libMesh::SparseMatrix< T > Class Template Reference

Generic sparse matrix. More...

#include <dof_map.h>

Inheritance diagram for libMesh::SparseMatrix< T >:

Public Member Functions
	SparseMatrix (const Parallel::Communicator &comm)
	Constructor; initializes the matrix to be empty, without any structure, i.e. More...
virtual SparseMatrix< T > &	operator= (const SparseMatrix< T > &)
	This looks like a copy assignment operator, but note that, unlike normal copy assignment operators, it is pure virtual. More...
	SparseMatrix (SparseMatrix &&)=default
	These 3 special functions can be defaulted for this class, as it does not manage any memory itself. More...
	SparseMatrix (const SparseMatrix &)=default
SparseMatrix &	operator= (SparseMatrix &&)=default
virtual	~SparseMatrix ()=default
	While this class doesn't manage any memory, the derived class might and users may be deleting through a pointer to this base class. More...
virtual SolverPackage	solver_package ()=0
virtual bool	initialized () const
void	attach_dof_map (const DofMap &dof_map)
	Set a pointer to the DofMap to use. More...
void	attach_sparsity_pattern (const SparsityPattern::Build &sp)
	Set a pointer to a sparsity pattern to use. More...
virtual bool	need_full_sparsity_pattern () const
virtual bool	require_sparsity_pattern () const
virtual void	update_sparsity_pattern (const SparsityPattern::Graph &)
	Updates the matrix sparsity pattern. More...
virtual void	init (const numeric_index_type m, const numeric_index_type n, const numeric_index_type m_l, const numeric_index_type n_l, const numeric_index_type nnz=30, const numeric_index_type noz=10, const numeric_index_type blocksize=1)=0
	Initialize SparseMatrix with the specified sizes. More...
virtual void	init (ParallelType type=PARALLEL)=0
	Initialize this matrix using the sparsity structure computed by dof_map. More...
virtual void	clear ()=0
	Restores the SparseMatrix<T> to a pristine state. More...
virtual void	zero ()=0
	Set all entries to 0. More...
virtual std::unique_ptr< SparseMatrix< T > >	zero_clone () const =0
virtual std::unique_ptr< SparseMatrix< T > >	clone () const =0
virtual void	zero_rows (std::vector< numeric_index_type > &rows, T diag_value=0.0)
	Sets all row entries to 0 then puts diag_value in the diagonal entry. More...
virtual void	close ()=0
	Calls the SparseMatrix's internal assembly routines, ensuring that the values are consistent across processors. More...
virtual void	flush ()
	For PETSc matrix , this function is similar to close but without shrinking memory. More...
virtual numeric_index_type	m () const =0
virtual numeric_index_type	local_m () const
	Get the number of rows owned by this process. More...
virtual numeric_index_type	local_n () const
	Get the number of columns owned by this process. More...
virtual numeric_index_type	n () const =0
virtual numeric_index_type	row_start () const =0
virtual numeric_index_type	row_stop () const =0
virtual numeric_index_type	col_start () const =0
virtual numeric_index_type	col_stop () const =0
virtual void	set (const numeric_index_type i, const numeric_index_type j, const T value)=0
	Set the element (i,j) to value. More...
virtual void	add (const numeric_index_type i, const numeric_index_type j, const T value)=0
	Add value to the element (i,j). More...
virtual void	add_matrix (const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols)=0
	Add the full matrix dm to the SparseMatrix. More...
virtual void	add_matrix (const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &dof_indices)=0
	Same as add_matrix, but assumes the row and column maps are the same. More...
virtual void	add_block_matrix (const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &brows, const std::vector< numeric_index_type > &bcols)
	Add the full matrix dm to the SparseMatrix. More...
virtual void	add_block_matrix (const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &dof_indices)
	Same as add_block_matrix(), but assumes the row and column maps are the same. More...
virtual void	add (const T a, const SparseMatrix< T > &X)=0
	Compute \( A \leftarrow A + a*X \) for scalar a, matrix X. More...
virtual void	matrix_matrix_mult (SparseMatrix< T > &, SparseMatrix< T > &, bool)
	Compute Y = A*X for matrix X. More...
virtual void	add_sparse_matrix (const SparseMatrix< T > &, const std::map< numeric_index_type, numeric_index_type > &, const std::map< numeric_index_type, numeric_index_type > &, const T)
	Add scalar* spm to the rows and cols of this matrix (A): A(rows[i], cols[j]) += scalar * spm(i,j) More...
virtual T	operator() (const numeric_index_type i, const numeric_index_type j) const =0
