libMesh::EpetraMatrix< T > Class Template Reference

This class provides a nice interface to the Epetra data structures for parallel, sparse matrices. More...

#include <trilinos_epetra_matrix.h>

Inheritance diagram for libMesh::EpetraMatrix< T >:

Public Member Functions
	EpetraMatrix (const Parallel::Communicator &comm)
	Constructor; initializes the matrix to be empty, without any structure, i.e. More...
	EpetraMatrix (Epetra_FECrsMatrix *m, const Parallel::Communicator &comm)
	Constructor. More...
	EpetraMatrix (EpetraMatrix &&)=delete
	This class manages the lifetime of an Epetra_FECrsMatrix manually, so we don't want to allow any automatic copy/move functions to be generated, and we can't default the destructor. More...
	EpetraMatrix (const EpetraMatrix &)=delete
EpetraMatrix &	operator= (const EpetraMatrix &)=delete
EpetraMatrix &	operator= (EpetraMatrix &&)=delete
virtual	~EpetraMatrix ()
virtual SparseMatrix< T > &	operator= (const SparseMatrix< T > &) override
	This looks like a copy assignment operator, but note that, unlike normal copy assignment operators, it is pure virtual. More...
virtual SolverPackage	solver_package () override
virtual bool	need_full_sparsity_pattern () const override
	The EpetraMatrix needs the full sparsity pattern. More...
virtual void	update_sparsity_pattern (const SparsityPattern::Graph &) override
	Updates the matrix sparsity pattern. More...
virtual void	init (const numeric_index_type m, const numeric_index_type n, const numeric_index_type m_l, const numeric_index_type n_l, const numeric_index_type nnz=30, const numeric_index_type noz=10, const numeric_index_type blocksize=1) override
	Initialize SparseMatrix with the specified sizes. More...
virtual void	init (ParallelType=PARALLEL) override
	Initialize this matrix using the sparsity structure computed by dof_map. More...
virtual void	clear () noexcept override
	clear() is called from the destructor, so it should not throw. More...
virtual void	zero () override
	Set all entries to 0. More...
virtual std::unique_ptr< SparseMatrix< T > >	zero_clone () const override
virtual std::unique_ptr< SparseMatrix< T > >	clone () const override
virtual void	close () override
	Calls the SparseMatrix's internal assembly routines, ensuring that the values are consistent across processors. More...
virtual numeric_index_type	m () const override
virtual numeric_index_type	n () const override
virtual numeric_index_type	row_start () const override
virtual numeric_index_type	row_stop () const override
virtual numeric_index_type	col_start () const override
virtual numeric_index_type	col_stop () const override
virtual void	set (const numeric_index_type i, const numeric_index_type j, const T value) override
	Set the element (i,j) to value. More...
virtual void	add (const numeric_index_type i, const numeric_index_type j, const T value) override
	Add value to the element (i,j). More...
virtual void	add_matrix (const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols) override
	Add the full matrix dm to the SparseMatrix. More...
virtual void	add_matrix (const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &dof_indices) override
	Same as add_matrix, but assumes the row and column maps are the same. More...
virtual void	add (const T a, const SparseMatrix< T > &X) override
	Compute A += a*X for scalar a, matrix X. More...
virtual T	operator() (const numeric_index_type i, const numeric_index_type j) const override
virtual Real	l1_norm () const override
virtual Real	linfty_norm () const override
virtual bool	closed () const override
virtual void	print_personal (std::ostream &os=libMesh::out) const override
	Print the contents of the matrix to the screen in a package-personalized style, if available. More...
virtual void	get_diagonal (NumericVector< T > &dest) const override
	Copies the diagonal part of the matrix into dest. More...
virtual void	get_transpose (SparseMatrix< T > &dest) const override
	Copies the transpose of the matrix into dest, which may be *this. More...
virtual void	get_row (numeric_index_type i, std::vector< numeric_index_type > &indices, std::vector< T > &values) const override
	Get a row from the matrix. More...
void	swap (EpetraMatrix< T > &)
	Swaps the internal data pointers, no actual values are swapped. More...
Epetra_FECrsMatrix *	mat ()
const Epetra_FECrsMatrix *	mat () const
virtual bool	initialized () const
void	attach_dof_map (const DofMap &dof_map)
	Set a pointer to the DofMap to use. More...
void	attach_sparsity_pattern (const SparsityPattern::Build &sp)
	Set a pointer to a sparsity pattern to use. More...
virtual bool	require_sparsity_pattern () const
virtual void	zero_rows (std::vector< numeric_index_type > &rows, T diag_value=0.0)
	Sets all row entries to 0 then puts diag_value in the diagonal entry. More...
virtual void	flush ()
	For PETSc matrix , this function is similar to close but without shrinking memory. More...
virtual numeric_index_type	local_m () const
	Get the number of rows owned by this process. More...
virtual numeric_index_type	local_n () const
	Get the number of columns owned by this process. More...
virtual void	add_block_matrix (const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &brows, const std::vector< numeric_index_type > &bcols)
	Add the full matrix dm to the SparseMatrix. More...
virtual void	add_block_matrix (const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &dof_indices)
	Same as add_block_matrix(), but assumes the row and column maps are the same. More...
virtual void	matrix_matrix_mult (SparseMatrix< T > &, SparseMatrix< T > &, bool)
	Compute Y = A*X for matrix X. More...
virtual void	add_sparse_matrix (const SparseMatrix< T > &, const std::map< numeric_index_type, numeric_index_type > &, const std::map< numeric_index_type, numeric_index_type > &, const T)
	Add scalar* spm to the rows and cols of this matrix (A): A(rows[i], cols[j]) += scalar * spm(i,j) More...
Real	l1_norm_diff (const SparseMatrix< T > &other_mat) const
virtual std::size_t	n_nonzeros () const
void	print (std::ostream &os=libMesh::out, const bool sparse=false) const
	Print the contents of the matrix to the screen in a uniform style, regardless of matrix/solver package being used. More...
void	print (const std::string &filename) const
	Print the contents of the matrix to a file, with a file format depending on the extension of filename. More...
template<>
void	print (std::ostream &os, const bool sparse) const
virtual void	print_coreform_hdf5 (const std::string &filename, const std::string &groupname="extraction") const
	Print the contents of the matrix to a file, with the HDF5 sparse matrix format used by CoreForm, putting CSR sparse matrix data in the group given by groupname. More...
virtual void	print_matlab (const std::string &="") const
	Print the contents of the matrix in Matlab's sparse matrix format. More...
virtual void	print_petsc_binary (const std::string &filename) const
	Write the contents of the matrix to a file in PETSc's binary sparse matrix format. More...
virtual void	print_petsc_hdf5 (const std::string &filename) const
	Write the contents of the matrix to a file in PETSc's HDF5 sparse matrix format. More...
virtual void	read (const std::string &filename)
	Read the contents of the matrix from a file, with the file format inferred from the extension of filename. More...
virtual void	read_coreform_hdf5 (const std::string &filename, const std::string &groupname="extraction")
	Read the contents of the matrix from a file, with the HDF5 sparse matrix format used by CoreForm, expecing sparse matrix data in the group given by groupname. More...
virtual void	read_matlab (const std::string &filename)
	Read the contents of the matrix from the Matlab-script sparse matrix format used by PETSc. More...
virtual void	read_petsc_binary (const std::string &filename)
	Read the contents of the matrix from a file in PETSc's binary sparse matrix format. More...
virtual void	read_petsc_hdf5 (const std::string &filename)
	Read the contents of the matrix from a file in PETSc's HDF5 sparse matrix format. More...
virtual void	create_submatrix (SparseMatrix< T > &submatrix, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols) const
	This function creates a matrix called "submatrix" which is defined by the row and column indices given in the "rows" and "cols" entries. More...
virtual void	create_submatrix_nosort (SparseMatrix< T > &, const std::vector< numeric_index_type > &, const std::vector< numeric_index_type > &) const
	Similar to the above function, this function creates a submatrix which is defined by the indices given in the rows and cols vectors. More...
virtual void	reinit_submatrix (SparseMatrix< T > &submatrix, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols) const
	This function is similar to the one above, but it allows you to reuse the existing sparsity pattern of "submatrix" instead of reallocating it again. More...
void	vector_mult (NumericVector< T > &dest, const NumericVector< T > &arg) const
	Multiplies the matrix by the NumericVector arg and stores the result in NumericVector dest. More...
void	vector_mult_add (NumericVector< T > &dest, const NumericVector< T > &arg) const
	Multiplies the matrix by the NumericVector arg and adds the result to the NumericVector dest. More...
virtual void	scale (const T scale)
	Scales all elements of this matrix by scale. More...
virtual bool	supports_hash_table () const
void	use_hash_table (bool use_hash)
	Sets whether to use hash table assembly. More...
bool	use_hash_table () const
virtual void	restore_original_nonzero_pattern ()
	Reset the memory storage of the matrix. More...
const Parallel::Communicator &	comm () const
processor_id_type	n_processors () const
processor_id_type	processor_id () const

Static Public Member Functions
static std::unique_ptr< SparseMatrix< T > >	build (const Parallel::Communicator &comm, const SolverPackage solver_package=libMesh::default_solver_package(), const MatrixBuildType matrix_build_type=MatrixBuildType::AUTOMATIC)
	Builds a SparseMatrix<T> using the linear solver package specified by solver_package. More...
static std::string	get_info ()
	Gets a string containing the reference information. More...
static void	print_info (std::ostream &out_stream=libMesh::out)
	Prints the reference information, by default to libMesh::out. More...
static unsigned int	n_objects ()
	Prints the number of outstanding (created, but not yet destroyed) objects. More...
static void	enable_print_counter_info ()
	Methods to enable/disable the reference counter output from print_info(). More...
static void	disable_print_counter_info ()

Protected Types
typedef std::map< std::string, std::pair< unsigned int, unsigned int > >	Counts
	Data structure to log the information. More...

Protected Member Functions
virtual void	_get_submatrix (SparseMatrix< T > &, const std::vector< numeric_index_type > &, const std::vector< numeric_index_type > &, const bool) const
	Protected implementation of the create_submatrix and reinit_submatrix routines. More...
void	increment_constructor_count (const std::string &name) noexcept
	Increments the construction counter. More...
void	increment_destructor_count (const std::string &name) noexcept
	Increments the destruction counter. More...

Protected Attributes
DofMap const *	_dof_map
	The DofMap object associated with this object. More...
SparsityPattern::Build const *	_sp
	The sparsity pattern associated with this object. More...
bool	_is_initialized
	Flag indicating whether or not the matrix has been initialized. More...
bool	_use_hash_table
	Flag indicating whether the matrix is assembled using a hash table. More...
const Parallel::Communicator &	_communicator

Static Protected Attributes
static Counts	_counts
	Actually holds the data. More...
static Threads::atomic< unsigned int >	_n_objects
	The number of objects. More...
static Threads::spin_mutex	_mutex
	Mutual exclusion object to enable thread-safe reference counting. More...
static bool	_enable_print_counter = true
	Flag to control whether reference count information is printed when print_info is called. More...

Private Attributes
Epetra_FECrsMatrix *	_mat
	Actual Epetra datatype to hold matrix entries. More...
Epetra_Map *	_map
	Holds the distributed Map. More...
Epetra_CrsGraph *	_graph
	Holds the sparsity pattern. More...
bool	_destroy_mat_on_exit
	This boolean value should only be set to false for the constructor which takes an Epetra_FECrsMatrix object. More...
bool	_use_transpose
	Epetra has no GetUseTranspose so we need to keep track of whether we're transposed manually. More...

Detailed Description

template<typename T>
class libMesh::EpetraMatrix< T >

This class provides a nice interface to the Epetra data structures for parallel, sparse matrices.

All overridden virtual functions are documented in sparse_matrix.h.

Author

Benjamin S. Kirk

Date

2008

Definition at line 63 of file trilinos_epetra_matrix.h.

Member Typedef Documentation

Counts

typedef std::map<std::string, std::pair<unsigned int, unsigned int> > libMesh::ReferenceCounter::Counts

protectedinherited

Data structure to log the information.

The log is identified by the class name.

Definition at line 119 of file reference_counter.h.

Constructor & Destructor Documentation

EpetraMatrix() [1/4]

template<typename T >

libMesh::EpetraMatrix< T >::EpetraMatrix

(

const Parallel::Communicator &

comm

)

Constructor; initializes the matrix to be empty, without any structure, i.e.

the matrix is not usable at all. This constructor is therefore only useful for matrices which are members of a class. All other matrices should be created at a point in the data flow where all necessary information is available.

You have to initialize the matrix before usage with init(...).

Definition at line 360 of file trilinos_epetra_matrix.C.

                                                               :
  SparseMatrix<T>(comm),
  _destroy_mat_on_exit(true),
  _use_transpose(false)
{}

EpetraMatrix() [2/4]

template<typename T >

libMesh::EpetraMatrix< T >::EpetraMatrix	(	Epetra_FECrsMatrix *	m,
		const Parallel::Communicator &	comm
	)

Constructor.

Creates a EpetraMatrix assuming you already have a valid Epetra_FECrsMatrix object. In this case, m is NOT destroyed by the EpetraMatrix destructor when this object goes out of scope. This allows ownership of m to remain with the original creator, and to simply provide additional functionality with the EpetraMatrix.

Definition at line 370 of file trilinos_epetra_matrix.C.

References libMesh::SparseMatrix< T >::_is_initialized, libMesh::EpetraMatrix< T >::_mat, and libMesh::EpetraMatrix< T >::m().

                                                                 :
  SparseMatrix<T>(comm),
  _destroy_mat_on_exit(false),
  _use_transpose(false) // dumb guess is the best we can do...
{
  this->_mat = m;
  this->_is_initialized = true;
}

EpetraMatrix() [3/4]

template<typename T>

libMesh::EpetraMatrix< T >::EpetraMatrix ( EpetraMatrix< T > &&  )

delete

This class manages the lifetime of an Epetra_FECrsMatrix manually, so we don't want to allow any automatic copy/move functions to be generated, and we can't default the destructor.

EpetraMatrix() [4/4]

template<typename T>

libMesh::EpetraMatrix< T >::EpetraMatrix ( const EpetraMatrix< T > &  )

delete

~EpetraMatrix()

template<typename T >

libMesh::EpetraMatrix< T >::~EpetraMatrix ( )

virtual

Definition at line 384 of file trilinos_epetra_matrix.C.

{
  this->clear();
}

Member Function Documentation

_get_submatrix()

template<typename T>

virtual void libMesh::SparseMatrix< T >::_get_submatrix ( SparseMatrix< T > &  , const std::vector< numeric_index_type > &  , const std::vector< numeric_index_type > &  , const bool    ) const

inlineprotectedvirtualinherited

Protected implementation of the create_submatrix and reinit_submatrix routines.

Note

This function must be overridden in derived classes for it to work properly!

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 654 of file sparse_matrix.h.

Referenced by libMesh::SparseMatrix< ValOut >::create_submatrix(), and libMesh::SparseMatrix< ValOut >::reinit_submatrix().

  {
    libmesh_not_implemented();
  }

add() [1/2]

template<typename T >

void libMesh::EpetraMatrix< T >::add ( const numeric_index_type  i, const numeric_index_type  j, const T  value  )

overridevirtual

Add value to the element (i,j).

Throws an error if the entry does not exist. Zero values can be "added" to non-existent entries.

Implements libMesh::SparseMatrix< T >.

Definition at line 487 of file trilinos_epetra_matrix.C.

References libMesh::initialized(), libMesh::libmesh_assert(), and value.

{
  libmesh_assert (this->initialized());

  int
    epetra_i = static_cast<int>(i),
    epetra_j = static_cast<int>(j);

  T epetra_value = value;

  _mat->SumIntoGlobalValues (epetra_i, 1, &epetra_value, &epetra_j);
}

add() [2/2]

template<typename T >

void libMesh::EpetraMatrix< T >::add ( const T  a, const SparseMatrix< T > &  X  )

overridevirtual

Compute A += a*X for scalar a, matrix X.

Note

It is advisable to not only allocate appropriate memory with init(), but also explicitly zero the terms of this whenever you add a non-zero value to X.

X will be closed, if not already done, before performing any work.

Implements libMesh::SparseMatrix< T >.

Definition at line 514 of file trilinos_epetra_matrix.C.

References libMesh::initialized(), libMesh::libmesh_assert(), libMesh::SparseMatrix< T >::m(), and libMesh::SparseMatrix< T >::n().

{
#ifdef LIBMESH_TRILINOS_HAVE_EPETRAEXT
  libmesh_assert (this->initialized());

  // sanity check. but this cannot avoid
  // crash due to incompatible sparsity structure...
  libmesh_assert_equal_to (this->m(), X_in.m());
  libmesh_assert_equal_to (this->n(), X_in.n());

  const EpetraMatrix<T> * X =
    cast_ptr<const EpetraMatrix<T> *> (&X_in);

  EpetraExt::MatrixMatrix::Add (*X->_mat, false, a_in, *_mat, 1.);
#else
  libmesh_error_msg("ERROR: EpetraExt is required for EpetraMatrix::add()!");
#endif
}

add_block_matrix() [1/2]

template<typename T>

void libMesh::SparseMatrix< T >::add_block_matrix ( const DenseMatrix< T > &  dm, const std::vector< numeric_index_type > &  brows, const std::vector< numeric_index_type > &  bcols  )

virtualinherited

Add the full matrix dm to the SparseMatrix.

