libMesh::FEMSystem Class Reference

#include <fem_system.h>

Inheritance diagram for libMesh::FEMSystem:

Public Types

typedef FEMSystem sys_type
 
typedef DifferentiableSystem 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 Number(* ValueFunctionPointer) (const Point &p, const Parameters &Parameters, const std::string &sys_name, const std::string &unknown_name)
 
typedef Gradient(* GradientFunctionPointer) (const Point &p, const Parameters &parameters, const std::string &sys_name, const std::string &unknown_name)
 
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

 FEMSystem (EquationSystems &es, const std::string &name, const unsigned int number)
 
virtual ~FEMSystem ()
 
virtual void assembly (bool get_residual, bool get_jacobian, bool apply_heterogeneous_constraints=false, bool apply_no_constraints=false) override
 
virtual void solve () override
 
void mesh_position_get ()
 
void mesh_position_set ()
 
virtual std::unique_ptr< DiffContextbuild_context () override
 
virtual void init_context (DiffContext &) override
 
virtual void postprocess () override
 
virtual void assemble_qoi (const QoISet &indices=QoISet()) override
 
virtual void assemble_qoi_derivative (const QoISet &qoi_indices=QoISet(), bool include_liftfunc=true, bool apply_constraints=true) 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 clear () override
 
virtual void reinit () override
 
virtual void assemble () override
 
virtual LinearSolver< Number > * get_linear_solver () const override
 
virtual std::pair< unsigned int, Realget_linear_solve_parameters () const override
 
virtual void release_linear_solver (LinearSolver< Number > *) const override
 
virtual std::pair< unsigned int, Realadjoint_solve (const QoISet &qoi_indices=QoISet()) override
 
virtual std::unique_ptr< DifferentiablePhysicsclone_physics () override
 
virtual std::unique_ptr< DifferentiableQoIclone () 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 (std::unique_ptr< 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 () override
 
virtual std::string system_type () const override
 
virtual void assemble_residual_derivatives (const ParameterVector &parameters) override
 
virtual std::pair< unsigned int, Realsensitivity_solve (const ParameterVector &parameters) override
 
virtual std::pair< unsigned int, Realweighted_sensitivity_solve (const ParameterVector &parameters, const ParameterVector &weights) override
 
virtual std::pair< unsigned int, Realweighted_sensitivity_adjoint_solve (const ParameterVector &parameters, const ParameterVector &weights, const QoISet &qoi_indices=QoISet()) override
 
virtual void adjoint_qoi_parameter_sensitivity (const QoISet &qoi_indices, const ParameterVector &parameters, SensitivityData &sensitivities) override
 
virtual void forward_qoi_parameter_sensitivity (const QoISet &qoi_indices, const ParameterVector &parameters, SensitivityData &sensitivities) override
 
virtual void qoi_parameter_hessian (const QoISet &qoi_indices, const ParameterVector &parameters, SensitivityData &hessian) override
 
virtual void qoi_parameter_hessian_vector_product (const QoISet &qoi_indices, const ParameterVector &parameters, const ParameterVector &vector, SensitivityData &product) 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 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=nullptr) const
 
void project_solution (FEMFunctionBase< Number > *f, FEMFunctionBase< Gradient > *g=nullptr) const
 
void project_solution (ValueFunctionPointer fptr, GradientFunctionPointer gptr, const Parameters &parameters) const
 
void project_vector (NumericVector< Number > &new_vector, FunctionBase< Number > *f, FunctionBase< Gradient > *g=nullptr, int is_adjoint=-1) const
 
void project_vector (NumericVector< Number > &new_vector, FEMFunctionBase< Number > *f, FEMFunctionBase< Gradient > *g=nullptr, int is_adjoint=-1) const
 
void project_vector (ValueFunctionPointer fptr, GradientFunctionPointer gptr, 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=nullptr)
 
void boundary_project_solution (const std::set< boundary_id_type > &b, const std::vector< unsigned int > &variables, ValueFunctionPointer fptr, GradientFunctionPointer gptr, 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=nullptr, int is_adjoint=-1) const
 
void boundary_project_vector (const std::set< boundary_id_type > &b, const std::vector< unsigned int > &variables, ValueFunctionPointer fptr, GradientFunctionPointer gptr, 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=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=nullptr)
 
unsigned int add_variables (const std::vector< std::string > &vars, const FEType &type, const std::set< subdomain_id_type > *const active_subdomains=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=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=nullptr) const
 
Real calculate_norm (const NumericVector< Number > &v, const SystemNorm &norm, std::set< unsigned int > *skip_dimensions=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
 
unsigned int n_qois () 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 ()
 
void projection_matrix (SparseMatrix< Number > &proj_mat) const
 
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 mass_residual (bool request_jacobian, DiffContext &)
 
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)
 
virtual void finalize_derivative (NumericVector< Number > &derivatives, std::size_t qoi_index)
 
virtual bool eulerian_residual (bool request_jacobian, DiffContext &context) override
 
virtual bool mass_residual (bool request_jacobian, DiffContext &) override
 

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

bool fe_reinit_during_postprocess
 
Real numerical_jacobian_h
 
Real verify_analytic_jacobians
 
std::unique_ptr< 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
 
std::unique_ptr< NumericVector< Number > > solution
 
std::unique_ptr< 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

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

Protected Member Functions

virtual void init_data () 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

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 Attributes

std::vector< Real_numerical_jacobian_h_for_var
 

Detailed Description

This class provides a specific system class. It aims at nonlinear implicit systems, requiring only a cell residual calculation from the user.

Note
Additional vectors/matrices can be added via parent class interfaces.

This class is part of the new DifferentiableSystem framework, which is still experimental. Users of this framework should beware of bugs and future API changes.

Author
Roy H. Stogner
Date
2006

Definition at line 53 of file fem_system.h.

Member Typedef Documentation

◆ const_matrices_iterator

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

Definition at line 306 of file implicit_system.h.

◆ const_vectors_iterator

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

Definition at line 749 of file system.h.

◆ Counts

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

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

Definition at line 117 of file reference_counter.h.

◆ GradientFunctionPointer

typedef Gradient(* libMesh::System::GradientFunctionPointer) (const Point &p, const Parameters &parameters, const std::string &sys_name, const std::string &unknown_name)
inherited

Definition at line 524 of file system.h.

◆ matrices_iterator

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

Matrix iterator typedefs.

Definition at line 305 of file implicit_system.h.

◆ Parent

The type of the parent.

Definition at line 79 of file fem_system.h.

◆ sys_type

The type of system.

Definition at line 74 of file fem_system.h.

◆ TimeSolverResPtr

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

Syntax sugar to make numerical_jacobian() declaration easier.

Definition at line 214 of file fem_system.h.

◆ ValueFunctionPointer

typedef Number(* libMesh::System::ValueFunctionPointer) (const Point &p, const Parameters &Parameters, const std::string &sys_name, const std::string &unknown_name)
inherited

Projects arbitrary functions onto the current solution. 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.

Definition at line 520 of file system.h.

◆ vectors_iterator

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

Vector iterator typedefs.

Definition at line 748 of file system.h.

Constructor & Destructor Documentation

◆ FEMSystem()

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

Constructor. Optionally initializes required data structures.

Definition at line 830 of file fem_system.C.

833  : Parent(es, name_in, number_in),
837 {
838 }
Real verify_analytic_jacobians
Definition: fem_system.h:209
static const Real TOLERANCE
bool fe_reinit_during_postprocess
Definition: fem_system.h:170
DifferentiableSystem Parent
Definition: fem_system.h:79

◆ ~FEMSystem()

libMesh::FEMSystem::~FEMSystem ( )
virtual

Destructor.

Definition at line 841 of file fem_system.C.

842 {
843 }

Member Function Documentation

◆ _eulerian_time_deriv()

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(), and libMesh::NewmarkSolver::element_residual().

◆ activate()

void libMesh::System::activate ( )
inlineinherited

Activates the system. Only active systems are solved.

Definition at line 2073 of file system.h.

References libMesh::System::_active.

2074 {
2075  _active = true;
2076 }

◆ active()

bool libMesh::System::active ( ) const
inlineinherited
Returns
true if the system is active, false otherwise. An active system will be solved.

Definition at line 2065 of file system.h.

References libMesh::System::_active.

2066 {
2067  return _active;
2068 }

◆ add_adjoint_rhs()

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 1021 of file system.C.

References libMesh::System::add_vector().

Referenced by libMesh::ExplicitSystem::assemble_qoi_derivative(), and assemble_qoi_derivative().

1022 {
1023  std::ostringstream adjoint_rhs_name;
1024  adjoint_rhs_name << "adjoint_rhs" << i;
1025 
1026  return this->add_vector(adjoint_rhs_name.str(), false);
1027 }
NumericVector< Number > & add_vector(const std::string &vec_name, const bool projections=true, const ParallelType type=PARALLEL)
Definition: system.C:661

◆ add_adjoint_solution()

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 957 of file system.C.

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

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

958 {
959  std::ostringstream adjoint_name;
960  adjoint_name << "adjoint_solution" << i;
961 
962  NumericVector<Number> & returnval = this->add_vector(adjoint_name.str());
963  this->set_vector_as_adjoint(adjoint_name.str(), i);
964  return returnval;
965 }
void set_vector_as_adjoint(const std::string &vec_name, int qoi_num)
Definition: system.C:885
NumericVector< Number > & add_vector(const std::string &vec_name, const bool projections=true, const ParallelType type=PARALLEL)
Definition: system.C:661

◆ add_dot_var_dirichlet_bcs()

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 227 of file diff_system.C.

References libMesh::DofMap::add_dirichlet_boundary(), libMesh::DofMap::get_dirichlet_boundaries(), and libMesh::System::get_dof_map().

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

229 {
230  // We're assuming that there could be a lot more variables than
231  // boundary conditions, so we search each of the boundary conditions
232  // for this variable rather than looping over boundary conditions
233  // in a separate loop and searching through all the variables.
234  const DirichletBoundaries * all_dbcs =
236 
237  if (all_dbcs)
238  {
239  // We need to cache the DBCs to be added so that we add them
240  // after looping over the existing DBCs. Otherwise, we're polluting
241  // the thing we're looping over.
242  std::vector<DirichletBoundary *> new_dbcs;
243 
244  for (const auto & dbc : *all_dbcs)
245  {
246  libmesh_assert(dbc);
247 
248  // Look for second order variable in the current
249  // DirichletBoundary object
250  std::vector<unsigned int>::const_iterator dbc_var_it =
251  std::find( dbc->variables.begin(), dbc->variables.end(), var_idx );
252 
253  // If we found it, then we also need to add it's corresponding
254  // "dot" variable to a DirichletBoundary
255  std::vector<unsigned int> vars_to_add;
256  if (dbc_var_it != dbc->variables.end())
257  vars_to_add.push_back(dot_var_idx);
258 
259  if (!vars_to_add.empty())
260  {
261  // We need to check if the boundary condition is time-dependent.
262  // Currently, we cannot automatically differentiate w.r.t. time
263  // so if the user supplies a time-dependent Dirichlet BC, then
264  // we can't automatically support the Dirichlet BC for the
265  // "velocity" boundary condition, so we error. Otherwise,
266  // the "velocity boundary condition will just be zero.
267  bool is_time_evolving_bc = false;
268  if (dbc->f)
269  is_time_evolving_bc = dbc->f->is_time_dependent();
270  else if (dbc->f_fem)
271  // We it's a FEMFunctionBase object, it will be implicitly
272  // time-dependent since it is assumed to depend on the solution.
273  is_time_evolving_bc = true;
274  else
275  libmesh_error_msg("Could not find valid boundary function!");
276 
277  if (is_time_evolving_bc)
278  libmesh_error_msg("Cannot currently support time-dependent Dirichlet BC for dot variables!");
279 
280 
281  DirichletBoundary * new_dbc;
282 
283  if (dbc->f)
284  {
285  ZeroFunction<Number> zf;
286 
287  new_dbc = new DirichletBoundary(dbc->b, vars_to_add, zf);
288  }
289  else
290  libmesh_error();
291 
292  new_dbcs.push_back(new_dbc);
293  }
294  }
295 
296  // Let the DofMap make its own deep copy of the DirichletBC objects and delete our copy.
297  for (const auto & dbc : new_dbcs)
298  {
299  this->get_dof_map().add_dirichlet_boundary(*dbc);
300  delete dbc;
301  }
302 
303  } // if (all_dbcs)
304 }
const DirichletBoundaries * get_dirichlet_boundaries() const
Definition: dof_map.h:1223
void add_dirichlet_boundary(const DirichletBoundary &dirichlet_boundary)
const DofMap & get_dof_map() const
Definition: system.h:2049

◆ add_matrix()

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 203 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().

204 {
205  // only add matrices before initializing...
206  if (!_can_add_matrices)
207  libmesh_error_msg("ERROR: Too late. Cannot add matrices to the system after initialization"
208  << "\n any more. You should have done this earlier.");
209 
210  // Return the matrix if it is already there.
211  if (this->have_matrix(mat_name))
212  return *(_matrices[mat_name]);
213 
214  // Otherwise build the matrix and return it.
215  SparseMatrix<Number> * buf = SparseMatrix<Number>::build(this->comm()).release();
216  _matrices.insert (std::make_pair (mat_name, buf));
217 
218  return *buf;
219 }
static std::unique_ptr< SparseMatrix< T > > build(const Parallel::Communicator &comm, const SolverPackage solver_package=libMesh::default_solver_package())
bool have_matrix(const std::string &mat_name) const
const Parallel::Communicator & comm() const
std::map< std::string, SparseMatrix< Number > * > _matrices

◆ add_second_order_dot_vars()

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 (const auto & var_id : second_order_vars)
204  {
205  const Variable & var = this->variable(var_id);
206  std::string new_var_name = std::string("dot_")+var.name();
207 
208  unsigned int v_var_idx;
209 
210  if (var.active_subdomains().empty())
211  v_var_idx = this->add_variable( new_var_name, var.type() );
212  else
213  v_var_idx = this->add_variable( new_var_name, var.type(), &var.active_subdomains() );
214 
215  _second_order_dot_vars.insert(std::pair<unsigned int, unsigned int>(var_id, v_var_idx));
216 
217  // The new velocities are time evolving variables of first order
218  this->time_evolving( v_var_idx, 1 );
219 
220  // And if there are any boundary conditions set on the second order
221  // variable, we also need to set it on its velocity variable.
222  this->add_dot_var_dirichlet_bcs(var_id, v_var_idx);
223  }
224  }
225 }
const Variable & variable(unsigned int var) const
Definition: system.h:2133
void add_dot_var_dirichlet_bcs(unsigned int var_idx, unsigned int dot_var_idx)
Definition: diff_system.C:227
std::map< unsigned int, unsigned int > _second_order_dot_vars
Definition: diff_physics.h:571
const std::set< unsigned int > & get_second_order_vars() const
Definition: diff_physics.h:530
virtual void time_evolving(unsigned int var)
Definition: diff_physics.h:249
unsigned int add_variable(const std::string &var, const FEType &type, const std::set< subdomain_id_type > *const active_subdomains=nullptr)
Definition: system.C:1081

◆ add_sensitivity_rhs()

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 1051 of file system.C.

References libMesh::System::add_vector().

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

1052 {
1053  std::ostringstream sensitivity_rhs_name;
1054  sensitivity_rhs_name << "sensitivity_rhs" << i;
1055 
1056  return this->add_vector(sensitivity_rhs_name.str(), false);
1057 }
NumericVector< Number > & add_vector(const std::string &vec_name, const bool projections=true, const ParallelType type=PARALLEL)
Definition: system.C:661

◆ add_sensitivity_solution()

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 906 of file system.C.

References libMesh::System::add_vector().

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

907 {
908  std::ostringstream sensitivity_name;
909  sensitivity_name << "sensitivity_solution" << i;
910 
911  return this->add_vector(sensitivity_name.str());
912 }
NumericVector< Number > & add_vector(const std::string &vec_name, const bool projections=true, const ParallelType type=PARALLEL)
Definition: system.C:661

◆ add_variable() [1/2]

unsigned int libMesh::System::add_variable ( const std::string &  var,
const FEType type,
const std::set< subdomain_id_type > *const  active_subdomains = 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 1081 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::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::read_header().

1084 {
1085  libmesh_assert(!this->is_initialized());
1086 
1087  // Make sure the variable isn't there already
1088  // or if it is, that it's the type we want
1089  for (unsigned int v=0; v<this->n_vars(); v++)
1090  if (this->variable_name(v) == var)
1091  {
1092  if (this->variable_type(v) == type)
1093  return _variables[v].number();
1094 
1095  libmesh_error_msg("ERROR: incompatible variable " << var << " has already been added for this system!");
1096  }
1097 
1098  // Optimize for VariableGroups here - if the user is adding multiple
1099  // variables of the same FEType and subdomain restriction, catch
1100  // that here and add them as members of the same VariableGroup.
1101  //
1102  // start by setting this flag to whatever the user has requested
1103  // and then consider the conditions which should negate it.
1104  bool should_be_in_vg = this->identify_variable_groups();
1105 
1106  // No variable groups, nothing to add to
1107  if (!this->n_variable_groups())
1108  should_be_in_vg = false;
1109 
1110  else
1111  {
1112  VariableGroup & vg(_variable_groups.back());
1113 
1114  // get a pointer to their subdomain restriction, if any.
1115  const std::set<subdomain_id_type> * const
1116  their_active_subdomains (vg.implicitly_active() ?
1117  nullptr : &vg.active_subdomains());
1118 
1119  // Different types?
1120  if (vg.type() != type)
1121  should_be_in_vg = false;
1122 
1123  // they are restricted, we aren't?
1124  if (their_active_subdomains && !active_subdomains)
1125  should_be_in_vg = false;
1126 
1127  // they aren't restricted, we are?
1128  if (!their_active_subdomains && active_subdomains)
1129  should_be_in_vg = false;
1130 
1131  if (their_active_subdomains && active_subdomains)
1132  // restricted to different sets?
1133  if (*their_active_subdomains != *active_subdomains)
1134  should_be_in_vg = false;
1135 
1136  // OK, after all that, append the variable to the vg if none of the conditions
1137  // were violated
1138  if (should_be_in_vg)
1139  {
1140  const unsigned short curr_n_vars = cast_int<unsigned short>
1141  (this->n_vars());
1142 
1143  vg.append (var);
1144 
1145  _variables.push_back(vg(vg.n_variables()-1));
1146  _variable_numbers[var] = curr_n_vars;
1147  return curr_n_vars;
1148  }
1149  }
1150 
1151  // otherwise, fall back to adding a single variable group
1152  return this->add_variables (std::vector<std::string>(1, var),
1153  type,
1154  active_subdomains);
1155 }
unsigned int add_variables(const std::vector< std::string > &vars, const FEType &type, const std::set< subdomain_id_type > *const active_subdomains=nullptr)
Definition: system.C:1171
std::map< std::string, unsigned short int > _variable_numbers
Definition: system.h:1922
unsigned int n_variable_groups() const
Definition: system.h:2113
std::vector< Variable > _variables
Definition: system.h:1911
unsigned int number() const
Definition: system.h:2025
std::vector< VariableGroup > _variable_groups
Definition: system.h:1916
bool is_initialized()
Definition: system.h:2089
const std::string & variable_name(const unsigned int i) const
Definition: system.h:2153
bool identify_variable_groups() const
Definition: system.h:2201
const FEType & variable_type(const unsigned int i) const
Definition: system.h:2183
unsigned int n_vars() const
Definition: system.h:2105

◆ add_variable() [2/2]

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 = 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 1159 of file system.C.

References libMesh::System::add_variable().

1163 {
1164  return this->add_variable(var,
1165  FEType(order, family),
1166  active_subdomains);
1167 }
unsigned int add_variable(const std::string &var, const FEType &type, const std::set< subdomain_id_type > *const active_subdomains=nullptr)
Definition: system.C:1081

◆ add_variables() [1/2]

unsigned int libMesh::System::add_variables ( const std::vector< std::string > &  vars,
const FEType type,
const std::set< subdomain_id_type > *const  active_subdomains = 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 1171 of file system.C.

References libMesh::System::_variable_groups, libMesh::System::_variable_numbers, libMesh::System::_variables, libMesh::System::is_initialized(), 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(), and libMesh::System::add_variables().

1174 {
1175  libmesh_assert(!this->is_initialized());
1176 
1177  // Make sure the variable isn't there already
1178  // or if it is, that it's the type we want
1179  for (std::size_t ov=0; ov<vars.size(); ov++)
1180  for (unsigned int v=0; v<this->n_vars(); v++)
1181  if (this->variable_name(v) == vars[ov])
1182  {
1183  if (this->variable_type(v) == type)
1184  return _variables[v].number();
1185 
1186  libmesh_error_msg("ERROR: incompatible variable " << vars[ov] << " has already been added for this system!");
1187  }
1188 
1189  const unsigned short curr_n_vars = cast_int<unsigned short>
1190  (this->n_vars());
1191 
1192  const unsigned int next_first_component = this->n_components();
1193 
1194  // Add the variable group to the list
1195  _variable_groups.push_back((active_subdomains == nullptr) ?
1196  VariableGroup(this, vars, curr_n_vars,
1197  next_first_component, type) :
1198  VariableGroup(this, vars, curr_n_vars,
1199  next_first_component, type, *active_subdomains));
1200 
1201  const VariableGroup & vg (_variable_groups.back());
1202 
1203  // Add each component of the group individually
1204  for (auto v : IntRange<unsigned int>(0, vars.size()))
1205  {
1206  _variables.push_back (vg(v));
1207  _variable_numbers[vars[v]] = cast_int<unsigned short>
1208  (curr_n_vars+v);
1209  }
1210 
1211  libmesh_assert_equal_to ((curr_n_vars+vars.size()), this->n_vars());
1212 
1213  // BSK - Defer this now to System::init_data() so we can detect
1214  // VariableGroups 12/28/2012
1215  // // Add the variable group to the _dof_map
1216  // _dof_map->add_variable_group (vg);
1217 
1218  // Return the number of the new variable
1219  return cast_int<unsigned int>(curr_n_vars+vars.size()-1);
1220 }
std::map< std::string, unsigned short int > _variable_numbers
Definition: system.h:1922
unsigned int n_components() const
Definition: system.h:2121
std::vector< Variable > _variables
Definition: system.h:1911
unsigned int number() const
Definition: system.h:2025
std::vector< VariableGroup > _variable_groups
Definition: system.h:1916
bool is_initialized()
Definition: system.h:2089
const std::string & variable_name(const unsigned int i) const
Definition: system.h:2153
const FEType & variable_type(const unsigned int i) const
Definition: system.h:2183
unsigned int n_vars() const
Definition: system.h:2105

◆ add_variables() [2/2]

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 = 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 1224 of file system.C.

References libMesh::System::add_variables().

1228 {
1229  return this->add_variables(vars,
1230  FEType(order, family),
1231  active_subdomains);
1232 }
unsigned int add_variables(const std::vector< std::string > &vars, const FEType &type, const std::set< subdomain_id_type > *const active_subdomains=nullptr)
Definition: system.C:1171

◆ add_vector()

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 661 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(), libMesh::ContinuationSystem::init_data(), libMesh::NewmarkSystem::NewmarkSystem(), libMesh::System::read_header(), libMesh::FrequencySystem::set_frequencies(), libMesh::FrequencySystem::set_frequencies_by_range(), and libMesh::FrequencySystem::set_frequencies_by_steps().

664 {
665  // Return the vector if it is already there.
666  if (this->have_vector(vec_name))
667  return *(_vectors[vec_name]);
668 
669  // Otherwise build the vector
670  NumericVector<Number> * buf = NumericVector<Number>::build(this->comm()).release();
671  _vectors.insert (std::make_pair (vec_name, buf));
672  _vector_projections.insert (std::make_pair (vec_name, projections));
673 
674  _vector_types.insert (std::make_pair (vec_name, type));
675 
676  // Vectors are primal by default
677  _vector_is_adjoint.insert (std::make_pair (vec_name, -1));
678 
679  // Initialize it if necessary
680  if (_is_initialized)
681  {
682  if (type == GHOSTED)
683  {
684 #ifdef LIBMESH_ENABLE_GHOSTED
685  buf->init (this->n_dofs(), this->n_local_dofs(),
686  _dof_map->get_send_list(), false,
687  GHOSTED);
688 #else
689  libmesh_error_msg("Cannot initialize ghosted vectors when they are not enabled.");
690 #endif
691  }
692  else
693  buf->init (this->n_dofs(), this->n_local_dofs(), false, type);
694  }
695 
696  return *buf;
697 }
std::map< std::string, ParallelType > _vector_types
Definition: system.h:1952
bool _is_initialized
Definition: system.h:1971
std::unique_ptr< DofMap > _dof_map
Definition: system.h:1884
const Parallel::Communicator & comm() const
dof_id_type n_local_dofs() const
Definition: system.C:187
dof_id_type n_dofs() const
Definition: system.C:150
std::map< std::string, int > _vector_is_adjoint
Definition: system.h:1947
bool have_vector(const std::string &vec_name) const
Definition: system.h:2225
static std::unique_ptr< NumericVector< T > > build(const Parallel::Communicator &comm, const SolverPackage solver_package=libMesh::default_solver_package())
std::map< std::string, NumericVector< Number > *> _vectors
Definition: system.h:1935
std::map< std::string, bool > _vector_projections
Definition: system.h:1941

◆ add_weighted_sensitivity_adjoint_solution()

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 989 of file system.C.