virtual Real	l1_norm () const =0
virtual Real	linfty_norm () const =0
Real	l1_norm_diff (const SparseMatrix< T > &other_mat) const
virtual bool	closed () const =0
virtual std::size_t	n_nonzeros () const
void	print (std::ostream &os=libMesh::out, const bool sparse=false) const
	Print the contents of the matrix to the screen in a uniform style, regardless of matrix/solver package being used. More...
virtual void	print_personal (std::ostream &os=libMesh::out) const =0
	Print the contents of the matrix to the screen in a package-personalized style, if available. More...
void	print (const std::string &filename) const
	Print the contents of the matrix to a file, with a file format depending on the extension of filename. More...
virtual void	print_coreform_hdf5 (const std::string &filename, const std::string &groupname="extraction") const
	Print the contents of the matrix to a file, with the HDF5 sparse matrix format used by CoreForm, putting CSR sparse matrix data in the group given by groupname. More...
virtual void	print_matlab (const std::string &="") const
	Print the contents of the matrix in Matlab's sparse matrix format. More...
virtual void	print_petsc_binary (const std::string &filename) const
	Write the contents of the matrix to a file in PETSc's binary sparse matrix format. More...
virtual void	print_petsc_hdf5 (const std::string &filename) const
	Write the contents of the matrix to a file in PETSc's HDF5 sparse matrix format. More...
virtual void	read (const std::string &filename)
	Read the contents of the matrix from a file, with the file format inferred from the extension of filename. More...
virtual void	read_coreform_hdf5 (const std::string &filename, const std::string &groupname="extraction")
	Read the contents of the matrix from a file, with the HDF5 sparse matrix format used by CoreForm, expecing sparse matrix data in the group given by groupname. More...
virtual void	read_matlab (const std::string &filename)
	Read the contents of the matrix from the Matlab-script sparse matrix format used by PETSc. More...
virtual void	read_petsc_binary (const std::string &filename)
	Read the contents of the matrix from a file in PETSc's binary sparse matrix format. More...
virtual void	read_petsc_hdf5 (const std::string &filename)
	Read the contents of the matrix from a file in PETSc's HDF5 sparse matrix format. More...
virtual void	create_submatrix (SparseMatrix< T > &submatrix, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols) const
	This function creates a matrix called "submatrix" which is defined by the row and column indices given in the "rows" and "cols" entries. More...
virtual void	create_submatrix_nosort (SparseMatrix< T > &, const std::vector< numeric_index_type > &, const std::vector< numeric_index_type > &) const
	Similar to the above function, this function creates a submatrix which is defined by the indices given in the rows and cols vectors. More...
virtual void	reinit_submatrix (SparseMatrix< T > &submatrix, const std::vector< numeric_index_type > &rows, const std::vector< numeric_index_type > &cols) const
	This function is similar to the one above, but it allows you to reuse the existing sparsity pattern of "submatrix" instead of reallocating it again. More...
void	vector_mult (NumericVector< T > &dest, const NumericVector< T > &arg) const
	Multiplies the matrix by the NumericVector arg and stores the result in NumericVector dest. More...
void	vector_mult_add (NumericVector< T > &dest, const NumericVector< T > &arg) const
	Multiplies the matrix by the NumericVector arg and adds the result to the NumericVector dest. More...
virtual void	get_diagonal (NumericVector< T > &dest) const =0
	Copies the diagonal part of the matrix into dest. More...
virtual void	get_transpose (SparseMatrix< T > &dest) const =0
	Copies the transpose of the matrix into dest, which may be *this. More...
virtual void	get_row (numeric_index_type i, std::vector< numeric_index_type > &indices, std::vector< T > &values) const =0
	Get a row from the matrix. More...
virtual void	scale (const T scale)
	Scales all elements of this matrix by scale. More...
virtual bool	supports_hash_table () const
void	use_hash_table (bool use_hash)
	Sets whether to use hash table assembly. More...
bool	use_hash_table () const
virtual void	restore_original_nonzero_pattern ()
	Reset the memory storage of the matrix. More...
template<>
void	print (std::ostream &os, const bool sparse) const
const Parallel::Communicator &	comm () const
processor_id_type	n_processors () const
processor_id_type	processor_id () const

