The EigenSparseMatrix class wraps a sparse matrix object from the Eigen library. More...

#include <eigen_sparse_matrix.h>

Inheritance diagram for libMesh::EigenSparseMatrix< T >:

Public Types
typedef EigenSM	DataType
	Convenient typedefs.

typedef Eigen::Triplet< T, eigen_idx_type >	TripletType

Public Member Functions
	EigenSparseMatrix (const Parallel::Communicator &comm)
	Constructor; initializes the matrix to be empty, without any structure, i.e.

	EigenSparseMatrix (EigenSparseMatrix &&)=default
	The 5 special functions can be defaulted for this class, as it does not manage any memory itself.

	EigenSparseMatrix (const EigenSparseMatrix &)=default

EigenSparseMatrix &	operator= (const EigenSparseMatrix &)=default

EigenSparseMatrix &	operator= (EigenSparseMatrix &&)=default

virtual	~EigenSparseMatrix ()=default

virtual SolverPackage	solver_package () override

virtual SparseMatrix< T > &	operator= (const SparseMatrix< T > &v) override
	This looks like a copy assignment operator, but note that, unlike normal copy assignment operators, it is pure virtual.

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.

virtual void	init (ParallelType=PARALLEL) override
	Initialize this matrix using the sparsity structure computed by `dof_map`.

virtual void	clear () override
	Restores the `SparseMatrix<T>` to a pristine state.

virtual void	zero () override
	Set all entries to 0.

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.

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`.

virtual void	add (const numeric_index_type i, const numeric_index_type j, const T value) override
	Add `value` to the element (i,j).

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.

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.

virtual void	add (const T a, const SparseMatrix< T > &X) override
	Compute \( A \leftarrow A + a*X \) for scalar `a`, matrix `X`.

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.

virtual void	get_diagonal (NumericVector< T > &dest) const override
	Copies the diagonal part of the matrix into `dest`.

virtual void	get_transpose (SparseMatrix< T > &dest) const override
	Copies the transpose of the matrix into `dest`, which may be *this.

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.

virtual bool	initialized () const

void	attach_dof_map (const DofMap &dof_map)
	Set a pointer to the `DofMap` to use.

void	attach_sparsity_pattern (const SparsityPattern::Build &sp)
	Set a pointer to a sparsity pattern to use.

virtual bool	need_full_sparsity_pattern () const

virtual bool	require_sparsity_pattern () const

virtual void	update_sparsity_pattern (const SparsityPattern::Graph &)
	Updates the matrix sparsity pattern.

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.

virtual void	flush ()
	For PETSc matrix , this function is similar to close but without shrinking memory.

virtual numeric_index_type	local_m () const
	Get the number of rows owned by this process.

virtual numeric_index_type	local_n () const
	Get the number of columns owned by this process.

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.

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.

virtual void	matrix_matrix_mult (SparseMatrix< T > &, SparseMatrix< T > &, bool)
	Compute Y = A*X for matrix `X`.

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)

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.

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`.

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`.

virtual void	print_matlab (const std::string &="") const
	Print the contents of the matrix in Matlab's sparse matrix format.

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.

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.

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`.

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`.

virtual void	read_matlab (const std::string &filename)
	Read the contents of the matrix from the Matlab-script sparse matrix format used by PETSc.

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.

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.

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.

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.

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.

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`.

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`.

virtual void	scale (const T scale)
	Scales all elements of this matrix by `scale`.

virtual bool	supports_hash_table () const

void	use_hash_table (bool use_hash)
	Sets whether to use hash table assembly.

bool	use_hash_table () const

virtual void	restore_original_nonzero_pattern ()
	Reset the memory storage of the matrix.

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`.

static std::string	get_info ()
	Gets a string containing the reference information.

static void	print_info (std::ostream &out_stream=libMesh::out)
	Prints the reference information, by default to `libMesh::out`.

static unsigned int	n_objects ()
	Prints the number of outstanding (created, but not yet destroyed) objects.

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

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.

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.

void	increment_constructor_count (const std::string &name) noexcept
	Increments the construction counter.

void	increment_destructor_count (const std::string &name) noexcept
	Increments the destruction counter.

Protected Attributes
DofMap const *	_dof_map
	The `DofMap` object associated with this object.