This is useful for adding an element matrix at assembly time. The matrix is assumed blocked, and brow, bcol correspond to the block row and column indices.

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 119 of file sparse_matrix.C.

Referenced by libMesh::SparseMatrix< ValOut >::add_block_matrix().

{
  libmesh_assert_equal_to (dm.m() / brows.size(), dm.n() / bcols.size());

  const numeric_index_type blocksize = cast_int<numeric_index_type>
    (dm.m() / brows.size());

  libmesh_assert_equal_to (dm.m()%blocksize, 0);
  libmesh_assert_equal_to (dm.n()%blocksize, 0);

  std::vector<numeric_index_type> rows, cols;

  rows.reserve(blocksize*brows.size());
  cols.reserve(blocksize*bcols.size());

  for (auto & row : brows)
    {
      numeric_index_type i = row * blocksize;

      for (unsigned int v=0; v<blocksize; v++)
        rows.push_back(i++);
    }

  for (auto & col : bcols)
    {
      numeric_index_type j = col * blocksize;

      for (unsigned int v=0; v<blocksize; v++)
        cols.push_back(j++);
    }

  this->add_matrix (dm, rows, cols);
}

add_block_matrix() [2/2]

template<typename T>

virtual void libMesh::SparseMatrix< T >::add_block_matrix ( const DenseMatrix< T > &  dm, const std::vector< numeric_index_type > &  dof_indices  )

inlinevirtualinherited

Same as add_block_matrix(), but assumes the row and column maps are the same.

Thus the matrix dm must be square.

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 337 of file sparse_matrix.h.

  { this->add_block_matrix (dm, dof_indices, dof_indices); }

add_matrix() [1/2]

template<typename T >

void libMesh::EpetraMatrix< T >::add_matrix ( const DenseMatrix< T > &  dm, const std::vector< numeric_index_type > &  rows, const std::vector< numeric_index_type > &  cols  )

overridevirtual

Add the full matrix dm to the SparseMatrix.

This is useful for adding an element matrix at assembly time.

Implements libMesh::SparseMatrix< T >.

Definition at line 274 of file trilinos_epetra_matrix.C.

References libMesh::DenseMatrix< T >::get_values(), libMesh::initialized(), libMesh::libmesh_assert(), libMesh::DenseMatrixBase< T >::m(), libMesh::DenseMatrixBase< T >::n(), and libMesh::numeric_trilinos_cast().

{
  libmesh_assert (this->initialized());

  const numeric_index_type m = dm.m();
  const numeric_index_type n = dm.n();

  libmesh_assert_equal_to (rows.size(), m);
  libmesh_assert_equal_to (cols.size(), n);

  _mat->SumIntoGlobalValues(m, numeric_trilinos_cast(rows.data()),
                            n, numeric_trilinos_cast(cols.data()),
                            dm.get_values().data());
}

add_matrix() [2/2]

template<typename T >

void libMesh::EpetraMatrix< T >::add_matrix ( const DenseMatrix< T > &  dm, const std::vector< numeric_index_type > &  dof_indices  )

overridevirtual

Same as add_matrix, but assumes the row and column maps are the same.

Thus the matrix dm must be square.

Implements libMesh::SparseMatrix< T >.

Definition at line 505 of file trilinos_epetra_matrix.C.

{
  this->add_matrix (dm, dof_indices, dof_indices);
}

add_sparse_matrix()

template<typename T>

virtual void libMesh::SparseMatrix< T >::add_sparse_matrix ( const SparseMatrix< T > &  , const std::map< numeric_index_type, numeric_index_type > &  , const std::map< numeric_index_type, numeric_index_type > &  , const T    )

inlinevirtualinherited

Add scalar* spm to the rows and cols of this matrix (A): A(rows[i], cols[j]) += scalar * spm(i,j)

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 356 of file sparse_matrix.h.

  { libmesh_not_implemented(); }

attach_dof_map()

template<typename T >

void libMesh::SparseMatrix< T >::attach_dof_map ( const DofMap &  dof_map )

inherited

Set a pointer to the DofMap to use.

If a separate sparsity pattern is not being used, use the one from the DofMap.

The lifetime of dof_map must exceed the lifetime of this.

Definition at line 100 of file sparse_matrix.C.

Referenced by libMesh::__libmesh_tao_hessian(), DMlibMeshJacobian(), libMesh::libmesh_petsc_snes_jacobian(), and libMesh::DofMap::update_sparsity_pattern().

{
  _dof_map = &dof_map;
  if (!_sp)
    _sp = dof_map.get_sparsity_pattern();
}

attach_sparsity_pattern()

template<typename T >

void libMesh::SparseMatrix< T >::attach_sparsity_pattern ( const SparsityPattern::Build &  sp )

inherited

Set a pointer to a sparsity pattern to use.

Useful in cases where a matrix requires a wider (or for efficiency narrower) pattern than most matrices in the system, or in cases where no system sparsity pattern is being calculated by the DofMap.

The lifetime of sp must exceed the lifetime of this.

Definition at line 110 of file sparse_matrix.C.

Referenced by libMesh::DofMap::update_sparsity_pattern().

{
  _sp = &sp;
}

build()

template<typename T >

std::unique_ptr< SparseMatrix< T > > libMesh::SparseMatrix< T >::build ( const Parallel::Communicator &  comm, const SolverPackage  solver_package = libMesh::default_solver_package(), const MatrixBuildType  matrix_build_type = MatrixBuildType::AUTOMATIC  )

staticinherited

Builds a SparseMatrix<T> using the linear solver package specified by solver_package.

Definition at line 193 of file sparse_matrix.C.

Referenced by libMesh::CondensedEigenSystem::add_matrices(), libMesh::System::add_matrix(), libMesh::TransientRBConstruction::allocate_data_structures(), libMesh::RBConstruction::allocate_data_structures(), libMesh::CondensedEigenSystem::copy_super_to_sub(), libMesh::StaticCondensation::init(), main(), libMesh::DofMap::process_mesh_constraint_rows(), ConstraintOperatorTest::test1DCoarseningNewNodes(), ConstraintOperatorTest::test1DCoarseningOperator(), ConstraintOperatorTest::testCoreform(), ConnectedComponentsTest::testEdge(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), and SystemsTest::testProjectMatrix3D().

{
  // Avoid unused parameter warnings when no solver packages are enabled.
  libmesh_ignore(comm);

  if (matrix_build_type == MatrixBuildType::DIAGONAL)
    return std::make_unique<DiagonalMatrix<T>>(comm);

  // Build the appropriate vector
  switch (solver_package)
    {

#ifdef LIBMESH_HAVE_LASPACK
    case LASPACK_SOLVERS:
      return std::make_unique<LaspackMatrix<T>>(comm);
#endif


#ifdef LIBMESH_HAVE_PETSC
    case PETSC_SOLVERS:
      return std::make_unique<PetscMatrix<T>>(comm);
#endif


#ifdef LIBMESH_TRILINOS_HAVE_EPETRA
    case TRILINOS_SOLVERS:
      return std::make_unique<EpetraMatrix<T>>(comm);
#endif


#ifdef LIBMESH_HAVE_EIGEN
    case EIGEN_SOLVERS:
      return std::make_unique<EigenSparseMatrix<T>>(comm);
#endif

    default:
      libmesh_error_msg("ERROR:  Unrecognized solver package: " << solver_package);
    }
}

clear()

template<typename T >

void libMesh::EpetraMatrix< T >::clear ( )

overridevirtualnoexcept

clear() is called from the destructor, so it should not throw.

Implements libMesh::SparseMatrix< T >.

Definition at line 236 of file trilinos_epetra_matrix.C.

References libMesh::libMeshPrivateData::_is_initialized.

{
  // FIXME: clear() doesn't actually free the memory managed by this
  // class, so it probably leaks memory.
  // delete _mat;
  // delete _map;

  this->_is_initialized = false;
}

clone()

template<typename T >

std::unique_ptr< SparseMatrix< T > > libMesh::EpetraMatrix< T >::clone ( ) const

overridevirtual

Returns

A smart pointer to a copy of this matrix.

Note

This must be overridden in the derived classes.

Implements libMesh::SparseMatrix< T >.

Definition at line 223 of file trilinos_epetra_matrix.C.

{
  // We don't currently have a faster implementation than making a
  // zero clone and then filling in the values.
  auto mat_copy = this->zero_clone();
  mat_copy->add(1., *this);

  return mat_copy;
}

close()

template<typename T >

void libMesh::EpetraMatrix< T >::close ( )

overridevirtual

Calls the SparseMatrix's internal assembly routines, ensuring that the values are consistent across processors.

Implements libMesh::SparseMatrix< T >.

Definition at line 392 of file trilinos_epetra_matrix.C.

References libMesh::libmesh_assert().

Referenced by libMesh::AztecLinearSolver< T >::solve().

{
  libmesh_assert(_mat);

  _mat->GlobalAssemble();
}

closed()

template<typename T >

bool libMesh::EpetraMatrix< T >::closed ( ) const

overridevirtual

Returns

true if the matrix has been assembled.

Implements libMesh::SparseMatrix< T >.

Definition at line 572 of file trilinos_epetra_matrix.C.

References libMesh::initialized(), and libMesh::libmesh_assert().

{
  libmesh_assert (this->initialized());
  libmesh_assert(this->_mat);

  return this->_mat->Filled();
}

col_start()

template<typename T >

numeric_index_type libMesh::EpetraMatrix< T >::col_start ( ) const

overridevirtual

Returns

The index of the first matrix column owned by this processor.

Implements libMesh::SparseMatrix< T >.

Definition at line 444 of file trilinos_epetra_matrix.C.

References libMesh::initialized(), and libMesh::libmesh_assert().

{
  libmesh_assert (this->initialized());
  libmesh_assert(_map);

  return static_cast<numeric_index_type>(_map->MinMyGID());
}

col_stop()

template<typename T >

numeric_index_type libMesh::EpetraMatrix< T >::col_stop ( ) const

overridevirtual

Returns

The index of the last matrix column (+1) owned by this processor.

Implements libMesh::SparseMatrix< T >.

Definition at line 455 of file trilinos_epetra_matrix.C.

References libMesh::initialized(), and libMesh::libmesh_assert().

{
  libmesh_assert (this->initialized());
  libmesh_assert(_map);

  return static_cast<numeric_index_type>(_map->MaxMyGID())+1;
}

comm()

const Parallel::Communicator& libMesh::ParallelObject::comm ( ) const

inlineinherited

Returns

A reference to the Parallel::Communicator object used by this mesh.

Definition at line 97 of file parallel_object.h.

References libMesh::ParallelObject::_communicator.