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

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

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

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

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

Friends
std::ostream &	operator<< (std::ostream &os, const SparseMatrix< T > &m)
	Same as the print method above, but allows you to print to a stream in the standard syntax. More...

Detailed Description

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

Generic sparse matrix.

This class contains pure virtual members that must be overridden in derived classes. Using a common base class allows for uniform access to sparse matrices from various different solver packages in different formats.

Author

Benjamin S. Kirk

Date

2003

Definition at line 46 of file vector_fe_ex5.C.

Member Typedef Documentation

Counts

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

protectedinherited

Data structure to log the information.

The log is identified by the class name.

Definition at line 119 of file reference_counter.h.

Constructor & Destructor Documentation

SparseMatrix() [1/3]

template<typename T >

libMesh::SparseMatrix< T >::SparseMatrix ( const Parallel::Communicator &  comm )

explicit

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 89 of file sparse_matrix.C.

                                                                   :
  ParallelObject(comm_in),
  _dof_map(nullptr),
  _sp(nullptr),
  _is_initialized(false),
  _use_hash_table(false)
{}

SparseMatrix() [2/3]

template<typename T>

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

default

These 3 special functions can be defaulted for this class, as it does not manage any memory itself.

SparseMatrix() [3/3]

template<typename T>

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

default

~SparseMatrix()

template<typename T>

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

virtualdefault

While this class doesn't manage any memory, the derived class might and users may be deleting through a pointer to this base class.

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

inlineprotectedvirtual

Protected implementation of the create_submatrix and reinit_submatrix routines.

Note

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

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 654 of file sparse_matrix.h.

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

  {
    libmesh_not_implemented();
  }

add() [1/2]

template<typename T>

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

pure virtual

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.

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, libMesh::PetscMFFDMatrix< Number >, and libMesh::LumpedMassMatrix< T >.

Referenced by add_M_C_K_helmholtz(), libMesh::RBConstruction::add_scaled_Aq(), libMesh::TransientRBConstruction::add_scaled_mass_matrix(), assemble_shell(), libMesh::NewmarkSystem::compute_matrix(), libMesh::RBConstruction::compute_residual_dual_norm_slow(), AssembleOptimization::hessian(), libMesh::HDGProblem::jacobian(), libMesh::RBSCMConstruction::load_matrix_B(), LinearElasticityWithContact::residual_and_jacobian(), libMesh::ClawSystem::solve_conservation_law(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), SystemsTest::testProjectMatrix3D(), libMesh::TransientRBConstruction::truth_assembly(), and libMesh::RBConstruction::truth_assembly().

add() [2/2]

template<typename T>

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

pure virtual

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

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, libMesh::PetscMFFDMatrix< Number >, and libMesh::LumpedMassMatrix< T >.

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  )

virtual

Add the full matrix dm to the SparseMatrix.

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

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 119 of file sparse_matrix.C.

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

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

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

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

  std::vector<numeric_index_type> rows, cols;

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

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

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

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

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

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

add_block_matrix() [2/2]

template<typename T>

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

inlinevirtual

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

Thus the matrix dm must be square.

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 337 of file sparse_matrix.h.

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

add_matrix() [1/2]

template<typename T>

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

pure virtual

Add the full matrix dm to the SparseMatrix.

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

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, and libMesh::PetscMFFDMatrix< Number >.

Referenced by libMesh::HDGProblem::add_matrix(), libMesh::RBConstruction::add_scaled_matrix_and_vector(), assemble(), LinearElasticity::assemble(), assemble_1D(), AssembleOptimization::assemble_A_and_F(), assemble_biharmonic(), assemble_divgrad(), assemble_elasticity(), assemble_ellipticdg(), assemble_func(), assemble_graddiv(), assemble_helmholtz(), assemble_laplace(), assemble_mass(), assemble_matrices(), assemble_matrix_and_rhs(), assemble_poisson(), assemble_SchroedingerEquation(), assemble_shell(), assemble_stokes(), assemble_temperature_jump(), assemble_wave(), assembly_with_dg_fem_context(), compute_jacobian(), fe_assembly(), LaplaceYoung::jacobian(), LargeDeformationElasticity::jacobian(), periodic_bc_test_poisson(), Biharmonic::JR::residual_and_jacobian(), LinearElasticityWithContact::residual_and_jacobian(), and OverlappingCouplingGhostingTest::run_sparsity_pattern_test().

add_matrix() [2/2]

template<typename T>

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

pure virtual

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

Thus the matrix dm must be square.

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, and libMesh::PetscMFFDMatrix< Number >.

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    )

inlinevirtual

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

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 356 of file sparse_matrix.h.

  { libmesh_not_implemented(); }

attach_dof_map()

template<typename T >

void libMesh::SparseMatrix< T >::attach_dof_map

(

const DofMap &

dof_map

)

Set a pointer to the DofMap to use.

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

The lifetime of dof_map must exceed the lifetime of this.

Definition at line 100 of file sparse_matrix.C.

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

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

attach_sparsity_pattern()

template<typename T >

void libMesh::SparseMatrix< T >::attach_sparsity_pattern

(

const SparsityPattern::Build &

sp

)

Set a pointer to a sparsity pattern to use.

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

The lifetime of sp must exceed the lifetime of this.

