libMesh::PetscNonlinearSolver< T > Class Template Reference

This class provides an interface to PETSc iterative solvers that is compatible with the libMesh NonlinearSolver<> More...

#include <petsc_nonlinear_solver.h>

Inheritance diagram for libMesh::PetscNonlinearSolver< T >:

Classes
class	ComputeLineSearchObject
	Abstract base class to be used to implement a custom line-search algorithm. More...

Public Types
typedef NonlinearImplicitSystem	sys_type
	The type of system. More...

Public Member Functions
	PetscNonlinearSolver (sys_type &system)
	Constructor. More...
	~PetscNonlinearSolver ()
	Destructor. More...
virtual void	clear () override
	Release all memory and clear data structures. More...
virtual void	init (const char *name=nullptr) override
	Initialize data structures if not done so already. More...
SNES	snes ()
virtual std::pair< unsigned int, Real >	solve (SparseMatrix< T > &, NumericVector< T > &, NumericVector< T > &, const double, const unsigned int) override
	Call the Petsc solver. More...
virtual void	print_converged_reason () override
	Prints a useful message about why the latest nonlinear solve con(di)verged. More...
SNESConvergedReason	get_converged_reason ()
virtual int	get_total_linear_iterations () override
	Get the total number of linear iterations done in the last solve. More...
virtual unsigned	get_current_nonlinear_iteration_number () const override
void	set_residual_zero_out (bool state)
	Set if the residual should be zeroed out in the callback. More...
void	set_jacobian_zero_out (bool state)
	Set if the jacobian should be zeroed out in the callback. More...
void	use_default_monitor (bool state)
	Set to true to use the libMesh's default monitor, set to false to use your own. More...
void	set_snesmf_reuse_base (bool state)
	Set to true to let PETSc reuse the base vector. More...
bool	initialized () const
const sys_type &	system () const
sys_type &	system ()
void	attach_preconditioner (Preconditioner< T > *preconditioner)
	Attaches a Preconditioner object to be used during the linear solves. More...
void	set_solver_configuration (SolverConfiguration &solver_configuration)
	Set the solver configuration object. More...
const Parallel::Communicator &	comm () const
processor_id_type	n_processors () const
processor_id_type	processor_id () const

Static Public Member Functions
static std::unique_ptr< NonlinearSolver< T > >	build (sys_type &s, const SolverPackage solver_package=libMesh::default_solver_package())
	Builds a NonlinearSolver using the nonlinear 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=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 ()

Public Attributes
std::unique_ptr< ComputeLineSearchObject >	linesearch_object
	A callable object that can be used to specify a custom line-search. More...
void(*	residual )(const NumericVector< Number > &X, NumericVector< Number > &R, sys_type &S)
	Function that computes the residual R(X) of the nonlinear system at the input iterate X. More...
NonlinearImplicitSystem::ComputeResidual *	residual_object
	Object that computes the residual R(X) of the nonlinear system at the input iterate X. More...
NonlinearImplicitSystem::ComputeResidual *	fd_residual_object
	Object that computes the residual R(X) of the nonlinear system at the input iterate X for the purpose of forming a finite-differenced Jacobian. More...
NonlinearImplicitSystem::ComputeResidual *	mffd_residual_object
	Object that computes the residual R(X) of the nonlinear system at the input iterate X for the purpose of forming Jacobian-vector products via finite differencing. More...
void(*	jacobian )(const NumericVector< Number > &X, SparseMatrix< Number > &J, sys_type &S)
	Function that computes the Jacobian J(X) of the nonlinear system at the input iterate X. More...
NonlinearImplicitSystem::ComputeJacobian *	jacobian_object
	Object that computes the Jacobian J(X) of the nonlinear system at the input iterate X. More...
void(*	matvec )(const NumericVector< Number > &X, NumericVector< Number > *R, SparseMatrix< Number > *J, sys_type &S)
	Function that computes either the residual \( R(X) \) or the Jacobian \( J(X) \) of the nonlinear system at the input iterate \( X \). More...
NonlinearImplicitSystem::ComputeResidualandJacobian *	residual_and_jacobian_object
	Object that computes either the residual \( R(X) \) or the Jacobian \( J(X) \) of the nonlinear system at the input iterate \( X \). More...
void(*	bounds )(NumericVector< Number > &XL, NumericVector< Number > &XU, sys_type &S)
	Function that computes the lower and upper bounds XL and XU on the solution of the nonlinear system. More...
NonlinearImplicitSystem::ComputeBounds *	bounds_object
	Object that computes the bounds vectors \( XL \) and \( XU \). More...
void(*	nullspace )(std::vector< NumericVector< Number > * > &sp, sys_type &S)
	Function that computes a basis for the Jacobian's nullspace – the kernel or the "zero energy modes" – that can be used in solving a degenerate problem iteratively, if the solver supports it (e.g., PETSc's KSP). More...
NonlinearImplicitSystem::ComputeVectorSubspace *	nullspace_object
	A callable object that computes a basis for the Jacobian's nullspace – the kernel or the "zero energy modes" – that can be used in solving a degenerate problem iteratively, if the solver supports it (e.g., PETSc's KSP). More...
void(*	transpose_nullspace )(std::vector< NumericVector< Number > * > &sp, sys_type &S)
	Function that computes a basis for the transpose Jacobian's nullspace – when solving a degenerate problem iteratively, if the solver supports it (e.g., PETSc's KSP), it is used to remove contributions outside of R(jac) More...
NonlinearImplicitSystem::ComputeVectorSubspace *	transpose_nullspace_object
	A callable object that computes a basis for the transpose Jacobian's nullspace – when solving a degenerate problem iteratively, if the solver supports it (e.g., PETSc's KSP), it is used to remove contributions outside of R(jac) More...
void(*	nearnullspace )(std::vector< NumericVector< Number > * > &sp, sys_type &S)
	Function that computes a basis for the Jacobian's near nullspace – the set of "low energy modes" – that can be used for AMG coarsening, if the solver supports it (e.g., ML, PETSc's GAMG). More...
NonlinearImplicitSystem::ComputeVectorSubspace *	nearnullspace_object
	A callable object that computes a basis for the Jacobian's near nullspace – the set of "low energy modes" – that can be used for AMG coarsening, if the solver supports it (e.g., ML, PETSc's GAMG). More...
void(*	user_presolve )(sys_type &S)
	Customizable function pointer which users can attach to the solver. More...
void(*	postcheck )(const NumericVector< Number > &old_soln, NumericVector< Number > &search_direction, NumericVector< Number > &new_soln, bool &changed_search_direction, bool &changed_new_soln, sys_type &S)
	Function that performs a "check" on the Newton search direction and solution after each nonlinear step. More...
NonlinearImplicitSystem::ComputePostCheck *	postcheck_object
	A callable object that is executed after each nonlinear iteration. More...
unsigned int	max_nonlinear_iterations
	Maximum number of non-linear iterations. More...
unsigned int	max_function_evaluations
	Maximum number of function evaluations. More...
double	absolute_residual_tolerance
	The NonlinearSolver should exit after the residual is reduced to either less than absolute_residual_tolerance or less than relative_residual_tolerance times the initial residual. More...
double	relative_residual_tolerance
double	divergence_tolerance
	The NonlinearSolver should exit if the residual becomes greater than the initial residual times the divergence_tolerance. More...
double	absolute_step_tolerance
	The NonlinearSolver should exit after the full nonlinear step norm is reduced to either less than absolute_step_tolerance or less than relative_step_tolerance times the largest nonlinear solution which has been seen so far. More...
double	relative_step_tolerance
unsigned int	max_linear_iterations
	Each linear solver step should exit after max_linear_iterations is exceeded. More...
double	initial_linear_tolerance
	Any required linear solves will at first be done with this tolerance; the NonlinearSolver may tighten the tolerance for later solves. More...
double	minimum_linear_tolerance
	The tolerance for linear solves is kept above this minimum. More...
bool	converged
	After a call to solve this will reflect whether or not the nonlinear solve was successful. More...

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

Protected Member Functions
void	build_mat_null_space (NonlinearImplicitSystem::ComputeVectorSubspace *computeSubspaceObject, void(*)(std::vector< NumericVector< Number > * > &, sys_type &), MatNullSpace *)
void	increment_constructor_count (const std::string &name)
	Increments the construction counter. More...
void	increment_destructor_count (const std::string &name)
	Increments the destruction counter. More...

