libMesh
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libMesh::PetscMatrixShellMatrix< T > Class Template Referenceabstract

This class allows to use a PETSc shell matrix as a PetscMatrix. More...

#include <petsc_matrix_shell_matrix.h>

Inheritance diagram for libMesh::PetscMatrixShellMatrix< T >:
[legend]

Public Member Functions

 PetscMatrixShellMatrix (const Parallel::Communicator &comm_in)
 
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=30, const numeric_index_type=10, const numeric_index_type blocksize=1) override
 Initialize SparseMatrix with the specified sizes. More...
 
virtual void init (ParallelType=PARALLEL) override
 Initialize this matrix using the sparsity structure computed by dof_map. More...
 
virtual SparseMatrix< T > & operator= (const SparseMatrix< T > &) override
 This looks like a copy assignment operator, but note that, unlike normal copy assignment operators, it is pure virtual. More...
 
virtual bool require_sparsity_pattern () const override
 
virtual SolverPackage solver_package () override
 
Mat mat ()
 
Mat mat () const
 
virtual void clear () noexcept override
 clear() is called from the destructor, so it should not throw. More...
 
void set_destroy_mat_on_exit (bool destroy=true)
 If set to false, we don't delete the Mat on destruction and allow instead for PETSc to manage it. More...
 
void swap (PetscMatrixBase< T > &)
 Swaps the internal data pointers of two PetscMatrices, no actual values are swapped. More...
 
void set_context ()
 Set the context (ourself) for _mat. More...
 
virtual numeric_index_type m () const override
 
virtual numeric_index_type local_m () const final
 Get the number of rows owned by this process. More...
 
virtual numeric_index_type n () const override
 
virtual numeric_index_type local_n () const final
 Get the number of columns owned by this process. More...
 
virtual numeric_index_type row_start () const override
 
virtual numeric_index_type row_stop () const override
 
virtual numeric_index_type col_start () const override
 
virtual numeric_index_type col_stop () const override
 
virtual void close () override
 Calls the SparseMatrix's internal assembly routines, ensuring that the values are consistent across processors. More...
 
virtual bool closed () const override
 
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 void update_sparsity_pattern (const SparsityPattern::Graph &)
 Updates the matrix sparsity pattern. 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 flush ()
 For PETSc matrix , this function is similar to close but without shrinking memory. More...
 
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 (const T a, const SparseMatrix< T > &X)=0
 Compute \( A \leftarrow A + a*X \) for scalar a, matrix X. 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 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 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...
 
template<>
void print (std::ostream &os, const bool sparse) const
 
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...
 
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)
 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)
 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...
 
const Parallel::Communicatorcomm () const
 
processor_id_type n_processors () const
 
processor_id_type processor_id () const
 

Static Public Member Functions

static PetscMatrixBase< T > * get_context (Mat mat, const TIMPI::Communicator &comm)
 
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

Mat _mat
 PETSc matrix datatype to store values. More...
 
bool _destroy_mat_on_exit
 This boolean value should only be set to false for the constructor which takes a PETSc Mat object. More...
 
DofMap const * _dof_map
 The DofMap object associated with this object. More...
 
SparsityPattern::Build const * _sp
 The sparsity pattern associated with this object. More...
 
bool _is_initialized
 Flag indicating whether or not the matrix has been initialized. More...
 
bool _use_hash_table
 Flag indicating whether the matrix is assembled using a hash table. More...
 
const Parallel::Communicator_communicator
 

Static Protected Attributes

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

Private Attributes

const bool _omit_constrained_dofs
 Whether to omit constrained degrees of freedom. More...
 

Friends

void init_shell_mat (PetscMatrixShellMatrix< T > &obj)
 
void init_shell_mat (PetscMatrixShellMatrix< T > &obj, 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 blocksize_in)
 

Detailed Description

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

This class allows to use a PETSc shell matrix as a PetscMatrix.

Author
Alexander Lindsay
Date
2024

Definition at line 38 of file petsc_matrix_shell_matrix.h.

Member Typedef Documentation

◆ Counts

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

Data structure to log the information.

The log is identified by the class name.

Definition at line 119 of file reference_counter.h.

Constructor & Destructor Documentation

◆ PetscMatrixShellMatrix()

template<typename T >
libMesh::PetscMatrixShellMatrix< T >::PetscMatrixShellMatrix ( const Parallel::Communicator comm_in)
explicit

Definition at line 81 of file petsc_matrix_shell_matrix.h.

82  : PetscMatrixBase<T>(comm_in), _omit_constrained_dofs(false)
83 {
84 }
const bool _omit_constrained_dofs
Whether to omit constrained degrees of freedom.

Member Function Documentation

◆ _get_submatrix()

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

Protected implementation of the create_submatrix and reinit_submatrix routines.

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

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 640 of file sparse_matrix.h.

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

644  {
645  libmesh_not_implemented();
646  }

◆ 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 virtualinherited

◆ add() [2/2]

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

◆ add_block_matrix() [1/2]

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

Add the full matrix dm to the SparseMatrix.

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

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 96 of file sparse_matrix.C.

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

99 {
100  libmesh_assert_equal_to (dm.m() / brows.size(), dm.n() / bcols.size());
101 
102  const numeric_index_type blocksize = cast_int<numeric_index_type>
103  (dm.m() / brows.size());
104 
105  libmesh_assert_equal_to (dm.m()%blocksize, 0);
106  libmesh_assert_equal_to (dm.n()%blocksize, 0);
107 
108  std::vector<numeric_index_type> rows, cols;
109 
110  rows.reserve(blocksize*brows.size());
111  cols.reserve(blocksize*bcols.size());
112 
113  for (auto & row : brows)
114  {
115  numeric_index_type i = row * blocksize;
116 
117  for (unsigned int v=0; v<blocksize; v++)
118  rows.push_back(i++);
119  }
120 
121  for (auto & col : bcols)
122  {
123  numeric_index_type j = col * blocksize;
124 
125  for (unsigned int v=0; v<blocksize; v++)
126  cols.push_back(j++);
127  }
128 
129  this->add_matrix (dm, rows, cols);
130 }
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.
dof_id_type numeric_index_type
Definition: id_types.h:99

◆ add_block_matrix() [2/2]

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

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

Thus the matrix dm must be square.

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 337 of file sparse_matrix.h.

339  { this->add_block_matrix (dm, dof_indices, dof_indices); }
virtual void add_block_matrix(const DenseMatrix< T > &dm, const std::vector< numeric_index_type > &brows, const std::vector< numeric_index_type > &bcols)
Add the full matrix dm to the SparseMatrix.
Definition: sparse_matrix.C:96

◆ 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 virtualinherited

◆ 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 virtualinherited

◆ add_sparse_matrix()

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

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

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 356 of file sparse_matrix.h.

360  { libmesh_not_implemented(); }

◆ attach_dof_map()

template<typename T >
void libMesh::SparseMatrix< T >::attach_dof_map ( const DofMap dof_map)
inherited

Set a pointer to the DofMap to use.

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

The lifetime of dof_map must exceed the lifetime of this.

Definition at line 77 of file sparse_matrix.C.

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

78 {
79  _dof_map = &dof_map;
80  if (!_sp)
81  _sp = dof_map.get_sparsity_pattern();
82 }
SparsityPattern::Build const * _sp
The sparsity pattern associated with this object.
const SparsityPattern::Graph & get_sparsity_pattern() const
Rows of sparse matrix indices, indexed by the offset from the first DoF on this processor.
DofMap const * _dof_map
The DofMap object associated with this object.

◆ attach_sparsity_pattern()

template<typename T >
void libMesh::SparseMatrix< T >::attach_sparsity_pattern ( const SparsityPattern::Build sp)
inherited

Set a pointer to a sparsity pattern to use.

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

The lifetime of sp must exceed the lifetime of this.

Definition at line 87 of file sparse_matrix.C.

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

88 {
89  _sp = &sp;
90 }
SparsityPattern::Build const * _sp
The sparsity pattern associated with this object.

◆ build()

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

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

Definition at line 170 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().

173 {
174  // Avoid unused parameter warnings when no solver packages are enabled.
176 
177  if (matrix_build_type == MatrixBuildType::DIAGONAL)
178  return std::make_unique<DiagonalMatrix<T>>(comm);
179 
180  // Build the appropriate vector
181  switch (solver_package)
182  {
183 
184 #ifdef LIBMESH_HAVE_LASPACK
185  case LASPACK_SOLVERS:
186  return std::make_unique<LaspackMatrix<T>>(comm);
187 #endif
188 
189 
190 #ifdef LIBMESH_HAVE_PETSC
191  case PETSC_SOLVERS:
192  return std::make_unique<PetscMatrix<T>>(comm);
193 #endif
194 
195 
196 #ifdef LIBMESH_TRILINOS_HAVE_EPETRA
197  case TRILINOS_SOLVERS:
198  return std::make_unique<EpetraMatrix<T>>(comm);
199 #endif
200 
201 
202 #ifdef LIBMESH_HAVE_EIGEN
203  case EIGEN_SOLVERS:
204  return std::make_unique<EigenSparseMatrix<T>>(comm);
205 #endif
206 
207  default:
208  libmesh_error_msg("ERROR: Unrecognized solver package: " << solver_package);
209  }
210 }
const Parallel::Communicator & comm() const
void libmesh_ignore(const Args &...)
virtual SolverPackage solver_package()=0

◆ clear()

template<typename T >
void libMesh::PetscMatrixBase< T >::clear ( )
overridevirtualnoexceptinherited

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

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 74 of file petsc_matrix_base.C.

