libMesh Namespace Reference

Namespaces
namespace	libMeshPrivateData
Classes
class	LogicError
class	NotImplemented
class	FileError
class	ConvergenceFailure
class	DynamicCastFailure
Functions
void	_init (int &argc, char **&argv) void _init(int &argc
void	init (int &argc, char **&argv)
void	init (int &argc, char **&argv, MPI_Comm COMM_WORLD_IN=MPI_COMM_WORLD)
bool	initialized ()
int	close ()
bool	closed ()
bool	on_command_line (const std::string &arg)
template<typename T >
T	command_line_value (const std::string &, T)
SolverPackage	default_solver_package ()
unsigned int	n_processors ()
unsigned int	processor_id ()
unsigned int	n_threads ()
Variables
void char **&	argv
PerfLog	perflog
const Number	imaginary
const Real	pi = 3.1415926535897932384626433832795029L
const Number	zero = 0.
const unsigned int	invalid_uint = static_cast<unsigned int>(-1)
MPI_Comm	COMM_WORLD = MPI_COMM_NULL

---

Detailed Description

The libMesh namespace provides an interface to certain functionality in the library. It provides a uniform init() method that initializes any other dependent libraries (e.g. MPI or PETSC), and a close() method for closing those libraries. It also provides a centralized place for performance logging and other functionality.

---

Function Documentation

void libMesh::_init	(	int &	argc,
		char **&	argv
	)

Referenced by init(), and LibMeshInit::LibMeshInit().

int libMesh::close

(

)

Stop using the mesh library. This will call PetscFinalize() if PETSC is available. This method should be called after all other library objects have gone out of scope, as it interrogates the ReferenceCounter object to look for memory leaks.

libMesh::init() and libMesh::close() are a deprecated method of library initialization. Create a LibMeshInit object to begin using the library; when the LibMeshInit object is destroyed the library will be closed.

Definition at line 368 of file libmesh.C.

{
  libmesh_deprecated();  // Use LibMeshInit instead
  return libMesh::_close();
}

bool libMesh::closed

(

)

[inline]

Checks that the library has been closed. This should always return false when called from a library object. It is useful to libmesh_assert(!libMeshclosed()) in library object destructors.

Definition at line 231 of file libmesh.h.

References initialized().

Referenced by MeshBase::~MeshBase(), System::~System(), and UnstructuredMesh::~UnstructuredMesh().

{
  return !libMesh::initialized();
}

template<typename T >

T libMesh::command_line_value	(	const std::string &	name,
		T	value
	)			[inline]

Returns:

the value associated with name on the command line if it is specified, otherwise return the default, provided value.

Definition at line 423 of file libmesh.C.

References EXTERN_C_FOR_PETSC_END::command_line.

{
  // Make sure the command line parser is ready for use
  libmesh_assert (command_line.get() != NULL);
  
    // only if the variable exists in the file
    if (command_line->have_variable(name.c_str()))
      value = (*command_line)(name.c_str(), value);      

    return value;
}

SolverPackage libMesh::default_solver_package

(

)

Returns:

the default solver interface to use. The value depends on which solver packages were available when the library was configured. The command-line is also checked, allowing the user to override the compiled default. For example, --use-petsc will force the use of PETSc solvers, and --use-laspack will force the use of LASPACK solvers.

Definition at line 436 of file libmesh.C.

References libMesh::libMeshPrivateData::_solver_package, initialized(), INVALID_SOLVER_PACKAGE, LASPACK_SOLVERS, on_command_line(), libMeshEnums::PETSC_SOLVERS, and TRILINOS_SOLVERS.

{
  libmesh_assert (libMesh::initialized());
  
  static bool called = false;

  // Check the command line.  Since the command line is
  // unchanging it is sufficient to do this only once.
  if (!called)
    {
      called = true;

#ifdef LIBMESH_HAVE_PETSC
      if (libMesh::on_command_line ("--use-petsc"))
        libMeshPrivateData::_solver_package = PETSC_SOLVERS;
#endif

#ifdef LIBMESH_HAVE_TRILINOS
      if (libMesh::on_command_line ("--use-trilinos") ||
          libMesh::on_command_line ("--disable-petsc"))
        libMeshPrivateData::_solver_package = TRILINOS_SOLVERS;
#endif
      