Protected Attributes
SNES	_snes
	Nonlinear solver context. More...
SNESConvergedReason	_reason
	Store the reason for SNES convergence/divergence for use even after the _snes has been cleared. More...
PetscInt	_n_linear_iterations
	Stores the total number of linear iterations from the last solve. More...
unsigned	_current_nonlinear_iteration_number
	Stores the current nonlinear iteration number. More...
bool	_zero_out_residual
	true to zero out residual before going into application level call-back, otherwise false More...
bool	_zero_out_jacobian
	true to zero out jacobian before going into application level call-back, otherwise false More...
bool	_default_monitor
	true if we want the default monitor to be set, false for no monitor (i.e. More...
bool	_snesmf_reuse_base
	True, If we want the base vector to be used for differencing even if the function provided to SNESSetFunction() is not the same as that provided to MatMFFDSetFunction(). More...
sys_type &	_system
	A reference to the system we are solving. More...
bool	_is_initialized
	Flag indicating if the data structures have been initialized. More...
Preconditioner< T > *	_preconditioner
	Holds the Preconditioner object to be used for the linear solves. More...
SolverConfiguration *	_solver_configuration
	Optionally store a SolverOptions object that can be used to set parameters like solver type, tolerances and iteration limits. More...
const Parallel::Communicator &	_communicator

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

Friends
ResidualContext	libmesh_petsc_snes_residual_helper (SNES snes, Vec x, void *ctx)
PetscErrorCode	libmesh_petsc_snes_residual (SNES snes, Vec x, Vec r, void *ctx)
PetscErrorCode	libmesh_petsc_snes_fd_residual (SNES snes, Vec x, Vec r, void *ctx)
PetscErrorCode	libmesh_petsc_snes_mffd_residual (SNES snes, Vec x, Vec r, void *ctx)
PetscErrorCode	libmesh_petsc_snes_jacobian (SNES snes, Vec x, Mat *jac, Mat *pc, MatStructure *msflag, void *ctx)
PetscErrorCode	libmesh_petsc_snes_jacobian (SNES snes, Vec x, Mat jac, Mat pc, void *ctx)

Detailed Description

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

This class provides an interface to PETSc iterative solvers that is compatible with the libMesh NonlinearSolver<>

Author

Benjamin Kirk

Date

2002-2007

Definition at line 99 of file petsc_nonlinear_solver.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 117 of file reference_counter.h.

sys_type

template<typename T>

typedef NonlinearImplicitSystem libMesh::PetscNonlinearSolver< T >::sys_type

The type of system.

Definition at line 105 of file petsc_nonlinear_solver.h.

Constructor & Destructor Documentation

PetscNonlinearSolver()

template<typename T >

libMesh::PetscNonlinearSolver< T >::PetscNonlinearSolver ( sys_type &  system )

explicit

Constructor.

Initializes Petsc data structures

Definition at line 543 of file petsc_nonlinear_solver.C.

                                                                   :
  NonlinearSolver<T>(system_in),
  linesearch_object(nullptr),
  _reason(SNES_CONVERGED_ITERATING/*==0*/), // Arbitrary initial value...
  _n_linear_iterations(0),
  _current_nonlinear_iteration_number(0),
  _zero_out_residual(true),
  _zero_out_jacobian(true),
  _default_monitor(true),
  _snesmf_reuse_base(true)
{
}

~PetscNonlinearSolver()

template<typename T >

libMesh::PetscNonlinearSolver< T >::~PetscNonlinearSolver

(

)

Destructor.

Definition at line 559 of file petsc_nonlinear_solver.C.

{
  this->clear ();
}

Member Function Documentation

attach_preconditioner()

template<typename T>

void libMesh::NonlinearSolver< T >::attach_preconditioner ( Preconditioner< T > *  preconditioner )

inherited

Attaches a Preconditioner object to be used during the linear solves.

Definition at line 71 of file nonlinear_solver.C.

{
  if (this->_is_initialized)
    libmesh_error_msg("Preconditioner must be attached before the solver is initialized!");
 
  _preconditioner = preconditioner;
}

build()

template<typename T >

std::unique_ptr< NonlinearSolver< T > > libMesh::NonlinearSolver< T >::build ( sys_type &  s, const SolverPackage  solver_package = libMesh::default_solver_package()  )

staticinherited

Builds a NonlinearSolver using the nonlinear solver package specified by solver_package.

Definition at line 37 of file nonlinear_solver.C.

{
  // Build the appropriate solver
  switch (solver_package)
    {
 
#ifdef LIBMESH_HAVE_PETSC
    case PETSC_SOLVERS:
      return libmesh_make_unique<PetscNonlinearSolver<T>>(s);
#endif // LIBMESH_HAVE_PETSC
 
#if defined(LIBMESH_TRILINOS_HAVE_NOX) && defined(LIBMESH_TRILINOS_HAVE_EPETRA)
    case TRILINOS_SOLVERS:
      return libmesh_make_unique<NoxNonlinearSolver<T>>(s);
#endif
 
    default:
      libmesh_error_msg("ERROR:  Unrecognized solver package: " << solver_package);
    }
}

build_mat_null_space()

template<typename T >

void libMesh::PetscNonlinearSolver< T >::build_mat_null_space ( NonlinearImplicitSystem::ComputeVectorSubspace *  computeSubspaceObject, void(*)(std::vector< NumericVector< Number > * > &, sys_type &)  computeSubspace, MatNullSpace *  msp  )

protected

Definition at line 690 of file petsc_nonlinear_solver.C.

{
  PetscErrorCode ierr;
  std::vector<NumericVector<Number> *> sp;
  if (computeSubspaceObject)
    (*computeSubspaceObject)(sp, this->system());
  else
    (*computeSubspace)(sp, this->system());
 
  *msp = PETSC_NULL;
  if (sp.size())
    {
      Vec * modes;
      PetscScalar * dots;
      PetscInt nmodes = cast_int<PetscInt>(sp.size());
 
#if PETSC_RELEASE_LESS_THAN(3,5,0)
      ierr = PetscMalloc2(nmodes,Vec,&modes,nmodes,PetscScalar,&dots);
#else
      ierr = PetscMalloc2(nmodes,&modes,nmodes,&dots);
#endif
      LIBMESH_CHKERR(ierr);
 
      for (PetscInt i=0; i<nmodes; ++i)
        {
          PetscVector<T> * pv = cast_ptr<PetscVector<T> *>(sp[i]);
          Vec v = pv->vec();
 
          ierr = VecDuplicate(v, modes+i);
          LIBMESH_CHKERR(ierr);
 
          ierr = VecCopy(v,modes[i]);
          LIBMESH_CHKERR(ierr);
        }
 
      // Normalize.
      ierr = VecNormalize(modes[0],PETSC_NULL);
      LIBMESH_CHKERR(ierr);
 
      for (PetscInt i=1; i<nmodes; i++)
        {
          // Orthonormalize vec[i] against vec[0:i-1]
          ierr = VecMDot(modes[i],i,modes,dots);
          LIBMESH_CHKERR(ierr);
 
          for (PetscInt j=0; j<i; j++)
            dots[j] *= -1.;
 
          ierr = VecMAXPY(modes[i],i,dots,modes);
          LIBMESH_CHKERR(ierr);
 
          ierr = VecNormalize(modes[i],PETSC_NULL);
          LIBMESH_CHKERR(ierr);
        }
 
      ierr = MatNullSpaceCreate(this->comm().get(), PETSC_FALSE, nmodes, modes, msp);
      LIBMESH_CHKERR(ierr);
 
      for (PetscInt i=0; i<nmodes; ++i)
        {
          ierr = VecDestroy(modes+i);
          LIBMESH_CHKERR(ierr);
        }
 
      ierr = PetscFree2(modes,dots);
      LIBMESH_CHKERR(ierr);
    }
}

clear()

template<typename T >

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

overridevirtual

Release all memory and clear data structures.

Reimplemented from libMesh::NonlinearSolver< T >.

Definition at line 567 of file petsc_nonlinear_solver.C.

{
  if (this->initialized())
    {
      this->_is_initialized = false;
 
      PetscErrorCode ierr=0;
 
      ierr = LibMeshSNESDestroy(&_snes);
      LIBMESH_CHKERR(ierr);
 
      // Reset the nonlinear iteration counter.  This information is only relevant
      // *during* the solve().  After the solve is completed it should return to
      // the default value of 0.
      _current_nonlinear_iteration_number = 0;
    }
}

comm()

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

inlineinherited

Returns

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

Definition at line 94 of file parallel_object.h.