SparsityPattern::Build const *	_sp
	The `sparsity` pattern associated with this object.

bool	_is_initialized
	Flag indicating whether or not the matrix has been initialized.

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

const Parallel::Communicator &	_communicator

Static Protected Attributes
static Counts	_counts
	Actually holds the data.

static Threads::atomic< unsigned int >	_n_objects
	The number of objects.

static Threads::spin_mutex	_mutex
	Mutual exclusion object to enable thread-safe reference counting.

static bool	_enable_print_counter = true
	Flag to control whether reference count information is printed when print_info is called.

Private Attributes
DataType	_mat
	Actual Eigen::SparseMatrix<> we are wrapping.

bool	_closed
	Flag indicating if the matrix has been closed yet.

Friends
class	EigenSparseVector< T >
	Make other Eigen datatypes friends.

class	EigenSparseLinearSolver< T >

Detailed Description

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

The EigenSparseMatrix class wraps a sparse matrix object from the Eigen library.

All overridden virtual functions are documented in sparse_matrix.h.

Author: Benjamin S. Kirk

Date: 2013

Definition at line 54 of file eigen_sparse_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.

◆ DataType

template<typename T >

typedef EigenSM libMesh::EigenSparseMatrix< T >::DataType

Convenient typedefs.

Definition at line 94 of file eigen_sparse_matrix.h.

◆ TripletType

template<typename T >

typedef Eigen::Triplet<T,eigen_idx_type> libMesh::EigenSparseMatrix< T >::TripletType

Definition at line 95 of file eigen_sparse_matrix.h.

Constructor & Destructor Documentation

◆ EigenSparseMatrix() [1/3]

template<typename T >

libMesh::EigenSparseMatrix< T >::EigenSparseMatrix ( 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 166 of file eigen_sparse_matrix.C.

                                                                             :
  SparseMatrix<T>(comm_in),
  _closed (false)
{
}

◆ EigenSparseMatrix() [2/3]

template<typename T >

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

default

The 5 special functions can be defaulted for this class, as it does not manage any memory itself.

◆ EigenSparseMatrix() [3/3]

template<typename T >

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

default

◆ ~EigenSparseMatrix()

template<typename T >

virtual libMesh::EigenSparseMatrix< T >::~EigenSparseMatrix ( )

virtualdefault

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.

  {
    libmesh_not_implemented();
  }

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

◆ add() [1/2]

template<typename T >

void libMesh::EigenSparseMatrix< 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 289 of file eigen_sparse_matrix.C.

{
  libmesh_assert (this->initialized());
  libmesh_assert_less (i, this->m());
  libmesh_assert_less (j, this->n());
 
  _mat.coeffRef(i,j) += value;
}

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

◆ add() [2/2]

template<typename T >

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

overridevirtual

Compute \( A \leftarrow A + a*X \) for scalar a, matrix X.

Implements libMesh::SparseMatrix< T >.

Definition at line 312 of file eigen_sparse_matrix.C.

{
  libmesh_assert (this->initialized());
  libmesh_assert_equal_to (this->m(), X_in.m());
  libmesh_assert_equal_to (this->n(), X_in.n());
 
  const EigenSparseMatrix<T> & X =
    cast_ref<const EigenSparseMatrix<T> &> (X_in);
 
  _mat += X._mat*a_in;
}

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

◆ 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.

{
  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);
}

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

◆ 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.

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

libMesh::SparseMatrix::add_block_matrix

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.

Definition sparse_matrix.C:119

References libMesh::SparseMatrix< T >::add_block_matrix().

◆ add_matrix() [1/2]

template<typename T >

void libMesh::EigenSparseMatrix< 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 303 of file eigen_sparse_matrix.C.

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

◆ add_matrix() [2/2]

template<typename T >

void libMesh::EigenSparseMatrix< 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 121 of file eigen_sparse_matrix.C.

{
  libmesh_assert (this->initialized());
  unsigned int n_rows = cast_int<unsigned int>(rows.size());
  unsigned int n_cols = cast_int<unsigned int>(cols.size());
  libmesh_assert_equal_to (dm.m(), n_rows);
  libmesh_assert_equal_to (dm.n(), n_cols);
 
 
  for (unsigned int i=0; i<n_rows; i++)
    for (unsigned int j=0; j<n_cols; j++)
      this->add(rows[i],cols[j],dm(i,j));
}

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

◆ 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.