Referenced by libMesh::__libmesh_petsc_diff_solver_jacobian(), libMesh::__libmesh_petsc_diff_solver_monitor(), libMesh::__libmesh_petsc_diff_solver_residual(), libMesh::__libmesh_tao_equality_constraints(), libMesh::__libmesh_tao_equality_constraints_jacobian(), libMesh::__libmesh_tao_gradient(), libMesh::__libmesh_tao_hessian(), libMesh::__libmesh_tao_inequality_constraints(), libMesh::__libmesh_tao_inequality_constraints_jacobian(), libMesh::__libmesh_tao_objective(), libMesh::MeshRefinement::_coarsen_elements(), libMesh::ExactSolution::_compute_error(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::Partitioner::_find_global_index_by_pid_map(), libMesh::BoundaryInfo::_find_id_maps(), libMesh::PetscLinearSolver< Number >::_petsc_shell_matrix_get_diagonal(), libMesh::SlepcEigenSolver< libMesh::Number >::_petsc_shell_matrix_get_diagonal(), libMesh::PetscLinearSolver< Number >::_petsc_shell_matrix_mult(), libMesh::SlepcEigenSolver< libMesh::Number >::_petsc_shell_matrix_mult(), libMesh::PetscLinearSolver< Number >::_petsc_shell_matrix_mult_add(), libMesh::MeshRefinement::_refine_elements(), libMesh::MeshRefinement::_smooth_flags(), libMesh::DofMap::add_constraints_to_send_list(), add_cube_convex_hull_to_mesh(), libMesh::PetscDMWrapper::add_dofs_helper(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::TransientRBConstruction::add_IC_to_RB_space(), libMesh::RBEIMEvaluation::add_interpolation_data(), libMesh::CondensedEigenSystem::add_matrices(), libMesh::EigenSystem::add_matrices(), libMesh::System::add_matrix(), libMesh::RBConstruction::add_scaled_matrix_and_vector(), libMesh::DofMap::add_variable(), libMesh::DofMap::add_variables(), libMesh::System::add_vector(), libMesh::MeshTools::Modification::all_tri(), libMesh::LaplaceMeshSmoother::allgather_graph(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::TransientRBConstruction::allocate_data_structures(), libMesh::RBConstruction::allocate_data_structures(), libMesh::TransientRBConstruction::assemble_affine_expansion(), libMesh::AdvectionSystem::assemble_claw_rhs(), libMesh::FEMSystem::assemble_qoi(), libMesh::Nemesis_IO::assert_symmetric_cmaps(), libMesh::MeshCommunication::assign_global_indices(), libMesh::Partitioner::assign_partitioning(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::Partitioner::build_graph(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::PetscDMWrapper::build_section(), libMesh::PetscDMWrapper::build_sf(), libMesh::MeshBase::cache_elem_data(), libMesh::System::calculate_norm(), libMesh::DofMap::check_dirichlet_bcid_consistency(), libMesh::MeshTetInterface::check_hull_integrity(), libMesh::MeshBase::complete_preparation(), libMesh::RBConstruction::compute_Fq_representor_innerprods(), libMesh::RBConstruction::compute_max_error_bound(), libMesh::Nemesis_IO_Helper::compute_num_global_elem_blocks(), libMesh::Nemesis_IO_Helper::compute_num_global_nodesets(), libMesh::Nemesis_IO_Helper::compute_num_global_sidesets(), libMesh::RBConstruction::compute_output_dual_innerprods(), libMesh::RBConstruction::compute_residual_dual_norm_slow(), libMesh::RBSCMConstruction::compute_SCM_bounds_on_training_set(), libMesh::DofMap::computed_sparsity_already(), libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), libMesh::ContinuationSystem::ContinuationSystem(), libMesh::MeshBase::copy_constraint_rows(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::CondensedEigenSystem::copy_super_to_sub(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::MeshTools::create_bounding_box(), libMesh::DofMap::create_dof_constraints(), libMesh::MeshTools::create_nodal_bounding_box(), libMesh::MeshRefinement::create_parent_error_vector(), libMesh::MeshTools::create_processor_bounding_box(), libMesh::MeshTools::create_subdomain_bounding_box(), libMesh::PetscMatrix< T >::create_submatrix_nosort(), create_wrapped_function(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::RBEIMEvaluation::distribute_bfs(), DMlibMeshFunction(), DMlibMeshJacobian(), DMlibMeshSetSystem_libMesh(), DMVariableBounds_libMesh(), libMesh::DTKSolutionTransfer::DTKSolutionTransfer(), libMesh::MeshRefinement::eliminate_unrefined_patches(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_interiors(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_nodes(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_sides(), libMesh::TransientRBConstruction::enrich_RB_space(), libMesh::EpetraVector< T >::EpetraVector(), AssembleOptimization::equality_constraints(), libMesh::PatchRecoveryErrorEstimator::estimate_error(), libMesh::WeightedPatchRecoveryErrorEstimator::estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::SmoothnessEstimator::estimate_smoothness(), libMesh::MeshRefinement::flag_elements_by_elem_fraction(), libMesh::MeshRefinement::flag_elements_by_error_fraction(), libMesh::MeshRefinement::flag_elements_by_error_tolerance(), libMesh::MeshRefinement::flag_elements_by_mean_stddev(), libMesh::MeshRefinement::flag_elements_by_nelem_target(), libMesh::RBEIMEvaluation::gather_bfs(), libMesh::DofMap::gather_constraints(), libMesh::MeshfreeInterpolation::gather_remote_data(), libMesh::CondensedEigenSystem::get_eigenpair(), libMesh::RBEIMEvaluation::get_eim_basis_function_node_value(), libMesh::RBEIMEvaluation::get_eim_basis_function_side_value(), libMesh::RBEIMEvaluation::get_eim_basis_function_value(), libMesh::System::get_info(), libMesh::MeshBase::get_info(), libMesh::DofMap::get_info(), libMesh::RBEIMEvaluation::get_interior_basis_functions_as_vecs(), libMesh::ImplicitSystem::get_linear_solver(), libMesh::RBEIMConstruction::get_max_abs_value(), libMesh::RBEIMConstruction::get_node_max_abs_value(), libMesh::RBEIMEvaluation::get_parametrized_function_node_value(), libMesh::RBEIMEvaluation::get_parametrized_function_side_value(), libMesh::RBEIMEvaluation::get_parametrized_function_value(), libMesh::RBEIMConstruction::get_random_point(), libMesh::MeshTetInterface::improve_hull_integrity(), AssembleOptimization::inequality_constraints(), AssembleOptimization::inequality_constraints_jacobian(), libMesh::LocationMap< T >::init(), libMesh::TimeSolver::init(), libMesh::StaticCondensation::init(), libMesh::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_and_attach_petscdm(), libMesh::AdvectionSystem::init_data(), libMesh::ClawSystem::init_data(), libMesh::PetscDMWrapper::init_petscdm(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::OptimizationSystem::initialize_equality_constraints_storage(), libMesh::OptimizationSystem::initialize_inequality_constraints_storage(), libMesh::RBEIMConstruction::initialize_parametrized_functions_in_training_set(), libMesh::RBEIMConstruction::inner_product(), integrate_function(), libMesh::MeshTools::libmesh_assert_consistent_distributed(), libMesh::MeshTools::libmesh_assert_consistent_distributed_nodes(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_equal_connectivity(), libMesh::MeshTools::libmesh_assert_equal_points(), libMesh::MeshTools::libmesh_assert_parallel_consistent_new_node_procids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_topology_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_valid_boundary_ids(), libMesh::MeshTools::libmesh_assert_valid_constraint_rows(), libMesh::MeshTools::libmesh_assert_valid_dof_ids(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_flags(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_object_ids(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_p_levels(), libMesh::MeshTools::libmesh_assert_valid_refinement_flags(), libMesh::MeshTools::libmesh_assert_valid_unique_ids(), libMesh::libmesh_petsc_linesearch_shellfunc(), libMesh::libmesh_petsc_preconditioner_apply(), libMesh::libmesh_petsc_recalculate_monitor(), libMesh::libmesh_petsc_snes_fd_residual(), libMesh::libmesh_petsc_snes_jacobian(), libMesh::libmesh_petsc_snes_mffd_interface(), libMesh::libmesh_petsc_snes_mffd_residual(), libMesh::libmesh_petsc_snes_postcheck(), libMesh::libmesh_petsc_snes_precheck(), libMesh::libmesh_petsc_snes_residual(), libMesh::libmesh_petsc_snes_residual_helper(), libMesh::MeshRefinement::limit_level_mismatch_at_edge(), libMesh::MeshRefinement::limit_level_mismatch_at_node(), libMesh::MeshRefinement::limit_overrefined_boundary(), libMesh::MeshRefinement::limit_underrefined_boundary(), libMesh::LinearImplicitSystem::LinearImplicitSystem(), main(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshCommunication::make_elems_parallel_consistent(), libMesh::MeshRefinement::make_flags_parallel_consistent(), libMesh::MeshCommunication::make_new_node_proc_ids_parallel_consistent(), libMesh::MeshCommunication::make_new_nodes_parallel_consistent(), libMesh::MeshCommunication::make_node_bcids_parallel_consistent(), libMesh::MeshCommunication::make_node_ids_parallel_consistent(), libMesh::MeshCommunication::make_node_proc_ids_parallel_consistent(), libMesh::MeshCommunication::make_node_unique_ids_parallel_consistent(), libMesh::MeshCommunication::make_nodes_parallel_consistent(), libMesh::MeshCommunication::make_p_levels_parallel_consistent(), libMesh::MeshRefinement::make_refinement_compatible(), libMesh::TransientRBConstruction::mass_matrix_scaled_matvec(), libMesh::FEMSystem::mesh_position_set(), libMesh::TriangulatorInterface::MeshedHole::MeshedHole(), LinearElasticityWithContact::move_mesh(), libMesh::DistributedMesh::n_active_elem(), libMesh::MeshTools::n_active_levels(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::MeshTools::n_connected_components(), libMesh::DofMap::n_constrained_dofs(), libMesh::MeshBase::n_constraint_rows(), libMesh::DofMap::n_dofs(), libMesh::DofMap::n_dofs_per_processor(), libMesh::BoundaryInfo::n_edge_conds(), libMesh::CondensedEigenSystem::n_global_non_condensed_dofs(), libMesh::MeshTools::n_levels(), MixedOrderTest::n_neighbor_links(), libMesh::BoundaryInfo::n_nodeset_conds(), libMesh::SparsityPattern::Build::n_nonzeros(), libMesh::MeshTools::n_p_levels(), libMesh::BoundaryInfo::n_shellface_conds(), libMesh::RBEIMEvaluation::node_distribute_bfs(), libMesh::RBEIMEvaluation::node_gather_bfs(), libMesh::RBEIMConstruction::node_inner_product(), libMesh::PetscVector< libMesh::Number >::operator=(), libMesh::MeshBase::operator==(), libMesh::DistributedMesh::parallel_max_elem_id(), libMesh::DistributedMesh::parallel_max_node_id(), libMesh::ReplicatedMesh::parallel_max_unique_id(), libMesh::DistributedMesh::parallel_max_unique_id(), libMesh::DistributedMesh::parallel_n_elem(), libMesh::DistributedMesh::parallel_n_nodes(), libMesh::SparsityPattern::Build::parallel_sync(), libMesh::BoundaryInfo::parallel_sync_node_ids(), libMesh::BoundaryInfo::parallel_sync_side_ids(), libMesh::MeshTools::paranoid_n_levels(), libMesh::Partitioner::partition(), libMesh::Partitioner::partition_unpartitioned_elements(), libMesh::petsc_auto_fieldsplit(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::MeshBase::print_constraint_rows(), libMesh::DofMap::print_dof_constraints(), libMesh::DofMap::process_mesh_constraint_rows(), libMesh::Partitioner::processor_pairs_to_interface_nodes(), libMesh::InterMeshProjection::project_system_vectors(), FEMParameters::read(), libMesh::Nemesis_IO::read(), libMesh::XdrIO::read(), libMesh::EquationSystems::read(), libMesh::ExodusII_IO::read_header(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::System::read_header(), libMesh::RBEIMEvaluation::read_in_interior_basis_functions(), libMesh::RBEIMEvaluation::read_in_node_basis_functions(), libMesh::RBEIMEvaluation::read_in_side_basis_functions(), libMesh::RBEvaluation::read_in_vectors_from_multiple_files(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), libMesh::System::read_SCALAR_dofs(), libMesh::XdrIO::read_serialized_bc_names(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::System::read_serialized_vector(), libMesh::Nemesis_IO_Helper::read_var_names_impl(), MeshFunctionTest::read_variable_info_from_output_data(), libMesh::MeshBase::recalculate_n_partitions(), libMesh::MeshRefinement::refine_and_coarsen_elements(), libMesh::SimplexRefiner::refine_via_edges(), libMesh::StaticCondensationDofMap::reinit(), libMesh::BoundaryInfo::remove_edge_id(), libMesh::BoundaryInfo::remove_node_id(), libMesh::BoundaryInfo::remove_shellface_id(), libMesh::BoundaryInfo::remove_side_id(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::DistributedMesh::renumber_nodes_and_elements(), LinearElasticityWithContact::residual_and_jacobian(), OverlappingAlgebraicGhostingTest::run_ghosting_test(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), scale_mesh_and_plot(), libMesh::DofMap::scatter_constraints(), libMesh::CheckpointIO::select_split_config(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::send_and_insert_dof_values(), libMesh::TransientRBConstruction::set_error_temporal_data(), libMesh::Partitioner::set_interface_node_processor_ids_BFS(), libMesh::Partitioner::set_interface_node_processor_ids_linear(), libMesh::Partitioner::set_interface_node_processor_ids_petscpartitioner(), libMesh::Partitioner::set_node_processor_ids(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::Partitioner::set_parent_processor_ids(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::PetscDiffSolver::setup_petsc_data(), libMesh::RBEIMEvaluation::side_distribute_bfs(), libMesh::RBEIMEvaluation::side_gather_bfs(), libMesh::RBEIMConstruction::side_inner_product(), libMesh::Partitioner::single_partition(), libMesh::LaplaceMeshSmoother::smooth(), libMesh::VariationalMeshSmoother::smooth(), libMesh::ClawSystem::solve_conservation_law(), libMesh::split_mesh(), libMesh::RBEIMConstruction::store_eim_solutions_for_training_set(), libMesh::MeshBase::subdomain_ids(), libMesh::BoundaryInfo::sync(), libMesh::MeshBase::sync_subdomain_name_map(), ConstraintOperatorTest::test1DCoarseningNewNodes(), ConstraintOperatorTest::test1DCoarseningOperator(), MeshFunctionTest::test_bad_gradient_var_with_out_of_mesh_value(), MeshFunctionTest::test_bad_hessian_var_with_out_of_mesh_value(), libMesh::MeshRefinement::test_level_one(), MeshfunctionDFEM::test_mesh_function_dfem(), MeshfunctionDFEM::test_mesh_function_dfem_grad(), MeshFunctionTest::test_p_level(), libMesh::MeshRefinement::test_unflagged(), DofMapTest::testBadElemFECombo(), SystemsTest::testBlockRestrictedVarNDofs(), BoundaryInfoTest::testBoundaryOnChildrenErrors(), VolumeTest::testC0PolygonMethods(), VolumeTest::testC0PolyhedronMethods(), ConstraintOperatorTest::testCoreform(), ConnectedComponentsTest::testEdge(), MeshInputTest::testExodusIGASidesets(), MeshTriangulationTest::testFoundCenters(), PointLocatorTest::testLocator(), BoundaryInfoTest::testMesh(), PointLocatorTest::testPlanar(), MeshTriangulationTest::testPoly2TriRefinementBase(), SystemsTest::testProjectCubeWithMeshFunction(), BoundaryInfoTest::testRenumber(), BoundaryInfoTest::testSelectiveRenumber(), CheckpointIOTest::testSplitter(), MeshInputTest::testTetgenIO(), MeshTriangulationTest::testTriangulatorInterp(), MeshTriangulationTest::testTriangulatorMeshedHoles(), MeshTriangulationTest::testTriangulatorRoundHole(), MeshSmootherTest::testVariationalSmoother(), libMesh::MeshTools::total_weight(), libMesh::RBConstruction::train_reduced_basis_with_POD(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::MeshfreeSolutionTransfer::transfer(), libMesh::Poly2TriTriangulator::triangulate(), libMesh::TransientRBConstruction::truth_assembly(), libMesh::RBConstruction::truth_assembly(), libMesh::MeshRefinement::uniformly_coarsen(), update_current_local_solution(), libMesh::TransientRBConstruction::update_RB_initial_condition_all_N(), libMesh::TransientRBConstruction::update_RB_system_matrices(), libMesh::RBConstruction::update_RB_system_matrices(), libMesh::TransientRBConstruction::update_residual_terms(), libMesh::RBConstruction::update_residual_terms(), libMesh::MeshTools::volume(), libMesh::STLIO::write(), libMesh::NameBasedIO::write(), libMesh::XdrIO::write(), libMesh::VTKIO::write_nodal_data(), libMesh::RBEIMEvaluation::write_out_interior_basis_functions(), libMesh::RBEIMEvaluation::write_out_node_basis_functions(), libMesh::RBEIMEvaluation::write_out_side_basis_functions(), libMesh::RBEvaluation::write_out_vectors(), libMesh::TransientRBConstruction::write_riesz_representors_to_files(), libMesh::RBConstruction::write_riesz_representors_to_files(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), libMesh::XdrIO::write_serialized_nodesets(), libMesh::RBDataSerialization::RBEvaluationSerialization::write_to_file(), libMesh::RBDataSerialization::TransientRBEvaluationSerialization::write_to_file(), libMesh::RBDataSerialization::RBEIMEvaluationSerialization::write_to_file(), and libMesh::RBDataSerialization::RBSCMEvaluationSerialization::write_to_file().

  { return _communicator; }

create_submatrix()

template<typename T>

virtual void libMesh::SparseMatrix< T >::create_submatrix ( SparseMatrix< T > &  submatrix, const std::vector< numeric_index_type > &  rows, const std::vector< numeric_index_type > &  cols  ) const

inlinevirtualinherited

This function creates a matrix called "submatrix" which is defined by the row and column indices given in the "rows" and "cols" entries.

Currently this operation is only defined for the PetscMatrixBase subclasses. Note: The rows and cols vectors need to be sorted; Use the nosort version below if rows and cols vectors are not sorted; The rows and cols only contain indices that are owned by this processor.

Definition at line 534 of file sparse_matrix.h.

Referenced by libMesh::CondensedEigenSystem::copy_super_to_sub(), libMesh::libmesh_petsc_DMCreateInterpolation(), and libMesh::CondensedEigenSystem::solve().

  {
    this->_get_submatrix(submatrix,
                         rows,
                         cols,
                         false); // false means DO NOT REUSE submatrix
  }

create_submatrix_nosort()

template<typename T>

virtual void libMesh::SparseMatrix< T >::create_submatrix_nosort ( SparseMatrix< T > &  , const std::vector< numeric_index_type > &  , const std::vector< numeric_index_type > &    ) const

inlinevirtualinherited

Similar to the above function, this function creates a submatrix which is defined by the indices given in the rows and cols vectors.

Note: Both rows and cols can be unsorted; Use the above function for better efficiency if your indices are sorted; rows and cols can contain indices that are owned by other processors.

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 552 of file sparse_matrix.h.

  {
    libmesh_not_implemented();
  }

disable_print_counter_info()

void libMesh::ReferenceCounter::disable_print_counter_info ( )

staticinherited

Definition at line 100 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

{
  _enable_print_counter = false;
  return;
}

enable_print_counter_info()

void libMesh::ReferenceCounter::enable_print_counter_info ( )

staticinherited

Methods to enable/disable the reference counter output from print_info().

Enabled by default.

Definition at line 94 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

Referenced by libMesh::LibMeshInit::~LibMeshInit().

{
  _enable_print_counter = true;
  return;
}

flush()

template<typename T>

virtual void libMesh::SparseMatrix< T >::flush ( )

inlinevirtualinherited

For PETSc matrix , this function is similar to close but without shrinking memory.

This is useful when we want to switch between ADD_VALUES and INSERT_VALUES. close should be called before using the matrix.

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 244 of file sparse_matrix.h.

{ close(); }

get_diagonal()

template<typename T >

void libMesh::EpetraMatrix< T >::get_diagonal ( NumericVector< T > &  dest ) const

overridevirtual

Copies the diagonal part of the matrix into dest.

Implements libMesh::SparseMatrix< T >.

Definition at line 297 of file trilinos_epetra_matrix.C.

References libMesh::EpetraVector< T >::vec().

{
  // Convert vector to EpetraVector.
  EpetraVector<T> * epetra_dest = cast_ptr<EpetraVector<T> *>(&dest);

  // Call Epetra function.
  _mat->ExtractDiagonalCopy(*(epetra_dest->vec()));
}

get_info()

std::string libMesh::ReferenceCounter::get_info ( )

staticinherited

Gets a string containing the reference information.

Definition at line 47 of file reference_counter.C.

References libMesh::ReferenceCounter::_counts, and libMesh::Quality::name().

Referenced by libMesh::ReferenceCounter::print_info().

{
#if defined(LIBMESH_ENABLE_REFERENCE_COUNTING) && defined(DEBUG)

  std::ostringstream oss;

  oss << '\n'
      << " ---------------------------------------------------------------------------- \n"
      << "| Reference count information                                                |\n"
      << " ---------------------------------------------------------------------------- \n";

  for (const auto & [name, cd] : _counts)
    oss << "| " << name << " reference count information:\n"
        << "|  Creations:    " << cd.first    << '\n'
        << "|  Destructions: " << cd.second << '\n';

  oss << " ---------------------------------------------------------------------------- \n";

  return oss.str();

#else

  return "";

#endif
}

get_row()

template<typename T >

void libMesh::EpetraMatrix< T >::get_row ( numeric_index_type  i, std::vector< numeric_index_type > &  indices, std::vector< T > &  values  ) const

overridevirtual

Get a row from the matrix.

Parameters

i	The matrix row to get
indices	A container that will be filled with the column indices corresponding to (possibly) non-zero values
values	A container holding the column values

Implements libMesh::SparseMatrix< T >.

Definition at line 328 of file trilinos_epetra_matrix.C.

References libMesh::initialized(), libMesh::libmesh_assert(), and libMesh::make_range().

{
  libmesh_assert (this->initialized());
  libmesh_assert(this->_mat);
  libmesh_assert (this->_mat->MyGlobalRow(static_cast<int>(i)));
  libmesh_assert_greater_equal (i, this->row_start());
  libmesh_assert_less (i, this->row_stop());

  int row_length;
  int * row_indices;
  double * row_values;

  _mat->ExtractMyRowView (i-this->row_start(),
                          row_length,
                          row_values,
                          row_indices);

  indices.resize(row_length);
  values.resize(row_length);

  for (auto i : make_range(row_length))
    {
      indices[i] = row_indices[i];
      values[i] = row_values[i];
    }
}

get_transpose()

template<typename T >

void libMesh::EpetraMatrix< T >::get_transpose ( SparseMatrix< T > &  dest ) const

overridevirtual

Copies the transpose of the matrix into dest, which may be *this.

Implements libMesh::SparseMatrix< T >.

Definition at line 309 of file trilinos_epetra_matrix.C.

References libMesh::EpetraMatrix< T >::_mat, and libMesh::EpetraMatrix< T >::_use_transpose.

{
  // Make sure the SparseMatrix passed in is really a EpetraMatrix
  EpetraMatrix<T> & epetra_dest = cast_ref<EpetraMatrix<T> &>(dest);

  // We currently only support calling get_transpose() with ourself
  // as the destination. Previously, this called the default copy
  // constructor which was not safe because this class manually
  // manages memory.
  if (&epetra_dest != this)
    libmesh_not_implemented();

  epetra_dest._use_transpose = !epetra_dest._use_transpose;
  epetra_dest._mat->SetUseTranspose(epetra_dest._use_transpose);
}

increment_constructor_count()

void libMesh::ReferenceCounter::increment_constructor_count ( const std::string &  name )

inlineprotectednoexceptinherited

Increments the construction counter.