#ifdef LIBMESH_HAVE_LASPACK
      if (libMesh::on_command_line ("--use-laspack"  ) ||
          libMesh::on_command_line ("--disable-petsc"))
        libMeshPrivateData::_solver_package = LASPACK_SOLVERS;
#endif

      if (libMesh::on_command_line ("--disable-laspack") &&
          libMesh::on_command_line ("--disable-trilinos") &&
          libMesh::on_command_line ("--disable-petsc"))
        libMeshPrivateData::_solver_package = INVALID_SOLVER_PACKAGE;
    }
  
  
  return libMeshPrivateData::_solver_package;  
}

void libMesh::init	(	int &	argc,
		char **&	argv,
		MPI_Comm	COMM_WORLD_IN = MPI_COMM_WORLD
	)

Initialize the library for use. This will call PetscInitialize if PETSC is available. This method takes an optional parameter

You must perform an initialization before using any of the library functionality, but libMesh::init() is a deprecated way to do so. Create a LibMeshInit object instead.

Definition at line 357 of file libmesh.C.

References _init().

{
  libmesh_deprecated();  // Use LibMeshInit instead
  libMesh::_init(argc, argv, COMM_WORLD_IN);
}

void libMesh::init	(	int &	argc,
		char **&	argv
	)

Initialize the library for use. This will call PetscInitialize if PETSC is available.

You must perform an initialization before using any of the library functionality, but libMesh::init() is a deprecated way to do so. Create a LibMeshInit object instead.

Definition at line 351 of file libmesh.C.

References _init().

{
  libmesh_deprecated();  // Use LibMeshInit instead
  libMesh::_init(argc, argv);
}

bool libMesh::initialized

(

)

[inline]

Checks that library initialization has been done. If it hasn't an error message is printed and the code aborts. It is useful to libmesh_assert(libMesh::initialized()) in library object constructors.

Definition at line 223 of file libmesh.h.

References libMesh::libMeshPrivateData::_is_initialized.

Referenced by closed(), default_solver_package(), MeshBase::MeshBase(), and UnstructuredMesh::UnstructuredMesh().

{
  return libMeshPrivateData::_is_initialized;
}

unsigned int libMesh::n_processors

(

)

[inline]

Returns:

the number of processors used in the current simulation.

Definition at line 76 of file libmesh_base.h.

References libMesh::libMeshPrivateData::_n_processors.

Referenced by ParmetisPartitioner::_do_repartition(), DofMap::add_constraints_to_send_list(), DofMap::allgather_recursive_constraints(), MeshCommunication::assign_global_indices(), ParmetisPartitioner::assign_partitioning(), AztecLinearSolver< T >::AztecLinearSolver(), MeshCommunication::broadcast(), AztecLinearSolver< T >::clear(), PetscLinearSolver< T >::clear(), DofMap::distribute_dofs(), DofMap::distribute_local_dofs_node_major(), DofMap::distribute_local_dofs_var_major(), EnsightIO::EnsightIO(), MeshCommunication::find_global_indices(), PerfLog::get_info_header(), PetscMatrix< T >::init(), EquationSystems::init(), ParmetisPartitioner::initialize(), MeshTools::libmesh_assert_valid_node_procids(), MeshTools::libmesh_assert_valid_refinement_flags(), EpetraVector< T >::localize_to_one(), MeshBase::n_active_elem_on_proc(), MeshBase::n_elem_on_proc(), MeshBase::n_nodes_on_proc(), Partitioner::partition_unpartitioned_elements(), PetscLinearSolver< T >::PetscLinearSolver(), SparseMatrix< T >::print(), MeshTools::processor_bounding_box(), System::project_vector(), Nemesis_IO::read(), System::read_serialized_blocked_dof_objects(), System::read_serialized_vector(), ParallelMesh::renumber_dof_objects(), Partitioner::set_node_processor_ids(), DofMap::set_nonlocal_dof_objects(), Parallel::sync_dofobject_data_by_id(), Parallel::sync_dofobject_data_by_xyz(), Parallel::sync_element_data_by_parent_id(), XdrIO::write_serialized_bcs(), System::write_serialized_blocked_dof_objects(), XdrIO::write_serialized_connectivity(), and XdrIO::write_serialized_nodes().

{
#ifdef LIBMESH_HAVE_MPI
  return static_cast<unsigned int>(libMeshPrivateData::_n_processors);
#else
  return 1;
#endif
}

unsigned int libMesh::n_threads

(

)

[inline]

Returns:

the maximum number of threads used in the simulation.

Definition at line 101 of file libmesh_base.h.

References libMesh::libMeshPrivateData::_n_threads.

Referenced by Threads::parallel_for(), and Threads::parallel_reduce().