360 { 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.

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

References libMesh::DofMap::get_sparsity_pattern().

Referenced by libMesh::Problem_Interface::computeJacobian(), DMlibMeshJacobian(), and libMesh::DofMap::update_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.

{
  _sp = &sp;
}

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

◆ 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.

{
  // 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);
    }
}

References libMesh::DIAGONAL, libMesh::EIGEN_SOLVERS, libMesh::LASPACK_SOLVERS, libMesh::libmesh_ignore(), libMesh::PETSC_SOLVERS, and libMesh::TRILINOS_SOLVERS.

Referenced by libMesh::CondensedEigenSystem::add_matrices(), libMesh::System::add_matrix(), libMesh::RBConstruction::allocate_data_structures(), libMesh::TransientRBConstruction::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().

◆ clear()

template<typename T >

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

overridevirtual

Restores the SparseMatrix<T> to a pristine state.

Implements libMesh::SparseMatrix< T >.

Definition at line 175 of file eigen_sparse_matrix.C.

{
  _mat.resize(0,0);
 
  _closed = false;
  this->_is_initialized = false;
}

◆ clone()

template<typename T >

std::unique_ptr< SparseMatrix< T > > libMesh::EigenSparseMatrix< 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 215 of file eigen_sparse_matrix.C.

{
  return std::make_unique<EigenSparseMatrix<T>>(*this);
}

◆ close()

template<typename T >

virtual void libMesh::EigenSparseMatrix< T >::close ( )

inlineoverridevirtual

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

Implements libMesh::SparseMatrix< T >.

Definition at line 115 of file eigen_sparse_matrix.h.

115{ this->_closed = true; }

References libMesh::EigenSparseMatrix< T >::_closed.

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

◆ closed()

template<typename T >

virtual bool libMesh::EigenSparseMatrix< T >::closed ( ) const

inlineoverridevirtual

Returns: true if the matrix has been assembled.

Implements libMesh::SparseMatrix< T >.

Definition at line 153 of file eigen_sparse_matrix.h.

153{ return _closed; }

References libMesh::EigenSparseMatrix< T >::_closed.

◆ col_start()

template<typename T >

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

overridevirtual

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

Implements libMesh::SparseMatrix< T >.

Definition at line 259 of file eigen_sparse_matrix.C.

{
  return 0;
}

◆ col_stop()

template<typename T >

numeric_index_type libMesh::EigenSparseMatrix< 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 267 of file eigen_sparse_matrix.C.

{
  return this->n();
}

◆ 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.

98 { return _communicator; }

libMesh::ParallelObject::_communicator

const Parallel::Communicator & _communicator

Definition parallel_object.h:120

References libMesh::ParallelObject::_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.

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

References libMesh::SparseMatrix< T >::_get_submatrix().

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

◆ 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.

{
  _enable_print_counter = false;
  return;
}

References libMesh::ReferenceCounter::_enable_print_counter.

◆ 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.

{
  _enable_print_counter = true;
  return;
}

References libMesh::ReferenceCounter::_enable_print_counter.

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

◆ 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.

244{ close(); }

libMesh::SparseMatrix::close

virtual void close()=0

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

References libMesh::SparseMatrix< T >::close().

◆ get_diagonal()

template<typename T >

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

overridevirtual

Copies the diagonal part of the matrix into dest.

Implements libMesh::SparseMatrix< T >.

Definition at line 141 of file eigen_sparse_matrix.C.

{
  EigenSparseVector<T> & dest = cast_ref<EigenSparseVector<T> &>(dest_in);
 
  dest._vec = _mat.diagonal();
 
  dest.close();
}

References libMesh::EigenSparseVector< T >::_vec, and libMesh::EigenSparseVector< T >::close().

◆ 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.

{
#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
}

References libMesh::ReferenceCounter::_counts.

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

◆ get_row()

template<typename T >

void libMesh::EigenSparseMatrix< 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 386 of file eigen_sparse_matrix.C.