Referenced by libMesh::StaticCondensation::clear().

75 {
76  if ((this->initialized()) && (this->_destroy_mat_on_exit))
77  {
78  exceptionless_semiparallel_only();
79 
80  // If we encounter an error here, print a warning but otherwise
81  // keep going since we may be recovering from an exception.
82  PetscErrorCode ierr = MatDestroy (&_mat);
83  if (ierr)
84  libmesh_warning("Warning: MatDestroy returned a non-zero error code which we ignored.");
85 
86  this->_is_initialized = false;
87  }
88 }
virtual bool initialized() const
bool _destroy_mat_on_exit
This boolean value should only be set to false for the constructor which takes a PETSc Mat object...
bool _is_initialized
Flag indicating whether or not the matrix has been initialized.
Mat _mat
PETSc matrix datatype to store values.

◆ clone()

template<typename T>
virtual std::unique_ptr<SparseMatrix<T> > libMesh::SparseMatrix< T >::clone ( ) const
pure virtualinherited

◆ close()

template<typename T >
void libMesh::PetscMatrixBase< T >::close ( )
overridevirtualinherited

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

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 226 of file petsc_matrix_base.C.

Referenced by libMesh::PetscMatrix< T >::_get_submatrix(), libMesh::PetscMatrix< T >::create_submatrix_nosort(), DMlibMeshJacobian(), libMesh::PetscMatrix< T >::get_transpose(), libMesh::libmesh_petsc_snes_jacobian(), and libMesh::PetscLinearSolver< Number >::solve_common().

227 {
228  semiparallel_only();
229 
230  // BSK - 1/19/2004
231  // strictly this check should be OK, but it seems to
232  // fail on matrix-free matrices. Do they falsely
233  // state they are assembled? Check with the developers...
234  // if (this->closed())
235  // return;
236 
237  MatAssemblyBeginEnd(this->comm(), this->_mat, MAT_FINAL_ASSEMBLY);
238 }
const Parallel::Communicator & comm() const
Mat _mat
PETSc matrix datatype to store values.

◆ closed()

template<typename T >
bool libMesh::PetscMatrixBase< T >::closed ( ) const
overridevirtualinherited
Returns
true if the matrix has been assembled.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 241 of file petsc_matrix_base.C.

Referenced by libMesh::PetscMatrix< T >::add().

242 {
243  libmesh_assert (this->initialized());
244 
245  PetscBool assembled;
246 
247  LibmeshPetscCall(MatAssembled(this->_mat, &assembled));
248 
249  return (assembled == PETSC_TRUE);
250 }
virtual bool initialized() const
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.

◆ col_start()

template<typename T >
numeric_index_type libMesh::PetscMatrixBase< T >::col_start ( ) const
overridevirtualinherited
Returns
The index of the first matrix column owned by this processor.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 202 of file petsc_matrix_base.C.

203 {
204  libmesh_assert (this->initialized());
205 
206  PetscInt start=0, stop=0;
207 
208  LibmeshPetscCall(MatGetOwnershipRangeColumn(this->_mat, &start, &stop));
209 
210  return static_cast<numeric_index_type>(start);
211 }
virtual bool initialized() const
dof_id_type numeric_index_type
Definition: id_types.h:99
libmesh_assert(ctx)
void stop(const char *file, int line, const char *date, const char *time)
Mat _mat
PETSc matrix datatype to store values.

◆ col_stop()

template<typename T >
numeric_index_type libMesh::PetscMatrixBase< T >::col_stop ( ) const
overridevirtualinherited
Returns
The index of the last matrix column (+1) owned by this processor.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 214 of file petsc_matrix_base.C.

215 {
216  libmesh_assert (this->initialized());
217 
218  PetscInt start=0, stop=0;
219 
220  LibmeshPetscCall(MatGetOwnershipRangeColumn(this->_mat, &start, &stop));
221 
222  return static_cast<numeric_index_type>(stop);
223 }
virtual bool initialized() const
dof_id_type numeric_index_type
Definition: id_types.h:99
libmesh_assert(ctx)
void stop(const char *file, int line, const char *date, const char *time)
Mat _mat
PETSc matrix datatype to store values.

◆ 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::System::add_variable(), libMesh::System::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::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::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::MeshBase::get_info(), libMesh::System::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(), 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::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::prepare_for_use(), 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::System::read_legacy_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::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::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(), ConstraintOperatorTest::test1DCoarseningNewNodes(), ConstraintOperatorTest::test1DCoarseningOperator(), 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(), 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().

98  { return _communicator; }
const Parallel::Communicator & _communicator

◆ create_submatrix()

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

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

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

Definition at line 520 of file sparse_matrix.h.

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

523  {
524  this->_get_submatrix(submatrix,
525  rows,
526  cols,
527  false); // false means DO NOT REUSE submatrix
528  }
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.

◆ create_submatrix_nosort()

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

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

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

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 538 of file sparse_matrix.h.

541  {
542  libmesh_not_implemented();
543  }

◆ 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.

101 {
102  _enable_print_counter = false;
103  return;
104 }
static bool _enable_print_counter
Flag to control whether reference count information is printed when print_info is called...

◆ enable_print_counter_info()

void libMesh::ReferenceCounter::enable_print_counter_info ( )
staticinherited

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

Definition at line 94 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

95 {
96  _enable_print_counter = true;
97  return;
98 }
static bool _enable_print_counter
Flag to control whether reference count information is printed when print_info is called...

◆ flush()

template<typename T>
virtual void libMesh::SparseMatrix< T >::flush ( )
inlinevirtualinherited

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

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

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 244 of file sparse_matrix.h.

244 { close(); }
virtual void close()=0
Calls the SparseMatrix&#39;s internal assembly routines, ensuring that the values are consistent across p...

◆ get_context()

template<typename T >
PetscMatrixBase< T > * libMesh::PetscMatrixBase< T >::get_context ( Mat  mat,
const TIMPI::Communicator comm 
)
staticinherited
Returns
The context for mat if it exists, else a nullptr

Definition at line 116 of file petsc_matrix_base.C.

Referenced by DMlibMeshJacobian(), form_matrixA(), and libMesh::libmesh_petsc_snes_jacobian().

117 {
118  void * ctx;
119  PetscContainer container;
120  LibmeshPetscCall2(comm, PetscObjectQuery((PetscObject)mat, "PetscMatrixCtx", (PetscObject *)&container));
121  if (!container)
122  return nullptr;
123 
124  LibmeshPetscCall2(comm, PetscContainerGetPointer(container, &ctx));
126  return static_cast<PetscMatrixBase<T> *>(ctx);
127 }
const Parallel::Communicator & comm() const
libmesh_assert(ctx)
void * ctx

◆ get_diagonal()

template<typename T>
virtual void libMesh::SparseMatrix< T >::get_diagonal ( NumericVector< T > &  dest) const
pure virtualinherited

◆ 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().

48 {
49 #if defined(LIBMESH_ENABLE_REFERENCE_COUNTING) && defined(DEBUG)
50 
51  std::ostringstream oss;
52 
53  oss << '\n'
54  << " ---------------------------------------------------------------------------- \n"
55  << "| Reference count information |\n"
56  << " ---------------------------------------------------------------------------- \n";
57 
58  for (const auto & [name, cd] : _counts)
59  oss << "| " << name << " reference count information:\n"
60  << "| Creations: " << cd.first << '\n'
61  << "| Destructions: " << cd.second << '\n';
62 
63  oss << " ---------------------------------------------------------------------------- \n";
64 
65  return oss.str();
66 
67 #else
68 
69  return "";
70 
71 #endif
72 }
std::string name(const ElemQuality q)
This function returns a string containing some name for q.
Definition: elem_quality.C:42
static Counts _counts
Actually holds the data.

◆ 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 virtualinherited

Get a row from the matrix.

Parameters
iThe matrix row to get
indicesA container that will be filled with the column indices corresponding to (possibly) non-zero values
valuesA 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 virtualinherited

◆ 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().

184 {
185  libmesh_try
186  {
187  Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
188  std::pair<unsigned int, unsigned int> & p = _counts[name];
189  p.first++;
190  }
191  libmesh_catch (...)
192  {
193  auto stream = libMesh::err.get();
194  stream->exceptions(stream->goodbit); // stream must not throw
195  libMesh::err << "Encountered unrecoverable error while calling "
196  << "ReferenceCounter::increment_constructor_count() "
197  << "for a(n) " << name << " object." << std::endl;
198  std::terminate();
199  }
200 }
std::string name(const ElemQuality q)
This function returns a string containing some name for q.
Definition: elem_quality.C:42
OStreamProxy err
static Counts _counts
Actually holds the data.
streamT * get()
Rather than implement every ostream/ios/ios_base function, we&#39;ll be lazy and make esoteric uses go th...
spin_mutex spin_mtx
A convenient spin mutex object which can be used for obtaining locks.
Definition: threads.C:30

◆ 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().