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

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

990 {
991  std::ostringstream adjoint_name;
992  adjoint_name << "weighted_sensitivity_adjoint_solution" << i;
993 
994  NumericVector<Number> & returnval = this->add_vector(adjoint_name.str());
995  this->set_vector_as_adjoint(adjoint_name.str(), i);
996  return returnval;
997 }
void set_vector_as_adjoint(const std::string &vec_name, int qoi_num)
Definition: system.C:885
NumericVector< Number > & add_vector(const std::string &vec_name, const bool projections=true, const ParallelType type=PARALLEL)
Definition: system.C:661

◆ add_weighted_sensitivity_solution()

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 936 of file system.C.

References libMesh::System::add_vector().

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

937 {
938  return this->add_vector("weighted_sensitivity_solution");
939 }
NumericVector< Number > & add_vector(const std::string &vec_name, const bool projections=true, const ParallelType type=PARALLEL)
Definition: system.C:661

◆ adjoint_qoi_parameter_sensitivity()

void libMesh::ImplicitSystem::adjoint_qoi_parameter_sensitivity ( const QoISet qoi_indices,
const ParameterVector parameters,
SensitivityData sensitivities 
)
overridevirtualinherited

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 697 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::n_qois(), libMesh::System::qoi, libMesh::Real, libMesh::ParameterVector::size(), and libMesh::TOLERANCE.

700 {
701  ParameterVector & parameters =
702  const_cast<ParameterVector &>(parameters_in);
703 
704  const unsigned int Np = cast_int<unsigned int>
705  (parameters.size());
706  const unsigned int Nq = this->n_qois();
707 
708  // An introduction to the problem:
709  //
710  // Residual R(u(p),p) = 0
711  // partial R / partial u = J = system matrix
712  //
713  // This implies that:
714  // d/dp(R) = 0
715  // (partial R / partial p) +
716  // (partial R / partial u) * (partial u / partial p) = 0
717 
718  // We first do an adjoint solve:
719  // J^T * z = (partial q / partial u)
720  // if we havent already or dont have an initial condition for the adjoint
721  if (!this->is_adjoint_already_solved())
722  {
723  this->adjoint_solve(qoi_indices);
724  }
725 
726  this->assemble_residual_derivatives(parameters_in);
727 
728  // Get ready to fill in sensitivities:
729  sensitivities.allocate_data(qoi_indices, *this, parameters);
730 
731  // We use the identities:
732  // dq/dp = (partial q / partial p) + (partial q / partial u) *
733  // (partial u / partial p)
734  // dq/dp = (partial q / partial p) + (J^T * z) *
735  // (partial u / partial p)
736  // dq/dp = (partial q / partial p) + z * J *
737  // (partial u / partial p)
738 
739  // Leading to our final formula:
740  // dq/dp = (partial q / partial p) - z * (partial R / partial p)
741 
742  // In the case of adjoints with heterogenous Dirichlet boundary
743  // function phi, where
744  // q := S(u) - R(u,phi)
745  // the final formula works out to:
746  // dq/dp = (partial S / partial p) - z * (partial R / partial p)
747  // Because we currently have no direct access to
748  // (partial S / partial p), we use the identity
749  // (partial S / partial p) = (partial q / partial p) +
750  // phi * (partial R / partial p)
751  // to derive an equivalent equation:
752  // dq/dp = (partial q / partial p) - (z-phi) * (partial R / partial p)
753 
754  // Since z-phi degrees of freedom are zero for constrained indices,
755  // we can use the same constrained -(partial R / partial p) that we
756  // use for forward sensitivity solves, taking into account the
757  // differing sign convention.
758  //
759  // Since that vector is constrained, its constrained indices are
760  // zero, so its product with phi is zero, so we can neglect the
761  // evaluation of phi terms.
762 
763  for (unsigned int j=0; j != Np; ++j)
764  {
765  // We currently get partial derivatives via central differencing
766 
767  // (partial q / partial p) ~= (q(p+dp)-q(p-dp))/(2*dp)
768  // (partial R / partial p) ~= (rhs(p+dp) - rhs(p-dp))/(2*dp)
769 
770  Number old_parameter = *parameters[j];
771 
772  const Real delta_p =
773  TOLERANCE * std::max(std::abs(old_parameter), 1e-3);
774 
775  *parameters[j] = old_parameter - delta_p;
776  this->assemble_qoi(qoi_indices);
777  std::vector<Number> qoi_minus = this->qoi;
778 
779  NumericVector<Number> & neg_partialR_partialp = this->get_sensitivity_rhs(j);
780 
781  *parameters[j] = old_parameter + delta_p;
782  this->assemble_qoi(qoi_indices);
783  std::vector<Number> & qoi_plus = this->qoi;
784 
785  std::vector<Number> partialq_partialp(Nq, 0);
786  for (unsigned int i=0; i != Nq; ++i)
787  if (qoi_indices.has_index(i))
788  partialq_partialp[i] = (qoi_plus[i] - qoi_minus[i]) / (2.*delta_p);
789 
790  // Don't leave the parameter changed
791  *parameters[j] = old_parameter;
792 
793  for (unsigned int i=0; i != Nq; ++i)
794  if (qoi_indices.has_index(i))
795  sensitivities[i][j] = partialq_partialp[i] +
796  neg_partialR_partialp.dot(this->get_adjoint_solution(i));
797  }
798 
799  // All parameters have been reset.
800  // Reset the original qoi.
801 
802  this->assemble_qoi(qoi_indices);
803 }
double abs(double a)
unsigned int n_qois() const
Definition: system.h:2278
NumericVector< Number > & get_sensitivity_rhs(unsigned int i=0)
Definition: system.C:1061
static const Real TOLERANCE
virtual std::pair< unsigned int, Real > adjoint_solve(const QoISet &qoi_indices=QoISet()) override
long double max(long double a, double b)
std::vector< Number > qoi
Definition: system.h:1558
bool is_adjoint_already_solved() const
Definition: system.h:388
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
virtual void assemble_qoi(const QoISet &qoi_indices=QoISet()) override
virtual void assemble_residual_derivatives(const ParameterVector &parameters) override

◆ adjoint_solve()

std::pair< unsigned int, Real > libMesh::DifferentiableSystem::adjoint_solve ( const QoISet qoi_indices = QoISet())
overridevirtualinherited

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()) override
void set_is_adjoint(bool _is_adjoint_value)
Definition: time_solver.h:240
TimeSolver & get_time_solver()
Definition: diff_system.h:415

◆ assemble()

void libMesh::DifferentiableSystem::assemble ( )
overridevirtualinherited

Prepares matrix and rhs for matrix assembly. Users should not reimplement this. Note that in some cases only current_local_solution is used during assembly, and, therefore, if solution has been altered without update() being called, then the user must call update() before calling this function.

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) override=0

◆ assemble_qoi()

void libMesh::FEMSystem::assemble_qoi ( const QoISet indices = QoISet())
overridevirtual

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 1121 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::System::n_qois(), libMesh::DifferentiableQoI::parallel_op(), libMesh::Threads::parallel_reduce(), libMesh::System::qoi, libMesh::StoredRange< iterator_type, object_type >::reset(), and libMesh::System::update().

1122 {
1123  LOG_SCOPE("assemble_qoi()", "FEMSystem");
1124 
1125  const MeshBase & mesh = this->get_mesh();
1126 
1127  this->update();
1128 
1129  const unsigned int Nq = this->n_qois();
1130 
1131  // the quantity of interest is assumed to be a sum of element and
1132  // side terms
1133  for (unsigned int i=0; i != Nq; ++i)
1134  if (qoi_indices.has_index(i))
1135  qoi[i] = 0;
1136 
1137  // Create a non-temporary qoi_contributions object, so we can query
1138  // its results after the reduction
1139  QoIContributions qoi_contributions(*this, *(this->diff_qoi), qoi_indices);
1140 
1141  // Loop over every active mesh element on this processor
1144  qoi_contributions);
1145 
1146  this->diff_qoi->parallel_op( this->comm(), this->qoi, qoi_contributions.qoi, qoi_indices );
1147 }
unsigned int n_qois() const
Definition: system.h:2278
MeshBase & mesh
const Parallel::Communicator & comm() const
const MeshBase & get_mesh() const
Definition: system.h:2033
Base class for Mesh.
Definition: mesh_base.h:77
DifferentiableQoI * diff_qoi
Definition: diff_system.h:378
virtual void parallel_op(const Parallel::Communicator &communicator, std::vector< Number > &sys_qoi, std::vector< Number > &local_qoi, const QoISet &qoi_indices)
std::vector< Number > qoi
Definition: system.h:1558
virtual element_iterator active_local_elements_begin()=0
virtual void update()
Definition: system.C:408
void parallel_reduce(const Range &range, Body &body)
Definition: threads_none.h:101
virtual element_iterator active_local_elements_end()=0

◆ assemble_qoi_derivative()

void libMesh::FEMSystem::assemble_qoi_derivative ( const QoISet qoi_indices = QoISet(),
bool  include_liftfunc = true,
bool  apply_constraints = true 
)
overridevirtual

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 1151 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::DifferentiableQoI::finalize_derivative(), libMesh::System::get_mesh(), libMesh::QoISet::has_index(), mesh, libMesh::System::n_qois(), libMesh::Threads::parallel_for(), libMesh::StoredRange< iterator_type, object_type >::reset(), libMesh::System::update(), and libMesh::NumericVector< T >::zero().

1154 {
1155  LOG_SCOPE("assemble_qoi_derivative()", "FEMSystem");
1156 
1157  const MeshBase & mesh = this->get_mesh();
1158 
1159  this->update();
1160 
1161  // The quantity of interest derivative assembly accumulates on
1162  // initially zero vectors
1163  for (unsigned int i=0; i != this->n_qois(); ++i)
1164  if (qoi_indices.has_index(i))
1165  this->add_adjoint_rhs(i).zero();
1166 
1167  // Loop over every active mesh element on this processor
1170  QoIDerivativeContributions(*this, qoi_indices,
1171  *(this->diff_qoi),
1172  include_liftfunc,
1173  apply_constraints));
1174 
1175  for (unsigned int i=0; i != this->n_qois(); ++i)
1176  if (qoi_indices.has_index(i))
1177  this->diff_qoi->finalize_derivative(this->get_adjoint_rhs(i),i);
1178 }
virtual void finalize_derivative(NumericVector< Number > &derivatives, std::size_t qoi_index)
void parallel_for(const Range &range, const Body &body)
Definition: threads_none.h:73
unsigned int n_qois() const
Definition: system.h:2278
MeshBase & mesh
const MeshBase & get_mesh() const
Definition: system.h:2033
Base class for Mesh.
Definition: mesh_base.h:77
virtual void zero()=0
DifferentiableQoI * diff_qoi
Definition: diff_system.h:378
bool has_index(std::size_t) const
Definition: qoi_set.h:221
virtual element_iterator active_local_elements_begin()=0
NumericVector< Number > & add_adjoint_rhs(unsigned int i=0)
Definition: system.C:1021
virtual void update()
Definition: system.C:408
virtual element_iterator active_local_elements_end()=0

◆ assemble_residual_derivatives()

void libMesh::ImplicitSystem::assemble_residual_derivatives ( const ParameterVector parameters)
overridevirtualinherited

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 654 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(), and libMesh::ImplicitSystem::sensitivity_solve().

655 {
656  ParameterVector & parameters =
657  const_cast<ParameterVector &>(parameters_in);
658 
659  const unsigned int Np = cast_int<unsigned int>
660  (parameters.size());
661 
662  for (unsigned int p=0; p != Np; ++p)
663  {
664  NumericVector<Number> & sensitivity_rhs = this->add_sensitivity_rhs(p);
665 
666  // Approximate -(partial R / partial p) by
667  // (R(p-dp) - R(p+dp)) / (2*dp)
668 
669  Number old_parameter = *parameters[p];
670 
671  const Real delta_p =
672  TOLERANCE * std::max(std::abs(old_parameter), 1e-3);
673 
674  *parameters[p] -= delta_p;
675 
676  // this->assembly(true, false, true);
677  this->assembly(true, false, false);
678  this->rhs->close();
679  sensitivity_rhs = *this->rhs;
680 
681  *parameters[p] = old_parameter + delta_p;
682 
683  // this->assembly(true, false, true);
684  this->assembly(true, false, false);
685  this->rhs->close();
686 
687  sensitivity_rhs -= *this->rhs;
688  sensitivity_rhs /= (2*delta_p);
689  sensitivity_rhs.close();
690 
691  *parameters[p] = old_parameter;
692  }
693 }
double abs(double a)
NumericVector< Number > * rhs
NumericVector< Number > & add_sensitivity_rhs(unsigned int i=0)
Definition: system.C:1051
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

◆ assembly()

void libMesh::FEMSystem::assembly ( bool  get_residual,
bool  get_jacobian,
bool  apply_heterogeneous_constraints = false,
bool  apply_no_constraints = false 
)
overridevirtual

Prepares matrix or rhs for matrix assembly. Users may reimplement this to add pre- or post-assembly code before or after calling FEMSystem::assembly(). Note that in some cases only current_local_solution is used during assembly, and, therefore, if solution has been altered without update() being called, then the user must call update() before calling this function.

Implements libMesh::DifferentiableSystem.

Definition at line 854 of file fem_system.C.

References libMesh::MeshBase::active_local_elements_begin(), libMesh::MeshBase::active_local_elements_end(), libMesh::DenseMatrix< T >::add(), 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(), init_context(), libMesh::NumericVector< T >::l1_norm(), libMesh::SparseMatrix< T >::l1_norm(), libMesh::DenseMatrix< T >::l1_norm(), libMesh::ImplicitSystem::matrix, std::max(), mesh, libMesh::ParallelObject::n_processors(), libMesh::System::n_variable_groups(), 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::variable_group(), verify_analytic_jacobians, libMesh::DenseMatrix< T >::zero(), libMesh::SparseMatrix< T >::zero(), and libMesh::NumericVector< T >::zero().

Referenced by libMesh::ContinuationSystem::continuation_solve(), and libMesh::ContinuationSystem::solve_tangent().

857 {
858  libmesh_assert(get_residual || get_jacobian);
859 
860  // Log residual and jacobian and combined performance separately
861 #ifdef LIBMESH_ENABLE_PERFORMANCE_LOGGING
862  const char * log_name;
863  if (get_residual && get_jacobian)
864  log_name = "assembly()";
865  else if (get_residual)
866  log_name = "assembly(get_residual)";
867  else
868  log_name = "assembly(get_jacobian)";
869 
870  LOG_SCOPE(log_name, "FEMSystem");
871 #endif
872 
873  const MeshBase & mesh = this->get_mesh();
874 
876  {
877  this->solution->close();
878 
879  std::streamsize old_precision = libMesh::out.precision();
881  libMesh::out << "|U| = "
882  << this->solution->l1_norm()
883  << std::endl;
884  libMesh::out.precision(old_precision);
885  }
886  if (print_solutions)
887  {
888  std::streamsize old_precision = libMesh::out.precision();
890  libMesh::out << "U = [" << *(this->solution)
891  << "];" << std::endl;
892  libMesh::out.precision(old_precision);
893  }
894 
895  // Is this definitely necessary? [RHS]
896  // Yes. [RHS 2012]
897  if (get_jacobian)
898  matrix->zero();
899  if (get_residual)
900  rhs->zero();
901 
902  // Stupid C++ lets you set *Real* verify_analytic_jacobians = true!
903  if (verify_analytic_jacobians > 0.5)
904  {
905  libMesh::err << "WARNING! verify_analytic_jacobians was set "
906  << "to absurdly large value of "
907  << verify_analytic_jacobians << std::endl;
908  libMesh::err << "Resetting to 1e-6!" << std::endl;
910  }
911 
912  // In time-dependent problems, the nonlinear function we're trying
913  // to solve at each timestep may depend on the particular solver
914  // we're using
915  libmesh_assert(time_solver.get());
916 
917  // Build the residual and jacobian contributions on every active
918  // mesh element on this processor
920  (elem_range.reset(mesh.active_local_elements_begin(),
922  AssemblyContributions(*this, get_residual, get_jacobian,
923  apply_heterogeneous_constraints,
924  apply_no_constraints));
925 
926  // Check and see if we have SCALAR variables
927  bool have_scalar = false;
928  for (unsigned int i=0; i != this->n_variable_groups(); ++i)
929  {
930  if (this->variable_group(i).type().family == SCALAR)
931  {
932  have_scalar = true;
933  break;
934  }
935  }
936 
937  // SCALAR dofs are stored on the last processor, so we'll evaluate
938  // their equation terms there and only if we have a SCALAR variable
939  if (this->processor_id() == (this->n_processors()-1) && have_scalar)
940  {
941  std::unique_ptr<DiffContext> con = this->build_context();
942  FEMContext & _femcontext = cast_ref<FEMContext &>(*con);
943  this->init_context(_femcontext);
944  _femcontext.pre_fe_reinit(*this, nullptr);
945 
946  bool jacobian_computed =
947  this->time_solver->nonlocal_residual(get_jacobian, _femcontext);
948 
949  // Nonlocal residuals are likely to be length 0, in which case we
950  // don't need to do any more. And we shouldn't try to do any
951  // more; lots of DenseVector/DenseMatrix code assumes rank>0.
952  if (_femcontext.get_elem_residual().size())
953  {
954  // Compute a numeric jacobian if we have to
955  if (get_jacobian && !jacobian_computed)
956  {
957  // Make sure we didn't compute a jacobian and lie about it
958  libmesh_assert_equal_to (_femcontext.get_elem_jacobian().l1_norm(), 0.0);
959  // Logging of numerical jacobians is done separately
960  this->numerical_nonlocal_jacobian(_femcontext);
961  }
962 
963  // Compute a numeric jacobian if we're asked to verify the
964  // analytic jacobian we got
965  if (get_jacobian && jacobian_computed &&
966  this->verify_analytic_jacobians != 0.0)
967  {
968  DenseMatrix<Number> analytic_jacobian(_femcontext.get_elem_jacobian());
969 
970  _femcontext.get_elem_jacobian().zero();
971  // Logging of numerical jacobians is done separately
972  this->numerical_nonlocal_jacobian(_femcontext);
973 
974  Real analytic_norm = analytic_jacobian.l1_norm();
975  Real numerical_norm = _femcontext.get_elem_jacobian().l1_norm();
976 
977  // If we can continue, we'll probably prefer the analytic jacobian
978  analytic_jacobian.swap(_femcontext.get_elem_jacobian());
979 
980  // The matrix "analytic_jacobian" will now hold the error matrix
981  analytic_jacobian.add(-1.0, _femcontext.get_elem_jacobian());
982  Real error_norm = analytic_jacobian.l1_norm();
983 
984  Real relative_error = error_norm /
985  std::max(analytic_norm, numerical_norm);
986 
987  if (relative_error > this->verify_analytic_jacobians)
988  {
989  libMesh::err << "Relative error " << relative_error
990  << " detected in analytic jacobian on nonlocal dofs!"
991  << std::endl;
992 
993  std::streamsize old_precision = libMesh::out.precision();
995  libMesh::out << "J_analytic nonlocal = "
996  << _femcontext.get_elem_jacobian() << std::endl;
997  analytic_jacobian.add(1.0, _femcontext.get_elem_jacobian());
998  libMesh::out << "J_numeric nonlocal = "
999  << analytic_jacobian << std::endl;
1000 
1001  libMesh::out.precision(old_precision);
1002 
1003  libmesh_error_msg("Relative error too large, exiting!");
1004  }
1005  }
1006 
1007  add_element_system
1008  (*this, get_residual, get_jacobian,
1009  apply_heterogeneous_constraints, apply_no_constraints, _femcontext);
1010  }
1011  }
1012 
1013  if (get_residual && (print_residual_norms || print_residuals))
1014  this->rhs->close();
1015  if (get_residual && print_residual_norms)
1016  {
1017  std::streamsize old_precision = libMesh::out.precision();
1018  libMesh::out.precision(16);
1019  libMesh::out << "|F| = " << this->rhs->l1_norm() << std::endl;
1020  libMesh::out.precision(old_precision);
1021  }
1022  if (get_residual && print_residuals)
1023  {
1024  std::streamsize old_precision = libMesh::out.precision();
1025  libMesh::out.precision(16);
1026  libMesh::out << "F = [" << *(this->rhs) << "];" << std::endl;
1027  libMesh::out.precision(old_precision);
1028  }
1029 
1030  if (get_jacobian && (print_jacobian_norms || print_jacobians))
1031  this->matrix->close();
1032  if (get_jacobian && print_jacobian_norms)
1033  {
1034  std::streamsize old_precision = libMesh::out.precision();
1035  libMesh::out.precision(16);
1036  libMesh::out << "|J| = " << this->matrix->l1_norm() << std::endl;
1037  libMesh::out.precision(old_precision);
1038  }
1039  if (get_jacobian && print_jacobians)
1040  {
1041  std::streamsize old_precision = libMesh::out.precision();
1042  libMesh::out.precision(16);
1043  libMesh::out << "J = [" << *(this->matrix) << "];" << std::endl;
1044  libMesh::out.precision(old_precision);
1045  }
1046 }
virtual unsigned int size() const override
Definition: dense_vector.h:92
FEFamily family
Definition: fe_type.h:204
const DenseMatrix< Number > & get_elem_jacobian() const
Definition: diff_context.h:283
Real verify_analytic_jacobians
Definition: fem_system.h:209
virtual void pre_fe_reinit(const System &, const Elem *e)
Definition: fem_context.C:1552
std::streamsize precision() const
void parallel_for(const Range &range, const Body &body)
Definition: threads_none.h:73
unsigned int n_variable_groups() const
Definition: system.h:2113
std::unique_ptr< TimeSolver > time_solver
Definition: diff_system.h:234
MeshBase & mesh
NumericVector< Number > * rhs
long double max(long double a, double b)
const MeshBase & get_mesh() const
Definition: system.h:2033
Base class for Mesh.
Definition: mesh_base.h:77
virtual void zero()=0
Real l1_norm() const
Definition: dense_matrix.h:991
processor_id_type n_processors() const
virtual void zero()=0
virtual element_iterator active_local_elements_begin()=0
boostcopy::enable_if_c< ScalarTraits< T2 >::value, void >::type add(const T2 factor, const DenseMatrix< T3 > &mat)
Definition: dense_matrix.h:884
std::unique_ptr< NumericVector< Number > > solution
Definition: system.h:1523
void numerical_nonlocal_jacobian(FEMContext &context) const
Definition: fem_system.C:1310
OStreamProxy err(std::cerr)
virtual Real l1_norm() const =0
virtual void close()=0
const DenseVector< Number > & get_elem_residual() const
Definition: diff_context.h:249
virtual void close()=0
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
virtual void zero() override
Definition: dense_matrix.h:808
SparseMatrix< Number > * matrix
virtual void init_context(DiffContext &) override
Definition: fem_system.C:1342
virtual std::unique_ptr< DiffContext > build_context() override
Definition: fem_system.C:1318
virtual Real l1_norm() const =0
processor_id_type processor_id() const
OStreamProxy out(std::cout)
virtual element_iterator active_local_elements_end()=0
const VariableGroup & variable_group(unsigned int vg) const
Definition: system.h:2143
const FEType & type() const
Definition: variable.h:119

◆ attach_assemble_function()

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 1777 of file system.C.

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

1779 {
1780  libmesh_assert(fptr);
1781 
1782  if (_assemble_system_object != nullptr)
1783  {
1784  libmesh_here();
1785  libMesh::out << "WARNING: Cannot specify both assembly function and object!"
1786  << std::endl;
1787 
1788  _assemble_system_object = nullptr;
1789  }
1790 
1792 }
Assembly * _assemble_system_object
Definition: system.h:1841
void(* _assemble_system_function)(EquationSystems &es, const std::string &name)
Definition: system.h:1835
OStreamProxy out(std::cout)

◆ attach_assemble_object()

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 1796 of file system.C.

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

1797 {
1798  if (_assemble_system_function != nullptr)
1799  {
1800  libmesh_here();
1801  libMesh::out << "WARNING: Cannot specify both assembly object and function!"
1802  << std::endl;
1803 
1804  _assemble_system_function = nullptr;
1805  }
1806 
1807  _assemble_system_object = &assemble_in;
1808 }
Assembly * _assemble_system_object
Definition: system.h:1841
void(* _assemble_system_function)(EquationSystems &es, const std::string &name)
Definition: system.h:1835
OStreamProxy out(std::cout)

◆ attach_constraint_function()

void libMesh::System::attach_constraint_function ( void   fptrEquationSystems &es, const std::string &name)
inherited

Register a user function for imposing constraints.

Definition at line 1812 of file system.C.

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

1814 {
1815  libmesh_assert(fptr);
1816 
1817  if (_constrain_system_object != nullptr)
1818  {
1819  libmesh_here();
1820  libMesh::out << "WARNING: Cannot specify both constraint function and object!"
1821  << std::endl;
1822 
1823  _constrain_system_object = nullptr;
1824  }
1825 
1827 }
void(* _constrain_system_function)(EquationSystems &es, const std::string &name)
Definition: system.h:1846
Constraint * _constrain_system_object
Definition: system.h:1852
OStreamProxy out(std::cout)

◆ attach_constraint_object()

void libMesh::System::attach_constraint_object ( System::Constraint constrain)
inherited

Register a user object for imposing constraints.