  { return _communicator; }

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::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::EquationSystems::_read_impl(), 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::ImplicitSystem::add_matrix(), libMesh::RBConstruction::add_scaled_matrix_and_vector(), libMesh::DynaIO::add_spline_constraints(), libMesh::System::add_vector(), libMesh::UnstructuredMesh::all_second_order(), 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::FEMSystem::assemble_qoi(), libMesh::MeshCommunication::assign_global_indices(), libMesh::DofMap::attach_matrix(), libMesh::MeshTools::Generation::build_extrusion(), 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::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::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_scalar_solution(), 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::MeshCommunication::delete_remote_elements(), libMesh::DofMap::distribute_dofs(), DMlibMeshFunction(), DMlibMeshJacobian(), DMlibMeshSetSystem_libMesh(), DMVariableBounds_libMesh(), libMesh::DTKSolutionTransfer::DTKSolutionTransfer(), libMesh::MeshRefinement::eliminate_unrefined_patches(), libMesh::RBEIMConstruction::enrich_RB_space(), libMesh::TransientRBConstruction::enrich_RB_space(), libMesh::RBConstruction::enrich_RB_space(), libMesh::EpetraVector< T >::EpetraVector(), AssembleOptimization::equality_constraints(), libMesh::WeightedPatchRecoveryErrorEstimator::estimate_error(), libMesh::PatchRecoveryErrorEstimator::estimate_error(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::RBEIMConstruction::evaluate_mesh_function(), 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::DofMap::gather_constraints(), libMesh::MeshfreeInterpolation::gather_remote_data(), libMesh::CondensedEigenSystem::get_eigenpair(), libMesh::DofMap::get_info(), libMesh::ImplicitSystem::get_linear_solver(), AssembleOptimization::inequality_constraints(), AssembleOptimization::inequality_constraints_jacobian(), libMesh::LocationMap< T >::init(), libMesh::TimeSolver::init(), libMesh::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_and_attach_petscdm(), libMesh::EigenSystem::init_matrices(), libMesh::OptimizationSystem::initialize_equality_constraints_storage(), libMesh::OptimizationSystem::initialize_inequality_constraints_storage(), libMesh::RBEIMConstruction::initialize_rb_construction(), 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_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::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_preconditioner_apply(), libMesh::libmesh_petsc_snes_fd_residual(), libMesh::libmesh_petsc_snes_jacobian(), libMesh::libmesh_petsc_snes_mffd_residual(), libMesh::libmesh_petsc_snes_postcheck(), 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(), 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_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(), LinearElasticityWithContact::move_mesh(), libMesh::DistributedMesh::n_active_elem(), libMesh::MeshTools::n_active_levels(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::DofMap::n_constrained_dofs(), libMesh::BoundaryInfo::n_edge_conds(), libMesh::CondensedEigenSystem::n_global_non_condensed_dofs(), libMesh::MeshTools::n_levels(), libMesh::BoundaryInfo::n_nodeset_conds(), libMesh::MeshTools::n_p_levels(), libMesh::BoundaryInfo::n_shellface_conds(), 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::MeshTools::paranoid_n_levels(), libMesh::petsc_auto_fieldsplit(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::DofMap::print_dof_constraints(), FEMParameters::read(), libMesh::Nemesis_IO::read(), libMesh::XdrIO::read(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::System::read_header(), 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::MeshRefinement::refine_and_coarsen_elements(), libMesh::DistributedMesh::renumber_dof_objects(), LinearElasticityWithContact::residual_and_jacobian(), OverlappingAlgebraicGhostingTest::run_ghosting_test(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), libMesh::DofMap::scatter_constraints(), libMesh::CheckpointIO::select_split_config(), libMesh::TransientRBConstruction::set_error_temporal_data(), libMesh::RBEIMConstruction::set_explicit_sys_subvector(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::PetscDiffSolver::setup_petsc_data(), libMesh::LaplaceMeshSmoother::smooth(), libMesh::split_mesh(), libMesh::BoundaryInfo::sync(), libMesh::MeshRefinement::test_level_one(), MeshfunctionDFEM::test_mesh_function_dfem(), MeshfunctionDFEM::test_mesh_function_dfem_grad(), MeshFunctionTest::test_p_level(), libMesh::MeshRefinement::test_unflagged(), SystemsTest::testBlockRestrictedVarNDofs(), PointLocatorTest::testLocator(), BoundaryInfoTest::testMesh(), SystemsTest::testProjectCubeWithMeshFunction(), CheckpointIOTest::testSplitter(), libMesh::MeshTools::total_weight(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::MeshfreeSolutionTransfer::transfer(), libMesh::TransientRBConstruction::truth_assembly(), libMesh::RBConstruction::truth_assembly(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::TransientRBConstruction::update_RB_initial_condition_all_N(), libMesh::RBEIMConstruction::update_RB_system_matrices(), libMesh::TransientRBConstruction::update_RB_system_matrices(), libMesh::RBConstruction::update_RB_system_matrices(), libMesh::TransientRBConstruction::update_residual_terms(), libMesh::RBConstruction::update_residual_terms(), libMesh::NameBasedIO::write(), libMesh::XdrIO::write(), libMesh::VTKIO::write_nodal_data(), 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().

disable_print_counter_info()

void libMesh::ReferenceCounter::disable_print_counter_info ( )

staticinherited

Definition at line 106 of file reference_counter.C.

{
  _enable_print_counter = false;
  return;
}

References libMesh::ReferenceCounter::_enable_print_counter.

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

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 100 of file reference_counter.C.

{
  _enable_print_counter = true;
  return;
}

References libMesh::ReferenceCounter::_enable_print_counter.

get_converged_reason()

template<typename T >

SNESConvergedReason libMesh::PetscNonlinearSolver< T >::get_converged_reason

(

)

Returns

The currently-available (or most recently obtained, if the SNES object has been destroyed) convergence reason.

Refer to PETSc docs for the meaning of different SNESConvergedReasons.

Definition at line 981 of file petsc_nonlinear_solver.C.

{
  PetscErrorCode ierr=0;
 
  if (this->initialized())
    {
      ierr = SNESGetConvergedReason(_snes, &_reason);
      LIBMESH_CHKERR(ierr);
    }
 
  return _reason;
}

get_current_nonlinear_iteration_number()

template<typename T>

virtual unsigned libMesh::PetscNonlinearSolver< T >::get_current_nonlinear_iteration_number ( ) const

inlineoverridevirtual

Returns

The current nonlinear iteration number if called during the solve(), for example by the user-specified residual or Jacobian function.

Implements libMesh::NonlinearSolver< T >.

Definition at line 170 of file petsc_nonlinear_solver.h.

  { return _current_nonlinear_iteration_number; }

get_info()

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

staticinherited

Gets a string containing the reference information.

Definition at line 47 of file reference_counter.C.

{
#if defined(LIBMESH_ENABLE_REFERENCE_COUNTING) && defined(DEBUG)
 
  std::ostringstream oss;
 
  oss << '\n'
      << " ---------------------------------------------------------------------------- \n"
      << "| Reference count information                                                |\n"
      << " ---------------------------------------------------------------------------- \n";
 
  for (const auto & pr : _counts)
    {
      const std::string name(pr.first);
      const unsigned int creations    = pr.second.first;
      const unsigned int destructions = pr.second.second;
 
      oss << "| " << name << " reference count information:\n"
          << "|  Creations:    " << creations    << '\n'
          << "|  Destructions: " << destructions << '\n';
    }
 
  oss << " ---------------------------------------------------------------------------- \n";
 
  return oss.str();
 
#else
 
  return "";
 
#endif
}

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

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

get_total_linear_iterations()

template<typename T >

int libMesh::PetscNonlinearSolver< T >::get_total_linear_iterations ( )

overridevirtual

Get the total number of linear iterations done in the last solve.

Implements libMesh::NonlinearSolver< T >.

Definition at line 995 of file petsc_nonlinear_solver.C.

{
  return _n_linear_iterations;
}

increment_constructor_count()

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

inlineprotectedinherited

Increments the construction counter.

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

Definition at line 181 of file reference_counter.h.

{
  Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
  std::pair<unsigned int, unsigned int> & p = _counts[name];
 
  p.first++;
}

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

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

increment_destructor_count()

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

inlineprotectedinherited

Increments the destruction counter.

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

Definition at line 194 of file reference_counter.h.

{
  Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
  std::pair<unsigned int, unsigned int> & p = _counts[name];
 
  p.second++;
}

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

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

init()

template<typename T >

void libMesh::PetscNonlinearSolver< T >::init ( const char *  name = nullptr )

overridevirtual

Initialize data structures if not done so already.

May assign a name to the solver in some implementations

Implements libMesh::NonlinearSolver< T >.

Definition at line 588 of file petsc_nonlinear_solver.C.