Definition at line 110 of file sparse_matrix.C.

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

{
  _sp = &sp;
}

build()

template<typename T >

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

static

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

Definition at line 193 of file sparse_matrix.C.

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

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

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

  // Build the appropriate vector
  switch (solver_package)
    {

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


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


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


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

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

clear()

template<typename T>

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

pure virtual

Restores the SparseMatrix<T> to a pristine state.

Implemented in libMesh::StaticCondensation, libMesh::EpetraMatrix< T >, libMesh::PetscMatrixBase< T >, libMesh::PetscMatrixBase< libMesh::Number >, libMesh::PetscMatrixBase< Number >, libMesh::DiagonalMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::EigenSparseMatrix< T >, and libMesh::StaticCondensation.

Referenced by libMesh::PetscMatrix< T >::_get_submatrix(), and libMesh::PetscMatrix< T >::get_transpose().

clone()

template<typename T>

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

pure virtual

Returns

A smart pointer to a copy of this matrix.

Note

This must be overridden in the derived classes.

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, libMesh::PetscMFFDMatrix< Number >, and libMesh::LumpedMassMatrix< T >.

close()

template<typename T>

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

pure virtual

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

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrixBase< T >, libMesh::PetscMatrixBase< libMesh::Number >, libMesh::PetscMatrixBase< Number >, libMesh::EpetraMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::EigenSparseMatrix< T >, and libMesh::StaticCondensation.

Referenced by add_M_C_K_helmholtz(), libMesh::RBConstruction::add_scaled_Aq(), libMesh::RBConstruction::add_scaled_matrix_and_vector(), libMesh::LinearSolver< Number >::adjoint_solve(), assemble(), AssembleOptimization::assemble_A_and_F(), libMesh::ClawSystem::assemble_boundary_condition_matrices(), assemble_func(), assemble_matrix_and_rhs(), assemble_poisson(), assemble_temperature_jump(), libMesh::FEMSystem::assembly(), libMesh::LinearImplicitSystem::assembly(), libMesh::NewmarkSystem::compute_matrix(), libMesh::ContinuationSystem::continuation_solve(), libMesh::SparseMatrix< ValOut >::flush(), form_matrixA(), libMesh::ImplicitSystem::forward_qoi_parameter_sensitivity(), libMesh::CondensedEigenSystem::initialize_condensed_matrices(), libMesh::RBSCMConstruction::load_matrix_B(), main(), periodic_bc_test_poisson(), libMesh::ImplicitSystem::qoi_parameter_hessian(), libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), libMesh::ImplicitSystem::sensitivity_solve(), libMesh::NewtonSolver::solve(), libMesh::CondensedEigenSystem::solve(), libMesh::ClawSystem::solve_conservation_law(), ConstraintOperatorTest::test1DCoarseningOperator(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), SystemsTest::testProjectMatrix3D(), libMesh::TransientRBConstruction::truth_assembly(), libMesh::RBConstruction::truth_assembly(), libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve(), and libMesh::ImplicitSystem::weighted_sensitivity_solve().

closed()

template<typename T>

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

pure virtual

Returns

true if the matrix has been assembled.

Implemented in libMesh::StaticCondensation, libMesh::EpetraMatrix< T >, libMesh::PetscMatrixBase< T >, libMesh::PetscMatrixBase< libMesh::Number >, libMesh::PetscMatrixBase< Number >, libMesh::LaspackMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::EigenSparseMatrix< T >, and libMesh::StaticCondensation.

col_start()

template<typename T>

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

pure virtual

Returns

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

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrixBase< T >, libMesh::PetscMatrixBase< libMesh::Number >, libMesh::PetscMatrixBase< Number >, libMesh::EpetraMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::EigenSparseMatrix< T >, and libMesh::StaticCondensation.

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

col_stop()

template<typename T>

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

pure virtual

Returns

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

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrixBase< T >, libMesh::PetscMatrixBase< libMesh::Number >, libMesh::PetscMatrixBase< Number >, libMesh::EpetraMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::EigenSparseMatrix< T >, and libMesh::StaticCondensation.

Referenced by libMesh::SparseMatrix< ValOut >::local_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.

References libMesh::ParallelObject::_communicator.

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

  { return _communicator; }

create_submatrix()

template<typename T>

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

inlinevirtual

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

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

Definition at line 534 of file sparse_matrix.h.

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

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

create_submatrix_nosort()

template<typename T>

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

inlinevirtual

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

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

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 552 of file sparse_matrix.h.

  {
    libmesh_not_implemented();
  }

disable_print_counter_info()

void libMesh::ReferenceCounter::disable_print_counter_info ( )

staticinherited

Definition at line 100 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

{
  _enable_print_counter = false;
  return;
}

enable_print_counter_info()

void libMesh::ReferenceCounter::enable_print_counter_info ( )

staticinherited

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

Enabled by default.