208 {
209  libmesh_try
210  {
211  Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
212  std::pair<unsigned int, unsigned int> & p = _counts[name];
213  p.second++;
214  }
215  libmesh_catch (...)
216  {
217  auto stream = libMesh::err.get();
218  stream->exceptions(stream->goodbit); // stream must not throw
219  libMesh::err << "Encountered unrecoverable error while calling "
220  << "ReferenceCounter::increment_destructor_count() "
221  << "for a(n) " << name << " object." << std::endl;
222  std::terminate();
223  }
224 }
std::string name(const ElemQuality q)
This function returns a string containing some name for q.
Definition: elem_quality.C:42
OStreamProxy err
static Counts _counts
Actually holds the data.
streamT * get()
Rather than implement every ostream/ios/ios_base function, we&#39;ll be lazy and make esoteric uses go th...
spin_mutex spin_mtx
A convenient spin mutex object which can be used for obtaining locks.
Definition: threads.C:30

◆ init() [1/2]

template<typename T >
void libMesh::PetscMatrixShellMatrix< T >::init ( const numeric_index_type  m,
const numeric_index_type  n,
const numeric_index_type  m_l,
const numeric_index_type  n_l,
const numeric_index_type  nnz = 30,
const numeric_index_type  noz = 10,
const numeric_index_type  blocksize = 1 
)
overridevirtual

Initialize SparseMatrix with the specified sizes.

Parameters
mThe global number of rows.
nThe global number of columns.
m_lThe local number of rows.
n_lThe local number of columns.
nnzThe number of on-diagonal nonzeros per row (defaults to 30).
nozThe number of off-diagonal nonzeros per row (defaults to 10).
blocksizeOptional value indicating dense coupled blocks for systems with multiple variables all of the same type.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 30 of file petsc_matrix_shell_matrix.C.

Referenced by libMesh::StaticCondensation::init().

37 {
38  init_shell_mat(*this, m, n, m_l, n_l, blocksize);
39  this->set_context();
40 }
virtual numeric_index_type n() const override
virtual numeric_index_type m() const override
void set_context()
Set the context (ourself) for _mat.
friend void init_shell_mat(PetscMatrixShellMatrix< T > &obj)

◆ init() [2/2]

template<typename T>
virtual void libMesh::PetscMatrixShellMatrix< T >::init ( ParallelType  = PARALLEL)
overridevirtual

Initialize this matrix using the sparsity structure computed by dof_map.

Parameters
typeThe serial/parallel/ghosted type of the matrix

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

◆ initialized()

template<typename T>
virtual bool libMesh::SparseMatrix< T >::initialized ( ) const
inlinevirtualinherited
Returns
true if the matrix has been initialized, false otherwise.

Reimplemented in libMesh::StaticCondensation.

Definition at line 133 of file sparse_matrix.h.

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

133 { return _is_initialized; }
bool _is_initialized
Flag indicating whether or not the matrix has been initialized.

◆ l1_norm()

template<typename T>
virtual Real libMesh::SparseMatrix< T >::l1_norm ( ) const
pure virtualinherited
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
inherited
Returns
The l1_norm() of the difference of this and other_mat

Definition at line 1124 of file sparse_matrix.C.

1125 {
1126  auto diff_mat = this->clone();
1127  diff_mat->add(-1.0, other_mat);
1128  return diff_mat->l1_norm();
1129 }
virtual std::unique_ptr< SparseMatrix< T > > clone() const =0

◆ linfty_norm()

template<typename T>
virtual Real libMesh::SparseMatrix< T >::linfty_norm ( ) const
pure virtualinherited
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 >
numeric_index_type libMesh::PetscMatrixBase< T >::local_m ( ) const
finalvirtualinherited

Get the number of rows owned by this process.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 142 of file petsc_matrix_base.C.

143 {
144  libmesh_assert (this->initialized());
145 
146  PetscInt m = 0;
147 
148  LibmeshPetscCall(MatGetLocalSize (this->_mat, &m, NULL));
149 
150  return static_cast<numeric_index_type>(m);
151 }
virtual bool initialized() const
virtual numeric_index_type m() const override
dof_id_type numeric_index_type
Definition: id_types.h:99
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.

◆ local_n()

template<typename T >
numeric_index_type libMesh::PetscMatrixBase< T >::local_n ( ) const
finalvirtualinherited

Get the number of columns owned by this process.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 166 of file petsc_matrix_base.C.

167 {
168  libmesh_assert (this->initialized());
169 
170  PetscInt n = 0;
171 
172  LibmeshPetscCall(MatGetLocalSize (this->_mat, NULL, &n));
173 
174  return static_cast<numeric_index_type>(n);
175 }
virtual numeric_index_type n() const override
virtual bool initialized() const
dof_id_type numeric_index_type
Definition: id_types.h:99
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.

◆ m()

template<typename T >
numeric_index_type libMesh::PetscMatrixBase< T >::m ( ) const
overridevirtualinherited
Returns
The row-dimension of the matrix.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 130 of file petsc_matrix_base.C.

131 {
132  libmesh_assert (this->initialized());
133 
134  PetscInt petsc_m=0, petsc_n=0;
135 
136  LibmeshPetscCall(MatGetSize (this->_mat, &petsc_m, &petsc_n));
137 
138  return static_cast<numeric_index_type>(petsc_m);
139 }
virtual bool initialized() const
dof_id_type numeric_index_type
Definition: id_types.h:99
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.

◆ mat() [1/2]

template<typename T>
Mat libMesh::PetscMatrixBase< T >::mat ( )
inlineinherited
Returns
The raw PETSc matrix pointer.
Note
This is generally not required in user-level code.
Don't do anything crazy like calling MatDestroy() on it, or very bad things will likely happen!

Definition at line 120 of file petsc_matrix_base.h.

Referenced by libMesh::StaticCondensation::add_matrix(), libMesh::PetscLinearSolver< Number >::init(), libMesh::libmesh_petsc_DMCreateInterpolation(), libMesh::libmesh_petsc_DMCreateRestriction(), libMesh::PetscDiffSolver::solve(), libMesh::TaoOptimizationSolver< T >::solve(), libMesh::PetscNonlinearSolver< Number >::solve(), and libMesh::PetscLinearSolver< Number >::solve_common().

120 { libmesh_assert (_mat); return _mat; }
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.

◆ mat() [2/2]

template<typename T>
Mat libMesh::PetscMatrixBase< T >::mat ( ) const
inlineinherited

Definition at line 121 of file petsc_matrix_base.h.

121 { libmesh_assert(_mat); return _mat; }
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.

◆ matrix_matrix_mult()

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

Compute Y = A*X for matrix X.

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 349 of file sparse_matrix.h.

350  { libmesh_not_implemented(); }

◆ n()

template<typename T >
numeric_index_type libMesh::PetscMatrixBase< T >::n ( ) const
overridevirtualinherited
Returns
The column-dimension of the matrix.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 154 of file petsc_matrix_base.C.

155 {
156  libmesh_assert (this->initialized());
157 
158  PetscInt petsc_m=0, petsc_n=0;
159 
160  LibmeshPetscCall(MatGetSize (this->_mat, &petsc_m, &petsc_n));
161 
162  return static_cast<numeric_index_type>(petsc_n);
163 }
virtual bool initialized() const
dof_id_type numeric_index_type
Definition: id_types.h:99
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.

◆ n_nonzeros()

template<typename T >
std::size_t libMesh::SparseMatrix< T >::n_nonzeros ( ) const
virtualinherited
Returns
the global number of non-zero entries in the matrix sparsity pattern

Definition at line 243 of file sparse_matrix.C.

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

244 {
245  if (!_sp)
246  return 0;
247  return _sp->n_nonzeros();
248 }
std::size_t n_nonzeros() const
The total number of nonzeros in the global matrix.
SparsityPattern::Build const * _sp
The sparsity pattern associated with this object.

◆ 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().

86  { return _n_objects; }
static Threads::atomic< unsigned int > _n_objects
The number of 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::ExodusII_IO::copy_scalar_solution(), libMesh::Nemesis_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::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().

104  {
105  processor_id_type returnval =
106  cast_int<processor_id_type>(_communicator.size());
107  libmesh_assert(returnval); // We never have an empty comm
108  return returnval;
109  }
const Parallel::Communicator & _communicator
processor_id_type size() const
uint8_t processor_id_type
libmesh_assert(ctx)

◆ need_full_sparsity_pattern()

template<typename T>
virtual bool libMesh::SparseMatrix< T >::need_full_sparsity_pattern ( ) const
inlinevirtualinherited
Returns
true if this sparse matrix format needs to be fed the graph of the sparse matrix.

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

Reimplemented in libMesh::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().

163  { return false; }

◆ operator()()

template<typename T>
virtual T libMesh::SparseMatrix< T >::operator() ( const numeric_index_type  i,
const numeric_index_type  j 
) const
pure virtualinherited
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=()

template<typename T>
SparseMatrix< T > & libMesh::PetscMatrixShellMatrix< T >::operator= ( const SparseMatrix< T > &  )
overridevirtual

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

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

Returns
A reference to *this as the base type.

Reimplemented from libMesh::SparseMatrix< T >.

Definition at line 88 of file petsc_matrix_shell_matrix.h.

89 {
90  libmesh_error();
91 }

◆ print() [1/2]

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

Definition at line 136 of file sparse_matrix.C.