{
  // Initialize the data structures if not done so already.
  if (!this->initialized())
    {
      this->_is_initialized = true;
 
      PetscErrorCode ierr=0;
 
      ierr = SNESCreate(this->comm().get(),&_snes);
      LIBMESH_CHKERR(ierr);
 
      if (name)
        {
          ierr = SNESSetOptionsPrefix(_snes, name);
          LIBMESH_CHKERR(ierr);
        }
 
#if !PETSC_RELEASE_LESS_THAN(3,3,0)
      // Attaching a DM to SNES.
      DM dm;
      ierr = DMCreate(this->comm().get(), &dm);LIBMESH_CHKERR(ierr);
      ierr = DMSetType(dm,DMLIBMESH);LIBMESH_CHKERR(ierr);
      ierr = DMlibMeshSetSystem(dm,this->system());LIBMESH_CHKERR(ierr);
      if (name)
        {
          ierr = DMSetOptionsPrefix(dm,name);    LIBMESH_CHKERR(ierr);
        }
      ierr = DMSetFromOptions(dm);               LIBMESH_CHKERR(ierr);
      ierr = DMSetUp(dm);                        LIBMESH_CHKERR(ierr);
      ierr = SNESSetDM(this->_snes, dm);         LIBMESH_CHKERR(ierr);
      // SNES now owns the reference to dm.
      ierr = DMDestroy(&dm);                     LIBMESH_CHKERR(ierr);
 
#endif
 
      if (_default_monitor)
        {
          ierr = SNESMonitorSet (_snes, libmesh_petsc_snes_monitor,
                                 this, PETSC_NULL);
          LIBMESH_CHKERR(ierr);
        }
 
      // If the SolverConfiguration object is provided, use it to set
      // options during solver initialization.
      if (this->_solver_configuration)
        {
          this->_solver_configuration->set_options_during_init();
        }
 
#if PETSC_VERSION_LESS_THAN(3,1,0)
      // Cannot call SNESSetOptions before SNESSetFunction when using
      // any matrix free options with PETSc 3.1.0+
      ierr = SNESSetFromOptions(_snes);
      LIBMESH_CHKERR(ierr);
#endif
 
      if (this->_preconditioner)
        {
          KSP ksp;
          ierr = SNESGetKSP (_snes, &ksp);
          LIBMESH_CHKERR(ierr);
          PC pc;
          ierr = KSPGetPC(ksp,&pc);
          LIBMESH_CHKERR(ierr);
 
          this->_preconditioner->init();
 
          PCSetType(pc, PCSHELL);
          PCShellSetContext(pc,(void *)this->_preconditioner);
 
          //Re-Use the shell functions from petsc_linear_solver
          PCShellSetSetUp(pc,libmesh_petsc_preconditioner_setup);
          PCShellSetApply(pc,libmesh_petsc_preconditioner_apply);
        }
    }
 
 
  // Tell PETSc about our linesearch "post-check" function, but only
  // if the user has provided one.  There seem to be extra,
  // unnecessary residual calculations if a postcheck function is
  // attached for no reason.
  if (this->postcheck || this->postcheck_object)
    {
#if PETSC_VERSION_LESS_THAN(3,3,0)
      PetscErrorCode ierr = SNESLineSearchSetPostCheck(_snes, libmesh_petsc_snes_postcheck, this);
      LIBMESH_CHKERR(ierr);
 
#else
      SNESLineSearch linesearch;
      PetscErrorCode ierr = SNESGETLINESEARCH(_snes, &linesearch);
      LIBMESH_CHKERR(ierr);
 
      ierr = SNESLineSearchSetPostCheck(linesearch, libmesh_petsc_snes_postcheck, this);
      LIBMESH_CHKERR(ierr);
#endif
    }
}

Referenced by libMesh::PetscNonlinearSolver< Number >::snes().

initialized()

template<typename T>

bool libMesh::NonlinearSolver< T >::initialized ( ) const

inlineinherited

Returns

true if the data structures are initialized, false otherwise.

Definition at line 91 of file nonlinear_solver.h.

{ return _is_initialized; }

n_objects()

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

inlinestaticinherited

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

Definition at line 83 of file reference_counter.h.

  { return _n_objects; }

References libMesh::ReferenceCounter::_n_objects.

n_processors()

processor_id_type libMesh::ParallelObject::n_processors ( ) const

inlineinherited

Returns

The number of processors in the group.

Definition at line 100 of file parallel_object.h.

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

References libMesh::ParallelObject::_communicator.

Referenced by 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::LaplaceMeshSmoother::allgather_graph(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::FEMSystem::assembly(), libMesh::AztecLinearSolver< T >::AztecLinearSolver(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::DistributedMesh::clear(), libMesh::Nemesis_IO_Helper::compute_border_node_ids(), libMesh::Nemesis_IO_Helper::construct_nemesis_filename(), libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::UnstructuredMesh::create_pid_mesh(), libMesh::MeshTools::create_processor_bounding_box(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_local_dofs_node_major(), libMesh::DofMap::distribute_local_dofs_var_major(), libMesh::EnsightIO::EnsightIO(), libMesh::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_and_attach_petscdm(), libMesh::Nemesis_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::partition(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::DofMap::prepare_send_list(), 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(), OverlappingFunctorTest::run_partitioner_test(), libMesh::DofMap::scatter_constraints(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::PetscDMWrapper::set_point_range_in_section(), CheckpointIOTest::testSplitter(), WriteVecAndScalar::testWrite(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::DistributedMesh::update_parallel_id_counts(), libMesh::GMVIO::write_binary(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::VTKIO::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().

print_converged_reason()

template<typename T >

void libMesh::PetscNonlinearSolver< T >::print_converged_reason ( )

overridevirtual

Prints a useful message about why the latest nonlinear solve con(di)verged.

Reimplemented from libMesh::NonlinearSolver< T >.

Definition at line 971 of file petsc_nonlinear_solver.C.

{
 
  libMesh::out << "Nonlinear solver convergence/divergence reason: "
               << SNESConvergedReasons[this->get_converged_reason()] << std::endl;
}

print_info()

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

staticinherited

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

Definition at line 87 of file reference_counter.C.

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

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

processor_id()

processor_id_type libMesh::ParallelObject::processor_id ( ) const

inlineinherited

Returns

The rank of this processor in the group.

Definition at line 106 of file parallel_object.h.

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

References libMesh::ParallelObject::_communicator.

Referenced by libMesh::BoundaryInfo::_find_id_maps(), libMesh::EquationSystems::_read_impl(), 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::UnstructuredMesh::all_second_order(), libMesh::MeshTools::Modification::all_tri(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::FEMSystem::assembly(), libMesh::Nemesis_IO_Helper::build_element_and_node_maps(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::DistributedMesh::clear(), 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_scalar_solution(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::ExodusII_IO_Helper::create(), libMesh::DistributedMesh::delete_elem(), libMesh::DistributedMesh::delete_node(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_local_dofs_node_major(), libMesh::DofMap::distribute_local_dofs_var_major(), libMesh::DistributedMesh::DistributedMesh(), libMesh::DofMap::end_dof(), libMesh::DofMap::end_old_dof(), libMesh::EnsightIO::EnsightIO(), libMesh::RBEIMConstruction::evaluate_mesh_function(), libMesh::MeshFunction::find_element(), libMesh::MeshFunction::find_elements(), libMesh::UnstructuredMesh::find_neighbors(), libMesh::DofMap::first_dof(), libMesh::DofMap::first_old_dof(), 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::DofMap::get_info(), libMesh::Nemesis_IO_Helper::get_init_global(), libMesh::Nemesis_IO_Helper::get_init_info(), libMesh::Nemesis_IO_Helper::get_loadbal_param(), libMesh::DofMap::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::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_and_attach_petscdm(), 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::DofMap::last_dof(), libMesh::TransientRBEvaluation::legacy_write_offline_data_to_files(), libMesh::RBEIMEvaluation::legacy_write_offline_data_to_files(), libMesh::RBEvaluation::legacy_write_offline_data_to_files(), libMesh::RBSCMEvaluation::legacy_write_offline_data_to_files(), libMesh::RBEIMEvaluation::legacy_write_out_interpolation_points_elem(), 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::MeshBase::n_active_local_elem(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::BoundaryInfo::n_edge_conds(), libMesh::DofMap::n_local_dofs(), libMesh::System::n_local_dofs(), libMesh::MeshBase::n_local_elem(), libMesh::MeshBase::n_local_nodes(), libMesh::BoundaryInfo::n_nodeset_conds(), libMesh::BoundaryInfo::n_shellface_conds(), libMesh::SparsityPattern::Build::operator()(), libMesh::DistributedMesh::own_node(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::DofMap::print_dof_constraints(), 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::ExodusII_IO_Helper::read_elem_num_map(), libMesh::ExodusII_IO_Helper::read_global_values(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::System::read_header(), libMesh::RBEvaluation::read_in_vectors_from_multiple_files(), libMesh::System::read_legacy_data(), 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::DistributedMesh::renumber_dof_objects(), libMesh::DofMap::scatter_constraints(), libMesh::CheckpointIO::select_split_config(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::LaplaceMeshSmoother::smooth(), DefaultCouplingTest::testCoupling(), PointNeighborCouplingTest::testCoupling(), MeshInputTest::testDynaReadElem(), MeshInputTest::testDynaReadPatch(), MeshInputTest::testExodusCopyElementSolution(), MeshInputTest::testExodusWriteElementDataFromDiscontinuousNodalData(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), SystemsTest::testProjectMatrix3D(), BoundaryInfoTest::testShellFaceConstraints(), CheckpointIOTest::testSplitter(), WriteVecAndScalar::testWrite(), libMesh::MeshTools::total_weight(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::Parallel::Packing< Node * >::unpack(), libMesh::Parallel::Packing< Elem * >::unpack(), libMesh::DistributedMesh::update_parallel_id_counts(), libMesh::DTKAdapter::update_variable_values(), 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::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::VTKIO::write_nodal_data(), libMesh::UCDIO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data_discontinuous(), libMesh::ExodusII_IO_Helper::write_nodal_values(), libMesh::Nemesis_IO_Helper::write_nodesets(), libMesh::ExodusII_IO_Helper::write_nodesets(), libMesh::RBEvaluation::write_out_vectors(), 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().

set_jacobian_zero_out()

template<typename T>

void libMesh::PetscNonlinearSolver< T >::set_jacobian_zero_out ( bool  state )

inline

Set if the jacobian should be zeroed out in the callback.