{
  return static_cast<unsigned int>(libMeshPrivateData::_n_threads);
}

bool libMesh::on_command_line

(

const std::string &

arg

)

Returns:

true if the argument arg was specified on the command line, false otherwise.

Definition at line 412 of file libmesh.C.

References EXTERN_C_FOR_PETSC_END::command_line.

Referenced by default_solver_package(), DofMap::distribute_dofs(), LibMeshInit::LibMeshInit(), System::read_header(), and DofMap::use_coupled_neighbor_dofs().

{
  // Make sure the command line parser is ready for use
  libmesh_assert (command_line.get() != NULL);
  
  return command_line->search (arg);
}

unsigned int libMesh::processor_id

(

)

[inline]

Returns:

the index of the local processor.

Definition at line 88 of file libmesh_base.h.

References libMesh::libMeshPrivateData::_processor_id.

Referenced by EquationSystems::_read_impl(), Predicates::ActiveLocal< T >::ActiveLocal(), Predicates::ActiveLocalSubdomain< T >::ActiveLocalSubdomain(), Predicates::ActiveNotLocal< T >::ActiveNotLocal(), ParallelMesh::add_elem(), Patch::add_local_face_neighbors(), Patch::add_local_point_neighbors(), DofMap::add_neighbors_to_send_list(), ParallelMesh::add_node(), DofMap::allgather_recursive_constraints(), MeshCommunication::assign_global_indices(), ParmetisPartitioner::assign_partitioning(), Patch::build_around_element(), ParmetisPartitioner::build_graph(), InfElemBuilder::build_inf_elem(), VTKIO::cells_to_vtk(), DofMap::distribute_dofs(), DofMap::distribute_local_dofs_node_major(), DofMap::distribute_local_dofs_var_major(), EnsightIO::EnsightIO(), MeshCommunication::find_global_indices(), MeshRefinement::flag_elements_by_elem_fraction(), MeshRefinement::flag_elements_by_mean_stddev(), MeshRefinement::flag_elements_by_nelem_target(), Nemesis_IO_Helper::get_cmap_params(), Nemesis_IO_Helper::get_eb_info_global(), Nemesis_IO_Helper::get_elem_cmap(), Nemesis_IO_Helper::get_elem_map(), PerfLog::get_info_header(), Nemesis_IO_Helper::get_init_global(), Nemesis_IO_Helper::get_init_info(), Nemesis_IO_Helper::get_loadbal_param(), Nemesis_IO_Helper::get_node_cmap(), Nemesis_IO_Helper::get_node_map(), Nemesis_IO_Helper::get_ns_param_global(), Nemesis_IO_Helper::get_ss_param_global(), ParmetisPartitioner::initialize(), ParallelMesh::libmesh_assert_valid_parallel_object_ids(), LibMeshInit::LibMeshInit(), Predicates::Local< T >::Local(), local_file_name(), Predicates::LocalLevel< T >::LocalLevel(), Predicates::LocalNotLevel< T >::LocalNotLevel(), MeshRefinement::make_coarsening_compatible(), MeshInput< MT >::MeshInput(), MeshOutput< MT >::MeshOutput(), MeshBase::n_active_local_elem(), BoundaryInfo::n_boundary_conds(), System::n_local_dofs(), DofMap::n_local_dofs(), MeshBase::n_local_elem(), MeshBase::n_local_nodes(), VTKIO::nodes_to_vtk(), Predicates::NotLocal< T >::NotLocal(), StatisticsVector< T >::plot_histogram(), SparseMatrix< T >::print(), NumericVector< T >::print_global(), System::project_vector(), XdrIO::read(), VTKIO::read(), UnstructuredMesh::read(), TetGenIO::read(), Nemesis_IO::read(), LegacyXdrIO::read(), GMVIO::read(), ExodusII_IO_Helper::read_elem_num_map(), System::read_header(), UCDIO::read_implementation(), System::read_legacy_data(), LegacyXdrIO::read_mesh(), GmshIO::read_mesh(), ExodusII_IO_Helper::read_node_num_map(), XdrIO::read_serialized_bcs(), System::read_serialized_blocked_dof_objects(), XdrIO::read_serialized_connectivity(), System::read_serialized_data(), XdrIO::read_serialized_nodes(), System::read_serialized_vector(), OFFIO::read_stream(), MatlabIO::read_stream(), ParallelMesh::renumber_dof_objects(), Partitioner::set_node_processor_ids(), DofMap::set_nonlocal_dof_objects(), VTKIO::solution_to_vtk(), Parallel::sync_dofobject_data_by_id(), Parallel::sync_dofobject_data_by_xyz(), Parallel::sync_element_data_by_parent_id(), VTKIO::system_vectors_to_vtk(), MeshTools::total_weight(), unzip_file(), EpetraMatrix< T >::update_sparsity_pattern(), XdrIO::write(), VTKIO::write(), UnstructuredMesh::write(), TecplotIO::write(), PostscriptIO::write(), MEDITIO::write(), GnuPlotIO::write(), GMVIO::write(), GmshIO::write(), FroIO::write(), EquationSystems::write(), TecplotIO::write_ascii(), GMVIO::write_ascii_old_impl(), TecplotIO::write_binary(), VTKIO::write_equation_systems(), LegacyXdrIO::write_mesh(), TecplotIO::write_nodal_data(), MEDITIO::write_nodal_data(), GnuPlotIO::write_nodal_data(), GMVIO::write_nodal_data(), GmshIO::write_nodal_data(), GmshIO::write_post(), XdrIO::write_serialized_bcs(), System::write_serialized_blocked_dof_objects(), XdrIO::write_serialized_connectivity(), System::write_serialized_data(), XdrIO::write_serialized_nodes(), System::write_serialized_vector(), GnuPlotIO::write_solution(), zip_file(), and ExodusII_IO::~ExodusII_IO().