Definition at line 1831 of file system.C.

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

1832 {
1833  if (_constrain_system_function != nullptr)
1834  {
1835  libmesh_here();
1836  libMesh::out << "WARNING: Cannot specify both constraint object and function!"
1837  << std::endl;
1838 
1839  _constrain_system_function = nullptr;
1840  }
1841 
1842  _constrain_system_object = &constrain;
1843 }
void(* _constrain_system_function)(EquationSystems &es, const std::string &name)
Definition: system.h:1846
Constraint * _constrain_system_object
Definition: system.h:1852
OStreamProxy out(std::cout)

◆ attach_init_function()

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 1742 of file system.C.

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

1744 {
1745  libmesh_assert(fptr);
1746 
1747  if (_init_system_object != nullptr)
1748  {
1749  libmesh_here();
1750  libMesh::out << "WARNING: Cannot specify both initialization function and object!"
1751  << std::endl;
1752 
1753  _init_system_object = nullptr;
1754  }
1755 
1756  _init_system_function = fptr;
1757 }
Initialization * _init_system_object
Definition: system.h:1830
void(* _init_system_function)(EquationSystems &es, const std::string &name)
Definition: system.h:1824
OStreamProxy out(std::cout)

◆ attach_init_object()

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 1761 of file system.C.

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

1762 {
1763  if (_init_system_function != nullptr)
1764  {
1765  libmesh_here();
1766  libMesh::out << "WARNING: Cannot specify both initialization object and function!"
1767  << std::endl;
1768 
1769  _init_system_function = nullptr;
1770  }
1771 
1772  _init_system_object = &init_in;
1773 }
Initialization * _init_system_object
Definition: system.h:1830
void(* _init_system_function)(EquationSystems &es, const std::string &name)
Definition: system.h:1824
OStreamProxy out(std::cout)

◆ attach_physics()

void libMesh::DifferentiableSystem::attach_physics ( DifferentiablePhysics physics_in)
inlineinherited

Attach external Physics object.

Definition at line 197 of file diff_system.h.

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

198  { this->_diff_physics = (physics_in->clone_physics()).release();
199  this->_diff_physics->init_physics(*this);}
DifferentiablePhysics * _diff_physics
Definition: diff_system.h:371
virtual void init_physics(const System &sys)

◆ attach_qoi()

void libMesh::DifferentiableSystem::attach_qoi ( DifferentiableQoI qoi_in)
inlineinherited

Attach external QoI object.

Definition at line 225 of file diff_system.h.

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

226  { this->diff_qoi = (qoi_in->clone()).release();
227  // User needs to resize qoi system qoi accordingly
228  this->diff_qoi->init_qoi( this->qoi );}
DifferentiableQoI * diff_qoi
Definition: diff_system.h:378
std::vector< Number > qoi
Definition: system.h:1558
virtual void init_qoi(std::vector< Number > &)
Definition: diff_qoi.h:69

◆ attach_QOI_derivative()

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 1883 of file system.C.

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

1885 {
1886  libmesh_assert(fptr);
1887 
1888  if (_qoi_evaluate_derivative_object != nullptr)
1889  {
1890  libmesh_here();
1891  libMesh::out << "WARNING: Cannot specify both QOI derivative function and object!"
1892  << std::endl;
1893 
1895  }
1896 
1898 }
QOIDerivative * _qoi_evaluate_derivative_object
Definition: system.h:1878
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:1869

◆ attach_QOI_derivative_object()

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 1902 of file system.C.

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

1903 {
1904  if (_qoi_evaluate_derivative_function != nullptr)
1905  {
1906  libmesh_here();
1907  libMesh::out << "WARNING: Cannot specify both QOI derivative object and function!"
1908  << std::endl;
1909 
1911  }
1912 
1913  _qoi_evaluate_derivative_object = &qoi_derivative;
1914 }
QOIDerivative * _qoi_evaluate_derivative_object
Definition: system.h:1878
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:1869

◆ attach_QOI_function()

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 1847 of file system.C.

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

1850 {
1851  libmesh_assert(fptr);
1852 
1853  if (_qoi_evaluate_object != nullptr)
1854  {
1855  libmesh_here();
1856  libMesh::out << "WARNING: Cannot specify both QOI function and object!"
1857  << std::endl;
1858 
1859  _qoi_evaluate_object = nullptr;
1860  }
1861 
1862  _qoi_evaluate_function = fptr;
1863 }
void(* _qoi_evaluate_function)(EquationSystems &es, const std::string &name, const QoISet &qoi_indices)
Definition: system.h:1857
QOI * _qoi_evaluate_object
Definition: system.h:1864
OStreamProxy out(std::cout)

◆ attach_QOI_object()

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 1867 of file system.C.

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

1868 {
1869  if (_qoi_evaluate_function != nullptr)
1870  {
1871  libmesh_here();
1872  libMesh::out << "WARNING: Cannot specify both QOI object and function!"
1873  << std::endl;
1874 
1875  _qoi_evaluate_function = nullptr;
1876  }
1877 
1878  _qoi_evaluate_object = &qoi_in;
1879 }
void(* _qoi_evaluate_function)(EquationSystems &es, const std::string &name, const QoISet &qoi_indices)
Definition: system.h:1857
QOI * _qoi_evaluate_object
Definition: system.h:1864
OStreamProxy out(std::cout)

◆ boundary_project_solution() [1/2]

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 = 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 985 of file system_projection.C.

989 {
990  this->boundary_project_vector(b, variables, *solution, f, g);
991 
992  solution->localize(*current_local_solution);
993 }
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=nullptr, int is_adjoint=-1) const
std::unique_ptr< NumericVector< Number > > solution
Definition: system.h:1523
std::unique_ptr< NumericVector< Number > > current_local_solution
Definition: system.h:1535

◆ boundary_project_solution() [2/2]

void libMesh::System::boundary_project_solution ( const std::set< boundary_id_type > &  b,
const std::vector< unsigned int > &  variables,
ValueFunctionPointer  fptr,
GradientFunctionPointer  gptr,
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.

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

Definition at line 968 of file system_projection.C.

973 {
974  WrappedFunction<Number> f(*this, fptr, &parameters);
975  WrappedFunction<Gradient> g(*this, gptr, &parameters);
976  this->boundary_project_solution(b, variables, &f, &g);
977 }
void boundary_project_solution(const std::set< boundary_id_type > &b, const std::vector< unsigned int > &variables, FunctionBase< Number > *f, FunctionBase< Gradient > *g=nullptr)

◆ boundary_project_vector() [1/2]

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 = 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 1021 of file system_projection.C.

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

1027 {
1028  LOG_SCOPE ("boundary_project_vector()", "System");
1029 
1031  (ConstElemRange (this->get_mesh().active_local_elements_begin(),
1032  this->get_mesh().active_local_elements_end() ),
1033  BoundaryProjectSolution(b, variables, *this, f, g,
1034  this->get_equation_systems().parameters,
1035  new_vector)
1036  );
1037 
1038  // We don't do SCALAR dofs when just projecting the boundary, so
1039  // we're done here.
1040 
1041  new_vector.close();
1042 
1043 #ifdef LIBMESH_ENABLE_CONSTRAINTS
1044  if (is_adjoint == -1)
1045  this->get_dof_map().enforce_constraints_exactly(*this, &new_vector);
1046  else if (is_adjoint >= 0)
1048  is_adjoint);
1049 #endif
1050 }
void parallel_for(const Range &range, const Body &body)
Definition: threads_none.h:73
const EquationSystems & get_equation_systems() const
Definition: system.h:712
const MeshBase & get_mesh() const
Definition: system.h:2033
StoredRange< MeshBase::const_element_iterator, const Elem * > ConstElemRange
Definition: elem_range.h:34
void enforce_adjoint_constraints_exactly(NumericVector< Number > &v, unsigned int q) const
virtual void close()=0
const DofMap & get_dof_map() const
Definition: system.h:2049
void enforce_constraints_exactly(const System &system, NumericVector< Number > *v=nullptr, bool homogeneous=false) const

◆ boundary_project_vector() [2/2]

void libMesh::System::boundary_project_vector ( const std::set< boundary_id_type > &  b,
const std::vector< unsigned int > &  variables,
ValueFunctionPointer  fptr,
GradientFunctionPointer  gptr,
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.

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

Definition at line 1003 of file system_projection.C.

1010 {
1011  WrappedFunction<Number> f(*this, fptr, &parameters);
1012  WrappedFunction<Gradient> g(*this, gptr, &parameters);
1013  this->boundary_project_vector(b, variables, new_vector, &f, &g,
1014  is_adjoint);
1015 }
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=nullptr, int is_adjoint=-1) const

◆ build_context()

std::unique_ptr< DiffContext > libMesh::FEMSystem::build_context ( )
overridevirtual

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::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 assembly(), mesh_position_get(), and 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 std::unique_ptr<DiffContext>(fc);
1338 }
unsigned int get_mesh_x_var() const
Definition: diff_physics.h:636
void set_mesh_z_var(unsigned int z_var)
Definition: fem_context.h:859
void set_mesh_x_var(unsigned int x_var)
Definition: fem_context.h:831
const System * get_mesh_system() const
Definition: diff_physics.h:624
bool is_adjoint() const
Definition: diff_context.h:470
virtual void set_mesh_system(System *sys)
Definition: fem_context.h:805
unsigned int get_mesh_y_var() const
Definition: diff_physics.h:642
bool is_adjoint() const
Definition: time_solver.h:233
const DifferentiablePhysics * get_physics() const
Definition: diff_system.h:182
void set_mesh_y_var(unsigned int y_var)
Definition: fem_context.h:845
unsigned int get_mesh_z_var() const
Definition: diff_physics.h:648
void set_deltat_pointer(Real *dt)
Definition: diff_context.C:103
TimeSolver & get_time_solver()
Definition: diff_system.h:415

◆ calculate_norm() [1/2]

Real libMesh::System::calculate_norm ( const NumericVector< Number > &  v,
unsigned int  var,
FEMNormType  norm_type,
std::set< unsigned int > *  skip_dimensions = 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 1378 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(), and libMesh::UnsteadySolver::du().

1382 {
1383  //short circuit to save time
1384  if (norm_type == DISCRETE_L1 ||
1385  norm_type == DISCRETE_L2 ||
1386  norm_type == DISCRETE_L_INF)
1387  return discrete_var_norm(v,var,norm_type);
1388 
1389  // Not a discrete norm
1390  std::vector<FEMNormType> norms(this->n_vars(), L2);
1391  std::vector<Real> weights(this->n_vars(), 0.0);
1392  norms[var] = norm_type;
1393  weights[var] = 1.0;
1394  Real val = this->calculate_norm(v, SystemNorm(norms, weights), skip_dimensions);
1395  return val;
1396 }
Real calculate_norm(const NumericVector< Number > &v, unsigned int var, FEMNormType norm_type, std::set< unsigned int > *skip_dimensions=nullptr) const
Definition: system.C:1378
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
Real discrete_var_norm(const NumericVector< Number > &v, unsigned int var, FEMNormType norm_type) const
Definition: system.C:1359
unsigned int n_vars() const
Definition: system.h:2105

◆ calculate_norm() [2/2]

Real libMesh::System::calculate_norm ( const NumericVector< Number > &  v,
const SystemNorm norm,
std::set< unsigned int > *  skip_dimensions = 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 1400 of file system.C.

References libMesh::System::_dof_map, libMesh::System::_mesh, std::abs(), 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::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::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().

1403 {
1404  // This function must be run on all processors at once
1405  parallel_object_only();
1406 
1407  LOG_SCOPE ("calculate_norm()", "System");
1408 
1409  // Zero the norm before summation
1410  Real v_norm = 0.;
1411 
1412  if (norm.is_discrete())
1413  {
1414  //Check to see if all weights are 1.0 and all types are equal
1415  FEMNormType norm_type0 = norm.type(0);
1416  unsigned int check_var = 0;
1417  for (; check_var != this->n_vars(); ++check_var)
1418  if ((norm.weight(check_var) != 1.0) || (norm.type(check_var) != norm_type0))
1419  break;
1420 
1421  //All weights were 1.0 so just do the full vector discrete norm
1422  if (check_var == this->n_vars())
1423  {
1424  if (norm_type0 == DISCRETE_L1)
1425  return v.l1_norm();
1426  if (norm_type0 == DISCRETE_L2)
1427  return v.l2_norm();
1428  if (norm_type0 == DISCRETE_L_INF)
1429  return v.linfty_norm();
1430  else
1431  libmesh_error_msg("Invalid norm_type0 = " << norm_type0);
1432  }
1433 
1434  for (unsigned int var=0; var != this->n_vars(); ++var)
1435  {
1436  // Skip any variables we don't need to integrate
1437  if (norm.weight(var) == 0.0)
1438  continue;
1439 
1440  v_norm += norm.weight(var) * discrete_var_norm(v, var, norm.type(var));
1441  }
1442 
1443  return v_norm;
1444  }
1445 
1446  // Localize the potentially parallel vector
1447  std::unique_ptr<NumericVector<Number>> local_v = NumericVector<Number>::build(this->comm());
1448  local_v->init(v.size(), true, SERIAL);
1449  v.localize (*local_v, _dof_map->get_send_list());
1450 
1451  // I'm not sure how best to mix Hilbert norms on some variables (for
1452  // which we'll want to square then sum then square root) with norms
1453  // like L_inf (for which we'll just want to take an absolute value
1454  // and then sum).
1455  bool using_hilbert_norm = true,
1456  using_nonhilbert_norm = true;
1457 
1458  // Loop over all variables
1459  for (unsigned int var=0; var != this->n_vars(); ++var)
1460  {
1461  // Skip any variables we don't need to integrate
1462  Real norm_weight_sq = norm.weight_sq(var);
1463  if (norm_weight_sq == 0.0)
1464  continue;
1465  Real norm_weight = norm.weight(var);
1466 
1467  // Check for unimplemented norms (rather than just returning 0).
1468  FEMNormType norm_type = norm.type(var);
1469  if ((norm_type==H1) ||
1470  (norm_type==H2) ||
1471  (norm_type==L2) ||
1472  (norm_type==H1_SEMINORM) ||
1473  (norm_type==H2_SEMINORM))
1474  {
1475  if (!using_hilbert_norm)
1476  libmesh_not_implemented();
1477  using_nonhilbert_norm = false;
1478  }
1479  else if ((norm_type==L1) ||
1480  (norm_type==L_INF) ||
1481  (norm_type==W1_INF_SEMINORM) ||
1482  (norm_type==W2_INF_SEMINORM))
1483  {
1484  if (!using_nonhilbert_norm)
1485  libmesh_not_implemented();
1486  using_hilbert_norm = false;
1487  }
1488  else
1489  libmesh_not_implemented();
1490 
1491  const FEType & fe_type = this->get_dof_map().variable_type(var);
1492 
1493  // Allow space for dims 0-3, even if we don't use them all
1494  std::vector<std::unique_ptr<FEBase>> fe_ptrs(4);
1495  std::vector<std::unique_ptr<QBase>> q_rules(4);
1496 
1497  const std::set<unsigned char> & elem_dims = _mesh.elem_dimensions();
1498 
1499  // Prepare finite elements for each dimension present in the mesh
1500  for (const auto & dim : elem_dims)
1501  {
1502  if (skip_dimensions && skip_dimensions->find(dim) != skip_dimensions->end())
1503  continue;
1504 
1505  // Construct quadrature and finite element objects
1506  q_rules[dim] = fe_type.default_quadrature_rule (dim);
1507  fe_ptrs[dim] = FEBase::build(dim, fe_type);
1508 
1509  // Attach quadrature rule to FE object
1510  fe_ptrs[dim]->attach_quadrature_rule (q_rules[dim].get());
1511  }
1512 
1513  std::vector<dof_id_type> dof_indices;
1514 
1515  // Begin the loop over the elements
1516  for (const auto & elem : this->get_mesh().active_local_element_ptr_range())
1517  {
1518  const unsigned int dim = elem->dim();
1519 
1520 #ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
1521 
1522  // One way for implementing this would be to exchange the fe with the FEInterface- class.
1523  // However, it needs to be discussed whether integral-norms make sense for infinite elements.
1524  // or in which sense they could make sense.
1525  if (elem->infinite() )
1526  libmesh_not_implemented();
1527 
1528 #endif
1529 
1530  if (skip_dimensions && skip_dimensions->find(dim) != skip_dimensions->end())
1531  continue;
1532 
1533  FEBase * fe = fe_ptrs[dim].get();
1534  QBase * qrule = q_rules[dim].get();
1535  libmesh_assert(fe);
1536  libmesh_assert(qrule);
1537 
1538  const std::vector<Real> & JxW = fe->get_JxW();
1539  const std::vector<std::vector<Real>> * phi = nullptr;
1540  if (norm_type == H1 ||
1541  norm_type == H2 ||
1542  norm_type == L2 ||
1543  norm_type == L1 ||
1544  norm_type == L_INF)
1545  phi = &(fe->get_phi());
1546 
1547  const std::vector<std::vector<RealGradient>> * dphi = nullptr;
1548  if (norm_type == H1 ||
1549  norm_type == H2 ||
1550  norm_type == H1_SEMINORM ||
1551  norm_type == W1_INF_SEMINORM)
1552  dphi = &(fe->get_dphi());
1553 #ifdef LIBMESH_ENABLE_SECOND_DERIVATIVES
1554  const std::vector<std::vector<RealTensor>> * d2phi = nullptr;
1555  if (norm_type == H2 ||
1556  norm_type == H2_SEMINORM ||
1557  norm_type == W2_INF_SEMINORM)
1558  d2phi = &(fe->get_d2phi());
1559 #endif
1560 
1561  fe->reinit (elem);
1562 
1563  this->get_dof_map().dof_indices (elem, dof_indices, var);
1564 
1565  const unsigned int n_qp = qrule->n_points();
1566 
1567  const unsigned int n_sf = cast_int<unsigned int>
1568  (dof_indices.size());
1569 
1570  // Begin the loop over the Quadrature points.
1571  for (unsigned int qp=0; qp<n_qp; qp++)
1572  {
1573  if (norm_type == L1)
1574  {
1575  Number u_h = 0.;
1576  for (unsigned int i=0; i != n_sf; ++i)
1577  u_h += (*phi)[i][qp] * (*local_v)(dof_indices[i]);
1578  v_norm += norm_weight *
1579  JxW[qp] * std::abs(u_h);
1580  }
1581 
1582  if (norm_type == L_INF)
1583  {
1584  Number u_h = 0.;
1585  for (unsigned int i=0; i != n_sf; ++i)
1586  u_h += (*phi)[i][qp] * (*local_v)(dof_indices[i]);
1587  v_norm = std::max(v_norm, norm_weight * std::abs(u_h));
1588  }
1589 
1590  if (norm_type == H1 ||
1591  norm_type == H2 ||
1592  norm_type == L2)
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_sq *
1598  JxW[qp] * TensorTools::norm_sq(u_h);
1599  }
1600 
1601  if (norm_type == H1 ||
1602  norm_type == H2 ||
1603  norm_type == H1_SEMINORM)
1604  {
1605  Gradient grad_u_h;
1606  for (unsigned int i=0; i != n_sf; ++i)
1607  grad_u_h.add_scaled((*dphi)[i][qp], (*local_v)(dof_indices[i]));
1608  v_norm += norm_weight_sq *
1609  JxW[qp] * grad_u_h.norm_sq();
1610  }
1611 
1612  if (norm_type == W1_INF_SEMINORM)
1613  {
1614  Gradient grad_u_h;
1615  for (unsigned int i=0; i != n_sf; ++i)
1616  grad_u_h.add_scaled((*dphi)[i][qp], (*local_v)(dof_indices[i]));
1617  v_norm = std::max(v_norm, norm_weight * grad_u_h.norm());
1618  }
1619 
1620 #ifdef LIBMESH_ENABLE_SECOND_DERIVATIVES
1621  if (norm_type == H2 ||
1622  norm_type == H2_SEMINORM)
1623  {
1624  Tensor hess_u_h;
1625  for (unsigned int i=0; i != n_sf; ++i)
1626  hess_u_h.add_scaled((*d2phi)[i][qp], (*local_v)(dof_indices[i]));
1627  v_norm += norm_weight_sq *
1628  JxW[qp] * hess_u_h.norm_sq();
1629  }
1630 
1631  if (norm_type == W2_INF_SEMINORM)
1632  {
1633  Tensor hess_u_h;
1634  for (unsigned int i=0; i != n_sf; ++i)
1635  hess_u_h.add_scaled((*d2phi)[i][qp], (*local_v)(dof_indices[i]));
1636  v_norm = std::max(v_norm, norm_weight * hess_u_h.norm());
1637  }
1638 #endif
1639  }
1640  }
1641  }
1642 
1643  if (using_hilbert_norm)
1644  {
1645  this->comm().sum(v_norm);
1646  v_norm = std::sqrt(v_norm);
1647  }
1648  else
1649  {
1650  this->comm().max(v_norm);
1651  }
1652 
1653  return v_norm;
1654 }
double abs(double a)
void dof_indices(const Elem *const elem, std::vector< dof_id_type > &di) const
Definition: dof_map.C:1930
void add_scaled(const TypeTensor< T2 > &, const T)
Definition: type_tensor.h:808
void add_scaled(const TypeVector< T2 > &, const T)
Definition: type_vector.h:627
virtual numeric_index_type size() const =0
const FEType & variable_type(const unsigned int c) const
Definition: dof_map.h:1792
std::unique_ptr< DofMap > _dof_map
Definition: system.h:1884
const Parallel::Communicator & comm() const
long double max(long double a, double b)
const MeshBase & get_mesh() const
Definition: system.h:2033
virtual Real l2_norm() const =0
NumberVectorValue Gradient
static std::unique_ptr< FEGenericBase > build(const unsigned int dim, const FEType &type)
const std::set< unsigned char > & elem_dimensions() const
Definition: mesh_base.h:220
FEGenericBase< Real > FEBase
virtual Real l1_norm() const =0
static std::unique_ptr< NumericVector< T > > build(const Parallel::Communicator &comm, const SolverPackage solver_package=libMesh::default_solver_package())
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
NumberTensorValue Tensor
Real discrete_var_norm(const NumericVector< Number > &v, unsigned int var, FEMNormType norm_type) const
Definition: system.C:1359
unsigned int n_vars() const
Definition: system.h:2105
const DofMap & get_dof_map() const
Definition: system.h:2049
MeshBase & _mesh
Definition: system.h:1896
virtual Real linfty_norm() const =0
virtual void localize(std::vector< T > &v_local) const =0

◆ clear()

void libMesh::DifferentiableSystem::clear ( )
overridevirtualinherited

Clear all the data structures associated with the system.

Reimplemented from libMesh::ImplicitSystem.

Reimplemented in libMesh::ContinuationSystem.

Definition at line 69 of file diff_system.C.

References libMesh::DifferentiableSystem::_diff_physics, libMesh::DifferentiablePhysics::clear_physics(), libMesh::DifferentiableQoI::clear_qoi(), libMesh::DifferentiableSystem::diff_qoi, and libMesh::System::use_fixed_solution.

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

70 {
71  // If we had an attached Physics object, delete it.
72  if (this->_diff_physics != this)
73  {
74  delete this->_diff_physics;
75  this->_diff_physics = this;
76  }
77  // If we had no attached Physics object, clear our own Physics data
78  else
79  this->clear_physics();
80 
81  // If we had an attached QoI object, delete it.
82  if (this->diff_qoi != this)
83  {
84  delete this->diff_qoi;
85  this->diff_qoi = this;
86  }
87  // If we had no attached QoI object, clear our own QoI data
88  else
89  this->clear_qoi();
90 
91  use_fixed_solution = false;
92 }
DifferentiableQoI * diff_qoi
Definition: diff_system.h:378
DifferentiablePhysics * _diff_physics
Definition: diff_system.h:371
bool use_fixed_solution
Definition: system.h:1493
virtual void clear_qoi()
Definition: diff_qoi.h:75

◆ clear_physics()

virtual void libMesh::DifferentiablePhysics::clear_physics ( )
virtualinherited

Clear any data structures associated with the physics.

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

◆ clear_qoi()

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

Clear all the data structures associated with the QoI.

Definition at line 75 of file diff_qoi.h.

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

75 {}

◆ clone()

virtual std::unique_ptr<DifferentiableQoI> libMesh::DifferentiableSystem::clone ( )
inlineoverridevirtualinherited

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

Implements libMesh::DifferentiableQoI.

Definition at line 169 of file diff_system.h.

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

170  {
171  libmesh_not_implemented();
172  // dummy
173  return std::unique_ptr<DifferentiableQoI>(this);
174  }

◆ clone_physics()

virtual std::unique_ptr<DifferentiablePhysics> libMesh::DifferentiableSystem::clone_physics ( )
inlineoverridevirtualinherited

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

Implements libMesh::DifferentiablePhysics.

Definition at line 159 of file diff_system.h.