Definition at line 181 of file petsc_nonlinear_solver.h.

{ _zero_out_jacobian = state; }

set_residual_zero_out()

template<typename T>

void libMesh::PetscNonlinearSolver< T >::set_residual_zero_out ( bool  state )

inline

Set if the residual should be zeroed out in the callback.

Definition at line 176 of file petsc_nonlinear_solver.h.

{ _zero_out_residual = state; }

set_snesmf_reuse_base()

template<typename T>

void libMesh::PetscNonlinearSolver< T >::set_snesmf_reuse_base ( bool  state )

inline

Set to true to let PETSc reuse the base vector.

Definition at line 191 of file petsc_nonlinear_solver.h.

{ _snesmf_reuse_base = state; }

set_solver_configuration()

template<typename T >

void libMesh::NonlinearSolver< T >::set_solver_configuration ( SolverConfiguration &  solver_configuration )

inherited

Set the solver configuration object.

Definition at line 80 of file nonlinear_solver.C.

{
  _solver_configuration = &solver_configuration;
}

snes()

template<typename T>

SNES libMesh::PetscNonlinearSolver< T >::snes ( )

inline

Returns

The raw PETSc snes context pointer.

Definition at line 132 of file petsc_nonlinear_solver.h.

{ this->init(); return _snes; }

Referenced by libMesh::libmesh_petsc_snes_mffd_interface().

solve()

template<typename T>

std::pair< unsigned int, Real > libMesh::PetscNonlinearSolver< T >::solve ( SparseMatrix< T > &  pre_in, NumericVector< T > &  x_in, NumericVector< T > &  r_in, const double  , const unsigned int    )

overridevirtual

Call the Petsc solver.

It calls the method below, using the same matrix for the system and preconditioner matrices.

Implements libMesh::NonlinearSolver< T >.

Definition at line 764 of file petsc_nonlinear_solver.C.

{
  LOG_SCOPE("solve()", "PetscNonlinearSolver");
  this->init ();
 
  // Make sure the data passed in are really of Petsc types
  PetscMatrix<T> * pre = cast_ptr<PetscMatrix<T> *>(&pre_in);
  PetscVector<T> * x   = cast_ptr<PetscVector<T> *>(&x_in);
  PetscVector<T> * r   = cast_ptr<PetscVector<T> *>(&r_in);
 
  PetscErrorCode ierr=0;
  PetscInt n_iterations =0;
  // Should actually be a PetscReal, but I don't know which version of PETSc first introduced PetscReal
  Real final_residual_norm=0.;
 
  ierr = SNESSetFunction (_snes, r->vec(), libmesh_petsc_snes_residual, this);
  LIBMESH_CHKERR(ierr);
 
  // Only set the jacobian function if we've been provided with something to call.
  // This allows a user to set their own jacobian function if they want to
  if (this->jacobian || this->jacobian_object || this->residual_and_jacobian_object)
    {
      ierr = SNESSetJacobian (_snes, pre->mat(), pre->mat(), libmesh_petsc_snes_jacobian, this);
      LIBMESH_CHKERR(ierr);
    }
 
 
#if !PETSC_VERSION_LESS_THAN(3,3,0)
  // Only set the nullspace if we have a way of computing it and the result is non-empty.
  if (this->nullspace || this->nullspace_object)
    {
      MatNullSpace msp;
      this->build_mat_null_space(this->nullspace_object, this->nullspace, &msp);
      if (msp)
        {
          ierr = MatSetNullSpace(pre->mat(), msp);
          LIBMESH_CHKERR(ierr);
          ierr = MatNullSpaceDestroy(&msp);
          LIBMESH_CHKERR(ierr);
        }
    }
 
  // Only set the transpose nullspace if we have a way of computing it and the result is non-empty.
  if (this->transpose_nullspace || this->transpose_nullspace_object)
    {
#if PETSC_VERSION_LESS_THAN(3,6,0)
      libmesh_warning("MatSetTransposeNullSpace is only supported for PETSc >= 3.6, transpose nullspace will be ignored.");
#else
      MatNullSpace msp = PETSC_NULL;
      this->build_mat_null_space(this->transpose_nullspace_object, this->transpose_nullspace, &msp);
      if (msp)
        {
          ierr = MatSetTransposeNullSpace(pre->mat(), msp);
          LIBMESH_CHKERR(ierr);
          ierr = MatNullSpaceDestroy(&msp);
          LIBMESH_CHKERR(ierr);
        }
#endif
    }
 
  // Only set the nearnullspace if we have a way of computing it and the result is non-empty.
  if (this->nearnullspace || this->nearnullspace_object)
    {
      MatNullSpace msp = PETSC_NULL;
      this->build_mat_null_space(this->nearnullspace_object, this->nearnullspace, &msp);
 
      if (msp)
        {
          ierr = MatSetNearNullSpace(pre->mat(), msp);
          LIBMESH_CHKERR(ierr);
          ierr = MatNullSpaceDestroy(&msp);
          LIBMESH_CHKERR(ierr);
        }
    }
#endif
 
  // Have the Krylov subspace method use our good initial guess rather than 0
  KSP ksp;
  ierr = SNESGetKSP (_snes, &ksp);
  LIBMESH_CHKERR(ierr);
 
  // Set the tolerances for the iterative solver.  Use the user-supplied
  // tolerance for the relative residual & leave the others at default values
  ierr = KSPSetTolerances (ksp, this->initial_linear_tolerance, PETSC_DEFAULT,
                           PETSC_DEFAULT, this->max_linear_iterations);
  LIBMESH_CHKERR(ierr);
 
  // Set the tolerances for the non-linear solver.
  ierr = SNESSetTolerances(_snes, this->absolute_residual_tolerance, this->relative_residual_tolerance,
                           this->relative_step_tolerance, this->max_nonlinear_iterations, this->max_function_evaluations);
  LIBMESH_CHKERR(ierr);
 
  // Set the divergence tolerance for the non-linear solver
#if !PETSC_VERSION_LESS_THAN(3,8,0)
  ierr = SNESSetDivergenceTolerance(_snes, this->divergence_tolerance);
  LIBMESH_CHKERR(ierr);
#endif
 
  //Pull in command-line options
#if PETSC_VERSION_LESS_THAN(3,7,0)
  KSPSetFromOptions(ksp);
#endif
  SNESSetFromOptions(_snes);
 
  if (this->user_presolve)
    this->user_presolve(this->system());
 
  //Set the preconditioning matrix
  if (this->_preconditioner)
    {
      this->_preconditioner->set_matrix(pre_in);
      this->_preconditioner->init();
    }
 
  // If the SolverConfiguration object is provided, use it to override
  // solver options.
  if (this->_solver_configuration)
    {
      this->_solver_configuration->configure_solver();
    }
 
  // In PETSc versions before 3.5.0, it is not possible to call
  // SNESSetUp() before the solution and rhs vectors are initialized, as
  // this triggers the
  //
  // "Solution vector cannot be right hand side vector!"
  //
  // error message. It is also not possible to call SNESSetSolution()
  // in those versions of PETSc to work around the problem, since that
  // API was removed in 3.0.0 and only restored in 3.6.0. The
  // overzealous check was moved out of SNESSetUp in PETSc 3.5.0
  // (petsc/petsc@154060b), so this code block should be safe to use
  // in 3.5.0 and later.
#if !PETSC_VERSION_LESS_THAN(3,5,0)
#if !PETSC_VERSION_LESS_THAN(3,6,0)
  ierr = SNESSetSolution(_snes, x->vec());
  LIBMESH_CHKERR(ierr);
#endif
  ierr = SNESSetUp(_snes);
  LIBMESH_CHKERR(ierr);
 
  Mat J;
  ierr = SNESGetJacobian(_snes,&J,PETSC_NULL,PETSC_NULL,PETSC_NULL);
  LIBMESH_CHKERR(ierr);
  ierr = MatMFFDSetFunction(J, libmesh_petsc_snes_mffd_interface, this);
  LIBMESH_CHKERR(ierr);
#if !PETSC_VERSION_LESS_THAN(3, 8, 4)
  // Resue the residual vector from SNES
  ierr = MatSNESMFSetReuseBase(J, static_cast<PetscBool>(_snesmf_reuse_base));
  LIBMESH_CHKERR(ierr);
#endif
#endif
 
