libMesh::ContinuationSystem Class Reference

#include <continuation_system.h>

Inheritance diagram for libMesh::ContinuationSystem:

Public Types

enum  Predictor { Euler, AB2, Invalid_Predictor }
 
typedef ContinuationSystem sys_type
 
typedef FEMSystem Parent
 
typedef bool(TimeSolver::* TimeSolverResPtr) (bool, DiffContext &)
 
typedef std::map< std::string, SparseMatrix< Number > * >::iterator matrices_iterator
 
typedef std::map< std::string, SparseMatrix< Number > * >::const_iterator const_matrices_iterator
 
typedef std::map< std::string, NumericVector< Number > * >::iterator vectors_iterator
 
typedef std::map< std::string, NumericVector< Number > * >::const_iterator const_vectors_iterator
 

Public Member Functions

 ContinuationSystem (EquationSystems &es, const std::string &name, const unsigned int number)
 
virtual ~ContinuationSystem ()
 
virtual void clear () libmesh_override
 
virtual void solve () libmesh_override
 
void continuation_solve ()
 
void advance_arcstep ()
 
void set_max_arclength_stepsize (Real maxds)
 
void save_current_solution ()
 
virtual void assembly (bool get_residual, bool get_jacobian, bool apply_heterogeneous_constraints=false, bool apply_no_constraints=false) libmesh_override
 
void mesh_position_get ()
 
void mesh_position_set ()
 
virtual UniquePtr< DiffContextbuild_context () libmesh_override
 
virtual void init_context (DiffContext &) libmesh_override
 
virtual void postprocess () libmesh_override
 
virtual void assemble_qoi (const QoISet &indices=QoISet()) libmesh_override
 
virtual void assemble_qoi_derivative (const QoISet &qoi_indices=QoISet(), bool include_liftfunc=true, bool apply_constraints=true) libmesh_override
 
Real numerical_jacobian_h_for_var (unsigned int var_num) const
 
void set_numerical_jacobian_h_for_var (unsigned int var_num, Real new_h)
 
void numerical_jacobian (TimeSolverResPtr res, FEMContext &context) const
 
void numerical_elem_jacobian (FEMContext &context) const
 
void numerical_side_jacobian (FEMContext &context) const
 
void numerical_nonlocal_jacobian (FEMContext &context) const
 
virtual void reinit () libmesh_override
 
virtual void assemble () libmesh_override
 
virtual LinearSolver< Number > * get_linear_solver () const libmesh_override
 
virtual std::pair< unsigned int, Realget_linear_solve_parameters () const libmesh_override
 
virtual void release_linear_solver (LinearSolver< Number > *) const libmesh_override
 
virtual std::pair< unsigned int, Realadjoint_solve (const QoISet &qoi_indices=QoISet()) libmesh_override
 
virtual UniquePtr< DifferentiablePhysicsclone_physics () libmesh_override
 
virtual UniquePtr< DifferentiableQoIclone () libmesh_override
 
const DifferentiablePhysicsget_physics () const
 
DifferentiablePhysicsget_physics ()
 
void attach_physics (DifferentiablePhysics *physics_in)
 
void swap_physics (DifferentiablePhysics *&swap_physics)
 
const DifferentiableQoIget_qoi () const
 
DifferentiableQoIget_qoi ()
 
void attach_qoi (DifferentiableQoI *qoi_in)
 
void set_time_solver (UniquePtr< TimeSolver > _time_solver)
 
TimeSolverget_time_solver ()
 
const TimeSolverget_time_solver () const
 
virtual void element_postprocess (DiffContext &)
 
virtual void side_postprocess (DiffContext &)
 
unsigned int get_second_order_dot_var (unsigned int var) const
 
bool have_first_order_scalar_vars () const
 
bool have_second_order_scalar_vars () const
 
sys_typesystem ()
 
virtual void disable_cache () libmesh_override
 
virtual std::string system_type () const libmesh_override
 
virtual void assemble_residual_derivatives (const ParameterVector &parameters) libmesh_override
 
virtual std::pair< unsigned int, Realsensitivity_solve (const ParameterVector &parameters) libmesh_override
 
virtual std::pair< unsigned int, Realweighted_sensitivity_solve (const ParameterVector &parameters, const ParameterVector &weights) libmesh_override
 
virtual std::pair< unsigned int, Realweighted_sensitivity_adjoint_solve (const ParameterVector &parameters, const ParameterVector &weights, const QoISet &qoi_indices=QoISet()) libmesh_override
 
virtual void adjoint_qoi_parameter_sensitivity (const QoISet &qoi_indices, const ParameterVector &parameters, SensitivityData &sensitivities) libmesh_override
 
virtual void forward_qoi_parameter_sensitivity (const QoISet &qoi_indices, const ParameterVector &parameters, SensitivityData &sensitivities) libmesh_override
 
virtual void qoi_parameter_hessian (const QoISet &qoi_indices, const ParameterVector &parameters, SensitivityData &hessian) libmesh_override
 
virtual void qoi_parameter_hessian_vector_product (const QoISet &qoi_indices, const ParameterVector &parameters, const ParameterVector &vector, SensitivityData &product) libmesh_override
 
SparseMatrix< Number > & add_matrix (const std::string &mat_name)
 
void remove_matrix (const std::string &mat_name)
 
bool have_matrix (const std::string &mat_name) const
 
const SparseMatrix< Number > * request_matrix (const std::string &mat_name) const
 
SparseMatrix< Number > * request_matrix (const std::string &mat_name)
 
const SparseMatrix< Number > & get_matrix (const std::string &mat_name) const
 
SparseMatrix< Number > & get_matrix (const std::string &mat_name)
 
virtual unsigned int n_matrices () const libmesh_override
 
void init ()
 
virtual void reinit_constraints ()
 
bool is_initialized ()
 
virtual void update ()
 
virtual void restrict_solve_to (const SystemSubset *subset, const SubsetSolveMode subset_solve_mode=SUBSET_ZERO)
 
bool is_adjoint_already_solved () const
 
void set_adjoint_already_solved (bool setting)
 
virtual void qoi_parameter_sensitivity (const QoISet &qoi_indices, const ParameterVector &parameters, SensitivityData &sensitivities)
 
virtual bool compare (const System &other_system, const Real threshold, const bool verbose) const
 
const std::string & name () const
 
void project_solution (FunctionBase< Number > *f, FunctionBase< Gradient > *g=libmesh_nullptr) const
 
void project_solution (FEMFunctionBase< Number > *f, FEMFunctionBase< Gradient > *g=libmesh_nullptr) const
 
void project_solution (Number fptr(const Point &p, const Parameters &parameters, const std::string &sys_name, const std::string &unknown_name), Gradient gptr(const Point &p, const Parameters &parameters, const std::string &sys_name, const std::string &unknown_name), const Parameters &parameters) const
 
void project_vector (NumericVector< Number > &new_vector, FunctionBase< Number > *f, FunctionBase< Gradient > *g=libmesh_nullptr, int is_adjoint=-1) const
 
void project_vector (NumericVector< Number > &new_vector, FEMFunctionBase< Number > *f, FEMFunctionBase< Gradient > *g=libmesh_nullptr, int is_adjoint=-1) const
 
void project_vector (Number fptr(const Point &p, const Parameters &parameters, const std::string &sys_name, const std::string &unknown_name), Gradient gptr(const Point &p, const Parameters &parameters, const std::string &sys_name, const std::string &unknown_name), const Parameters &parameters, NumericVector< Number > &new_vector, int is_adjoint=-1) const
 
void boundary_project_solution (const std::set< boundary_id_type > &b, const std::vector< unsigned int > &variables, FunctionBase< Number > *f, FunctionBase< Gradient > *g=libmesh_nullptr)
 
void boundary_project_solution (const std::set< boundary_id_type > &b, const std::vector< unsigned int > &variables, Number fptr(const Point &p, const Parameters &parameters, const std::string &sys_name, const std::string &unknown_name), Gradient gptr(const Point &p, const Parameters &parameters, const std::string &sys_name, const std::string &unknown_name), const Parameters &parameters)
 
void boundary_project_vector (const std::set< boundary_id_type > &b, const std::vector< unsigned int > &variables, NumericVector< Number > &new_vector, FunctionBase< Number > *f, FunctionBase< Gradient > *g=libmesh_nullptr, int is_adjoint=-1) const
 
void boundary_project_vector (const std::set< boundary_id_type > &b, const std::vector< unsigned int > &variables, Number fptr(const Point &p, const Parameters &parameters, const std::string &sys_name, const std::string &unknown_name), Gradient gptr(const Point &p, const Parameters &parameters, const std::string &sys_name, const std::string &unknown_name), const Parameters &parameters, NumericVector< Number > &new_vector, int is_adjoint=-1) const
 
unsigned int number () const
 
void update_global_solution (std::vector< Number > &global_soln) const
 
void update_global_solution (std::vector< Number > &global_soln, const processor_id_type dest_proc) const
 
const MeshBaseget_mesh () const
 
MeshBaseget_mesh ()
 
const DofMapget_dof_map () const
 
DofMapget_dof_map ()
 
const EquationSystemsget_equation_systems () const
 
EquationSystemsget_equation_systems ()
 
bool active () const
 
void activate ()
 
void deactivate ()
 
void set_basic_system_only ()
 
vectors_iterator vectors_begin ()
 
const_vectors_iterator vectors_begin () const
 
vectors_iterator vectors_end ()
 
const_vectors_iterator vectors_end () const
 
NumericVector< Number > & add_vector (const std::string &vec_name, const bool projections=true, const ParallelType type=PARALLEL)
 
void remove_vector (const std::string &vec_name)
 
bool & project_solution_on_reinit (void)
 
bool have_vector (const std::string &vec_name) const
 
const NumericVector< Number > * request_vector (const std::string &vec_name) const
 
NumericVector< Number > * request_vector (const std::string &vec_name)
 
const NumericVector< Number > * request_vector (const unsigned int vec_num) const
 
NumericVector< Number > * request_vector (const unsigned int vec_num)
 
const NumericVector< Number > & get_vector (const std::string &vec_name) const
 
NumericVector< Number > & get_vector (const std::string &vec_name)
 
const NumericVector< Number > & get_vector (const unsigned int vec_num) const
 
NumericVector< Number > & get_vector (const unsigned int vec_num)
 
const std::string & vector_name (const unsigned int vec_num) const
 
const std::string & vector_name (const NumericVector< Number > &vec_reference) const
 
void set_vector_as_adjoint (const std::string &vec_name, int qoi_num)
 
int vector_is_adjoint (const std::string &vec_name) const
 
void set_vector_preservation (const std::string &vec_name, bool preserve)
 
bool vector_preservation (const std::string &vec_name) const
 
NumericVector< Number > & add_adjoint_solution (unsigned int i=0)
 
NumericVector< Number > & get_adjoint_solution (unsigned int i=0)
 
const NumericVector< Number > & get_adjoint_solution (unsigned int i=0) const
 
NumericVector< Number > & add_sensitivity_solution (unsigned int i=0)
 
NumericVector< Number > & get_sensitivity_solution (unsigned int i=0)
 
const NumericVector< Number > & get_sensitivity_solution (unsigned int i=0) const
 
NumericVector< Number > & add_weighted_sensitivity_adjoint_solution (unsigned int i=0)
 
NumericVector< Number > & get_weighted_sensitivity_adjoint_solution (unsigned int i=0)
 
const NumericVector< Number > & get_weighted_sensitivity_adjoint_solution (unsigned int i=0) const
 
NumericVector< Number > & add_weighted_sensitivity_solution ()
 
NumericVector< Number > & get_weighted_sensitivity_solution ()
 
const NumericVector< Number > & get_weighted_sensitivity_solution () const
 
NumericVector< Number > & add_adjoint_rhs (unsigned int i=0)
 
NumericVector< Number > & get_adjoint_rhs (unsigned int i=0)
 
const NumericVector< Number > & get_adjoint_rhs (unsigned int i=0) const
 
NumericVector< Number > & add_sensitivity_rhs (unsigned int i=0)
 
NumericVector< Number > & get_sensitivity_rhs (unsigned int i=0)
 
const NumericVector< Number > & get_sensitivity_rhs (unsigned int i=0) const
 
unsigned int n_vectors () const
 
unsigned int n_vars () const
 
unsigned int n_variable_groups () const
 
unsigned int n_components () const
 
dof_id_type n_dofs () const
 
dof_id_type n_active_dofs () const
 
dof_id_type n_constrained_dofs () const
 
dof_id_type n_local_constrained_dofs () const
 
dof_id_type n_local_dofs () const
 
unsigned int add_variable (const std::string &var, const FEType &type, const std::set< subdomain_id_type > *const active_subdomains=libmesh_nullptr)
 
unsigned int add_variable (const std::string &var, const Order order=FIRST, const FEFamily=LAGRANGE, const std::set< subdomain_id_type > *const active_subdomains=libmesh_nullptr)
 
unsigned int add_variables (const std::vector< std::string > &vars, const FEType &type, const std::set< subdomain_id_type > *const active_subdomains=libmesh_nullptr)
 
unsigned int add_variables (const std::vector< std::string > &vars, const Order order=FIRST, const FEFamily=LAGRANGE, const std::set< subdomain_id_type > *const active_subdomains=libmesh_nullptr)
 
const Variablevariable (unsigned int var) const
 
const VariableGroupvariable_group (unsigned int vg) const
 
bool has_variable (const std::string &var) const
 
const std::string & variable_name (const unsigned int i) const
 
unsigned short int variable_number (const std::string &var) const
 
void get_all_variable_numbers (std::vector< unsigned int > &all_variable_numbers) const
 
unsigned int variable_scalar_number (const std::string &var, unsigned int component) const
 
unsigned int variable_scalar_number (unsigned int var_num, unsigned int component) const
 
const FETypevariable_type (const unsigned int i) const
 
const FETypevariable_type (const std::string &var) const
 
bool identify_variable_groups () const
 
void identify_variable_groups (const bool)
 
Real calculate_norm (const NumericVector< Number > &v, unsigned int var, FEMNormType norm_type, std::set< unsigned int > *skip_dimensions=libmesh_nullptr) const
 
Real calculate_norm (const NumericVector< Number > &v, const SystemNorm &norm, std::set< unsigned int > *skip_dimensions=libmesh_nullptr) const
 
void read_header (Xdr &io, const std::string &version, const bool read_header=true, const bool read_additional_data=true, const bool read_legacy_format=false)
 
void read_legacy_data (Xdr &io, const bool read_additional_data=true)
 
template<typename ValType >
void read_serialized_data (Xdr &io, const bool read_additional_data=true)
 
void read_serialized_data (Xdr &io, const bool read_additional_data=true)
 
template<typename InValType >
std::size_t read_serialized_vectors (Xdr &io, const std::vector< NumericVector< Number > * > &vectors) const
 
std::size_t read_serialized_vectors (Xdr &io, const std::vector< NumericVector< Number > * > &vectors) const
 
template<typename InValType >
void read_parallel_data (Xdr &io, const bool read_additional_data)
 
void read_parallel_data (Xdr &io, const bool read_additional_data)
 
void write_header (Xdr &io, const std::string &version, const bool write_additional_data) const
 
void write_serialized_data (Xdr &io, const bool write_additional_data=true) const
 
std::size_t write_serialized_vectors (Xdr &io, const std::vector< const NumericVector< Number > * > &vectors) const
 
void write_parallel_data (Xdr &io, const bool write_additional_data) const
 
std::string get_info () const
 
void attach_init_function (void fptr(EquationSystems &es, const std::string &name))
 
void attach_init_object (Initialization &init)
 
void attach_assemble_function (void fptr(EquationSystems &es, const std::string &name))
 
void attach_assemble_object (Assembly &assemble)
 
void attach_constraint_function (void fptr(EquationSystems &es, const std::string &name))
 
void attach_constraint_object (Constraint &constrain)
 
void attach_QOI_function (void fptr(EquationSystems &es, const std::string &name, const QoISet &qoi_indices))
 
void attach_QOI_object (QOI &qoi)
 
void attach_QOI_derivative (void fptr(EquationSystems &es, const std::string &name, const QoISet &qoi_indices, bool include_liftfunc, bool apply_constraints))
 
void attach_QOI_derivative_object (QOIDerivative &qoi_derivative)
 
virtual void user_initialization ()
 
virtual void user_assembly ()
 
virtual void user_constrain ()
 
virtual void user_QOI (const QoISet &qoi_indices)
 
virtual void user_QOI_derivative (const QoISet &qoi_indices=QoISet(), bool include_liftfunc=true, bool apply_constraints=true)
 
virtual void re_update ()
 
virtual void restrict_vectors ()
 
virtual void prolong_vectors ()
 
Number current_solution (const dof_id_type global_dof_number) const
 
Number point_value (unsigned int var, const Point &p, const bool insist_on_success=true) const
 
Number point_value (unsigned int var, const Point &p, const Elem &e) const
 
Number point_value (unsigned int var, const Point &p, const Elem *e) const
 
Gradient point_gradient (unsigned int var, const Point &p, const bool insist_on_success=true) const
 
Gradient point_gradient (unsigned int var, const Point &p, const Elem &e) const
 
Gradient point_gradient (unsigned int var, const Point &p, const Elem *e) const
 
Tensor point_hessian (unsigned int var, const Point &p, const bool insist_on_success=true) const
 
Tensor point_hessian (unsigned int var, const Point &p, const Elem &e) const
 
Tensor point_hessian (unsigned int var, const Point &p, const Elem *e) const
 
void local_dof_indices (const unsigned int var, std::set< dof_id_type > &var_indices) const
 
void zero_variable (NumericVector< Number > &v, unsigned int var_num) const
 
bool & hide_output ()
 
const Parallel::Communicatorcomm () const
 
processor_id_type n_processors () const
 
processor_id_type processor_id () const
 
virtual void clear_physics ()
 
virtual void init_physics (const System &sys)
 
virtual bool element_time_derivative (bool request_jacobian, DiffContext &)
 
virtual bool element_constraint (bool request_jacobian, DiffContext &)
 
virtual bool side_time_derivative (bool request_jacobian, DiffContext &)
 
virtual bool side_constraint (bool request_jacobian, DiffContext &)
 
virtual bool nonlocal_time_derivative (bool request_jacobian, DiffContext &)
 
virtual bool nonlocal_constraint (bool request_jacobian, DiffContext &)
 
virtual void time_evolving (unsigned int var)
 
virtual void time_evolving (unsigned int var, unsigned int order)
 
bool is_time_evolving (unsigned int var) const
 
virtual bool eulerian_residual (bool request_jacobian, DiffContext &)
 
virtual bool eulerian_residual (bool request_jacobian, DiffContext &context) libmesh_override
 
virtual bool mass_residual (bool request_jacobian, DiffContext &)
 
virtual bool mass_residual (bool request_jacobian, DiffContext &) libmesh_override
 
virtual bool side_mass_residual (bool request_jacobian, DiffContext &)
 
virtual bool nonlocal_mass_residual (bool request_jacobian, DiffContext &c)
 
virtual bool damping_residual (bool request_jacobian, DiffContext &)
 
virtual bool side_damping_residual (bool request_jacobian, DiffContext &)
 
virtual bool nonlocal_damping_residual (bool request_jacobian, DiffContext &)
 
virtual void set_mesh_system (System *sys)
 
const Systemget_mesh_system () const
 
Systemget_mesh_system ()
 
virtual void set_mesh_x_var (unsigned int var)
 
unsigned int get_mesh_x_var () const
 
virtual void set_mesh_y_var (unsigned int var)
 
unsigned int get_mesh_y_var () const
 
virtual void set_mesh_z_var (unsigned int var)
 
unsigned int get_mesh_z_var () const
 
bool _eulerian_time_deriv (bool request_jacobian, DiffContext &)
 
bool have_first_order_vars () const
 
const std::set< unsigned int > & get_first_order_vars () const
 
bool is_first_order_var (unsigned int var) const
 
bool have_second_order_vars () const
 
const std::set< unsigned int > & get_second_order_vars () const
 
bool is_second_order_var (unsigned int var) const
 
virtual void init_qoi (std::vector< Number > &)
 
virtual void clear_qoi ()
 
virtual void element_qoi (DiffContext &, const QoISet &)
 
virtual void element_qoi_derivative (DiffContext &, const QoISet &)
 
virtual void side_qoi (DiffContext &, const QoISet &)
 
virtual void side_qoi_derivative (DiffContext &, const QoISet &)
 
virtual void thread_join (std::vector< Number > &qoi, const std::vector< Number > &other_qoi, const QoISet &qoi_indices)
 
virtual void parallel_op (const Parallel::Communicator &communicator, std::vector< Number > &sys_qoi, std::vector< Number > &local_qoi, const QoISet &qoi_indices)
 

Static Public Member Functions

static std::string get_info ()
 
static void print_info (std::ostream &out=libMesh::out)
 
static unsigned int n_objects ()
 
static void enable_print_counter_info ()
 
static void disable_print_counter_info ()
 

Public Attributes

Realcontinuation_parameter
 
bool quiet
 
Real continuation_parameter_tolerance
 
Real solution_tolerance
 
Real initial_newton_tolerance
 
Real old_continuation_parameter
 
Real min_continuation_parameter
 
Real max_continuation_parameter
 
Real Theta
 
Real Theta_LOCA
 
unsigned int n_backtrack_steps
 
unsigned int n_arclength_reductions
 
Real ds_min
 
Predictor predictor
 
Real newton_stepgrowth_aggressiveness
 
bool newton_progress_check
 
bool fe_reinit_during_postprocess
 
Real numerical_jacobian_h
 
Real verify_analytic_jacobians
 
UniquePtr< TimeSolvertime_solver
 
Real deltat
 
bool postprocess_sides
 
bool print_solution_norms
 
bool print_solutions
 
bool print_residual_norms
 
bool print_residuals
 
bool print_jacobian_norms
 
bool print_jacobians
 
bool print_element_solutions
 
bool print_element_residuals
 
bool print_element_jacobians
 
SparseMatrix< Number > * matrix
 
bool zero_out_matrix_and_rhs
 
NumericVector< Number > * rhs
 
bool assemble_before_solve
 
bool use_fixed_solution
 
int extra_quadrature_order
 
UniquePtr< NumericVector< Number > > solution
 
UniquePtr< NumericVector< Number > > current_local_solution
 
Real time
 
std::vector< Numberqoi
 
bool compute_internal_sides
 
bool assemble_qoi_sides
 
bool assemble_qoi_internal_sides
 
bool assemble_qoi_elements
 

Protected Types

enum  RHS_Mode { Residual, G_Lambda }
 
typedef std::map< std::string, std::pair< unsigned int, unsigned int > > Counts
 

Protected Member Functions

virtual void init_data () libmesh_override
 
void add_second_order_dot_vars ()
 
void add_dot_var_dirichlet_bcs (unsigned int var_idx, unsigned int dot_var_idx)
 
virtual void init_matrices ()
 
void project_vector (NumericVector< Number > &, int is_adjoint=-1) const
 
void project_vector (const NumericVector< Number > &, NumericVector< Number > &, int is_adjoint=-1) const
 
void increment_constructor_count (const std::string &name)
 
void increment_destructor_count (const std::string &name)
 

Protected Attributes

RHS_Mode rhs_mode
 
DifferentiablePhysics_diff_physics
 
DifferentiableQoIdiff_qoi
 
const Parallel::Communicator_communicator
 
System_mesh_sys
 
unsigned int _mesh_x_var
 
unsigned int _mesh_y_var
 
unsigned int _mesh_z_var
 
std::vector< unsigned int > _time_evolving
 
std::set< unsigned int > _first_order_vars
 
std::set< unsigned int > _second_order_vars
 
std::map< unsigned int, unsigned int > _second_order_dot_vars
 

Static Protected Attributes

static Counts _counts
 
static Threads::atomic< unsigned int > _n_objects
 
static Threads::spin_mutex _mutex
 
static bool _enable_print_counter = true
 

Private Member Functions

void initialize_tangent ()
 
void solve_tangent ()
 
void update_solution ()
 
void set_Theta ()
 
void set_Theta_LOCA ()
 
void apply_predictor ()
 

Private Attributes

NumericVector< Number > * du_ds
 
NumericVector< Number > * previous_du_ds
 
NumericVector< Number > * previous_u
 
NumericVector< Number > * y
 
NumericVector< Number > * y_old
 
NumericVector< Number > * z
 
NumericVector< Number > * delta_u
 
UniquePtr< LinearSolver< Number > > linear_solver
 
bool tangent_initialized
 
NewtonSolvernewton_solver
 
Real dlambda_ds
 
Real ds
 
Real ds_current
 
Real previous_dlambda_ds
 
Real previous_ds
 
unsigned int newton_step
 

Detailed Description

This class inherits from the FEMSystem. It can be used to do arclength continuation. Most of the ideas and the notation here come from HB Keller's 1977 paper:

* @InProceedings{Kell-1977,
*   author    = {H.~B.~Keller},
*   title     = {{Numerical solution of bifurcation and nonlinear eigenvalue problems}},
*   booktitle = {Applications of Bifurcation Theory, P.~H.~Rabinowitz (ed.)},
*   year      = 1977,
*   publisher = {Academic Press},
*   pages     = {359--389},
*   notes     = {QA 3 U45 No.\ 38 (PMA)}
* }
* 
Author
John W. Peterson
Date
2007

Definition at line 55 of file continuation_system.h.