160  {
161  libmesh_not_implemented();
162  // dummy
163  return std::unique_ptr<DifferentiablePhysics>(this);
164  }

◆ comm()

const Parallel::Communicator& libMesh::ParallelObject::comm ( ) const
inlineinherited
Returns
A reference to the Parallel::Communicator object used by this mesh.

Definition at line 89 of file parallel_object.h.

References libMesh::ParallelObject::_communicator.

Referenced by libMesh::__libmesh_petsc_diff_solver_jacobian(), libMesh::__libmesh_petsc_diff_solver_monitor(), libMesh::__libmesh_petsc_diff_solver_residual(), libMesh::__libmesh_tao_equality_constraints(), libMesh::__libmesh_tao_equality_constraints_jacobian(), libMesh::__libmesh_tao_gradient(), libMesh::__libmesh_tao_hessian(), libMesh::__libmesh_tao_inequality_constraints(), libMesh::__libmesh_tao_inequality_constraints_jacobian(), libMesh::__libmesh_tao_objective(), libMesh::MeshRefinement::_coarsen_elements(), libMesh::ExactSolution::_compute_error(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::BoundaryInfo::_find_id_maps(), libMesh::SlepcEigenSolver< T >::_petsc_shell_matrix_get_diagonal(), libMesh::PetscLinearSolver< T >::_petsc_shell_matrix_get_diagonal(), libMesh::SlepcEigenSolver< T >::_petsc_shell_matrix_mult(), libMesh::PetscLinearSolver< 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::PetscDMWrapper::add_dofs_helper(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::ImplicitSystem::add_matrix(), libMesh::System::add_vector(), libMesh::UnstructuredMesh::all_second_order(), libMesh::MeshTools::Modification::all_tri(), libMesh::LaplaceMeshSmoother::allgather_graph(), assemble_qoi(), libMesh::MeshCommunication::assign_global_indices(), libMesh::DofMap::attach_matrix(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::PetscDMWrapper::build_section(), libMesh::PetscDMWrapper::build_sf(), libMesh::MeshBase::cache_elem_dims(), libMesh::System::calculate_norm(), libMesh::DofMap::check_dirichlet_bcid_consistency(), libMesh::PetscDMWrapper::check_section_n_dofs(), 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::ExodusII_IO::copy_elemental_solution(), 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::CondensedEigenSystem::get_eigenpair(), libMesh::DofMap::get_info(), libMesh::ImplicitSystem::get_linear_solver(), libMesh::LocationMap< T >::init(), libMesh::TimeSolver::init(), libMesh::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_and_attach_petscdm(), libMesh::EigenSystem::init_data(), libMesh::EigenSystem::init_matrices(), libMesh::OptimizationSystem::initialize_equality_constraints_storage(), libMesh::OptimizationSystem::initialize_inequality_constraints_storage(), libMesh::MeshTools::libmesh_assert_consistent_distributed(), libMesh::MeshTools::libmesh_assert_consistent_distributed_nodes(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_new_node_procids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_topology_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_valid_boundary_ids(), libMesh::MeshTools::libmesh_assert_valid_dof_ids(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_flags(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_object_ids(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_p_levels(), libMesh::MeshTools::libmesh_assert_valid_refinement_flags(), libMesh::MeshTools::libmesh_assert_valid_unique_ids(), libMesh::libmesh_petsc_snes_fd_residual(), libMesh::libmesh_petsc_snes_jacobian(), libMesh::libmesh_petsc_snes_mffd_residual(), libMesh::libmesh_petsc_snes_postcheck(), libMesh::libmesh_petsc_snes_residual(), libMesh::libmesh_petsc_snes_residual_helper(), libMesh::MeshRefinement::limit_level_mismatch_at_edge(), libMesh::MeshRefinement::limit_level_mismatch_at_node(), libMesh::MeshRefinement::limit_overrefined_boundary(), libMesh::MeshRefinement::limit_underrefined_boundary(), 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(), mesh_position_set(), 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::petsc_auto_fieldsplit(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::MeshBase::prepare_for_use(), libMesh::Nemesis_IO::read(), libMesh::XdrIO::read(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::System::read_header(), libMesh::System::read_legacy_data(), libMesh::System::read_SCALAR_dofs(), libMesh::XdrIO::read_serialized_bc_names(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::System::read_serialized_vector(), libMesh::MeshBase::recalculate_n_partitions(), libMesh::MeshRefinement::refine_and_coarsen_elements(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::CheckpointIO::select_split_config(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::PetscDiffSolver::setup_petsc_data(), libMesh::LaplaceMeshSmoother::smooth(), libMesh::split_mesh(), libMesh::MeshBase::subdomain_ids(), libMesh::BoundaryInfo::sync(), libMesh::MeshRefinement::test_level_one(), libMesh::MeshRefinement::test_unflagged(), libMesh::MeshTools::total_weight(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::NameBasedIO::write(), libMesh::XdrIO::write(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), and libMesh::XdrIO::write_serialized_nodesets().

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

◆ compare()

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 514 of file system.C.

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

Referenced by libMesh::EquationSystems::compare().

517 {
518  // we do not care for matrices, but for vectors
519  libmesh_assert (_is_initialized);
520  libmesh_assert (other_system._is_initialized);
521 
522  if (verbose)
523  {
524  libMesh::out << " Systems \"" << _sys_name << "\"" << std::endl;
525  libMesh::out << " comparing matrices not supported." << std::endl;
526  libMesh::out << " comparing names...";
527  }
528 
529  // compare the name: 0 means identical
530  const int name_result = _sys_name.compare(other_system.name());
531  if (verbose)
532  {
533  if (name_result == 0)
534  libMesh::out << " identical." << std::endl;
535  else
536  libMesh::out << " names not identical." << std::endl;
537  libMesh::out << " comparing solution vector...";
538  }
539 
540 
541  // compare the solution: -1 means identical
542  const int solu_result = solution->compare (*other_system.solution.get(),
543  threshold);
544 
545  if (verbose)
546  {
547  if (solu_result == -1)
548  libMesh::out << " identical up to threshold." << std::endl;
549  else
550  libMesh::out << " first difference occurred at index = "
551  << solu_result << "." << std::endl;
552  }
553 
554 
555  // safety check, whether we handle at least the same number
556  // of vectors
557  std::vector<int> ov_result;
558 
559  if (this->n_vectors() != other_system.n_vectors())
560  {
561  if (verbose)
562  {
563  libMesh::out << " Fatal difference. This system handles "
564  << this->n_vectors() << " add'l vectors," << std::endl
565  << " while the other system handles "
566  << other_system.n_vectors()
567  << " add'l vectors." << std::endl
568  << " Aborting comparison." << std::endl;
569  }
570  return false;
571  }
572  else if (this->n_vectors() == 0)
573  {
574  // there are no additional vectors...
575  ov_result.clear ();
576  }
577  else
578  {
579  // compare other vectors
580  for (auto & pr : _vectors)
581  {
582  if (verbose)
583  libMesh::out << " comparing vector \""
584  << pr.first << "\" ...";
585 
586  // assume they have the same name
587  const NumericVector<Number> & other_system_vector =
588  other_system.get_vector(pr.first);
589 
590  ov_result.push_back(pr.second->compare (other_system_vector,
591  threshold));
592 
593  if (verbose)
594  {
595  if (ov_result[ov_result.size()-1] == -1)
596  libMesh::out << " identical up to threshold." << std::endl;
597  else
598  libMesh::out << " first difference occurred at" << std::endl
599  << " index = " << ov_result[ov_result.size()-1] << "." << std::endl;
600  }
601  }
602  } // finished comparing additional vectors
603 
604 
605  bool overall_result;
606 
607  // sum up the results
608  if ((name_result==0) && (solu_result==-1))
609  {
610  if (ov_result.size()==0)
611  overall_result = true;
612  else
613  {
614  bool ov_identical;
615  unsigned int n = 0;
616  do
617  {
618  ov_identical = (ov_result[n]==-1);
619  n++;
620  }
621  while (ov_identical && n<ov_result.size());
622  overall_result = ov_identical;
623  }
624  }
625  else
626  overall_result = false;
627 
628  if (verbose)
629  {
630  libMesh::out << " finished comparisons, ";
631  if (overall_result)
632  libMesh::out << "found no differences." << std::endl << std::endl;
633  else
634  libMesh::out << "found differences." << std::endl << std::endl;
635  }
636 
637  return overall_result;
638 }
bool _is_initialized
Definition: system.h:1971
unsigned int n_vectors() const
Definition: system.h:2233
std::unique_ptr< NumericVector< Number > > solution
Definition: system.h:1523
std::map< std::string, NumericVector< Number > *> _vectors
Definition: system.h:1935
const std::string _sys_name
Definition: system.h:1901
OStreamProxy out(std::cout)

◆ current_solution()

Number libMesh::System::current_solution ( const dof_id_type  global_dof_number) const
inherited

◆ damping_residual()

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 374 of file diff_physics.h.

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

375  {
376  return request_jacobian;
377  }

◆ deactivate()

void libMesh::System::deactivate ( )
inlineinherited

Deactivates the system. Only active systems are solved.

Definition at line 2081 of file system.h.

References libMesh::System::_active.

2082 {
2083  _active = false;
2084 }

◆ disable_cache()

void libMesh::ImplicitSystem::disable_cache ( )
overridevirtualinherited

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 306 of file implicit_system.C.

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

306  {
307  this->assemble_before_solve = true;
308  this->get_linear_solver()->reuse_preconditioner(false);
309 }
virtual LinearSolver< Number > * get_linear_solver() const
virtual void reuse_preconditioner(bool)
bool assemble_before_solve
Definition: system.h:1477

◆ disable_print_counter_info()

void libMesh::ReferenceCounter::disable_print_counter_info ( )
staticinherited

Definition at line 106 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

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

107 {
108  _enable_print_counter = false;
109  return;
110 }

◆ element_constraint()

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 142 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().

143  {
144  return request_jacobian;
145  }

◆ element_postprocess()

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 282 of file diff_system.h.

282 {}

◆ element_qoi()

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 108 of file diff_qoi.h.

110  {}

◆ element_qoi_derivative()

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 120 of file diff_qoi.h.

122  {}

◆ element_time_derivative()

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 124 of file diff_physics.h.

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

125  {
126  return request_jacobian;
127  }

◆ enable_print_counter_info()

void libMesh::ReferenceCounter::enable_print_counter_info ( )
staticinherited

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

Definition at line 100 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

101 {
102  _enable_print_counter = true;
103  return;
104 }

◆ eulerian_residual() [1/2]

virtual bool libMesh::FEMPhysics::eulerian_residual ( bool  request_jacobian,
DiffContext context 
)
overridevirtualinherited

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.

◆ eulerian_residual() [2/2]

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 294 of file diff_physics.h.

295  {
296  return request_jacobian;
297  }

◆ finalize_derivative()

virtual void libMesh::DifferentiableQoI::finalize_derivative ( NumericVector< Number > &  derivatives,
std::size_t  qoi_index 
)
virtualinherited

Method to finalize qoi derivatives which require more than just a simple sum of element contributions.

Referenced by assemble_qoi_derivative().

◆ forward_qoi_parameter_sensitivity()

void libMesh::ImplicitSystem::forward_qoi_parameter_sensitivity ( const QoISet qoi_indices,
const ParameterVector parameters,
SensitivityData sensitivities 
)
overridevirtualinherited

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 807 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::n_qois(), libMesh::System::qoi, libMesh::Real, libMesh::ExplicitSystem::rhs, libMesh::ImplicitSystem::sensitivity_solve(), libMesh::ParameterVector::size(), and libMesh::TOLERANCE.

810 {
811  ParameterVector & parameters =
812  const_cast<ParameterVector &>(parameters_in);
813 
814  const unsigned int Np = cast_int<unsigned int>
815  (parameters.size());
816  const unsigned int Nq = this->n_qois();
817 
818  // An introduction to the problem:
819  //
820  // Residual R(u(p),p) = 0
821  // partial R / partial u = J = system matrix
822  //
823  // This implies that:
824  // d/dp(R) = 0
825  // (partial R / partial p) +
826  // (partial R / partial u) * (partial u / partial p) = 0
827 
828  // We first solve for (partial u / partial p) for each parameter:
829  // J * (partial u / partial p) = - (partial R / partial p)
830 
831  this->sensitivity_solve(parameters);
832 
833  // Get ready to fill in sensitivities:
834  sensitivities.allocate_data(qoi_indices, *this, parameters);
835 
836  // We use the identity:
837  // dq/dp = (partial q / partial p) + (partial q / partial u) *
838  // (partial u / partial p)
839 
840  // We get (partial q / partial u) from the user
841  this->assemble_qoi_derivative(qoi_indices,
842  /* include_liftfunc = */ true,
843  /* apply_constraints = */ false);
844 
845  // We don't need these to be closed() in this function, but libMesh
846  // standard practice is to have them closed() by the time the
847  // function exits
848  for (unsigned int i=0; i != this->n_qois(); ++i)
849  if (qoi_indices.has_index(i))
850  this->get_adjoint_rhs(i).close();
851 
852  for (unsigned int j=0; j != Np; ++j)
853  {
854  // We currently get partial derivatives via central differencing
855 
856  // (partial q / partial p) ~= (q(p+dp)-q(p-dp))/(2*dp)
857 
858  Number old_parameter = *parameters[j];
859 
860  const Real delta_p =
861  TOLERANCE * std::max(std::abs(old_parameter), 1e-3);
862 
863  *parameters[j] = old_parameter - delta_p;
864  this->assemble_qoi(qoi_indices);
865  std::vector<Number> qoi_minus = this->qoi;
866 
867  *parameters[j] = old_parameter + delta_p;
868  this->assemble_qoi(qoi_indices);
869  std::vector<Number> & qoi_plus = this->qoi;
870 
871  std::vector<Number> partialq_partialp(Nq, 0);
872  for (unsigned int i=0; i != Nq; ++i)
873  if (qoi_indices.has_index(i))
874  partialq_partialp[i] = (qoi_plus[i] - qoi_minus[i]) / (2.*delta_p);
875 
876  // Don't leave the parameter changed
877  *parameters[j] = old_parameter;
878 
879  for (unsigned int i=0; i != Nq; ++i)
880  if (qoi_indices.has_index(i))
881  sensitivities[i][j] = partialq_partialp[i] +
882  this->get_adjoint_rhs(i).dot(this->get_sensitivity_solution(j));
883  }
884 
885  // All parameters have been reset.
886  // We didn't cache the original rhs or matrix for memory reasons,
887  // but we can restore them to a state consistent solution -
888  // principle of least surprise.
889  this->assembly(true, true);
890  this->rhs->close();
891  this->matrix->close();
892  this->assemble_qoi(qoi_indices);
893 }
double abs(double a)
unsigned int n_qois() const
Definition: system.h:2278
NumericVector< Number > & get_sensitivity_solution(unsigned int i=0)
Definition: system.C:916
NumericVector< Number > * rhs
virtual std::pair< unsigned int, Real > sensitivity_solve(const ParameterVector &parameters) override
static const Real TOLERANCE
virtual T dot(const NumericVector< T > &v) const =0
long double max(long double a, double b)
virtual void assembly(bool, bool, bool=false, bool=false)
std::vector< Number > qoi
Definition: system.h:1558
virtual void close()=0
virtual void close()=0
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
SparseMatrix< Number > * matrix
virtual void assemble_qoi(const QoISet &qoi_indices=QoISet()) override
virtual void assemble_qoi_derivative(const QoISet &qoi_indices=QoISet(), bool include_liftfunc=true, bool apply_constraints=true) override
NumericVector< Number > & get_adjoint_rhs(unsigned int i=0)
Definition: system.C:1031

◆ get_adjoint_rhs() [1/2]

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 1031 of file system.C.

References libMesh::System::get_vector().

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

1032 {
1033  std::ostringstream adjoint_rhs_name;
1034  adjoint_rhs_name << "adjoint_rhs" << i;
1035 
1036  return this->get_vector(adjoint_rhs_name.str());
1037 }
const NumericVector< Number > & get_vector(const std::string &vec_name) const
Definition: system.C:774

◆ get_adjoint_rhs() [2/2]

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 1041 of file system.C.

References libMesh::System::get_vector().

1042 {
1043  std::ostringstream adjoint_rhs_name;
1044  adjoint_rhs_name << "adjoint_rhs" << i;
1045 
1046  return this->get_vector(adjoint_rhs_name.str());
1047 }
const NumericVector< Number > & get_vector(const std::string &vec_name) const
Definition: system.C:774

◆ get_adjoint_solution() [1/2]

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 969 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::ImplicitSystem::qoi_parameter_hessian(), libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product(), and libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve().

970 {
971  std::ostringstream adjoint_name;
972  adjoint_name << "adjoint_solution" << i;
973 
974  return this->get_vector(adjoint_name.str());
975 }
const NumericVector< Number > & get_vector(const std::string &vec_name) const
Definition: system.C:774

◆ get_adjoint_solution() [2/2]

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 979 of file system.C.

References libMesh::System::get_vector().

980 {
981  std::ostringstream adjoint_name;
982  adjoint_name << "adjoint_solution" << i;
983 
984  return this->get_vector(adjoint_name.str());
985 }
const NumericVector< Number > & get_vector(const std::string &vec_name) const
Definition: system.C:774

◆ get_all_variable_numbers()

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 1258 of file system.C.

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

1259 {
1260  all_variable_numbers.resize(n_vars());
1261 
1262  // Make sure the variable exists
1263  std::map<std::string, unsigned short int>::const_iterator
1264  it = _variable_numbers.begin();
1265  std::map<std::string, unsigned short int>::const_iterator
1266  it_end = _variable_numbers.end();
1267 
1268  unsigned int count = 0;
1269  for ( ; it != it_end; ++it)
1270  {
1271  all_variable_numbers[count] = it->second;
1272  count++;
1273  }
1274 }
std::map< std::string, unsigned short int > _variable_numbers
Definition: system.h:1922
unsigned int n_vars() const
Definition: system.h:2105

◆ get_dof_map() [1/2]

const DofMap & libMesh::System::get_dof_map ( ) const
inlineinherited
Returns
A constant reference to this system's _dof_map.

Definition at line 2049 of file system.h.

References libMesh::System::_dof_map.

Referenced by libMesh::__libmesh_petsc_diff_solver_jacobian(), libMesh::__libmesh_petsc_diff_solver_residual(), 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_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::PetscDMWrapper::build_sf(), 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::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::libmesh_petsc_snes_jacobian(), libMesh::libmesh_petsc_snes_postcheck(), libMesh::libmesh_petsc_snes_residual_helper(), 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::WeightedPatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::PatchRecoveryErrorEstimator::EstimateError::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::System::read_parallel_data(), libMesh::System::read_SCALAR_dofs(), libMesh::SecondOrderUnsteadySolver::reinit(), libMesh::UnsteadySolver::reinit(), libMesh::EigenSystem::reinit(), libMesh::ImplicitSystem::reinit(), libMesh::System::reinit_constraints(), libMesh::EquationSystems::reinit_solutions(), libMesh::UnsteadySolver::retrieve_timestep(), libMesh::HPCoarsenTest::select_refinement(), libMesh::ImplicitSystem::sensitivity_solve(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::NewtonSolver::solve(), libMesh::PetscDiffSolver::solve(), libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve(), libMesh::ImplicitSystem::weighted_sensitivity_solve(), libMesh::System::write_parallel_data(), libMesh::EnsightIO::write_scalar_ascii(), libMesh::System::write_SCALAR_dofs(), and libMesh::EnsightIO::write_vector_ascii().

2050 {
2051  return *_dof_map;
2052 }
std::unique_ptr< DofMap > _dof_map
Definition: system.h:1884

◆ get_dof_map() [2/2]

DofMap & libMesh::System::get_dof_map ( )
inlineinherited
Returns
A writable reference to this system's _dof_map.

Definition at line 2057 of file system.h.

References libMesh::System::_dof_map.

2058 {
2059  return *_dof_map;
2060 }
std::unique_ptr< DofMap > _dof_map
Definition: system.h:1884

◆ get_equation_systems() [1/2]

◆ get_equation_systems() [2/2]

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.

717 { return _equation_systems; }
EquationSystems & _equation_systems
Definition: system.h:1890

◆ get_first_order_vars()

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 517 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_first_order_vars.

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

518  { return _first_order_vars; }
std::set< unsigned int > _first_order_vars
Definition: diff_physics.h:559

◆ get_info() [1/2]

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

Gets a string containing the reference information.

Definition at line 47 of file reference_counter.C.

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

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

48 {
49 #if defined(LIBMESH_ENABLE_REFERENCE_COUNTING) && defined(DEBUG)
50 
51  std::ostringstream oss;
52 
53  oss << '\n'
54  << " ---------------------------------------------------------------------------- \n"
55  << "| Reference count information |\n"
56  << " ---------------------------------------------------------------------------- \n";
57 
58  for (const auto & pr : _counts)
59  {
60  const std::string name(pr.first);
61  const unsigned int creations = pr.second.first;
62  const unsigned int destructions = pr.second.second;
63 
64  oss << "| " << name << " reference count information:\n"
65  << "| Creations: " << creations << '\n'
66  << "| Destructions: " << destructions << '\n';
67  }
68 
69  oss << " ---------------------------------------------------------------------------- \n";
70 
71  return oss.str();
72 
73 #else
74 
75  return "";
76 
77 #endif
78 }
std::string name(const ElemQuality q)
Definition: elem_quality.C:42

◆ get_info() [2/2]

std::string libMesh::System::get_info ( ) const
inherited
Returns
A string containing information about the system.

Definition at line 1658 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().

1659 {
1660  std::ostringstream oss;
1661 
1662 
1663  const std::string & sys_name = this->name();
1664 
1665  oss << " System #" << this->number() << ", \"" << sys_name << "\"\n"
1666  << " Type \"" << this->system_type() << "\"\n"
1667  << " Variables=";
1668 
1669  for (unsigned int vg=0; vg<this->n_variable_groups(); vg++)
1670  {
1671  const VariableGroup & vg_description (this->variable_group(vg));
1672 
1673  if (vg_description.n_variables() > 1) oss << "{ ";
1674  for (unsigned int vn=0; vn<vg_description.n_variables(); vn++)
1675  oss << "\"" << vg_description.name(vn) << "\" ";
1676  if (vg_description.n_variables() > 1) oss << "} ";
1677  }
1678 
1679  oss << '\n';
1680 
1681  oss << " Finite Element Types=";
1682 #ifndef LIBMESH_ENABLE_INFINITE_ELEMENTS
1683  for (unsigned int vg=0; vg<this->n_variable_groups(); vg++)
1684  oss << "\""
1685  << Utility::enum_to_string<FEFamily>(this->get_dof_map().variable_group(vg).type().family)
1686  << "\" ";
1687 #else
1688  for (unsigned int vg=0; vg<this->n_variable_groups(); vg++)
1689  {
1690  oss << "\""
1691  << Utility::enum_to_string<FEFamily>(this->get_dof_map().variable_group(vg).type().family)
1692  << "\", \""
1693  << Utility::enum_to_string<FEFamily>(this->get_dof_map().variable_group(vg).type().radial_family)
1694  << "\" ";
1695  }
1696 
1697  oss << '\n' << " Infinite Element Mapping=";
1698  for (unsigned int vg=0; vg<this->n_variable_groups(); vg++)
1699  oss << "\""
1700  << Utility::enum_to_string<InfMapType>(this->get_dof_map().variable_group(vg).type().inf_map)
1701  << "\" ";
1702 #endif
1703 
1704  oss << '\n';
1705 
1706  oss << " Approximation Orders=";
1707  for (unsigned int vg=0; vg<this->n_variable_groups(); vg++)
1708  {
1709 #ifndef LIBMESH_ENABLE_INFINITE_ELEMENTS
1710  oss << "\""
1711  << Utility::enum_to_string<Order>(this->get_dof_map().variable_group(vg).type().order)
1712  << "\" ";
1713 #else
1714  oss << "\""
1715  << Utility::enum_to_string<Order>(this->get_dof_map().variable_group(vg).type().order)
1716  << "\", \""
1717  << Utility::enum_to_string<Order>(this->get_dof_map().variable_group(vg).type().radial_order)
1718  << "\" ";
1719 #endif
1720  }
1721 
1722  oss << '\n';
1723 
1724  oss << " n_dofs()=" << this->n_dofs() << '\n';
1725  oss << " n_local_dofs()=" << this->n_local_dofs() << '\n';
1726 #ifdef LIBMESH_ENABLE_CONSTRAINTS
1727  oss << " n_constrained_dofs()=" << this->n_constrained_dofs() << '\n';
1728  oss << " n_local_constrained_dofs()=" << this->n_local_constrained_dofs() << '\n';
1729 #endif
1730 
1731  oss << " " << "n_vectors()=" << this->n_vectors() << '\n';
1732  oss << " " << "n_matrices()=" << this->n_matrices() << '\n';
1733  // oss << " " << "n_additional_matrices()=" << this->n_additional_matrices() << '\n';
1734 
1735  oss << this->get_dof_map().get_info();
1736 
1737  return oss.str();
1738 }
FEFamily family
Definition: fe_type.h:204
OrderWrapper radial_order
Definition: fe_type.h:237
unsigned int n_variable_groups() const
Definition: system.h:2113
OrderWrapper order
Definition: fe_type.h:198
dof_id_type n_local_dofs() const
Definition: system.C:187
std::string get_info() const
Definition: dof_map.C:2703
dof_id_type n_dofs() const
Definition: system.C:150
unsigned int number() const
Definition: system.h:2025
unsigned int n_vectors() const
Definition: system.h:2233
const VariableGroup & variable_group(const unsigned int c) const
Definition: dof_map.h:1752
InfMapType inf_map
Definition: fe_type.h:258
virtual unsigned int n_matrices() const
Definition: system.h:2239
FEFamily radial_family
Definition: fe_type.h:250
virtual std::string system_type() const
Definition: system.h:487
dof_id_type n_local_constrained_dofs() const
Definition: system.C:172
const std::string & name() const
Definition: system.h:2017
const DofMap & get_dof_map() const
Definition: system.h:2049
const VariableGroup & variable_group(unsigned int vg) const
Definition: system.h:2143
dof_id_type n_constrained_dofs() const
Definition: system.C:157
const FEType & type() const
Definition: variable.h:119

◆ get_linear_solve_parameters()

std::pair< unsigned int, Real > libMesh::DifferentiableSystem::get_linear_solve_parameters ( ) const
overridevirtualinherited
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::DifferentiableSystem::time_solver.