{
  indices.clear();
  values.clear();
 
  // InnerIterator is over rows in RowMajor ordering
  static_assert(EigenSM::IsRowMajor);
 
  for (EigenSM::InnerIterator it(_mat, i); it; ++it)
    {
      indices.push_back(it.col());
      values.push_back(it.value());
    }
}

◆ get_transpose()

template<typename T >

void libMesh::EigenSparseMatrix< 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 153 of file eigen_sparse_matrix.C.

{
  EigenSparseMatrix<T> & dest = cast_ref<EigenSparseMatrix<T> &>(dest_in);
 
  dest._mat = _mat.transpose();
 
  dest._is_initialized = true;
  dest._closed = true;
}

References libMesh::EigenSparseMatrix< T >::_closed, libMesh::SparseMatrix< T >::_is_initialized, and libMesh::EigenSparseMatrix< T >::_mat.

◆ 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.

{
  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();
  }
}

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

Referenced by libMesh::ReferenceCountedObject< T >::ReferenceCountedObject(), libMesh::ReferenceCountedObject< T >::ReferenceCountedObject(), and libMesh::ReferenceCountedObject< T >::ReferenceCountedObject().

◆ 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.

{
  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();
  }
}

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

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

◆ init() [1/2]

template<typename T >

virtual void libMesh::EigenSparseMatrix< 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::EigenSparseMatrix< 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 64 of file eigen_sparse_matrix.C.

{
  // Ignore calls on initialized objects
  if (this->initialized())
    return;
 
  // We need the DofMap for this!
  libmesh_assert(this->_dof_map);
 
  // Clear initialized matrices
  if (this->initialized())
    this->clear();
 
  const numeric_index_type n_rows   = this->_dof_map->n_dofs();
  const numeric_index_type n_cols   = n_rows;
 
#ifndef NDEBUG
  // The following variables are only used for assertions,
  // so avoid declaring them when asserts are inactive.
  const numeric_index_type n_l = this->_dof_map->n_dofs_on_processor(0);
  const numeric_index_type m_l = n_l;
#endif
 
  // Eigen Matrices only work for uniprocessor cases
  libmesh_assert_equal_to (m_l, n_rows);
  libmesh_assert_equal_to (n_l, n_cols);
 
  const std::vector<numeric_index_type> & n_nz = this->_sp->get_n_nz();
 
#ifndef NDEBUG
  // The following variables are only used for assertions,
  // so avoid declaring them when asserts are inactive.
  const std::vector<numeric_index_type> & n_oz = this->_sp->get_n_oz();
#endif
 
  // 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);
 
  if (n_rows==0)
    {
      _mat.resize(0,0);
      return;
    }
 
  _mat.resize(n_rows,n_cols);
  _mat.reserve(n_nz);
 
  this->_is_initialized = true;
 
  libmesh_assert_equal_to (n_rows, this->m());
  libmesh_assert_equal_to (n_cols, this->n());
}

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

◆ 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.

133{ return _is_initialized; }

References libMesh::SparseMatrix< T >::_is_initialized.

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

◆ l1_norm()

template<typename T >

Real libMesh::EigenSparseMatrix< 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 341 of file eigen_sparse_matrix.C.

{
  // There does not seem to be a straightforward way to iterate over
  // the columns of an EigenSparseMatrix.  So we use some extra
  // storage and keep track of the column sums while going over the
  // row entries...
  std::vector<Real> abs_col_sums(this->n());
 
  // For a row-major Eigen SparseMatrix like we're using, the
  // InnerIterator iterates over the non-zero entries of rows.
  for (auto row : make_range(this->m()))
    {
      EigenSM::InnerIterator it(_mat, row);
      for (; it; ++it)
        abs_col_sums[it.col()] += std::abs(it.value());
    }
 
  return *(std::max_element(abs_col_sums.begin(), abs_col_sums.end()));
}

References libMesh::make_range().

◆ 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();
}

Referenced by libMesh::l1_norm_diff().

◆ linfty_norm()

template<typename T >

Real libMesh::EigenSparseMatrix< 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 364 of file eigen_sparse_matrix.C.

{
  Real max_abs_row_sum = 0.;
 
  // For a row-major Eigen SparseMatrix like we're using, the
  // InnerIterator iterates over the non-zero entries of rows.
  for (auto row : make_range(this->m()))
    {
      Real current_abs_row_sum = 0.;
      EigenSM::InnerIterator it(_mat, row);
      for (; it; ++it)
        current_abs_row_sum += std::abs(it.value());
 
      max_abs_row_sum = std::max(max_abs_row_sum, current_abs_row_sum);
    }
 
  return max_abs_row_sum;
}

References libMesh::make_range(), and libMesh::Real.