Member Typedef Documentation

typedef std::map<std::string, SparseMatrix<Number> *>::const_iterator libMesh::ImplicitSystem::const_matrices_iterator
inherited

Definition at line 283 of file implicit_system.h.

typedef std::map<std::string, NumericVector<Number> *>::const_iterator libMesh::System::const_vectors_iterator
inherited

Definition at line 749 of file system.h.

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

Data structure to log the information. The log is identified by the class name.

Definition at line 119 of file reference_counter.h.

typedef std::map<std::string, SparseMatrix<Number> *>::iterator libMesh::ImplicitSystem::matrices_iterator
inherited

Matrix iterator typedefs.

Definition at line 282 of file implicit_system.h.

The type of the parent.

Definition at line 79 of file continuation_system.h.

The type of system.

Definition at line 74 of file continuation_system.h.

typedef bool(TimeSolver::* libMesh::FEMSystem::TimeSolverResPtr) (bool, DiffContext &)
inherited

Syntax sugar to make numerical_jacobian() declaration easier.

Definition at line 208 of file fem_system.h.

typedef std::map<std::string, NumericVector<Number> *>::iterator libMesh::System::vectors_iterator
inherited

Vector iterator typedefs.

Definition at line 748 of file system.h.

Member Enumeration Documentation

The code provides the ability to select from different predictor schemes for getting the initial guess for the solution at the next point on the solution arc.

Enumerator
Euler 

First-order Euler predictor

AB2 

Second-order explicit Adams-Bashforth predictor

Invalid_Predictor 

Invalid predictor

Definition at line 221 of file continuation_system.h.

There are (so far) two different vectors which may be assembled using the assembly routine: 1.) The Residual = the normal PDE weighted residual 2.) G_Lambda = the derivative wrt the parameter lambda of the PDE weighted residual

It is up to the derived class to handle writing separate assembly code for the different cases. Usually something like: switch (rhs_mode) { case Residual: { Fu(i) += ... // normal PDE residual break; }

case G_Lambda: { Fu(i) += ... // derivative wrt control parameter break; }

Enumerator
Residual 
G_Lambda 

Definition at line 286 of file continuation_system.h.

Constructor & Destructor Documentation

libMesh::ContinuationSystem::ContinuationSystem ( EquationSystems es,
const std::string &  name,
const unsigned int  number 
)

Constructor. Optionally initializes required data structures.

Definition at line 29 of file continuation_system.C.

References linear_solver, libMesh::System::name(), and libMesh::on_command_line().

31  :
32  Parent(es, name_in, number_in),
34  quiet(true),
36  solution_tolerance(1.e-6),
41  Theta(1.),
42  Theta_LOCA(1.),
45  ds_min(1.e-8),
51  tangent_initialized(false),
53  dlambda_ds(0.707),
54  ds(0.1),
55  ds_current(0.1),
57  previous_ds(0.),
58  newton_step(0)
59 {
60  // Warn about using untested code
61  libmesh_experimental();
62 
63  if (libMesh::on_command_line("--solver_system_names"))
64  linear_solver->init((this->name()+"_").c_str());
65  else
66  linear_solver->init();
67 }
UniquePtr< LinearSolver< Number > > linear_solver
static UniquePtr< LinearSolver< Number > > build(const libMesh::Parallel::Communicator &comm_in, const SolverPackage solver_package=libMesh::default_solver_package())
const class libmesh_nullptr_t libmesh_nullptr
const std::string & name() const
Definition: system.h:1996
bool on_command_line(const std::string &arg)
Definition: libmesh.C:921
libMesh::ContinuationSystem::~ContinuationSystem ( )
virtual

Destructor.

Definition at line 72 of file continuation_system.C.

References clear().

73 {
74  this->clear();
75 }
virtual void clear() libmesh_override

Member Function Documentation

bool libMesh::DifferentiablePhysics::_eulerian_time_deriv ( bool  request_jacobian,
DiffContext  
)
inherited

This method simply combines element_time_derivative() and eulerian_residual(), which makes its address useful as a pointer-to-member-function when refactoring.

Referenced by libMesh::EulerSolver::element_residual(), libMesh::Euler2Solver::element_residual(), libMesh::NewmarkSolver::element_residual(), and libMesh::DifferentiablePhysics::init_context().

void libMesh::System::activate ( )
inlineinherited

Activates the system. Only active systems are solved.

Definition at line 2052 of file system.h.

References libMesh::System::_active.

Referenced by libMesh::System::get_equation_systems().

2053 {
2054  _active = true;
2055 }
bool libMesh::System::active ( ) const
inlineinherited
Returns
true if the system is active, false otherwise. An active system will be solved.

Definition at line 2044 of file system.h.

References libMesh::System::_active.

Referenced by libMesh::System::get_equation_systems().

2045 {
2046  return _active;
2047 }
NumericVector< Number > & libMesh::System::add_adjoint_rhs ( unsigned int  i = 0)
inherited
Returns
A reference to one of the system's adjoint rhs vectors, by default the one corresponding to the first qoi. Creates the vector if it doesn't already exist.

Definition at line 1039 of file system.C.

References libMesh::System::add_vector().

Referenced by libMesh::ExplicitSystem::assemble_qoi_derivative(), libMesh::FEMSystem::assemble_qoi_derivative(), and libMesh::System::project_solution_on_reinit().

1040 {
1041  std::ostringstream adjoint_rhs_name;
1042  adjoint_rhs_name << "adjoint_rhs" << i;
1043 
1044  return this->add_vector(adjoint_rhs_name.str(), false);
1045 }
NumericVector< Number > & add_vector(const std::string &vec_name, const bool projections=true, const ParallelType type=PARALLEL)
Definition: system.C:679
NumericVector< Number > & libMesh::System::add_adjoint_solution ( unsigned int  i = 0)
inherited
Returns
A reference to one of the system's adjoint solution vectors, by default the one corresponding to the first qoi. Creates the vector if it doesn't already exist.

Definition at line 975 of file system.C.

References libMesh::System::add_vector(), and libMesh::System::set_vector_as_adjoint().

Referenced by libMesh::ImplicitSystem::adjoint_solve(), and libMesh::System::project_solution_on_reinit().

976 {
977  std::ostringstream adjoint_name;
978  adjoint_name << "adjoint_solution" << i;
979 
980  NumericVector<Number> & returnval = this->add_vector(adjoint_name.str());
981  this->set_vector_as_adjoint(adjoint_name.str(), i);
982  return returnval;
983 }
void set_vector_as_adjoint(const std::string &vec_name, int qoi_num)
Definition: system.C:903
NumericVector< Number > & add_vector(const std::string &vec_name, const bool projections=true, const ParallelType type=PARALLEL)
Definition: system.C:679
void libMesh::DifferentiableSystem::add_dot_var_dirichlet_bcs ( unsigned int  var_idx,
unsigned int  dot_var_idx 
)
protectedinherited

Helper function to and Dirichlet boundary conditions to "dot" variable cousins of second order variables in the system. The function takes the second order variable index, it's corresponding "dot" variable index and then searches for DirichletBoundary objects for var_idx and then adds a DirichletBoundary object for dot_var_idx using the same boundary ids and functors for the var_idx DirichletBoundary.

Definition at line 228 of file diff_system.C.

References libMesh::DofMap::add_dirichlet_boundary(), libMesh::DirichletBoundary::b, libMesh::DirichletBoundary::f, libMesh::DirichletBoundary::f_fem, libMesh::DofMap::get_dirichlet_boundaries(), libMesh::System::get_dof_map(), libMesh::libmesh_assert(), and libMesh::DirichletBoundary::variables.

Referenced by libMesh::DifferentiableSystem::add_second_order_dot_vars().

230 {
231  // We're assuming that there could be a lot more variables than
232  // boundary conditions, so we search each of the boundary conditions
233  // for this variable rather than looping over boundary conditions
234  // in a separate loop and searching through all the variables.
235  const DirichletBoundaries * all_dbcs =
237 
238  if (all_dbcs)
239  {
240  // We need to cache the DBCs to be added so that we add them
241  // after looping over the existing DBCs. Otherwise, we're polluting
242  // the thing we're looping over.
243  std::vector<DirichletBoundary*> new_dbcs;
244 
245  DirichletBoundaries::const_iterator dbc_it = all_dbcs->begin();
246  for ( ; dbc_it != all_dbcs->end(); ++dbc_it )
247  {
248  libmesh_assert(*dbc_it);
249  DirichletBoundary & dbc = *(*dbc_it);
250 
251  // Look for second order variable in the current
252  // DirichletBoundary object
253  std::vector<unsigned int>::const_iterator dbc_var_it =
254  std::find( dbc.variables.begin(), dbc.variables.end(), var_idx );
255 
256  // If we found it, then we also need to add it's corresponding
257  // "dot" variable to a DirichletBoundary
258  std::vector<unsigned int> vars_to_add;
259  if (dbc_var_it != dbc.variables.end())
260  vars_to_add.push_back(dot_var_idx);
261 
262  if (!vars_to_add.empty())
263  {
264  // We need to check if the boundary condition is time-dependent.
265  // Currently, we cannot automatically differentiate w.r.t. time
266  // so if the user supplies a time-dependent Dirichlet BC, then
267  // we can't automatically support the Dirichlet BC for the
268  // "velocity" boundary condition, so we error. Otherwise,
269  // the "velocity boundary condition will just be zero.
270  bool is_time_evolving_bc = false;
271  if (dbc.f)
272  is_time_evolving_bc = dbc.f->is_time_dependent();
273  else if (dbc.f_fem)
274  // We it's a FEMFunctionBase object, it will be implicitly
275  // time-dependent since it is assumed to depend on the solution.
276  is_time_evolving_bc = true;
277  else
278  libmesh_error_msg("Could not find valid boundary function!");
279 
280  if (is_time_evolving_bc)
281  libmesh_error_msg("Cannot currently support time-dependent Dirichlet BC for dot variables!");
282 
283 
284  DirichletBoundary * new_dbc;
285 
286  if (dbc.f)
287  {
288  ZeroFunction<Number> zf;
289 
290  new_dbc = new DirichletBoundary(dbc.b, vars_to_add, zf);
291  }
292  else
293  libmesh_error();
294 
295  new_dbcs.push_back(new_dbc);
296  }
297  }
298 
299  // Now add the new DBCs for the "dot" vars to the DofMap
300  std::vector<DirichletBoundary*>::iterator new_dbc_it =
301  new_dbcs.begin();
302 
303  for ( ; new_dbc_it != new_dbcs.end(); ++new_dbc_it )
304  {
305  const DirichletBoundary & dbc = *(*new_dbc_it);
306  this->get_dof_map().add_dirichlet_boundary(dbc);
307  delete *new_dbc_it;
308  }
309 
310  } // if (all_dbcs)
311 }
libmesh_assert(j)
const DofMap & get_dof_map() const
Definition: system.h:2028
const DirichletBoundaries * get_dirichlet_boundaries() const
Definition: dof_map.h:1134
void add_dirichlet_boundary(const DirichletBoundary &dirichlet_boundary)
SparseMatrix< Number > & libMesh::ImplicitSystem::add_matrix ( const std::string &  mat_name)
inherited

Adds the additional matrix mat_name to this system. Only allowed prior to assemble(). All additional matrices have the same sparsity pattern as the matrix used during solution. When not System but the user wants to initialize the mayor matrix, then all the additional matrices, if existent, have to be initialized by the user, too.

Definition at line 210 of file implicit_system.C.

References libMesh::ImplicitSystem::_can_add_matrices, libMesh::ImplicitSystem::_matrices, libMesh::SparseMatrix< T >::build(), libMesh::ParallelObject::comm(), and libMesh::ImplicitSystem::have_matrix().

Referenced by libMesh::ImplicitSystem::add_system_matrix(), libMesh::EigenTimeSolver::init(), and libMesh::NewmarkSystem::NewmarkSystem().

211 {
212  // only add matrices before initializing...
213  if (!_can_add_matrices)
214  libmesh_error_msg("ERROR: Too late. Cannot add matrices to the system after initialization"
215  << "\n any more. You should have done this earlier.");
216 
217  // Return the matrix if it is already there.
218  if (this->have_matrix(mat_name))
219  return *(_matrices[mat_name]);
220 
221  // Otherwise build the matrix and return it.
222  SparseMatrix<Number> * buf = SparseMatrix<Number>::build(this->comm()).release();
223  _matrices.insert (std::make_pair (mat_name, buf));
224 
225  return *buf;
226 }
static UniquePtr< SparseMatrix< T > > build(const Parallel::Communicator &comm, const SolverPackage solver_package=libMesh::default_solver_package())
std::map< std::string, SparseMatrix< Number > * > _matrices
bool have_matrix(const std::string &mat_name) const
const Parallel::Communicator & comm() const
void libMesh::DifferentiableSystem::add_second_order_dot_vars ( )
protectedinherited

Helper function to add "velocity" variables that are cousins to second order-in-time variables in the DifferentiableSystem. This function is only called if the TimeSolver is a FirstOrderUnsteadySolver.

Definition at line 198 of file diff_system.C.

References libMesh::DifferentiablePhysics::_second_order_dot_vars, libMesh::Variable::active_subdomains(), libMesh::DifferentiableSystem::add_dot_var_dirichlet_bcs(), libMesh::System::add_variable(), libMesh::DifferentiablePhysics::get_second_order_vars(), libMesh::Variable::name(), libMesh::DifferentiablePhysics::time_evolving(), libMesh::Variable::type(), and libMesh::System::variable().

Referenced by libMesh::DifferentiableSystem::init_data().

199 {
200  const std::set<unsigned int> & second_order_vars = this->get_second_order_vars();
201  if (!second_order_vars.empty())
202  {
203  for (std::set<unsigned int>::const_iterator var_it = second_order_vars.begin();
204  var_it != second_order_vars.end(); ++var_it)
205  {
206  const Variable & var = this->variable(*var_it);
207  std::string new_var_name = std::string("dot_")+var.name();
208 
209  unsigned int v_var_idx;
210 
211  if (var.active_subdomains().empty())
212  v_var_idx = this->add_variable( new_var_name, var.type() );
213  else
214  v_var_idx = this->add_variable( new_var_name, var.type(), &var.active_subdomains() );
215 
216  _second_order_dot_vars.insert( std::pair<unsigned int,unsigned int>(*var_it,v_var_idx) );
217 
218  // The new velocities are time evolving variables of first order
219  this->time_evolving( v_var_idx, 1 );
220 
221  // And if there are any boundary conditions set on the second order
222  // variable, we also need to set it on its velocity variable.
223  this->add_dot_var_dirichlet_bcs( *var_it, v_var_idx );
224  }
225  }
226 }
const std::set< unsigned int > & get_second_order_vars() const
Definition: diff_physics.h:527
unsigned int add_variable(const std::string &var, const FEType &type, const std::set< subdomain_id_type > *const active_subdomains=libmesh_nullptr)
Definition: system.C:1099
void add_dot_var_dirichlet_bcs(unsigned int var_idx, unsigned int dot_var_idx)
Definition: diff_system.C:228
std::map< unsigned int, unsigned int > _second_order_dot_vars
Definition: diff_physics.h:568
const Variable & variable(unsigned int var) const
Definition: system.h:2112
virtual void time_evolving(unsigned int var)
Definition: diff_physics.h:247
NumericVector< Number > & libMesh::System::add_sensitivity_rhs ( unsigned int  i = 0)
inherited
Returns
A reference to one of the system's sensitivity rhs vectors, by default the one corresponding to the first parameter. Creates the vector if it doesn't already exist.

Definition at line 1069 of file system.C.

References libMesh::System::add_vector().

Referenced by libMesh::ImplicitSystem::assemble_residual_derivatives(), and libMesh::System::project_solution_on_reinit().

1070 {
1071  std::ostringstream sensitivity_rhs_name;
1072  sensitivity_rhs_name << "sensitivity_rhs" << i;
1073 
1074  return this->add_vector(sensitivity_rhs_name.str(), false);
1075 }
NumericVector< Number > & add_vector(const std::string &vec_name, const bool projections=true, const ParallelType type=PARALLEL)
Definition: system.C:679
NumericVector< Number > & libMesh::System::add_sensitivity_solution ( unsigned int  i = 0)
inherited
Returns
A reference to one of the system's solution sensitivity vectors, by default the one corresponding to the first parameter. Creates the vector if it doesn't already exist.

Definition at line 924 of file system.C.

References libMesh::System::add_vector().

Referenced by libMesh::System::project_solution_on_reinit(), and libMesh::ImplicitSystem::sensitivity_solve().

925 {
926  std::ostringstream sensitivity_name;
927  sensitivity_name << "sensitivity_solution" << i;
928 
929  return this->add_vector(sensitivity_name.str());
930 }
NumericVector< Number > & add_vector(const std::string &vec_name, const bool projections=true, const ParallelType type=PARALLEL)
Definition: system.C:679
unsigned int libMesh::System::add_variable ( const std::string &  var,
const FEType type,
const std::set< subdomain_id_type > *const  active_subdomains = libmesh_nullptr 
)
inherited

Adds the variable var to the list of variables for this system.

Returns
The index number for the new variable.

Definition at line 1099 of file system.C.

References libMesh::System::_variable_groups, libMesh::System::_variable_numbers, libMesh::System::_variables, libMesh::System::add_variables(), libMesh::VariableGroup::append(), libMesh::System::identify_variable_groups(), libMesh::System::is_initialized(), libMesh::libmesh_assert(), libmesh_nullptr, libMesh::System::n_variable_groups(), libMesh::System::n_vars(), libMesh::System::number(), libMesh::System::variable_name(), and libMesh::System::variable_type().

Referenced by libMesh::DifferentiableSystem::add_second_order_dot_vars(), libMesh::System::add_variable(), libMesh::ErrorVector::plot_error(), and libMesh::System::project_solution_on_reinit().

1102 {
1103  libmesh_assert(!this->is_initialized());
1104 
1105  // Make sure the variable isn't there already
1106  // or if it is, that it's the type we want
1107  for (unsigned int v=0; v<this->n_vars(); v++)
1108  if (this->variable_name(v) == var)
1109  {
1110  if (this->variable_type(v) == type)
1111  return _variables[v].number();
1112 
1113  libmesh_error_msg("ERROR: incompatible variable " << var << " has already been added for this system!");
1114  }
1115 
1116  // Optimize for VariableGroups here - if the user is adding multiple
1117  // variables of the same FEType and subdomain restriction, catch
1118  // that here and add them as members of the same VariableGroup.
1119  //
1120  // start by setting this flag to whatever the user has requested
1121  // and then consider the conditions which should negate it.
1122  bool should_be_in_vg = this->identify_variable_groups();
1123 
1124  // No variable groups, nothing to add to
1125  if (!this->n_variable_groups())
1126  should_be_in_vg = false;
1127 
1128  else
1129  {
1130  VariableGroup & vg(_variable_groups.back());
1131 
1132  // get a pointer to their subdomain restriction, if any.
1133  const std::set<subdomain_id_type> * const
1134  their_active_subdomains (vg.implicitly_active() ?
1135  libmesh_nullptr : &vg.active_subdomains());
1136 
1137  // Different types?
1138  if (vg.type() != type)
1139  should_be_in_vg = false;
1140 
1141  // they are restricted, we aren't?
1142  if (their_active_subdomains && !active_subdomains)
1143  should_be_in_vg = false;
1144 
1145  // they aren't restricted, we are?
1146  if (!their_active_subdomains && active_subdomains)
1147  should_be_in_vg = false;
1148 
1149  if (their_active_subdomains && active_subdomains)
1150  // restricted to different sets?
1151  if (*their_active_subdomains != *active_subdomains)
1152  should_be_in_vg = false;
1153 
1154  // OK, after all that, append the variable to the vg if none of the conditions
1155  // were violated
1156  if (should_be_in_vg)
1157  {
1158  const unsigned short curr_n_vars = cast_int<unsigned short>
1159  (this->n_vars());
1160 
1161  vg.append (var);
1162 
1163  _variables.push_back(vg(vg.n_variables()-1));
1164  _variable_numbers[var] = curr_n_vars;
1165  return curr_n_vars;
1166  }
1167  }
1168 
1169  // otherwise, fall back to adding a single variable group
1170  return this->add_variables (std::vector<std::string>(1, var),
1171  type,
1172  active_subdomains);
1173 }
std::map< std::string, unsigned short int > _variable_numbers
Definition: system.h:1901
const std::string & variable_name(const unsigned int i) const
Definition: system.h:2132
const class libmesh_nullptr_t libmesh_nullptr
std::vector< Variable > _variables
Definition: system.h:1890
const FEType & variable_type(const unsigned int i) const
Definition: system.h:2162
libmesh_assert(j)
unsigned int n_variable_groups() const
Definition: system.h:2092
std::vector< VariableGroup > _variable_groups
Definition: system.h:1895
bool is_initialized()
Definition: system.h:2068
bool identify_variable_groups() const
Definition: system.h:2180
unsigned int number() const
Definition: system.h:2004
unsigned int add_variables(const std::vector< std::string > &vars, const FEType &type, const std::set< subdomain_id_type > *const active_subdomains=libmesh_nullptr)
Definition: system.C:1189
unsigned int n_vars() const
Definition: system.h:2084
unsigned int libMesh::System::add_variable ( const std::string &  var,
const Order  order = FIRST,
const FEFamily  family = LAGRANGE,
const std::set< subdomain_id_type > *const  active_subdomains = libmesh_nullptr 
)
inherited

Adds the variable var to the list of variables for this system. Same as before, but assumes LAGRANGE as default value for FEType.family.

Definition at line 1177 of file system.C.

References libMesh::System::add_variable().

1181 {
1182  return this->add_variable(var,
1183  FEType(order, family),
1184  active_subdomains);
1185 }
unsigned int add_variable(const std::string &var, const FEType &type, const std::set< subdomain_id_type > *const active_subdomains=libmesh_nullptr)
Definition: system.C:1099
unsigned int libMesh::System::add_variables ( const std::vector< std::string > &  vars,
const FEType type,
const std::set< subdomain_id_type > *const  active_subdomains = libmesh_nullptr 
)
inherited

Adds the variable var to the list of variables for this system.

Returns
The index number for the new variable.

Definition at line 1189 of file system.C.

References libMesh::System::_variable_groups, libMesh::System::_variable_numbers, libMesh::System::_variables, libMesh::System::is_initialized(), libMesh::libmesh_assert(), libmesh_nullptr, libMesh::System::n_components(), libMesh::System::n_vars(), libMesh::System::number(), libMesh::System::variable_name(), and libMesh::System::variable_type().

Referenced by libMesh::System::add_variable(), libMesh::System::add_variables(), and libMesh::System::project_solution_on_reinit().