185 {
186  libmesh_assert(time_solver.get());
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 }
std::unique_ptr< TimeSolver > time_solver
Definition: diff_system.h:234

◆ get_linear_solver()

LinearSolver< Number > * libMesh::DifferentiableSystem::get_linear_solver ( ) const
overridevirtualinherited
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::DifferentiableSystem::time_solver.

176 {
177  libmesh_assert(time_solver.get());
178  libmesh_assert_equal_to (&(time_solver->system()), this);
179  return this->time_solver->linear_solver().get();
180 }
std::unique_ptr< TimeSolver > time_solver
Definition: diff_system.h:234

◆ get_matrix() [1/2]

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 263 of file implicit_system.C.

References libMesh::ImplicitSystem::_matrices.

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

264 {
265  // Make sure the matrix exists
266  const_matrices_iterator pos = _matrices.find (mat_name);
267 
268  if (pos == _matrices.end())
269  libmesh_error_msg("ERROR: matrix " << mat_name << " does not exist in this system!");
270 
271  return *(pos->second);
272 }
std::map< std::string, SparseMatrix< Number > * > _matrices
std::map< std::string, SparseMatrix< Number > * >::const_iterator const_matrices_iterator

◆ get_matrix() [2/2]

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 276 of file implicit_system.C.

References libMesh::ImplicitSystem::_matrices.

277 {
278  // Make sure the matrix exists
279  matrices_iterator pos = _matrices.find (mat_name);
280 
281  if (pos == _matrices.end())
282  libmesh_error_msg("ERROR: matrix " << mat_name << " does not exist in this system!");
283 
284  return *(pos->second);
285 }
std::map< std::string, SparseMatrix< Number > * > _matrices
std::map< std::string, SparseMatrix< Number > * >::iterator matrices_iterator

◆ get_mesh() [1/2]

const MeshBase & libMesh::System::get_mesh ( ) const
inlineinherited
Returns
A constant reference to this systems's _mesh.

Definition at line 2033 of file system.h.

References libMesh::System::_mesh.

Referenced by libMesh::ExactSolution::_compute_error(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::HPCoarsenTest::add_projection(), assemble_qoi(), assemble_qoi_derivative(), assembly(), libMesh::System::calculate_norm(), DMCreateDomainDecomposition_libMesh(), DMCreateFieldDecomposition_libMesh(), DMlibMeshSetSystem_libMesh(), libMesh::WeightedPatchRecoveryErrorEstimator::estimate_error(), libMesh::PatchRecoveryErrorEstimator::estimate_error(), libMesh::JumpErrorEstimator::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(), mesh_position_get(), mesh_position_set(), libMesh::WeightedPatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::PatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::petsc_auto_fieldsplit(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), postprocess(), libMesh::System::read_header(), libMesh::System::read_legacy_data(), libMesh::System::read_parallel_data(), libMesh::System::read_serialized_vector(), libMesh::System::read_serialized_vectors(), libMesh::EigenSystem::reinit(), libMesh::ImplicitSystem::reinit(), libMesh::HPSingularity::select_refinement(), libMesh::HPCoarsenTest::select_refinement(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::System::write_header(), libMesh::System::write_parallel_data(), libMesh::System::write_serialized_vector(), libMesh::System::write_serialized_vectors(), and libMesh::System::zero_variable().

2034 {
2035  return _mesh;
2036 }
MeshBase & _mesh
Definition: system.h:1896

◆ get_mesh() [2/2]

MeshBase & libMesh::System::get_mesh ( )
inlineinherited
Returns
A reference to this systems's _mesh.

Definition at line 2041 of file system.h.

References libMesh::System::_mesh.

2042 {
2043  return _mesh;
2044 }
MeshBase & _mesh
Definition: system.h:1896

◆ get_mesh_system() [1/2]

const System * libMesh::DifferentiablePhysics::get_mesh_system ( ) const
inlineinherited
Returns
A const reference to the system with variables corresponding to mesh nodal coordinates, or nullptr if the mesh is fixed. Useful for ALE calculations.

Definition at line 624 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_mesh_sys.

Referenced by build_context().

625 {
626  return _mesh_sys;
627 }

◆ get_mesh_system() [2/2]

System * libMesh::DifferentiablePhysics::get_mesh_system ( )
inlineinherited
Returns
A reference to the system with variables corresponding to mesh nodal coordinates, or nullptr if the mesh is fixed.

Definition at line 630 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_mesh_sys.

631 {
632  return _mesh_sys;
633 }

◆ get_mesh_x_var()

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 636 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_mesh_x_var.

Referenced by build_context().

637 {
638  return _mesh_x_var;
639 }

◆ get_mesh_y_var()

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 642 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_mesh_y_var.

Referenced by build_context().

643 {
644  return _mesh_y_var;
645 }

◆ get_mesh_z_var()

unsigned int libMesh::DifferentiablePhysics::get_mesh_z_var ( ) const
inlineinherited
Returns
The variable number corresponding to the mesh z coordinate. Useful for ALE calculations.

Definition at line 648 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_mesh_z_var.

Referenced by build_context().

649 {
650  return _mesh_z_var;
651 }

◆ get_physics() [1/2]

◆ get_physics() [2/2]

DifferentiablePhysics* libMesh::DifferentiableSystem::get_physics ( )
inlineinherited
Returns
A reference to a DifferentiablePhysics object.
Note
If no external Physics object is attached, the default is this.

Definition at line 191 of file diff_system.h.

References libMesh::DifferentiableSystem::_diff_physics.

192  { return this->_diff_physics; }
DifferentiablePhysics * _diff_physics
Definition: diff_system.h:371

◆ get_qoi() [1/2]

const DifferentiableQoI* libMesh::DifferentiableSystem::get_qoi ( ) const
inlineinherited
Returns
A const reference to a DifferentiableQoI object.
Note
If no external QoI object is attached, the default is this.

Definition at line 211 of file diff_system.h.

References libMesh::DifferentiableSystem::diff_qoi.

212  { return this->diff_qoi; }
DifferentiableQoI * diff_qoi
Definition: diff_system.h:378

◆ get_qoi() [2/2]

DifferentiableQoI* libMesh::DifferentiableSystem::get_qoi ( )
inlineinherited
Returns
A reference to a DifferentiableQoI object.
Note
If no external QoI object is attached, the default is this.

Definition at line 219 of file diff_system.h.

References libMesh::DifferentiableSystem::diff_qoi.

220  { return this->diff_qoi; }
DifferentiableQoI * diff_qoi
Definition: diff_system.h:378

◆ get_second_order_dot_var()

unsigned int libMesh::DifferentiableSystem::get_second_order_dot_var ( unsigned int  var) const
inherited

For a given second order (in time) variable var, this method will return the index to the corresponding "dot" variable. For FirstOrderUnsteadySolver classes, the "dot" variable would automatically be added and the returned index will correspond to that variable. For SecondOrderUnsteadySolver classes, this method will return var as there this is no "dot" variable per se, but having this function allows one to use the interface to treat both FirstOrderUnsteadySolver and SecondOrderUnsteadySolver simultaneously.

Definition at line 306 of file diff_system.C.

References libMesh::DifferentiablePhysics::_second_order_dot_vars, libMesh::UnsteadySolver::time_order(), and libMesh::DifferentiableSystem::time_solver.

Referenced by libMesh::FirstOrderUnsteadySolver::compute_second_order_eqns().

307 {
308  // For SteadySolver or SecondOrderUnsteadySolvers, we just give back var
309  unsigned int dot_var = var;
310 
311  if (!time_solver->is_steady())
312  {
313  const UnsteadySolver & unsteady_solver =
314  cast_ref<const UnsteadySolver &>(*(time_solver.get()));
315 
316  if (unsteady_solver.time_order() == 1)
317  dot_var = this->_second_order_dot_vars.find(var)->second;
318  }
319 
320  return dot_var;
321 }
std::unique_ptr< TimeSolver > time_solver
Definition: diff_system.h:234
std::map< unsigned int, unsigned int > _second_order_dot_vars
Definition: diff_physics.h:571

◆ get_second_order_vars()

const std::set<unsigned int>& libMesh::DifferentiablePhysics::get_second_order_vars ( ) const
inlineinherited

◆ get_sensitivity_rhs() [1/2]

NumericVector< Number > & libMesh::System::get_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. By default these vectors are built by the library, using finite differences, when assemble_residual_derivatives() is called.

When assembled, this vector should hold -(partial R / partial p_i)

Definition at line 1061 of file system.C.

References libMesh::System::get_vector().

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

1062 {
1063  std::ostringstream sensitivity_rhs_name;
1064  sensitivity_rhs_name << "sensitivity_rhs" << i;
1065 
1066  return this->get_vector(sensitivity_rhs_name.str());
1067 }
const NumericVector< Number > & get_vector(const std::string &vec_name) const
Definition: system.C:774

◆ get_sensitivity_rhs() [2/2]

const NumericVector< Number > & libMesh::System::get_sensitivity_rhs ( unsigned int  i = 0) const
inherited
Returns
A reference to one of the system's sensitivity rhs vectors, by default the one corresponding to the first parameter.

Definition at line 1071 of file system.C.

References libMesh::System::get_vector().

1072 {
1073  std::ostringstream sensitivity_rhs_name;
1074  sensitivity_rhs_name << "sensitivity_rhs" << i;
1075 
1076  return this->get_vector(sensitivity_rhs_name.str());
1077 }
const NumericVector< Number > & get_vector(const std::string &vec_name) const
Definition: system.C:774

◆ get_sensitivity_solution() [1/2]

NumericVector< Number > & libMesh::System::get_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.

Definition at line 916 of file system.C.

References libMesh::System::get_vector().

Referenced by libMesh::ImplicitSystem::forward_qoi_parameter_sensitivity(), libMesh::ImplicitSystem::qoi_parameter_hessian(), and libMesh::ImplicitSystem::sensitivity_solve().

917 {
918  std::ostringstream sensitivity_name;
919  sensitivity_name << "sensitivity_solution" << i;
920 
921  return this->get_vector(sensitivity_name.str());
922 }
const NumericVector< Number > & get_vector(const std::string &vec_name) const
Definition: system.C:774

◆ get_sensitivity_solution() [2/2]

const NumericVector< Number > & libMesh::System::get_sensitivity_solution ( unsigned int  i = 0) const
inherited
Returns
A reference to one of the system's solution sensitivity vectors, by default the one corresponding to the first parameter.

Definition at line 926 of file system.C.

References libMesh::System::get_vector().

927 {
928  std::ostringstream sensitivity_name;
929  sensitivity_name << "sensitivity_solution" << i;
930 
931  return this->get_vector(sensitivity_name.str());
932 }
const NumericVector< Number > & get_vector(const std::string &vec_name) const
Definition: system.C:774

◆ get_time_solver() [1/2]

TimeSolver & libMesh::DifferentiableSystem::get_time_solver ( )
inlineinherited
Returns
A pointer to the time solver attached to the calling system

Definition at line 415 of file diff_system.h.

References libMesh::DifferentiableSystem::time_solver.

Referenced by libMesh::DifferentiableSystem::adjoint_solve(), build_context(), libMesh::DiffContext::DiffContext(), postprocess(), libMesh::FEMContext::pre_fe_reinit(), and libMesh::DifferentiableSystem::solve().

416 {
417  libmesh_assert(time_solver.get());
418  libmesh_assert_equal_to (&(time_solver->system()), this);
419  return *time_solver;
420 }
std::unique_ptr< TimeSolver > time_solver
Definition: diff_system.h:234

◆ get_time_solver() [2/2]

const TimeSolver & libMesh::DifferentiableSystem::get_time_solver ( ) const
inlineinherited

Non-const version of the above

Definition at line 423 of file diff_system.h.

References libMesh::DifferentiableSystem::time_solver.

424 {
425  libmesh_assert(time_solver.get());
426  libmesh_assert_equal_to (&(time_solver->system()), this);
427  return *time_solver;
428 }
std::unique_ptr< TimeSolver > time_solver
Definition: diff_system.h:234

◆ get_vector() [1/4]

const NumericVector< Number > & libMesh::System::get_vector ( const std::string &  vec_name) const
inherited
Returns
A const reference to this system's additional vector named vec_name. Access is only granted when the vector is already properly initialized.

Definition at line 774 of file system.C.

References libMesh::System::_vectors.

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::UnsteadySolver::adjoint_advance_timestep(), libMesh::NewmarkSolver::advance_timestep(), libMesh::AdaptiveTimeSolver::advance_timestep(), libMesh::UnsteadySolver::advance_timestep(), libMesh::System::compare(), libMesh::NewmarkSolver::compute_initial_accel(), libMesh::UnsteadySolver::du(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::System::get_adjoint_rhs(), libMesh::System::get_adjoint_solution(), libMesh::System::get_sensitivity_rhs(), libMesh::System::get_sensitivity_solution(), libMesh::System::get_weighted_sensitivity_adjoint_solution(), libMesh::System::get_weighted_sensitivity_solution(), libMesh::NewmarkSystem::initial_conditions(), libMesh::NewmarkSolver::project_initial_accel(), libMesh::SecondOrderUnsteadySolver::project_initial_rate(), libMesh::SecondOrderUnsteadySolver::reinit(), libMesh::UnsteadySolver::reinit(), libMesh::MemorySolutionHistory::retrieve(), libMesh::UnsteadySolver::retrieve_timestep(), libMesh::TwostepTimeSolver::solve(), libMesh::FrequencySystem::solve(), libMesh::NewmarkSystem::update_rhs(), and libMesh::NewmarkSystem::update_u_v_a().

775 {
776  // Make sure the vector exists
777  const_vectors_iterator pos = _vectors.find(vec_name);
778 
779  if (pos == _vectors.end())
780  libmesh_error_msg("ERROR: vector " << vec_name << " does not exist in this system!");
781 
782  return *(pos->second);
783 }
std::map< std::string, NumericVector< Number > * >::const_iterator const_vectors_iterator
Definition: system.h:749
std::map< std::string, NumericVector< Number > *> _vectors
Definition: system.h:1935

◆ get_vector() [2/4]

NumericVector< Number > & libMesh::System::get_vector ( const std::string &  vec_name)
inherited
Returns
A writable reference to this system's additional vector named vec_name. Access is only granted when the vector is already properly initialized.

Definition at line 787 of file system.C.

References libMesh::System::_vectors.

788 {
789  // Make sure the vector exists
790  vectors_iterator pos = _vectors.find(vec_name);
791 
792  if (pos == _vectors.end())
793  libmesh_error_msg("ERROR: vector " << vec_name << " does not exist in this system!");
794 
795  return *(pos->second);
796 }
std::map< std::string, NumericVector< Number > * >::iterator vectors_iterator
Definition: system.h:748
std::map< std::string, NumericVector< Number > *> _vectors
Definition: system.h:1935

◆ get_vector() [3/4]

const NumericVector< Number > & libMesh::System::get_vector ( const unsigned int  vec_num) const
inherited
Returns
A const reference to this system's additional vector number vec_num (where the vectors are counted starting with 0).

Definition at line 800 of file system.C.

References libMesh::System::vectors_begin(), and libMesh::System::vectors_end().

801 {
804  unsigned int num = 0;
805  while ((num<vec_num) && (v!=v_end))
806  {
807  num++;
808  ++v;
809  }
810  libmesh_assert (v != v_end);
811  return *(v->second);
812 }
vectors_iterator vectors_end()
Definition: system.h:2257
std::map< std::string, NumericVector< Number > * >::const_iterator const_vectors_iterator
Definition: system.h:749
vectors_iterator vectors_begin()
Definition: system.h:2245

◆ get_vector() [4/4]

NumericVector< Number > & libMesh::System::get_vector ( const unsigned int  vec_num)
inherited
Returns
A writable reference to this system's additional vector number vec_num (where the vectors are counted starting with 0).

Definition at line 816 of file system.C.

References libMesh::System::vectors_begin(), and libMesh::System::vectors_end().

817 {
819  vectors_iterator v_end = vectors_end();
820  unsigned int num = 0;
821  while ((num<vec_num) && (v!=v_end))
822  {
823  num++;
824  ++v;
825  }
826  libmesh_assert (v != v_end);
827  return *(v->second);
828 }
vectors_iterator vectors_end()
Definition: system.h:2257
vectors_iterator vectors_begin()
Definition: system.h:2245
std::map< std::string, NumericVector< Number > * >::iterator vectors_iterator
Definition: system.h:748

◆ get_weighted_sensitivity_adjoint_solution() [1/2]

NumericVector< Number > & libMesh::System::get_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.

Definition at line 1001 of file system.C.

References libMesh::System::get_vector().

Referenced by libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product(), and libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve().

1002 {
1003  std::ostringstream adjoint_name;
1004  adjoint_name << "weighted_sensitivity_adjoint_solution" << i;
1005 
1006  return this->get_vector(adjoint_name.str());
1007 }
const NumericVector< Number > & get_vector(const std::string &vec_name) const
Definition: system.C:774

◆ get_weighted_sensitivity_adjoint_solution() [2/2]

const NumericVector< Number > & libMesh::System::get_weighted_sensitivity_adjoint_solution ( unsigned int  i = 0) const
inherited
Returns
A reference to one of the system's weighted sensitivity adjoint solution vectors, by default the one corresponding to the first qoi.

Definition at line 1011 of file system.C.

References libMesh::System::get_vector().

1012 {
1013  std::ostringstream adjoint_name;
1014  adjoint_name << "weighted_sensitivity_adjoint_solution" << i;
1015 
1016  return this->get_vector(adjoint_name.str());
1017 }
const NumericVector< Number > & get_vector(const std::string &vec_name) const
Definition: system.C:774

◆ get_weighted_sensitivity_solution() [1/2]

NumericVector< Number > & libMesh::System::get_weighted_sensitivity_solution ( )
inherited
Returns
A reference to the solution of the last weighted sensitivity solve

Definition at line 943 of file system.C.

References libMesh::System::get_vector().

Referenced by libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product(), and libMesh::ImplicitSystem::weighted_sensitivity_solve().

944 {
945  return this->get_vector("weighted_sensitivity_solution");
946 }
const NumericVector< Number > & get_vector(const std::string &vec_name) const
Definition: system.C:774

◆ get_weighted_sensitivity_solution() [2/2]

const NumericVector< Number > & libMesh::System::get_weighted_sensitivity_solution ( ) const
inherited
Returns
A reference to the solution of the last weighted sensitivity solve

Definition at line 950 of file system.C.

References libMesh::System::get_vector().

951 {
952  return this->get_vector("weighted_sensitivity_solution");
953 }
const NumericVector< Number > & get_vector(const std::string &vec_name) const
Definition: system.C:774

◆ has_variable()

bool libMesh::System::has_variable ( const std::string &  var) const
inherited
Returns
true if a variable named var exists in this System

Definition at line 1236 of file system.C.

References libMesh::System::_variable_numbers.

Referenced by libMesh::GMVIO::copy_nodal_solution().

1237 {
1238  return _variable_numbers.count(var);
1239 }
std::map< std::string, unsigned short int > _variable_numbers
Definition: system.h:1922

◆ have_first_order_scalar_vars()

bool libMesh::DifferentiableSystem::have_first_order_scalar_vars ( ) const
inherited

Check for any first order vars that are also belong to FEFamily::SCALAR

Definition at line 323 of file diff_system.C.

References libMesh::DifferentiablePhysics::get_first_order_vars(), libMesh::DifferentiablePhysics::have_first_order_vars(), libMesh::SCALAR, and libMesh::System::variable().

324 {
325  bool have_first_order_scalar_vars = false;
326 
327  if (this->have_first_order_vars())
328  for (const auto & var : this->get_first_order_vars())
329  if (this->variable(var).type().family == SCALAR)
331 
333 }
const Variable & variable(unsigned int var) const
Definition: system.h:2133
const std::set< unsigned int > & get_first_order_vars() const
Definition: diff_physics.h:517
bool have_first_order_scalar_vars() const
Definition: diff_system.C:323

◆ have_first_order_vars()

bool libMesh::DifferentiablePhysics::have_first_order_vars ( ) const
inlineinherited

Definition at line 511 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_first_order_vars.

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

512  { return !_first_order_vars.empty(); }
std::set< unsigned int > _first_order_vars
Definition: diff_physics.h:559

◆ have_matrix()

bool libMesh::ImplicitSystem::have_matrix ( const std::string &  mat_name) const
inlineinherited
Returns
true if this System has a matrix associated with the given name, false otherwise.

Definition at line 419 of file implicit_system.h.

References libMesh::ImplicitSystem::_matrices.

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

420 {
421  return (_matrices.count(mat_name));
422 }
std::map< std::string, SparseMatrix< Number > * > _matrices

◆ have_second_order_scalar_vars()

bool libMesh::DifferentiableSystem::have_second_order_scalar_vars ( ) const
inherited

Check for any second order vars that are also belong to FEFamily::SCALAR

Definition at line 335 of file diff_system.C.

References libMesh::DifferentiablePhysics::get_second_order_vars(), libMesh::DifferentiablePhysics::have_second_order_vars(), libMesh::SCALAR, and libMesh::System::variable().

Referenced by libMesh::EulerSolver::nonlocal_residual(), and libMesh::Euler2Solver::nonlocal_residual().

336 {
337  bool have_second_order_scalar_vars = false;
338 
339  if (this->have_second_order_vars())
340  for (const auto & var : this->get_second_order_vars())
341  if (this->variable(var).type().family == SCALAR)
343 
345 }
const Variable & variable(unsigned int var) const
Definition: system.h:2133
const std::set< unsigned int > & get_second_order_vars() const
Definition: diff_physics.h:530
bool have_second_order_scalar_vars() const
Definition: diff_system.C:335

◆ have_second_order_vars()

bool libMesh::DifferentiablePhysics::have_second_order_vars ( ) const
inlineinherited

◆ have_vector()

bool libMesh::System::have_vector ( const std::string &  vec_name) const
inlineinherited
Returns
true if this System has a vector associated with the given name, false otherwise.

Definition at line 2225 of file system.h.

References libMesh::System::_vectors.

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

2226 {
2227  return (_vectors.count(vec_name));
2228 }
std::map< std::string, NumericVector< Number > *> _vectors
Definition: system.h:1935

◆ hide_output()

bool& libMesh::System::hide_output ( )
inlineinherited
Returns
A writable reference to a boolean that determines if this system can be written to file or not. If set to true, then EquationSystems::write will ignore this system.

Definition at line 1662 of file system.h.

References libMesh::System::_hide_output.

1662 { return _hide_output; }
bool _hide_output
Definition: system.h:2009

◆ identify_variable_groups() [1/2]

bool libMesh::System::identify_variable_groups ( ) const
inlineinherited
Returns
true when VariableGroup structures should be automatically identified, false otherwise.

Definition at line 2201 of file system.h.

References libMesh::System::_identify_variable_groups.

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

2202 {
2204 }
bool _identify_variable_groups
Definition: system.h:1977

◆ identify_variable_groups() [2/2]

void libMesh::System::identify_variable_groups ( const bool  ivg)
inlineinherited

Toggle automatic VariableGroup identification.

Definition at line 2209 of file system.h.

References libMesh::System::_identify_variable_groups.

2210 {
2212 }
bool _identify_variable_groups
Definition: system.h:1977

◆ increment_constructor_count()

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

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

Definition at line 181 of file reference_counter.h.

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

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

182 {
183  Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
184  std::pair<unsigned int, unsigned int> & p = _counts[name];
185 
186  p.first++;
187 }
std::string name(const ElemQuality q)
Definition: elem_quality.C:42
spin_mutex spin_mtx
Definition: threads.C:29

◆ increment_destructor_count()

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

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

Definition at line 194 of file reference_counter.h.

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

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

195 {
196  Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
197  std::pair<unsigned int, unsigned int> & p = _counts[name];
198 
199  p.second++;
200 }
std::string name(const ElemQuality q)
Definition: elem_quality.C:42
spin_mutex spin_mtx
Definition: threads.C:29

◆ init()

void libMesh::System::init ( )
inherited

Initializes degrees of freedom on the current mesh. Sets the

Definition at line 237 of file system.C.

References libMesh::System::_basic_system_only, libMesh::System::init_data(), libMesh::System::is_initialized(), libMesh::System::n_vars(), and libMesh::System::user_initialization().