Should be called in the constructor of any derived class that will be reference counted.

Definition at line 183 of file reference_counter.h.

References libMesh::err, libMesh::BasicOStreamProxy< charT, traits >::get(), libMesh::Quality::name(), and libMesh::Threads::spin_mtx.

Referenced by libMesh::ReferenceCountedObject< RBParametrized >::ReferenceCountedObject().

{
  libmesh_try
  {
    Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
    std::pair<unsigned int, unsigned int> & p = _counts[name];
    p.first++;
  }
  libmesh_catch (...)
  {
    auto stream = libMesh::err.get();
    stream->exceptions(stream->goodbit); // stream must not throw
    libMesh::err << "Encountered unrecoverable error while calling "
                 << "ReferenceCounter::increment_constructor_count() "
                 << "for a(n) " << name << " object." << std::endl;
    std::terminate();
  }
}

increment_destructor_count()

void libMesh::ReferenceCounter::increment_destructor_count ( const std::string &  name )

inlineprotectednoexceptinherited

Increments the destruction counter.

Should be called in the destructor of any derived class that will be reference counted.

Definition at line 207 of file reference_counter.h.

References libMesh::err, libMesh::BasicOStreamProxy< charT, traits >::get(), libMesh::Quality::name(), and libMesh::Threads::spin_mtx.

Referenced by libMesh::ReferenceCountedObject< RBParametrized >::~ReferenceCountedObject().

{
  libmesh_try
  {
    Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
    std::pair<unsigned int, unsigned int> & p = _counts[name];
    p.second++;
  }
  libmesh_catch (...)
  {
    auto stream = libMesh::err.get();
    stream->exceptions(stream->goodbit); // stream must not throw
    libMesh::err << "Encountered unrecoverable error while calling "
                 << "ReferenceCounter::increment_destructor_count() "
                 << "for a(n) " << name << " object." << std::endl;
    std::terminate();
  }
}

init() [1/2]

template<typename T>

virtual void libMesh::EpetraMatrix< T >::init ( const numeric_index_type  m, const numeric_index_type  n, const numeric_index_type  m_l, const numeric_index_type  n_l, const numeric_index_type  nnz = 30, const numeric_index_type  noz = 10, const numeric_index_type  blocksize = 1  )

overridevirtual

Initialize SparseMatrix with the specified sizes.

Parameters

m	The global number of rows.
n	The global number of columns.
m_l	The local number of rows.
n_l	The local number of columns.
nnz	The number of on-diagonal nonzeros per row (defaults to 30).
noz	The number of off-diagonal nonzeros per row (defaults to 10).
blocksize	Optional value indicating dense coupled blocks for systems with multiple variables all of the same type.

Implements libMesh::SparseMatrix< T >.

init() [2/2]

template<typename T >

void libMesh::EpetraMatrix< T >::init ( ParallelType  type = PARALLEL )

overridevirtual

Initialize this matrix using the sparsity structure computed by dof_map.

Parameters

type	The serial/parallel/ghosted type of the matrix

Implements libMesh::SparseMatrix< T >.

Definition at line 177 of file trilinos_epetra_matrix.C.

References libMesh::libMeshPrivateData::_is_initialized, libMesh::initialized(), and libMesh::libmesh_assert().

{
  libmesh_assert(this->_dof_map);

  {
    // Clear initialized matrices
    if (this->initialized())
      this->clear();

    this->_is_initialized = true;
  }


  _mat = new Epetra_FECrsMatrix (Copy, *_graph);
}

initialized()

template<typename T>

virtual bool libMesh::SparseMatrix< T >::initialized ( ) const

inlinevirtualinherited

Returns

true if the matrix has been initialized, false otherwise.

Reimplemented in libMesh::StaticCondensation.

Definition at line 133 of file sparse_matrix.h.

Referenced by libMesh::PetscMatrix< T >::_get_submatrix(), libMesh::ImplicitSystem::assemble(), libMesh::System::init_matrices(), and libMesh::StaticCondensation::initialized().

{ return _is_initialized; }

l1_norm()

template<typename T >

Real libMesh::EpetraMatrix< T >::l1_norm ( ) const

overridevirtual

Returns

The \( \ell_1 \)-norm of the matrix, that is the max column sum: \( |M|_1 = \max_{j} \sum_{i} |M_{ij}| \)

This is the natural matrix norm that is compatible with the \( \ell_1 \)-norm for vectors, i.e. \( |Mv|_1 \leq |M|_1 |v|_1 \). (cf. Haemmerlin-Hoffmann : Numerische Mathematik)

Implements libMesh::SparseMatrix< T >.

Definition at line 249 of file trilinos_epetra_matrix.C.

References libMesh::initialized(), libMesh::libmesh_assert(), and libMesh::Real.

{
  libmesh_assert (this->initialized());

  libmesh_assert(_mat);

  return static_cast<Real>(_mat->NormOne());
}

l1_norm_diff()

template<typename T>

Real libMesh::SparseMatrix< T >::l1_norm_diff ( const SparseMatrix< T > &  other_mat ) const

inherited

Returns

The l1_norm() of the difference of this and other_mat

Definition at line 1362 of file sparse_matrix.C.

{
  auto diff_mat = this->clone();
  diff_mat->add(-1.0, other_mat);
  return diff_mat->l1_norm();
}

linfty_norm()

template<typename T >

Real libMesh::EpetraMatrix< T >::linfty_norm ( ) const

overridevirtual

Returns

The \( \ell_{\infty} \)-norm of the matrix, that is the max row sum:

\( |M|_{\infty} = \max_{i} \sum_{j} |M_{ij}| \)

This is the natural matrix norm that is compatible to the \( \ell_{\infty} \)-norm of vectors, i.e. \( |Mv|_{\infty} \leq |M|_{\infty} |v|_{\infty} \). (cf. Haemmerlin-Hoffmann : Numerische Mathematik)

Implements libMesh::SparseMatrix< T >.

Definition at line 261 of file trilinos_epetra_matrix.C.

References libMesh::initialized(), libMesh::libmesh_assert(), and libMesh::Real.

{
  libmesh_assert (this->initialized());


  libmesh_assert(_mat);

  return static_cast<Real>(_mat->NormInf());
}

local_m()

template<typename T>

virtual numeric_index_type libMesh::SparseMatrix< T >::local_m ( ) const

inlinevirtualinherited

Get the number of rows owned by this process.

Reimplemented in libMesh::PetscMatrixBase< T >, libMesh::PetscMatrixBase< libMesh::Number >, and libMesh::PetscMatrixBase< Number >.

Definition at line 254 of file sparse_matrix.h.

Referenced by libMesh::CondensedEigenSystem::copy_super_to_sub().

{ return row_stop() - row_start(); }

local_n()

template<typename T>

virtual numeric_index_type libMesh::SparseMatrix< T >::local_n ( ) const

inlinevirtualinherited

Get the number of columns owned by this process.

Reimplemented in libMesh::PetscMatrixBase< T >, libMesh::PetscMatrixBase< libMesh::Number >, and libMesh::PetscMatrixBase< Number >.

Definition at line 259 of file sparse_matrix.h.

{ return col_stop() - col_start(); }

m()

template<typename T >

numeric_index_type libMesh::EpetraMatrix< T >::m ( ) const

overridevirtual

Returns

The row-dimension of the matrix.

Implements libMesh::SparseMatrix< T >.

Definition at line 402 of file trilinos_epetra_matrix.C.

References libMesh::initialized(), and libMesh::libmesh_assert().

Referenced by libMesh::EpetraMatrix< T >::EpetraMatrix().

{
  libmesh_assert (this->initialized());

  return static_cast<numeric_index_type>(_mat->NumGlobalRows());
}

mat() [1/2]

template<typename T>

Epetra_FECrsMatrix* libMesh::EpetraMatrix< T >::mat ( )

inline

Returns

The raw Epetra_FECrsMatrix pointer.

Note

This is generally not required in user-level code.

Don't do anything crazy like deleting the pointer, or very bad things will likely happen!

Definition at line 217 of file trilinos_epetra_matrix.h.

References libMesh::EpetraMatrix< T >::_mat, and libMesh::libmesh_assert().

Referenced by libMesh::TrilinosPreconditioner< T >::init(), libMesh::NoxNonlinearSolver< Number >::solve(), and libMesh::AztecLinearSolver< T >::solve().

{ libmesh_assert(_mat); return _mat; }

mat() [2/2]

template<typename T>

const Epetra_FECrsMatrix* libMesh::EpetraMatrix< T >::mat ( ) const

inline

Definition at line 219 of file trilinos_epetra_matrix.h.

References libMesh::EpetraMatrix< T >::_mat, and libMesh::libmesh_assert().

{ libmesh_assert(_mat); return _mat; }

matrix_matrix_mult()

template<typename T>

virtual void libMesh::SparseMatrix< T >::matrix_matrix_mult ( SparseMatrix< T > &  , SparseMatrix< T > &  , bool    )

inlinevirtualinherited

Compute Y = A*X for matrix X.

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 349 of file sparse_matrix.h.

  { libmesh_not_implemented(); }

n()

template<typename T >

numeric_index_type libMesh::EpetraMatrix< T >::n ( ) const

overridevirtual

Returns

The column-dimension of the matrix.

Implements libMesh::SparseMatrix< T >.

Definition at line 412 of file trilinos_epetra_matrix.C.

References libMesh::initialized(), and libMesh::libmesh_assert().

{
  libmesh_assert (this->initialized());

  return static_cast<numeric_index_type>(_mat->NumGlobalCols());
}

n_nonzeros()

template<typename T >

std::size_t libMesh::SparseMatrix< T >::n_nonzeros ( ) const

virtualinherited

Returns

the global number of non-zero entries in the matrix sparsity pattern

Definition at line 266 of file sparse_matrix.C.

Referenced by libMesh::SparseMatrix< ValOut >::n_nonzeros().

{
  if (!_sp)
    return 0;
  return _sp->n_nonzeros();
}

n_objects()

static unsigned int libMesh::ReferenceCounter::n_objects ( )

inlinestaticinherited

Prints the number of outstanding (created, but not yet destroyed) objects.

Definition at line 85 of file reference_counter.h.

References libMesh::ReferenceCounter::_n_objects.

Referenced by libMesh::LibMeshInit::~LibMeshInit().

  { return _n_objects; }

n_processors()

processor_id_type libMesh::ParallelObject::n_processors ( ) const

inlineinherited

Returns

The number of processors in the group.

Definition at line 103 of file parallel_object.h.

References libMesh::ParallelObject::_communicator, libMesh::libmesh_assert(), and TIMPI::Communicator::size().

Referenced by libMesh::Partitioner::_find_global_index_by_pid_map(), libMesh::BoundaryInfo::_find_id_maps(), libMesh::DofMap::add_constraints_to_send_list(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::DistributedMesh::add_elem(), libMesh::DofMap::add_neighbors_to_send_list(), libMesh::DistributedMesh::add_node(), libMesh::System::add_vector(), libMesh::LaplaceMeshSmoother::allgather_graph(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::FEMSystem::assembly(), libMesh::Nemesis_IO::assert_symmetric_cmaps(), libMesh::Partitioner::assign_partitioning(), libMesh::AztecLinearSolver< T >::AztecLinearSolver(), libMesh::Partitioner::build_graph(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::DistributedMesh::clear(), libMesh::DistributedMesh::clear_elems(), libMesh::Nemesis_IO_Helper::compute_border_node_ids(), libMesh::Nemesis_IO_Helper::construct_nemesis_filename(), libMesh::UnstructuredMesh::copy_nodes_and_elements(), libMesh::Nemesis_IO::copy_scalar_solution(), libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::UnstructuredMesh::create_pid_mesh(), libMesh::MeshTools::create_processor_bounding_box(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_scalar_dofs(), libMesh::DistributedMesh::DistributedMesh(), libMesh::EnsightIO::EnsightIO(), libMesh::RBEIMEvaluation::gather_bfs(), libMesh::MeshBase::get_info(), libMesh::StaticCondensation::init(), libMesh::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_petscdm(), libMesh::Nemesis_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::DistributedMesh::insert_elem(), libMesh::NumericVector< Number >::is_effectively_ghosted(), libMesh::NumericVector< Number >::is_effectively_serial(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_new_node_procids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_topology_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_valid_boundary_ids(), libMesh::MeshTools::libmesh_assert_valid_dof_ids(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::MeshTools::libmesh_assert_valid_refinement_flags(), libMesh::DofMap::local_variable_indices(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshBase::n_active_elem_on_proc(), libMesh::DofMap::n_dofs_per_processor(), libMesh::MeshBase::n_elem_on_proc(), libMesh::MeshBase::n_nodes_on_proc(), libMesh::RBEIMEvaluation::node_gather_bfs(), libMesh::Partitioner::partition(), libMesh::MeshBase::partition(), libMesh::Partitioner::partition_unpartitioned_elements(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::DofMap::prepare_send_list(), libMesh::MeshBase::print_constraint_rows(), libMesh::DofMap::print_dof_constraints(), libMesh::NameBasedIO::read(), libMesh::Nemesis_IO::read(), libMesh::CheckpointIO::read(), libMesh::CheckpointIO::read_connectivity(), libMesh::XdrIO::read_header(), libMesh::CheckpointIO::read_nodes(), libMesh::System::read_parallel_data(), libMesh::System::read_SCALAR_dofs(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::System::read_serialized_vector(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::Partitioner::repartition(), OverlappingFunctorTest::run_partitioner_test(), libMesh::DofMap::scatter_constraints(), libMesh::DistributedMesh::set_next_unique_id(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::PetscDMWrapper::set_point_range_in_section(), WriteVecAndScalar::setupTests(), libMesh::RBEIMEvaluation::side_gather_bfs(), DistributedMeshTest::testRemoteElemError(), CheckpointIOTest::testSplitter(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::DistributedMesh::update_parallel_id_counts(), libMesh::GMVIO::write_binary(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::ExodusII_IO_Helper::write_nodal_coordinates(), libMesh::VTKIO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data(), libMesh::System::write_parallel_data(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), and libMesh::XdrIO::write_serialized_nodesets().

  {
    processor_id_type returnval =
      cast_int<processor_id_type>(_communicator.size());
    libmesh_assert(returnval); // We never have an empty comm
    return returnval;
  }

need_full_sparsity_pattern()

template<typename T>

virtual bool libMesh::EpetraMatrix< T >::need_full_sparsity_pattern ( ) const

inlineoverridevirtual

The EpetraMatrix needs the full sparsity pattern.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 113 of file trilinos_epetra_matrix.h.

  { return true; }

operator()()

template<typename T >

T libMesh::EpetraMatrix< T >::operator() ( const numeric_index_type  i, const numeric_index_type  j  ) const

overridevirtual

Returns

A copy of matrix entry (i,j).

Note

This may be an expensive operation, and you should always be careful where you call this function.

Implements libMesh::SparseMatrix< T >.

Definition at line 537 of file trilinos_epetra_matrix.C.

References libMesh::initialized(), and libMesh::libmesh_assert().

{
  libmesh_assert (this->initialized());
  libmesh_assert(this->_mat);
  libmesh_assert (this->_mat->MyGlobalRow(static_cast<int>(i)));
  libmesh_assert_greater_equal (i, this->row_start());
  libmesh_assert_less (i, this->row_stop());


  int row_length;
  int * row_indices;
  double * values;

  _mat->ExtractMyRowView (i-this->row_start(),
                          row_length,
                          values,
                          row_indices);

  //libMesh::out << "row_length=" << row_length << std::endl;

  int * index = std::lower_bound (row_indices, row_indices+row_length, j);

  libmesh_assert_less (*index, row_length);
  libmesh_assert_equal_to (static_cast<numeric_index_type>(row_indices[*index]), j);

  //libMesh::out << "val=" << values[*index] << std::endl;

  return values[*index];
}

operator=() [1/3]

template<typename T>

EpetraMatrix& libMesh::EpetraMatrix< T >::operator= ( const EpetraMatrix< T > &  )

delete

operator=() [2/3]

template<typename T>

EpetraMatrix& libMesh::EpetraMatrix< T >::operator= ( EpetraMatrix< T > &&  )

delete

operator=() [3/3]

template<typename T>

virtual SparseMatrix<T>& libMesh::EpetraMatrix< T >::operator= ( const SparseMatrix< T > &  )

inlineoverridevirtual

This looks like a copy assignment operator, but note that, unlike normal copy assignment operators, it is pure virtual.

This function should be overridden in derived classes so that they can be copied correctly via references to the base class. This design usually isn't a good idea in general, but in this context it works because we usually don't have a mix of different kinds of SparseMatrix active in the library at a single time.

Returns

A reference to *this as the base type.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 99 of file trilinos_epetra_matrix.h.

  {
    libmesh_not_implemented();
    return *this;
  }

print() [1/3]

template<>

void libMesh::SparseMatrix< Complex >::print ( std::ostream &  os, const bool  sparse  ) const

inherited

Definition at line 159 of file sparse_matrix.C.