1192 {
1193  libmesh_assert(!this->is_initialized());
1194 
1195  // Make sure the variable isn't there already
1196  // or if it is, that it's the type we want
1197  for (std::size_t ov=0; ov<vars.size(); ov++)
1198  for (unsigned int v=0; v<this->n_vars(); v++)
1199  if (this->variable_name(v) == vars[ov])
1200  {
1201  if (this->variable_type(v) == type)
1202  return _variables[v].number();
1203 
1204  libmesh_error_msg("ERROR: incompatible variable " << vars[ov] << " has already been added for this system!");
1205  }
1206 
1207  const unsigned short curr_n_vars = cast_int<unsigned short>
1208  (this->n_vars());
1209 
1210  const unsigned int next_first_component = this->n_components();
1211 
1212  // Add the variable group to the list
1213  _variable_groups.push_back((active_subdomains == libmesh_nullptr) ?
1214  VariableGroup(this, vars, curr_n_vars,
1215  next_first_component, type) :
1216  VariableGroup(this, vars, curr_n_vars,
1217  next_first_component, type, *active_subdomains));
1218 
1219  const VariableGroup & vg (_variable_groups.back());
1220 
1221  // Add each component of the group individually
1222  for (std::size_t v=0; v<vars.size(); v++)
1223  {
1224  _variables.push_back (vg(v));
1225  _variable_numbers[vars[v]] = cast_int<unsigned short>
1226  (curr_n_vars+v);
1227  }
1228 
1229  libmesh_assert_equal_to ((curr_n_vars+vars.size()), this->n_vars());
1230 
1231  // BSK - Defer this now to System::init_data() so we can detect
1232  // VariableGroups 12/28/2012
1233  // // Add the variable group to the _dof_map
1234  // _dof_map->add_variable_group (vg);
1235 
1236  // Return the number of the new variable
1237  return cast_int<unsigned int>(curr_n_vars+vars.size()-1);
1238 }
std::map< std::string, unsigned short int > _variable_numbers
Definition: system.h:1901
const std::string & variable_name(const unsigned int i) const
Definition: system.h:2132
const class libmesh_nullptr_t libmesh_nullptr
std::vector< Variable > _variables
Definition: system.h:1890
const FEType & variable_type(const unsigned int i) const
Definition: system.h:2162
libmesh_assert(j)
unsigned int n_components() const
Definition: system.h:2100
std::vector< VariableGroup > _variable_groups
Definition: system.h:1895
bool is_initialized()
Definition: system.h:2068
unsigned int number() const
Definition: system.h:2004
unsigned int n_vars() const
Definition: system.h:2084
unsigned int libMesh::System::add_variables ( const std::vector< std::string > &  vars,
const Order  order = FIRST,
const FEFamily  family = LAGRANGE,
const std::set< subdomain_id_type > *const  active_subdomains = libmesh_nullptr 
)
inherited

Adds the variable var to the list of variables for this system. Same as before, but assumes LAGRANGE as default value for FEType.family.

Definition at line 1242 of file system.C.

References libMesh::System::add_variables().

1246 {
1247  return this->add_variables(vars,
1248  FEType(order, family),
1249  active_subdomains);
1250 }
unsigned int add_variables(const std::vector< std::string > &vars, const FEType &type, const std::set< subdomain_id_type > *const active_subdomains=libmesh_nullptr)
Definition: system.C:1189
NumericVector< Number > & libMesh::System::add_vector ( const std::string &  vec_name,
const bool  projections = true,
const ParallelType  type = PARALLEL 
)
inherited

Adds the additional vector vec_name to this system. All the additional vectors are similarly distributed, like the solution, and initialized to zero.

By default vectors added by add_vector are projected to changed grids by reinit(). To zero them instead (more efficient), pass "false" as the second argument

Definition at line 679 of file system.C.

References libMesh::System::_dof_map, libMesh::System::_is_initialized, libMesh::System::_vector_is_adjoint, libMesh::System::_vector_projections, libMesh::System::_vector_types, libMesh::System::_vectors, libMesh::NumericVector< T >::build(), libMesh::ParallelObject::comm(), libMesh::GHOSTED, libMesh::System::have_vector(), libMesh::NumericVector< T >::init(), libMesh::System::n_dofs(), and libMesh::System::n_local_dofs().

Referenced by libMesh::System::add_adjoint_rhs(), libMesh::System::add_adjoint_solution(), libMesh::System::add_sensitivity_rhs(), libMesh::System::add_sensitivity_solution(), libMesh::ExplicitSystem::add_system_rhs(), libMesh::System::add_weighted_sensitivity_adjoint_solution(), libMesh::System::add_weighted_sensitivity_solution(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::SecondOrderUnsteadySolver::init(), libMesh::UnsteadySolver::init(), libMesh::OptimizationSystem::init_data(), init_data(), libMesh::NewmarkSystem::NewmarkSystem(), libMesh::FrequencySystem::set_frequencies(), libMesh::FrequencySystem::set_frequencies_by_range(), and libMesh::FrequencySystem::set_frequencies_by_steps().

682 {
683  // Return the vector if it is already there.
684  if (this->have_vector(vec_name))
685  return *(_vectors[vec_name]);
686 
687  // Otherwise build the vector
688  NumericVector<Number> * buf = NumericVector<Number>::build(this->comm()).release();
689  _vectors.insert (std::make_pair (vec_name, buf));
690  _vector_projections.insert (std::make_pair (vec_name, projections));
691 
692  _vector_types.insert (std::make_pair (vec_name, type));
693 
694  // Vectors are primal by default
695  _vector_is_adjoint.insert (std::make_pair (vec_name, -1));
696 
697  // Initialize it if necessary
698  if (_is_initialized)
699  {
700  if (type == GHOSTED)
701  {
702 #ifdef LIBMESH_ENABLE_GHOSTED
703  buf->init (this->n_dofs(), this->n_local_dofs(),
704  _dof_map->get_send_list(), false,
705  GHOSTED);
706 #else
707  libmesh_error_msg("Cannot initialize ghosted vectors when they are not enabled.");
708 #endif
709  }
710  else
711  buf->init (this->n_dofs(), this->n_local_dofs(), false, type);
712  }
713 
714  return *buf;
715 }
std::map< std::string, ParallelType > _vector_types
Definition: system.h:1931
bool _is_initialized
Definition: system.h:1950
UniquePtr< DofMap > _dof_map
Definition: system.h:1863
static UniquePtr< NumericVector< T > > build(const Parallel::Communicator &comm, const SolverPackage solver_package=libMesh::default_solver_package())
bool have_vector(const std::string &vec_name) const
Definition: system.h:2204
std::map< std::string, int > _vector_is_adjoint
Definition: system.h:1926
dof_id_type n_local_dofs() const
Definition: system.C:183
std::map< std::string, NumericVector< Number > * > _vectors
Definition: system.h:1914
const Parallel::Communicator & comm() const
std::map< std::string, bool > _vector_projections
Definition: system.h:1920
dof_id_type n_dofs() const
Definition: system.C:146
NumericVector< Number > & libMesh::System::add_weighted_sensitivity_adjoint_solution ( unsigned int  i = 0)
inherited
Returns
A reference to one of the system's weighted sensitivity adjoint solution vectors, by default the one corresponding to the first qoi. Creates the vector if it doesn't already exist.

Definition at line 1007 of file system.C.

References libMesh::System::add_vector(), and libMesh::System::set_vector_as_adjoint().

Referenced by libMesh::System::project_solution_on_reinit(), and libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve().

1008 {
1009  std::ostringstream adjoint_name;
1010  adjoint_name << "weighted_sensitivity_adjoint_solution" << i;
1011 
1012  NumericVector<Number> & returnval = this->add_vector(adjoint_name.str());
1013  this->set_vector_as_adjoint(adjoint_name.str(), i);
1014  return returnval;
1015 }
void set_vector_as_adjoint(const std::string &vec_name, int qoi_num)
Definition: system.C:903
NumericVector< Number > & add_vector(const std::string &vec_name, const bool projections=true, const ParallelType type=PARALLEL)
Definition: system.C:679
NumericVector< Number > & libMesh::System::add_weighted_sensitivity_solution ( )
inherited
Returns
A reference to the solution of the last weighted sensitivity solve Creates the vector if it doesn't already exist.

Definition at line 954 of file system.C.

References libMesh::System::add_vector().

Referenced by libMesh::System::project_solution_on_reinit(), and libMesh::ImplicitSystem::weighted_sensitivity_solve().

955 {
956  return this->add_vector("weighted_sensitivity_solution");
957 }
NumericVector< Number > & add_vector(const std::string &vec_name, const bool projections=true, const ParallelType type=PARALLEL)
Definition: system.C:679
void libMesh::ImplicitSystem::adjoint_qoi_parameter_sensitivity ( const QoISet qoi_indices,
const ParameterVector parameters,
SensitivityData sensitivities 
)
virtualinherited

Solves for the derivative of each of the system's quantities of interest q in qoi[qoi_indices] with respect to each parameter in parameters, placing the result for qoi i and parameter j into sensitivities[i][j].

Uses adjoint_solve() and the adjoint sensitivity method.

Currently uses finite differenced derivatives (partial q / partial p) and (partial R / partial p).

Reimplemented from libMesh::System.

Definition at line 708 of file implicit_system.C.

References std::abs(), libMesh::ImplicitSystem::adjoint_solve(), libMesh::SensitivityData::allocate_data(), libMesh::ExplicitSystem::assemble_qoi(), libMesh::ImplicitSystem::assemble_residual_derivatives(), libMesh::NumericVector< T >::dot(), libMesh::System::get_sensitivity_rhs(), libMesh::QoISet::has_index(), libMesh::System::is_adjoint_already_solved(), std::max(), libMesh::System::qoi, libMesh::Real, libMesh::ParameterVector::size(), and libMesh::TOLERANCE.

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

711 {
712  ParameterVector & parameters =
713  const_cast<ParameterVector &>(parameters_in);
714 
715  const unsigned int Np = cast_int<unsigned int>
716  (parameters.size());
717  const unsigned int Nq = cast_int<unsigned int>
718  (qoi.size());
719 
720  // An introduction to the problem:
721  //
722  // Residual R(u(p),p) = 0
723  // partial R / partial u = J = system matrix
724  //
725  // This implies that:
726  // d/dp(R) = 0
727  // (partial R / partial p) +
728  // (partial R / partial u) * (partial u / partial p) = 0
729 
730  // We first do an adjoint solve:
731  // J^T * z = (partial q / partial u)
732  // if we havent already or dont have an initial condition for the adjoint
733  if (!this->is_adjoint_already_solved())
734  {
735  this->adjoint_solve(qoi_indices);
736  }
737 
738  this->assemble_residual_derivatives(parameters_in);
739 
740  // Get ready to fill in sensitivities:
741  sensitivities.allocate_data(qoi_indices, *this, parameters);
742 
743  // We use the identities:
744  // dq/dp = (partial q / partial p) + (partial q / partial u) *
745  // (partial u / partial p)
746  // dq/dp = (partial q / partial p) + (J^T * z) *
747  // (partial u / partial p)
748  // dq/dp = (partial q / partial p) + z * J *
749  // (partial u / partial p)
750 
751  // Leading to our final formula:
752  // dq/dp = (partial q / partial p) - z * (partial R / partial p)
753 
754  // In the case of adjoints with heterogenous Dirichlet boundary
755  // function phi, where
756  // q := S(u) - R(u,phi)
757  // the final formula works out to:
758  // dq/dp = (partial S / partial p) - z * (partial R / partial p)
759  // Because we currently have no direct access to
760  // (partial S / partial p), we use the identity
761  // (partial S / partial p) = (partial q / partial p) +
762  // phi * (partial R / partial p)
763  // to derive an equivalent equation:
764  // dq/dp = (partial q / partial p) - (z-phi) * (partial R / partial p)
765 
766  // Since z-phi degrees of freedom are zero for constrained indices,
767  // we can use the same constrained -(partial R / partial p) that we
768  // use for forward sensitivity solves, taking into account the
769  // differing sign convention.
770  //
771  // Since that vector is constrained, its constrained indices are
772  // zero, so its product with phi is zero, so we can neglect the
773  // evaluation of phi terms.
774 
775  for (unsigned int j=0; j != Np; ++j)
776  {
777  // We currently get partial derivatives via central differencing
778 
779  // (partial q / partial p) ~= (q(p+dp)-q(p-dp))/(2*dp)
780  // (partial R / partial p) ~= (rhs(p+dp) - rhs(p-dp))/(2*dp)
781 
782  Number old_parameter = *parameters[j];
783 
784  const Real delta_p =
785  TOLERANCE * std::max(std::abs(old_parameter), 1e-3);
786 
787  *parameters[j] = old_parameter - delta_p;
788  this->assemble_qoi(qoi_indices);
789  std::vector<Number> qoi_minus = this->qoi;
790 
791  NumericVector<Number> & neg_partialR_partialp = this->get_sensitivity_rhs(j);
792 
793  *parameters[j] = old_parameter + delta_p;
794  this->assemble_qoi(qoi_indices);
795  std::vector<Number> & qoi_plus = this->qoi;
796 
797  std::vector<Number> partialq_partialp(Nq, 0);
798  for (unsigned int i=0; i != Nq; ++i)
799  if (qoi_indices.has_index(i))
800  partialq_partialp[i] = (qoi_plus[i] - qoi_minus[i]) / (2.*delta_p);
801 
802  // Don't leave the parameter changed
803  *parameters[j] = old_parameter;
804 
805  for (unsigned int i=0; i != Nq; ++i)
806  if (qoi_indices.has_index(i))
807  sensitivities[i][j] = partialq_partialp[i] +
808  neg_partialR_partialp.dot(this->get_adjoint_solution(i));
809  }
810 
811  // All parameters have been reset.
812  // Reset the original qoi.
813 
814  this->assemble_qoi(qoi_indices);
815 }
double abs(double a)
virtual std::pair< unsigned int, Real > adjoint_solve(const QoISet &qoi_indices=QoISet()) libmesh_override
NumericVector< Number > & get_sensitivity_rhs(unsigned int i=0)
Definition: system.C:1079
static const Real TOLERANCE
long double max(long double a, double b)
std::vector< Number > qoi
Definition: system.h:1551
bool is_adjoint_already_solved() const
Definition: system.h:372
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
virtual void assemble_qoi(const QoISet &qoi_indices=QoISet()) libmesh_override
virtual void assemble_residual_derivatives(const ParameterVector &parameters) libmesh_override
std::pair< unsigned int, Real > libMesh::DifferentiableSystem::adjoint_solve ( const QoISet qoi_indices = QoISet())
virtualinherited

This function sets the _is_adjoint boolean member of TimeSolver to true and then calls the adjoint_solve in implicit system

Reimplemented from libMesh::ImplicitSystem.

Definition at line 164 of file diff_system.C.

References libMesh::ImplicitSystem::adjoint_solve(), libMesh::DifferentiableSystem::get_time_solver(), and libMesh::TimeSolver::set_is_adjoint().

165 {
166  // Get the time solver object associated with the system, and tell it that
167  // we are solving the adjoint problem
168  this->get_time_solver().set_is_adjoint(true);
169 
170  return this->ImplicitSystem::adjoint_solve(qoi_indices);
171 }
virtual std::pair< unsigned int, Real > adjoint_solve(const QoISet &qoi_indices=QoISet()) libmesh_override
void set_is_adjoint(bool _is_adjoint_value)
Definition: time_solver.h:239
TimeSolver & get_time_solver()
Definition: diff_system.h:402
void libMesh::ContinuationSystem::advance_arcstep ( )

Call this function after a continuation solve to compute the tangent and get the next initial guess.

Definition at line 936 of file continuation_system.C.

References solve_tangent(), and update_solution().

937 {
938  // Solve for the updated tangent du1/ds, d(lambda1)/ds
939  solve_tangent();
940 
941  // Advance the solution and the parameter to the next value.
942  update_solution();
943 }
void libMesh::ContinuationSystem::apply_predictor ( )
private

Applies the predictor to the current solution to get a guess for the next solution.

Definition at line 1375 of file continuation_system.C.

References AB2, continuation_parameter, dlambda_ds, ds_current, du_ds, Euler, predictor, previous_dlambda_ds, previous_ds, previous_du_ds, libMesh::Real, and libMesh::System::solution.

Referenced by continuation_solve(), and update_solution().

1376 {
1377  if (predictor == Euler)
1378  {
1379  // 1.) Euler Predictor
1380  // Predict next the solution
1381  solution->add(ds_current, *du_ds);
1382  solution->close();
1383 
1384  // Predict next parameter value
1386  }
1387 
1388 
1389  else if (predictor == AB2)
1390  {
1391  // 2.) 2nd-order explicit AB predictor
1392  libmesh_assert_not_equal_to (previous_ds, 0.0);
1393  const Real stepratio = ds_current/previous_ds;
1394 
1395  // Build up next solution value.
1396  solution->add( 0.5*ds_current*(2.+stepratio), *du_ds);
1397  solution->add(-0.5*ds_current*stepratio , *previous_du_ds);
1398  solution->close();
1399 
1400  // Next parameter value
1402  0.5*ds_current*((2.+stepratio)*dlambda_ds -
1403  stepratio*previous_dlambda_ds);
1404  }
1405 
1406  else
1407  libmesh_error_msg("Unknown predictor!");
1408 }
NumericVector< Number > * previous_du_ds
NumericVector< Number > * du_ds
UniquePtr< NumericVector< Number > > solution
Definition: system.h:1521
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
void libMesh::DifferentiableSystem::assemble ( )
virtualinherited

Prepares matrix and rhs for matrix assembly. Users should not reimplement this

Reimplemented from libMesh::ImplicitSystem.

Definition at line 145 of file diff_system.C.

References libMesh::DifferentiableSystem::assembly().

146 {
147  this->assembly(true, true);
148 }
virtual void assembly(bool get_residual, bool get_jacobian, bool apply_heterogeneous_constraints=false, bool apply_no_constraints=false) libmesh_override=0
void libMesh::FEMSystem::assemble_qoi ( const QoISet indices = QoISet())
virtualinherited

Runs a qoi assembly loop over all elements, and if assemble_qoi_sides is true over all sides.

Users may have to override this function if they have any quantities of interest that are not expressible as a sum of element qois.

Reimplemented from libMesh::ExplicitSystem.

Definition at line 1128 of file fem_system.C.

References libMesh::MeshBase::active_local_elements_begin(), libMesh::MeshBase::active_local_elements_end(), libMesh::ParallelObject::comm(), libMesh::DifferentiableSystem::diff_qoi, libMesh::System::get_mesh(), libMesh::QoISet::has_index(), mesh, libMesh::DifferentiableQoI::parallel_op(), libMesh::Threads::parallel_reduce(), libMesh::System::qoi, libMesh::StoredRange< iterator_type, object_type >::reset(), and libMesh::System::update().

1129 {
1130  LOG_SCOPE("assemble_qoi()", "FEMSystem");
1131 
1132  const MeshBase & mesh = this->get_mesh();
1133 
1134  this->update();
1135 
1136  const unsigned int Nq = cast_int<unsigned int>(qoi.size());
1137 
1138  // the quantity of interest is assumed to be a sum of element and
1139  // side terms
1140  for (unsigned int i=0; i != Nq; ++i)
1141  if (qoi_indices.has_index(i))
1142  qoi[i] = 0;
1143 
1144  // Create a non-temporary qoi_contributions object, so we can query
1145  // its results after the reduction
1146  QoIContributions qoi_contributions(*this, *(this->diff_qoi), qoi_indices);
1147 
1148  // Loop over every active mesh element on this processor
1149  Threads::parallel_reduce(elem_range.reset(mesh.active_local_elements_begin(),
1150  mesh.active_local_elements_end()),
1151  qoi_contributions);
1152 
1153  this->diff_qoi->parallel_op( this->comm(), this->qoi, qoi_contributions.qoi, qoi_indices );
1154 }
MeshBase & mesh
Base class for Mesh.
Definition: mesh_base.h:67
DifferentiableQoI * diff_qoi
Definition: diff_system.h:365
virtual void parallel_op(const Parallel::Communicator &communicator, std::vector< Number > &sys_qoi, std::vector< Number > &local_qoi, const QoISet &qoi_indices)
const MeshBase & get_mesh() const
Definition: system.h:2012
std::vector< Number > qoi
Definition: system.h:1551
virtual element_iterator active_local_elements_begin()=0
virtual void update()
Definition: system.C:423
const Parallel::Communicator & comm() const
void parallel_reduce(const Range &range, Body &body)
Definition: threads_none.h:101
virtual element_iterator active_local_elements_end()=0
void libMesh::FEMSystem::assemble_qoi_derivative ( const QoISet qoi_indices = QoISet(),
bool  include_liftfunc = true,
bool  apply_constraints = true 
)
virtualinherited

Runs a qoi derivative assembly loop over all elements, and if assemble_qoi_sides is true over all sides.

Users may have to override this function for quantities of interest that are not expressible as a sum of element qois.

Reimplemented from libMesh::ExplicitSystem.

Definition at line 1158 of file fem_system.C.

References libMesh::MeshBase::active_local_elements_begin(), libMesh::MeshBase::active_local_elements_end(), libMesh::System::add_adjoint_rhs(), libMesh::DifferentiableSystem::diff_qoi, libMesh::System::get_mesh(), libMesh::QoISet::has_index(), mesh, libMesh::Threads::parallel_for(), libMesh::System::qoi, libMesh::StoredRange< iterator_type, object_type >::reset(), libMesh::System::update(), and libMesh::NumericVector< T >::zero().

1161 {
1162  LOG_SCOPE("assemble_qoi_derivative()", "FEMSystem");
1163 
1164  const MeshBase & mesh = this->get_mesh();
1165 
1166  this->update();
1167 
1168  // The quantity of interest derivative assembly accumulates on
1169  // initially zero vectors
1170  for (std::size_t i=0; i != qoi.size(); ++i)
1171  if (qoi_indices.has_index(i))
1172  this->add_adjoint_rhs(i).zero();
1173 
1174  // Loop over every active mesh element on this processor
1175  Threads::parallel_for (elem_range.reset(mesh.active_local_elements_begin(),
1176  mesh.active_local_elements_end()),
1177  QoIDerivativeContributions(*this, qoi_indices,
1178  *(this->diff_qoi),
1179  include_liftfunc,
1180  apply_constraints));
1181 }
void parallel_for(const Range &range, const Body &body)
Definition: threads_none.h:73
MeshBase & mesh
Base class for Mesh.
Definition: mesh_base.h:67
virtual void zero()=0
DifferentiableQoI * diff_qoi
Definition: diff_system.h:365
const MeshBase & get_mesh() const
Definition: system.h:2012
std::vector< Number > qoi
Definition: system.h:1551
virtual element_iterator active_local_elements_begin()=0
NumericVector< Number > & add_adjoint_rhs(unsigned int i=0)
Definition: system.C:1039
virtual void update()
Definition: system.C:423
virtual element_iterator active_local_elements_end()=0
bool has_index(unsigned int) const
Definition: qoi_set.h:221
void libMesh::ImplicitSystem::assemble_residual_derivatives ( const ParameterVector parameters)
virtualinherited

Residual parameter derivative function.

Uses finite differences by default.

This will assemble the sensitivity rhs vectors to hold -(partial R / partial p_i), making them ready to solve the forward sensitivity equation.

Can be overridden in derived classes.

Reimplemented from libMesh::System.

Definition at line 665 of file implicit_system.C.

References std::abs(), libMesh::System::add_sensitivity_rhs(), libMesh::ImplicitSystem::assembly(), libMesh::NumericVector< T >::close(), std::max(), libMesh::Real, libMesh::ExplicitSystem::rhs, libMesh::ParameterVector::size(), and libMesh::TOLERANCE.

Referenced by libMesh::ImplicitSystem::adjoint_qoi_parameter_sensitivity(), libMesh::ImplicitSystem::assembly(), and libMesh::ImplicitSystem::sensitivity_solve().