#if PETSC_VERSION_LESS_THAN(3, 3, 0)
  if (linesearch_object)
    libmesh_error_msg("Line search setter interface introduced in petsc version 3.3!");
#else
  SNESLineSearch linesearch;
  if (linesearch_object)
  {
    ierr = SNESGETLINESEARCH(_snes, &linesearch);
    LIBMESH_CHKERR(ierr);
    ierr = SNESLineSearchSetType(linesearch, SNESLINESEARCHSHELL);
    LIBMESH_CHKERR(ierr);
    ierr = SNESLineSearchShellSetUserFunc(linesearch, libmesh_petsc_linesearch_shellfunc, this);
    LIBMESH_CHKERR(ierr);
  }
#endif
 
  ierr = SNESSolve (_snes, PETSC_NULL, x->vec());
  LIBMESH_CHKERR(ierr);
 
  ierr = SNESGetIterationNumber(_snes,&n_iterations);
  LIBMESH_CHKERR(ierr);
 
  ierr = SNESGetLinearSolveIterations(_snes, &_n_linear_iterations);
  LIBMESH_CHKERR(ierr);
 
  // SNESGetFunction has been around forever and should work on all
  // versions of PETSc.  This is also now the recommended approach
  // according to the documentation for the PETSc 3.5.1 release:
  // http://www.mcs.anl.gov/petsc/documentation/changes/35.html
  Vec f;
  ierr = SNESGetFunction(_snes, &f, 0, 0);
  LIBMESH_CHKERR(ierr);
  ierr = VecNorm(f, NORM_2, pPR(&final_residual_norm));
  LIBMESH_CHKERR(ierr);
 
  // Get and store the reason for convergence
  SNESGetConvergedReason(_snes, &_reason);
 
  //Based on Petsc 2.3.3 documentation all diverged reasons are negative
  this->converged = (_reason >= 0);
 
  this->clear();
 
  // return the # of its. and the final residual norm.
  return std::make_pair(n_iterations, final_residual_norm);
}

system() [1/2]

template<typename T>

sys_type& libMesh::NonlinearSolver< T >::system ( )

inlineinherited

Returns

A writable reference to the system we are solving.

Definition at line 284 of file nonlinear_solver.h.

{ return _system; }

system() [2/2]

template<typename T>

const sys_type& libMesh::NonlinearSolver< T >::system ( ) const

inlineinherited

Returns

A constant reference to the system we are solving.

Definition at line 279 of file nonlinear_solver.h.

{ return _system; }

Referenced by libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), libMesh::libmesh_petsc_snes_jacobian(), libMesh::libmesh_petsc_snes_postcheck(), and libMesh::libmesh_petsc_snes_residual_helper().

use_default_monitor()

template<typename T>

void libMesh::PetscNonlinearSolver< T >::use_default_monitor ( bool  state )

inline

Set to true to use the libMesh's default monitor, set to false to use your own.

Definition at line 186 of file petsc_nonlinear_solver.h.

{ _default_monitor = state; }

Friends And Related Function Documentation

libmesh_petsc_snes_fd_residual

template<typename T>

PetscErrorCode libmesh_petsc_snes_fd_residual ( SNES  snes, Vec  x, Vec  r, void *  ctx  )

friend

Definition at line 206 of file petsc_nonlinear_solver.C.

  {
    ResidualContext rc = libmesh_petsc_snes_residual_helper(snes, x, ctx);
 
    libmesh_assert(r);
    PetscVector<Number> R(r, rc.sys.comm());
 
    if (rc.solver->_zero_out_residual)
      R.zero();
 
    if (rc.solver->fd_residual_object != nullptr)
      rc.solver->fd_residual_object->residual(*rc.sys.current_local_solution.get(), R, rc.sys);
 
    else if (rc.solver->residual_object != nullptr)
      rc.solver->residual_object->residual(*rc.sys.current_local_solution.get(), R, rc.sys);
 
    else
      libmesh_error_msg("Error! Unable to compute residual for forming finite difference Jacobian!");
 
    R.close();
    PetscVector<Number> X(x, rc.sys.comm());
    rc.sys.get_dof_map().enforce_constraints_on_residual(rc.sys, &R, &X);
 
    R.close();
 
    return rc.ierr;
  }

libmesh_petsc_snes_jacobian [1/2]

template<typename T>

PetscErrorCode libmesh_petsc_snes_jacobian ( SNES  snes, Vec  x, Mat *  jac, Mat *  pc, MatStructure *  msflag, void *  ctx  )

friend

libmesh_petsc_snes_jacobian [2/2]

template<typename T>

PetscErrorCode libmesh_petsc_snes_jacobian ( SNES  snes, Vec  x, Mat  jac, Mat  pc, void *  ctx  )

friend

libmesh_petsc_snes_mffd_residual

template<typename T>

PetscErrorCode libmesh_petsc_snes_mffd_residual ( SNES  snes, Vec  x, Vec  r, void *  ctx  )

friend

Definition at line 247 of file petsc_nonlinear_solver.C.

  {
    ResidualContext rc = libmesh_petsc_snes_residual_helper(snes, x, ctx);
 
    libmesh_assert(r);
    PetscVector<Number> R(r, rc.sys.comm());
 
    if (rc.solver->_zero_out_residual)
      R.zero();
 
    if (rc.solver->mffd_residual_object != nullptr)
      rc.solver->mffd_residual_object->residual(*rc.sys.current_local_solution.get(), R, rc.sys);
 
    else if (rc.solver->residual_object != nullptr)
      rc.solver->residual_object->residual(*rc.sys.current_local_solution.get(), R, rc.sys);
 
    else
      libmesh_error_msg("Error! Unable to compute residual for forming finite differenced"
                        "Jacobian-vector products!");
 
    R.close();
    PetscVector<Number> X(x, rc.sys.comm());
    rc.sys.get_dof_map().enforce_constraints_on_residual(rc.sys, &R, &X);
 
    R.close();
 
    return rc.ierr;
  }

libmesh_petsc_snes_residual

template<typename T>

PetscErrorCode libmesh_petsc_snes_residual ( SNES  snes, Vec  x, Vec  r, void *  ctx  )

friend

Definition at line 151 of file petsc_nonlinear_solver.C.

  {
    ResidualContext rc = libmesh_petsc_snes_residual_helper(snes, x, ctx);
 
    libmesh_assert(r);
    PetscVector<Number> R(r, rc.sys.comm());
 
    if (rc.solver->_zero_out_residual)
      R.zero();
 
    //-----------------------------------------------------------------------------
    // if the user has provided both function pointers and objects only the pointer
    // will be used, so catch that as an error
    if (rc.solver->residual && rc.solver->residual_object)
      libmesh_error_msg("ERROR: cannot specify both a function and object to compute the Residual!");
 
    if (rc.solver->matvec && rc.solver->residual_and_jacobian_object)
      libmesh_error_msg("ERROR: cannot specify both a function and object to compute the combined Residual & Jacobian!");
 
    if (rc.solver->residual != nullptr)
      rc.solver->residual(*rc.sys.current_local_solution.get(), R, rc.sys);
 
    else if (rc.solver->residual_object != nullptr)
      rc.solver->residual_object->residual(*rc.sys.current_local_solution.get(), R, rc.sys);
 
    else if (rc.solver->matvec != nullptr)
      rc.solver->matvec (*rc.sys.current_local_solution.get(), &R, nullptr, rc.sys);
 
    else if (rc.solver->residual_and_jacobian_object != nullptr)
      rc.solver->residual_and_jacobian_object->residual_and_jacobian (*rc.sys.current_local_solution.get(), &R, nullptr, rc.sys);
 
    else
      libmesh_error_msg("Error! Unable to compute residual and/or Jacobian!");
 
    PetscVector<Number> X(x, rc.sys.comm());
 
    R.close();
    rc.sys.get_dof_map().enforce_constraints_on_residual(rc.sys, &R, &X);
    R.close();
 
    return rc.ierr;
  }

libmesh_petsc_snes_residual_helper

template<typename T>

ResidualContext libmesh_petsc_snes_residual_helper ( SNES  snes, Vec  x, void *  ctx  )

friend

Definition at line 65 of file petsc_nonlinear_solver.C.