137 {
138  // std::complex<>::operator<<() is defined, but use this form
139 
140  if (sparse)
141  {
142  libmesh_not_implemented();
143  }
144 
145  os << "Real part:" << std::endl;
146  for (auto i : make_range(this->m()))
147  {
148  for (auto j : make_range(this->n()))
149  os << std::setw(8) << (*this)(i,j).real() << " ";
150  os << std::endl;
151  }
152 
153  os << std::endl << "Imaginary part:" << std::endl;
154  for (auto i : make_range(this->m()))
155  {
156  for (auto j : make_range(this->n()))
157  os << std::setw(8) << (*this)(i,j).imag() << " ";
158  os << std::endl;
159  }
160 }
boost::multiprecision::float128 real(const boost::multiprecision::float128 in)
virtual numeric_index_type m() const =0
IntRange< T > make_range(T beg, T end)
The 2-parameter make_range() helper function returns an IntRange<T> when both input parameters are of...
Definition: int_range.h:140
boost::multiprecision::float128 imag(const boost::multiprecision::float128)
virtual numeric_index_type n() const =0

◆ print() [2/2]

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

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

Definition at line 252 of file sparse_matrix.C.

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

253 {
254  parallel_object_only();
255 
256  libmesh_assert (this->initialized());
257 
258  const numeric_index_type first_dof = this->row_start(),
259  end_dof = this->row_stop();
260 
261  // We'll print the matrix from processor 0 to make sure
262  // it's serialized properly
263  if (this->processor_id() == 0)
264  {
265  libmesh_assert_equal_to (first_dof, 0);
266  for (numeric_index_type i : make_range(end_dof))
267  {
268  if (sparse)
269  {
270  for (auto j : make_range(this->n()))
271  {
272  T c = (*this)(i,j);
273  if (c != static_cast<T>(0.0))
274  {
275  os << i << " " << j << " " << c << std::endl;
276  }
277  }
278  }
279  else
280  {
281  for (auto j : make_range(this->n()))
282  os << (*this)(i,j) << " ";
283  os << std::endl;
284  }
285  }
286 
287  std::vector<numeric_index_type> ibuf, jbuf;
288  std::vector<T> cbuf;
289  numeric_index_type currenti = end_dof;
290  for (auto p : IntRange<processor_id_type>(1, this->n_processors()))
291  {
292  this->comm().receive(p, ibuf);
293  this->comm().receive(p, jbuf);
294  this->comm().receive(p, cbuf);
295  libmesh_assert_equal_to (ibuf.size(), jbuf.size());
296  libmesh_assert_equal_to (ibuf.size(), cbuf.size());
297 
298  if (ibuf.empty())
299  continue;
300  libmesh_assert_greater_equal (ibuf.front(), currenti);
301  libmesh_assert_greater_equal (ibuf.back(), ibuf.front());
302 
303  std::size_t currentb = 0;
304  for (;currenti <= ibuf.back(); ++currenti)
305  {
306  if (sparse)
307  {
308  for (numeric_index_type j=0; j<this->n(); j++)
309  {
310  if (currentb < ibuf.size() &&
311  ibuf[currentb] == currenti &&
312  jbuf[currentb] == j)
313  {
314  os << currenti << " " << j << " " << cbuf[currentb] << std::endl;
315  currentb++;
316  }
317  }
318  }
319  else
320  {
321  for (auto j : make_range(this->n()))
322  {
323  if (currentb < ibuf.size() &&
324  ibuf[currentb] == currenti &&
325  jbuf[currentb] == j)
326  {
327  os << cbuf[currentb] << " ";
328  currentb++;
329  }
330  else
331  os << static_cast<T>(0.0) << " ";
332  }
333  os << std::endl;
334  }
335  }
336  }
337  if (!sparse)
338  {
339  for (; currenti != this->m(); ++currenti)
340  {
341  for (numeric_index_type j=0; j<this->n(); j++)
342  os << static_cast<T>(0.0) << " ";
343  os << std::endl;
344  }
345  }
346  }
347  else
348  {
349  std::vector<numeric_index_type> ibuf, jbuf;
350  std::vector<T> cbuf;
351 
352  // We'll assume each processor has access to entire
353  // matrix rows, so (*this)(i,j) is valid if i is a local index.
354  for (numeric_index_type i : make_range(first_dof, end_dof))
355  {
356  for (auto j : make_range(this->n()))
357  {
358  T c = (*this)(i,j);
359  if (c != static_cast<T>(0.0))
360  {
361  ibuf.push_back(i);
362  jbuf.push_back(j);
363  cbuf.push_back(c);
364  }
365  }
366  }
367  this->comm().send(0,ibuf);
368  this->comm().send(0,jbuf);
369  this->comm().send(0,cbuf);
370  }
371 }
virtual bool initialized() const
const Parallel::Communicator & comm() const
virtual numeric_index_type row_stop() const =0
processor_id_type n_processors() const
Status receive(const unsigned int dest_processor_id, T &buf, const MessageTag &tag=any_tag) const
dof_id_type numeric_index_type
Definition: id_types.h:99
virtual numeric_index_type m() const =0
libmesh_assert(ctx)
virtual numeric_index_type row_start() const =0
void send(const unsigned int dest_processor_id, const T &buf, const MessageTag &tag=no_tag) const
IntRange< T > make_range(T beg, T end)
The 2-parameter make_range() helper function returns an IntRange<T> when both input parameters are of...
Definition: int_range.h:140
processor_id_type processor_id() const
virtual numeric_index_type n() const =0

◆ 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().

82 {
84  out_stream << ReferenceCounter::get_info();
85 }
static std::string get_info()
Gets a string containing the reference information.
static bool _enable_print_counter
Flag to control whether reference count information is printed when print_info is called...

◆ print_matlab()

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

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

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

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 375 of file sparse_matrix.C.

376 {
377  parallel_object_only();
378 
379  libmesh_assert (this->initialized());
380 
381  const numeric_index_type first_dof = this->row_start(),
382  end_dof = this->row_stop();
383 
384  // We'll print the matrix from processor 0 to make sure
385  // it's serialized properly
386  if (this->processor_id() == 0)
387  {
388  std::unique_ptr<std::ofstream> file;
389 
390  if (name != "")
391  file = std::make_unique<std::ofstream>(name.c_str());
392 
393  std::ostream & os = (name == "") ? libMesh::out : *file;
394 
395  std::size_t sparsity_nonzeros = this->n_nonzeros();
396 
397  std::size_t real_nonzeros = 0;
398 
399  libmesh_assert_equal_to(first_dof, 0);
400  for (numeric_index_type i : make_range(end_dof))
401  {
402  for (auto j : make_range(this->n()))
403  {
404  T c = (*this)(i,j);
405  if (c != static_cast<T>(0.0))
406  ++real_nonzeros;
407  }
408  }
409 
410 
411  for (auto p : IntRange<processor_id_type>(1, this->n_processors()))
412  {
413  std::size_t nonzeros_on_p = 0;
414  this->comm().receive(p, nonzeros_on_p);
415  real_nonzeros += nonzeros_on_p;
416  }
417 
418  if (sparsity_nonzeros &&
419  sparsity_nonzeros != real_nonzeros)
420  libmesh_warning(sparsity_nonzeros <<
421  " nonzeros allocated, but " <<
422  real_nonzeros << " used.");
423 
424  // We probably want to be more consistent than that, if our
425  // sparsity is overallocated.
426 
427  // Print a header similar to PETSc's mat_view ascii_matlab
428  os << "%Mat Object: () " << this->n_processors() << " MPI processes\n"
429  << "% type: " << (this->n_processors() > 1 ? "mpi" : "seq") << "aij\n"
430  << "% Size = " << this->m() << ' ' << this->n() << '\n'
431  << "% Nonzeros = " << real_nonzeros << '\n'
432  << "zzz = zeros(" << real_nonzeros << ",3);\n"
433  << "zzz = [\n";
434 
435  for (numeric_index_type i : make_range(end_dof))
436  {
437  // FIXME - we need a base class way to iterate over a
438  // SparseMatrix row.
439  for (auto j : make_range(this->n()))
440  {
441  T c = (*this)(i,j);
442  if (c != static_cast<T>(0.0))
443  {
444  // Convert from 0-based to 1-based indexing
445  os << (i+1) << ' ' << (j+1) << " " << c << '\n';
446  }
447  }
448  }
449 
450  std::vector<numeric_index_type> ibuf, jbuf;
451  std::vector<T> cbuf;
452  for (auto p : IntRange<processor_id_type>(1, this->n_processors()))
453  {
454  this->comm().receive(p, ibuf);
455  this->comm().receive(p, jbuf);
456  this->comm().receive(p, cbuf);
457  libmesh_assert_equal_to (ibuf.size(), jbuf.size());
458  libmesh_assert_equal_to (ibuf.size(), cbuf.size());
459 
460  for (auto n : index_range(ibuf))
461  os << ibuf[n] << ' ' << jbuf[n] << " " << cbuf[n] << '\n';
462  }
463 
464  os << "];\n" << "Mat_sparse = spconvert(zzz);" << std::endl;
465  }
466  else
467  {
468  std::vector<numeric_index_type> ibuf, jbuf;
469  std::vector<T> cbuf;
470  std::size_t my_nonzeros = 0;
471 
472  // We'll assume each processor has access to entire
473  // matrix rows, so (*this)(i,j) is valid if i is a local index.
474  for (numeric_index_type i : make_range(first_dof, end_dof))
475  {
476  for (auto j : make_range(this->n()))
477  {
478  T c = (*this)(i,j);
479  if (c != static_cast<T>(0.0))
480  {
481  ibuf.push_back(i);
482  jbuf.push_back(j);
483  cbuf.push_back(c);
484  ++my_nonzeros;
485  }
486  }
487  }
488  this->comm().send(0,my_nonzeros);
489  this->comm().send(0,ibuf);
490  this->comm().send(0,jbuf);
491  this->comm().send(0,cbuf);
492  }
493 }
std::string name(const ElemQuality q)
This function returns a string containing some name for q.
Definition: elem_quality.C:42
virtual bool initialized() const
virtual std::size_t n_nonzeros() const
const Parallel::Communicator & comm() const
virtual numeric_index_type row_stop() const =0
processor_id_type n_processors() const
Status receive(const unsigned int dest_processor_id, T &buf, const MessageTag &tag=any_tag) const
dof_id_type numeric_index_type
Definition: id_types.h:99
virtual numeric_index_type m() const =0
libmesh_assert(ctx)
virtual numeric_index_type row_start() const =0
void send(const unsigned int dest_processor_id, const T &buf, const MessageTag &tag=no_tag) const
OStreamProxy out
IntRange< T > make_range(T beg, T end)
The 2-parameter make_range() helper function returns an IntRange<T> when both input parameters are of...
Definition: int_range.h:140
processor_id_type processor_id() const
auto index_range(const T &sizable)
Helper function that returns an IntRange<std::size_t> representing all the indices of the passed-in v...
Definition: int_range.h:117
virtual numeric_index_type n() const =0