666 {
667  ParameterVector & parameters =
668  const_cast<ParameterVector &>(parameters_in);
669 
670  const unsigned int Np = cast_int<unsigned int>
671  (parameters.size());
672 
673  for (unsigned int p=0; p != Np; ++p)
674  {
675  NumericVector<Number> & sensitivity_rhs = this->add_sensitivity_rhs(p);
676 
677  // Approximate -(partial R / partial p) by
678  // (R(p-dp) - R(p+dp)) / (2*dp)
679 
680  Number old_parameter = *parameters[p];
681 
682  const Real delta_p =
683  TOLERANCE * std::max(std::abs(old_parameter), 1e-3);
684 
685  *parameters[p] -= delta_p;
686 
687  // this->assembly(true, false, true);
688  this->assembly(true, false, false);
689  this->rhs->close();
690  sensitivity_rhs = *this->rhs;
691 
692  *parameters[p] = old_parameter + delta_p;
693 
694  // this->assembly(true, false, true);
695  this->assembly(true, false, false);
696  this->rhs->close();
697 
698  sensitivity_rhs -= *this->rhs;
699  sensitivity_rhs /= (2*delta_p);
700  sensitivity_rhs.close();
701 
702  *parameters[p] = old_parameter;
703  }
704 }
double abs(double a)
NumericVector< Number > * rhs
NumericVector< Number > & add_sensitivity_rhs(unsigned int i=0)
Definition: system.C:1069
static const Real TOLERANCE
long double max(long double a, double b)
virtual void assembly(bool, bool, bool=false, bool=false)
virtual void close()=0
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
void libMesh::FEMSystem::assembly ( bool  get_residual,
bool  get_jacobian,
bool  apply_heterogeneous_constraints = false,
bool  apply_no_constraints = false 
)
virtualinherited

Prepares matrix or rhs for matrix assembly. Users may reimplement this to add pre- or post-assembly code before or after calling FEMSystem::assembly()

Implements libMesh::DifferentiableSystem.

Definition at line 852 of file fem_system.C.

References libMesh::DenseMatrix< T >::add(), libMesh::FEMSystem::build_context(), libMesh::NumericVector< T >::close(), libMesh::SparseMatrix< T >::close(), libMesh::err, libMesh::FEType::family, libMesh::DiffContext::get_elem_jacobian(), libMesh::DiffContext::get_elem_residual(), libMesh::System::get_mesh(), libMesh::FEMSystem::init_context(), libMesh::NumericVector< T >::l1_norm(), libMesh::SparseMatrix< T >::l1_norm(), libMesh::DenseMatrix< T >::l1_norm(), libMesh::libmesh_assert(), libmesh_nullptr, libMesh::ImplicitSystem::matrix, std::max(), mesh, libMesh::ParallelObject::n_processors(), libMesh::System::n_variable_groups(), libMesh::FEMSystem::numerical_nonlocal_jacobian(), libMesh::out, libMesh::Threads::parallel_for(), libMesh::FEMContext::pre_fe_reinit(), libMesh::BasicOStreamProxy< charT, traits >::precision(), libMesh::DifferentiableSystem::print_jacobian_norms, libMesh::DifferentiableSystem::print_jacobians, libMesh::DifferentiableSystem::print_residual_norms, libMesh::DifferentiableSystem::print_residuals, libMesh::DifferentiableSystem::print_solution_norms, libMesh::DifferentiableSystem::print_solutions, libMesh::ParallelObject::processor_id(), libMesh::Real, libMesh::StoredRange< iterator_type, object_type >::reset(), libMesh::ExplicitSystem::rhs, libMesh::SCALAR, libMesh::DenseVector< T >::size(), libMesh::System::solution, libMesh::DifferentiableSystem::time_solver, libMesh::Variable::type(), libMesh::System::update(), libMesh::System::variable_group(), libMesh::FEMSystem::verify_analytic_jacobians, libMesh::DenseMatrix< T >::zero(), libMesh::SparseMatrix< T >::zero(), and libMesh::NumericVector< T >::zero().

Referenced by continuation_solve(), and solve_tangent().

855 {
856  libmesh_assert(get_residual || get_jacobian);
857  std::string log_name;
858  if (get_residual && get_jacobian)
859  log_name = "assembly()";
860  else if (get_residual)
861  log_name = "assembly(get_residual)";
862  else
863  log_name = "assembly(get_jacobian)";
864 
865  LOG_SCOPE(log_name.c_str(), "FEMSystem");
866 
867  const MeshBase & mesh = this->get_mesh();
868 
869  // this->get_vector("_nonlinear_solution").localize
870  // (*current_local_nonlinear_solution,
871  // dof_map.get_send_list());
872  this->update();
873 
875  {
876  // this->get_vector("_nonlinear_solution").close();
877  this->solution->close();
878 
879  std::streamsize old_precision = libMesh::out.precision();
881  libMesh::out << "|U| = "
882  // << this->get_vector("_nonlinear_solution").l1_norm()
883  << this->solution->l1_norm()
884  << std::endl;
885  libMesh::out.precision(old_precision);
886  }
887  if (print_solutions)
888  {
889  std::streamsize old_precision = libMesh::out.precision();
891  // libMesh::out << "U = [" << this->get_vector("_nonlinear_solution")
892  libMesh::out << "U = [" << *(this->solution)
893  << "];" << std::endl;
894  libMesh::out.precision(old_precision);
895  }
896 
897  // Is this definitely necessary? [RHS]
898  // Yes. [RHS 2012]
899  if (get_jacobian)
900  matrix->zero();
901  if (get_residual)
902  rhs->zero();
903 
904  // Stupid C++ lets you set *Real* verify_analytic_jacobians = true!
905  if (verify_analytic_jacobians > 0.5)
906  {
907  libMesh::err << "WARNING! verify_analytic_jacobians was set "
908  << "to absurdly large value of "
909  << verify_analytic_jacobians << std::endl;
910  libMesh::err << "Resetting to 1e-6!" << std::endl;
912  }
913 
914  // In time-dependent problems, the nonlinear function we're trying
915  // to solve at each timestep may depend on the particular solver
916  // we're using
918 
919  // Build the residual and jacobian contributions on every active
920  // mesh element on this processor
922  (elem_range.reset(mesh.active_local_elements_begin(),
923  mesh.active_local_elements_end()),
924  AssemblyContributions(*this, get_residual, get_jacobian,
925  apply_heterogeneous_constraints,
926  apply_no_constraints));
927 
928  // Check and see if we have SCALAR variables
929  bool have_scalar = false;
930  for (unsigned int i=0; i != this->n_variable_groups(); ++i)
931  {
932  if (this->variable_group(i).type().family == SCALAR)
933  {
934  have_scalar = true;
935  break;
936  }
937  }
938 
939  // SCALAR dofs are stored on the last processor, so we'll evaluate
940  // their equation terms there and only if we have a SCALAR variable
941  if (this->processor_id() == (this->n_processors()-1) && have_scalar)
942  {
944  FEMContext & _femcontext = cast_ref<FEMContext &>(*con);
945  this->init_context(_femcontext);
946  _femcontext.pre_fe_reinit(*this, libmesh_nullptr);
947 
948  bool jacobian_computed =
949  this->time_solver->nonlocal_residual(get_jacobian, _femcontext);
950 
951  // Nonlocal residuals are likely to be length 0, in which case we
952  // don't need to do any more. And we shouldn't try to do any
953  // more; lots of DenseVector/DenseMatrix code assumes rank>0.
954  if (_femcontext.get_elem_residual().size())
955  {
956  // Compute a numeric jacobian if we have to
957  if (get_jacobian && !jacobian_computed)
958  {
959  // Make sure we didn't compute a jacobian and lie about it
960  libmesh_assert_equal_to (_femcontext.get_elem_jacobian().l1_norm(), 0.0);
961  // Logging of numerical jacobians is done separately
962  this->numerical_nonlocal_jacobian(_femcontext);
963  }
964 
965  // Compute a numeric jacobian if we're asked to verify the
966  // analytic jacobian we got
967  if (get_jacobian && jacobian_computed &&
968  this->verify_analytic_jacobians != 0.0)
969  {
970  DenseMatrix<Number> analytic_jacobian(_femcontext.get_elem_jacobian());
971 
972  _femcontext.get_elem_jacobian().zero();
973  // Logging of numerical jacobians is done separately
974  this->numerical_nonlocal_jacobian(_femcontext);
975 
976  Real analytic_norm = analytic_jacobian.l1_norm();
977  Real numerical_norm = _femcontext.get_elem_jacobian().l1_norm();
978 
979  // If we can continue, we'll probably prefer the analytic jacobian
980  analytic_jacobian.swap(_femcontext.get_elem_jacobian());
981 
982  // The matrix "analytic_jacobian" will now hold the error matrix
983  analytic_jacobian.add(-1.0, _femcontext.get_elem_jacobian());
984  Real error_norm = analytic_jacobian.l1_norm();
985 
986  Real relative_error = error_norm /
987  std::max(analytic_norm, numerical_norm);
988 
989  if (relative_error > this->verify_analytic_jacobians)
990  {
991  libMesh::err << "Relative error " << relative_error
992  << " detected in analytic jacobian on nonlocal dofs!"
993  << std::endl;
994 
995  std::streamsize old_precision = libMesh::out.precision();
997  libMesh::out << "J_analytic nonlocal = "
998  << _femcontext.get_elem_jacobian() << std::endl;
999  analytic_jacobian.add(1.0, _femcontext.get_elem_jacobian());
1000  libMesh::out << "J_numeric nonlocal = "
1001  << analytic_jacobian << std::endl;
1002 
1003  libMesh::out.precision(old_precision);
1004 
1005  libmesh_error_msg("Relative error too large, exiting!");
1006  }
1007  }
1008 
1009  add_element_system
1010  (*this, get_residual, get_jacobian,
1011  apply_heterogeneous_constraints, apply_no_constraints, _femcontext);
1012  }
1013  }
1014 
1015  if (get_residual && (print_residual_norms || print_residuals))
1016  this->rhs->close();
1017  if (get_residual && print_residual_norms)
1018  {
1019  std::streamsize old_precision = libMesh::out.precision();
1020  libMesh::out.precision(16);
1021  libMesh::out << "|F| = " << this->rhs->l1_norm() << std::endl;
1022  libMesh::out.precision(old_precision);
1023  }
1024  if (get_residual && print_residuals)
1025  {
1026  std::streamsize old_precision = libMesh::out.precision();
1027  libMesh::out.precision(16);
1028  libMesh::out << "F = [" << *(this->rhs) << "];" << std::endl;
1029  libMesh::out.precision(old_precision);
1030  }
1031 
1032  if (get_jacobian && (print_jacobian_norms || print_jacobians))
1033  this->matrix->close();
1034  if (get_jacobian && print_jacobian_norms)
1035  {
1036  std::streamsize old_precision = libMesh::out.precision();
1037  libMesh::out.precision(16);
1038  libMesh::out << "|J| = " << this->matrix->l1_norm() << std::endl;
1039  libMesh::out.precision(old_precision);
1040  }
1041  if (get_jacobian && print_jacobians)
1042  {
1043  std::streamsize old_precision = libMesh::out.precision();
1044  libMesh::out.precision(16);
1045  libMesh::out << "J = [" << *(this->matrix) << "];" << std::endl;
1046  libMesh::out.precision(old_precision);
1047  }
1048 }
FEFamily family
Definition: fe_type.h:203
const FEType & type() const
Definition: variable.h:119
UniquePtr< TimeSolver > time_solver
Definition: diff_system.h:221
void numerical_nonlocal_jacobian(FEMContext &context) const
Definition: fem_system.C:1310
Real verify_analytic_jacobians
Definition: fem_system.h:203
virtual void pre_fe_reinit(const System &, const Elem *e)
Definition: fem_context.C:1580
virtual void zero() libmesh_override
Definition: dense_matrix.h:792
void parallel_for(const Range &range, const Body &body)
Definition: threads_none.h:73
processor_id_type n_processors() const
MeshBase & mesh
Real l1_norm() const
Definition: dense_matrix.h:990
const class libmesh_nullptr_t libmesh_nullptr
NumericVector< Number > * rhs
const VariableGroup & variable_group(unsigned int vg) const
Definition: system.h:2122
const DenseVector< Number > & get_elem_residual() const
Definition: diff_context.h:248
virtual unsigned int size() const libmesh_override
Definition: dense_vector.h:87
virtual Real l1_norm() const =0
long double max(long double a, double b)
Base class for Mesh.
Definition: mesh_base.h:67
virtual void zero()=0
libmesh_assert(j)
std::unique_ptr< T > UniquePtr
Definition: auto_ptr.h:46
const DenseMatrix< Number > & get_elem_jacobian() const
Definition: diff_context.h:282
unsigned int n_variable_groups() const
Definition: system.h:2092
const MeshBase & get_mesh() const
Definition: system.h:2012
virtual void zero()=0
virtual void init_context(DiffContext &) libmesh_override
Definition: fem_system.C:1342
boostcopy::enable_if_c< ScalarTraits< T2 >::value, void >::type add(const T2 factor, const DenseMatrix< T3 > &mat)
Definition: dense_matrix.h:883
UniquePtr< NumericVector< Number > > solution
Definition: system.h:1521
OStreamProxy err(std::cerr)
virtual void close()=0
virtual void update()
Definition: system.C:423
virtual void close()=0
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
SparseMatrix< Number > * matrix
virtual UniquePtr< DiffContext > build_context() libmesh_override
Definition: fem_system.C:1318
OStreamProxy out(std::cout)
virtual Real l1_norm() const =0
std::streamsize precision() const
processor_id_type processor_id() const
void libMesh::System::attach_assemble_function ( void   fptrEquationSystems &es, const std::string &name)
inherited

Register a user function to use in assembling the system matrix and RHS.

Definition at line 1805 of file system.C.

References libMesh::System::_assemble_system_function, libMesh::System::_assemble_system_object, libMesh::libmesh_assert(), libmesh_nullptr, and libMesh::out.

Referenced by libMesh::System::read_parallel_data().

1807 {
1808  libmesh_assert(fptr);
1809 
1811  {
1812  libmesh_here();
1813  libMesh::out << "WARNING: Cannot specify both assembly function and object!"
1814  << std::endl;
1815 
1817  }
1818 
1820 }
Assembly * _assemble_system_object
Definition: system.h:1820
const class libmesh_nullptr_t libmesh_nullptr
libmesh_assert(j)
void(* _assemble_system_function)(EquationSystems &es, const std::string &name)
Definition: system.h:1814
OStreamProxy out(std::cout)
void libMesh::System::attach_assemble_object ( System::Assembly assemble_in)
inherited

Register a user object to use in assembling the system matrix and RHS.

Definition at line 1824 of file system.C.

References libMesh::System::_assemble_system_function, libMesh::System::_assemble_system_object, libmesh_nullptr, and libMesh::out.

Referenced by libMesh::System::read_parallel_data().

1825 {
1827  {
1828  libmesh_here();
1829  libMesh::out << "WARNING: Cannot specify both assembly object and function!"
1830  << std::endl;
1831 
1833  }
1834 
1835  _assemble_system_object = &assemble_in;
1836 }
Assembly * _assemble_system_object
Definition: system.h:1820
const class libmesh_nullptr_t libmesh_nullptr
void(* _assemble_system_function)(EquationSystems &es, const std::string &name)
Definition: system.h:1814
OStreamProxy out(std::cout)
void libMesh::System::attach_constraint_function ( void   fptrEquationSystems &es, const std::string &name)
inherited

Register a user function for imposing constraints.

Definition at line 1840 of file system.C.

References libMesh::System::_constrain_system_function, libMesh::System::_constrain_system_object, libMesh::libmesh_assert(), libmesh_nullptr, and libMesh::out.

Referenced by libMesh::System::read_parallel_data().

1842 {
1843  libmesh_assert(fptr);
1844 
1846  {
1847  libmesh_here();
1848  libMesh::out << "WARNING: Cannot specify both constraint function and object!"
1849  << std::endl;
1850 
1852  }
1853 
1855 }
void(* _constrain_system_function)(EquationSystems &es, const std::string &name)
Definition: system.h:1825
Constraint * _constrain_system_object
Definition: system.h:1831
const class libmesh_nullptr_t libmesh_nullptr
libmesh_assert(j)
OStreamProxy out(std::cout)
void libMesh::System::attach_constraint_object ( System::Constraint constrain)
inherited

Register a user object for imposing constraints.

Definition at line 1859 of file system.C.

References libMesh::System::_constrain_system_function, libMesh::System::_constrain_system_object, libmesh_nullptr, and libMesh::out.

Referenced by libMesh::System::read_parallel_data().

1860 {
1862  {
1863  libmesh_here();
1864  libMesh::out << "WARNING: Cannot specify both constraint object and function!"
1865  << std::endl;
1866 
1868  }
1869 
1870  _constrain_system_object = &constrain;
1871 }
void(* _constrain_system_function)(EquationSystems &es, const std::string &name)
Definition: system.h:1825
Constraint * _constrain_system_object
Definition: system.h:1831
const class libmesh_nullptr_t libmesh_nullptr
OStreamProxy out(std::cout)
void libMesh::System::attach_init_function ( void   fptrEquationSystems &es, const std::string &name)
inherited

Register a user function to use in initializing the system.

Definition at line 1770 of file system.C.

References libMesh::System::_init_system_function, libMesh::System::_init_system_object, libMesh::libmesh_assert(), libmesh_nullptr, and libMesh::out.

Referenced by libMesh::System::read_parallel_data().

1772 {
1773  libmesh_assert(fptr);
1774 
1776  {
1777  libmesh_here();
1778  libMesh::out << "WARNING: Cannot specify both initialization function and object!"
1779  << std::endl;
1780 
1782  }
1783 
1784  _init_system_function = fptr;
1785 }
const class libmesh_nullptr_t libmesh_nullptr
libmesh_assert(j)
Initialization * _init_system_object
Definition: system.h:1809
void(* _init_system_function)(EquationSystems &es, const std::string &name)
Definition: system.h:1803
OStreamProxy out(std::cout)
void libMesh::System::attach_init_object ( System::Initialization init_in)
inherited

Register a user class to use to initialize the system.

Note
This is exclusive with the attach_init_function.

Definition at line 1789 of file system.C.

References libMesh::System::_init_system_function, libMesh::System::_init_system_object, libmesh_nullptr, and libMesh::out.

Referenced by libMesh::System::read_parallel_data().

1790 {
1792  {
1793  libmesh_here();
1794  libMesh::out << "WARNING: Cannot specify both initialization object and function!"
1795  << std::endl;
1796 
1798  }
1799 
1800  _init_system_object = &init_in;
1801 }
const class libmesh_nullptr_t libmesh_nullptr
Initialization * _init_system_object
Definition: system.h:1809
void(* _init_system_function)(EquationSystems &es, const std::string &name)
Definition: system.h:1803
OStreamProxy out(std::cout)
void libMesh::DifferentiableSystem::attach_physics ( DifferentiablePhysics physics_in)
inlineinherited

Attach external Physics object.

Definition at line 184 of file diff_system.h.

References libMesh::DifferentiableSystem::_diff_physics, libMesh::DifferentiablePhysics::clone_physics(), libMesh::DifferentiablePhysics::init_physics(), and libMesh::DifferentiableSystem::swap_physics().

185  { this->_diff_physics = (physics_in->clone_physics()).release();
186  this->_diff_physics->init_physics(*this);}
DifferentiablePhysics * _diff_physics
Definition: diff_system.h:358
virtual void init_physics(const System &sys)
void libMesh::DifferentiableSystem::attach_qoi ( DifferentiableQoI qoi_in)
inlineinherited

Attach external QoI object.

Definition at line 212 of file diff_system.h.

References libMesh::DifferentiableQoI::clone(), libMesh::DifferentiableSystem::diff_qoi, libMesh::DifferentiableQoI::init_qoi(), and libMesh::System::qoi.

213  { this->diff_qoi = (qoi_in->clone()).release();
214  // User needs to resize qoi system qoi accordingly
215  this->diff_qoi->init_qoi( this->qoi );}
DifferentiableQoI * diff_qoi
Definition: diff_system.h:365
std::vector< Number > qoi
Definition: system.h:1551
virtual void init_qoi(std::vector< Number > &)
Definition: diff_qoi.h:67
void libMesh::System::attach_QOI_derivative ( void   fptrEquationSystems &es, const std::string &name, const QoISet &qoi_indices, bool include_liftfunc, bool apply_constraints)
inherited

Register a user function for evaluating derivatives of a quantity of interest with respect to test functions, whose values should be placed in System::rhs

Definition at line 1911 of file system.C.

References libMesh::System::_qoi_evaluate_derivative_function, libMesh::System::_qoi_evaluate_derivative_object, libMesh::libmesh_assert(), libmesh_nullptr, and libMesh::out.

Referenced by libMesh::System::read_parallel_data().

1913 {
1914  libmesh_assert(fptr);
1915 
1917  {
1918  libmesh_here();
1919  libMesh::out << "WARNING: Cannot specify both QOI derivative function and object!"
1920  << std::endl;
1921 
1923  }
1924 
1926 }
const class libmesh_nullptr_t libmesh_nullptr
libmesh_assert(j)
QOIDerivative * _qoi_evaluate_derivative_object
Definition: system.h:1857
OStreamProxy out(std::cout)
void(* _qoi_evaluate_derivative_function)(EquationSystems &es, const std::string &name, const QoISet &qoi_indices, bool include_liftfunc, bool apply_constraints)
Definition: system.h:1848
void libMesh::System::attach_QOI_derivative_object ( QOIDerivative qoi_derivative)
inherited

Register a user object for evaluating derivatives of a quantity of interest with respect to test functions, whose values should be placed in System::rhs

Definition at line 1930 of file system.C.

References libMesh::System::_qoi_evaluate_derivative_function, libMesh::System::_qoi_evaluate_derivative_object, libmesh_nullptr, and libMesh::out.

Referenced by libMesh::System::read_parallel_data().

1931 {
1933  {
1934  libmesh_here();
1935  libMesh::out << "WARNING: Cannot specify both QOI derivative object and function!"
1936  << std::endl;
1937 
1939  }
1940 
1941  _qoi_evaluate_derivative_object = &qoi_derivative;
1942 }
const class libmesh_nullptr_t libmesh_nullptr
QOIDerivative * _qoi_evaluate_derivative_object
Definition: system.h:1857
OStreamProxy out(std::cout)
void(* _qoi_evaluate_derivative_function)(EquationSystems &es, const std::string &name, const QoISet &qoi_indices, bool include_liftfunc, bool apply_constraints)
Definition: system.h:1848
void libMesh::System::attach_QOI_function ( void   fptrEquationSystems &es, const std::string &name, const QoISet &qoi_indices)
inherited

Register a user function for evaluating the quantities of interest, whose values should be placed in System::qoi

Definition at line 1875 of file system.C.

References libMesh::System::_qoi_evaluate_function, libMesh::System::_qoi_evaluate_object, libMesh::libmesh_assert(), libmesh_nullptr, and libMesh::out.

Referenced by libMesh::System::read_parallel_data().

1878 {
1879  libmesh_assert(fptr);
1880 
1882  {
1883  libmesh_here();
1884  libMesh::out << "WARNING: Cannot specify both QOI function and object!"
1885  << std::endl;
1886 
1888  }
1889 
1890  _qoi_evaluate_function = fptr;
1891 }
const class libmesh_nullptr_t libmesh_nullptr
void(* _qoi_evaluate_function)(EquationSystems &es, const std::string &name, const QoISet &qoi_indices)
Definition: system.h:1836
libmesh_assert(j)
QOI * _qoi_evaluate_object
Definition: system.h:1843
OStreamProxy out(std::cout)
void libMesh::System::attach_QOI_object ( QOI qoi)
inherited

Register a user object for evaluating the quantities of interest, whose values should be placed in System::qoi

Definition at line 1895 of file system.C.

References libMesh::System::_qoi_evaluate_function, libMesh::System::_qoi_evaluate_object, libmesh_nullptr, and libMesh::out.

Referenced by libMesh::System::read_parallel_data().

1896 {
1898  {
1899  libmesh_here();
1900  libMesh::out << "WARNING: Cannot specify both QOI object and function!"
1901  << std::endl;
1902 
1904  }
1905 
1906  _qoi_evaluate_object = &qoi_in;
1907 }
const class libmesh_nullptr_t libmesh_nullptr
void(* _qoi_evaluate_function)(EquationSystems &es, const std::string &name, const QoISet &qoi_indices)
Definition: system.h:1836
QOI * _qoi_evaluate_object
Definition: system.h:1843
OStreamProxy out(std::cout)
void libMesh::System::boundary_project_solution ( const std::set< boundary_id_type > &  b,
const std::vector< unsigned int > &  variables,
FunctionBase< Number > *  f,
FunctionBase< Gradient > *  g = libmesh_nullptr 
)
inherited

Projects arbitrary boundary functions onto a vector of degree of freedom values for the current system. Only degrees of freedom which affect the function's trace on a boundary in the set b are affected. Only degrees of freedom associated with the variables listed in the vector variables are projected. The function value f and its gradient g are user-provided cloneable functors. A gradient g is only required/used for projecting onto finite element spaces with continuous derivatives. If non-default Parameters are to be used, they can be provided in the parameters argument.