Definition at line 94 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

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

{
  _enable_print_counter = true;
  return;
}

flush()

template<typename T>

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

inlinevirtual

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

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

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 244 of file sparse_matrix.h.

{ close(); }

get_diagonal()

template<typename T>

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

pure virtual

Copies the diagonal part of the matrix into dest.

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, and libMesh::PetscMFFDMatrix< Number >.

Referenced by libMesh::LumpedMassMatrix< T >::add(), and libMesh::DiagonalMatrix< T >::add().

get_info()

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

staticinherited

Gets a string containing the reference information.

Definition at line 47 of file reference_counter.C.

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

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

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

  std::ostringstream oss;

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

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

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

  return oss.str();

#else

  return "";

#endif
}

get_row()

template<typename T>

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

pure virtual

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

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, and libMesh::PetscMFFDMatrix< Number >.

Referenced by libMesh::MeshBase::copy_constraint_rows().

get_transpose()

template<typename T>

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

pure virtual

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

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, and libMesh::PetscMFFDMatrix< Number >.

Referenced by libMesh::EigenSparseLinearSolver< T >::adjoint_solve(), libMesh::LinearSolver< Number >::adjoint_solve(), and libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve().

increment_constructor_count()

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

inlineprotectednoexceptinherited

Increments the construction counter.

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

Definition at line 183 of file reference_counter.h.

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

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

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

increment_destructor_count()

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

inlineprotectednoexceptinherited

Increments the destruction counter.

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

Definition at line 207 of file reference_counter.h.

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

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

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

init() [1/2]

template<typename T>

virtual void libMesh::SparseMatrix< 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  )

pure virtual

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.

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, libMesh::PetscMFFDMatrix< Number >, libMesh::PetscMatrixShellMatrix< T >, and libMesh::PetscMatrixShellMatrix< Number >.

Referenced by libMesh::CondensedEigenSystem::initialize_condensed_matrices(), libMesh::System::late_matrix_init(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), ConstraintOperatorTest::test1DCoarseningOperator(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), and SystemsTest::testProjectMatrix3D().

init() [2/2]

template<typename T>

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

pure virtual

Initialize this matrix using the sparsity structure computed by dof_map.

Parameters

type	The serial/parallel/ghosted type of the matrix

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, libMesh::PetscMFFDMatrix< Number >, libMesh::PetscMatrixShellMatrix< T >, and libMesh::PetscMatrixShellMatrix< Number >.

initialized()

template<typename T>

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

inlinevirtual

Returns

true if the matrix has been initialized, false otherwise.

Reimplemented in libMesh::StaticCondensation.

Definition at line 133 of file sparse_matrix.h.

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

{ return _is_initialized; }

l1_norm()

template<typename T>

virtual Real libMesh::SparseMatrix< T >::l1_norm ( ) const

pure virtual

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)

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, and libMesh::PetscMFFDMatrix< Number >.

Referenced by libMesh::FEMSystem::assembly().

l1_norm_diff()

template<typename T>

Real libMesh::SparseMatrix< T >::l1_norm_diff

(

const SparseMatrix< T > &

other_mat

)

const

Returns

The l1_norm() of the difference of this and other_mat

Definition at line 1362 of file sparse_matrix.C.

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

linfty_norm()

template<typename T>

virtual Real libMesh::SparseMatrix< T >::linfty_norm ( ) const

pure virtual

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)

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, and libMesh::PetscMFFDMatrix< Number >.

Referenced by SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), and SystemsTest::testProjectMatrix3D().

local_m()

template<typename T>

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

inlinevirtual

Get the number of rows owned by this process.

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

Definition at line 254 of file sparse_matrix.h.

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

{ return row_stop() - row_start(); }

local_n()

template<typename T>

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

inlinevirtual

Get the number of columns owned by this process.

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

Definition at line 259 of file sparse_matrix.h.

{ return col_stop() - col_start(); }

m()

template<typename T>

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

pure virtual

Returns

The row-dimension of the matrix.

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrixBase< T >, libMesh::PetscMatrixBase< libMesh::Number >, libMesh::PetscMatrixBase< Number >, libMesh::EpetraMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::EigenSparseMatrix< T >, and libMesh::StaticCondensation.

Referenced by libMesh::EigenSparseMatrix< T >::add(), libMesh::LaspackMatrix< T >::add(), libMesh::EpetraMatrix< T >::add(), libMesh::PetscMatrix< T >::add(), libMesh::PetscMatrix< T >::add_sparse_matrix(), libMesh::MeshBase::copy_constraint_rows(), and libMesh::PetscMatrix< T >::matrix_matrix_mult().

matrix_matrix_mult()

template<typename T>

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

inlinevirtual

Compute Y = A*X for matrix X.