◆ print_personal()

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

◆ print_petsc_binary()

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

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

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 498 of file sparse_matrix.C.

499 {
500  libmesh_not_implemented_msg
501  ("libMesh cannot write PETSc binary-format files from non-PETSc matrices");
502 }

◆ print_petsc_hdf5()

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

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

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 507 of file sparse_matrix.C.

508 {
509  libmesh_not_implemented_msg
510  ("libMesh cannot write PETSc HDF5-format files from non-PETSc matrices");
511 }

◆ 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::ExodusII_IO::copy_scalar_solution(), libMesh::Nemesis_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::System::read_legacy_data(), 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(), ExodusTest< elem_type >::test_read_gold(), ExodusTest< elem_type >::test_write(), MeshInputTest::testAbaqusRead(), MeshInputTest::testBadGmsh(), 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(), MeshInputTest::testLowOrderEdgeBlocks(), SystemsTest::testProjectMatrix3D(), BoundaryInfoTest::testShellFaceConstraints(), MeshInputTest::testSingleElementImpl(), WriteVecAndScalar::testSolution(), CheckpointIOTest::testSplitter(), MeshInputTest::testTetgenIO(), 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().

115  { return cast_int<processor_id_type>(_communicator.rank()); }
processor_id_type rank() const
const Parallel::Communicator & _communicator

◆ read()

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

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

Definition at line 516 of file sparse_matrix.C.

517 {
518  {
519  std::ifstream in (filename.c_str());
520  libmesh_error_msg_if
521  (!in.good(), "ERROR: cannot read file:\n\t" <<
522  filename);
523  }
524 
525  std::string_view basename = Utility::basename_of(filename);
526 
527  const bool gzipped_file = Utility::ends_with(filename, ".gz");
528 
529  if (gzipped_file)
530  basename.remove_suffix(3);
531 
532  if (Utility::ends_with(basename, ".matlab") ||
533  Utility::ends_with(basename, ".m"))
534  this->read_matlab(filename);
535  else if (Utility::ends_with(basename, ".petsc64"))
536  {
537 #ifndef LIBMESH_HAVE_PETSC
538  libmesh_error_msg("Cannot load PETSc matrix file " <<
539  filename << " without PETSc-enabled libMesh.");
540 #endif
541 #if LIBMESH_DOF_ID_BYTES != 8
542  libmesh_error_msg("Cannot load 64-bit PETSc matrix file " <<
543  filename << " with non-64-bit libMesh.");
544 #endif
545  this->read_petsc_binary(filename);
546  }
547  else if (Utility::ends_with(basename, ".petsc32"))
548  {
549 #ifndef LIBMESH_HAVE_PETSC
550  libmesh_error_msg("Cannot load PETSc matrix file " <<
551  filename << " without PETSc-enabled libMesh.");
552 #endif
553 #if LIBMESH_DOF_ID_BYTES != 4
554  libmesh_error_msg("Cannot load 32-bit PETSc matrix file " <<
555  filename << " with non-32-bit libMesh.");
556 #endif
557  this->read_petsc_binary(filename);
558  }
559  else if (Utility::ends_with(basename, ".h5"))
560  {
561  this->read_coreform_hdf5(filename);
562  }
563  else
564  libmesh_error_msg(" ERROR: Unrecognized matrix file extension on: "
565  << basename
566  << "\n I understand the following:\n\n"
567  << " *.h5 -- CoreForm HDF5 sparse matrix format\n"
568  << " *.matlab -- Matlab sparse matrix format\n"
569  << " *.m -- Matlab sparse matrix format\n"
570  << " *.petsc32 -- PETSc binary format, 32-bit\n"
571  << " *.petsc64 -- PETSc binary format, 64-bit\n"
572  );
573 }
bool ends_with(std::string_view superstring, std::string_view suffix)
Look for a substring at the very end of a string.
Definition: utility.C:213
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...
virtual void read_matlab(const std::string &filename)
Read the contents of the matrix from the Matlab-script sparse matrix format used by PETSc...
virtual void read_petsc_binary(const std::string &filename)
Read the contents of the matrix from a file in PETSc&#39;s binary sparse matrix format.
std::string_view basename_of(const std::string &fullname)
Definition: utility.C:108

◆ read_coreform_hdf5()

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

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

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

Definition at line 578 of file sparse_matrix.C.