This method projects an arbitrary boundary function onto the solution via L2 projections and nodal interpolations on each element.

Definition at line 999 of file system_projection.C.

References libMesh::System::boundary_project_vector().

Referenced by libMesh::System::project_vector(), and libMesh::System::system_type().

1003 {
1004  this->boundary_project_vector(b, variables, *solution, f, g);
1005 
1006  solution->localize(*current_local_solution);
1007 }
void boundary_project_vector(const std::set< boundary_id_type > &b, const std::vector< unsigned int > &variables, NumericVector< Number > &new_vector, FunctionBase< Number > *f, FunctionBase< Gradient > *g=libmesh_nullptr, int is_adjoint=-1) const
UniquePtr< NumericVector< Number > > current_local_solution
Definition: system.h:1533
UniquePtr< NumericVector< Number > > solution
Definition: system.h:1521
void libMesh::System::boundary_project_solution ( const std::set< boundary_id_type > &  b,
const std::vector< unsigned int > &  variables,
Number   fptrconst Point &p, const Parameters &parameters, const std::string &sys_name, const std::string &unknown_name,
Gradient   gptrconst Point &p, const Parameters &parameters, const std::string &sys_name, const std::string &unknown_name,
const Parameters parameters 
)
inherited

Projects arbitrary boundary functions onto a vector of degree of freedom values for the current system. Only degrees of freedom which affect the function's trace on a boundary in the set b are affected. Only degrees of freedom associated with the variables listed in the vector variables are projected. The function value fptr and its gradient gptr are represented by function pointers. A gradient gptr is only required/used for projecting onto finite element spaces with continuous derivatives.

void libMesh::System::boundary_project_vector ( const std::set< boundary_id_type > &  b,
const std::vector< unsigned int > &  variables,
NumericVector< Number > &  new_vector,
FunctionBase< Number > *  f,
FunctionBase< Gradient > *  g = libmesh_nullptr,
int  is_adjoint = -1 
) const
inherited

Projects arbitrary boundary functions onto a vector of degree of freedom values for the current system. Only degrees of freedom which affect the function's trace on a boundary in the set b are affected. Only degrees of freedom associated with the variables listed in the vector variables are projected. The function value f and its gradient g are user-provided cloneable functors. A gradient g is only required/used for projecting onto finite element spaces with continuous derivatives. If non-default Parameters are to be used, they can be provided in the parameters argument.

Constrain the new vector using the requested adjoint rather than primal constraints if is_adjoint is non-negative.

This method projects an arbitrary function via L2 projections and nodal interpolations on each element.

Definition at line 1041 of file system_projection.C.

References libMesh::NumericVector< T >::close(), libMesh::get_dof_map(), and libMesh::Threads::parallel_for().

Referenced by libMesh::System::boundary_project_solution(), and libMesh::System::system_type().

1047 {
1048  LOG_SCOPE ("boundary_project_vector()", "System");
1049 
1051  (ConstElemRange (this->get_mesh().active_local_elements_begin(),
1052  this->get_mesh().active_local_elements_end() ),
1053  BoundaryProjectSolution(b, variables, *this, f, g,
1054  this->get_equation_systems().parameters,
1055  new_vector)
1056  );
1057 
1058  // We don't do SCALAR dofs when just projecting the boundary, so
1059  // we're done here.
1060 
1061  new_vector.close();
1062 
1063 #ifdef LIBMESH_ENABLE_CONSTRAINTS
1064  if (is_adjoint == -1)
1065  this->get_dof_map().enforce_constraints_exactly(*this, &new_vector);
1066  else if (is_adjoint >= 0)
1068  is_adjoint);
1069 #endif
1070 }
void parallel_for(const Range &range, const Body &body)
Definition: threads_none.h:73
StoredRange< MeshBase::const_element_iterator, const Elem * > ConstElemRange
Definition: elem_range.h:34
const MeshBase & get_mesh() const
Definition: system.h:2012
const DofMap & get_dof_map() const
Definition: system.h:2028
void enforce_constraints_exactly(const System &system, NumericVector< Number > *v=libmesh_nullptr, bool homogeneous=false) const
virtual void close()=0
const EquationSystems & get_equation_systems() const
Definition: system.h:712
void enforce_adjoint_constraints_exactly(NumericVector< Number > &v, unsigned int q) const
void libMesh::System::boundary_project_vector ( const std::set< boundary_id_type > &  b,
const std::vector< unsigned int > &  variables,
Number   fptrconst Point &p, const Parameters &parameters, const std::string &sys_name, const std::string &unknown_name,
Gradient   gptrconst Point &p, const Parameters &parameters, const std::string &sys_name, const std::string &unknown_name,
const Parameters parameters,
NumericVector< Number > &  new_vector,
int  is_adjoint = -1 
) const
inherited

Projects arbitrary boundary functions onto a vector of degree of freedom values for the current system. Only degrees of freedom which affect the function's trace on a boundary in the set b are affected. Only degrees of freedom associated with the variables listed in the vector variables are projected. The function value fptr and its gradient gptr are represented by function pointers. A gradient gptr is only required/used for projecting onto finite element spaces with continuous derivatives.

Constrain the new vector using the requested adjoint rather than primal constraints if is_adjoint is non-negative.

UniquePtr< DiffContext > libMesh::FEMSystem::build_context ( )
virtualinherited

Builds a FEMContext object with enough information to do evaluations on each element.

For most problems, the default FEMSystem implementation is correct; users who subclass FEMContext will need to also reimplement this method to build it.

Reimplemented from libMesh::DifferentiableSystem.

Definition at line 1318 of file fem_system.C.

References libMesh::DifferentiableSystem::deltat, libMesh::DifferentiablePhysics::get_mesh_system(), libMesh::DifferentiablePhysics::get_mesh_x_var(), libMesh::DifferentiablePhysics::get_mesh_y_var(), libMesh::DifferentiablePhysics::get_mesh_z_var(), libMesh::DifferentiableSystem::get_physics(), libMesh::DifferentiableSystem::get_time_solver(), libMesh::TimeSolver::is_adjoint(), libMesh::DiffContext::is_adjoint(), libMesh::libmesh_assert(), libMesh::DiffContext::set_deltat_pointer(), libMesh::FEMContext::set_mesh_system(), libMesh::FEMContext::set_mesh_x_var(), libMesh::FEMContext::set_mesh_y_var(), and libMesh::FEMContext::set_mesh_z_var().

Referenced by libMesh::FEMSystem::assembly(), libMesh::FEMSystem::mesh_position_get(), and libMesh::FEMSystem::mesh_position_set().

1319 {
1320  FEMContext * fc = new FEMContext(*this);
1321 
1322  DifferentiablePhysics * phys = this->get_physics();
1323 
1324  libmesh_assert (phys);
1325 
1326  // If we are solving a moving mesh problem, tell that to the Context
1327  fc->set_mesh_system(phys->get_mesh_system());
1328  fc->set_mesh_x_var(phys->get_mesh_x_var());
1329  fc->set_mesh_y_var(phys->get_mesh_y_var());
1330  fc->set_mesh_z_var(phys->get_mesh_z_var());
1331 
1332  fc->set_deltat_pointer( &deltat );
1333 
1334  // If we are solving the adjoint problem, tell that to the Context
1335  fc->is_adjoint() = this->get_time_solver().is_adjoint();
1336 
1337  return UniquePtr<DiffContext>(fc);
1338 }
bool is_adjoint() const
Definition: time_solver.h:232
void set_mesh_z_var(unsigned int z_var)
Definition: fem_context.h:857
void set_mesh_x_var(unsigned int x_var)
Definition: fem_context.h:829
bool is_adjoint() const
Definition: diff_context.h:453
libmesh_assert(j)
std::unique_ptr< T > UniquePtr
Definition: auto_ptr.h:46
const System * get_mesh_system() const
Definition: diff_physics.h:621
unsigned int get_mesh_x_var() const
Definition: diff_physics.h:633
virtual void set_mesh_system(System *sys)
Definition: fem_context.h:803
const DifferentiablePhysics * get_physics() const
Definition: diff_system.h:169
unsigned int get_mesh_z_var() const
Definition: diff_physics.h:645
unsigned int get_mesh_y_var() const
Definition: diff_physics.h:639
void set_mesh_y_var(unsigned int y_var)
Definition: fem_context.h:843
void set_deltat_pointer(Real *dt)
Definition: diff_context.C:138
TimeSolver & get_time_solver()
Definition: diff_system.h:402
Real libMesh::System::calculate_norm ( const NumericVector< Number > &  v,
unsigned int  var,
FEMNormType  norm_type,
std::set< unsigned int > *  skip_dimensions = libmesh_nullptr 
) const
inherited
Returns
A norm of variable var in the vector v, in the specified norm (e.g. L2, L_INF, H1)

Definition at line 1397 of file system.C.

References libMesh::DISCRETE_L1, libMesh::DISCRETE_L2, libMesh::DISCRETE_L_INF, libMesh::System::discrete_var_norm(), libMesh::L2, libMesh::System::n_vars(), and libMesh::Real.

Referenced by libMesh::AdaptiveTimeSolver::calculate_norm(), libMesh::UnsteadySolver::du(), and libMesh::System::project_solution_on_reinit().

1401 {
1402  //short circuit to save time
1403  if (norm_type == DISCRETE_L1 ||
1404  norm_type == DISCRETE_L2 ||
1405  norm_type == DISCRETE_L_INF)
1406  return discrete_var_norm(v,var,norm_type);
1407 
1408  // Not a discrete norm
1409  std::vector<FEMNormType> norms(this->n_vars(), L2);
1410  std::vector<Real> weights(this->n_vars(), 0.0);
1411  norms[var] = norm_type;
1412  weights[var] = 1.0;
1413  Real val = this->calculate_norm(v, SystemNorm(norms, weights), skip_dimensions);
1414  return val;
1415 }
Real calculate_norm(const NumericVector< Number > &v, unsigned int var, FEMNormType norm_type, std::set< unsigned int > *skip_dimensions=libmesh_nullptr) const
Definition: system.C:1397
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
unsigned int n_vars() const
Definition: system.h:2084
Real discrete_var_norm(const NumericVector< Number > &v, unsigned int var, FEMNormType norm_type) const
Definition: system.C:1378
Real libMesh::System::calculate_norm ( const NumericVector< Number > &  v,
const SystemNorm norm,
std::set< unsigned int > *  skip_dimensions = libmesh_nullptr 
) const
inherited
Returns
A norm of the vector v, using component_norm and component_scale to choose and weight the norms of each variable.

Definition at line 1419 of file system.C.

References libMesh::System::_dof_map, libMesh::System::_mesh, std::abs(), libMesh::MeshBase::active_local_elements_begin(), libMesh::MeshBase::active_local_elements_end(), libMesh::TypeVector< T >::add_scaled(), libMesh::TypeTensor< T >::add_scaled(), libMesh::FEGenericBase< OutputType >::build(), libMesh::NumericVector< T >::build(), libMesh::ParallelObject::comm(), libMesh::FEType::default_quadrature_rule(), libMesh::Elem::dim(), libMesh::DISCRETE_L1, libMesh::DISCRETE_L2, libMesh::DISCRETE_L_INF, libMesh::System::discrete_var_norm(), libMesh::DofMap::dof_indices(), libMesh::MeshBase::elem_dimensions(), libMesh::FEGenericBase< OutputType >::get_d2phi(), libMesh::System::get_dof_map(), libMesh::FEGenericBase< OutputType >::get_dphi(), libMesh::FEAbstract::get_JxW(), libMesh::System::get_mesh(), libMesh::FEGenericBase< OutputType >::get_phi(), libMesh::H1, libMesh::H1_SEMINORM, libMesh::H2, libMesh::H2_SEMINORM, libMesh::SystemNorm::is_discrete(), libMesh::L1, libMesh::NumericVector< T >::l1_norm(), libMesh::L2, libMesh::NumericVector< T >::l2_norm(), libMesh::L_INF, libMesh::libmesh_assert(), libmesh_nullptr, libMesh::NumericVector< T >::linfty_norm(), libMesh::NumericVector< T >::localize(), std::max(), libMesh::Parallel::Communicator::max(), libMesh::QBase::n_points(), libMesh::System::n_vars(), libMesh::TypeVector< T >::norm(), libMesh::TypeTensor< T >::norm(), libMesh::TensorTools::norm_sq(), libMesh::TypeVector< T >::norm_sq(), libMesh::TypeTensor< T >::norm_sq(), libMesh::Real, libMesh::FEAbstract::reinit(), libMesh::SERIAL, libMesh::NumericVector< T >::size(), libMesh::Parallel::Communicator::sum(), libMesh::SystemNorm::type(), libMesh::DofMap::variable_type(), libMesh::W1_INF_SEMINORM, libMesh::W2_INF_SEMINORM, libMesh::SystemNorm::weight(), and libMesh::SystemNorm::weight_sq().

1422 {
1423  // This function must be run on all processors at once
1424  parallel_object_only();
1425 
1426  LOG_SCOPE ("calculate_norm()", "System");
1427 
1428  // Zero the norm before summation
1429  Real v_norm = 0.;
1430 
1431  if (norm.is_discrete())
1432  {
1433  //Check to see if all weights are 1.0 and all types are equal
1434  FEMNormType norm_type0 = norm.type(0);
1435  unsigned int check_var = 0;
1436  for (; check_var != this->n_vars(); ++check_var)
1437  if ((norm.weight(check_var) != 1.0) || (norm.type(check_var) != norm_type0))
1438  break;
1439 
1440  //All weights were 1.0 so just do the full vector discrete norm
1441  if (check_var == this->n_vars())
1442  {
1443  if (norm_type0 == DISCRETE_L1)
1444  return v.l1_norm();
1445  if (norm_type0 == DISCRETE_L2)
1446  return v.l2_norm();
1447  if (norm_type0 == DISCRETE_L_INF)
1448  return v.linfty_norm();
1449  else
1450  libmesh_error_msg("Invalid norm_type0 = " << norm_type0);
1451  }
1452 
1453  for (unsigned int var=0; var != this->n_vars(); ++var)
1454  {
1455  // Skip any variables we don't need to integrate
1456  if (norm.weight(var) == 0.0)
1457  continue;
1458 
1459  v_norm += norm.weight(var) * discrete_var_norm(v, var, norm.type(var));
1460  }
1461 
1462  return v_norm;
1463  }
1464 
1465  // Localize the potentially parallel vector
1466  UniquePtr<NumericVector<Number> > local_v = NumericVector<Number>::build(this->comm());
1467  local_v->init(v.size(), true, SERIAL);
1468  v.localize (*local_v, _dof_map->get_send_list());
1469 
1470  // I'm not sure how best to mix Hilbert norms on some variables (for
1471  // which we'll want to square then sum then square root) with norms
1472  // like L_inf (for which we'll just want to take an absolute value
1473  // and then sum).
1474  bool using_hilbert_norm = true,
1475  using_nonhilbert_norm = true;
1476 
1477  // Loop over all variables
1478  for (unsigned int var=0; var != this->n_vars(); ++var)
1479  {
1480  // Skip any variables we don't need to integrate
1481  Real norm_weight_sq = norm.weight_sq(var);
1482  if (norm_weight_sq == 0.0)
1483  continue;
1484  Real norm_weight = norm.weight(var);
1485 
1486  // Check for unimplemented norms (rather than just returning 0).
1487  FEMNormType norm_type = norm.type(var);
1488  if ((norm_type==H1) ||
1489  (norm_type==H2) ||
1490  (norm_type==L2) ||
1491  (norm_type==H1_SEMINORM) ||
1492  (norm_type==H2_SEMINORM))
1493  {
1494  if (!using_hilbert_norm)
1495  libmesh_not_implemented();
1496  using_nonhilbert_norm = false;
1497  }
1498  else if ((norm_type==L1) ||
1499  (norm_type==L_INF) ||
1500  (norm_type==W1_INF_SEMINORM) ||
1501  (norm_type==W2_INF_SEMINORM))
1502  {
1503  if (!using_nonhilbert_norm)
1504  libmesh_not_implemented();
1505  using_hilbert_norm = false;
1506  }
1507  else
1508  libmesh_not_implemented();
1509 
1510  const FEType & fe_type = this->get_dof_map().variable_type(var);
1511 
1512  // Allow space for dims 0-3, even if we don't use them all
1513  std::vector<FEBase *> fe_ptrs(4,libmesh_nullptr);
1514  std::vector<QBase *> q_rules(4,libmesh_nullptr);
1515 
1516  const std::set<unsigned char> & elem_dims = _mesh.elem_dimensions();
1517 
1518  // Prepare finite elements for each dimension present in the mesh
1519  for (std::set<unsigned char>::const_iterator d_it = elem_dims.begin();
1520  d_it != elem_dims.end(); ++d_it)
1521  {
1522  if (skip_dimensions && skip_dimensions->find(*d_it) != skip_dimensions->end())
1523  continue;
1524 
1525  q_rules[*d_it] =
1526  fe_type.default_quadrature_rule (*d_it).release();
1527 
1528  // Construct finite element object
1529 
1530  fe_ptrs[*d_it] = FEBase::build(*d_it, fe_type).release();
1531 
1532  // Attach quadrature rule to FE object
1533  fe_ptrs[*d_it]->attach_quadrature_rule (q_rules[*d_it]);
1534  }
1535 
1536  std::vector<dof_id_type> dof_indices;
1537 
1538  // Begin the loop over the elements
1539  MeshBase::const_element_iterator el =
1541  const MeshBase::const_element_iterator end_el =
1543 
1544  for ( ; el != end_el; ++el)
1545  {
1546  const Elem * elem = *el;
1547  const unsigned int dim = elem->dim();
1548 
1549  if (skip_dimensions && skip_dimensions->find(dim) != skip_dimensions->end())
1550  continue;
1551 
1552  FEBase * fe = fe_ptrs[dim];
1553  QBase * qrule = q_rules[dim];
1554  libmesh_assert(fe);
1555  libmesh_assert(qrule);
1556 
1557  const std::vector<Real> & JxW = fe->get_JxW();
1558  const std::vector<std::vector<Real> > * phi = libmesh_nullptr;
1559  if (norm_type == H1 ||
1560  norm_type == H2 ||
1561  norm_type == L2 ||
1562  norm_type == L1 ||
1563  norm_type == L_INF)
1564  phi = &(fe->get_phi());
1565 
1566  const std::vector<std::vector<RealGradient> > * dphi = libmesh_nullptr;
1567  if (norm_type == H1 ||
1568  norm_type == H2 ||
1569  norm_type == H1_SEMINORM ||
1570  norm_type == W1_INF_SEMINORM)
1571  dphi = &(fe->get_dphi());
1572 #ifdef LIBMESH_ENABLE_SECOND_DERIVATIVES
1573  const std::vector<std::vector<RealTensor> > * d2phi = libmesh_nullptr;
1574  if (norm_type == H2 ||
1575  norm_type == H2_SEMINORM ||
1576  norm_type == W2_INF_SEMINORM)
1577  d2phi = &(fe->get_d2phi());
1578 #endif
1579 
1580  fe->reinit (elem);
1581 
1582  this->get_dof_map().dof_indices (elem, dof_indices, var);
1583 
1584  const unsigned int n_qp = qrule->n_points();
1585 
1586  const unsigned int n_sf = cast_int<unsigned int>
1587  (dof_indices.size());
1588 
1589  // Begin the loop over the Quadrature points.
1590  for (unsigned int qp=0; qp<n_qp; qp++)
1591  {
1592  if (norm_type == L1)
1593  {
1594  Number u_h = 0.;
1595  for (unsigned int i=0; i != n_sf; ++i)
1596  u_h += (*phi)[i][qp] * (*local_v)(dof_indices[i]);
1597  v_norm += norm_weight *
1598  JxW[qp] * std::abs(u_h);
1599  }
1600 
1601  if (norm_type == L_INF)
1602  {
1603  Number u_h = 0.;
1604  for (unsigned int i=0; i != n_sf; ++i)
1605  u_h += (*phi)[i][qp] * (*local_v)(dof_indices[i]);
1606  v_norm = std::max(v_norm, norm_weight * std::abs(u_h));
1607  }
1608 
1609  if (norm_type == H1 ||
1610  norm_type == H2 ||
1611  norm_type == L2)
1612  {
1613  Number u_h = 0.;
1614  for (unsigned int i=0; i != n_sf; ++i)
1615  u_h += (*phi)[i][qp] * (*local_v)(dof_indices[i]);
1616  v_norm += norm_weight_sq *
1617  JxW[qp] * TensorTools::norm_sq(u_h);
1618  }
1619 
1620  if (norm_type == H1 ||
1621  norm_type == H2 ||
1622  norm_type == H1_SEMINORM)
1623  {
1624  Gradient grad_u_h;
1625  for (unsigned int i=0; i != n_sf; ++i)
1626  grad_u_h.add_scaled((*dphi)[i][qp], (*local_v)(dof_indices[i]));
1627  v_norm += norm_weight_sq *
1628  JxW[qp] * grad_u_h.norm_sq();
1629  }
1630 
1631  if (norm_type == W1_INF_SEMINORM)
1632  {
1633  Gradient grad_u_h;
1634  for (unsigned int i=0; i != n_sf; ++i)
1635  grad_u_h.add_scaled((*dphi)[i][qp], (*local_v)(dof_indices[i]));
1636  v_norm = std::max(v_norm, norm_weight * grad_u_h.norm());
1637  }
1638 
1639 #ifdef LIBMESH_ENABLE_SECOND_DERIVATIVES
1640  if (norm_type == H2 ||
1641  norm_type == H2_SEMINORM)
1642  {
1643  Tensor hess_u_h;
1644  for (unsigned int i=0; i != n_sf; ++i)
1645  hess_u_h.add_scaled((*d2phi)[i][qp], (*local_v)(dof_indices[i]));
1646  v_norm += norm_weight_sq *
1647  JxW[qp] * hess_u_h.norm_sq();
1648  }
1649 
1650  if (norm_type == W2_INF_SEMINORM)
1651  {
1652  Tensor hess_u_h;
1653  for (unsigned int i=0; i != n_sf; ++i)
1654  hess_u_h.add_scaled((*d2phi)[i][qp], (*local_v)(dof_indices[i]));
1655  v_norm = std::max(v_norm, norm_weight * hess_u_h.norm());
1656  }
1657 #endif
1658  }
1659  }
1660 
1661  // Need to delete the FE and quadrature objects to prevent a memory leak
1662  for (std::size_t i=0; i<fe_ptrs.size(); i++)
1663  if (fe_ptrs[i])
1664  delete fe_ptrs[i];
1665 
1666  for (std::size_t i=0; i<q_rules.size(); i++)
1667  if (q_rules[i])
1668  delete q_rules[i];
1669  }
1670 
1671  if (using_hilbert_norm)
1672  {
1673  this->comm().sum(v_norm);
1674  v_norm = std::sqrt(v_norm);
1675  }
1676  else
1677  {
1678  this->comm().max(v_norm);
1679  }
1680 
1681  return v_norm;
1682 }
double abs(double a)
virtual numeric_index_type size() const =0
const FEType & variable_type(const unsigned int c) const
Definition: dof_map.h:1686
void add_scaled(const TypeTensor< T2 > &, const T)
Definition: type_tensor.h:773
void add_scaled(const TypeVector< T2 > &, const T)
Definition: type_vector.h:620
virtual Real l2_norm() const =0
const class libmesh_nullptr_t libmesh_nullptr
virtual Real l1_norm() const =0
long double max(long double a, double b)
UniquePtr< DofMap > _dof_map
Definition: system.h:1863
libmesh_assert(j)
static UniquePtr< NumericVector< T > > build(const Parallel::Communicator &comm, const SolverPackage solver_package=libMesh::default_solver_package())
const MeshBase & get_mesh() const
Definition: system.h:2012
const DofMap & get_dof_map() const
Definition: system.h:2028
virtual element_iterator active_local_elements_begin()=0
NumberVectorValue Gradient
const std::set< unsigned char > & elem_dimensions() const
Definition: mesh_base.h:203
FEGenericBase< Real > FEBase
virtual Real linfty_norm() const =0
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
NumberTensorValue Tensor
const Parallel::Communicator & comm() const
ParallelType type() const
unsigned int n_vars() const
Definition: system.h:2084
virtual element_iterator active_local_elements_end()=0
MeshBase & _mesh
Definition: system.h:1875
virtual void localize(std::vector< T > &v_local) const =0
Real discrete_var_norm(const NumericVector< Number > &v, unsigned int var, FEMNormType norm_type) const
Definition: system.C:1378
void dof_indices(const Elem *const elem, std::vector< dof_id_type > &di) const
Definition: dof_map.C:2005
static UniquePtr< FEGenericBase > build(const unsigned int dim, const FEType &type)
void libMesh::ContinuationSystem::clear ( )
virtual

Clear all the data structures associated with the system.