{
  // std::complex<>::operator<<() is defined, but use this form

  if (sparse)
    {
      libmesh_not_implemented();
    }

  os << "Real part:" << std::endl;
  for (auto i : make_range(this->m()))
    {
      for (auto j : make_range(this->n()))
        os << std::setw(8) << (*this)(i,j).real() << " ";
      os << std::endl;
    }

  os << std::endl << "Imaginary part:" << std::endl;
  for (auto i : make_range(this->m()))
    {
      for (auto j : make_range(this->n()))
        os << std::setw(8) << (*this)(i,j).imag() << " ";
      os << std::endl;
    }
}

print() [2/3]

template<typename T >

void libMesh::SparseMatrix< T >::print ( std::ostream &  os = libMesh::out, const bool  sparse = false  ) const

inherited

Print the contents of the matrix to the screen in a uniform style, regardless of matrix/solver package being used.

Definition at line 275 of file sparse_matrix.C.

Referenced by libMesh::EigenSparseMatrix< T >::print_personal(), and libMesh::LaspackMatrix< T >::print_personal().

{
  parallel_object_only();

  libmesh_assert (this->initialized());

  const numeric_index_type first_dof = this->row_start(),
                           end_dof   = this->row_stop();

  // We'll print the matrix from processor 0 to make sure
  // it's serialized properly
  if (this->processor_id() == 0)
    {
      libmesh_assert_equal_to (first_dof, 0);
      for (numeric_index_type i : make_range(end_dof))
        {
          if (sparse)
            {
              for (auto j : make_range(this->n()))
                {
                  T c = (*this)(i,j);
                  if (c != static_cast<T>(0.0))
                    {
                      os << i << " " << j << " " << c << std::endl;
                    }
                }
            }
          else
            {
              for (auto j : make_range(this->n()))
                os << (*this)(i,j) << " ";
              os << std::endl;
            }
        }

      std::vector<numeric_index_type> ibuf, jbuf;
      std::vector<T> cbuf;
      numeric_index_type currenti = end_dof;
      for (auto p : IntRange<processor_id_type>(1, this->n_processors()))
        {
          this->comm().receive(p, ibuf);
          this->comm().receive(p, jbuf);
          this->comm().receive(p, cbuf);
          libmesh_assert_equal_to (ibuf.size(), jbuf.size());
          libmesh_assert_equal_to (ibuf.size(), cbuf.size());

          if (ibuf.empty())
            continue;
          libmesh_assert_greater_equal (ibuf.front(), currenti);
          libmesh_assert_greater_equal (ibuf.back(), ibuf.front());

          std::size_t currentb = 0;
          for (;currenti <= ibuf.back(); ++currenti)
            {
              if (sparse)
                {
                  for (numeric_index_type j=0; j<this->n(); j++)
                    {
                      if (currentb < ibuf.size() &&
                          ibuf[currentb] == currenti &&
                          jbuf[currentb] == j)
                        {
                          os << currenti << " " << j << " " << cbuf[currentb] << std::endl;
                          currentb++;
                        }
                    }
                }
              else
                {
                  for (auto j : make_range(this->n()))
                    {
                      if (currentb < ibuf.size() &&
                          ibuf[currentb] == currenti &&
                          jbuf[currentb] == j)
                        {
                          os << cbuf[currentb] << " ";
                          currentb++;
                        }
                      else
                        os << static_cast<T>(0.0) << " ";
                    }
                  os << std::endl;
                }
            }
        }
      if (!sparse)
        {
          for (; currenti != this->m(); ++currenti)
            {
              for (numeric_index_type j=0; j<this->n(); j++)
                os << static_cast<T>(0.0) << " ";
              os << std::endl;
            }
        }
    }
  else
    {
      std::vector<numeric_index_type> ibuf, jbuf;
      std::vector<T> cbuf;

      // We'll assume each processor has access to entire
      // matrix rows, so (*this)(i,j) is valid if i is a local index.
      for (numeric_index_type i : make_range(first_dof, end_dof))
        {
          for (auto j : make_range(this->n()))
            {
              T c = (*this)(i,j);
              if (c != static_cast<T>(0.0))
                {
                  ibuf.push_back(i);
                  jbuf.push_back(j);
                  cbuf.push_back(c);
                }
            }
        }
      this->comm().send(0,ibuf);
      this->comm().send(0,jbuf);
      this->comm().send(0,cbuf);
    }
}

print() [3/3]

template<typename T >

void libMesh::SparseMatrix< T >::print ( const std::string &  filename ) const

inherited

Print the contents of the matrix to a file, with a file format depending on the extension of filename.

Definition at line 754 of file sparse_matrix.C.

{
  {
    std::ofstream outstr (filename.c_str());
    libmesh_error_msg_if
      (!outstr.good(), "ERROR: cannot write to file:\n\t" <<
       filename);
  }

  std::string_view basename = Utility::basename_of(filename);

  const bool gzipped_file = Utility::ends_with(filename, ".gz");

  if (gzipped_file)
    basename.remove_suffix(3);

  if (Utility::ends_with(basename, ".matlab") ||
      Utility::ends_with(basename, ".m"))
    this->print_matlab(filename);
  else if (Utility::ends_with(basename, ".petsc64"))
    {
#ifndef LIBMESH_HAVE_PETSC
      libmesh_error_msg("Cannot load PETSc matrix file " <<
                        filename << " without PETSc-enabled libMesh.");
#elif LIBMESH_DOF_ID_BYTES != 8
      libmesh_error_msg("Cannot load 64-bit PETSc matrix file " <<
                        filename << " with non-64-bit libMesh.");
#endif
      if (gzipped_file)
        libmesh_not_implemented_msg("Gzipped PETSc matrices are not currently supported");
      this->print_petsc_binary(filename);
    }
  else if (Utility::ends_with(basename, ".petsc32"))
    {
#ifndef LIBMESH_HAVE_PETSC
      libmesh_error_msg("Cannot load PETSc matrix file " <<
                        filename << " without PETSc-enabled libMesh.");
#elif LIBMESH_DOF_ID_BYTES != 4
      libmesh_error_msg("Cannot load 32-bit PETSc matrix file " <<
                        filename << " with non-32-bit libMesh.");
#endif
      if (gzipped_file)
        libmesh_not_implemented_msg("Gzipped PETSc matrices are not currently supported");
      this->print_petsc_binary(filename);
    }
  else if (Utility::ends_with(basename, ".h5"))
    {
      if (gzipped_file)
        libmesh_not_implemented_msg("Gzipped HDF5 matrices are not currently supported");
      this->print_coreform_hdf5(filename);
    }
  else
    libmesh_error_msg(" ERROR: Unrecognized matrix file extension on: "
                      << basename
                      << "\n   I understand the following:\n\n"
                      << "     *.h5        -- CoreForm HDF5 sparse matrix format\n"
                      << "     *.matlab    -- Matlab sparse matrix format\n"
                      << "     *.matlab.gz -- Matlab sparse matrix format, gzipped\n"
                      << "     *.m         -- Matlab sparse matrix format\n"
                      << "     *.m.gz      -- Matlab sparse matrix format, gzipped\n"
                      << "     *.petsc32   -- PETSc binary format, 32-bit\n"
                      << "     *.petsc64   -- PETSc binary format, 64-bit\n"
                     );
}

print_coreform_hdf5()

template<typename T >

void libMesh::SparseMatrix< T >::print_coreform_hdf5 ( const std::string &  filename, const std::string &  groupname = "extraction"  ) const

virtualinherited

Print the contents of the matrix to a file, with the HDF5 sparse matrix format used by CoreForm, putting CSR sparse matrix data in the group given by groupname.

Definition at line 521 of file sparse_matrix.C.

{
#if defined(LIBMESH_USE_COMPLEX_NUMBERS) || !defined(LIBMESH_HAVE_HDF5)
  // TODO: HDF5 version 2.0.0 and later adds native support for
  // complex numbers with the H5T_NATIVE_DOUBLE_COMPLEX type [0], so
  // we could consider supporting T==std::complex<Real> in the future.
  // [0]: https://forum.hdfgroup.org/t/coming-in-the-next-hdf5-release-native-support-for-complex-number-datatypes/13543
  libmesh_ignore(filename, groupname);
  libmesh_error_msg("ERROR: need HDF5 support to handle .h5 files!!!");
#else
  LOG_SCOPE("print_coreform_hdf5()", "SparseMatrix");

  // In this implementation, we copy the SparseMatrix entries into a
  // std::vector<double>, so this won't work for any Number type for
  // which sizeof(Number) > sizeof(double).
  if constexpr (sizeof(T) > sizeof(double))
    libmesh_not_implemented();

  const numeric_index_type first_dof = this->row_start(),
                           end_dof   = this->row_stop();

  std::vector<std::size_t> cols, row_offsets;
  std::vector<double> vals;

  if (this->processor_id() == 0)
    row_offsets.push_back(0);

  for (numeric_index_type i : make_range(first_dof, end_dof))
    {
      for (auto j : make_range(this->n()))
        {
          T c = (*this)(i,j);
          if (c != static_cast<T>(0.0))
            {
              cols.push_back(j);
              vals.push_back(c);
            }
        }
      // This is a *local* row offset; proc 0 may need to adjust later
      row_offsets.push_back(cols.size());
    }

  if (this->processor_id() == 0)
    {
      const hid_t file = H5Fcreate(filename.c_str(), H5F_ACC_TRUNC,
                                   H5P_DEFAULT, H5P_DEFAULT);
      if (file == H5I_INVALID_HID)
        libmesh_file_error(filename);

      const hid_t group =
        H5Gcreate2(file, groupname.c_str(), H5P_DEFAULT, H5P_DEFAULT,
                   H5P_DEFAULT);
      check_open(filename, group, groupname);

      auto write_size_attribute = [&filename, &group]
        (const std::string & attribute_name, unsigned long long writeval)
      {
        const hid_t fspace = H5Screate(H5S_SCALAR);
        check_hdf5(filename, fspace, attribute_name + " fspace");

        const hid_t attr = H5Acreate2(group, attribute_name.c_str(),
                                      H5T_STD_I64LE, fspace,
                                      H5P_DEFAULT, H5P_DEFAULT);
        check_hdf5(filename, attr, attribute_name);

        // HDF5 is supposed to handle both upscaling and endianness
        // conversions here
        const herr_t errval = H5Awrite(attr, H5T_NATIVE_ULLONG, &writeval);
        check_hdf5(filename, errval, attribute_name + " write");

        H5Aclose(attr);
        H5Sclose(fspace);
      };

      write_size_attribute("num_cols", this->n());
      write_size_attribute("num_rows", this->m());

      auto write_vector = [&filename, &group]
        (const std::string & dataname, auto hdf5_file_type,
         auto hdf5_native_type, auto & datavec)
      {
        const hsize_t len[1] = {cast_int<hsize_t>(datavec.size())};

        const hid_t space = H5Screate_simple(1, len, nullptr);
        check_hdf5(filename, space, dataname + " space");

        const hid_t data =
          H5Dcreate2(group, dataname.c_str(), hdf5_file_type, space,
                     H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
        check_hdf5(filename, data, dataname + " data");

        const hid_t errval =
          H5Dwrite(data, hdf5_native_type, H5S_ALL, H5S_ALL,
                   H5P_DEFAULT, datavec.data());
        check_hdf5(filename, errval, dataname + " write");

        H5Dclose(data);
        H5Sclose(space);
      };

      std::vector<std::size_t> vals_sizes, first_dofs;
      this->comm().gather(0, vals.size(), vals_sizes);
      this->comm().gather(0, cast_int<std::size_t>(first_dof), first_dofs);
      first_dofs.push_back(this->m());

      this->comm().allgather(cols);
      this->comm().allgather(vals);
      this->comm().allgather(row_offsets);

      libmesh_assert_equal_to(vals.size(),
                              cols.size());
      libmesh_assert_equal_to(vals.size(),
                              std::accumulate(vals_sizes.begin(),
                                              vals_sizes.end(),
                                              std::size_t(0)));

      std::size_t extra_offset = 0;
      for (auto p : make_range(processor_id_type(1), this->n_processors()))
        {
          extra_offset += vals_sizes[p-1];
          for (auto i : make_range(first_dofs[p]+1, first_dofs[p+1]+1))
            row_offsets[i] += extra_offset;
        }

      write_vector("cols", H5T_STD_U64LE, H5T_NATIVE_ULLONG, cols);
      write_vector("row_offsets", H5T_STD_U64LE, H5T_NATIVE_ULLONG, row_offsets);
      write_vector("vals", H5T_IEEE_F64LE, H5T_NATIVE_DOUBLE, vals);

      H5Gclose(group);
      H5Fclose(file);
    }
  else
    {
      std::vector<std::size_t> dummy;
      this->comm().gather(0, vals.size(), dummy);
      this->comm().gather(0, cast_int<std::size_t>(first_dof), dummy);
      this->comm().allgather(cols);
      this->comm().allgather(vals);
      this->comm().allgather(row_offsets);
    }
#endif // LIBMESH_HAVE_HDF5
}

print_info()

void libMesh::ReferenceCounter::print_info ( std::ostream &  out_stream = libMesh::out )

staticinherited

Prints the reference information, by default to libMesh::out.

Definition at line 81 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter, and libMesh::ReferenceCounter::get_info().

Referenced by libMesh::LibMeshInit::~LibMeshInit().

{
  if (_enable_print_counter)
    out_stream << ReferenceCounter::get_info();
}

print_matlab()

template<typename T >

void libMesh::SparseMatrix< T >::print_matlab ( const std::string &  name = "" ) const

virtualinherited

Print the contents of the matrix in Matlab's sparse matrix format.

Optionally prints the matrix to the file named name. If name is not specified it is dumped to the screen.

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 398 of file sparse_matrix.C.

{
  parallel_object_only();

  libmesh_assert (this->initialized());

  const numeric_index_type first_dof = this->row_start(),
                           end_dof   = this->row_stop();

  // We'll print the matrix from processor 0 to make sure
  // it's serialized properly
  if (this->processor_id() == 0)
    {
      std::unique_ptr<std::ofstream> file;

      if (name != "")
        file = std::make_unique<std::ofstream>(name.c_str());

      std::ostream & os = (name == "") ? libMesh::out : *file;

      std::size_t sparsity_nonzeros = this->n_nonzeros();

      std::size_t real_nonzeros = 0;

      libmesh_assert_equal_to(first_dof, 0);
      for (numeric_index_type i : make_range(end_dof))
        {
          for (auto j : make_range(this->n()))
            {
              T c = (*this)(i,j);
              if (c != static_cast<T>(0.0))
                ++real_nonzeros;
            }
        }


      for (auto p : IntRange<processor_id_type>(1, this->n_processors()))
        {
          std::size_t nonzeros_on_p = 0;
          this->comm().receive(p, nonzeros_on_p);
          real_nonzeros += nonzeros_on_p;
        }

      if (sparsity_nonzeros &&
          sparsity_nonzeros != real_nonzeros)
        libmesh_warning(sparsity_nonzeros <<
                        " nonzeros allocated, but " <<
                        real_nonzeros << " used.");

      // We probably want to be more consistent than that, if our
      // sparsity is overallocated.

      // Print a header similar to PETSc's mat_view ascii_matlab
      os << "%Mat Object: () " << this->n_processors() << " MPI processes\n"
         << "%  type: " << (this->n_processors() > 1 ? "mpi" : "seq") << "aij\n"
         << "% Size = " << this->m() << ' ' << this->n() << '\n'
         << "% Nonzeros = " << real_nonzeros << '\n'
         << "zzz = zeros(" << real_nonzeros << ",3);\n"
         << "zzz = [\n";

      for (numeric_index_type i : make_range(end_dof))
        {
          // FIXME - we need a base class way to iterate over a
          // SparseMatrix row.
          for (auto j : make_range(this->n()))
            {
              T c = (*this)(i,j);
              if (c != static_cast<T>(0.0))
                {
                  // Convert from 0-based to 1-based indexing
                  os << (i+1) << ' ' << (j+1) << "  " << c << '\n';
                }
            }
        }

      std::vector<numeric_index_type> ibuf, jbuf;
      std::vector<T> cbuf;
      for (auto p : IntRange<processor_id_type>(1, this->n_processors()))
        {
          this->comm().receive(p, ibuf);
          this->comm().receive(p, jbuf);
          this->comm().receive(p, cbuf);
          libmesh_assert_equal_to (ibuf.size(), jbuf.size());
          libmesh_assert_equal_to (ibuf.size(), cbuf.size());

          for (auto n : index_range(ibuf))
            os << ibuf[n] << ' ' << jbuf[n] << "  " << cbuf[n] << '\n';
        }

      os << "];\n" << "Mat_sparse = spconvert(zzz);" << std::endl;
    }
  else
    {
      std::vector<numeric_index_type> ibuf, jbuf;
      std::vector<T> cbuf;
      std::size_t my_nonzeros = 0;

      // We'll assume each processor has access to entire
      // matrix rows, so (*this)(i,j) is valid if i is a local index.
      for (numeric_index_type i : make_range(first_dof, end_dof))
        {
          for (auto j : make_range(this->n()))
            {
              T c = (*this)(i,j);
              if (c != static_cast<T>(0.0))
                {
                  ibuf.push_back(i);
                  jbuf.push_back(j);
                  cbuf.push_back(c);
                  ++my_nonzeros;
                }
            }
        }
      this->comm().send(0,my_nonzeros);
      this->comm().send(0,ibuf);
      this->comm().send(0,jbuf);
      this->comm().send(0,cbuf);
    }
}

print_personal()

template<typename T >

void libMesh::EpetraMatrix< T >::print_personal ( std::ostream &  os = libMesh::out ) const

overridevirtual

Print the contents of the matrix to the screen in a package-personalized style, if available.