580 {
581 #ifndef LIBMESH_HAVE_HDF5
582  libmesh_ignore(filename, groupname);
583  libmesh_error_msg("ERROR: need HDF5 support to handle .h5 files!!!");
584 #else
585  LOG_SCOPE("read_coreform_hdf5()", "SparseMatrix");
586 
587  std::size_t num_rows, num_cols;
588 
589  hid_t group;
590 
591  auto check_open = [&filename](hid_t id, const std::string & objname)
592  {
593  if (id == H5I_INVALID_HID)
594  libmesh_error_msg("Couldn't open " + objname + " in " + filename);
595  };
596 
597  auto check_hdf5 = [&filename](auto hdf5val, const std::string & objname)
598  {
599  if (hdf5val < 0)
600  libmesh_error_msg("HDF5 error from " + objname + " in " + filename);
601  };
602 
603 
604  if (this->processor_id() == 0)
605  {
606  const hid_t file = H5Fopen(filename.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
607 
608  if (file == H5I_INVALID_HID)
609  libmesh_file_error(filename);
610 
611  group = H5Gopen(file, groupname.c_str(), H5P_DEFAULT);
612  check_open(group, groupname);
613 
614  auto read_size_attribute = [&filename, &group, &check_open, &check_hdf5]
615  (const std::string & attribute_name)
616  {
617  unsigned long long returnval = 0;
618 
619  const hid_t attr = H5Aopen(group, attribute_name.c_str(), H5P_DEFAULT);
620  check_open(attr, attribute_name);
621 
622  const hid_t attr_type = H5Aget_type(attr);
623  check_hdf5(attr_type, attribute_name + " type");
624 
625  // HDF5 will convert between the file's integer type and ours, but
626  // we do expect an integer type.
627  if (H5Tget_class(attr_type) != H5T_INTEGER)
628  libmesh_error_msg("Non-integer type for " + attribute_name + " in " + filename);
629 
630  H5Tclose(attr_type);
631 
632  // HDF5 is supposed to handle both upscaling and endianness
633  // conversions here
634  herr_t errval = H5Aread(attr, H5T_NATIVE_ULLONG, &returnval);
635  check_hdf5(errval, attribute_name + " read");
636 
637  H5Aclose(attr);
638 
639  return returnval;
640  };
641 
642  num_cols = read_size_attribute("num_cols");
643  num_rows = read_size_attribute("num_rows");
644 
645  this->comm().broadcast(num_cols);
646  this->comm().broadcast(num_rows);
647  }
648  else
649  {
650  this->comm().broadcast(num_cols);
651  this->comm().broadcast(num_rows);
652  }
653 
654  numeric_index_type new_row_start, new_row_stop,
655  new_col_start, new_col_stop;
656 
657  // If we need to reinit, we need to determine which rows+columns
658  // each processor is in charge of.
659  std::vector<numeric_index_type> new_row_starts, new_row_stops,
660  new_col_starts, new_col_stops;
661 
662  if (this->initialized() &&
663  num_cols == this->m() &&
664  num_rows == this->n())
665  {
666  new_row_start = this->row_start(),
667  new_row_stop = this->row_stop();
668 
669  new_col_start = this->col_start(),
670  new_col_stop = this->col_stop();
671  }
672  else
673  {
674  // Determine which rows/columns each processor will be in charge of
675  new_row_start = this->processor_id() * num_rows / this->n_processors(),
676  new_row_stop = (this->processor_id()+1) * num_rows / this->n_processors();
677 
678  new_col_start = this->processor_id() * num_cols / this->n_processors(),
679  new_col_stop = (this->processor_id()+1) * num_cols / this->n_processors();
680  }
681 
682  this->comm().gather(0, new_row_start, new_row_starts);
683  this->comm().gather(0, new_row_stop, new_row_stops);
684  this->comm().gather(0, new_col_start, new_col_starts);
685  this->comm().gather(0, new_col_stop, new_col_stops);
686 
687  numeric_index_type on_diagonal_nonzeros = 0,
688  off_diagonal_nonzeros = 0;
689 
690  std::vector<std::size_t> cols, row_offsets;
691  std::vector<double> vals;
692 
693  if (this->processor_id() == 0)
694  {
695  auto read_vector = [&filename, &group, &check_open, &check_hdf5]
696  (const std::string & dataname, auto hdf5_class,
697  auto hdf5_type, auto & datavec)
698  {
699  const hid_t data = H5Dopen1(group, dataname.c_str());
700  check_open(data, dataname.c_str());
701 
702  const hid_t data_type = H5Dget_type(data);
703  check_hdf5(data_type, dataname + " type");
704 
705  // HDF5 will convert between the file's integer type and ours, but
706  // we do expect an integer type.
707  if (H5Tget_class(data_type) != hdf5_class)
708  libmesh_error_msg("Unexpected type for " + dataname + " in " + filename);
709 
710  H5Tclose(data_type);
711 
712  const hid_t dataspace = H5Dget_space(data);
713  check_hdf5(dataspace, dataname + " space");
714 
715  int ndims = H5Sget_simple_extent_ndims(dataspace);
716  if (ndims != 1)
717  libmesh_error_msg("Non-vector space for " + dataname + " in " + filename);
718 
719  hsize_t len, maxlen;
720  herr_t errval = H5Sget_simple_extent_dims(dataspace, &len, &maxlen);
721  check_hdf5(errval, dataname + " dims");
722 
723  datavec.resize(len);
724 
725  errval = H5Dread(data, hdf5_type, H5S_ALL, H5S_ALL, H5P_DEFAULT, datavec.data());
726  check_hdf5(errval, dataname + " read");
727  };
728 
729  read_vector("cols", H5T_INTEGER, H5T_NATIVE_ULLONG, cols);
730  read_vector("row_offsets", H5T_INTEGER, H5T_NATIVE_ULLONG, row_offsets);
731  read_vector("vals", H5T_FLOAT, H5T_NATIVE_DOUBLE, vals);
732 
733  if (cols.size() != vals.size())
734  libmesh_error_msg("Inconsistent cols/vals sizes in " + filename);
735 
736  if (row_offsets.size() != num_rows + 1)
737  libmesh_error_msg("Inconsistent row_offsets size in " + filename);
738 
739  // Data for the row we're working on
740  numeric_index_type current_row = 0;
741  processor_id_type current_proc = 0;
742  numeric_index_type current_on_diagonal_nonzeros = 0;
743  numeric_index_type current_off_diagonal_nonzeros = 0;
744  if (row_offsets[0] != 0)
745  libmesh_error_msg("Unexpected row_offsets[0] in " + filename);
746 
747  for (auto i : index_range(cols))
748  {
749  while (row_offsets[current_row+1] <= i)
750  {
751  ++current_row;
752  if (row_offsets[current_row] < row_offsets[current_row-1])
753  libmesh_error_msg("Non-monotonic row_offsets in " + filename);
754  current_on_diagonal_nonzeros = 0;
755  current_off_diagonal_nonzeros = 0;
756  }
757 
758  while (current_row >= (new_row_stops[current_proc]+1))
759  ++current_proc;
760 
761  // 0-based indexing in file
762  if (cols[i] >= new_col_starts[current_proc] &&
763  cols[i] < new_col_stops[current_proc])
764  {
765  ++current_on_diagonal_nonzeros;
766  on_diagonal_nonzeros =
767  std::max(on_diagonal_nonzeros,
768  current_on_diagonal_nonzeros);
769  }
770  else
771  {
772  ++current_off_diagonal_nonzeros;
773  off_diagonal_nonzeros =
774  std::max(off_diagonal_nonzeros,
775  current_off_diagonal_nonzeros);
776  }
777  }
778  }
779 
780  this->comm().broadcast(on_diagonal_nonzeros);
781  this->comm().broadcast(off_diagonal_nonzeros);
782 
783  this->init(num_rows, num_cols,
784  new_row_stop-new_row_start,
785  new_col_stop-new_col_start,
786  on_diagonal_nonzeros,
787  off_diagonal_nonzeros);
788 
789  // Set the matrix values last.
790  if (this->processor_id() == 0)
791  {
792  numeric_index_type current_row = 0;
793  for (auto i : index_range(cols))
794  {
795  while (row_offsets[current_row+1] <= i)
796  {
797  ++current_row;
798  libmesh_assert_greater_equal (row_offsets[current_row],
799  row_offsets[current_row-1]);
800  }
801  this->set(current_row, cols[i], vals[i]);
802  }
803  }
804 
805  this->close();
806 #endif // LIBMESH_HAVE_HDF5
807 }
virtual bool initialized() const
MPI_Datatype data_type
void gather(const unsigned int root_id, const T &send_data, std::vector< T, A > &recv) const
const Parallel::Communicator & comm() const
virtual numeric_index_type row_stop() const =0
uint8_t processor_id_type
processor_id_type n_processors() const
void libmesh_ignore(const Args &...)
dof_id_type numeric_index_type
Definition: id_types.h:99
virtual numeric_index_type m() const =0
virtual numeric_index_type col_stop() const =0
virtual numeric_index_type col_start() const =0
void broadcast(T &data, const unsigned int root_id=0, const bool identical_sizes=false) const
virtual void close()=0
Calls the SparseMatrix&#39;s internal assembly routines, ensuring that the values are consistent across p...
virtual numeric_index_type row_start() const =0
processor_id_type processor_id() const
auto index_range(const T &sizable)
Helper function that returns an IntRange<std::size_t> representing all the indices of the passed-in v...
Definition: int_range.h:117
virtual numeric_index_type n() const =0
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.

◆ read_matlab()

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

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

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

Definition at line 812 of file sparse_matrix.C.

Referenced by ConstraintOperatorTest::test1DCoarseningNewNodes().