Reimplemented from libMesh::DifferentiableSystem.

Definition at line 80 of file continuation_system.C.

References libMesh::DifferentiableSystem::clear().

Referenced by ~ContinuationSystem().

81 {
82  // FIXME: Do anything here, e.g. zero vectors, etc?
83 
84  // Call the Parent's clear function
85  Parent::clear();
86 }
virtual void clear() libmesh_override
Definition: diff_system.C:69
virtual void libMesh::DifferentiablePhysics::clear_physics ( )
virtualinherited

Clear any data structures associated with the physics.

Referenced by libMesh::DifferentiableSystem::clear(), and libMesh::DifferentiablePhysics::DifferentiablePhysics().

virtual void libMesh::DifferentiableQoI::clear_qoi ( )
inlinevirtualinherited

Clear all the data structures associated with the QoI.

Definition at line 73 of file diff_qoi.h.

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

73 {}
virtual UniquePtr<DifferentiableQoI> libMesh::DifferentiableSystem::clone ( )
inlinevirtualinherited

We don't allow systems to be attached to each other

Implements libMesh::DifferentiableQoI.

Definition at line 156 of file diff_system.h.

Referenced by libMesh::AdjointRefinementEstimator::estimate_error().

157  {
158  libmesh_not_implemented();
159  // dummy
160  return UniquePtr<DifferentiableQoI>(this);
161  }
virtual UniquePtr<DifferentiablePhysics> libMesh::DifferentiableSystem::clone_physics ( )
inlinevirtualinherited

We don't allow systems to be attached to each other

Implements libMesh::DifferentiablePhysics.

Definition at line 146 of file diff_system.h.

147  {
148  libmesh_not_implemented();
149  // dummy
150  return UniquePtr<DifferentiablePhysics>(this);
151  }
const Parallel::Communicator& libMesh::ParallelObject::comm ( ) const
inlineinherited
Returns
A reference to the Parallel::Communicator object used by this mesh.

Definition at line 87 of file parallel_object.h.

References libMesh::ParallelObject::_communicator.

Referenced by libMesh::__libmesh_petsc_diff_solver_monitor(), libMesh::__libmesh_petsc_diff_solver_residual(), libMesh::__libmesh_petsc_snes_jacobian(), libMesh::__libmesh_petsc_snes_postcheck(), libMesh::__libmesh_petsc_snes_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::ParmetisPartitioner::_do_repartition(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::BoundaryInfo::_find_id_maps(), libMesh::PetscLinearSolver< T >::_petsc_shell_matrix_get_diagonal(), libMesh::SlepcEigenSolver< T >::_petsc_shell_matrix_get_diagonal(), libMesh::PetscLinearSolver< T >::_petsc_shell_matrix_mult(), libMesh::SlepcEigenSolver< T >::_petsc_shell_matrix_mult(), libMesh::PetscLinearSolver< T >::_petsc_shell_matrix_mult_add(), libMesh::EquationSystems::_read_impl(), libMesh::MeshRefinement::_refine_elements(), libMesh::MeshRefinement::_smooth_flags(), libMesh::ImplicitSystem::add_matrix(), libMesh::System::add_vector(), libMesh::EigenSparseLinearSolver< T >::adjoint_solve(), libMesh::UnstructuredMesh::all_second_order(), libMesh::MeshTools::Modification::all_tri(), libMesh::LaplaceMeshSmoother::allgather_graph(), libMesh::FEMSystem::assemble_qoi(), libMesh::MeshCommunication::assign_global_indices(), libMesh::ParmetisPartitioner::assign_partitioning(), libMesh::DofMap::attach_matrix(), libMesh::Parallel::BinSorter< KeyType, IdxType >::binsort(), libMesh::Parallel::Sort< KeyType, IdxType >::binsort(), libMesh::MeshCommunication::broadcast(), libMesh::SparseMatrix< T >::build(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::Parallel::Histogram< KeyType, IdxType >::build_histogram(), libMesh::PetscNonlinearSolver< T >::build_mat_null_space(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::MeshBase::cache_elem_dims(), libMesh::System::calculate_norm(), libMesh::DofMap::check_dirichlet_bcid_consistency(), libMesh::DistributedVector< T >::clone(), libMesh::EigenSparseVector< T >::clone(), libMesh::LaspackVector< T >::clone(), libMesh::EpetraVector< T >::clone(), libMesh::PetscVector< T >::clone(), libMesh::EpetraVector< T >::close(), libMesh::Parallel::Sort< KeyType, IdxType >::communicate_bins(), 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::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::MeshTools::create_bounding_box(), 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::MeshRefinement::eliminate_unrefined_patches(), libMesh::EpetraVector< T >::EpetraVector(), libMesh::WeightedPatchRecoveryErrorEstimator::estimate_error(), libMesh::PatchRecoveryErrorEstimator::estimate_error(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::MeshRefinement::flag_elements_by_elem_fraction(), libMesh::MeshRefinement::flag_elements_by_error_fraction(), libMesh::MeshRefinement::flag_elements_by_nelem_target(), libMesh::MeshCommunication::gather(), libMesh::MeshCommunication::gather_neighboring_elements(), libMesh::CondensedEigenSystem::get_eigenpair(), libMesh::DofMap::get_info(), libMesh::ImplicitSystem::get_linear_solver(), libMesh::EquationSystems::get_solution(), libMesh::LocationMap< T >::init(), libMesh::PetscDiffSolver::init(), libMesh::TimeSolver::init(), libMesh::TopologyMap::init(), libMesh::TaoOptimizationSolver< T >::init(), libMesh::PetscNonlinearSolver< T >::init(), libMesh::DistributedVector< T >::init(), libMesh::EpetraVector< T >::init(), libMesh::PetscVector< T >::init(), libMesh::SystemSubsetBySubdomain::init(), libMesh::EigenSystem::init_data(), libMesh::EigenSystem::init_matrices(), libMesh::ParmetisPartitioner::initialize(), libMesh::OptimizationSystem::initialize_equality_constraints_storage(), libMesh::OptimizationSystem::initialize_inequality_constraints_storage(), 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::MeshRefinement::limit_level_mismatch_at_edge(), libMesh::MeshRefinement::limit_level_mismatch_at_node(), libMesh::MeshRefinement::limit_overrefined_boundary(), libMesh::MeshRefinement::limit_underrefined_boundary(), 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::DistributedVector< T >::max(), libMesh::FEMSystem::mesh_position_set(), libMesh::MeshSerializer::MeshSerializer(), libMesh::DistributedVector< T >::min(), libMesh::DistributedMesh::n_active_elem(), libMesh::MeshTools::n_active_levels(), libMesh::BoundaryInfo::n_boundary_conds(), 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::Partitioner::partition(), libMesh::MetisPartitioner::partition_range(), libMesh::Partitioner::partition_unpartitioned_elements(), libMesh::petsc_auto_fieldsplit(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::MeshBase::prepare_for_use(), libMesh::SparseMatrix< T >::print(), libMesh::Nemesis_IO::read(), libMesh::CheckpointIO::read(), libMesh::XdrIO::read(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_serialized_bc_names(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::MeshBase::recalculate_n_partitions(), libMesh::MeshCommunication::redistribute(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::MeshCommunication::send_coarse_ghosts(), libMesh::Partitioner::set_node_processor_ids(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::Partitioner::set_parent_processor_ids(), libMesh::LaplaceMeshSmoother::smooth(), libMesh::Parallel::Sort< KeyType, IdxType >::sort(), libMesh::MeshBase::subdomain_ids(), libMesh::BoundaryInfo::sync(), libMesh::Parallel::sync_element_data_by_parent_id(), libMesh::Parallel::sync_node_data_by_element_id(), libMesh::MeshRefinement::test_level_one(), libMesh::MeshRefinement::test_unflagged(), libMesh::MeshTools::total_weight(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::NameBasedIO::write(), libMesh::XdrIO::write(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), libMesh::XdrIO::write_serialized_nodesets(), libMesh::DistributedVector< T >::zero_clone(), libMesh::LaspackVector< T >::zero_clone(), libMesh::EigenSparseVector< T >::zero_clone(), libMesh::EpetraVector< T >::zero_clone(), and libMesh::PetscVector< T >::zero_clone().

88  { return _communicator; }
const Parallel::Communicator & _communicator
bool libMesh::System::compare ( const System other_system,
const Real  threshold,
const bool  verbose 
) const
virtualinherited
Returns
true when the other system contains identical data, up to the given threshold. Outputs some diagnostic info when verbose is set.

Definition at line 529 of file system.C.

References libMesh::System::_is_initialized, libMesh::System::_sys_name, libMesh::System::_vectors, libMesh::System::get_vector(), libMesh::libmesh_assert(), libMesh::System::n_vectors(), libMesh::System::name(), libMesh::out, and libMesh::System::solution.

Referenced by libMesh::EquationSystems::compare(), and libMesh::System::set_adjoint_already_solved().

532 {
533  // we do not care for matrices, but for vectors
535  libmesh_assert (other_system._is_initialized);
536 
537  if (verbose)
538  {
539  libMesh::out << " Systems \"" << _sys_name << "\"" << std::endl;
540  libMesh::out << " comparing matrices not supported." << std::endl;
541  libMesh::out << " comparing names...";
542  }
543 
544  // compare the name: 0 means identical
545  const int name_result = _sys_name.compare(other_system.name());
546  if (verbose)
547  {
548  if (name_result == 0)
549  libMesh::out << " identical." << std::endl;
550  else
551  libMesh::out << " names not identical." << std::endl;
552  libMesh::out << " comparing solution vector...";
553  }
554 
555 
556  // compare the solution: -1 means identical
557  const int solu_result = solution->compare (*other_system.solution.get(),
558  threshold);
559 
560  if (verbose)
561  {
562  if (solu_result == -1)
563  libMesh::out << " identical up to threshold." << std::endl;
564  else
565  libMesh::out << " first difference occurred at index = "
566  << solu_result << "." << std::endl;
567  }
568 
569 
570  // safety check, whether we handle at least the same number
571  // of vectors
572  std::vector<int> ov_result;
573 
574  if (this->n_vectors() != other_system.n_vectors())
575  {
576  if (verbose)
577  {
578  libMesh::out << " Fatal difference. This system handles "
579  << this->n_vectors() << " add'l vectors," << std::endl
580  << " while the other system handles "
581  << other_system.n_vectors()
582  << " add'l vectors." << std::endl
583  << " Aborting comparison." << std::endl;
584  }
585  return false;
586  }
587  else if (this->n_vectors() == 0)
588  {
589  // there are no additional vectors...
590  ov_result.clear ();
591  }
592  else
593  {
594  // compare other vectors
595  for (const_vectors_iterator pos = _vectors.begin();
596  pos != _vectors.end(); ++pos)
597  {
598  if (verbose)
599  libMesh::out << " comparing vector \""
600  << pos->first << "\" ...";
601 
602  // assume they have the same name
603  const NumericVector<Number> & other_system_vector =
604  other_system.get_vector(pos->first);
605 
606  ov_result.push_back(pos->second->compare (other_system_vector,
607  threshold));
608 
609  if (verbose)
610  {
611  if (ov_result[ov_result.size()-1] == -1)
612  libMesh::out << " identical up to threshold." << std::endl;
613  else
614  libMesh::out << " first difference occurred at" << std::endl
615  << " index = " << ov_result[ov_result.size()-1] << "." << std::endl;
616  }
617 
618  }
619 
620  } // finished comparing additional vectors
621 
622 
623  bool overall_result;
624 
625  // sum up the results
626  if ((name_result==0) && (solu_result==-1))
627  {
628  if (ov_result.size()==0)
629  overall_result = true;
630  else
631  {
632  bool ov_identical;
633  unsigned int n = 0;
634  do
635  {
636  ov_identical = (ov_result[n]==-1);
637  n++;
638  }
639  while (ov_identical && n<ov_result.size());
640  overall_result = ov_identical;
641  }
642  }
643  else
644  overall_result = false;
645 
646  if (verbose)
647  {
648  libMesh::out << " finished comparisons, ";
649  if (overall_result)
650  libMesh::out << "found no differences." << std::endl << std::endl;
651  else
652  libMesh::out << "found differences." << std::endl << std::endl;
653  }
654 
655  return overall_result;
656 }
bool _is_initialized
Definition: system.h:1950
std::map< std::string, NumericVector< Number > * >::const_iterator const_vectors_iterator
Definition: system.h:749
libmesh_assert(j)
UniquePtr< NumericVector< Number > > solution
Definition: system.h:1521
std::map< std::string, NumericVector< Number > * > _vectors
Definition: system.h:1914
const std::string _sys_name
Definition: system.h:1880
OStreamProxy out(std::cout)
unsigned int n_vectors() const
Definition: system.h:2212
void libMesh::ContinuationSystem::continuation_solve ( )

Perform a continuation solve of the system. In general, you can only begin the continuation solves after either reading in or solving for two previous values of the control parameter. The prior two solutions are required for starting up the continuation method.

Definition at line 358 of file continuation_system.C.

References std::abs(), libMesh::NumericVector< T >::add(), apply_predictor(), libMesh::FEMSystem::assembly(), libMesh::NumericVector< T >::close(), libMesh::SparseMatrix< T >::close(), continuation_parameter, continuation_parameter_tolerance, delta_u, dlambda_ds, libMesh::NumericVector< T >::dot(), ds_current, du_ds, G_Lambda, initial_newton_tolerance, initialize_tangent(), libMesh::NumericVector< T >::l2_norm(), libMesh::libmesh_real(), linear_solver, libMesh::ImplicitSystem::matrix, max_continuation_parameter, libMesh::DiffSolver::max_linear_iterations, libMesh::DiffSolver::max_nonlinear_iterations, std::min(), min_continuation_parameter, n_arclength_reductions, n_backtrack_steps, newton_progress_check, newton_solver, newton_step, old_continuation_parameter, libMesh::out, std::pow(), libMesh::BasicOStreamProxy< charT, traits >::precision(), previous_u, quiet, libMesh::Real, Residual, libMesh::ExplicitSystem::rhs, rhs_mode, libMesh::NumericVector< T >::scale(), libMesh::BasicOStreamProxy< charT, traits >::setf(), libMesh::System::solution, solution_tolerance, tangent_initialized, Theta, Theta_LOCA, libMesh::DifferentiableSystem::time_solver, libMesh::BasicOStreamProxy< charT, traits >::unsetf(), y, y_old, z, and libMesh::NumericVector< T >::zero().