Implements libMesh::SparseMatrix< T >.

Definition at line 593 of file trilinos_epetra_matrix.C.

References libMesh::initialized(), and libMesh::libmesh_assert().

{
  libmesh_assert (this->initialized());
  libmesh_assert(_mat);

  os << *_mat;
}

print_petsc_binary()

template<typename T >

void libMesh::SparseMatrix< T >::print_petsc_binary ( const std::string &  filename ) const

virtualinherited

Write the contents of the matrix to a file in PETSc's binary sparse matrix format.

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 668 of file sparse_matrix.C.

{
  libmesh_not_implemented_msg
    ("libMesh cannot write PETSc binary-format files from non-PETSc matrices");
}

print_petsc_hdf5()

template<typename T >

void libMesh::SparseMatrix< T >::print_petsc_hdf5 ( const std::string &  filename ) const

virtualinherited

Write the contents of the matrix to a file in PETSc's HDF5 sparse matrix format.

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 677 of file sparse_matrix.C.

{
  libmesh_not_implemented_msg
    ("libMesh cannot write PETSc HDF5-format files from non-PETSc matrices");
}

processor_id()

processor_id_type libMesh::ParallelObject::processor_id ( ) const

inlineinherited

Returns

The rank of this processor in the group.

Definition at line 114 of file parallel_object.h.

References libMesh::ParallelObject::_communicator, and TIMPI::Communicator::rank().

Referenced by libMesh::BoundaryInfo::_find_id_maps(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::DistributedMesh::add_elem(), libMesh::BoundaryInfo::add_elements(), libMesh::DofMap::add_neighbors_to_send_list(), libMesh::DistributedMesh::add_node(), libMesh::MeshTools::Modification::all_tri(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::FEMSystem::assembly(), libMesh::Nemesis_IO::assert_symmetric_cmaps(), libMesh::Partitioner::assign_partitioning(), libMesh::Nemesis_IO_Helper::build_element_and_node_maps(), libMesh::Partitioner::build_graph(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::MeshFunction::check_found_elem(), libMesh::DistributedMesh::clear(), libMesh::DistributedMesh::clear_elems(), libMesh::ExodusII_IO_Helper::close(), libMesh::Nemesis_IO_Helper::compute_border_node_ids(), libMesh::Nemesis_IO_Helper::compute_communication_map_parameters(), libMesh::Nemesis_IO_Helper::compute_internal_and_border_elems_and_internal_nodes(), libMesh::RBConstruction::compute_max_error_bound(), libMesh::Nemesis_IO_Helper::compute_node_communication_maps(), libMesh::Nemesis_IO_Helper::compute_num_global_elem_blocks(), libMesh::Nemesis_IO_Helper::compute_num_global_nodesets(), libMesh::Nemesis_IO_Helper::compute_num_global_sidesets(), libMesh::Nemesis_IO_Helper::construct_nemesis_filename(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::Nemesis_IO::copy_scalar_solution(), libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::ExodusII_IO_Helper::create(), libMesh::DistributedMesh::delete_elem(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_scalar_dofs(), libMesh::DistributedMesh::DistributedMesh(), libMesh::DofMapBase::end_dof(), libMesh::DofMapBase::end_old_dof(), libMesh::EnsightIO::EnsightIO(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::SubFunctor::find_dofs_to_send(), libMesh::UnstructuredMesh::find_neighbors(), libMesh::DofMapBase::first_dof(), libMesh::DofMapBase::first_old_dof(), libMesh::RBEIMEvaluation::gather_bfs(), libMesh::Nemesis_IO_Helper::get_cmap_params(), libMesh::Nemesis_IO_Helper::get_eb_info_global(), libMesh::Nemesis_IO_Helper::get_elem_cmap(), libMesh::Nemesis_IO_Helper::get_elem_map(), libMesh::MeshBase::get_info(), libMesh::DofMap::get_info(), libMesh::Nemesis_IO_Helper::get_init_global(), libMesh::Nemesis_IO_Helper::get_init_info(), libMesh::RBEIMEvaluation::get_interior_basis_functions_as_vecs(), libMesh::Nemesis_IO_Helper::get_loadbal_param(), libMesh::DofMap::get_local_constraints(), libMesh::MeshBase::get_local_constraints(), libMesh::Nemesis_IO_Helper::get_node_cmap(), libMesh::Nemesis_IO_Helper::get_node_map(), libMesh::Nemesis_IO_Helper::get_ns_param_global(), libMesh::Nemesis_IO_Helper::get_ss_param_global(), libMesh::SparsityPattern::Build::handle_vi_vj(), libMesh::LaplaceMeshSmoother::init(), libMesh::SystemSubsetBySubdomain::init(), HeatSystem::init_data(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::initialize_element_variables(), libMesh::ExodusII_IO_Helper::initialize_global_variables(), libMesh::ExodusII_IO_Helper::initialize_nodal_variables(), libMesh::DistributedMesh::insert_elem(), libMesh::DofMap::is_evaluable(), libMesh::SparsityPattern::Build::join(), libMesh::TransientRBEvaluation::legacy_write_offline_data_to_files(), libMesh::RBSCMEvaluation::legacy_write_offline_data_to_files(), libMesh::RBEvaluation::legacy_write_offline_data_to_files(), libMesh::MeshTools::libmesh_assert_consistent_distributed(), libMesh::MeshTools::libmesh_assert_consistent_distributed_nodes(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_object_ids(), libMesh::DofMap::local_variable_indices(), main(), libMesh::MeshRefinement::make_coarsening_compatible(), AugmentSparsityOnInterface::mesh_reinit(), libMesh::TriangulatorInterface::MeshedHole::MeshedHole(), libMesh::MeshBase::n_active_local_elem(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::MeshTools::n_connected_components(), libMesh::MeshBase::n_constraint_rows(), libMesh::BoundaryInfo::n_edge_conds(), libMesh::DofMapBase::n_local_dofs(), libMesh::MeshBase::n_local_elem(), libMesh::MeshBase::n_local_nodes(), libMesh::BoundaryInfo::n_nodeset_conds(), libMesh::BoundaryInfo::n_shellface_conds(), libMesh::RBEIMEvaluation::node_gather_bfs(), libMesh::DistributedMesh::own_node(), libMesh::BoundaryInfo::parallel_sync_node_ids(), libMesh::BoundaryInfo::parallel_sync_side_ids(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::MeshBase::print_constraint_rows(), libMesh::DofMap::print_dof_constraints(), libMesh::DofMap::process_mesh_constraint_rows(), libMesh::Nemesis_IO_Helper::put_cmap_params(), libMesh::Nemesis_IO_Helper::put_elem_cmap(), libMesh::Nemesis_IO_Helper::put_elem_map(), libMesh::Nemesis_IO_Helper::put_loadbal_param(), libMesh::Nemesis_IO_Helper::put_node_cmap(), libMesh::Nemesis_IO_Helper::put_node_map(), libMesh::NameBasedIO::read(), libMesh::Nemesis_IO::read(), libMesh::XdrIO::read(), libMesh::CheckpointIO::read(), libMesh::EquationSystems::read(), libMesh::ExodusII_IO_Helper::read_elem_num_map(), libMesh::ExodusII_IO_Helper::read_global_values(), libMesh::ExodusII_IO::read_header(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::System::read_header(), libMesh::DynaIO::read_mesh(), libMesh::ExodusII_IO_Helper::read_node_num_map(), libMesh::System::read_parallel_data(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), libMesh::System::read_SCALAR_dofs(), libMesh::XdrIO::read_serialized_bc_names(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::System::read_serialized_data(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::System::read_serialized_vector(), libMesh::System::read_serialized_vectors(), libMesh::Nemesis_IO_Helper::read_var_names_impl(), libMesh::SimplexRefiner::refine_via_edges(), libMesh::StaticCondensationDofMap::reinit(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::DistributedMesh::renumber_nodes_and_elements(), libMesh::DofMap::scatter_constraints(), libMesh::CheckpointIO::select_split_config(), libMesh::DistributedMesh::set_next_unique_id(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::RBEIMEvaluation::side_gather_bfs(), MeshFunctionTest::test_bad_gradient_var_with_out_of_mesh_value(), MeshFunctionTest::test_bad_hessian_var_with_out_of_mesh_value(), ExodusTest< elem_type >::test_read_gold(), ExodusTest< elem_type >::test_write(), MeshInputTest::testAbaqusRead(), MeshInputTest::testBadGmsh(), BoundaryInfoTest::testBoundaryIDs(), MeshInputTest::testCopyElementSolutionImpl(), MeshInputTest::testCopyElementVectorImpl(), MeshInputTest::testCopyNodalSolutionImpl(), DefaultCouplingTest::testCoupling(), PointNeighborCouplingTest::testCoupling(), MeshInputTest::testDynaFileMappings(), MeshInputTest::testDynaNoSplines(), MeshInputTest::testDynaReadElem(), MeshInputTest::testDynaReadPatch(), MeshInputTest::testExodusFileMappings(), MeshInputTest::testExodusIGASidesets(), MeshInputTest::testExodusWriteElementDataFromDiscontinuousNodalData(), MeshInputTest::testGmshBCIDOverlap(), MeshInputTest::testGoodGmsh(), MeshInputTest::testGoodSTL(), MeshInputTest::testGoodSTLBinary(), BoundaryInfoTest::testInternalBoundary(), MeshInputTest::testLowOrderEdgeBlocks(), SystemsTest::testProjectMatrix3D(), BoundaryInfoTest::testShellFaceConstraints(), MeshInputTest::testSingleElementImpl(), WriteVecAndScalar::testSolution(), CheckpointIOTest::testSplitter(), MeshInputTest::testTetgenIO(), MeshSmootherTest::testVariationalSmoother(), libMesh::MeshTools::total_weight(), libMesh::NetGenMeshInterface::triangulate(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::DistributedMesh::update_parallel_id_counts(), libMesh::DTKAdapter::update_variable_values(), libMesh::MeshTools::volume(), libMesh::STLIO::write(), libMesh::NameBasedIO::write(), libMesh::XdrIO::write(), libMesh::CheckpointIO::write(), libMesh::EquationSystems::write(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::ExodusII_IO::write_element_data(), libMesh::ExodusII_IO_Helper::write_element_values(), libMesh::ExodusII_IO_Helper::write_element_values_element_major(), libMesh::ExodusII_IO_Helper::write_elements(), libMesh::ExodusII_IO_Helper::write_elemset_data(), libMesh::ExodusII_IO_Helper::write_elemsets(), libMesh::ExodusII_IO::write_global_data(), libMesh::ExodusII_IO_Helper::write_global_values(), libMesh::System::write_header(), libMesh::ExodusII_IO::write_information_records(), libMesh::ExodusII_IO_Helper::write_information_records(), libMesh::ExodusII_IO_Helper::write_nodal_coordinates(), libMesh::UCDIO::write_nodal_data(), libMesh::VTKIO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data_common(), libMesh::ExodusII_IO::write_nodal_data_discontinuous(), libMesh::ExodusII_IO_Helper::write_nodal_values(), libMesh::ExodusII_IO_Helper::write_nodeset_data(), libMesh::Nemesis_IO_Helper::write_nodesets(), libMesh::ExodusII_IO_Helper::write_nodesets(), libMesh::RBEIMEvaluation::write_out_interior_basis_functions(), libMesh::RBEIMEvaluation::write_out_node_basis_functions(), libMesh::RBEIMEvaluation::write_out_side_basis_functions(), write_output_solvedata(), libMesh::System::write_parallel_data(), libMesh::RBConstruction::write_riesz_representors_to_files(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bc_names(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::System::write_serialized_data(), libMesh::XdrIO::write_serialized_nodes(), libMesh::XdrIO::write_serialized_nodesets(), libMesh::XdrIO::write_serialized_subdomain_names(), libMesh::System::write_serialized_vector(), libMesh::System::write_serialized_vectors(), libMesh::ExodusII_IO_Helper::write_sideset_data(), libMesh::Nemesis_IO_Helper::write_sidesets(), libMesh::ExodusII_IO_Helper::write_sidesets(), libMesh::ExodusII_IO::write_timestep(), libMesh::ExodusII_IO_Helper::write_timestep(), and libMesh::ExodusII_IO::write_timestep_discontinuous().

  { return cast_int<processor_id_type>(_communicator.rank()); }

read()

template<typename T >

void libMesh::SparseMatrix< T >::read ( const std::string &  filename )

virtualinherited

Read the contents of the matrix from a file, with the file format inferred from the extension of filename.

Definition at line 686 of file sparse_matrix.C.

{
  {
    std::ifstream in (filename.c_str());
    libmesh_error_msg_if
      (!in.good(), "ERROR: cannot read file:\n\t" <<
       filename);
  }

  std::string_view basename = Utility::basename_of(filename);

  const bool gzipped_file = Utility::ends_with(filename, ".gz");

  if (gzipped_file)
    basename.remove_suffix(3);

  if (Utility::ends_with(basename, ".matlab") ||
      Utility::ends_with(basename, ".m"))
    this->read_matlab(filename);
  else if (Utility::ends_with(basename, ".petsc64"))
    {
#ifndef LIBMESH_HAVE_PETSC
      libmesh_error_msg("Cannot load PETSc matrix file " <<
                        filename << " without PETSc-enabled libMesh.");
#elif LIBMESH_DOF_ID_BYTES != 8
      libmesh_error_msg("Cannot load 64-bit PETSc matrix file " <<
                        filename << " with non-64-bit libMesh.");
#endif
      if (gzipped_file)
        libmesh_not_implemented_msg("Gzipped PETSc matrices are not currently supported");
      this->read_petsc_binary(filename);
    }
  else if (Utility::ends_with(basename, ".petsc32"))
    {
#ifndef LIBMESH_HAVE_PETSC
      libmesh_error_msg("Cannot load PETSc matrix file " <<
                        filename << " without PETSc-enabled libMesh.");
#elif LIBMESH_DOF_ID_BYTES != 4
      libmesh_error_msg("Cannot load 32-bit PETSc matrix file " <<
                        filename << " with non-32-bit libMesh.");
#endif
      if (gzipped_file)
        libmesh_not_implemented_msg("Gzipped PETSc matrices are not currently supported");
      this->read_petsc_binary(filename);
    }
  else if (Utility::ends_with(basename, ".h5"))
    {
      if (gzipped_file)
        libmesh_not_implemented_msg("Gzipped HDF5 matrices are not currently supported");
      this->read_coreform_hdf5(filename);
    }
  else
    libmesh_error_msg(" ERROR: Unrecognized matrix file extension on: "
                      << basename
                      << "\n   I understand the following:\n\n"
                      << "     *.h5        -- CoreForm HDF5 sparse matrix format\n"
                      << "     *.matlab    -- Matlab sparse matrix format\n"
                      << "     *.matlab.gz -- Matlab sparse matrix format, gzipped\n"
                      << "     *.m         -- Matlab sparse matrix format\n"
                      << "     *.m.gz      -- Matlab sparse matrix format, gzipped\n"
                      << "     *.petsc32   -- PETSc binary format, 32-bit\n"
                      << "     *.petsc64   -- PETSc binary format, 64-bit\n"
                     );
}

read_coreform_hdf5()

template<typename T >

void libMesh::SparseMatrix< T >::read_coreform_hdf5 ( const std::string &  filename, const std::string &  groupname = "extraction"  )

virtualinherited

Read the contents of the matrix from a file, with the HDF5 sparse matrix format used by CoreForm, expecing sparse matrix data in the group given by groupname.

This will be initialized with the sparsity from the file, linearly partitioned onto the number of processors available unless this matrix is pre-sized and pre-partitionsed.

Definition at line 822 of file sparse_matrix.C.