813 {
814  LOG_SCOPE("read_matlab()", "SparseMatrix");
815 
816 #ifndef LIBMESH_HAVE_CXX11_REGEX
817  libmesh_not_implemented(); // What is your compiler?!? Email us!
818  libmesh_ignore(filename);
819 #else
820  parallel_object_only();
821 
822  const bool gzipped_file = Utility::ends_with(filename, ".gz");
823 
824  // The sizes we get from the file
825  std::size_t m = 0,
826  n = 0;
827 
828  // If we don't already have this size, we'll need to reinit, and
829  // determine which rows+columns each processor is in charge of.
830  std::vector<numeric_index_type> new_row_starts, new_row_stops,
831  new_col_starts, new_col_stops;
832 
833  numeric_index_type new_row_start, new_row_stop,
834  new_col_start, new_col_stop;
835 
836  // We'll read through the file three times: once to get a reliable
837  // value for the matrix size (so we can divvy it up among
838  // processors), then again to get the sparsity to send to each
839  // processor, then a final time to get the entries to send to each
840  // processor.
841  //
842  // We'll use an istream here; it might be an ifstream if we're
843  // opening a raw ASCII file or a gzstream if we're opening a
844  // compressed one.
845  std::unique_ptr<std::istream> file;
846 
847  // We'll need a temporary structure to cache matrix entries, because
848  // we need to read through the whole file before we know the size
849  // and sparsity structure with which we can init().
850  //
851  // Reading through the file three times via `seekg` doesn't work
852  // with our gzstream wrapper, and seems to take three times as long
853  // even with a plain ifstream. What happened to disk caching!?
854  std::vector<std::tuple<numeric_index_type, numeric_index_type, T>> entries;
855 
856  // First read through the file, saving size and entry data
857  {
858  // We'll read the matrix on processor 0 rather than try to juggle
859  // parallel I/O.
860  if (this->processor_id() == 0)
861  {
862  // We'll be using regular expressions to make ourselves slightly
863  // more robust to formatting.
864  const std::regex start_regex // assignment like "zzz = ["
865  ("\\s*\\w+\\s*=\\s*\\[");
866  const std::regex end_regex // end of assignment
867  ("^[^%]*\\]");
868 
869  if (gzipped_file)
870  {
871 #ifdef LIBMESH_HAVE_GZSTREAM
872  auto inf = std::make_unique<igzstream>();
873  libmesh_assert(inf);
874  inf->open(filename.c_str(), std::ios::in);
875  file = std::move(inf);
876 #else
877  libmesh_error_msg("ERROR: need gzstream to handle .gz files!!!");
878 #endif
879  }
880  else
881  {
882  auto inf = std::make_unique<std::ifstream>();
883  libmesh_assert(inf);
884 
885  std::string new_name = Utility::unzip_file(filename);
886 
887  inf->open(new_name.c_str(), std::ios::in);
888  file = std::move(inf);
889  }
890 
891  // If we have a matrix with all-zero trailing rows, the only
892  // way to get the size is if it ended up in a comment
893  const std::regex size_regex // comment like "% size = 8 8"
894  ("%\\s*[Ss][Ii][Zz][Ee]\\s*=\\s*(\\d+)\\s+(\\d+)");
895  const std::string whitespace = " \t";
896 
897  bool have_started = false;
898  bool have_ended = false;
899  std::size_t largest_i_seen = 0, largest_j_seen = 0;
900 
901  // Data for the row we're working on
902  // Use 1-based indexing for current_row, as in the file
903  std::size_t current_row = 1;
904 
905  for (std::string line; std::getline(*file, line);)
906  {
907  std::smatch sm;
908 
909  // First, try to match an entry. This is the most common
910  // case so we won't rely on slow std::regex for it.
911  // stringstream is at least an improvement over that.
912 
913  // Look for row/col/val like "1 1 -2.0e-4"
914 
915  std::istringstream l(line);
916 
917  std::size_t i, j;
918  T value;
919 
920  l >> i >> j >> value;
921 
922  if (!l.fail())
923  {
924  libmesh_error_msg_if
925  (!have_started, "Confused by premature entries in matrix file " << filename);
926 
927  entries.emplace_back(cast_int<numeric_index_type>(i),
928  cast_int<numeric_index_type>(j),
929  value);
930 
931  libmesh_error_msg_if
932  (!i || !j, "Expected 1-based indexing in matrix file "
933  << filename);
934 
935  current_row = std::max(current_row, i);
936 
937  libmesh_error_msg_if
938  (i < current_row,
939  "Can't handle out-of-order entries in matrix file "
940  << filename);
941 
942  largest_i_seen = std::max(i, largest_i_seen);
943  largest_j_seen = std::max(j, largest_j_seen);
944  }
945 
946  else if (std::regex_search(line, sm, size_regex))
947  {
948  const std::string msize = sm[1];
949  const std::string nsize = sm[2];
950  m = std::stoull(msize);
951  n = std::stoull(nsize);
952  }
953 
954  else if (std::regex_search(line, start_regex))
955  have_started = true;
956 
957  else if (std::regex_search(line, end_regex))
958  {
959  have_ended = true;
960  break;
961  }
962  }
963 
964  libmesh_error_msg_if
965  (!have_started, "Confused by missing assignment beginning in matrix file " << filename);
966 
967  libmesh_error_msg_if
968  (!have_ended, "Confused by missing assignment ending in matrix file " << filename);
969 
970  libmesh_error_msg_if
971  (m > largest_i_seen, "Confused by missing final row(s) in matrix file " << filename);
972 
973  libmesh_error_msg_if
974  (m > 0 && m < largest_i_seen, "Confused by extra final row(s) in matrix file " << filename);
975 
976  if (!m)
977  m = largest_i_seen;
978 
979  libmesh_error_msg_if
980  (n > largest_j_seen, "Confused by missing final column(s) in matrix file " << filename);
981 
982  libmesh_error_msg_if
983  (n > 0 && n < largest_j_seen, "Confused by extra final column(s) in matrix file " << filename);
984 
985  if (!n)
986  n = largest_j_seen;
987 
988  this->comm().broadcast(m);
989  this->comm().broadcast(n);
990  }
991  else
992  {
993  this->comm().broadcast(m);
994  this->comm().broadcast(n);
995  }
996 
997  if (this->initialized() &&
998  m == this->m() &&
999  n == this->n())
1000  {
1001  new_row_start = this->row_start(),
1002  new_row_stop = this->row_stop();
1003 
1004  new_col_start = this->col_start(),
1005  new_col_stop = this->col_stop();
1006  }
1007  else
1008  {
1009  // Determine which rows/columns each processor will be in charge of
1010  new_row_start = this->processor_id() * m / this->n_processors(),
1011  new_row_stop = (this->processor_id()+1) * m / this->n_processors();
1012 
1013  new_col_start = this->processor_id() * n / this->n_processors(),
1014  new_col_stop = (this->processor_id()+1) * n / this->n_processors();
1015  }
1016 
1017  this->comm().gather(0, new_row_start, new_row_starts);
1018  this->comm().gather(0, new_row_stop, new_row_stops);
1019  this->comm().gather(0, new_col_start, new_col_starts);
1020  this->comm().gather(0, new_col_stop, new_col_stops);
1021 
1022  } // Done reading entry data and broadcasting matrix size
1023 
1024  // Calculate the matrix sparsity and initialize it second
1025  {
1026  // Deduce the sparsity pattern, or at least the maximum number of
1027  // on- and off- diagonal non-zeros per row.
1028  numeric_index_type on_diagonal_nonzeros =0,
1029  off_diagonal_nonzeros =0;
1030 
1031  if (this->processor_id() == 0)
1032  {
1033  // Data for the row we're working on
1034  // Use 1-based indexing for current_row, as in the file
1035  numeric_index_type current_row = 1;
1036  processor_id_type current_proc = 0;
1037  numeric_index_type current_on_diagonal_nonzeros = 0;
1038  numeric_index_type current_off_diagonal_nonzeros = 0;
1039 
1040  for (auto [i, j, value] : entries)
1041  {
1042  if (i > current_row)
1043  {
1044  current_row = i;
1045  // +1 for 1-based indexing in file
1046  while (current_row >= (new_row_stops[current_proc]+1))
1047  ++current_proc;
1048  current_on_diagonal_nonzeros = 0;
1049  current_off_diagonal_nonzeros = 0;
1050  }
1051 
1052  // +1 for 1-based indexing in file
1053  if (j >= (new_col_starts[current_proc]+1) &&
1054  j < (new_col_stops[current_proc]+1))
1055  {
1056  ++current_on_diagonal_nonzeros;
1057  on_diagonal_nonzeros =
1058  std::max(on_diagonal_nonzeros,
1059  current_on_diagonal_nonzeros);
1060  }
1061  else
1062  {
1063  ++current_off_diagonal_nonzeros;
1064  off_diagonal_nonzeros =
1065  std::max(off_diagonal_nonzeros,
1066  current_off_diagonal_nonzeros);
1067  }
1068  }
1069  }
1070 
1071  this->comm().broadcast(on_diagonal_nonzeros);
1072  this->comm().broadcast(off_diagonal_nonzeros);
1073 
1074  this->init(m, n,
1075  new_row_stop-new_row_start,
1076  new_col_stop-new_col_start,
1077  on_diagonal_nonzeros,
1078  off_diagonal_nonzeros);
1079  }
1080 
1081  // Set the matrix values last.
1082  // Convert from 1-based to 0-based indexing
1083  if (this->processor_id() == 0)
1084  for (auto [i, j, value] : entries)
1085  this->set(i-1, j-1, value);
1086 
1087  this->close();
1088 #endif
1089 }
virtual bool initialized() const
bool ends_with(std::string_view superstring, std::string_view suffix)
Look for a substring at the very end of a string.
Definition: utility.C:213
void gather(const unsigned int root_id, const T &send_data, std::vector< T, A > &recv) const
const Parallel::Communicator & comm() const
virtual numeric_index_type row_stop() const =0
uint8_t processor_id_type
processor_id_type n_processors() const
void libmesh_ignore(const Args &...)
dof_id_type numeric_index_type
Definition: id_types.h:99
virtual numeric_index_type m() const =0
std::string unzip_file(std::string_view name)
Create an unzipped copy of a bz2 or xz file, returning the name of the now-unzipped file that can be ...
Definition: utility.C:164
libmesh_assert(ctx)
virtual numeric_index_type col_stop() const =0
virtual numeric_index_type col_start() const =0
void broadcast(T &data, const unsigned int root_id=0, const bool identical_sizes=false) const
virtual void close()=0
Calls the SparseMatrix&#39;s internal assembly routines, ensuring that the values are consistent across p...
virtual numeric_index_type row_start() const =0
static const bool value
Definition: xdr_io.C:55
processor_id_type processor_id() const
virtual numeric_index_type n() const =0
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.

◆ read_petsc_binary()

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

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

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 1094 of file sparse_matrix.C.

1095 {
1096  libmesh_not_implemented_msg
1097  ("libMesh cannot read PETSc binary-format files into non-PETSc matrices");
1098 }

◆ read_petsc_hdf5()

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

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

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 1103 of file sparse_matrix.C.

1104 {
1105  libmesh_not_implemented_msg
1106  ("libMesh cannot read PETSc HDF5-format files into non-PETSc matrices");
1107 }

◆ reinit_submatrix()

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

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

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

Definition at line 551 of file sparse_matrix.h.

554  {
555  this->_get_submatrix(submatrix,
556  rows,
557  cols,
558  true); // true means REUSE submatrix
559  }
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.

◆ require_sparsity_pattern()

template<typename T>
virtual bool libMesh::PetscMatrixShellMatrix< T >::require_sparsity_pattern ( ) const
inlineoverridevirtual
Returns
Whether this matrix needs the sparsity pattern computed by the DofMap

Reimplemented from libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation.

Definition at line 59 of file petsc_matrix_shell_matrix.h.

59 { return false; }

◆ restore_original_nonzero_pattern()

template<typename T>
virtual void libMesh::SparseMatrix< T >::restore_original_nonzero_pattern ( )
inlinevirtualinherited

Reset the memory storage of the matrix.

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

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

Definition at line 630 of file sparse_matrix.h.

630 { libmesh_not_implemented(); }

◆ row_start()

template<typename T >
numeric_index_type libMesh::PetscMatrixBase< T >::row_start ( ) const
overridevirtualinherited
Returns
The index of the first matrix row stored on this processor.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 178 of file petsc_matrix_base.C.