359 {
360  // Be sure the user has set the continuation parameter pointer
362  libmesh_error_msg("You must set the continuation_parameter pointer " \
363  << "to a member variable of the derived class, preferably in the " \
364  << "Derived class's init_data function. This is how the ContinuationSystem " \
365  << "updates the continuation parameter.");
366 
367  // Use extra precision for all the numbers printed in this function.
368  std::streamsize old_precision = libMesh::out.precision();
370  libMesh::out.setf(std::ios_base::scientific);
371 
372  // We can't start solving the augmented PDE system unless the tangent
373  // vectors have been initialized. This only needs to occur once.
374  if (!tangent_initialized)
376 
377  // Save the old value of -du/dlambda. This will be used after the Newton iterations
378  // to compute the angle between previous tangent vectors. This cosine of this angle is
379  //
380  // tau := abs( (du/d(lambda)_i , du/d(lambda)_{i-1}) / (||du/d(lambda)_i|| * ||du/d(lambda)_{i-1}||) )
381  //
382  // The scaling factor tau (which should vary between 0 and 1) is used to shrink the step-size ds
383  // when we are approaching a turning point. Note that it can only shrink the step size.
384  *y_old = *y;
385 
386  // Set pointer to underlying Newton solver
387  if (!newton_solver)
388  newton_solver = cast_ptr<NewtonSolver *> (this->time_solver->diff_solver().get());
389 
390  // A pair for catching return values from linear system solves.
391  std::pair<unsigned int, Real> rval;
392 
393  // Convergence flag for the entire arcstep
394  bool arcstep_converged = false;
395 
396  // Begin loop over arcstep reductions.
397  for (unsigned int ns=0; ns<n_arclength_reductions; ++ns)
398  {
399  if (!quiet)
400  {
401  libMesh::out << "Current arclength stepsize, ds_current=" << ds_current << std::endl;
402  libMesh::out << "Current parameter value, lambda=" << *continuation_parameter << std::endl;
403  }
404 
405  // Upon exit from the nonlinear loop, the newton_converged flag
406  // will tell us the convergence status of Newton's method.
407  bool newton_converged = false;
408 
409  // The nonlinear residual before *any* nonlinear steps have been taken.
410  Real nonlinear_residual_firststep = 0.;
411 
412  // The nonlinear residual from the current "k" Newton step, before the Newton step
413  Real nonlinear_residual_beforestep = 0.;
414 
415  // The nonlinear residual from the current "k" Newton step, after the Newton step
416  Real nonlinear_residual_afterstep = 0.;
417 
418  // The linear solver tolerance, can be updated dynamically at each Newton step.
419  Real current_linear_tolerance = 0.;
420 
421  // The nonlinear loop
423  {
424  libMesh::out << "\n === Starting Newton step " << newton_step << " ===" << std::endl;
425 
426  // Set the linear system solver tolerance
427  // // 1.) Set the current linear tolerance based as a multiple of the current residual of the system.
428  // const Real residual_multiple = 1.e-4;
429  // Real current_linear_tolerance = residual_multiple*nonlinear_residual_beforestep;
430 
431  // // But if the current residual isn't small, don't let the solver exit with zero iterations!
432  // if (current_linear_tolerance > 1.)
433  // current_linear_tolerance = residual_multiple;
434 
435  // 2.) Set the current linear tolerance based on the method based on technique of Eisenstat & Walker.
436  if (newton_step==0)
437  {
438  // At first step, only try reducing the residual by a small amount
439  current_linear_tolerance = initial_newton_tolerance;//0.01;
440  }
441 
442  else
443  {
444  // The new tolerance is based on the ratio of the most recent tolerances
445  const Real alp=0.5*(1.+std::sqrt(5.));
446  const Real gam=0.9;
447 
448  libmesh_assert_not_equal_to (nonlinear_residual_beforestep, 0.0);
449  libmesh_assert_not_equal_to (nonlinear_residual_afterstep, 0.0);
450 
451  current_linear_tolerance = std::min(gam*std::pow(nonlinear_residual_afterstep/nonlinear_residual_beforestep, alp),
452  current_linear_tolerance*current_linear_tolerance
453  );
454 
455  // Don't let it get ridiculously small!!
456  if (current_linear_tolerance < 1.e-12)
457  current_linear_tolerance = 1.e-12;
458  }
459 
460  if (!quiet)
461  libMesh::out << "Using current_linear_tolerance=" << current_linear_tolerance << std::endl;
462 
463 
464  // Assemble the residual (and Jacobian).
465  rhs_mode = Residual;
466  assembly(true, // Residual
467  true); // Jacobian
468  rhs->close();
469 
470  // Save the current nonlinear residual. We don't need to recompute the residual unless
471  // this is the first step, since it was already computed as part of the convergence check
472  // at the end of the last loop iteration.
473  if (newton_step==0)
474  {
475  nonlinear_residual_beforestep = rhs->l2_norm();
476 
477  // Store the residual before any steps have been taken. This will *not*
478  // be updated at each step, and can be used to see if any progress has
479  // been made from the initial residual at later steps.
480  nonlinear_residual_firststep = nonlinear_residual_beforestep;
481 
482  const Real old_norm_u = solution->l2_norm();
483  libMesh::out << " (before step) ||R||_{L2} = " << nonlinear_residual_beforestep << std::endl;
484  libMesh::out << " (before step) ||R||_{L2}/||u|| = " << nonlinear_residual_beforestep / old_norm_u << std::endl;
485 
486  // In rare cases (very small arcsteps), it's possible that the residual is
487  // already below our absolute linear tolerance.
488  if (nonlinear_residual_beforestep < solution_tolerance)
489  {
490  if (!quiet)
491  libMesh::out << "Initial guess satisfied linear tolerance, exiting with zero Newton iterations!" << std::endl;
492 
493  // Since we go straight from here to the solve of the next tangent, we
494  // have to close the matrix before it can be assembled again.
495  matrix->close();
496  newton_converged=true;
497  break; // out of Newton iterations, with newton_converged=true
498  }
499  }
500 
501  else
502  {
503  nonlinear_residual_beforestep = nonlinear_residual_afterstep;
504  }
505 
506 
507  // Solve the linear system G_u*z = G
508  // Initial guess?
509  z->zero(); // It seems to be extremely important to zero z here, otherwise the solver quits early.
510  z->close();
511 
512  // It's possible that we have selected the current_linear_tolerance so large that
513  // a guess of z=zero yields a linear system residual |Az + R| small enough that the
514  // linear solver exits in zero iterations. If this happens, we will reduce the
515  // current_linear_tolerance until the linear solver does at least 1 iteration.
516  do
517  {
518  rval =
519  linear_solver->solve(*matrix,
520  *z,
521  *rhs,
522  //1.e-12,
523  current_linear_tolerance,
524  newton_solver->max_linear_iterations); // max linear iterations
525 
526  if (rval.first==0)
527  {
528  if (newton_step==0)
529  {
530  libMesh::out << "Repeating initial solve with smaller linear tolerance!" << std::endl;
531  current_linear_tolerance *= initial_newton_tolerance; // reduce the linear tolerance to force the solver to do some work
532  }
533  else
534  // We shouldn't get here ... it means the linear solver did no work on a Newton
535  // step other than the first one. If this happens, we need to think more about our
536  // tolerance selection.
537  libmesh_error_msg("Linear solver did no work!");
538  }
539 
540  } while (rval.first==0);
541 
542 
543  if (!quiet)
544  libMesh::out << " G_u*z = G solver converged at step "
545  << rval.first
546  << " linear tolerance = "
547  << rval.second
548  << "."
549  << std::endl;
550 
551  // Sometimes (I am not sure why) the linear solver exits after zero iterations.
552  // Perhaps it is hitting PETSc's divergence tolerance dtol??? If this occurs,
553  // we should break out of the Newton iteration loop because nothing further is
554  // going to happen... Of course if the tolerance is already small enough after
555  // zero iterations (how can this happen?!) we should not quit.
556  if ((rval.first == 0) && (rval.second > current_linear_tolerance*nonlinear_residual_beforestep))
557  {
558  if (!quiet)
559  libMesh::out << "Linear solver exited in zero iterations!" << std::endl;
560 
561  // Try to find out the reason for convergence/divergence
562  linear_solver->print_converged_reason();
563 
564  break; // out of Newton iterations
565  }
566 
567  // Note: need to scale z by -1 since our code always solves Jx=R
568  // instead of Jx=-R.
569  z->scale(-1.);
570  z->close();
571 
572 
573 
574 
575 
576 
577  // Assemble the G_Lambda vector, skip residual.
578  rhs_mode = G_Lambda;
579 
580  // Assemble both rhs and Jacobian
581  assembly(true, // Residual
582  false); // Jacobian
583 
584  // Not sure if this is really necessary
585  rhs->close();
586  const Real yrhsnorm=rhs->l2_norm();
587  if (yrhsnorm == 0.0)
588  libmesh_error_msg("||G_Lambda|| = 0");
589 
590  // We select a tolerance for the y-system which is based on the inexact Newton
591  // tolerance but scaled by an extra term proportional to the RHS (which is not -> 0 in this case)
592  const Real ysystemtol=current_linear_tolerance*(nonlinear_residual_beforestep/yrhsnorm);
593  if (!quiet)
594  libMesh::out << "ysystemtol=" << ysystemtol << std::endl;
595 
596  // Solve G_u*y = G_{\lambda}
597  // FIXME: Initial guess? This is really a solve for -du/dlambda so we could try
598  // initializing it with the latest approximation to that... du/dlambda ~ du/ds * ds/dlambda
599  //*y = *solution;
600  //y->add(-1., *previous_u);
601  //y->scale(-1. / (*continuation_parameter - old_continuation_parameter)); // Be careful of divide by zero...
602  //y->close();
603 
604  // const unsigned int max_attempts=1;
605  // unsigned int attempt=0;
606  // do
607  // {
608  // if (!quiet)
609  // libMesh::out << "Trying to solve tangent system, attempt " << attempt << std::endl;
610 
611  rval =
612  linear_solver->solve(*matrix,
613  *y,
614  *rhs,
615  //1.e-12,
616  ysystemtol,
617  newton_solver->max_linear_iterations); // max linear iterations
618 
619  if (!quiet)
620  libMesh::out << " G_u*y = G_{lambda} solver converged at step "
621  << rval.first
622  << ", linear tolerance = "
623  << rval.second
624  << "."
625  << std::endl;
626 
627  // Sometimes (I am not sure why) the linear solver exits after zero iterations.
628  // Perhaps it is hitting PETSc's divergence tolerance dtol??? If this occurs,
629  // we should break out of the Newton iteration loop because nothing further is
630  // going to happen...
631  if ((rval.first == 0) && (rval.second > ysystemtol))
632  {
633  if (!quiet)
634  libMesh::out << "Linear solver exited in zero iterations!" << std::endl;
635 
636  break; // out of Newton iterations
637  }
638 
639  // ++attempt;
640  // } while ((attempt<max_attempts) && (rval.first==newton_solver->max_linear_iterations));
641 
642 
643 
644 
645 
646  // Compute N, the residual of the arclength constraint eqn.
647  // Note 1: N(u,lambda,s) := (u-u_{old}, du_ds) + (lambda-lambda_{old}, dlambda_ds) - _ds
648  // We temporarily use the delta_u vector as a temporary vector for this calculation.
649  *delta_u = *solution;
650  delta_u->add(-1., *previous_u);
651 
652  // First part of the arclength constraint
654  const Number N2 = ((*continuation_parameter) - old_continuation_parameter)*dlambda_ds;
655  const Number N3 = ds_current;
656 
657  if (!quiet)
658  {
659  libMesh::out << " N1=" << N1 << std::endl;
660  libMesh::out << " N2=" << N2 << std::endl;
661  libMesh::out << " N3=" << N3 << std::endl;
662  }
663 
664  // The arclength constraint value
665  const Number N = N1+N2-N3;
666 
667  if (!quiet)
668  libMesh::out << " N=" << N << std::endl;
669 
670  const Number duds_dot_z = du_ds->dot(*z);
671  const Number duds_dot_y = du_ds->dot(*y);
672 
673  //libMesh::out << "duds_dot_z=" << duds_dot_z << std::endl;
674  //libMesh::out << "duds_dot_y=" << duds_dot_y << std::endl;
675  //libMesh::out << "dlambda_ds=" << dlambda_ds << std::endl;
676 
677  const Number delta_lambda_numerator = -(N + Theta_LOCA*Theta_LOCA*Theta*duds_dot_z);
678  const Number delta_lambda_denominator = (dlambda_ds - Theta_LOCA*Theta_LOCA*Theta*duds_dot_y);
679 
680  libmesh_assert_not_equal_to (delta_lambda_denominator, 0.0);
681 
682  // Now, we are ready to compute the step delta_lambda
683  const Number delta_lambda_comp = delta_lambda_numerator /
684  delta_lambda_denominator;
685  // Lambda is real-valued
686  const Real delta_lambda = libmesh_real(delta_lambda_comp);
687 
688  // Knowing delta_lambda, we are ready to update delta_u
689  // delta_u = z - delta_lambda*y
690  delta_u->zero();
691  delta_u->add(1., *z);
692  delta_u->add(-delta_lambda, *y);
693  delta_u->close();
694 
695  // Update the system solution and the continuation parameter.
696  solution->add(1., *delta_u);
697  solution->close();
698  *continuation_parameter += delta_lambda;
699 
700  // Did the Newton step actually reduce the residual?
701  rhs_mode = Residual;
702  assembly(true, // Residual
703  false); // Jacobian
704  rhs->close();
705  nonlinear_residual_afterstep = rhs->l2_norm();
706 
707 
708  // In a "normal" Newton step, ||du||/||R|| > 1 since the most recent
709  // step is where you "just were" and the current residual is where
710  // you are now. It can occur that ||du||/||R|| < 1, but these are
711  // likely not good cases to attempt backtracking (?).
712  const Real norm_du_norm_R = delta_u->l2_norm() / nonlinear_residual_afterstep;
713  if (!quiet)
714  libMesh::out << " norm_du_norm_R=" << norm_du_norm_R << std::endl;
715 
716 
717  // Factor to decrease the stepsize by for backtracking
718  Real newton_stepfactor = 1.;
719 
720  const bool attempt_backtracking =
721  (nonlinear_residual_afterstep > solution_tolerance)
722  && (nonlinear_residual_afterstep > nonlinear_residual_beforestep)
723  && (n_backtrack_steps>0)
724  && (norm_du_norm_R > 1.)
725  ;
726 
727  // If residual is not reduced, do Newton back tracking.
728  if (attempt_backtracking)
729  {
730  if (!quiet)
731  libMesh::out << "Newton step did not reduce residual." << std::endl;
732 
733  // back off the previous step.
734  solution->add(-1., *delta_u);
735  solution->close();
736  *continuation_parameter -= delta_lambda;
737 
738  // Backtracking: start cutting the Newton stepsize by halves until
739  // the new residual is actually smaller...
740  for (unsigned int backtrack_step=0; backtrack_step<n_backtrack_steps; ++backtrack_step)
741  {
742  newton_stepfactor *= 0.5;
743 
744  if (!quiet)
745  libMesh::out << "Shrinking step size by " << newton_stepfactor << std::endl;
746 
747  // Take fractional step
748  solution->add(newton_stepfactor, *delta_u);
749  solution->close();
750  *continuation_parameter += newton_stepfactor*delta_lambda;
751 
752  rhs_mode = Residual;
753  assembly(true, // Residual
754  false); // Jacobian
755  rhs->close();
756  nonlinear_residual_afterstep = rhs->l2_norm();
757 
758  if (!quiet)
759  libMesh::out << "At shrink step "
760  << backtrack_step
761  << ", nonlinear_residual_afterstep="
762  << nonlinear_residual_afterstep
763  << std::endl;
764 
765  if (nonlinear_residual_afterstep < nonlinear_residual_beforestep)
766  {
767  if (!quiet)
768  libMesh::out << "Backtracking succeeded!" << std::endl;
769 
770  break; // out of backtracking loop
771  }
772 
773  else
774  {
775  // Back off that step
776  solution->add(-newton_stepfactor, *delta_u);
777  solution->close();
778  *continuation_parameter -= newton_stepfactor*delta_lambda;
779  }
780 
781  // Save a copy of the solution from before the Newton step.
782  //UniquePtr<NumericVector<Number> > prior_iterate = solution->clone();
783  }
784  } // end if (attempte_backtracking)
785 
786 
787  // If we tried backtracking but the residual is still not reduced, print message.
788  if ((attempt_backtracking) && (nonlinear_residual_afterstep > nonlinear_residual_beforestep))
789  {
790  //libMesh::err << "Backtracking failed." << std::endl;
791  libMesh::out << "Backtracking failed." << std::endl;
792 
793  // 1.) Quit, exit program.
794  //libmesh_error_msg("Backtracking failed!");
795 
796  // 2.) Continue with last newton_stepfactor
797  if (newton_step<3)
798  {
799  solution->add(newton_stepfactor, *delta_u);
800  solution->close();
801  *continuation_parameter += newton_stepfactor*delta_lambda;
802  if (!quiet)
803  libMesh::out << "Backtracking could not reduce residual ... continuing anyway!" << std::endl;
804  }
805 
806  // 3.) Break out of Newton iteration loop with newton_converged = false,
807  // reduce the arclength stepsize, and try again.
808  else
809  {
810  break; // out of Newton iteration loop, with newton_converged=false
811  }
812  }
813 
814  // Another type of convergence check: suppose the residual has not been reduced
815  // from its initial value after half of the allowed Newton steps have occurred.
816  // In our experience, this typically means that it isn't going to converge and
817  // we could probably save time by dropping out of the Newton iteration loop and
818  // trying a smaller arcstep.
819  if (this->newton_progress_check)
820  {
821  if ((nonlinear_residual_afterstep > nonlinear_residual_firststep) &&
822  (newton_step+1 > static_cast<unsigned int>(0.5*newton_solver->max_nonlinear_iterations)))
823  {
824  libMesh::out << "Progress check failed: the current residual: "
825  << nonlinear_residual_afterstep
826  << ", is\n"
827  << "larger than the initial residual, and half of the allowed\n"
828  << "number of Newton iterations have elapsed.\n"
829  << "Exiting Newton iterations with converged==false." << std::endl;
830 
831  break; // out of Newton iteration loop, newton_converged = false
832  }
833  }
834 
835  // Safety check: Check the current continuation parameter against user-provided min-allowable parameter value
837  {
838  libMesh::out << "Continuation parameter fell below min-allowable value." << std::endl;
839  break; // out of Newton iteration loop, newton_converged = false
840  }
841 
842  // Safety check: Check the current continuation parameter against user-provided max-allowable parameter value
843  if ( (max_continuation_parameter != 0.0) &&
845  {
846  libMesh::out << "Current continuation parameter value: "
848  << " exceeded max-allowable value."
849  << std::endl;
850  break; // out of Newton iteration loop, newton_converged = false
851  }
852 
853 
854  // Check the convergence of the parameter and the solution. If they are small
855  // enough, we can break out of the Newton iteration loop.
856  const Real norm_delta_u = delta_u->l2_norm();
857  const Real norm_u = solution->l2_norm();
858  libMesh::out << " delta_lambda = " << delta_lambda << std::endl;
859  libMesh::out << " newton_stepfactor*delta_lambda = " << newton_stepfactor*delta_lambda << std::endl;
860  libMesh::out << " lambda_current = " << *continuation_parameter << std::endl;
861  libMesh::out << " ||delta_u|| = " << norm_delta_u << std::endl;
862  libMesh::out << " ||delta_u||/||u|| = " << norm_delta_u / norm_u << std::endl;
863 
864 
865  // Evaluate the residual at the current Newton iterate. We don't want to detect
866  // convergence due to a small Newton step when the residual is still not small.
867  rhs_mode = Residual;
868  assembly(true, // Residual
869  false); // Jacobian
870  rhs->close();
871  const Real norm_residual = rhs->l2_norm();
872  libMesh::out << " ||R||_{L2} = " << norm_residual << std::endl;
873  libMesh::out << " ||R||_{L2}/||u|| = " << norm_residual / norm_u << std::endl;
874 
875 
876  // FIXME: The norm_delta_u tolerance (at least) should be relative.
877  // It doesn't make sense to converge a solution whose size is ~ 10^5 to
878  // a tolerance of 1.e-6. Oh, and we should also probably check the
879  // (relative) size of the residual as well, instead of just the step.
880  if ((std::abs(delta_lambda) < continuation_parameter_tolerance) &&
881  //(norm_delta_u < solution_tolerance) && // This is a *very* strict criterion we can probably skip
882  (norm_residual < solution_tolerance))
883  {
884  if (!quiet)
885  libMesh::out << "Newton iterations converged!" << std::endl;
886 
887  newton_converged = true;
888  break; // out of Newton iterations
889  }
890  } // end nonlinear loop
891 
892  if (!newton_converged)
893  {
894  libMesh::out << "Newton iterations of augmented system did not converge!" << std::endl;
895 
896  // Reduce ds_current, recompute the solution and parameter, and continue to next
897  // arcstep, if there is one.
898  ds_current *= 0.5;
899 
900  // Go back to previous solution and parameter value.
901  *solution = *previous_u;
903 
904  // Compute new predictor with smaller ds
905  apply_predictor();
906  }
907  else
908  {
909  // Set step convergence and break out
910  arcstep_converged=true;
911  break; // out of arclength reduction loop
912  }
913 
914  } // end loop over arclength reductions
915 
916  // Check for convergence of the whole arcstep. If not converged at this
917  // point, we have no choice but to quit.
918  if (!arcstep_converged)
919  libmesh_error_msg("Arcstep failed to converge after max number of reductions! Exiting...");
920 
921  // Print converged solution control parameter and max value.
922  libMesh::out << "lambda_current=" << *continuation_parameter << std::endl;
923  //libMesh::out << "u_max=" << solution->max() << std::endl;
924 
925  // Reset old stream precision and flags.
926  libMesh::out.precision(old_precision);
927  libMesh::out.unsetf(std::ios_base::scientific);
928 
929  // Note: we don't want to go on to the next guess yet, since the user may
930  // want to post-process this data. It's up to the user to call advance_arcstep()
931  // when they are ready to go on.
932 }
T libmesh_real(T a)
double abs(double a)
UniquePtr< TimeSolver > time_solver
Definition: diff_system.h:221
NumericVector< Number > * previous_u
UniquePtr< LinearSolver< Number > > linear_solver
virtual Real l2_norm() const =0
unsigned int max_nonlinear_iterations
Definition: diff_solver.h:156
NumericVector< Number > * delta_u
NumericVector< Number > * rhs
virtual void zero()=0
virtual void scale(const T factor)=0
NumericVector< Number > * du_ds
virtual void assembly(bool get_residual, bool get_jacobian, bool apply_heterogeneous_constraints=false, bool apply_no_constraints=false) libmesh_override
Definition: fem_system.C:852
NumericVector< Number > * z
unsigned int max_linear_iterations
Definition: diff_solver.h:148
NumericVector< Number > * y_old
NumericVector< Number > * y
void unsetf(std::ios_base::fmtflags mask)
UniquePtr< NumericVector< Number > > solution
Definition: system.h:1521
double pow(double a, int b)
virtual void close()=0
virtual void close()=0
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
std::ios_base::fmtflags setf(std::ios_base::fmtflags fmtfl)
SparseMatrix< Number > * matrix
virtual T dot(const NumericVector< T > &v) const =0
virtual void add(const numeric_index_type i, const T value)=0
OStreamProxy out(std::cout)
long double min(long double a, double b)
std::streamsize precision() const
Number libMesh::System::current_solution ( const dof_id_type  global_dof_number) const
inherited
Returns
The current solution for the specified global DOF.

Definition at line 190 of file system.C.

References libMesh::System::_dof_map, and libMesh::System::current_local_solution.

Referenced by libMesh::ExactSolution::_compute_error(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::HPCoarsenTest::add_projection(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::HPCoarsenTest::select_refinement(), libMesh::EnsightIO::write_scalar_ascii(), and libMesh::EnsightIO::write_vector_ascii().

191 {
192  // Check the sizes
193  libmesh_assert_less (global_dof_number, _dof_map->n_dofs());
194  libmesh_assert_less (global_dof_number, current_local_solution->size());
195 
196  return (*current_local_solution)(global_dof_number);
197 }
UniquePtr< NumericVector< Number > > current_local_solution
Definition: system.h:1533
UniquePtr< DofMap > _dof_map
Definition: system.h:1863
virtual bool libMesh::DifferentiablePhysics::damping_residual ( bool  request_jacobian,
DiffContext  
)
inlinevirtualinherited

Subtracts a damping vector contribution on elem from elem_residual. This method is not used in first-order-in-time problems. For second-order-in-time problems, this is the $ C(u,\ddot{u})\ddot{u} $ term. This method is only called for UnsteadySolver-based TimeSolvers.

If this method receives request_jacobian = true, then it should compute elem_jacobian and return true if possible. If elem_jacobian has not been computed then the method should return false.

If the problem has no damping, the default "do-nothing" is correct. Otherwise, this must be reimplemented.

Definition at line 371 of file diff_physics.h.

Referenced by libMesh::EulerSolver::element_residual(), libMesh::Euler2Solver::element_residual(), and libMesh::NewmarkSolver::element_residual().

372  {
373  return request_jacobian;
374  }
void libMesh::System::deactivate ( )
inlineinherited

Deactivates the system. Only active systems are solved.

Definition at line 2060 of file system.h.

References libMesh::System::_active.

Referenced by libMesh::System::get_equation_systems().

2061 {
2062  _active = false;
2063 }
void libMesh::ImplicitSystem::disable_cache ( )
virtualinherited

Avoids use of any cached data that might affect any solve result. Should be overridden in derived systems.

Reimplemented from libMesh::System.

Definition at line 313 of file implicit_system.C.

References libMesh::System::assemble_before_solve, libMesh::ImplicitSystem::get_linear_solver(), and libMesh::LinearSolver< T >::reuse_preconditioner().

313  {
314  this->assemble_before_solve = true;
315  this->get_linear_solver()->reuse_preconditioner(false);
316 }
virtual LinearSolver< Number > * get_linear_solver() const
virtual void reuse_preconditioner(bool)
bool assemble_before_solve
Definition: system.h:1475
void libMesh::ReferenceCounter::disable_print_counter_info ( )
staticinherited
virtual bool libMesh::DifferentiablePhysics::element_constraint ( bool  request_jacobian,
DiffContext  
)
inlinevirtualinherited

Adds the constraint contribution on elem to elem_residual. If this method receives request_jacobian = true, then it should compute elem_jacobian and return true if possible. If elem_jacobian has not been computed then the method should return false.

Users may need to reimplement this for their particular PDE.

To implement the constraint 0 = G(u), the user should examine u = elem_solution and add (G(u), phi_i) to elem_residual in elem_constraint().

Definition at line 141 of file diff_physics.h.

Referenced by libMesh::EulerSolver::element_residual(), libMesh::Euler2Solver::element_residual(), libMesh::SteadySolver::element_residual(), libMesh::EigenTimeSolver::element_residual(), and libMesh::NewmarkSolver::element_residual().

142  {
143  return request_jacobian;
144  }
virtual void libMesh::DifferentiableSystem::element_postprocess ( DiffContext )
inlinevirtualinherited

Does any work that needs to be done on elem in a postprocessing loop.

Definition at line 269 of file diff_system.h.

269 {}
virtual void libMesh::DifferentiableQoI::element_qoi ( DiffContext ,
const QoISet  
)
inlinevirtualinherited

Does any work that needs to be done on elem in a quantity of interest assembly loop, outputting to elem_qoi.

Only qois included in the supplied QoISet need to be assembled.

Definition at line 106 of file diff_qoi.h.

108  {}
virtual void libMesh::DifferentiableQoI::element_qoi_derivative ( DiffContext ,
const QoISet  
)
inlinevirtualinherited

Does any work that needs to be done on elem in a quantity of interest derivative assembly loop, outputting to elem_qoi_derivative

Only qois included in the supplied QoISet need their derivatives assembled.

Definition at line 118 of file diff_qoi.h.

120  {}
virtual bool libMesh::DifferentiablePhysics::element_time_derivative ( bool  request_jacobian,
DiffContext  
)
inlinevirtualinherited

Adds the time derivative contribution on elem to elem_residual. If this method receives request_jacobian = true, then it should compute elem_jacobian and return true if possible. If elem_jacobian has not been computed then the method should return false.

Users need to reimplement this for their particular PDE.

To implement the physics model du/dt = F(u), the user should examine u = elem_solution and add (F(u), phi_i) to elem_residual in elem_time_derivative().

Definition at line 123 of file diff_physics.h.

Referenced by libMesh::SteadySolver::element_residual(), and libMesh::EigenTimeSolver::element_residual().

124  {
125  return request_jacobian;
126  }
void libMesh::ReferenceCounter::enable_print_counter_info ( )
staticinherited

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

Definition at line 101 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

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

102 {
103  _enable_print_counter = true;
104  return;
105 }
virtual bool libMesh::FEMPhysics::eulerian_residual ( bool  request_jacobian,
DiffContext context 
)
virtualinherited

Adds a pseudo-convection contribution on elem to elem_residual, if the nodes of elem are being translated by a moving mesh.

This function assumes that the user's time derivative equations (except for any equations involving unknown mesh xyz coordinates themselves) are expressed in an Eulerian frame of reference, and that the user is satisfied with an unstabilized convection term. Lagrangian equations will probably require overriding eulerian_residual() with a blank function; ALE or stabilized formulations will require reimplementing eulerian_residual() entirely.

Reimplemented from libMesh::DifferentiablePhysics.

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

virtual bool libMesh::DifferentiablePhysics::eulerian_residual ( bool  request_jacobian,
DiffContext  
)
inlinevirtualinherited

Adds a pseudo-convection contribution on elem to elem_residual, if the nodes of elem are being translated by a moving mesh.

The library provides a basic implementation in FEMPhysics::eulerian_residual()

Reimplemented in libMesh::FEMPhysics.

Definition at line 291 of file diff_physics.h.

292  {
293  return request_jacobian;
294  }
void libMesh::ImplicitSystem::forward_qoi_parameter_sensitivity ( const QoISet qoi_indices,
const ParameterVector parameters,
SensitivityData sensitivities 
)
virtualinherited

Solves for the derivative of each of the system's quantities of interest q in qoi[qoi_indices] with respect to each parameter in parameters, placing the result for qoi i and parameter j into sensitivities[i][j].

Uses the forward sensitivity method.

Currently uses finite differenced derivatives (partial q / partial p) and (partial R / partial p).

Reimplemented from libMesh::System.

Definition at line 819 of file implicit_system.C.

References std::abs(), libMesh::SensitivityData::allocate_data(), libMesh::ExplicitSystem::assemble_qoi(), libMesh::ExplicitSystem::assemble_qoi_derivative(), libMesh::ImplicitSystem::assembly(), libMesh::NumericVector< T >::close(), libMesh::SparseMatrix< T >::close(), libMesh::NumericVector< T >::dot(), libMesh::System::get_adjoint_rhs(), libMesh::System::get_sensitivity_solution(), libMesh::QoISet::has_index(), libMesh::ImplicitSystem::matrix, std::max(), libMesh::System::qoi, libMesh::Real, libMesh::ExplicitSystem::rhs, libMesh::ImplicitSystem::sensitivity_solve(), libMesh::ParameterVector::size(), and libMesh::TOLERANCE.