◆ 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.

254{ return row_stop() - row_start(); }

libMesh::SparseMatrix::row_stop

virtual numeric_index_type row_stop() const =0

libMesh::SparseMatrix::row_start

virtual numeric_index_type row_start() const =0

References libMesh::SparseMatrix< T >::row_start(), and libMesh::SparseMatrix< T >::row_stop().

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

◆ 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.

259{ return col_stop() - col_start(); }

libMesh::SparseMatrix::col_stop

virtual numeric_index_type col_stop() const =0

libMesh::SparseMatrix::col_start

virtual numeric_index_type col_start() const =0

References libMesh::SparseMatrix< T >::col_start(), and libMesh::SparseMatrix< T >::col_stop().

◆ m()

template<typename T >

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

overridevirtual

Returns: The row-dimension of the matrix.

Implements libMesh::SparseMatrix< T >.

Definition at line 223 of file eigen_sparse_matrix.C.

{
  libmesh_assert (this->initialized());
 
  return cast_int<numeric_index_type>(_mat.rows());
}

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

◆ 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.

350 { libmesh_not_implemented(); }

◆ n()

template<typename T >

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

overridevirtual

Returns: The column-dimension of the matrix.

Implements libMesh::SparseMatrix< T >.

Definition at line 233 of file eigen_sparse_matrix.C.

{
  libmesh_assert (this->initialized());
 
  return cast_int<numeric_index_type>(_mat.cols());
}

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

◆ 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.

{
  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.

86 { return _n_objects; }

libMesh::ReferenceCounter::_n_objects

static Threads::atomic< unsigned int > _n_objects

The number of objects.

Definition reference_counter.h:132

References libMesh::ReferenceCounter::_n_objects.

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

◆ 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.

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

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

◆ need_full_sparsity_pattern()

template<typename T >

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

inlinevirtualinherited

Returns: true if this sparse matrix format needs to be fed the graph of the sparse matrix.

This is true for LaspackMatrix, but not PetscMatrixBase subclasses. In the case where the full graph is not required, we can efficiently approximate it to provide a good estimate of the required size of the sparse matrix.

Reimplemented in libMesh::LaspackMatrix< T >, and libMesh::EpetraMatrix< T >.

Definition at line 162 of file sparse_matrix.h.

163 { return false; }

Referenced by libMesh::DofMap::attach_matrix(), and libMesh::DofMap::update_sparsity_pattern().

◆ operator()()

template<typename T >

T libMesh::EigenSparseMatrix< 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 328 of file eigen_sparse_matrix.C.

{
  libmesh_assert (this->initialized());
  libmesh_assert_less (i, this->m());
  libmesh_assert_less (j, this->n());
 
  return _mat.coeff(i,j);
}

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

◆ operator=() [1/3]

template<typename T >

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

default

◆ operator=() [2/3]

template<typename T >

virtual SparseMatrix< T > & libMesh::EigenSparseMatrix< 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 85 of file eigen_sparse_matrix.h.

  {
    *this = cast_ref<const EigenSparseMatrix<T> &>(v);
    return *this;
  }

◆ operator=() [3/3]

template<typename T >

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

default

◆ print() [1/3]

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"
                     );
}

References libMesh::Utility::basename_of(), and libMesh::Utility::ends_with().

◆ print() [2/3]

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;
    }
}

References libMesh::make_range().

◆ print() [3/3]

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.

{
  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);
    }
}

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

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

◆ 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.

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

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

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

◆ 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);
    }
}

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

◆ print_personal()

template<typename T >

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

inlineoverridevirtual

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

Implements libMesh::SparseMatrix< T >.

Definition at line 155 of file eigen_sparse_matrix.h.

155{ this->print(os); }

libMesh::SparseMatrix::print

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 packag...

Definition sparse_matrix.C:275

References libMesh::SparseMatrix< T >::print().

◆ 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.