238 {
239  // Calling init() twice on the same system currently works evil
240  // magic, whether done directly or via EquationSystems::read()
241  libmesh_assert(!this->is_initialized());
242 
243  // First initialize any required data:
244  // either only the basic System data
245  if (_basic_system_only)
247  // or all the derived class' data too
248  else
249  this->init_data();
250 
251  // If no variables have been added to this system
252  // don't do anything
253  if (!this->n_vars())
254  return;
255 
256  // Then call the user-provided initialization function
257  this->user_initialization();
258 }
bool _basic_system_only
Definition: system.h:1965
virtual void init_data()
Definition: system.C:262
virtual void user_initialization()
Definition: system.C:1918
bool is_initialized()
Definition: system.h:2089
unsigned int n_vars() const
Definition: system.h:2105

◆ init_context()

void libMesh::FEMSystem::init_context ( DiffContext c)
overridevirtual

Reimplemented from libMesh::DifferentiablePhysics.

Definition at line 1342 of file fem_system.C.

References libMesh::DifferentiableSystem::deltat, libMesh::FEInterface::field_type(), libMesh::FEMContext::get_element_fe(), libMesh::FEAbstract::get_JxW(), libMesh::FEGenericBase< OutputType >::get_phi(), libMesh::DifferentiableSystem::get_physics(), libMesh::DifferentiablePhysics::is_time_evolving(), libMesh::System::n_vars(), libMesh::DiffContext::set_deltat_pointer(), libMesh::TYPE_SCALAR, libMesh::TYPE_VECTOR, and libMesh::System::variable_type().

Referenced by assembly(), mesh_position_get(), and mesh_position_set().

1343 {
1344  // Parent::init_context(c); // may be a good idea in derived classes
1345 
1346  // Although we do this in DiffSystem::build_context() and
1347  // FEMSystem::build_context() as well, we do it here just to be
1348  // extra sure that the deltat pointer gets set. Since the
1349  // intended behavior is for classes derived from FEMSystem to
1350  // call Parent::init_context() in their own init_context()
1351  // overloads, we can ensure that those classes get the correct
1352  // deltat pointers even if they have different build_context()
1353  // overloads.
1354  c.set_deltat_pointer ( &deltat );
1355 
1356  FEMContext & context = cast_ref<FEMContext &>(c);
1357 
1358  // Make sure we're prepared to do mass integration
1359  for (unsigned int var = 0; var != this->n_vars(); ++var)
1360  if (this->get_physics()->is_time_evolving(var))
1361  {
1362  // Request shape functions based on FEType
1363  switch( FEInterface::field_type( this->variable_type(var) ) )
1364  {
1365  case( TYPE_SCALAR ):
1366  {
1367  FEBase * elem_fe = nullptr;
1368  context.get_element_fe(var, elem_fe);
1369  elem_fe->get_JxW();
1370  elem_fe->get_phi();
1371  }
1372  break;
1373  case( TYPE_VECTOR ):
1374  {
1375  FEGenericBase<RealGradient> * elem_fe = nullptr;
1376  context.get_element_fe(var, elem_fe);
1377  elem_fe->get_JxW();
1378  elem_fe->get_phi();
1379  }
1380  break;
1381  default:
1382  libmesh_error_msg("Unrecognized field type!");
1383  }
1384  }
1385 }
static FEFieldType field_type(const FEType &fe_type)
const std::vector< Real > & get_JxW() const
Definition: fe_abstract.h:245
const DifferentiablePhysics * get_physics() const
Definition: diff_system.h:182
const FEType & variable_type(const unsigned int i) const
Definition: system.h:2183
void set_deltat_pointer(Real *dt)
Definition: diff_context.C:103
void get_element_fe(unsigned int var, FEGenericBase< OutputShape > *&fe) const
Definition: fem_context.h:262
bool is_time_evolving(unsigned int var) const
Definition: diff_physics.h:277
unsigned int n_vars() const
Definition: system.h:2105
const std::vector< std::vector< OutputShape > > & get_phi() const
Definition: fe_base.h:207

◆ init_data()

void libMesh::FEMSystem::init_data ( )
overrideprotectedvirtual

Initializes the member data fields associated with the system, so that, e.g., assemble() may be used.

Reimplemented from libMesh::DifferentiableSystem.

Reimplemented in libMesh::ContinuationSystem.

Definition at line 847 of file fem_system.C.

References libMesh::DifferentiableSystem::init_data().

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

848 {
849  // First initialize LinearImplicitSystem data
851 }
virtual void init_data() override
Definition: diff_system.C:108

◆ init_matrices()

void libMesh::ImplicitSystem::init_matrices ( )
protectedvirtualinherited

Initializes the matrices associated with this system.

Definition at line 106 of file implicit_system.C.

References libMesh::ImplicitSystem::_can_add_matrices, libMesh::ImplicitSystem::_matrices, libMesh::DofMap::attach_matrix(), libMesh::DofMap::compute_sparsity(), libMesh::System::get_dof_map(), libMesh::System::get_mesh(), libMesh::SparseMatrix< T >::initialized(), libMesh::DofMap::is_attached(), and libMesh::ImplicitSystem::matrix.

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

107 {
108  libmesh_assert(matrix);
109 
110  // Check for quick return in case the system matrix
111  // (and by extension all the matrices) has already
112  // been initialized
113  if (matrix->initialized())
114  return;
115 
116  // Get a reference to the DofMap
117  DofMap & dof_map = this->get_dof_map();
118 
119  // no chance to add other matrices
120  _can_add_matrices = false;
121 
122  // Tell the matrices about the dof map, and vice versa
123  for (auto & pr : _matrices)
124  {
125  SparseMatrix<Number> & m = *(pr.second);
126  libmesh_assert (!m.initialized());
127 
128  // We want to allow repeated init() on systems, but we don't
129  // want to attach the same matrix to the DofMap twice
130  if (!dof_map.is_attached(m))
131  dof_map.attach_matrix (m);
132  }
133 
134  // Compute the sparsity pattern for the current
135  // mesh and DOF distribution. This also updates
136  // additional matrices, \p DofMap now knows them
137  dof_map.compute_sparsity (this->get_mesh());
138 
139  // Initialize matrices
140  for (auto & pr : _matrices)
141  pr.second->init ();
142 
143  // Set the additional matrices to 0.
144  for (auto & pr : _matrices)
145  pr.second->zero ();
146 }
virtual bool initialized() const
std::map< std::string, SparseMatrix< Number > * > _matrices
const MeshBase & get_mesh() const
Definition: system.h:2033
SparseMatrix< Number > * matrix
const DofMap & get_dof_map() const
Definition: system.h:2049

◆ init_physics()

virtual void libMesh::DifferentiablePhysics::init_physics ( const System sys)
virtualinherited

Initialize any data structures associated with the physics.

Referenced by libMesh::DifferentiableSystem::attach_physics(), and libMesh::DifferentiableSystem::init_data().

◆ init_qoi()

virtual void libMesh::DifferentiableQoI::init_qoi ( std::vector< Number > &  )
inlinevirtualinherited

Initialize system qoi. By default, does nothing in order to maintain backward compatibility for FEMSystem applications that control qoi.

Definition at line 69 of file diff_qoi.h.

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

69 {}

◆ is_adjoint_already_solved()

◆ is_first_order_var()

bool libMesh::DifferentiablePhysics::is_first_order_var ( unsigned int  var) const
inlineinherited

Definition at line 520 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_first_order_vars.

521  { return _first_order_vars.find(var) != _first_order_vars.end(); }
std::set< unsigned int > _first_order_vars
Definition: diff_physics.h:559

◆ is_initialized()

bool libMesh::System::is_initialized ( )
inlineinherited
Returns
true iff this system has been initialized.

Definition at line 2089 of file system.h.

References libMesh::System::_is_initialized.

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

2090 {
2091  return _is_initialized;
2092 }
bool _is_initialized
Definition: system.h:1971

◆ is_second_order_var()

bool libMesh::DifferentiablePhysics::is_second_order_var ( unsigned int  var) const
inlineinherited

◆ is_time_evolving()

bool libMesh::DifferentiablePhysics::is_time_evolving ( unsigned int  var) const
inlineinherited
Returns
true iff variable var is evolving with respect to time. In general, the user's init() function should have set time_evolving() for any variables which behave like du/dt = F(u), and should not call time_evolving() for any variables which behave like 0 = G(u).

Definition at line 277 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_time_evolving.

Referenced by init_context().

278  {
279  libmesh_assert_less(var,_time_evolving.size());
280  libmesh_assert( _time_evolving[var] == 0 ||
281  _time_evolving[var] == 1 ||
282  _time_evolving[var] == 2 );
283  return _time_evolving[var];
284  }
std::vector< unsigned int > _time_evolving
Definition: diff_physics.h:554

◆ local_dof_indices()

void libMesh::System::local_dof_indices ( const unsigned int  var,
std::set< dof_id_type > &  var_indices 
) const
inherited

Fills the std::set with the degrees of freedom on the local processor corresponding the the variable number passed in.

Definition at line 1277 of file system.C.

References libMesh::DofMap::dof_indices(), libMesh::DofMap::end_dof(), libMesh::DofMap::first_dof(), libMesh::System::get_dof_map(), and libMesh::System::get_mesh().

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

1279 {
1280  // Make sure the set is clear
1281  var_indices.clear();
1282 
1283  std::vector<dof_id_type> dof_indices;
1284 
1285  const dof_id_type
1286  first_local = this->get_dof_map().first_dof(),
1287  end_local = this->get_dof_map().end_dof();
1288 
1289  // Begin the loop over the elements
1290  for (const auto & elem : this->get_mesh().active_local_element_ptr_range())
1291  {
1292  this->get_dof_map().dof_indices (elem, dof_indices, var);
1293 
1294  for (std::size_t i=0; i<dof_indices.size(); i++)
1295  {
1296  dof_id_type dof = dof_indices[i];
1297 
1298  //If the dof is owned by the local processor
1299  if (first_local <= dof && dof < end_local)
1300  var_indices.insert(dof_indices[i]);
1301  }
1302  }
1303 
1304  // we may have missed assigning DOFs to nodes that we own
1305  // but to which we have no connected elements matching our
1306  // variable restriction criterion. this will happen, for example,
1307  // if variable V is restricted to subdomain S. We may not own
1308  // any elements which live in S, but we may own nodes which are
1309  // *connected* to elements which do.
1310  for (const auto & node : this->get_mesh().local_node_ptr_range())
1311  {
1312  libmesh_assert(node);
1313  this->get_dof_map().dof_indices (node, dof_indices, var);
1314  for (auto dof : dof_indices)
1315  if (first_local <= dof && dof < end_local)
1316  var_indices.insert(dof);
1317  }
1318 }
void dof_indices(const Elem *const elem, std::vector< dof_id_type > &di) const
Definition: dof_map.C:1930
const MeshBase & get_mesh() const
Definition: system.h:2033
dof_id_type first_dof(const processor_id_type proc) const
Definition: dof_map.h:599
dof_id_type end_dof(const processor_id_type proc) const
Definition: dof_map.h:641
const DofMap & get_dof_map() const
Definition: system.h:2049
uint8_t dof_id_type
Definition: id_types.h:64

◆ mass_residual() [1/2]

virtual bool libMesh::FEMPhysics::mass_residual ( bool  request_jacobian,
DiffContext  
)
overridevirtualinherited

Subtracts a mass vector contribution on elem from 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.

Many problems can use the reimplementation in FEMPhysics::mass_residual which subtracts (du/dt,v) for each transient variable u; users with more complicated transient problems will need to reimplement this themselves.

Reimplemented from libMesh::DifferentiablePhysics.

◆ mass_residual() [2/2]

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

Subtracts a mass vector contribution on elem from elem_residual. For first-order-in-time problems, this is the $ M(u,\dot{u})\dot{u} $ term. For second-order-in-time problems, this is the $ M(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.

Many first-order-in-time problems can use the reimplementation in FEMPhysics::mass_residual which subtracts (du/dt,v) for each transient variable u; users with more complicated transient problems or second-order-in-time problems will need to reimplement this themselves.

Reimplemented in libMesh::FEMPhysics.

Definition at line 318 of file diff_physics.h.

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

319  {
320  return request_jacobian;
321  }

◆ mesh_position_get()

void libMesh::FEMSystem::mesh_position_get ( )

Tells the FEMSystem to set the degree of freedom coefficients which should correspond to mesh nodal coordinates.

Definition at line 1389 of file fem_system.C.

References libMesh::DifferentiablePhysics::_mesh_sys, libMesh::DifferentiablePhysics::_mesh_x_var, libMesh::DifferentiablePhysics::_mesh_y_var, libMesh::DifferentiablePhysics::_mesh_z_var, libMesh::MeshBase::active_local_element_ptr_range(), build_context(), libMesh::FEMContext::elem_position_get(), libMesh::DiffContext::get_dof_indices(), libMesh::DiffContext::get_elem_solution(), libMesh::System::get_mesh(), init_context(), libMesh::invalid_uint, mesh, libMesh::FEMContext::pre_fe_reinit(), libMesh::System::solution, and libMesh::System::update().

1390 {
1391  // This function makes no sense unless we've already picked out some
1392  // variable(s) to reflect mesh position coordinates
1393  if (!_mesh_sys)
1394  libmesh_error_msg("_mesh_sys was nullptr!");
1395 
1396  // We currently assume mesh variables are in our own system
1397  if (_mesh_sys != this)
1398  libmesh_not_implemented();
1399 
1400  // Loop over every active mesh element on this processor
1401  const MeshBase & mesh = this->get_mesh();
1402 
1403  std::unique_ptr<DiffContext> con = this->build_context();
1404  FEMContext & _femcontext = cast_ref<FEMContext &>(*con);
1405  this->init_context(_femcontext);
1406 
1407  // Get the solution's mesh variables from every element
1408  for (const auto & elem : mesh.active_local_element_ptr_range())
1409  {
1410  _femcontext.pre_fe_reinit(*this, elem);
1411 
1412  _femcontext.elem_position_get();
1413 
1415  this->solution->insert(_femcontext.get_elem_solution(_mesh_x_var),
1416  _femcontext.get_dof_indices(_mesh_x_var) );
1418  this->solution->insert(_femcontext.get_elem_solution(_mesh_y_var),
1419  _femcontext.get_dof_indices(_mesh_y_var));
1421  this->solution->insert(_femcontext.get_elem_solution(_mesh_z_var),
1422  _femcontext.get_dof_indices(_mesh_z_var));
1423  }
1424 
1425  this->solution->close();
1426 
1427  // And make sure the current_local_solution is up to date too
1428  this->System::update();
1429 }
virtual void pre_fe_reinit(const System &, const Elem *e)
Definition: fem_context.C:1552
const unsigned int invalid_uint
Definition: libmesh.h:245
MeshBase & mesh
const MeshBase & get_mesh() const
Definition: system.h:2033
Base class for Mesh.
Definition: mesh_base.h:77
virtual SimpleRange< element_iterator > active_local_element_ptr_range()=0
const DenseVector< Number > & get_elem_solution() const
Definition: diff_context.h:111
std::unique_ptr< NumericVector< Number > > solution
Definition: system.h:1523
const std::vector< dof_id_type > & get_dof_indices() const
Definition: diff_context.h:367
virtual void update()
Definition: system.C:408
virtual void init_context(DiffContext &) override
Definition: fem_system.C:1342
virtual std::unique_ptr< DiffContext > build_context() override
Definition: fem_system.C:1318

◆ mesh_position_set()

void libMesh::FEMSystem::mesh_position_set ( )

Tells the FEMSystem to set the mesh nodal coordinates which should correspond to degree of freedom coefficients.

Definition at line 1061 of file fem_system.C.

References libMesh::DifferentiablePhysics::_mesh_sys, libMesh::MeshBase::active_local_element_ptr_range(), build_context(), libMesh::ParallelObject::comm(), libMesh::FEMContext::elem_fe_reinit(), libMesh::FEMContext::elem_position_set(), libMesh::FEMContext::get_elem(), libMesh::System::get_mesh(), libMesh::Elem::has_children(), init_context(), mesh, libMesh::MeshBase::nodes_begin(), libMesh::MeshBase::nodes_end(), libMesh::FEMContext::pre_fe_reinit(), and libMesh::Parallel::sync_dofobject_data_by_id().

Referenced by solve().

1062 {
1063  // If we don't need to move the mesh, we're done
1064  if (_mesh_sys != this)
1065  return;
1066 
1067  MeshBase & mesh = this->get_mesh();
1068 
1069  std::unique_ptr<DiffContext> con = this->build_context();
1070  FEMContext & _femcontext = cast_ref<FEMContext &>(*con);
1071  this->init_context(_femcontext);
1072 
1073  // Move every mesh element we can
1074  for (const auto & elem : mesh.active_local_element_ptr_range())
1075  {
1076  // We need the algebraic data
1077  _femcontext.pre_fe_reinit(*this, elem);
1078  // And when asserts are on, we also need the FE so
1079  // we can assert that the mesh data is of the right type.
1080 #ifndef NDEBUG
1081  _femcontext.elem_fe_reinit();
1082 #endif
1083 
1084  // This code won't handle moving subactive elements
1085  libmesh_assert(!_femcontext.get_elem().has_children());
1086 
1087  _femcontext.elem_position_set(1.);
1088  }
1089 
1090  // We've now got positions set on all local nodes (and some
1091  // semilocal nodes); let's request positions for non-local nodes
1092  // from their processors.
1093 
1094  SyncNodalPositions sync_object(mesh);
1096  (this->comm(), mesh.nodes_begin(), mesh.nodes_end(), sync_object);
1097 }
void elem_position_set(Real theta)
Definition: fem_context.h:1197
virtual void pre_fe_reinit(const System &, const Elem *e)
Definition: fem_context.C:1552
const Elem & get_elem() const
Definition: fem_context.h:871
MeshBase & mesh
const Parallel::Communicator & comm() const
const MeshBase & get_mesh() const
Definition: system.h:2033
Base class for Mesh.
Definition: mesh_base.h:77
virtual void elem_fe_reinit(const std::vector< Point > *const pts=nullptr)
Definition: fem_context.C:1362
virtual node_iterator nodes_begin()=0
virtual SimpleRange< element_iterator > active_local_element_ptr_range()=0
void sync_dofobject_data_by_id(const Communicator &comm, const Iterator &range_begin, const Iterator &range_end, SyncFunctor &sync)
virtual node_iterator nodes_end()=0
virtual void init_context(DiffContext &) override
Definition: fem_system.C:1342
virtual std::unique_ptr< DiffContext > build_context() override
Definition: fem_system.C:1318
bool has_children() const
Definition: elem.h:2428

◆ n_active_dofs()

dof_id_type libMesh::System::n_active_dofs ( ) const
inlineinherited
Returns
The number of active degrees of freedom for this System.

Definition at line 2217 of file system.h.

References libMesh::System::n_constrained_dofs(), and libMesh::System::n_dofs().

2218 {
2219  return this->n_dofs() - this->n_constrained_dofs();
2220 }
dof_id_type n_dofs() const
Definition: system.C:150
dof_id_type n_constrained_dofs() const
Definition: system.C:157

◆ n_components()

unsigned int libMesh::System::n_components ( ) const
inlineinherited
Returns
The total number of scalar components in the system's variables. This will equal n_vars() in the case of all scalar-valued variables.

Definition at line 2121 of file system.h.

References libMesh::System::_variables, libMesh::Variable::first_scalar_number(), and libMesh::Variable::n_components().

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

2122 {
2123  if (_variables.empty())
2124  return 0;
2125 
2126  const Variable & last = _variables.back();
2127  return last.first_scalar_number() + last.n_components();
2128 }
std::vector< Variable > _variables
Definition: system.h:1911

◆ n_constrained_dofs()

dof_id_type libMesh::System::n_constrained_dofs ( ) const
inherited
Returns
The total number of constrained degrees of freedom in the system.

Definition at line 157 of file system.C.

References libMesh::System::_dof_map.

Referenced by libMesh::System::get_info(), and libMesh::System::n_active_dofs().

158 {
159 #ifdef LIBMESH_ENABLE_CONSTRAINTS
160 
161  return _dof_map->n_constrained_dofs();
162 
163 #else
164 
165  return 0;
166 
167 #endif
168 }
std::unique_ptr< DofMap > _dof_map
Definition: system.h:1884

◆ n_dofs()

◆ n_local_constrained_dofs()

dof_id_type libMesh::System::n_local_constrained_dofs ( ) const
inherited
Returns
The number of constrained degrees of freedom on this processor.

Definition at line 172 of file system.C.

References libMesh::System::_dof_map.

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

173 {
174 #ifdef LIBMESH_ENABLE_CONSTRAINTS
175 
176  return _dof_map->n_local_constrained_dofs();
177 
178 #else
179 
180  return 0;
181 
182 #endif
183 }
std::unique_ptr< DofMap > _dof_map
Definition: system.h:1884

◆ n_local_dofs()

◆ n_matrices()

unsigned int libMesh::ImplicitSystem::n_matrices ( ) const
inlineoverridevirtualinherited
Returns
The number of matrices handled by this system

Reimplemented from libMesh::System.

Definition at line 426 of file implicit_system.h.

References libMesh::ImplicitSystem::_matrices.

427 {
428  return cast_int<unsigned int>(_matrices.size());
429 }
std::map< std::string, SparseMatrix< Number > * > _matrices

◆ n_objects()

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

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

Definition at line 83 of file reference_counter.h.

References libMesh::ReferenceCounter::_n_objects.

84  { return _n_objects; }
static Threads::atomic< unsigned int > _n_objects

◆ n_processors()

processor_id_type libMesh::ParallelObject::n_processors ( ) const
inlineinherited
Returns
The number of processors in the group.

Definition at line 95 of file parallel_object.h.

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

Referenced by libMesh::BoundaryInfo::_find_id_maps(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::DistributedMesh::add_elem(), libMesh::DistributedMesh::add_node(), libMesh::LaplaceMeshSmoother::allgather_graph(), assembly(), libMesh::AztecLinearSolver< T >::AztecLinearSolver(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::DistributedMesh::clear(), libMesh::Nemesis_IO_Helper::compute_border_node_ids(), libMesh::Nemesis_IO_Helper::construct_nemesis_filename(), libMesh::UnstructuredMesh::create_pid_mesh(), libMesh::MeshTools::create_processor_bounding_box(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_local_dofs_node_major(), libMesh::DofMap::distribute_local_dofs_var_major(), libMesh::EnsightIO::EnsightIO(), libMesh::MeshBase::get_info(), libMesh::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_and_attach_petscdm(), libMesh::Nemesis_IO_Helper::initialize(), libMesh::DistributedMesh::insert_elem(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_new_node_procids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_topology_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_valid_boundary_ids(), libMesh::MeshTools::libmesh_assert_valid_dof_ids(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::MeshTools::libmesh_assert_valid_refinement_flags(), libMesh::DofMap::local_variable_indices(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshBase::n_active_elem_on_proc(), libMesh::MeshBase::n_elem_on_proc(), libMesh::MeshBase::n_nodes_on_proc(), libMesh::MeshBase::partition(), libMesh::PetscLinearSolver< T >::PetscLinearSolver(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::NameBasedIO::read(), libMesh::Nemesis_IO::read(), libMesh::CheckpointIO::read(), libMesh::CheckpointIO::read_connectivity(), libMesh::XdrIO::read_header(), libMesh::CheckpointIO::read_nodes(), libMesh::System::read_parallel_data(), libMesh::System::read_SCALAR_dofs(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::System::read_serialized_vector(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::DistributedMesh::update_parallel_id_counts(), libMesh::GMVIO::write_binary(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::System::write_parallel_data(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), and libMesh::XdrIO::write_serialized_nodesets().

96  { return cast_int<processor_id_type>(_communicator.size()); }
processor_id_type size() const
Definition: communicator.h:175
const Parallel::Communicator & _communicator

◆ n_qois()

◆ n_variable_groups()

unsigned int libMesh::System::n_variable_groups ( ) const
inlineinherited
Returns
The number of VariableGroup variable groups in the system

Definition at line 2113 of file system.h.

References libMesh::System::_variable_groups.

Referenced by libMesh::System::add_variable(), assembly(), libMesh::System::get_info(), and libMesh::System::init_data().

2114 {
2115  return cast_int<unsigned int>(_variable_groups.size());
2116 }
std::vector< VariableGroup > _variable_groups
Definition: system.h:1916

◆ n_vars()

unsigned int libMesh::System::n_vars ( ) const
inlineinherited
Returns
The number of variables in the system

Definition at line 2105 of file system.h.

References libMesh::System::_variables.