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

822 {
823  ParameterVector & parameters =
824  const_cast<ParameterVector &>(parameters_in);
825 
826  const unsigned int Np = cast_int<unsigned int>
827  (parameters.size());
828  const unsigned int Nq = cast_int<unsigned int>
829  (qoi.size());
830 
831  // An introduction to the problem:
832  //
833  // Residual R(u(p),p) = 0
834  // partial R / partial u = J = system matrix
835  //
836  // This implies that:
837  // d/dp(R) = 0
838  // (partial R / partial p) +
839  // (partial R / partial u) * (partial u / partial p) = 0
840 
841  // We first solve for (partial u / partial p) for each parameter:
842  // J * (partial u / partial p) = - (partial R / partial p)
843 
844  this->sensitivity_solve(parameters);
845 
846  // Get ready to fill in sensitivities:
847  sensitivities.allocate_data(qoi_indices, *this, parameters);
848 
849  // We use the identity:
850  // dq/dp = (partial q / partial p) + (partial q / partial u) *
851  // (partial u / partial p)
852 
853  // We get (partial q / partial u) from the user
854  this->assemble_qoi_derivative(qoi_indices,
855  /* include_liftfunc = */ true,
856  /* apply_constraints = */ false);
857 
858  // We don't need these to be closed() in this function, but libMesh
859  // standard practice is to have them closed() by the time the
860  // function exits
861  for (std::size_t i=0; i != this->qoi.size(); ++i)
862  if (qoi_indices.has_index(i))
863  this->get_adjoint_rhs(i).close();
864 
865  for (unsigned int j=0; j != Np; ++j)
866  {
867  // We currently get partial derivatives via central differencing
868 
869  // (partial q / partial p) ~= (q(p+dp)-q(p-dp))/(2*dp)
870 
871  Number old_parameter = *parameters[j];
872 
873  const Real delta_p =
874  TOLERANCE * std::max(std::abs(old_parameter), 1e-3);
875 
876  *parameters[j] = old_parameter - delta_p;
877  this->assemble_qoi(qoi_indices);
878  std::vector<Number> qoi_minus = this->qoi;
879 
880  *parameters[j] = old_parameter + delta_p;
881  this->assemble_qoi(qoi_indices);
882  std::vector<Number> & qoi_plus = this->qoi;
883 
884  std::vector<Number> partialq_partialp(Nq, 0);
885  for (unsigned int i=0; i != Nq; ++i)
886  if (qoi_indices.has_index(i))
887  partialq_partialp[i] = (qoi_plus[i] - qoi_minus[i]) / (2.*delta_p);
888 
889  // Don't leave the parameter changed
890  *parameters[j] = old_parameter;
891 
892  for (unsigned int i=0; i != Nq; ++i)
893  if (qoi_indices.has_index(i))
894  sensitivities[i][j] = partialq_partialp[i] +
895  this->get_adjoint_rhs(i).dot(this->get_sensitivity_solution(j));
896  }
897 
898  // All parameters have been reset.
899  // We didn't cache the original rhs or matrix for memory reasons,
900  // but we can restore them to a state consistent solution -
901  // principle of least surprise.
902  this->assembly(true, true);
903  this->rhs->close();
904  this->matrix->close();
905  this->assemble_qoi(qoi_indices);
906 }
double abs(double a)
NumericVector< Number > & get_sensitivity_solution(unsigned int i=0)
Definition: system.C:934
virtual std::pair< unsigned int, Real > sensitivity_solve(const ParameterVector &parameters) libmesh_override
NumericVector< Number > * rhs
static const Real TOLERANCE
long double max(long double a, double b)
virtual void assemble_qoi_derivative(const QoISet &qoi_indices=QoISet(), bool include_liftfunc=true, bool apply_constraints=true) libmesh_override
virtual void assembly(bool, bool, bool=false, bool=false)
std::vector< Number > qoi
Definition: system.h:1551
virtual void close()=0
virtual void close()=0
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
SparseMatrix< Number > * matrix
virtual T dot(const NumericVector< T > &v) const =0
virtual void assemble_qoi(const QoISet &qoi_indices=QoISet()) libmesh_override
NumericVector< Number > & get_adjoint_rhs(unsigned int i=0)
Definition: system.C:1049
NumericVector< Number > & libMesh::System::get_adjoint_rhs ( unsigned int  i = 0)
inherited
Returns
A reference to one of the system's adjoint rhs vectors, by default the one corresponding to the first qoi. This what the user's QoI derivative code should assemble when setting up an adjoint problem

Definition at line 1049 of file system.C.

References libMesh::System::get_vector().

Referenced by libMesh::ImplicitSystem::adjoint_solve(), libMesh::ImplicitSystem::forward_qoi_parameter_sensitivity(), libMesh::System::project_solution_on_reinit(), libMesh::ImplicitSystem::qoi_parameter_hessian(), libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product(), and libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve().

1050 {
1051  std::ostringstream adjoint_rhs_name;
1052  adjoint_rhs_name << "adjoint_rhs" << i;
1053 
1054  return this->get_vector(adjoint_rhs_name.str());
1055 }
const NumericVector< Number > & get_vector(const std::string &vec_name) const
Definition: system.C:792
const NumericVector< Number > & libMesh::System::get_adjoint_rhs ( unsigned int  i = 0) const
inherited
Returns
A reference to one of the system's adjoint rhs vectors, by default the one corresponding to the first qoi.

Definition at line 1059 of file system.C.

References libMesh::System::get_vector().

1060 {
1061  std::ostringstream adjoint_rhs_name;
1062  adjoint_rhs_name << "adjoint_rhs" << i;
1063 
1064  return this->get_vector(adjoint_rhs_name.str());
1065 }
const NumericVector< Number > & get_vector(const std::string &vec_name) const
Definition: system.C:792
NumericVector< Number > & libMesh::System::get_adjoint_solution ( unsigned int  i = 0)
inherited
Returns
A reference to one of the system's adjoint solution vectors, by default the one corresponding to the first qoi.

Definition at line 987 of file system.C.

References libMesh::System::get_vector().

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::ImplicitSystem::adjoint_solve(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::AdjointResidualErrorEstimator::estimate_error(), libMesh::System::project_solution_on_reinit(), libMesh::ImplicitSystem::qoi_parameter_hessian(), libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product(), and libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve().

988 {
989  std::ostringstream adjoint_name;
990  adjoint_name << "adjoint_solution" << i;
991 
992  return this->get_vector(adjoint_name.str());
993 }
const NumericVector< Number > & get_vector(const std::string &vec_name) const
Definition: system.C:792
const NumericVector< Number > & libMesh::System::get_adjoint_solution ( unsigned int  i = 0) const
inherited
Returns
A reference to one of the system's adjoint solution vectors, by default the one corresponding to the first qoi.

Definition at line 997 of file system.C.

References libMesh::System::get_vector().

998 {
999  std::ostringstream adjoint_name;
1000  adjoint_name << "adjoint_solution" << i;
1001 
1002  return this->get_vector(adjoint_name.str());
1003 }
const NumericVector< Number > & get_vector(const std::string &vec_name) const
Definition: system.C:792
void libMesh::System::get_all_variable_numbers ( std::vector< unsigned int > &  all_variable_numbers) const
inherited

Fills all_variable_numbers with all the variable numbers for the variables that have been added to this system.

Definition at line 1276 of file system.C.

References libMesh::System::_variable_numbers, and libMesh::System::n_vars().

Referenced by libMesh::System::project_solution_on_reinit().

1277 {
1278  all_variable_numbers.resize(n_vars());
1279 
1280  // Make sure the variable exists
1281  std::map<std::string, unsigned short int>::const_iterator
1282  it = _variable_numbers.begin();
1283  std::map<std::string, unsigned short int>::const_iterator
1284  it_end = _variable_numbers.end();
1285 
1286  unsigned int count = 0;
1287  for ( ; it != it_end; ++it)
1288  {
1289  all_variable_numbers[count] = it->second;
1290  count++;
1291  }
1292 }
std::map< std::string, unsigned short int > _variable_numbers
Definition: system.h:1901
unsigned int n_vars() const
Definition: system.h:2084
const DofMap & libMesh::System::get_dof_map ( ) const
inlineinherited
Returns
A constant reference to this system's _dof_map.

Definition at line 2028 of file system.h.

References libMesh::System::_dof_map.

Referenced by libMesh::__libmesh_petsc_diff_solver_residual(), libMesh::__libmesh_petsc_snes_postcheck(), libMesh::ExactSolution::_compute_error(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::DifferentiableSystem::add_dot_var_dirichlet_bcs(), libMesh::HPCoarsenTest::add_projection(), libMesh::UnsteadySolver::adjoint_advance_timestep(), libMesh::ImplicitSystem::adjoint_solve(), libMesh::NewmarkSolver::advance_timestep(), libMesh::UnsteadySolver::advance_timestep(), libMesh::EquationSystems::allgather(), libMesh::EquationSystems::build_discontinuous_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::System::calculate_norm(), libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), DMCreateDomainDecomposition_libMesh(), DMCreateFieldDecomposition_libMesh(), DMlibMeshFunction(), DMlibMeshJacobian(), DMlibMeshSetSystem_libMesh(), libMesh::DofMap::enforce_constraints_exactly(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::System::get_info(), libMesh::EquationSystems::get_solution(), libMesh::SystemSubsetBySubdomain::init(), libMesh::SecondOrderUnsteadySolver::init_data(), libMesh::UnsteadySolver::init_data(), libMesh::EigenSystem::init_matrices(), libMesh::ImplicitSystem::init_matrices(), libMesh::CondensedEigenSystem::initialize_condensed_dofs(), libMesh::OptimizationSystem::initialize_equality_constraints_storage(), libMesh::OptimizationSystem::initialize_inequality_constraints_storage(), libMesh::System::local_dof_indices(), libMesh::DofMap::max_constraint_error(), libMesh::DGFEMContext::neighbor_side_fe_reinit(), libMesh::UnsteadySolver::old_nonlinear_solution(), libMesh::SecondOrderUnsteadySolver::old_solution_accel(), libMesh::SecondOrderUnsteadySolver::old_solution_rate(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::operator()(), libMesh::BuildProjectionList::operator()(), libMesh::BoundaryProjectSolution::operator()(), libMesh::petsc_auto_fieldsplit(), libMesh::ErrorVector::plot_error(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::FEMContext::pre_fe_reinit(), libMesh::System::re_update(), libMesh::SecondOrderUnsteadySolver::reinit(), libMesh::UnsteadySolver::reinit(), libMesh::ImplicitSystem::reinit(), libMesh::EigenSystem::reinit(), libMesh::EquationSystems::reinit(), libMesh::System::reinit_constraints(), libMesh::UnsteadySolver::retrieve_timestep(), libMesh::HPCoarsenTest::select_refinement(), libMesh::ImplicitSystem::sensitivity_solve(), libMesh::NewtonSolver::solve(), libMesh::PetscDiffSolver::solve(), libMesh::PetscNonlinearSolver< T >::solve(), libMesh::System::system_type(), libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve(), libMesh::ImplicitSystem::weighted_sensitivity_solve(), libMesh::EnsightIO::write_scalar_ascii(), and libMesh::EnsightIO::write_vector_ascii().

2029 {
2030  return *_dof_map;
2031 }
UniquePtr< DofMap > _dof_map
Definition: system.h:1863
DofMap & libMesh::System::get_dof_map ( )
inlineinherited
Returns
A writable reference to this system's _dof_map.

Definition at line 2036 of file system.h.

References libMesh::System::_dof_map.

2037 {
2038  return *_dof_map;
2039 }
UniquePtr< DofMap > _dof_map
Definition: system.h:1863
EquationSystems& libMesh::System::get_equation_systems ( )
inlineinherited
Returns
A reference to this system's parent EquationSystems object.

Definition at line 717 of file system.h.

References libMesh::System::_equation_systems, libMesh::System::activate(), libMesh::System::active(), libMesh::System::deactivate(), and libMesh::System::set_basic_system_only().

717 { return _equation_systems; }
EquationSystems & _equation_systems
Definition: system.h:1869
const std::set<unsigned int>& libMesh::DifferentiablePhysics::get_first_order_vars ( ) const
inlineinherited
Returns
The set of first order in time variable indices. May be empty.

Definition at line 514 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_first_order_vars.

Referenced by libMesh::DifferentiableSystem::have_first_order_scalar_vars().

515  { return _first_order_vars; }
std::set< unsigned int > _first_order_vars
Definition: diff_physics.h:556
std::string libMesh::ReferenceCounter::get_info ( )
staticinherited

Gets a string containing the reference information.

Definition at line 47 of file reference_counter.C.

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

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

48 {
49 #if defined(LIBMESH_ENABLE_REFERENCE_COUNTING) && defined(DEBUG)
50 
51  std::ostringstream oss;
52 
53  oss << '\n'
54  << " ---------------------------------------------------------------------------- \n"
55  << "| Reference count information |\n"
56  << " ---------------------------------------------------------------------------- \n";
57 
58  for (Counts::iterator it = _counts.begin();
59  it != _counts.end(); ++it)
60  {
61  const std::string name(it->first);
62  const unsigned int creations = it->second.first;
63  const unsigned int destructions = it->second.second;
64 
65  oss << "| " << name << " reference count information:\n"
66  << "| Creations: " << creations << '\n'
67  << "| Destructions: " << destructions << '\n';
68  }
69 
70  oss << " ---------------------------------------------------------------------------- \n";
71 
72  return oss.str();
73 
74 #else
75 
76  return "";
77 
78 #endif
79 }
std::string name(const ElemQuality q)
Definition: elem_quality.C:39
std::string libMesh::System::get_info ( ) const
inherited
Returns
A string containing information about the system.

Definition at line 1686 of file system.C.

References libMesh::FEType::family, libMesh::System::get_dof_map(), libMesh::DofMap::get_info(), libMesh::FEType::inf_map, libMesh::System::n_constrained_dofs(), libMesh::System::n_dofs(), libMesh::System::n_local_constrained_dofs(), libMesh::System::n_local_dofs(), libMesh::System::n_matrices(), libMesh::System::n_variable_groups(), libMesh::VariableGroup::n_variables(), libMesh::System::n_vectors(), libMesh::VariableGroup::name(), libMesh::System::name(), libMesh::System::number(), libMesh::FEType::order, libMesh::FEType::radial_family, libMesh::FEType::radial_order, libMesh::System::system_type(), libMesh::Variable::type(), libMesh::DofMap::variable_group(), and libMesh::System::variable_group().

Referenced by libMesh::System::read_parallel_data().

1687 {
1688  std::ostringstream oss;
1689 
1690 
1691  const std::string & sys_name = this->name();
1692 
1693  oss << " System #" << this->number() << ", \"" << sys_name << "\"\n"
1694  << " Type \"" << this->system_type() << "\"\n"
1695  << " Variables=";
1696 
1697  for (unsigned int vg=0; vg<this->n_variable_groups(); vg++)
1698  {
1699  const VariableGroup & vg_description (this->variable_group(vg));
1700 
1701  if (vg_description.n_variables() > 1) oss << "{ ";
1702  for (unsigned int vn=0; vn<vg_description.n_variables(); vn++)
1703  oss << "\"" << vg_description.name(vn) << "\" ";
1704  if (vg_description.n_variables() > 1) oss << "} ";
1705  }
1706 
1707  oss << '\n';
1708 
1709  oss << " Finite Element Types=";
1710 #ifndef LIBMESH_ENABLE_INFINITE_ELEMENTS
1711  for (unsigned int vg=0; vg<this->n_variable_groups(); vg++)
1712  oss << "\""
1713  << Utility::enum_to_string<FEFamily>(this->get_dof_map().variable_group(vg).type().family)
1714  << "\" ";
1715 #else
1716  for (unsigned int vg=0; vg<this->n_variable_groups(); vg++)
1717  {
1718  oss << "\""
1719  << Utility::enum_to_string<FEFamily>(this->get_dof_map().variable_group(vg).type().family)
1720  << "\", \""
1721  << Utility::enum_to_string<FEFamily>(this->get_dof_map().variable_group(vg).type().radial_family)
1722  << "\" ";
1723  }
1724 
1725  oss << '\n' << " Infinite Element Mapping=";
1726  for (unsigned int vg=0; vg<this->n_variable_groups(); vg++)
1727  oss << "\""
1728  << Utility::enum_to_string<InfMapType>(this->get_dof_map().variable_group(vg).type().inf_map)
1729  << "\" ";
1730 #endif
1731 
1732  oss << '\n';
1733 
1734  oss << " Approximation Orders=";
1735  for (unsigned int vg=0; vg<this->n_variable_groups(); vg++)
1736  {
1737 #ifndef LIBMESH_ENABLE_INFINITE_ELEMENTS
1738  oss << "\""
1739  << Utility::enum_to_string<Order>(this->get_dof_map().variable_group(vg).type().order)
1740  << "\" ";
1741 #else
1742  oss << "\""
1743  << Utility::enum_to_string<Order>(this->get_dof_map().variable_group(vg).type().order)
1744  << "\", \""
1745  << Utility::enum_to_string<Order>(this->get_dof_map().variable_group(vg).type().radial_order)
1746  << "\" ";
1747 #endif
1748  }
1749 
1750  oss << '\n';
1751 
1752  oss << " n_dofs()=" << this->n_dofs() << '\n';
1753  oss << " n_local_dofs()=" << this->n_local_dofs() << '\n';
1754 #ifdef LIBMESH_ENABLE_CONSTRAINTS
1755  oss << " n_constrained_dofs()=" << this->n_constrained_dofs() << '\n';
1756  oss << " n_local_constrained_dofs()=" << this->n_local_constrained_dofs() << '\n';
1757 #endif
1758 
1759  oss << " " << "n_vectors()=" << this->n_vectors() << '\n';
1760  oss << " " << "n_matrices()=" << this->n_matrices() << '\n';
1761  // oss << " " << "n_additional_matrices()=" << this->n_additional_matrices() << '\n';
1762 
1763  oss << this->get_dof_map().get_info();
1764 
1765  return oss.str();
1766 }
FEFamily family
Definition: fe_type.h:203
dof_id_type n_constrained_dofs() const
Definition: system.C:153
const FEType & type() const
Definition: variable.h:119
std::string get_info() const
Definition: dof_map.C:2764
OrderWrapper radial_order
Definition: fe_type.h:236
OrderWrapper order
Definition: fe_type.h:197
const VariableGroup & variable_group(unsigned int vg) const
Definition: system.h:2122
const VariableGroup & variable_group(const unsigned int c) const
Definition: dof_map.h:1646
const std::string & name() const
Definition: system.h:1996
unsigned int n_variable_groups() const
Definition: system.h:2092
const DofMap & get_dof_map() const
Definition: system.h:2028
InfMapType inf_map
Definition: fe_type.h:257
virtual unsigned int n_matrices() const
Definition: system.h:2218
FEFamily radial_family
Definition: fe_type.h:249
dof_id_type n_local_dofs() const
Definition: system.C:183
virtual std::string system_type() const
Definition: system.h:471
dof_id_type n_local_constrained_dofs() const
Definition: system.C:168
unsigned int number() const
Definition: system.h:2004
dof_id_type n_dofs() const
Definition: system.C:146
unsigned int n_vectors() const
Definition: system.h:2212
std::pair< unsigned int, Real > libMesh::DifferentiableSystem::get_linear_solve_parameters ( ) const
virtualinherited
Returns
An integer corresponding to the upper iteration count limit and a Real corresponding to the convergence tolerance to be used in linear adjoint and/or sensitivity solves

Reimplemented from libMesh::ImplicitSystem.

Definition at line 184 of file diff_system.C.

References libMesh::libmesh_assert(), and libMesh::DifferentiableSystem::time_solver.

185 {
187  libmesh_assert_equal_to (&(time_solver->system()), this);
188  return std::make_pair(this->time_solver->diff_solver()->max_linear_iterations,
189  this->time_solver->diff_solver()->relative_residual_tolerance);
190 }
UniquePtr< TimeSolver > time_solver
Definition: diff_system.h:221
libmesh_assert(j)
LinearSolver< Number > * libMesh::DifferentiableSystem::get_linear_solver ( ) const
virtualinherited
Returns
A pointer to a linear solver appropriate for use in adjoint and/or sensitivity solves

Reimplemented from libMesh::ImplicitSystem.

Definition at line 175 of file diff_system.C.

References libMesh::libmesh_assert(), and libMesh::DifferentiableSystem::time_solver.

176 {
178  libmesh_assert_equal_to (&(time_solver->system()), this);
179  return this->time_solver->linear_solver().get();
180 }
UniquePtr< TimeSolver > time_solver
Definition: diff_system.h:221
libmesh_assert(j)
const SparseMatrix< Number > & libMesh::ImplicitSystem::get_matrix ( const std::string &  mat_name) const
inherited
Returns
A const reference to this system's additional matrix named mat_name.

None of these matrices is involved in the solution process. Access is only granted when the matrix is already properly initialized.

Definition at line 270 of file implicit_system.C.

References libMesh::ImplicitSystem::_matrices.

Referenced by libMesh::NewmarkSystem::compute_matrix(), libMesh::EigenTimeSolver::solve(), and libMesh::NewmarkSystem::update_rhs().

271 {
272  // Make sure the matrix exists
273  const_matrices_iterator pos = _matrices.find (mat_name);
274 
275  if (pos == _matrices.end())
276  libmesh_error_msg("ERROR: matrix " << mat_name << " does not exist in this system!");
277 
278  return *(pos->second);
279 }
std::map< std::string, SparseMatrix< Number > * > _matrices
std::map< std::string, SparseMatrix< Number > * >::const_iterator const_matrices_iterator
SparseMatrix< Number > & libMesh::ImplicitSystem::get_matrix ( const std::string &  mat_name)
inherited
Returns
A writable reference to this system's additional matrix named mat_name.

None of these matrices is involved in the solution process. Access is only granted when the matrix is already properly initialized.

Definition at line 283 of file implicit_system.C.

References libMesh::ImplicitSystem::_matrices.

284 {
285  // Make sure the matrix exists
286  matrices_iterator pos = _matrices.find (mat_name);
287 
288  if (pos == _matrices.end())
289  libmesh_error_msg("ERROR: matrix " << mat_name << " does not exist in this system!");
290 
291  return *(pos->second);
292 }
std::map< std::string, SparseMatrix< Number > * > _matrices
std::map< std::string, SparseMatrix< Number > * >::iterator matrices_iterator
const MeshBase & libMesh::System::get_mesh ( ) const
inlineinherited
Returns
A constant reference to this systems's _mesh.

Definition at line 2012 of file system.h.

References libMesh::System::_mesh.

Referenced by libMesh::ExactSolution::_compute_error(), libMesh::HPCoarsenTest::add_projection(), libMesh::FEMSystem::assemble_qoi(), libMesh::FEMSystem::assemble_qoi_derivative(), libMesh::FEMSystem::assembly(), libMesh::System::calculate_norm(), DMCreateDomainDecomposition_libMesh(), DMCreateFieldDecomposition_libMesh(), DMlibMeshSetSystem_libMesh(), libMesh::WeightedPatchRecoveryErrorEstimator::estimate_error(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::PatchRecoveryErrorEstimator::estimate_error(), libMesh::AdjointResidualErrorEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::SystemSubsetBySubdomain::init(), libMesh::System::init_data(), libMesh::EigenSystem::init_matrices(), libMesh::ImplicitSystem::init_matrices(), libMesh::System::local_dof_indices(), libMesh::DofMap::max_constraint_error(), libMesh::FEMSystem::mesh_position_get(), libMesh::FEMSystem::mesh_position_set(), libMesh::BoundaryProjectSolution::operator()(), libMesh::petsc_auto_fieldsplit(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::FEMSystem::postprocess(), libMesh::ImplicitSystem::reinit(), libMesh::EigenSystem::reinit(), libMesh::HPSingularity::select_refinement(), libMesh::HPCoarsenTest::select_refinement(), libMesh::System::system_type(), and libMesh::System::zero_variable().

2013 {
2014  return _mesh;
2015 }
MeshBase & _mesh
Definition: system.h:1875
MeshBase & libMesh::System::get_mesh ( )
inlineinherited
Returns
A reference to this systems's _mesh.

Definition at line 2020 of file system.h.

References libMesh::System::_mesh.

2021 {
2022  return _mesh;
2023 }
MeshBase & _mesh
Definition: system.h:1875
const System * libMesh::DifferentiablePhysics::get_mesh_system ( ) const
inlineinherited
Returns
A const reference to the system with variables corresponding to mesh nodal coordinates, or NULL if the mesh is fixed. Useful for ALE calculations.

Definition at line 621 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_mesh_sys.

Referenced by libMesh::FEMSystem::build_context(), and libMesh::DifferentiablePhysics::init_context().

622 {
623  return _mesh_sys;
624 }
System * libMesh::DifferentiablePhysics::get_mesh_system ( )
inlineinherited
Returns
A reference to the system with variables corresponding to mesh nodal coordinates, or NULL if the mesh is fixed.

Definition at line 627 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_mesh_sys.

628 {
629  return _mesh_sys;
630 }
unsigned int libMesh::DifferentiablePhysics::get_mesh_x_var ( ) const
inlineinherited
Returns
The variable number corresponding to the mesh x coordinate. Useful for ALE calculations.

Definition at line 633 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_mesh_x_var.

Referenced by libMesh::FEMSystem::build_context(), and libMesh::DifferentiablePhysics::init_context().

634 {
635  return _mesh_x_var;
636 }
unsigned int libMesh::DifferentiablePhysics::get_mesh_y_var ( ) const
inlineinherited
Returns
The variable number corresponding to the mesh y coordinate. Useful for ALE calculations.

Definition at line 639 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_mesh_y_var.

Referenced by libMesh::FEMSystem::build_context(), and libMesh::DifferentiablePhysics::init_context().

640 {
641  return _mesh_y_var;
642 }
unsigned int libMesh::DifferentiablePhysics::get_mesh_z_var