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

libMesh::Parallel::Communicator::rank

processor_id_type rank() const

References libMesh::ParallelObject::_communicator, and libMesh::Parallel::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"
                     );
}

References libMesh::Utility::basename_of(), and libMesh::Utility::ends_with().

◆ 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
}

References libMesh::index_range(), libMesh::initialized(), and libMesh::libmesh_ignore().

◆ 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.

{
  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
}

References libMesh::Utility::ends_with(), libMesh::initialized(), libMesh::libmesh_assert(), libMesh::libmesh_ignore(), libMesh::Utility::unzip_file(), and value.

Referenced by ConstraintOperatorTest::test1DCoarseningNewNodes(), and ConstraintOperatorTest::testCoreform().

◆ 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
  }

References libMesh::SparseMatrix< T >::_get_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::PetscMatrixShellMatrix< T >, libMesh::PetscMatrixShellMatrix< Number >, and libMesh::StaticCondensation.

Definition at line 168 of file sparse_matrix.h.

168{ return !this->use_hash_table(); }

libMesh::SparseMatrix::use_hash_table

bool use_hash_table() const

Definition sparse_matrix.h:634

References libMesh::SparseMatrix< T >::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::DiagonalMatrix< T >, and libMesh::PetscMatrix< T >.

Definition at line 644 of file sparse_matrix.h.

644{ libmesh_not_implemented(); }

◆ row_start()

template<typename T >

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

overridevirtual

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

Implements libMesh::SparseMatrix< T >.

Definition at line 243 of file eigen_sparse_matrix.C.

{
  return 0;
}

◆ row_stop()

template<typename T >

numeric_index_type libMesh::EigenSparseMatrix< 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 251 of file eigen_sparse_matrix.C.

{
  return this->m();
}

◆ 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);
}

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

◆ set()

template<typename T >

void libMesh::EigenSparseMatrix< 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 275 of file eigen_sparse_matrix.C.

{
  libmesh_assert (this->initialized());
  libmesh_assert_less (i, this->m());
  libmesh_assert_less (j, this->n());
 
  _mat.coeffRef(i,j) = value;
}

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

◆ solver_package()

template<typename T >

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

inlineoverridevirtual

Implements libMesh::SparseMatrix< T >.

Definition at line 80 of file eigen_sparse_matrix.h.

  {
    return EIGEN_SOLVERS;
  }

References libMesh::EIGEN_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.

619{ return false; }

◆ update_sparsity_pattern()

template<typename T >

virtual void libMesh::SparseMatrix< T >::update_sparsity_pattern ( const SparsityPattern::Graph & )

inlinevirtualinherited

Updates the matrix sparsity pattern.

When your SparseMatrix<T> implementation does not need this data, simply do not override this method.

Reimplemented in libMesh::LaspackMatrix< T >, and libMesh::EpetraMatrix< T >.

Definition at line 175 of file sparse_matrix.h.

175{}

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

◆ use_hash_table() [1/2]

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.

634{ return _use_hash_table; }

libMesh::SparseMatrix::_use_hash_table

bool _use_hash_table

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

Definition sparse_matrix.h:683

References libMesh::SparseMatrix< T >::_use_hash_table.

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

◆ use_hash_table() [2/2]

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.

{
  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;
}

Referenced by PetscMatrixTest::testPetscCopyFromHash().

◆ 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.

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

References libMesh::NumericVector< T >::zero().

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::RBConstruction::enrich_RB_space(), libMesh::TransientRBConstruction::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::RBConstruction::update_RB_system_matrices(), libMesh::TransientRBConstruction::update_RB_system_matrices(), libMesh::TransientRBConstruction::update_residual_terms(), and libMesh::RBConstruction::update_residual_terms().

◆ 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.

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

References libMesh::NumericVector< T >::add_vector().

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

◆ zero()

template<typename T >

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

overridevirtual

Set all entries to 0.

Implements libMesh::SparseMatrix< T >.

Definition at line 186 of file eigen_sparse_matrix.C.

{
  // This doesn't just zero, it clears the entire non-zero structure!
  _mat.setZero();
 
  if (this->_sp)
  {
    // Re-reserve our non-zero structure
    const std::vector<numeric_index_type> & n_nz = this->_sp->get_n_nz();
    _mat.reserve(n_nz);
  }
}

◆ zero_clone()

template<typename T >

std::unique_ptr< SparseMatrix< T > > libMesh::EigenSparseMatrix< 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 202 of file eigen_sparse_matrix.C.