{
  LOG_SCOPE("residual()", "PetscNonlinearSolver");
 
  PetscErrorCode ierr = 0;
 
  libmesh_assert(x);
  libmesh_assert(ctx);
 
  // No way to safety-check this cast, since we got a void *...
  PetscNonlinearSolver<Number> * solver =
    static_cast<PetscNonlinearSolver<Number> *> (ctx);
 
  // Get the current iteration number from the snes object,
  // store it in the PetscNonlinearSolver object for possible use
  // by the user's residual function.
  {
    PetscInt n_iterations = 0;
    ierr = SNESGetIterationNumber(snes, &n_iterations);
    CHKERRABORT(solver->comm().get(),ierr);
    solver->_current_nonlinear_iteration_number = cast_int<unsigned>(n_iterations);
  }
 
  NonlinearImplicitSystem & sys = solver->system();
 
  PetscVector<Number> & X_sys = *cast_ptr<PetscVector<Number> *>(sys.solution.get());
 
  PetscVector<Number> X_global(x, sys.comm());
 
  // Use the system's update() to get a good local version of the
  // parallel solution.  This operation does not modify the incoming
  // "x" vector, it only localizes information from "x" into
  // sys.current_local_solution.
  X_global.swap(X_sys);
  sys.update();
  X_global.swap(X_sys);
 
  // Enforce constraints (if any) exactly on the
  // current_local_solution.  This is the solution vector that is
  // actually used in the computation of the residual below, and is
  // not locked by debug-enabled PETSc the way that "x" is.
  sys.get_dof_map().enforce_constraints_exactly(sys, sys.current_local_solution.get());
 
  return ResidualContext(solver, sys, ierr);
}

Member Data Documentation

_communicator

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

protectedinherited

Definition at line 112 of file parallel_object.h.

Referenced by libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::ParallelObject::comm(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::operator=(), and libMesh::ParallelObject::processor_id().

_counts

ReferenceCounter::Counts libMesh::ReferenceCounter::_counts

staticprotectedinherited

Actually holds the data.

Definition at line 122 of file reference_counter.h.

Referenced by libMesh::ReferenceCounter::get_info(), libMesh::ReferenceCounter::increment_constructor_count(), and libMesh::ReferenceCounter::increment_destructor_count().

_current_nonlinear_iteration_number

template<typename T>

unsigned libMesh::PetscNonlinearSolver< T >::_current_nonlinear_iteration_number

protected

Stores the current nonlinear iteration number.

Definition at line 236 of file petsc_nonlinear_solver.h.

Referenced by libMesh::PetscNonlinearSolver< Number >::get_current_nonlinear_iteration_number(), libMesh::libmesh_petsc_snes_jacobian(), and libMesh::libmesh_petsc_snes_residual_helper().

_default_monitor

template<typename T>

bool libMesh::PetscNonlinearSolver< T >::_default_monitor

protected

true if we want the default monitor to be set, false for no monitor (i.e.

user code can use their own)

Definition at line 251 of file petsc_nonlinear_solver.h.

Referenced by libMesh::PetscNonlinearSolver< Number >::use_default_monitor().

_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 141 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::NonlinearSolver< T >::_is_initialized

protectedinherited

Flag indicating if the data structures have been initialized.

Definition at line 374 of file nonlinear_solver.h.

Referenced by libMesh::NonlinearSolver< Number >::initialized().

_mutex

Threads::spin_mutex libMesh::ReferenceCounter::_mutex

staticprotectedinherited

Mutual exclusion object to enable thread-safe reference counting.

Definition at line 135 of file reference_counter.h.

_n_linear_iterations

template<typename T>

PetscInt libMesh::PetscNonlinearSolver< T >::_n_linear_iterations

protected

Stores the total number of linear iterations from the last solve.

Definition at line 231 of file petsc_nonlinear_solver.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 130 of file reference_counter.h.

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

_preconditioner

template<typename T>

Preconditioner<T>* libMesh::NonlinearSolver< T >::_preconditioner

protectedinherited

Holds the Preconditioner object to be used for the linear solves.

Definition at line 379 of file nonlinear_solver.h.

_reason

template<typename T>

SNESConvergedReason libMesh::PetscNonlinearSolver< T >::_reason

protected

Store the reason for SNES convergence/divergence for use even after the _snes has been cleared.

Note

print_converged_reason() will always try to get the current reason with SNESGetConvergedReason(), but if the SNES object has already been cleared, it will fall back on this stored value. This value is therefore necessarily not cleared by the clear() function.

Definition at line 226 of file petsc_nonlinear_solver.h.

_snes

template<typename T>

SNES libMesh::PetscNonlinearSolver< T >::_snes

protected

Nonlinear solver context.

Definition at line 214 of file petsc_nonlinear_solver.h.

Referenced by libMesh::PetscNonlinearSolver< Number >::snes().

_snesmf_reuse_base

template<typename T>

bool libMesh::PetscNonlinearSolver< T >::_snesmf_reuse_base

protected

True, If we want the base vector to be used for differencing even if the function provided to SNESSetFunction() is not the same as that provided to MatMFFDSetFunction().

https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/SNES/MatSNESMFSetReuseBase.html

Definition at line 258 of file petsc_nonlinear_solver.h.

Referenced by libMesh::PetscNonlinearSolver< Number >::set_snesmf_reuse_base().

_solver_configuration

template<typename T>

SolverConfiguration* libMesh::NonlinearSolver< T >::_solver_configuration

protectedinherited

Optionally store a SolverOptions object that can be used to set parameters like solver type, tolerances and iteration limits.

Definition at line 385 of file nonlinear_solver.h.

_system

template<typename T>

sys_type& libMesh::NonlinearSolver< T >::_system

protectedinherited

A reference to the system we are solving.

Definition at line 369 of file nonlinear_solver.h.

Referenced by libMesh::NonlinearSolver< Number >::system().

_zero_out_jacobian

template<typename T>

bool libMesh::PetscNonlinearSolver< T >::_zero_out_jacobian

protected

true to zero out jacobian before going into application level call-back, otherwise false

Definition at line 246 of file petsc_nonlinear_solver.h.

Referenced by libMesh::libmesh_petsc_snes_jacobian(), and libMesh::PetscNonlinearSolver< Number >::set_jacobian_zero_out().

_zero_out_residual

template<typename T>

bool libMesh::PetscNonlinearSolver< T >::_zero_out_residual

protected

true to zero out residual before going into application level call-back, otherwise false

Definition at line 241 of file petsc_nonlinear_solver.h.

Referenced by libMesh::libmesh_petsc_snes_fd_residual(), libMesh::libmesh_petsc_snes_mffd_residual(), libMesh::libmesh_petsc_snes_residual(), and libMesh::PetscNonlinearSolver< Number >::set_residual_zero_out().

absolute_residual_tolerance

template<typename T>

double libMesh::NonlinearSolver< T >::absolute_residual_tolerance

inherited

The NonlinearSolver should exit after the residual is reduced to either less than absolute_residual_tolerance or less than relative_residual_tolerance times the initial residual.

Users should increase any of these tolerances that they want to use for a stopping condition.

Definition at line 311 of file nonlinear_solver.h.

absolute_step_tolerance

template<typename T>

double libMesh::NonlinearSolver< T >::absolute_step_tolerance

inherited

The NonlinearSolver should exit after the full nonlinear step norm is reduced to either less than absolute_step_tolerance or less than relative_step_tolerance times the largest nonlinear solution which has been seen so far.

Users should increase any of these tolerances that they want to use for a stopping condition.

Note

Not all NonlinearSolvers support relative_step_tolerance!

Definition at line 334 of file nonlinear_solver.h.

bounds

template<typename T>

void(* libMesh::NonlinearSolver< T >::bounds) (NumericVector< Number > &XL, NumericVector< Number > &XU, sys_type &S)

inherited

Function that computes the lower and upper bounds XL and XU on the solution of the nonlinear system.

Definition at line 198 of file nonlinear_solver.h.

bounds_object

template<typename T>

NonlinearImplicitSystem::ComputeBounds* libMesh::NonlinearSolver< T >::bounds_object

inherited

Object that computes the bounds vectors \( XL \) and \( XU \).

Definition at line 204 of file nonlinear_solver.h.

converged

template<typename T>

bool libMesh::NonlinearSolver< T >::converged

inherited

After a call to solve this will reflect whether or not the nonlinear solve was successful.

Definition at line 358 of file nonlinear_solver.h.

divergence_tolerance

template<typename T>

double libMesh::NonlinearSolver< T >::divergence_tolerance

inherited

The NonlinearSolver should exit if the residual becomes greater than the initial residual times the divergence_tolerance.

Users should adjust this tolerances to prevent divergence of the NonlinearSolver.

Definition at line 321 of file nonlinear_solver.h.

fd_residual_object

template<typename T>

NonlinearImplicitSystem::ComputeResidual* libMesh::NonlinearSolver< T >::fd_residual_object

inherited

Object that computes the residual R(X) of the nonlinear system at the input iterate X for the purpose of forming a finite-differenced Jacobian.

Definition at line 151 of file nonlinear_solver.h.

Referenced by libMesh::libmesh_petsc_snes_fd_residual().

initial_linear_tolerance

template<typename T>

double libMesh::NonlinearSolver< T >::initial_linear_tolerance

inherited

Any required linear solves will at first be done with this tolerance; the NonlinearSolver may tighten the tolerance for later solves.