179 {
180  libmesh_assert (this->initialized());
181 
182  PetscInt start=0, stop=0;
183 
184  LibmeshPetscCall(MatGetOwnershipRange(this->_mat, &start, &stop));
185 
186  return static_cast<numeric_index_type>(start);
187 }
virtual bool initialized() const
dof_id_type numeric_index_type
Definition: id_types.h:99
libmesh_assert(ctx)
void stop(const char *file, int line, const char *date, const char *time)
Mat _mat
PETSc matrix datatype to store values.

◆ row_stop()

template<typename T >
numeric_index_type libMesh::PetscMatrixBase< T >::row_stop ( ) const
overridevirtualinherited
Returns
The index of the last matrix row (+1) stored on this processor.

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 190 of file petsc_matrix_base.C.

191 {
192  libmesh_assert (this->initialized());
193 
194  PetscInt start=0, stop=0;
195 
196  LibmeshPetscCall(MatGetOwnershipRange(this->_mat, &start, &stop));
197 
198  return static_cast<numeric_index_type>(stop);
199 }
virtual bool initialized() const
dof_id_type numeric_index_type
Definition: id_types.h:99
libmesh_assert(ctx)
void stop(const char *file, int line, const char *date, const char *time)
Mat _mat
PETSc matrix datatype to store values.

◆ scale()

template<typename T>
void libMesh::SparseMatrix< T >::scale ( const T  scale)
virtualinherited

Scales all elements of this matrix by scale.

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 1112 of file sparse_matrix.C.

1113 {
1114  libmesh_assert(this->closed());
1115 
1116  for (const auto i : make_range(this->row_start(), this->row_stop()))
1117  for (const auto j : make_range(this->col_start(), this->col_stop()))
1118  this->set(i, j, (*this)(i, j) * scale);
1119 }
virtual numeric_index_type row_stop() const =0
libmesh_assert(ctx)
virtual numeric_index_type col_stop() const =0
virtual numeric_index_type col_start() const =0
virtual bool closed() const =0
virtual numeric_index_type row_start() const =0
IntRange< T > make_range(T beg, T end)
The 2-parameter make_range() helper function returns an IntRange<T> when both input parameters are of...
Definition: int_range.h:140
virtual void scale(const T scale)
Scales all elements of this matrix by 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 virtualinherited

◆ set_context()

template<typename T >
void libMesh::PetscMatrixBase< T >::set_context ( )
inherited

Set the context (ourself) for _mat.

Definition at line 105 of file petsc_matrix_base.C.

106 {
107  libmesh_assert(this->_mat);
108  PetscContainer container;
109  LibmeshPetscCall(PetscContainerCreate(this->comm().get(), &container));
110  LibmeshPetscCall(PetscContainerSetPointer(container, this));
111  LibmeshPetscCall(PetscObjectCompose((PetscObject)(Mat)this->_mat, "PetscMatrixCtx", (PetscObject)container));
112  LibmeshPetscCall(PetscContainerDestroy(&container));
113 }
const Parallel::Communicator & comm() const
libmesh_assert(ctx)
Mat _mat
PETSc matrix datatype to store values.

◆ set_destroy_mat_on_exit()

template<typename T >
void libMesh::PetscMatrixBase< T >::set_destroy_mat_on_exit ( bool  destroy = true)
inherited

If set to false, we don't delete the Mat on destruction and allow instead for PETSc to manage it.

Definition at line 91 of file petsc_matrix_base.C.

92 {
94 }
bool _destroy_mat_on_exit
This boolean value should only be set to false for the constructor which takes a PETSc Mat object...
void destroy(triangulateio &t, IO_Type)
Frees any memory which has been dynamically allocated by Triangle.

◆ solver_package()

template<typename T>
virtual SolverPackage libMesh::PetscMatrixBase< T >::solver_package ( )
inlineoverridevirtualinherited

Implements libMesh::SparseMatrix< T >.

Reimplemented in libMesh::StaticCondensation, and libMesh::StaticCondensation.

Definition at line 107 of file petsc_matrix_base.h.

108  {
109  return PETSC_SOLVERS;
110  }

◆ supports_hash_table()

template<typename T>
virtual bool libMesh::SparseMatrix< T >::supports_hash_table ( ) const
inlinevirtualinherited
Returns
Whether the matrix supports hash table assembly

Reimplemented in libMesh::PetscMatrix< T >.

Definition at line 605 of file sparse_matrix.h.

605 { return false; }

◆ swap()

template<typename T>
void libMesh::PetscMatrixBase< T >::swap ( PetscMatrixBase< T > &  m_in)
inherited

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

Definition at line 98 of file petsc_matrix_base.C.

Referenced by DMlibMeshJacobian().

99 {
100  std::swap(_mat, m_in._mat);
101  std::swap(_destroy_mat_on_exit, m_in._destroy_mat_on_exit);
102 }
bool _destroy_mat_on_exit
This boolean value should only be set to false for the constructor which takes a PETSc Mat object...
Mat _mat
PETSc matrix datatype to store values.

◆ update_sparsity_pattern()

template<typename T>
virtual void libMesh::SparseMatrix< T >::update_sparsity_pattern ( const SparsityPattern::Graph )
inlinevirtualinherited

Updates the matrix sparsity pattern.

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

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

Definition at line 175 of file sparse_matrix.h.

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

175 {}

◆ use_hash_table() [1/2]

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

Sets whether to use hash table assembly.

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

Definition at line 678 of file sparse_matrix.h.

Referenced by PetscMatrixTest::testPetscCopyFromHash().

679 {
680  libmesh_error_msg_if(use_hash && !this->supports_hash_table(),
681  "This matrix class does not support hash table assembly");
682  this->_use_hash_table = use_hash;
683 }
bool _use_hash_table
Flag indicating whether the matrix is assembled using a hash table.
virtual bool supports_hash_table() const

◆ use_hash_table() [2/2]

template<typename T>
bool libMesh::SparseMatrix< T >::use_hash_table ( ) const
inlineinherited
Returns
Whether this matrix is using hash table assembly. Hash table or hash map assembly means storing maps from i-j locations in the matrix to values. Because it is a hash map as opposed to a contiguous array of data, no preallocation is required to use it

Definition at line 620 of file sparse_matrix.h.

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

620 { return _use_hash_table; }
bool _use_hash_table
Flag indicating whether the matrix is assembled using a hash table.

◆ vector_mult()

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

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

Definition at line 214 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().

216 {
217  dest.zero();
218  this->vector_mult_add(dest,arg);
219 }
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...

◆ vector_mult_add()

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

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

Definition at line 224 of file sparse_matrix.C.

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

226 {
227  /* This functionality is actually implemented in the \p
228  NumericVector class. */
229  dest.add_vector(arg,*this);
230 }

◆ zero()

template<typename T>
virtual void libMesh::SparseMatrix< T >::zero ( )
pure virtualinherited

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 virtualinherited
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,
diag_value = 0.0 
)
virtualinherited

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

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

Definition at line 235 of file sparse_matrix.C.

236 {
237  /* This functionality isn't implemented or stubbed in every subclass yet */
238  libmesh_not_implemented();
239 }

Friends And Related Function Documentation

◆ init_shell_mat [1/2]

template<typename T>
void init_shell_mat ( PetscMatrixShellMatrix< T > &  obj)
friend

◆ init_shell_mat [2/2]

template<typename T>
void init_shell_mat ( PetscMatrixShellMatrix< T > &  obj,
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  blocksize_in 
)
friend

Member Data Documentation

◆ _communicator

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

◆ _counts

ReferenceCounter::Counts libMesh::ReferenceCounter::_counts
staticprotectedinherited

Actually holds the data.

Definition at line 124 of file reference_counter.h.

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

◆ _destroy_mat_on_exit

template<typename T>
bool libMesh::PetscMatrixBase< T >::_destroy_mat_on_exit
protectedinherited

This boolean value should only be set to false for the constructor which takes a PETSc Mat object.

Definition at line 186 of file petsc_matrix_base.h.

Referenced by libMesh::PetscMatrixBase< Number >::swap().

◆ _dof_map

template<typename T>
DofMap const* libMesh::SparseMatrix< T >::_dof_map
protectedinherited

The DofMap object associated with this object.

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

Definition at line 652 of file sparse_matrix.h.

◆ _enable_print_counter

bool libMesh::ReferenceCounter::_enable_print_counter = true
staticprotectedinherited

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

Definition at line 143 of file reference_counter.h.

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

◆ _is_initialized

template<typename T>
bool libMesh::SparseMatrix< T >::_is_initialized
protectedinherited

◆ _mat

template<typename T>
Mat libMesh::PetscMatrixBase< T >::_mat
protectedinherited

◆ _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().

◆ _omit_constrained_dofs

template<typename T>
const bool libMesh::PetscMatrixShellMatrix< T >::_omit_constrained_dofs
private

Whether to omit constrained degrees of freedom.

Definition at line 67 of file petsc_matrix_shell_matrix.h.

◆ _sp

template<typename T>
SparsityPattern::Build const* libMesh::SparseMatrix< T >::_sp
protectedinherited

The sparsity pattern associated with this object.

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

Definition at line 659 of file sparse_matrix.h.

◆ _use_hash_table

template<typename T>
bool libMesh::SparseMatrix< T >::_use_hash_table
protectedinherited

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

Definition at line 669 of file sparse_matrix.h.

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


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