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 349 of file sparse_matrix.h.

  { libmesh_not_implemented(); }

n()

template<typename T>

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

pure virtual

Returns

The column-dimension of the matrix.

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrixBase< T >, libMesh::PetscMatrixBase< libMesh::Number >, libMesh::PetscMatrixBase< Number >, libMesh::EpetraMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::EigenSparseMatrix< T >, and libMesh::StaticCondensation.

Referenced by libMesh::EigenSparseMatrix< T >::add(), libMesh::LaspackMatrix< T >::add(), libMesh::EpetraMatrix< T >::add(), libMesh::PetscMatrix< T >::add(), libMesh::PetscMatrix< T >::add_sparse_matrix(), and libMesh::MeshBase::copy_constraint_rows().

n_nonzeros()

template<typename T >

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

virtual

Returns

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

Definition at line 266 of file sparse_matrix.C.

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

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

n_objects()

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

inlinestaticinherited

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

Definition at line 85 of file reference_counter.h.

References libMesh::ReferenceCounter::_n_objects.

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

  { return _n_objects; }

n_processors()

processor_id_type libMesh::ParallelObject::n_processors ( ) const

inlineinherited

Returns

The number of processors in the group.

Definition at line 103 of file parallel_object.h.

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

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

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

need_full_sparsity_pattern()

template<typename T>

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

inlinevirtual

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

Definition at line 162 of file sparse_matrix.h.

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

  { return false; }

operator()()

template<typename T>

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

pure virtual

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.

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, and libMesh::PetscMFFDMatrix< Number >.

operator=() [1/2]

template<typename T>

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

inlinevirtual

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 in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::StaticCondensation, libMesh::DiagonalMatrix< T >, libMesh::PetscMFFDMatrix< T >, libMesh::PetscMFFDMatrix< Number >, libMesh::PetscMatrixShellMatrix< T >, libMesh::PetscMatrixShellMatrix< Number >, and libMesh::LumpedMassMatrix< T >.

Definition at line 98 of file sparse_matrix.h.

  {
    libmesh_not_implemented();
    return *this;
  }

operator=() [2/2]

template<typename T>

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

default

print() [1/3]

template<>

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

Definition at line 159 of file sparse_matrix.C.

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

  if (sparse)
    {
      libmesh_not_implemented();
    }

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

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

print() [2/3]

template<typename T >

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

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

Definition at line 275 of file sparse_matrix.C.

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

{
  parallel_object_only();

  libmesh_assert (this->initialized());

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

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

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

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

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

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

print() [3/3]

template<typename T >

void libMesh::SparseMatrix< T >::print

(

const std::string &

filename

)

const

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

Definition at line 754 of file sparse_matrix.C.

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

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

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

  if (gzipped_file)
    basename.remove_suffix(3);

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

print_coreform_hdf5()

template<typename T >

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

virtual

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

Definition at line 521 of file sparse_matrix.C.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

print_info()

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

staticinherited

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

Definition at line 81 of file reference_counter.C.

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

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

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

print_matlab()

template<typename T >

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

virtual

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

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

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 398 of file sparse_matrix.C.

{
  parallel_object_only();

  libmesh_assert (this->initialized());

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

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

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

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

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

      std::size_t real_nonzeros = 0;

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


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

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

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

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

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

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

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

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

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

print_personal()

template<typename T>

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

pure virtual

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

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, and libMesh::PetscMFFDMatrix< Number >.

print_petsc_binary()

template<typename T >

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

virtual

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

virtual

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

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 677 of file sparse_matrix.C.

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

processor_id()

processor_id_type libMesh::ParallelObject::processor_id ( ) const

inlineinherited

Returns

The rank of this processor in the group.

Definition at line 114 of file parallel_object.h.

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

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

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

read()

template<typename T >

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

virtual

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

Definition at line 686 of file sparse_matrix.C.

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

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

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

  if (gzipped_file)
    basename.remove_suffix(3);

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

read_coreform_hdf5()

template<typename T >

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

virtual

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

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

Definition at line 822 of file sparse_matrix.C.

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

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

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

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

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

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

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

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

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

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

        H5Tclose(attr_type);

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

        H5Aclose(attr);

        return returnval;
      };

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

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

  numeric_index_type new_row_start, new_row_stop,
                     new_col_start, new_col_stop;

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

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

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

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

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

  numeric_index_type on_diagonal_nonzeros = 0,
                     off_diagonal_nonzeros = 0;

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

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

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

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

        H5Tclose(data_type);

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

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

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

        datavec.resize(len);

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

        H5Dclose(data);
      };

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

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

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

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

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

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

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

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

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

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

      H5Gclose(group);
      H5Fclose(file);
    }

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

read_matlab()

template<typename T >

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

virtual

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

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

Definition at line 1050 of file sparse_matrix.C.