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::PetscDMWrapper::add_dofs_helper(), libMesh::DiffContext::add_localized_vector(), libMesh::System::add_variable(), libMesh::System::add_variables(), libMesh::EquationSystems::build_discontinuous_solution_vector(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::PetscDMWrapper::build_section(), libMesh::System::calculate_norm(), libMesh::DGFEMContext::DGFEMContext(), libMesh::DiffContext::DiffContext(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::AdjointResidualErrorEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::ErrorEstimator::estimate_errors(), libMesh::ExactSolution::ExactSolution(), libMesh::System::get_all_variable_numbers(), libMesh::System::init(), init_context(), libMesh::FEMContext::init_internal_data(), libMesh::DGFEMContext::neighbor_side_fe_reinit(), libMesh::WeightedPatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::PatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::petsc_auto_fieldsplit(), libMesh::FEMContext::pre_fe_reinit(), libMesh::System::re_update(), libMesh::System::read_legacy_data(), libMesh::System::read_parallel_data(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::System::read_serialized_vector(), libMesh::System::read_serialized_vectors(), libMesh::HPCoarsenTest::select_refinement(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::SystemSubsetBySubdomain::set_var_nums(), libMesh::System::write_header(), libMesh::System::write_parallel_data(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::System::write_serialized_vector(), libMesh::System::write_serialized_vectors(), and libMesh::System::zero_variable().

2106 {
2107  return cast_int<unsigned int>(_variables.size());
2108 }
std::vector< Variable > _variables
Definition: system.h:1911

◆ n_vectors()

unsigned int libMesh::System::n_vectors ( ) const
inlineinherited
Returns
The number of vectors (in addition to the solution) handled by this system This is the size of the _vectors map

Definition at line 2233 of file system.h.

References libMesh::System::_vectors.

Referenced by libMesh::ExplicitSystem::add_system_rhs(), libMesh::System::compare(), libMesh::System::get_info(), and libMesh::System::write_header().

2234 {
2235  return cast_int<unsigned int>(_vectors.size());
2236 }
std::map< std::string, NumericVector< Number > *> _vectors
Definition: system.h:1935

◆ name()

◆ nonlocal_constraint()

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

Adds any nonlocal constraint contributions (e.g. some components of constraints in scalar variable equations) to elem_residual

If this method receives request_jacobian = true, then it should also modify elem_jacobian and return true if possible. If the Jacobian changes have not been computed then the method should return false.

Users may need to reimplement this for PDEs on systems to which SCALAR variables with non-transient equations have been added.

Definition at line 227 of file diff_physics.h.

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

228  {
229  return request_jacobian;
230  }

◆ nonlocal_damping_residual()

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

Subtracts any nonlocal damping vector contributions (e.g. any first time derivative coefficients in scalar variable equations) from elem_residual

If this method receives request_jacobian = true, then it should also modify elem_jacobian and return true if possible. If the Jacobian changes have not been computed then the method should return false.

Definition at line 406 of file diff_physics.h.

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

407  {
408  return request_jacobian;
409  }

◆ nonlocal_mass_residual()

virtual bool libMesh::DifferentiablePhysics::nonlocal_mass_residual ( bool  request_jacobian,
DiffContext c 
)
virtualinherited

Subtracts any nonlocal mass vector contributions (e.g. any time derivative coefficients in scalar variable equations) from elem_residual

If this method receives request_jacobian = true, then it should also modify elem_jacobian and return true if possible. If the Jacobian changes have not been computed then the method should return false.

Many problems can use the reimplementation in FEMPhysics::mass_residual which subtracts (du/dt,v) for each transient scalar variable u; users with more complicated transient scalar variable equations will need to reimplement this themselves.

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

◆ nonlocal_time_derivative()

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

Adds any nonlocal time derivative contributions (e.g. some components of time derivatives in scalar variable equations) to elem_residual

If this method receives request_jacobian = true, then it should also modify elem_jacobian and return true if possible. If the Jacobian changes have not been computed then the method should return false.

Users may need to reimplement this for PDEs on systems to which SCALAR variables have been added.

Definition at line 209 of file diff_physics.h.

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

210  {
211  return request_jacobian;
212  }

◆ number()

◆ numerical_elem_jacobian()

void libMesh::FEMSystem::numerical_elem_jacobian ( FEMContext context) const

Uses the results of multiple element_residual() calls to numerically differentiate the corresponding jacobian on an element.

Definition at line 1294 of file fem_system.C.

References libMesh::TimeSolver::element_residual(), and numerical_jacobian().

1295 {
1296  LOG_SCOPE("numerical_elem_jacobian()", "FEMSystem");
1298 }
void numerical_jacobian(TimeSolverResPtr res, FEMContext &context) const
Definition: fem_system.C:1182
virtual bool element_residual(bool request_jacobian, DiffContext &)=0

◆ numerical_jacobian()

void libMesh::FEMSystem::numerical_jacobian ( TimeSolverResPtr  res,
FEMContext context 
) const

Uses the results of multiple res calls to numerically differentiate the corresponding jacobian.

Definition at line 1182 of file fem_system.C.

References libMesh::DifferentiablePhysics::_mesh_sys, libMesh::DifferentiablePhysics::_mesh_x_var, libMesh::DifferentiablePhysics::_mesh_y_var, libMesh::DifferentiablePhysics::_mesh_z_var, libMesh::DiffContext::get_dof_indices(), libMesh::FEMContext::get_elem(), libMesh::DiffContext::get_elem_jacobian(), libMesh::DiffContext::get_elem_residual(), libMesh::DiffContext::get_elem_solution(), libMesh::Elem::hmin(), libMesh::invalid_uint, libMesh::libmesh_real(), libMesh::System::n_dofs(), libMesh::DiffContext::n_vars(), numerical_jacobian_h, numerical_jacobian_h_for_var(), libMesh::Elem::point(), libMesh::Real, and libMesh::DenseVector< T >::zero().

Referenced by numerical_elem_jacobian(), numerical_nonlocal_jacobian(), and numerical_side_jacobian().

1184 {
1185  // Logging is done by numerical_elem_jacobian
1186  // or numerical_side_jacobian
1187 
1188  DenseVector<Number> original_residual(context.get_elem_residual());
1189  DenseVector<Number> backwards_residual(context.get_elem_residual());
1190  DenseMatrix<Number> numeric_jacobian(context.get_elem_jacobian());
1191 #ifdef DEBUG
1192  DenseMatrix<Number> old_jacobian(context.get_elem_jacobian());
1193 #endif
1194 
1195  Real numerical_point_h = 0.;
1196  if (_mesh_sys == this)
1197  numerical_point_h = numerical_jacobian_h * context.get_elem().hmin();
1198 
1199  const unsigned int n_dofs =
1200  cast_int<unsigned int>(context.get_dof_indices().size());
1201 
1202  for (unsigned int v = 0; v != context.n_vars(); ++v)
1203  {
1204  const Real my_h = this->numerical_jacobian_h_for_var(v);
1205 
1206  unsigned int j_offset = libMesh::invalid_uint;
1207 
1208  if (!context.get_dof_indices(v).empty())
1209  {
1210  for (auto i : IntRange<unsigned int>(0, n_dofs))
1211  if (context.get_dof_indices()[i] ==
1212  context.get_dof_indices(v)[0])
1213  j_offset = i;
1214 
1215  libmesh_assert_not_equal_to(j_offset, libMesh::invalid_uint);
1216  }
1217 
1218  for (auto j : IntRange<unsigned int>(0, context.get_dof_indices(v).size()))
1219  {
1220  const unsigned int total_j = j + j_offset;
1221 
1222  // Take the "minus" side of a central differenced first derivative
1223  Number original_solution = context.get_elem_solution(v)(j);
1224  context.get_elem_solution(v)(j) -= my_h;
1225 
1226  // Make sure to catch any moving mesh terms
1227  Real * coord = nullptr;
1228  if (_mesh_sys == this)
1229  {
1230  if (_mesh_x_var == v)
1231  coord = &(context.get_elem().point(j)(0));
1232  else if (_mesh_y_var == v)
1233  coord = &(context.get_elem().point(j)(1));
1234  else if (_mesh_z_var == v)
1235  coord = &(context.get_elem().point(j)(2));
1236  }
1237  if (coord)
1238  {
1239  // We have enough information to scale the perturbations
1240  // here appropriately
1241  context.get_elem_solution(v)(j) = original_solution - numerical_point_h;
1242  *coord = libmesh_real(context.get_elem_solution(v)(j));
1243  }
1244 
1245  context.get_elem_residual().zero();
1246  ((*time_solver).*(res))(false, context);
1247 #ifdef DEBUG
1248  libmesh_assert_equal_to (old_jacobian, context.get_elem_jacobian());
1249 #endif
1250  backwards_residual = context.get_elem_residual();
1251 
1252  // Take the "plus" side of a central differenced first derivative
1253  context.get_elem_solution(v)(j) = original_solution + my_h;
1254  if (coord)
1255  {
1256  context.get_elem_solution()(j) = original_solution + numerical_point_h;
1257  *coord = libmesh_real(context.get_elem_solution(v)(j));
1258  }
1259  context.get_elem_residual().zero();
1260  ((*time_solver).*(res))(false, context);
1261 #ifdef DEBUG
1262  libmesh_assert_equal_to (old_jacobian, context.get_elem_jacobian());
1263 #endif
1264 
1265  context.get_elem_solution(v)(j) = original_solution;
1266  if (coord)
1267  {
1268  *coord = libmesh_real(context.get_elem_solution(v)(j));
1269  for (auto i : IntRange<unsigned int>(0, n_dofs))
1270  {
1271  numeric_jacobian(i,total_j) =
1272  (context.get_elem_residual()(i) - backwards_residual(i)) /
1273  2. / numerical_point_h;
1274  }
1275  }
1276  else
1277  {
1278  for (auto i : IntRange<unsigned int>(0, n_dofs))
1279  {
1280  numeric_jacobian(i,total_j) =
1281  (context.get_elem_residual()(i) - backwards_residual(i)) /
1282  2. / my_h;
1283  }
1284  }
1285  }
1286  }
1287 
1288  context.get_elem_residual() = original_residual;
1289  context.get_elem_jacobian() = numeric_jacobian;
1290 }
T libmesh_real(T a)
const DenseMatrix< Number > & get_elem_jacobian() const
Definition: diff_context.h:283
const unsigned int invalid_uint
Definition: libmesh.h:245
const Elem & get_elem() const
Definition: fem_context.h:871
dof_id_type n_dofs() const
Definition: system.C:150
const DenseVector< Number > & get_elem_solution() const
Definition: diff_context.h:111
virtual Real hmin() const
Definition: elem.C:356
const std::vector< dof_id_type > & get_dof_indices() const
Definition: diff_context.h:367
const DenseVector< Number > & get_elem_residual() const
Definition: diff_context.h:249
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
unsigned int n_vars() const
Definition: diff_context.h:99
const Point & point(const unsigned int i) const
Definition: elem.h:1892
Real numerical_jacobian_h_for_var(unsigned int var_num) const
Definition: fem_system.h:259
virtual void zero() override
Definition: dense_vector.h:379

◆ numerical_jacobian_h_for_var()

Real libMesh::FEMSystem::numerical_jacobian_h_for_var ( unsigned int  var_num) const
inline

If numerical_jacobian_h_for_var(var_num) is changed from its default value (numerical_jacobian_h), the FEMSystem will perturb solution vector entries for variable var_num by that amount when calculating finite differences with respect to that variable.

This is useful in multiphysics problems which have not been normalized.

Definition at line 259 of file fem_system.h.

References _numerical_jacobian_h_for_var, numerical_jacobian_h, and libMesh::Real.

Referenced by numerical_jacobian().

260 {
261  if ((var_num >= _numerical_jacobian_h_for_var.size()) ||
262  _numerical_jacobian_h_for_var[var_num] == Real(0))
263  return numerical_jacobian_h;
264 
265  return _numerical_jacobian_h_for_var[var_num];
266 }
std::vector< Real > _numerical_jacobian_h_for_var
Definition: fem_system.h:252
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real

◆ numerical_nonlocal_jacobian()

void libMesh::FEMSystem::numerical_nonlocal_jacobian ( FEMContext context) const

Uses the results of multiple side_residual() calls to numerically differentiate the corresponding jacobian on nonlocal DoFs.

Definition at line 1310 of file fem_system.C.

References libMesh::TimeSolver::nonlocal_residual(), and numerical_jacobian().

Referenced by assembly().

1311 {
1312  LOG_SCOPE("numerical_nonlocal_jacobian()", "FEMSystem");
1314 }
void numerical_jacobian(TimeSolverResPtr res, FEMContext &context) const
Definition: fem_system.C:1182
virtual bool nonlocal_residual(bool request_jacobian, DiffContext &)=0

◆ numerical_side_jacobian()

void libMesh::FEMSystem::numerical_side_jacobian ( FEMContext context) const

Uses the results of multiple side_residual() calls to numerically differentiate the corresponding jacobian on an element's side.

Definition at line 1302 of file fem_system.C.

References numerical_jacobian(), and libMesh::TimeSolver::side_residual().

1303 {
1304  LOG_SCOPE("numerical_side_jacobian()", "FEMSystem");
1306 }
virtual bool side_residual(bool request_jacobian, DiffContext &)=0
void numerical_jacobian(TimeSolverResPtr res, FEMContext &context) const
Definition: fem_system.C:1182

◆ parallel_op()

virtual void libMesh::DifferentiableQoI::parallel_op ( const Parallel::Communicator communicator,
std::vector< Number > &  sys_qoi,
std::vector< Number > &  local_qoi,
const QoISet qoi_indices 
)
virtualinherited

Method to populate system qoi data structure with process-local qoi. By default, simply sums process qois into system qoi.

Referenced by assemble_qoi().

◆ point_gradient() [1/3]

Gradient libMesh::System::point_gradient ( unsigned int  var,
const Point p,
const bool  insist_on_success = true 
) const
inherited
Returns
The gradient of the solution variable var at the physical point p in the mesh, similarly to point_value.

Definition at line 2100 of file system.C.

References libMesh::Parallel::Communicator::broadcast(), libMesh::ParallelObject::comm(), libMesh::PointLocatorBase::enable_out_of_mesh_mode(), libMesh::System::get_dof_map(), libMesh::System::get_mesh(), mesh, libMesh::Parallel::Communicator::min(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::processor_id(), and libMesh::DofObject::processor_id().

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

2101 {
2102  // This function must be called on every processor; there's no
2103  // telling where in the partition p falls.
2104  parallel_object_only();
2105 
2106  // And every processor had better agree about which point we're
2107  // looking for
2108 #ifndef NDEBUG
2109  libmesh_assert(this->comm().verify(p(0)));
2110 #if LIBMESH_DIM > 1
2111  libmesh_assert(this->comm().verify(p(1)));
2112 #endif
2113 #if LIBMESH_DIM > 2
2114  libmesh_assert(this->comm().verify(p(2)));
2115 #endif
2116 #endif // NDEBUG
2117 
2118  // Get a reference to the mesh object associated with the system object that calls this function
2119  const MeshBase & mesh = this->get_mesh();
2120 
2121  // Use an existing PointLocator or create a new one
2122  std::unique_ptr<PointLocatorBase> locator_ptr = mesh.sub_point_locator();
2123  PointLocatorBase & locator = *locator_ptr;
2124 
2125  if (!insist_on_success || !mesh.is_serial())
2126  locator.enable_out_of_mesh_mode();
2127 
2128  // Get a pointer to the element that contains P
2129  const Elem * e = locator(p);
2130 
2131  Gradient grad_u;
2132 
2133  if (e && this->get_dof_map().is_evaluable(*e, var))
2134  grad_u = point_gradient(var, p, *e);
2135 
2136  // If I have an element containing p, then let's let everyone know
2137  processor_id_type lowest_owner =
2138  (e && (e->processor_id() == this->processor_id())) ?
2139  this->processor_id() : this->n_processors();
2140  this->comm().min(lowest_owner);
2141 
2142  // Everybody should get their value from a processor that was able
2143  // to compute it.
2144  // If nobody admits owning the point, we may have a problem.
2145  if (lowest_owner != this->n_processors())
2146  this->comm().broadcast(grad_u, lowest_owner);
2147  else
2148  libmesh_assert(!insist_on_success);
2149 
2150  return grad_u;
2151 }
Gradient point_gradient(unsigned int var, const Point &p, const bool insist_on_success=true) const
Definition: system.C:2100
MeshBase & mesh
uint8_t processor_id_type
Definition: id_types.h:99
const Parallel::Communicator & comm() const
const MeshBase & get_mesh() const
Definition: system.h:2033
processor_id_type n_processors() const
NumberVectorValue Gradient
processor_id_type processor_id() const
const DofMap & get_dof_map() const
Definition: system.h:2049
void broadcast(T &data, const unsigned int root_id=0) const

◆ point_gradient() [2/3]

Gradient libMesh::System::point_gradient ( unsigned int  var,
const Point p,
const Elem e 
) const
inherited
Returns
The gradient of the solution variable var at the physical point p in local Elem e in the mesh, similarly to point_value.

Definition at line 2154 of file system.C.

References libMesh::TypeVector< T >::add_scaled(), libMesh::FEGenericBase< OutputType >::build(), libMesh::Elem::contains_point(), libMesh::System::current_solution(), libMesh::Elem::dim(), libMesh::DofMap::dof_indices(), libMesh::System::get_dof_map(), libMesh::Elem::infinite(), libMesh::FEInterface::inverse_map(), libMesh::DofMap::is_evaluable(), and libMesh::DofMap::variable_type().

2155 {
2156  // Ensuring that the given point is really in the element is an
2157  // expensive assert, but as long as debugging is turned on we might
2158  // as well try to catch a particularly nasty potential error
2159  libmesh_assert (e.contains_point(p));
2160 
2161 #ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
2162  if (e.infinite())
2163  libmesh_not_implemented();
2164 #endif
2165 
2166  // Get the dof map to get the proper indices for our computation
2167  const DofMap & dof_map = this->get_dof_map();
2168 
2169  // Make sure we can evaluate on this element.
2170  libmesh_assert (dof_map.is_evaluable(e, var));
2171 
2172  // Need dof_indices for phi[i][j]
2173  std::vector<dof_id_type> dof_indices;
2174 
2175  // Fill in the dof_indices for our element
2176  dof_map.dof_indices (&e, dof_indices, var);
2177 
2178  // Get the no of dofs associated with this point
2179  const unsigned int num_dofs = cast_int<unsigned int>
2180  (dof_indices.size());
2181 
2182  FEType fe_type = dof_map.variable_type(var);
2183 
2184  // Build a FE again so we can calculate u(p)
2185  std::unique_ptr<FEBase> fe (FEBase::build(e.dim(), fe_type));
2186 
2187  // Map the physical co-ordinates to the master co-ordinates using the inverse_map from fe_interface.h
2188  // Build a vector of point co-ordinates to send to reinit
2189  std::vector<Point> coor(1, FEInterface::inverse_map(e.dim(), fe_type, &e, p));
2190 
2191  // Get the values of the shape function derivatives
2192  const std::vector<std::vector<RealGradient>> & dphi = fe->get_dphi();
2193 
2194  // Reinitialize the element and compute the shape function values at coor
2195  fe->reinit (&e, &coor);
2196 
2197  // Get ready to accumulate a gradient
2198  Gradient grad_u;
2199 
2200  for (unsigned int l=0; l<num_dofs; l++)
2201  {
2202  grad_u.add_scaled (dphi[l][0], this->current_solution (dof_indices[l]));
2203  }
2204 
2205  return grad_u;
2206 }
void add_scaled(const TypeVector< T2 > &, const T)
Definition: type_vector.h:627
Number current_solution(const dof_id_type global_dof_number) const
Definition: system.C:194
NumberVectorValue Gradient
static std::unique_ptr< FEGenericBase > build(const unsigned int dim, const FEType &type)
static Point inverse_map(const unsigned int dim, const FEType &fe_t, const Elem *elem, const Point &p, const Real tolerance=TOLERANCE, const bool secure=true)
Definition: fe_interface.C:590
const DofMap & get_dof_map() const
Definition: system.h:2049

◆ point_gradient() [3/3]

Gradient libMesh::System::point_gradient ( unsigned int  var,
const Point p,
const Elem e 
) const
inherited

Calls the version of point_gradient() which takes a reference. This function exists only to prevent people from calling the version of point_gradient() that has a boolean third argument, which would result in unnecessary PointLocator calls.

Definition at line 2210 of file system.C.

References libMesh::System::point_gradient().

2211 {
2212  libmesh_assert(e);
2213  return this->point_gradient(var, p, *e);
2214 }
Gradient point_gradient(unsigned int var, const Point &p, const bool insist_on_success=true) const
Definition: system.C:2100

◆ point_hessian() [1/3]

Tensor libMesh::System::point_hessian ( unsigned int  var,
const Point p,
const bool  insist_on_success = true 
) const
inherited
Returns
The second derivative tensor of the solution variable var at the physical point p in the mesh, similarly to point_value.

Definition at line 2220 of file system.C.

References libMesh::Parallel::Communicator::broadcast(), libMesh::ParallelObject::comm(), libMesh::PointLocatorBase::enable_out_of_mesh_mode(), libMesh::System::get_dof_map(), libMesh::System::get_mesh(), mesh, libMesh::Parallel::Communicator::min(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::processor_id(), and libMesh::DofObject::processor_id().

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

2221 {
2222  // This function must be called on every processor; there's no
2223  // telling where in the partition p falls.
2224  parallel_object_only();
2225 
2226  // And every processor had better agree about which point we're
2227  // looking for
2228 #ifndef NDEBUG
2229  libmesh_assert(this->comm().verify(p(0)));
2230 #if LIBMESH_DIM > 1
2231  libmesh_assert(this->comm().verify(p(1)));
2232 #endif
2233 #if LIBMESH_DIM > 2
2234  libmesh_assert(this->comm().verify(p(2)));
2235 #endif
2236 #endif // NDEBUG
2237 
2238  // Get a reference to the mesh object associated with the system object that calls this function
2239  const MeshBase & mesh = this->get_mesh();
2240 
2241  // Use an existing PointLocator or create a new one
2242  std::unique_ptr<PointLocatorBase> locator_ptr = mesh.sub_point_locator();
2243  PointLocatorBase & locator = *locator_ptr;
2244 
2245  if (!insist_on_success || !mesh.is_serial())
2246  locator.enable_out_of_mesh_mode();
2247 
2248  // Get a pointer to the element that contains P
2249  const Elem * e = locator(p);
2250 
2251  Tensor hess_u;
2252 
2253  if (e && this->get_dof_map().is_evaluable(*e, var))
2254  hess_u = point_hessian(var, p, *e);
2255 
2256  // If I have an element containing p, then let's let everyone know
2257  processor_id_type lowest_owner =
2258  (e && (e->processor_id() == this->processor_id())) ?
2259  this->processor_id() : this->n_processors();
2260  this->comm().min(lowest_owner);
2261 
2262  // Everybody should get their value from a processor that was able
2263  // to compute it.
2264  // If nobody admits owning the point, we may have a problem.
2265  if (lowest_owner != this->n_processors())
2266  this->comm().broadcast(hess_u, lowest_owner);
2267  else
2268  libmesh_assert(!insist_on_success);
2269 
2270  return hess_u;
2271 }
MeshBase & mesh
uint8_t processor_id_type
Definition: id_types.h:99
const Parallel::Communicator & comm() const
const MeshBase & get_mesh() const
Definition: system.h:2033
Tensor point_hessian(unsigned int var, const Point &p, const bool insist_on_success=true) const
Definition: system.C:2220
processor_id_type n_processors() const
NumberTensorValue Tensor
processor_id_type processor_id() const
const DofMap & get_dof_map() const
Definition: system.h:2049
void broadcast(T &data, const unsigned int root_id=0) const

◆ point_hessian() [2/3]

Tensor libMesh::System::point_hessian ( unsigned int  var,
const Point p,
const Elem e 
) const
inherited
Returns
The second derivative tensor of the solution variable var at the physical point p in local Elem e in the mesh, similarly to point_value.

Definition at line 2273 of file system.C.

References libMesh::TypeTensor< T >::add_scaled(), libMesh::FEGenericBase< OutputType >::build(), libMesh::Elem::contains_point(), libMesh::System::current_solution(), libMesh::Elem::dim(), libMesh::DofMap::dof_indices(), libMesh::System::get_dof_map(), libMesh::Elem::infinite(), libMesh::FEInterface::inverse_map(), libMesh::DofMap::is_evaluable(), and libMesh::DofMap::variable_type().