{
#ifdef LIBMESH_HAVE_MPI
  return static_cast<unsigned int>(libMeshPrivateData::_processor_id);
#else
  return 0;
#endif
}

---

Variable Documentation

void char** & libMesh::argv

Definition at line 127 of file libmesh.C.

MPI_Comm libMesh::COMM_WORLD = MPI_COMM_NULL

MPI Communicator to be used in the library.

Definition at line 75 of file libmesh.C.

Referenced by ParmetisPartitioner::_do_repartition(), PetscVector< T >::_get_array(), PetscMatrix< T >::_get_submatrix(), SlepcEigenSolver< T >::_petsc_shell_matrix_get_diagonal(), PetscLinearSolver< T >::_petsc_shell_matrix_get_diagonal(), SlepcEigenSolver< T >::_petsc_shell_matrix_mult(), PetscLinearSolver< T >::_petsc_shell_matrix_mult(), PetscVector< T >::_restore_array(), SlepcEigenSolver< T >::_solve_generalized_helper(), SlepcEigenSolver< T >::_solve_standard_helper(), PetscVector< T >::abs(), PetscVector< T >::add(), PetscMatrix< T >::add(), PetscMatrix< T >::add_matrix(), PetscVector< T >::add_vector(), MeshCommunication::assign_global_indices(), SlepcEigenSolver< T >::attach_deflation_space(), Parallel::Sort< KeyType >::binsort(), SlepcEigenSolver< T >::clear(), PetscVector< T >::clear(), PetscNonlinearSolver< T >::clear(), PetscMatrix< T >::clear(), PetscLinearSolver< T >::clear(), PetscDiffSolver::clear(), PetscVector< T >::close(), PetscMatrix< T >::close(), PetscMatrix< T >::closed(), Parallel::Sort< KeyType >::communicate_bins(), PetscVector< T >::create_subvector(), PetscVector< T >::dot(), MeshCommunication::find_global_indices(), PetscVector< T >::first_local_index(), PetscMatrix< T >::get_diagonal(), SlepcEigenSolver< T >::get_eigenpair(), PetscLinearSolver< T >::get_initial_residual(), SlepcEigenSolver< T >::get_relative_error(), PetscLinearSolver< T >::get_residual_history(), PetscMatrix< T >::get_transpose(), EpetraVector< T >::init(), EpetraMatrix< T >::init(), SlepcEigenSolver< T >::init(), PetscVector< T >::init(), PetscPreconditioner< T >::init(), PetscNonlinearSolver< T >::init(), PetscMatrix< T >::init(), PetscLinearSolver< T >::init(), PetscDiffSolver::init(), DistributedVector< T >::init(), PetscVector< T >::l1_norm(), PetscMatrix< T >::l1_norm(), PetscVector< T >::l2_norm(), PetscVector< T >::last_local_index(), PetscVector< T >::linfty_norm(), PetscMatrix< T >::linfty_norm(), PetscVector< T >::local_size(), PetscVector< T >::localize(), PetscVector< T >::localize_to_one(), PetscVector< T >::map_global_to_local_index(), PetscVector< T >::max(), PetscVector< T >::min(), PetscMatrix< T >::operator()(), PetscVector< T >::operator=(), PetscVector< T >::PetscVector(), PetscVector< T >::pointwise_mult(), PetscVector< T >::print_matlab(), PetscMatrix< T >::print_matlab(), PetscMatrix< T >::print_personal(), PetscMatrix< T >::row_start(), PetscMatrix< T >::row_stop(), PetscVector< T >::scale(), PetscVector< T >::set(), PetscMatrix< T >::set(), PetscPreconditioner< T >::set_petsc_preconditioner_type(), PetscLinearSolver< T >::set_petsc_solver_type(), SlepcEigenSolver< T >::set_slepc_position_of_spectrum(), SlepcEigenSolver< T >::set_slepc_problem_type(), SlepcEigenSolver< T >::set_slepc_solver_type(), PetscVector< T >::size(), PetscNonlinearSolver< T >::solve(), PetscLinearSolver< T >::solve(), PetscDiffSolver::solve(), SlepcEigenSolver< T >::solve_generalized(), SlepcEigenSolver< T >::solve_standard(), PetscVector< T >::sum(), EpetraMatrix< T >::update_sparsity_pattern(), PetscVector< T >::zero(), PetscMatrix< T >::zero(), and PetscMatrix< T >::zero_rows().