Referenced by ConstraintOperatorTest::test1DCoarseningNewNodes().

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

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

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

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

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

  numeric_index_type new_row_start, new_row_stop,
                     new_col_start, new_col_stop;

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

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

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

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

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

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

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

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

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

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

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

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

          std::istringstream l(line);

          std::size_t i, j;
          T value;

          l >> i >> j >> value;

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

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

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

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

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

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

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

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

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

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

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

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

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

      if (!m)
        m = largest_i_seen;

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

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

      if (!n)
        n = largest_j_seen;

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

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

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

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

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

  } // Done reading entry data and broadcasting matrix size

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

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

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

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

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

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

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

  this->close();
#endif
}

read_petsc_binary()

template<typename T >

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

virtual

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 )

virtual

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

inlinevirtual

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

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

Definition at line 565 of file sparse_matrix.h.

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

require_sparsity_pattern()

template<typename T>

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

inlinevirtual

Returns

Whether this matrix needs the sparsity pattern computed by the DofMap

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

Definition at line 168 of file sparse_matrix.h.

{ return !this->use_hash_table(); }

restore_original_nonzero_pattern()

template<typename T>

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

inlinevirtual

Reset the memory storage of the matrix.

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

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

Definition at line 644 of file sparse_matrix.h.

{ libmesh_not_implemented(); }

row_start()

template<typename T>

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

pure virtual

Returns

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

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrixBase< T >, libMesh::PetscMatrixBase< libMesh::Number >, libMesh::PetscMatrixBase< Number >, libMesh::EpetraMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::EigenSparseMatrix< T >, and libMesh::StaticCondensation.

Referenced by libMesh::MeshBase::copy_constraint_rows(), libMesh::MatrixFillAction< ValIn, ValOut >::insert(), libMesh::SparseMatrix< ValOut >::local_m(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), and SystemsTest::testProjectMatrix3D().

row_stop()

template<typename T>

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

pure virtual

Returns

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

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrixBase< T >, libMesh::PetscMatrixBase< libMesh::Number >, libMesh::PetscMatrixBase< Number >, libMesh::EpetraMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::EigenSparseMatrix< T >, and libMesh::StaticCondensation.

Referenced by libMesh::MeshBase::copy_constraint_rows(), libMesh::MatrixFillAction< ValIn, ValOut >::insert(), libMesh::SparseMatrix< ValOut >::local_m(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), and SystemsTest::testProjectMatrix3D().

scale()

template<typename T>

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

virtual

Scales all elements of this matrix by scale.

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 1350 of file sparse_matrix.C.

{
  libmesh_assert(this->closed());

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

set()

template<typename T>

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

pure virtual

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.

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, libMesh::PetscMFFDMatrix< Number >, and libMesh::LumpedMassMatrix< T >.

Referenced by AssembleOptimization::equality_constraints_jacobian(), AssembleOptimization::inequality_constraints_jacobian(), libMesh::MatrixFillAction< ValIn, ValOut >::insert(), libMesh::System::projection_matrix(), ConstraintOperatorTest::test1DCoarseningOperator(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), and SystemsTest::testProjectMatrix3D().

solver_package()

template<typename T>

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

pure virtual

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrixBase< T >, libMesh::PetscMatrixBase< libMesh::Number >, libMesh::PetscMatrixBase< Number >, libMesh::EpetraMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::StaticCondensation, libMesh::EigenSparseMatrix< T >, and libMesh::DiagonalMatrix< T >.

supports_hash_table()

template<typename T>

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

inlinevirtual

Returns

Whether the matrix supports hash table assembly

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 619 of file sparse_matrix.h.

{ return false; }

update_sparsity_pattern()

template<typename T>

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

inlinevirtual

Updates the matrix sparsity pattern.

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

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

Definition at line 175 of file sparse_matrix.h.

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

{}

use_hash_table() [1/2]

template<typename T >

void libMesh::SparseMatrix< T >::use_hash_table

(

bool

use_hash

)

Sets whether to use hash table assembly.

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

Definition at line 692 of file sparse_matrix.h.

Referenced by PetscMatrixTest::testPetscCopyFromHash().

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

use_hash_table() [2/2]

template<typename T>

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

inline

Returns

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

Definition at line 634 of file sparse_matrix.h.

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

{ return _use_hash_table; }

vector_mult()

template<typename T>

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

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

Definition at line 237 of file sparse_matrix.C.