{
  // TODO: If there is a more efficient way to make a zeroed-out copy
  // of an EigenSM, we should call that instead.
  auto ret = std::make_unique<EigenSparseMatrix<T>>(*this);
  ret->zero();
 
  return ret;
}

◆ 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::PetscMatrix< T >, and libMesh::DiagonalMatrix< T >.

Definition at line 258 of file sparse_matrix.C.

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

Friends And Related Symbol Documentation

◆ EigenSparseLinearSolver< T >

template<typename T >

friend class EigenSparseLinearSolver< T >

friend

Definition at line 174 of file eigen_sparse_matrix.h.

◆ EigenSparseVector< T >

template<typename T >

friend class EigenSparseVector< T >

friend

Make other Eigen datatypes friends.

Definition at line 174 of file eigen_sparse_matrix.h.

Member Data Documentation

◆ _closed

template<typename T >

bool libMesh::EigenSparseMatrix< T >::_closed

private

Flag indicating if the matrix has been closed yet.

Definition at line 174 of file eigen_sparse_matrix.h.

Referenced by libMesh::EigenSparseMatrix< T >::close(), libMesh::EigenSparseMatrix< T >::closed(), and libMesh::EigenSparseMatrix< T >::get_transpose().

◆ _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().

◆ _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().

◆ _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(), libMesh::SparseMatrix< T >::initialized(), and libMesh::PetscMatrixBase< T >::PetscMatrixBase().

◆ _mat

template<typename T >

DataType libMesh::EigenSparseMatrix< T >::_mat

private

Actual Eigen::SparseMatrix<> we are wrapping.

Definition at line 169 of file eigen_sparse_matrix.h.

Referenced by libMesh::EigenSparseMatrix< T >::add(), libMesh::EigenSparseMatrix< T >::get_transpose(), and libMesh::EigenSparseLinearSolver< T >::solve().

◆ _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(), libMesh::ReferenceCounter::ReferenceCounter(), 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< T >::use_hash_table().

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

include/numerics/eigen_sparse_matrix.h
src/numerics/eigen_sparse_matrix.C

Public Types

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Static Protected Attributes

Private Attributes

Friends

Detailed Description

Member Typedef Documentation

◆ Counts

◆ DataType

◆ TripletType

Constructor & Destructor Documentation

◆ EigenSparseMatrix() [1/3]

◆ EigenSparseMatrix() [2/3]

◆ EigenSparseMatrix() [3/3]

◆ ~EigenSparseMatrix()

Member Function Documentation

◆ _get_submatrix()

◆ add() [1/2]

◆ add() [2/2]

◆ add_block_matrix() [1/2]

◆ add_block_matrix() [2/2]

◆ add_matrix() [1/2]

◆ add_matrix() [2/2]

◆ add_sparse_matrix()

◆ attach_dof_map()

◆ attach_sparsity_pattern()

◆ build()

◆ clear()

◆ clone()

◆ close()

◆ closed()

◆ col_start()

◆ col_stop()

◆ comm()

◆ create_submatrix()

◆ create_submatrix_nosort()

◆ disable_print_counter_info()

◆ enable_print_counter_info()

◆ flush()

◆ get_diagonal()

◆ get_info()

◆ get_row()

◆ get_transpose()

◆ increment_constructor_count()

◆ increment_destructor_count()

◆ init() [1/2]

◆ init() [2/2]

◆ initialized()

◆ l1_norm()

◆ l1_norm_diff()

◆ linfty_norm()

◆ local_m()

◆ local_n()

◆ m()

◆ matrix_matrix_mult()

◆ n()

◆ n_nonzeros()

◆ n_objects()

◆ n_processors()

◆ need_full_sparsity_pattern()

◆ operator()()

◆ operator=() [1/3]

◆ operator=() [2/3]

◆ operator=() [3/3]

◆ print() [1/3]

◆ print() [2/3]

◆ print() [3/3]

◆ print_coreform_hdf5()

◆ print_info()

◆ print_matlab()

◆ print_personal()

◆ print_petsc_binary()

◆ print_petsc_hdf5()

◆ processor_id()

◆ read()

◆ read_coreform_hdf5()