Definition at line 347 of file nonlinear_solver.h.

jacobian

template<typename T>

void(* libMesh::NonlinearSolver< T >::jacobian) (const NumericVector< Number > &X, SparseMatrix< Number > &J, sys_type &S)

inherited

Function that computes the Jacobian J(X) of the nonlinear system at the input iterate X.

Definition at line 164 of file nonlinear_solver.h.

Referenced by libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), and libMesh::libmesh_petsc_snes_jacobian().

jacobian_object

template<typename T>

NonlinearImplicitSystem::ComputeJacobian* libMesh::NonlinearSolver< T >::jacobian_object

inherited

Object that computes the Jacobian J(X) of the nonlinear system at the input iterate X.

Definition at line 172 of file nonlinear_solver.h.

Referenced by libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), and libMesh::libmesh_petsc_snes_jacobian().

linesearch_object

template<typename T>

std::unique_ptr<ComputeLineSearchObject> libMesh::PetscNonlinearSolver< T >::linesearch_object

A callable object that can be used to specify a custom line-search.

Definition at line 207 of file petsc_nonlinear_solver.h.

Referenced by libMesh::libmesh_petsc_linesearch_shellfunc().

matvec

template<typename T>

void(* libMesh::NonlinearSolver< T >::matvec) (const NumericVector< Number > &X, NumericVector< Number > *R, SparseMatrix< Number > *J, sys_type &S)

inherited

Function that computes either the residual \( R(X) \) or the Jacobian \( J(X) \) of the nonlinear system at the input iterate \( X \).

Note

Either R or J could be nullptr.

Definition at line 181 of file nonlinear_solver.h.

Referenced by libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), libMesh::libmesh_petsc_snes_jacobian(), and libMesh::libmesh_petsc_snes_residual().

max_function_evaluations

template<typename T>

unsigned int libMesh::NonlinearSolver< T >::max_function_evaluations

inherited

Maximum number of function evaluations.

Definition at line 299 of file nonlinear_solver.h.

max_linear_iterations

template<typename T>

unsigned int libMesh::NonlinearSolver< T >::max_linear_iterations

inherited

Each linear solver step should exit after max_linear_iterations is exceeded.

Definition at line 341 of file nonlinear_solver.h.

max_nonlinear_iterations

template<typename T>

unsigned int libMesh::NonlinearSolver< T >::max_nonlinear_iterations

inherited

Maximum number of non-linear iterations.

Definition at line 294 of file nonlinear_solver.h.

mffd_residual_object

template<typename T>

NonlinearImplicitSystem::ComputeResidual* libMesh::NonlinearSolver< T >::mffd_residual_object

inherited

Object that computes the residual R(X) of the nonlinear system at the input iterate X for the purpose of forming Jacobian-vector products via finite differencing.

Definition at line 158 of file nonlinear_solver.h.

Referenced by libMesh::libmesh_petsc_snes_mffd_residual().

minimum_linear_tolerance

template<typename T>

double libMesh::NonlinearSolver< T >::minimum_linear_tolerance

inherited

The tolerance for linear solves is kept above this minimum.

Definition at line 352 of file nonlinear_solver.h.

nearnullspace

template<typename T>

void(* libMesh::NonlinearSolver< T >::nearnullspace) (std::vector< NumericVector< Number > * > &sp, sys_type &S)

inherited

Function that computes a basis for the Jacobian's near nullspace – the set of "low energy modes" – that can be used for AMG coarsening, if the solver supports it (e.g., ML, PETSc's GAMG).

Definition at line 241 of file nonlinear_solver.h.

nearnullspace_object

template<typename T>

NonlinearImplicitSystem::ComputeVectorSubspace* libMesh::NonlinearSolver< T >::nearnullspace_object

inherited

A callable object that computes a basis for the Jacobian's near nullspace – the set of "low energy modes" – that can be used for AMG coarsening, if the solver supports it (e.g., ML, PETSc's GAMG).

Definition at line 248 of file nonlinear_solver.h.

nullspace

template<typename T>

void(* libMesh::NonlinearSolver< T >::nullspace) (std::vector< NumericVector< Number > * > &sp, sys_type &S)

inherited

Function that computes a basis for the Jacobian's nullspace – the kernel or the "zero energy modes" – that can be used in solving a degenerate problem iteratively, if the solver supports it (e.g., PETSc's KSP).

Definition at line 212 of file nonlinear_solver.h.

nullspace_object

template<typename T>

NonlinearImplicitSystem::ComputeVectorSubspace* libMesh::NonlinearSolver< T >::nullspace_object

inherited

A callable object that computes a basis for the Jacobian's nullspace – the kernel or the "zero energy modes" – that can be used in solving a degenerate problem iteratively, if the solver supports it (e.g., PETSc's KSP).

Definition at line 220 of file nonlinear_solver.h.

postcheck

template<typename T>

void(* libMesh::NonlinearSolver< T >::postcheck) (const NumericVector< Number > &old_soln, NumericVector< Number > &search_direction, NumericVector< Number > &new_soln, bool &changed_search_direction, bool &changed_new_soln, sys_type &S)

inherited

Function that performs a "check" on the Newton search direction and solution after each nonlinear step.

See documentation for the NonlinearImplicitSystem::ComputePostCheck object for more information about the calling sequence.

Definition at line 262 of file nonlinear_solver.h.

Referenced by libMesh::libmesh_petsc_snes_postcheck().

postcheck_object

template<typename T>

NonlinearImplicitSystem::ComputePostCheck* libMesh::NonlinearSolver< T >::postcheck_object

inherited

A callable object that is executed after each nonlinear iteration.

Allows the user to modify both the search direction and the solution vector in an application-specific way.

Definition at line 274 of file nonlinear_solver.h.

Referenced by libMesh::libmesh_petsc_snes_postcheck().

relative_residual_tolerance

template<typename T>

double libMesh::NonlinearSolver< T >::relative_residual_tolerance

inherited

Definition at line 312 of file nonlinear_solver.h.

relative_step_tolerance

template<typename T>

double libMesh::NonlinearSolver< T >::relative_step_tolerance

inherited

Definition at line 335 of file nonlinear_solver.h.

residual

template<typename T>

void(* libMesh::NonlinearSolver< T >::residual) (const NumericVector< Number > &X, NumericVector< Number > &R, sys_type &S)

inherited

Function that computes the residual R(X) of the nonlinear system at the input iterate X.

Definition at line 137 of file nonlinear_solver.h.

Referenced by libMesh::Problem_Interface::computeF(), and libMesh::libmesh_petsc_snes_residual().

residual_and_jacobian_object

template<typename T>

NonlinearImplicitSystem::ComputeResidualandJacobian* libMesh::NonlinearSolver< T >::residual_and_jacobian_object

inherited

Object that computes either the residual \( R(X) \) or the Jacobian \( J(X) \) of the nonlinear system at the input iterate \( X \).

Note

Either R or J could be nullptr.

Definition at line 193 of file nonlinear_solver.h.

Referenced by libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), libMesh::libmesh_petsc_snes_jacobian(), and libMesh::libmesh_petsc_snes_residual().

residual_object

template<typename T>

NonlinearImplicitSystem::ComputeResidual* libMesh::NonlinearSolver< T >::residual_object

inherited

Object that computes the residual R(X) of the nonlinear system at the input iterate X.

Definition at line 145 of file nonlinear_solver.h.

Referenced by libMesh::Problem_Interface::computeF(), libMesh::libmesh_petsc_snes_fd_residual(), libMesh::libmesh_petsc_snes_mffd_residual(), and libMesh::libmesh_petsc_snes_residual().

transpose_nullspace

template<typename T>

void(* libMesh::NonlinearSolver< T >::transpose_nullspace) (std::vector< NumericVector< Number > * > &sp, sys_type &S)

inherited

Function that computes a basis for the transpose Jacobian's nullspace – when solving a degenerate problem iteratively, if the solver supports it (e.g., PETSc's KSP), it is used to remove contributions outside of R(jac)

Definition at line 227 of file nonlinear_solver.h.

transpose_nullspace_object

template<typename T>

NonlinearImplicitSystem::ComputeVectorSubspace* libMesh::NonlinearSolver< T >::transpose_nullspace_object

inherited

A callable object that computes a basis for the transpose Jacobian's nullspace – when solving a degenerate problem iteratively, if the solver supports it (e.g., PETSc's KSP), it is used to remove contributions outside of R(jac)

Definition at line 234 of file nonlinear_solver.h.

user_presolve

template<typename T>

void(* libMesh::NonlinearSolver< T >::user_presolve) (sys_type &S)

inherited

Customizable function pointer which users can attach to the solver.

Gets called prior to every call to solve().

Definition at line 254 of file nonlinear_solver.h.

---

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

• include/solvers/petsc_nonlinear_solver.h
• src/solvers/petsc_nonlinear_solver.C