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

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

vector_mult_add()

template<typename T>

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

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

Definition at line 247 of file sparse_matrix.C.

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

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

zero()

template<typename T>

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

pure virtual

Set all entries to 0.

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, and libMesh::PetscMFFDMatrix< Number >.

Referenced by add_M_C_K_helmholtz(), libMesh::RBSCMConstruction::Aq_inner_product(), libMesh::ImplicitSystem::assemble(), AssembleOptimization::assemble_A_and_F(), libMesh::RBConstruction::assemble_Aq_matrix(), libMesh::RBConstruction::assemble_inner_product_matrix(), libMesh::TransientRBConstruction::assemble_L2_matrix(), libMesh::TransientRBConstruction::assemble_mass_matrix(), libMesh::TransientRBConstruction::assemble_Mq_matrix(), libMesh::FEMSystem::assembly(), libMesh::NewmarkSystem::compute_matrix(), libMesh::RBConstruction::compute_residual_dual_norm_slow(), libMesh::RBSCMConstruction::compute_SCM_bounding_box(), DMlibMeshJacobian(), AssembleOptimization::equality_constraints_jacobian(), libMesh::RBSCMConstruction::evaluate_stability_constant(), AssembleOptimization::hessian(), AssembleOptimization::inequality_constraints_jacobian(), LargeDeformationElasticity::jacobian(), libMesh::libmesh_petsc_snes_jacobian(), libMesh::libmesh_petsc_snes_residual(), libMesh::RBSCMConstruction::load_matrix_B(), main(), LinearElasticityWithContact::residual_and_jacobian(), libMesh::ClawSystem::solve_conservation_law(), libMesh::TransientRBConstruction::truth_assembly(), and libMesh::RBConstruction::truth_assembly().

zero_clone()

template<typename T>

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

pure virtual

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.

Implemented in libMesh::StaticCondensation, libMesh::PetscMatrix< T >, libMesh::EpetraMatrix< T >, libMesh::DiagonalMatrix< T >, libMesh::LaspackMatrix< T >, libMesh::EigenSparseMatrix< T >, libMesh::StaticCondensation, libMesh::PetscMFFDMatrix< T >, libMesh::PetscMFFDMatrix< Number >, and libMesh::LumpedMassMatrix< T >.

zero_rows()

template<typename T>

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

virtual

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

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

Definition at line 258 of file sparse_matrix.C.

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

Friends And Related Function Documentation

operator<<

template<typename T>

std::ostream& operator<< ( std::ostream &  os, const SparseMatrix< T > &  m  )

friend

Same as the print method above, but allows you to print to a stream in the standard syntax.

template <typename U>
friend std::ostream & operator << (std::ostream & os, const SparseMatrix<U> & m);

Note

The above syntax, which does not require any prior declaration of operator<<, declares any instantiation of SparseMatrix<X> is friend to any instantiation of operator<<(ostream &, SparseMatrix<Y> &). It would not happen in practice, but in principle it means that SparseMatrix<Complex> would be friend to operator<<(ostream &, SparseMatrix<Real>).

The form below, which requires a previous declaration of the operator<<(stream &, SparseMatrix<T> &) function (see top of this file), means that any instantiation of SparseMatrix<T> is friend to the specialization operator<<(ostream &, SparseMatrix<T> &), but e.g. SparseMatrix<U> is not friend to the same function. So this is slightly different to the form above...

This method seems to be the "preferred" technique, see http://www.parashift.com/c++-faq-lite/template-friends.html

Definition at line 705 of file sparse_matrix.h.

{
  m.print(os);
  return os;
}

Member Data Documentation

_communicator

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

protectedinherited

Definition at line 120 of file parallel_object.h.

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

_counts

ReferenceCounter::Counts libMesh::ReferenceCounter::_counts

staticprotectedinherited

Actually holds the data.

Definition at line 124 of file reference_counter.h.

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

_dof_map

template<typename T>

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

protected

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

protected

Flag indicating whether or not the matrix has been initialized.

Definition at line 678 of file sparse_matrix.h.

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

_mutex

Threads::spin_mutex libMesh::ReferenceCounter::_mutex

staticprotectedinherited

Mutual exclusion object to enable thread-safe reference counting.

Definition at line 137 of file reference_counter.h.

_n_objects

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

staticprotectedinherited

The number of objects.

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

Definition at line 132 of file reference_counter.h.

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

_sp

template<typename T>

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

protected

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

protected

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

Definition at line 683 of file sparse_matrix.h.

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

---

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

• examples/vector_fe/vector_fe_ex5/vector_fe_ex5.C
• include/numerics/sparse_matrix.h
• src/numerics/sparse_matrix.C