const Number libMesh::imaginary

The imaginary unit, .

const unsigned int libMesh::invalid_uint = static_cast<unsigned int>(-1)

A number which is used quite often to represent an invalid or uninitialized value.

Definition at line 96 of file libmesh.C.

Referenced by SFCPartitioner::_do_partition(), InfFE< Dim, T_radial, T_map >::compute_node_indices_fast(), FEBase::compute_periodic_constraints(), InfFE< Dim, T_radial, T_map >::compute_shape_indices(), UnstructuredMesh::create_submesh(), Xdr::data_stream(), DofMap::dof_indices(), FEMContext::elem_position_get(), FEMContext::elem_position_set(), FEMContext::elem_reinit(), FEMContext::elem_side_reinit(), FEMSystem::eulerian_residual(), TreeNode< N >::find_element_in_children(), MeshRefinement::flag_elements_by_elem_fraction(), MeshRefinement::flag_elements_by_error_fraction(), MeshRefinement::flag_elements_by_mean_stddev(), DofObject::has_dofs(), MeshTools::Generation::Private::idx(), Elem::is_ancestor_of(), ParallelMesh::libmesh_assert_valid_parallel_flags(), FEMSystem::mesh_position_get(), FEMSystem::mesh_x_position(), FEMSystem::mesh_y_position(), FEMSystem::mesh_z_position(), DofObject::n_dofs(), Quad9::n_second_order_adjacent_vertices(), InfHex18::n_second_order_adjacent_vertices(), Hex27::n_second_order_adjacent_vertices(), FEMSystem::numerical_jacobian(), DofMap::old_dof_indices(), XdrIO::pack_element(), MeshDataUnvHeader::read(), System::read_serialized_blocked_dof_objects(), XdrIO::read_serialized_connectivity(), FEMContext::reinit(), Tet4::reselect_diagonal(), Prism18::second_order_adjacent_vertex(), FE< Dim, T >::shape_second_deriv(), BoundaryInfo::side_with_boundary_id(), Elem::which_neighbor_am_i(), and System::write_serialized_blocked_dof_objects().

PerfLog libMesh::perflog

A PerfLog object to log performance. If the library is configured with --enable-perflog then it will log key functions.

Referenced by Threads::parallel_for(), and Threads::parallel_reduce().

const Real libMesh::pi = 3.1415926535897932384626433832795029L

.

Definition at line 87 of file libmesh.C.

Referenced by MeshTools::Generation::build_cube(), InfFE< Dim, T_radial, T_map >::compute_data(), Tri3::min_and_max_angle(), TriangleInterface::PolygonHole::point(), VariationalMeshSmoother::readgr(), MeshTools::Modification::rotate(), and Sphere::surface_coords().

const Number libMesh::zero = 0.

.

Definition at line 93 of file libmesh.C.

Referenced by DenseMatrix< T >::_lu_back_substitute(), DenseMatrix< T >::_lu_decompose(), HPCoarsenTest::add_projection(), EquationSystems::build_solution_vector(), FEBase::coarsened_dof_values(), System::ProjectVector::operator()(), MeshData::operator()(), System::read_legacy_data(), and HPCoarsenTest::select_refinement().