{
#ifndef LIBMESH_HAVE_HDF5
  libmesh_ignore(filename, groupname);
  libmesh_error_msg("ERROR: need HDF5 support to handle .h5 files!!!");
#else
  LOG_SCOPE("read_coreform_hdf5()", "SparseMatrix");

  std::size_t num_rows = 0, num_cols = 0;

  // These are only used on pid 0, but avoid "uninitialized" warnings
  hid_t group = H5I_INVALID_HID;
  hid_t file = H5I_INVALID_HID;

  if (this->processor_id() == 0)
    {
      file = H5Fopen(filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);

      if (file == H5I_INVALID_HID)
        libmesh_file_error(filename);

      group = H5Gopen(file, groupname.c_str(), H5P_DEFAULT);
      check_open(filename, group, groupname);

      auto read_size_attribute = [&filename, &group]
        (const std::string & attribute_name)
      {
        unsigned long long returnval = 0;

        const hid_t attr = H5Aopen(group, attribute_name.c_str(), H5P_DEFAULT);
        check_open(filename, attr, attribute_name);

        const hid_t attr_type = H5Aget_type(attr);
        check_hdf5(filename, attr_type, attribute_name + " type");

        // HDF5 will convert between the file's integer type and ours, but
        // we do expect an integer type.
        if (H5Tget_class(attr_type) != H5T_INTEGER)
          libmesh_error_msg("Non-integer type for " + attribute_name + " in " + filename);

        H5Tclose(attr_type);

        // HDF5 is supposed to handle both upscaling and endianness
        // conversions here
        const herr_t errval = H5Aread(attr, H5T_NATIVE_ULLONG, &returnval);
        check_hdf5(filename, errval, attribute_name + " read");

        H5Aclose(attr);

        return returnval;
      };

      num_cols = read_size_attribute("num_cols");
      num_rows = read_size_attribute("num_rows");

      this->comm().broadcast(num_cols);
      this->comm().broadcast(num_rows);
    }
  else
    {
      this->comm().broadcast(num_cols);
      this->comm().broadcast(num_rows);
    }

  numeric_index_type new_row_start, new_row_stop,
                     new_col_start, new_col_stop;

  // If we need to reinit, we need to determine which rows+columns
  // each processor is in charge of.
  std::vector<numeric_index_type> new_row_starts, new_row_stops,
                                  new_col_starts, new_col_stops;

  if (this->initialized() &&
      num_cols == this->n() &&
      num_rows == this->m())
    {
      new_row_start = this->row_start(),
      new_row_stop  = this->row_stop();

      new_col_start = this->col_start(),
      new_col_stop  = this->col_stop();
    }
  else
    {
      // Determine which rows/columns each processor will be in charge of
      new_row_start =     this->processor_id() * num_rows / this->n_processors(),
      new_row_stop  = (this->processor_id()+1) * num_rows / this->n_processors();

      new_col_start =     this->processor_id() * num_cols / this->n_processors(),
      new_col_stop  = (this->processor_id()+1) * num_cols / this->n_processors();
    }

  this->comm().gather(0, new_row_start, new_row_starts);
  this->comm().gather(0, new_row_stop, new_row_stops);
  this->comm().gather(0, new_col_start, new_col_starts);
  this->comm().gather(0, new_col_stop, new_col_stops);

  numeric_index_type on_diagonal_nonzeros = 0,
                     off_diagonal_nonzeros = 0;

  std::vector<std::size_t> cols, row_offsets;
  std::vector<double> vals;

  if (this->processor_id() == 0)
    {
      auto read_vector = [&filename, &group]
        (const std::string & dataname, auto hdf5_class,
         auto hdf5_type, auto & datavec)
      {
        const hid_t data = H5Dopen1(group, dataname.c_str());
        check_open(filename, data, dataname.c_str());

        const hid_t data_type = H5Dget_type(data);
        check_hdf5(filename, data_type, dataname + " type");

        // HDF5 will convert between the file's integer type and ours, but
        // we do expect an integer type.
        if (H5Tget_class(data_type) != hdf5_class)
          libmesh_error_msg("Unexpected type for " + dataname + " in " + filename);

        H5Tclose(data_type);

        const hid_t dataspace = H5Dget_space(data);
        check_hdf5(filename, dataspace, dataname + " space");

        int ndims = H5Sget_simple_extent_ndims(dataspace);
        if (ndims != 1)
          libmesh_error_msg("Non-vector space for " + dataname + " in " + filename);

        hsize_t len, maxlen;
        herr_t errval = H5Sget_simple_extent_dims(dataspace, &len, &maxlen);
        check_hdf5(filename, errval, dataname + " dims");

        datavec.resize(len);

        errval = H5Dread(data, hdf5_type, H5S_ALL, H5S_ALL, H5P_DEFAULT, datavec.data());
        check_hdf5(filename, errval, dataname + " read");

        H5Dclose(data);
      };

      read_vector("cols", H5T_INTEGER, H5T_NATIVE_ULLONG, cols);
      read_vector("row_offsets", H5T_INTEGER, H5T_NATIVE_ULLONG, row_offsets);
      read_vector("vals", H5T_FLOAT, H5T_NATIVE_DOUBLE, vals);

      if (cols.size() != vals.size())
        libmesh_error_msg("Inconsistent cols/vals sizes in " + filename);

      if (row_offsets.size() != num_rows + 1)
        libmesh_error_msg("Inconsistent row_offsets size in " + filename);

      // Data for the row we're working on
      numeric_index_type current_row = 0;
      processor_id_type current_proc = 0;
      numeric_index_type current_on_diagonal_nonzeros = 0;
      numeric_index_type current_off_diagonal_nonzeros = 0;
      if (row_offsets[0] != 0)
        libmesh_error_msg("Unexpected row_offsets[0] in " + filename);

      for (auto i : index_range(cols))
        {
          while (row_offsets[current_row+1] <= i)
            {
              ++current_row;
              if (row_offsets[current_row] < row_offsets[current_row-1])
                libmesh_error_msg("Non-monotonic row_offsets in " + filename);
              current_on_diagonal_nonzeros = 0;
              current_off_diagonal_nonzeros = 0;
            }

          while (current_row >= new_row_stops[current_proc])
            ++current_proc;

          // 0-based indexing in file
          if (cols[i] >= new_col_starts[current_proc] &&
              cols[i] < new_col_stops[current_proc])
            {
              ++current_on_diagonal_nonzeros;
              on_diagonal_nonzeros =
                std::max(on_diagonal_nonzeros,
                         current_on_diagonal_nonzeros);
            }
          else
            {
              ++current_off_diagonal_nonzeros;
              off_diagonal_nonzeros =
                std::max(off_diagonal_nonzeros,
                         current_off_diagonal_nonzeros);
            }
        }
    }

  this->comm().broadcast(on_diagonal_nonzeros);
  this->comm().broadcast(off_diagonal_nonzeros);

  this->init(num_rows, num_cols,
             new_row_stop-new_row_start,
             new_col_stop-new_col_start,
             on_diagonal_nonzeros,
             off_diagonal_nonzeros);

  // Set the matrix values last.
  if (this->processor_id() == 0)
    {
      numeric_index_type current_row = 0;
      for (auto i : index_range(cols))
        {
          while (row_offsets[current_row+1] <= i)
            {
              ++current_row;
              libmesh_assert_greater_equal (row_offsets[current_row],
                                            row_offsets[current_row-1]);
            }
          this->set(current_row, cols[i], vals[i]);
        }

      H5Gclose(group);
      H5Fclose(file);
    }

  this->close();
#endif // LIBMESH_HAVE_HDF5
}

read_matlab()

template<typename T >

void libMesh::SparseMatrix< T >::read_matlab ( const std::string &  filename )

virtualinherited

Read the contents of the matrix from the Matlab-script sparse matrix format used by PETSc.

If the size and sparsity of the matrix in filename appears consistent with the existing sparsity of this then the existing parallel decomposition and sparsity will be retained. If not, then this will be initialized with the sparsity from the file, linearly partitioned onto the number of processors available.

Definition at line 1050 of file sparse_matrix.C.

Referenced by ConstraintOperatorTest::test1DCoarseningNewNodes().

{
  LOG_SCOPE("read_matlab()", "SparseMatrix");

#ifndef LIBMESH_HAVE_CXX11_REGEX
  libmesh_not_implemented();  // What is your compiler?!?  Email us!
  libmesh_ignore(filename);
#else
  parallel_object_only();

  const bool gzipped_file = Utility::ends_with(filename, ".gz");

  // The sizes we get from the file
  std::size_t m = 0,
              n = 0;

  // If we don't already have this size, we'll need to reinit, and
  // determine which rows+columns each processor is in charge of.
  std::vector<numeric_index_type> new_row_starts, new_row_stops,
                                  new_col_starts, new_col_stops;

  numeric_index_type new_row_start, new_row_stop,
                     new_col_start, new_col_stop;

  // We'll read through the file three times: once to get a reliable
  // value for the matrix size (so we can divvy it up among
  // processors), then again to get the sparsity to send to each
  // processor, then a final time to get the entries to send to each
  // processor.
  //
  // We'll use an istream here; it might be an ifstream if we're
  // opening a raw ASCII file or a gzstream if we're opening a
  // compressed one.
  std::unique_ptr<std::istream> file;

  // We'll need a temporary structure to cache matrix entries, because
  // we need to read through the whole file before we know the size
  // and sparsity structure with which we can init().
  //
  // Reading through the file three times via `seekg` doesn't work
  // with our gzstream wrapper, and seems to take three times as long
  // even with a plain ifstream.  What happened to disk caching!?
  std::vector<std::tuple<numeric_index_type, numeric_index_type, T>> entries;

  // First read through the file, saving size and entry data
  {
  // We'll read the matrix on processor 0 rather than try to juggle
  // parallel I/O.
  if (this->processor_id() == 0)
    {
      // We'll be using regular expressions to make ourselves slightly
      // more robust to formatting.
      const std::regex start_regex // assignment like "zzz = ["
        ("\\s*\\w+\\s*=\\s*\\[");
      const std::regex end_regex // end of assignment
        ("^[^%]*\\]");

      if (gzipped_file)
        {
#ifdef LIBMESH_HAVE_GZSTREAM
          auto inf = std::make_unique<igzstream>();
          libmesh_assert(inf);
          inf->open(filename.c_str(), std::ios::in);
          file = std::move(inf);
#else
          libmesh_error_msg("ERROR: need gzstream to handle .gz files!!!");
#endif
        }
      else
        {
          auto inf = std::make_unique<std::ifstream>();
          libmesh_assert(inf);

          std::string new_name = Utility::unzip_file(filename);

          inf->open(new_name.c_str(), std::ios::in);
          file = std::move(inf);
        }

      // If we have a matrix with all-zero trailing rows, the only
      // way to get the size is if it ended up in a comment
      const std::regex size_regex // comment like "% size = 8 8"
        ("%\\s*[Ss][Ii][Zz][Ee]\\s*=\\s*(\\d+)\\s+(\\d+)");
      const std::string whitespace = " \t";

      bool have_started = false;
      bool have_ended = false;
      std::size_t largest_i_seen = 0, largest_j_seen = 0;

      // Data for the row we're working on
      // Use 1-based indexing for current_row, as in the file
      std::size_t current_row = 1;

      for (std::string line; std::getline(*file, line);)
        {
          std::smatch sm;

          // First, try to match an entry.  This is the most common
          // case so we won't rely on slow std::regex for it.
          // stringstream is at least an improvement over that.

          // Look for row/col/val like "1 1 -2.0e-4"

          std::istringstream l(line);

          std::size_t i, j;
          T value;

          l >> i >> j >> value;

          if (!l.fail())
            {
              libmesh_error_msg_if
                (!have_started, "Confused by premature entries in matrix file " << filename);

              entries.emplace_back(cast_int<numeric_index_type>(i),
                                   cast_int<numeric_index_type>(j),
                                   value);

              libmesh_error_msg_if
                (!i || !j, "Expected 1-based indexing in matrix file "
                 << filename);

              current_row = std::max(current_row, i);

              libmesh_error_msg_if
                (i < current_row,
                 "Can't handle out-of-order entries in matrix file "
                 << filename);

              largest_i_seen = std::max(i, largest_i_seen);
              largest_j_seen = std::max(j, largest_j_seen);
            }

          else if (std::regex_search(line, sm, size_regex))
            {
              const std::string msize = sm[1];
              const std::string nsize = sm[2];
              m = std::stoull(msize);
              n = std::stoull(nsize);
            }

          else if (std::regex_search(line, start_regex))
            have_started = true;

          else if (std::regex_search(line, end_regex))
            {
              have_ended = true;
              break;
            }
        }

      libmesh_error_msg_if
        (!have_started, "Confused by missing assignment beginning in matrix file " << filename);

      libmesh_error_msg_if
        (!have_ended, "Confused by missing assignment ending in matrix file " << filename);

      libmesh_error_msg_if
        (m > largest_i_seen, "Confused by missing final row(s) in matrix file " << filename);

      libmesh_error_msg_if
        (m > 0 && m < largest_i_seen, "Confused by extra final row(s) in matrix file " << filename);

      if (!m)
        m = largest_i_seen;

      libmesh_error_msg_if
        (n > largest_j_seen, "Confused by missing final column(s) in matrix file " << filename);

      libmesh_error_msg_if
        (n > 0 && n < largest_j_seen, "Confused by extra final column(s) in matrix file " << filename);

      if (!n)
        n = largest_j_seen;

      this->comm().broadcast(m);
      this->comm().broadcast(n);
    }
  else
    {
      this->comm().broadcast(m);
      this->comm().broadcast(n);
    }

  if (this->initialized() &&
      m == this->m() &&
      n == this->n())
    {
      new_row_start = this->row_start(),
      new_row_stop  = this->row_stop();

      new_col_start = this->col_start(),
      new_col_stop  = this->col_stop();
    }
  else
    {
      // Determine which rows/columns each processor will be in charge of
      new_row_start =     this->processor_id() * m / this->n_processors(),
      new_row_stop  = (this->processor_id()+1) * m / this->n_processors();

      new_col_start =     this->processor_id() * n / this->n_processors(),
      new_col_stop  = (this->processor_id()+1) * n / this->n_processors();
    }

  this->comm().gather(0, new_row_start, new_row_starts);
  this->comm().gather(0, new_row_stop, new_row_stops);
  this->comm().gather(0, new_col_start, new_col_starts);
  this->comm().gather(0, new_col_stop, new_col_stops);

  } // Done reading entry data and broadcasting matrix size

  // Calculate the matrix sparsity and initialize it second
  {
  // Deduce the sparsity pattern, or at least the maximum number of
  // on- and off- diagonal non-zeros per row.
  numeric_index_type  on_diagonal_nonzeros =0,
                     off_diagonal_nonzeros =0;

  if (this->processor_id() == 0)
    {
      // Data for the row we're working on
      // Use 1-based indexing for current_row, as in the file
      numeric_index_type current_row = 1;
      processor_id_type current_proc = 0;
      numeric_index_type current_on_diagonal_nonzeros = 0;
      numeric_index_type current_off_diagonal_nonzeros = 0;

      for (auto [i, j, value] : entries)
        {
          if (i > current_row)
            {
              current_row = i;
              // +1 for 1-based indexing in file
              while (current_row >= (new_row_stops[current_proc]+1))
                ++current_proc;
              current_on_diagonal_nonzeros = 0;
              current_off_diagonal_nonzeros = 0;
            }

          // +1 for 1-based indexing in file
          if (j >= (new_col_starts[current_proc]+1) &&
              j < (new_col_stops[current_proc]+1))
            {
              ++current_on_diagonal_nonzeros;
              on_diagonal_nonzeros =
                std::max(on_diagonal_nonzeros,
                         current_on_diagonal_nonzeros);
            }
          else
            {
              ++current_off_diagonal_nonzeros;
              off_diagonal_nonzeros =
                std::max(off_diagonal_nonzeros,
                         current_off_diagonal_nonzeros);
            }
        }
    }

  this->comm().broadcast(on_diagonal_nonzeros);
  this->comm().broadcast(off_diagonal_nonzeros);

  this->init(m, n,
             new_row_stop-new_row_start,
             new_col_stop-new_col_start,
             on_diagonal_nonzeros,
             off_diagonal_nonzeros);
  }

  // Set the matrix values last.
  // Convert from 1-based to 0-based indexing
  if (this->processor_id() == 0)
    for (auto [i, j, value] : entries)
      this->set(i-1, j-1, value);

  this->close();
#endif
}

read_petsc_binary()

template<typename T >

void libMesh::SparseMatrix< T >::read_petsc_binary ( const std::string &  filename )

virtualinherited

Read the contents of the matrix from a file in PETSc's binary sparse matrix format.

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 1332 of file sparse_matrix.C.

{
  libmesh_not_implemented_msg
    ("libMesh cannot read PETSc binary-format files into non-PETSc matrices");
}

read_petsc_hdf5()

template<typename T >

void libMesh::SparseMatrix< T >::read_petsc_hdf5 ( const std::string &  filename )

virtualinherited

Read the contents of the matrix from a file in PETSc's HDF5 sparse matrix format.

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 1341 of file sparse_matrix.C.

{
  libmesh_not_implemented_msg
    ("libMesh cannot read PETSc HDF5-format files into non-PETSc matrices");
}

reinit_submatrix()

template<typename T>

virtual void libMesh::SparseMatrix< T >::reinit_submatrix ( SparseMatrix< T > &  submatrix, const std::vector< numeric_index_type > &  rows, const std::vector< numeric_index_type > &  cols  ) const

inlinevirtualinherited

This function is similar to the one above, but it allows you to reuse the existing sparsity pattern of "submatrix" instead of reallocating it again.

This should hopefully be more efficient if you are frequently extracting submatrices of the same size.

Definition at line 565 of file sparse_matrix.h.

  {
    this->_get_submatrix(submatrix,
                         rows,
                         cols,
                         true); // true means REUSE submatrix
  }

require_sparsity_pattern()

template<typename T>

virtual bool libMesh::SparseMatrix< T >::require_sparsity_pattern ( ) const

inlinevirtualinherited

Returns

Whether this matrix needs the sparsity pattern computed by the DofMap

Reimplemented in libMesh::StaticCondensation, libMesh::PetscMatrixShellMatrix< T >, and libMesh::PetscMatrixShellMatrix< Number >.

Definition at line 168 of file sparse_matrix.h.

{ return !this->use_hash_table(); }

restore_original_nonzero_pattern()

template<typename T>

virtual void libMesh::SparseMatrix< T >::restore_original_nonzero_pattern ( )

inlinevirtualinherited

Reset the memory storage of the matrix.

Unlike clear(), this does not destroy the matrix but rather will reset the matrix to use the original preallocation or when using hash table matrix assembly (see use_hash_table()) will reset (clear) the hash table used for assembly. In the words of the MatResetPreallocation documentation in PETSc, 'current values in the matrix are lost in this call', so a user can expect to have back their original sparsity pattern in a zeroed state

Reimplemented in libMesh::PetscMatrix< T >, and libMesh::DiagonalMatrix< T >.

Definition at line 644 of file sparse_matrix.h.

{ libmesh_not_implemented(); }

row_start()

template<typename T >

numeric_index_type libMesh::EpetraMatrix< T >::row_start ( ) const

overridevirtual

Returns

The index of the first matrix row stored on this processor.

Implements libMesh::SparseMatrix< T >.

Definition at line 422 of file trilinos_epetra_matrix.C.

References libMesh::initialized(), and libMesh::libmesh_assert().

{
  libmesh_assert (this->initialized());
  libmesh_assert(_map);

  return static_cast<numeric_index_type>(_map->MinMyGID());
}

row_stop()

template<typename T >

numeric_index_type libMesh::EpetraMatrix< T >::row_stop ( ) const

overridevirtual

Returns

The index of the last matrix row (+1) stored on this processor.

Implements libMesh::SparseMatrix< T >.

Definition at line 433 of file trilinos_epetra_matrix.C.

References libMesh::initialized(), and libMesh::libmesh_assert().

{
  libmesh_assert (this->initialized());
  libmesh_assert(_map);

  return static_cast<numeric_index_type>(_map->MaxMyGID())+1;
}

scale()

template<typename T>

void libMesh::SparseMatrix< T >::scale ( const T  scale )

virtualinherited

Scales all elements of this matrix by scale.

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 1350 of file sparse_matrix.C.

{
  libmesh_assert(this->closed());

  for (const auto i : make_range(this->row_start(), this->row_stop()))
    for (const auto j : make_range(this->col_start(), this->col_stop()))
      this->set(i, j, (*this)(i, j) * scale);
}

set()

template<typename T >

void libMesh::EpetraMatrix< T >::set ( const numeric_index_type  i, const numeric_index_type  j, const T  value  )

overridevirtual

Set the element (i,j) to value.

Throws an error if the entry does not exist. Zero values can be "stored" in non-existent fields.

Implements libMesh::SparseMatrix< T >.

Definition at line 466 of file trilinos_epetra_matrix.C.

References libMesh::initialized(), libMesh::libmesh_assert(), and value.

{
  libmesh_assert (this->initialized());

  int
    epetra_i = static_cast<int>(i),
    epetra_j = static_cast<int>(j);

  T epetra_value = value;

  if (_mat->Filled())
    _mat->ReplaceGlobalValues (epetra_i, 1, &epetra_value, &epetra_j);
  else
    _mat->InsertGlobalValues (epetra_i, 1, &epetra_value, &epetra_j);
}

solver_package()

template<typename T>

virtual SolverPackage libMesh::EpetraMatrix< T >::solver_package ( )

inlineoverridevirtual

Implements libMesh::SparseMatrix< T >.

Definition at line 105 of file trilinos_epetra_matrix.h.

References libMesh::TRILINOS_SOLVERS.

  {
    return TRILINOS_SOLVERS;
  }

supports_hash_table()

template<typename T>

virtual bool libMesh::SparseMatrix< T >::supports_hash_table ( ) const

inlinevirtualinherited

Returns

Whether the matrix supports hash table assembly

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 619 of file sparse_matrix.h.

{ return false; }

swap()

template<typename T >

void libMesh::EpetraMatrix< T >::swap

(

EpetraMatrix< T > &

m

)

Swaps the internal data pointers, no actual values are swapped.

Definition at line 582 of file trilinos_epetra_matrix.C.

References libMesh::EpetraMatrix< T >::_destroy_mat_on_exit, and libMesh::EpetraMatrix< T >::_mat.

{
  std::swap(_mat, m._mat);
  std::swap(_destroy_mat_on_exit, m._destroy_mat_on_exit);
}

update_sparsity_pattern()

template<typename T >

void libMesh::EpetraMatrix< T >::update_sparsity_pattern ( const SparsityPattern::Graph &  sparsity_pattern )

overridevirtual

Updates the matrix sparsity pattern.

This will tell the underlying matrix storage scheme how to map the \( (i,j) \) elements.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 42 of file trilinos_epetra_matrix.C.

References libMesh::index_range(), libMesh::TriangleWrapper::init(), libMesh::initialized(), and libMesh::libmesh_assert().

{
  // clear data, start over
  this->clear ();

  // big trouble if this fails!
  libmesh_assert(this->_dof_map);

  const numeric_index_type n_rows = cast_int<numeric_index_type>
    (sparsity_pattern.size());

  const numeric_index_type m   = this->_dof_map->n_dofs();
  const numeric_index_type n   = m;
  const numeric_index_type n_l = this->_dof_map->n_local_dofs();
  const numeric_index_type m_l = n_l;

  // error checking
#ifndef NDEBUG
  {
    libmesh_assert_equal_to (n, m);
    libmesh_assert_equal_to (n_l, m_l);

    numeric_index_type
      summed_m_l = m_l,
      summed_n_l = n_l;

    this->comm().sum (summed_m_l);
    this->comm().sum (summed_n_l);

    libmesh_assert_equal_to (m, summed_m_l);
    libmesh_assert_equal_to (n, summed_n_l);
  }
#endif

  // build a map defining the data distribution
  _map = new Epetra_Map (static_cast<int>(m),
                         m_l,
                         0,
                         Epetra_MpiComm (this->comm().get()));

  libmesh_assert_equal_to (static_cast<numeric_index_type>(_map->NumGlobalPoints()), m);
  libmesh_assert_equal_to (static_cast<numeric_index_type>(_map->MaxAllGID()+1), m);

  const std::vector<numeric_index_type> & n_nz = this->_sp->get_n_nz();
  const std::vector<numeric_index_type> & n_oz = this->_sp->get_n_oz();

  // Make sure the sparsity pattern isn't empty
  libmesh_assert_equal_to (n_nz.size(), n_l);
  libmesh_assert_equal_to (n_oz.size(), n_l);

  // Epetra wants the total number of nonzeros, both local and remote.
  std::vector<int> n_nz_tot;  n_nz_tot.reserve(n_nz.size());

  for (auto i : index_range(n_nz))
    n_nz_tot.push_back(std::min(n_nz[i] + n_oz[i], n));

  if (m==0)
    return;

  _graph = new Epetra_CrsGraph(Copy, *_map, n_nz_tot.data());

  // Tell the matrix about its structure.  Initialize it
  // to zero.
  for (numeric_index_type i=0; i<n_rows; i++)
    _graph->InsertGlobalIndices(_graph->GRID(i),
                                cast_int<numeric_index_type>(sparsity_pattern[i].size()),
                                const_cast<int *>(reinterpret_cast<const int *>(sparsity_pattern[i].data())));

  _graph->FillComplete();

  //Initialize the matrix
  libmesh_assert (!this->initialized());
  this->init ();
  libmesh_assert (this->initialized());
}

use_hash_table() [1/2]

template<typename T >

void libMesh::SparseMatrix< T >::use_hash_table ( bool  use_hash )

inherited

Sets whether to use hash table assembly.

This will error if the passed-in value is true and the matrix type does not support hash tables. Hash table or hash map assembly means storing maps from i-j locations in the matrix to values. Because it is a hash map as opposed to a contiguous array of data, no preallocation is required to use it

Definition at line 692 of file sparse_matrix.h.

Referenced by PetscMatrixTest::testPetscCopyFromHash().

{
  libmesh_error_msg_if(use_hash && !this->supports_hash_table(),
                       "This matrix class does not support hash table assembly");
  this->_use_hash_table = use_hash;
}

use_hash_table() [2/2]

template<typename T>

bool libMesh::SparseMatrix< T >::use_hash_table ( ) const

inlineinherited

Returns

Whether this matrix is using hash table assembly. Hash table or hash map assembly means storing maps from i-j locations in the matrix to values. Because it is a hash map as opposed to a contiguous array of data, no preallocation is required to use it

Definition at line 634 of file sparse_matrix.h.

Referenced by libMesh::SparseMatrix< ValOut >::require_sparsity_pattern().

{ return _use_hash_table; }

vector_mult()

template<typename T>

void libMesh::SparseMatrix< T >::vector_mult ( NumericVector< T > &  dest, const NumericVector< T > &  arg  ) const

inherited

Multiplies the matrix by the NumericVector arg and stores the result in NumericVector dest.

Definition at line 237 of file sparse_matrix.C.

Referenced by libMesh::TransientRBConstruction::add_IC_to_RB_space(), libMesh::RBSCMConstruction::Aq_inner_product(), libMesh::AdvectionSystem::assemble_claw_rhs(), libMesh::RBSCMConstruction::B_inner_product(), libMesh::RBConstruction::compute_Fq_representor_innerprods(), libMesh::RBConstruction::compute_output_dual_innerprods(), libMesh::RBConstruction::compute_residual_dual_norm_slow(), libMesh::TransientRBConstruction::enrich_RB_space(), libMesh::RBConstruction::enrich_RB_space(), AssembleOptimization::gradient(), libMesh::TransientRBConstruction::mass_matrix_scaled_matvec(), AssembleOptimization::objective(), libMesh::RBConstruction::print_basis_function_orthogonality(), libMesh::ImplicitSystem::qoi_parameter_hessian(), libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product(), libMesh::TransientRBConstruction::set_error_temporal_data(), libMesh::RBConstruction::train_reduced_basis_with_POD(), libMesh::TransientRBConstruction::truth_assembly(), libMesh::RBConstruction::truth_solve(), libMesh::TransientRBConstruction::update_RB_system_matrices(), libMesh::RBConstruction::update_RB_system_matrices(), libMesh::TransientRBConstruction::update_residual_terms(), and libMesh::RBConstruction::update_residual_terms().

{
  dest.zero();
  this->vector_mult_add(dest,arg);
}

vector_mult_add()

template<typename T>

void libMesh::SparseMatrix< T >::vector_mult_add ( NumericVector< T > &  dest, const NumericVector< T > &  arg  ) const

inherited

Multiplies the matrix by the NumericVector arg and adds the result to the NumericVector dest.

Definition at line 247 of file sparse_matrix.C.

Referenced by libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve().

{
  /* This functionality is actually implemented in the \p
     NumericVector class.  */
  dest.add_vector(arg,*this);
}

zero()

template<typename T >

void libMesh::EpetraMatrix< T >::zero ( )

overridevirtual

Set all entries to 0.

Implements libMesh::SparseMatrix< T >.

Definition at line 196 of file trilinos_epetra_matrix.C.

References libMesh::initialized(), and libMesh::libmesh_assert().

{
  libmesh_assert (this->initialized());

  _mat->Scale(0.0);
}

zero_clone()

template<typename T >

std::unique_ptr< SparseMatrix< T > > libMesh::EpetraMatrix< T >::zero_clone ( ) const

overridevirtual

Returns

A smart pointer to a copy of this matrix with the same type, size, and partitioning, but with all zero entries.

Note

This must be overridden in the derived classes.

Implements libMesh::SparseMatrix< T >.

Definition at line 206 of file trilinos_epetra_matrix.C.

{
  // This function is marked as "not implemented" since it hasn't been
  // tested, the code below might serve as a possible implementation.
  libmesh_not_implemented();

  // Make empty copy with matching comm, initialize, and return.
  auto mat_copy = std::make_unique<EpetraMatrix<T>>(this->comm());
  mat_copy->init();
  mat_copy->zero();

  return mat_copy;
}

zero_rows()

template<typename T>

void libMesh::SparseMatrix< T >::zero_rows ( std::vector< numeric_index_type > &  rows, T  diag_value = 0.0  )

virtualinherited

Sets all row entries to 0 then puts diag_value in the diagonal entry.

Reimplemented in libMesh::DiagonalMatrix< T >, and libMesh::PetscMatrix< T >.

Definition at line 258 of file sparse_matrix.C.

{
  /* This functionality isn't implemented or stubbed in every subclass yet */
  libmesh_not_implemented();
}

Member Data Documentation

_communicator

const Parallel::Communicator& libMesh::ParallelObject::_communicator

protectedinherited

Definition at line 120 of file parallel_object.h.

Referenced by libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::StaticCondensation::close(), libMesh::ParallelObject::comm(), libMesh::CondensedEigenSystem::initialize_condensed_matrices(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::operator=(), libMesh::ParallelObject::processor_id(), libMesh::BoundaryInfo::regenerate_id_sets(), libMesh::StaticCondensationDofMap::reinit(), and libMesh::BoundaryInfo::synchronize_global_id_set().

_counts

ReferenceCounter::Counts libMesh::ReferenceCounter::_counts

staticprotectedinherited

Actually holds the data.

Definition at line 124 of file reference_counter.h.

Referenced by libMesh::ReferenceCounter::get_info().

_destroy_mat_on_exit

template<typename T>

bool libMesh::EpetraMatrix< T >::_destroy_mat_on_exit

private

This boolean value should only be set to false for the constructor which takes an Epetra_FECrsMatrix object.

Definition at line 243 of file trilinos_epetra_matrix.h.

Referenced by libMesh::EpetraMatrix< T >::swap().

_dof_map

template<typename T>

DofMap const* libMesh::SparseMatrix< T >::_dof_map

protectedinherited

The DofMap object associated with this object.

May be queried for degree-of-freedom counts on processors.

Definition at line 666 of file sparse_matrix.h.

_enable_print_counter

bool libMesh::ReferenceCounter::_enable_print_counter = true

staticprotectedinherited

Flag to control whether reference count information is printed when print_info is called.

Definition at line 143 of file reference_counter.h.

Referenced by libMesh::ReferenceCounter::disable_print_counter_info(), libMesh::ReferenceCounter::enable_print_counter_info(), and libMesh::ReferenceCounter::print_info().

_graph

template<typename T>

Epetra_CrsGraph* libMesh::EpetraMatrix< T >::_graph

private

Holds the sparsity pattern.

Definition at line 237 of file trilinos_epetra_matrix.h.

_is_initialized

template<typename T>

bool libMesh::SparseMatrix< T >::_is_initialized

protectedinherited

Flag indicating whether or not the matrix has been initialized.

Definition at line 678 of file sparse_matrix.h.

Referenced by libMesh::PetscMatrix< T >::_get_submatrix(), libMesh::PetscMatrix< T >::create_submatrix_nosort(), libMesh::EpetraMatrix< T >::EpetraMatrix(), libMesh::EigenSparseMatrix< T >::get_transpose(), libMesh::LaspackMatrix< T >::get_transpose(), libMesh::PetscMatrix< T >::get_transpose(), and libMesh::SparseMatrix< ValOut >::initialized().

_map

template<typename T>

Epetra_Map* libMesh::EpetraMatrix< T >::_map

private

Holds the distributed Map.

Definition at line 232 of file trilinos_epetra_matrix.h.

_mat

template<typename T>

Epetra_FECrsMatrix* libMesh::EpetraMatrix< T >::_mat

private

Actual Epetra datatype to hold matrix entries.

Definition at line 227 of file trilinos_epetra_matrix.h.

Referenced by libMesh::EpetraMatrix< T >::EpetraMatrix(), libMesh::EpetraMatrix< T >::get_transpose(), libMesh::EpetraMatrix< T >::mat(), and libMesh::EpetraMatrix< T >::swap().

_mutex

Threads::spin_mutex libMesh::ReferenceCounter::_mutex

staticprotectedinherited

Mutual exclusion object to enable thread-safe reference counting.

Definition at line 137 of file reference_counter.h.

_n_objects

Threads::atomic< unsigned int > libMesh::ReferenceCounter::_n_objects

staticprotectedinherited

The number of objects.

Print the reference count information when the number returns to 0.

Definition at line 132 of file reference_counter.h.

Referenced by libMesh::ReferenceCounter::n_objects(), libMesh::ReferenceCounter::ReferenceCounter(), and libMesh::ReferenceCounter::~ReferenceCounter().

_sp

template<typename T>

SparsityPattern::Build const* libMesh::SparseMatrix< T >::_sp

protectedinherited

The sparsity pattern associated with this object.

Should be queried for entry counts (or with need_full_sparsity_pattern, patterns) when needed.

Definition at line 673 of file sparse_matrix.h.

_use_hash_table

template<typename T>

bool libMesh::SparseMatrix< T >::_use_hash_table

protectedinherited

Flag indicating whether the matrix is assembled using a hash table.

Definition at line 683 of file sparse_matrix.h.

Referenced by libMesh::SparseMatrix< ValOut >::use_hash_table().

_use_transpose

template<typename T>

bool libMesh::EpetraMatrix< T >::_use_transpose

private

Epetra has no GetUseTranspose so we need to keep track of whether we're transposed manually.

Definition at line 249 of file trilinos_epetra_matrix.h.

Referenced by libMesh::EpetraMatrix< T >::get_transpose().

---

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

• include/numerics/trilinos_epetra_matrix.h
• src/numerics/trilinos_epetra_matrix.C