2274 {
2275  // Ensuring that the given point is really in the element is an
2276  // expensive assert, but as long as debugging is turned on we might
2277  // as well try to catch a particularly nasty potential error
2278  libmesh_assert (e.contains_point(p));
2279 
2280 #ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
2281  if (e.infinite())
2282  libmesh_not_implemented();
2283 #endif
2284 
2285  // Get the dof map to get the proper indices for our computation
2286  const DofMap & dof_map = this->get_dof_map();
2287 
2288  // Make sure we can evaluate on this element.
2289  libmesh_assert (dof_map.is_evaluable(e, var));
2290 
2291  // Need dof_indices for phi[i][j]
2292  std::vector<dof_id_type> dof_indices;
2293 
2294  // Fill in the dof_indices for our element
2295  dof_map.dof_indices (&e, dof_indices, var);
2296 
2297  // Get the no of dofs associated with this point
2298  const unsigned int num_dofs = cast_int<unsigned int>
2299  (dof_indices.size());
2300 
2301  FEType fe_type = dof_map.variable_type(var);
2302 
2303  // Build a FE again so we can calculate u(p)
2304  std::unique_ptr<FEBase> fe (FEBase::build(e.dim(), fe_type));
2305 
2306  // Map the physical co-ordinates to the master co-ordinates using the inverse_map from fe_interface.h
2307  // Build a vector of point co-ordinates to send to reinit
2308  std::vector<Point> coor(1, FEInterface::inverse_map(e.dim(), fe_type, &e, p));
2309 
2310  // Get the values of the shape function derivatives
2311  const std::vector<std::vector<RealTensor>> & d2phi = fe->get_d2phi();
2312 
2313  // Reinitialize the element and compute the shape function values at coor
2314  fe->reinit (&e, &coor);
2315 
2316  // Get ready to accumulate a hessian
2317  Tensor hess_u;
2318 
2319  for (unsigned int l=0; l<num_dofs; l++)
2320  {
2321  hess_u.add_scaled (d2phi[l][0], this->current_solution (dof_indices[l]));
2322  }
2323 
2324  return hess_u;
2325 }
void add_scaled(const TypeTensor< T2 > &, const T)
Definition: type_tensor.h:808
Number current_solution(const dof_id_type global_dof_number) const
Definition: system.C:194
static std::unique_ptr< FEGenericBase > build(const unsigned int dim, const FEType &type)
static Point inverse_map(const unsigned int dim, const FEType &fe_t, const Elem *elem, const Point &p, const Real tolerance=TOLERANCE, const bool secure=true)
Definition: fe_interface.C:590
NumberTensorValue Tensor
const DofMap & get_dof_map() const
Definition: system.h:2049

◆ point_hessian() [3/3]

Tensor libMesh::System::point_hessian ( unsigned int  var,
const Point p,
const Elem e 
) const
inherited

Calls the version of point_hessian() which takes a reference. This function exists only to prevent people from calling the version of point_hessian() that has a boolean third argument, which would result in unnecessary PointLocator calls.

Definition at line 2329 of file system.C.

References libMesh::System::point_hessian().

2330 {
2331  libmesh_assert(e);
2332  return this->point_hessian(var, p, *e);
2333 }
Tensor point_hessian(unsigned int var, const Point &p, const bool insist_on_success=true) const
Definition: system.C:2220

◆ point_value() [1/3]

Number libMesh::System::point_value ( unsigned int  var,
const Point p,
const bool  insist_on_success = true 
) const
inherited
Returns
The value of the solution variable var at the physical point p in the mesh, without knowing a priori which element contains p.
Note
This function uses MeshBase::sub_point_locator(); users may or may not want to call MeshBase::clear_point_locator() afterward. Also, point_locator() is expensive (N log N for initial construction, log N for evaluations). Avoid using this function in any context where you are already looping over elements.

Because the element containing p may lie on any processor, this function is parallel-only.

By default this method expects the point to reside inside the domain and will abort if no element can be found which contains p. The optional parameter insist_on_success can be set to false to allow the method to return 0 when the point is not located.

Definition at line 1993 of file system.C.

References libMesh::Parallel::Communicator::broadcast(), libMesh::ParallelObject::comm(), libMesh::PointLocatorBase::enable_out_of_mesh_mode(), libMesh::System::get_dof_map(), libMesh::System::get_mesh(), mesh, libMesh::Parallel::Communicator::min(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::processor_id(), and libMesh::DofObject::processor_id().

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

1994 {
1995  // This function must be called on every processor; there's no
1996  // telling where in the partition p falls.
1997  parallel_object_only();
1998 
1999  // And every processor had better agree about which point we're
2000  // looking for
2001 #ifndef NDEBUG
2002  libmesh_assert(this->comm().verify(p(0)));
2003 #if LIBMESH_DIM > 1
2004  libmesh_assert(this->comm().verify(p(1)));
2005 #endif
2006 #if LIBMESH_DIM > 2
2007  libmesh_assert(this->comm().verify(p(2)));
2008 #endif
2009 #endif // NDEBUG
2010 
2011  // Get a reference to the mesh object associated with the system object that calls this function
2012  const MeshBase & mesh = this->get_mesh();
2013 
2014  // Use an existing PointLocator or create a new one
2015  std::unique_ptr<PointLocatorBase> locator_ptr = mesh.sub_point_locator();
2016  PointLocatorBase & locator = *locator_ptr;
2017 
2018  if (!insist_on_success || !mesh.is_serial())
2019  locator.enable_out_of_mesh_mode();
2020 
2021  // Get a pointer to the element that contains P
2022  const Elem * e = locator(p);
2023 
2024  Number u = 0;
2025 
2026  if (e && this->get_dof_map().is_evaluable(*e, var))
2027  u = point_value(var, p, *e);
2028 
2029  // If I have an element containing p, then let's let everyone know
2030  processor_id_type lowest_owner =
2031  (e && (e->processor_id() == this->processor_id())) ?
2032  this->processor_id() : this->n_processors();
2033  this->comm().min(lowest_owner);
2034 
2035  // Everybody should get their value from a processor that was able
2036  // to compute it.
2037  // If nobody admits owning the point, we have a problem.
2038  if (lowest_owner != this->n_processors())
2039  this->comm().broadcast(u, lowest_owner);
2040  else
2041  libmesh_assert(!insist_on_success);
2042 
2043  return u;
2044 }
MeshBase & mesh
uint8_t processor_id_type
Definition: id_types.h:99
const Parallel::Communicator & comm() const
const MeshBase & get_mesh() const
Definition: system.h:2033
processor_id_type n_processors() const
Number point_value(unsigned int var, const Point &p, const bool insist_on_success=true) const
Definition: system.C:1993
processor_id_type processor_id() const
const DofMap & get_dof_map() const
Definition: system.h:2049
void broadcast(T &data, const unsigned int root_id=0) const

◆ point_value() [2/3]

Number libMesh::System::point_value ( unsigned int  var,
const Point p,
const Elem e 
) const
inherited
Returns
The value of the solution variable var at the physical point p contained in local Elem e

This version of point_value can be run in serial, but assumes e is in the local mesh partition or is algebraically ghosted.

Definition at line 2046 of file system.C.

References libMesh::FEInterface::compute_data(), libMesh::Elem::contains_point(), libMesh::System::current_solution(), libMesh::Elem::dim(), libMesh::System::get_dof_map(), libMesh::System::get_equation_systems(), and libMesh::FEInterface::inverse_map().

2047 {
2048  // Ensuring that the given point is really in the element is an
2049  // expensive assert, but as long as debugging is turned on we might
2050  // as well try to catch a particularly nasty potential error
2051  libmesh_assert (e.contains_point(p));
2052 
2053  // Get the dof map to get the proper indices for our computation
2054  const DofMap & dof_map = this->get_dof_map();
2055 
2056  // Make sure we can evaluate on this element.
2057  libmesh_assert (dof_map.is_evaluable(e, var));
2058 
2059  // Need dof_indices for phi[i][j]
2060  std::vector<dof_id_type> dof_indices;
2061 
2062  // Fill in the dof_indices for our element
2063  dof_map.dof_indices (&e, dof_indices, var);
2064 
2065  // Get the no of dofs associated with this point
2066  const unsigned int num_dofs = cast_int<unsigned int>
2067  (dof_indices.size());
2068 
2069  FEType fe_type = dof_map.variable_type(var);
2070 
2071  // Map the physical co-ordinates to the master co-ordinates using the inverse_map from fe_interface.h.
2072  Point coor = FEInterface::inverse_map(e.dim(), fe_type, &e, p);
2073 
2074  // get the shape function value via the FEInterface to also handle the case
2075  // of infinite elements correcly, the shape function is not fe->phi().
2076  FEComputeData fe_data(this->get_equation_systems(), coor);
2077  FEInterface::compute_data(e.dim(), fe_type, &e, fe_data);
2078 
2079  // Get ready to accumulate a value
2080  Number u = 0;
2081 
2082  for (unsigned int l=0; l<num_dofs; l++)
2083  {
2084  u += fe_data.shape[l]*this->current_solution (dof_indices[l]);
2085  }
2086 
2087  return u;
2088 }
const EquationSystems & get_equation_systems() const
Definition: system.h:712
Number current_solution(const dof_id_type global_dof_number) const
Definition: system.C:194
static void compute_data(const unsigned int dim, const FEType &fe_t, const Elem *elem, FEComputeData &data)
Definition: fe_interface.C:837
static Point inverse_map(const unsigned int dim, const FEType &fe_t, const Elem *elem, const Point &p, const Real tolerance=TOLERANCE, const bool secure=true)
Definition: fe_interface.C:590
const DofMap & get_dof_map() const
Definition: system.h:2049

◆ point_value() [3/3]

Number libMesh::System::point_value ( unsigned int  var,
const Point p,
const Elem e 
) const
inherited

Calls the version of point_value() which takes a reference. This function exists only to prevent people from calling the version of point_value() that has a boolean third argument, which would result in unnecessary PointLocator calls.

Definition at line 2092 of file system.C.

References libMesh::System::point_value().

2093 {
2094  libmesh_assert(e);
2095  return this->point_value(var, p, *e);
2096 }
Number point_value(unsigned int var, const Point &p, const bool insist_on_success=true) const
Definition: system.C:1993

◆ postprocess()

void libMesh::FEMSystem::postprocess ( )
overridevirtual

Runs a postprocessing loop over all elements, and if postprocess_sides is true over all sides.

Reimplemented from libMesh::DifferentiableSystem.

Definition at line 1101 of file fem_system.C.

References libMesh::MeshBase::active_local_elements_begin(), libMesh::MeshBase::active_local_elements_end(), libMesh::System::get_mesh(), libMesh::DifferentiableSystem::get_time_solver(), mesh, libMesh::Threads::parallel_for(), libMesh::StoredRange< iterator_type, object_type >::reset(), libMesh::TimeSolver::set_is_adjoint(), and libMesh::System::update().

1102 {
1103  LOG_SCOPE("postprocess()", "FEMSystem");
1104 
1105  const MeshBase & mesh = this->get_mesh();
1106 
1107  this->update();
1108 
1109  // Get the time solver object associated with the system, and tell it that
1110  // we are not solving the adjoint problem
1111  this->get_time_solver().set_is_adjoint(false);
1112 
1113  // Loop over every active mesh element on this processor
1116  PostprocessContributions(*this));
1117 }
void parallel_for(const Range &range, const Body &body)
Definition: threads_none.h:73
MeshBase & mesh
const MeshBase & get_mesh() const
Definition: system.h:2033
Base class for Mesh.
Definition: mesh_base.h:77
void set_is_adjoint(bool _is_adjoint_value)
Definition: time_solver.h:240
virtual element_iterator active_local_elements_begin()=0
virtual void update()
Definition: system.C:408
virtual element_iterator active_local_elements_end()=0
TimeSolver & get_time_solver()
Definition: diff_system.h:415

◆ print_info()

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

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

Definition at line 87 of file reference_counter.C.

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

88 {
90  out_stream << ReferenceCounter::get_info();
91 }
static std::string get_info()

◆ processor_id()

processor_id_type libMesh::ParallelObject::processor_id ( ) const
inlineinherited
Returns
The rank of this processor in the group.

Definition at line 101 of file parallel_object.h.

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

Referenced by libMesh::BoundaryInfo::_find_id_maps(), libMesh::EquationSystems::_read_impl(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::DistributedMesh::add_elem(), libMesh::BoundaryInfo::add_elements(), libMesh::DofMap::add_neighbors_to_send_list(), libMesh::DistributedMesh::add_node(), libMesh::UnstructuredMesh::all_second_order(), libMesh::MeshTools::Modification::all_tri(), assembly(), libMesh::EquationSystems::build_discontinuous_solution_vector(), libMesh::Nemesis_IO_Helper::build_element_and_node_maps(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::DistributedMesh::clear(), libMesh::ExodusII_IO_Helper::close(), libMesh::Nemesis_IO_Helper::compute_border_node_ids(), libMesh::Nemesis_IO_Helper::compute_communication_map_parameters(), libMesh::Nemesis_IO_Helper::compute_internal_and_border_elems_and_internal_nodes(), libMesh::Nemesis_IO_Helper::compute_node_communication_maps(), libMesh::Nemesis_IO_Helper::compute_num_global_elem_blocks(), libMesh::Nemesis_IO_Helper::compute_num_global_nodesets(), libMesh::Nemesis_IO_Helper::compute_num_global_sidesets(), libMesh::Nemesis_IO_Helper::construct_nemesis_filename(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::ExodusII_IO_Helper::create(), libMesh::DistributedMesh::delete_elem(), libMesh::DistributedMesh::delete_node(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_local_dofs_node_major(), libMesh::DofMap::distribute_local_dofs_var_major(), libMesh::DistributedMesh::DistributedMesh(), libMesh::DofMap::end_dof(), libMesh::DofMap::end_old_dof(), libMesh::EnsightIO::EnsightIO(), libMesh::MeshFunction::find_element(), libMesh::MeshFunction::find_elements(), libMesh::UnstructuredMesh::find_neighbors(), libMesh::DofMap::first_dof(), libMesh::DofMap::first_old_dof(), libMesh::Nemesis_IO_Helper::get_cmap_params(), libMesh::Nemesis_IO_Helper::get_eb_info_global(), libMesh::Nemesis_IO_Helper::get_elem_cmap(), libMesh::Nemesis_IO_Helper::get_elem_map(), libMesh::MeshBase::get_info(), libMesh::DofMap::get_info(), libMesh::Nemesis_IO_Helper::get_init_global(), libMesh::Nemesis_IO_Helper::get_init_info(), libMesh::Nemesis_IO_Helper::get_loadbal_param(), libMesh::Nemesis_IO_Helper::get_node_cmap(), libMesh::Nemesis_IO_Helper::get_node_map(), libMesh::Nemesis_IO_Helper::get_ns_param_global(), libMesh::Nemesis_IO_Helper::get_ss_param_global(), libMesh::SparsityPattern::Build::handle_vi_vj(), libMesh::SystemSubsetBySubdomain::init(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::initialize_element_variables(), libMesh::ExodusII_IO_Helper::initialize_global_variables(), libMesh::ExodusII_IO_Helper::initialize_nodal_variables(), libMesh::DistributedMesh::insert_elem(), libMesh::DofMap::is_evaluable(), libMesh::SparsityPattern::Build::join(), libMesh::DofMap::last_dof(), libMesh::MeshTools::libmesh_assert_consistent_distributed(), libMesh::MeshTools::libmesh_assert_consistent_distributed_nodes(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_object_ids(), libMesh::DofMap::local_variable_indices(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshBase::n_active_local_elem(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::BoundaryInfo::n_edge_conds(), libMesh::DofMap::n_local_dofs(), libMesh::System::n_local_dofs(), libMesh::MeshBase::n_local_elem(), libMesh::MeshBase::n_local_nodes(), libMesh::BoundaryInfo::n_nodeset_conds(), libMesh::BoundaryInfo::n_shellface_conds(), libMesh::SparsityPattern::Build::operator()(), libMesh::DistributedMesh::own_node(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::Nemesis_IO_Helper::put_cmap_params(), libMesh::Nemesis_IO_Helper::put_elem_cmap(), libMesh::Nemesis_IO_Helper::put_elem_map(), libMesh::Nemesis_IO_Helper::put_loadbal_param(), libMesh::Nemesis_IO_Helper::put_node_cmap(), libMesh::Nemesis_IO_Helper::put_node_map(), libMesh::NameBasedIO::read(), libMesh::Nemesis_IO::read(), libMesh::XdrIO::read(), libMesh::CheckpointIO::read(), libMesh::ExodusII_IO_Helper::read_elem_num_map(), libMesh::ExodusII_IO_Helper::read_global_values(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::System::read_header(), libMesh::System::read_legacy_data(), libMesh::ExodusII_IO_Helper::read_node_num_map(), libMesh::System::read_parallel_data(), libMesh::System::read_SCALAR_dofs(), libMesh::XdrIO::read_serialized_bc_names(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::System::read_serialized_data(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::System::read_serialized_vector(), libMesh::System::read_serialized_vectors(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::CheckpointIO::select_split_config(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::LaplaceMeshSmoother::smooth(), libMesh::MeshTools::total_weight(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::Parallel::Packing< T >::unpack(), libMesh::DistributedMesh::update_parallel_id_counts(), libMesh::NameBasedIO::write(), libMesh::XdrIO::write(), libMesh::CheckpointIO::write(), libMesh::EquationSystems::write(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::ExodusII_IO::write_element_data(), libMesh::ExodusII_IO_Helper::write_element_values(), libMesh::ExodusII_IO_Helper::write_elements(), libMesh::ExodusII_IO::write_global_data(), libMesh::ExodusII_IO_Helper::write_global_values(), libMesh::System::write_header(), libMesh::ExodusII_IO::write_information_records(), libMesh::ExodusII_IO_Helper::write_information_records(), libMesh::ExodusII_IO_Helper::write_nodal_coordinates(), libMesh::UCDIO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data_discontinuous(), libMesh::ExodusII_IO_Helper::write_nodal_values(), libMesh::Nemesis_IO_Helper::write_nodesets(), libMesh::ExodusII_IO_Helper::write_nodesets(), libMesh::System::write_parallel_data(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bc_names(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::System::write_serialized_data(), libMesh::XdrIO::write_serialized_nodes(), libMesh::XdrIO::write_serialized_nodesets(), libMesh::XdrIO::write_serialized_subdomain_names(), libMesh::System::write_serialized_vector(), libMesh::System::write_serialized_vectors(), libMesh::Nemesis_IO_Helper::write_sidesets(), libMesh::ExodusII_IO_Helper::write_sidesets(), libMesh::ExodusII_IO::write_timestep(), libMesh::ExodusII_IO_Helper::write_timestep(), and libMesh::ExodusII_IO::write_timestep_discontinuous().

102  { return cast_int<processor_id_type>(_communicator.rank()); }
const Parallel::Communicator & _communicator
processor_id_type rank() const
Definition: communicator.h:173

◆ project_solution() [1/3]

void libMesh::System::project_solution ( FunctionBase< Number > *  f,
FunctionBase< Gradient > *  g = nullptr 
) const
inherited

Projects arbitrary functions onto the current solution. 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 function onto the solution via L2 projections and nodal interpolations on each element.

Definition at line 810 of file system_projection.C.

812 {
813  this->project_vector(*solution, f, g);
814 
815  solution->localize(*current_local_solution, _dof_map->get_send_list());
816 }
std::unique_ptr< DofMap > _dof_map
Definition: system.h:1884
std::unique_ptr< NumericVector< Number > > solution
Definition: system.h:1523
std::unique_ptr< NumericVector< Number > > current_local_solution
Definition: system.h:1535
void project_vector(NumericVector< Number > &new_vector, FunctionBase< Number > *f, FunctionBase< Gradient > *g=nullptr, int is_adjoint=-1) const

◆ project_solution() [2/3]

void libMesh::System::project_solution ( FEMFunctionBase< Number > *  f,
FEMFunctionBase< Gradient > *  g = nullptr 
) const
inherited

Projects arbitrary functions onto the current solution. 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 function onto the solution via L2 projections and nodal interpolations on each element.

Definition at line 823 of file system_projection.C.

825 {
826  this->project_vector(*solution, f, g);
827 
828  solution->localize(*current_local_solution, _dof_map->get_send_list());
829 }
std::unique_ptr< DofMap > _dof_map
Definition: system.h:1884
std::unique_ptr< NumericVector< Number > > solution
Definition: system.h:1523
std::unique_ptr< NumericVector< Number > > current_local_solution
Definition: system.h:1535
void project_vector(NumericVector< Number > &new_vector, FunctionBase< Number > *f, FunctionBase< Gradient > *g=nullptr, int is_adjoint=-1) const

◆ project_solution() [3/3]

void libMesh::System::project_solution ( ValueFunctionPointer  fptr,
GradientFunctionPointer  gptr,
const Parameters parameters 
) const
inherited

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

Definition at line 796 of file system_projection.C.

799 {
800  WrappedFunction<Number> f(*this, fptr, &parameters);
801  WrappedFunction<Gradient> g(*this, gptr, &parameters);
802  this->project_solution(&f, &g);
803 }
void project_solution(FunctionBase< Number > *f, FunctionBase< Gradient > *g=nullptr) const

◆ project_solution_on_reinit()

bool& libMesh::System::project_solution_on_reinit ( void  )
inlineinherited

Tells the System whether or not to project the solution vector onto new grids when the system is reinitialized. The solution will be projected unless project_solution_on_reinit() = false is called.

Definition at line 794 of file system.h.

References libMesh::System::_solution_projection.

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), and libMesh::MemorySolutionHistory::store().

795  { return _solution_projection; }
bool _solution_projection
Definition: system.h:1959

◆ project_vector() [1/5]

void libMesh::System::project_vector ( NumericVector< Number > &  new_vector,
FunctionBase< Number > *  f,
FunctionBase< Gradient > *  g = nullptr,
int  is_adjoint = -1 
) const
inherited

Projects arbitrary functions onto a vector of degree of freedom values for the current system. 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 851 of file system_projection.C.

Referenced by libMesh::NewmarkSolver::project_initial_accel(), libMesh::SecondOrderUnsteadySolver::project_initial_rate(), and libMesh::System::restrict_vectors().

855 {
856  LOG_SCOPE ("project_vector(FunctionBase)", "System");
857 
858  libmesh_assert(f);
859 
860  WrappedFunctor<Number> f_fem(*f);
861 
862  if (g)
863  {
864  WrappedFunctor<Gradient> g_fem(*g);
865 
866  this->project_vector(new_vector, &f_fem, &g_fem, is_adjoint);
867  }
868  else
869  this->project_vector(new_vector, &f_fem, nullptr, is_adjoint);
870 }
void project_vector(NumericVector< Number > &new_vector, FunctionBase< Number > *f, FunctionBase< Gradient > *g=nullptr, int is_adjoint=-1) const

◆ project_vector() [2/5]

void libMesh::System::project_vector ( NumericVector< Number > &  new_vector,
FEMFunctionBase< Number > *  f,
FEMFunctionBase< Gradient > *  g = nullptr,
int  is_adjoint = -1 
) const
inherited

Projects arbitrary functions onto a vector of degree of freedom values for the current system. 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 877 of file system_projection.C.

References libMesh::NumericVector< T >::close(), libMesh::FEMFunctionBase< Output >::component(), libMesh::Utility::iota(), n_vars, libMesh::Threads::parallel_for(), libMesh::FEMContext::pre_fe_reinit(), libMesh::SCALAR, libMesh::DofMap::SCALAR_dof_indices(), and libMesh::NumericVector< T >::set().

881 {
882  LOG_SCOPE ("project_fem_vector()", "System");
883 
884  libmesh_assert (f);
885 
886  ConstElemRange active_local_range
887  (this->get_mesh().active_local_elements_begin(),
888  this->get_mesh().active_local_elements_end() );
889 
890  VectorSetAction<Number> setter(new_vector);
891 
892  const unsigned int n_variables = this->n_vars();
893 
894  std::vector<unsigned int> vars(n_variables);
895  std::iota(vars.begin(), vars.end(), 0);
896 
897  // Use a typedef to make the calling sequence for parallel_for() a bit more readable
898  typedef
899  GenericProjector<FEMFunctionWrapper<Number>, FEMFunctionWrapper<Gradient>,
900  Number, VectorSetAction<Number>> FEMProjector;
901 
902  FEMFunctionWrapper<Number> fw(*f);
903 
904  if (g)
905  {
906  FEMFunctionWrapper<Gradient> gw(*g);
907 
909  (active_local_range,
910  FEMProjector(*this, fw, &gw, setter, vars));
911  }
912  else
914  (active_local_range,
915  FEMProjector(*this, fw, nullptr, setter, vars));
916 
917  // Also, load values into the SCALAR dofs
918  // Note: We assume that all SCALAR dofs are on the
919  // processor with highest ID
920  if (this->processor_id() == (this->n_processors()-1))
921  {
922  // FIXME: Do we want to first check for SCALAR vars before building this? [PB]
923  FEMContext context( *this );
924 
925  const DofMap & dof_map = this->get_dof_map();
926  for (unsigned int var=0; var<this->n_vars(); var++)
927  if (this->variable(var).type().family == SCALAR)
928  {
929  // FIXME: We reinit with an arbitrary element in case the user
930  // doesn't override FEMFunctionBase::component. Is there
931  // any use case we're missing? [PB]
932  Elem * el = const_cast<Elem *>(*(this->get_mesh().active_local_elements_begin()));
933  context.pre_fe_reinit(*this, el);
934 
935  std::vector<dof_id_type> SCALAR_indices;
936  dof_map.SCALAR_dof_indices (SCALAR_indices, var);
937  const unsigned int n_SCALAR_dofs =
938  cast_int<unsigned int>(SCALAR_indices.size());
939 
940  for (unsigned int i=0; i<n_SCALAR_dofs; i++)
941  {
942  const dof_id_type global_index = SCALAR_indices[i];
943  const unsigned int component_index =
944  this->variable_scalar_number(var,i);
945 
946  new_vector.set(global_index, f->component(context, component_index, Point(), this->time));
947  }
948  }
949  }
950 
951  new_vector.close();
952 
953 #ifdef LIBMESH_ENABLE_CONSTRAINTS
954  if (is_adjoint == -1)
955  this->get_dof_map().enforce_constraints_exactly(*this, &new_vector);
956  else if (is_adjoint >= 0)
958  is_adjoint);
959 #endif
960 }
FEFamily family
Definition: fe_type.h:204
unsigned int variable_scalar_number(const std::string &var, unsigned int component) const
Definition: system.h:2164
const Variable & variable(unsigned int var) const
Definition: system.h:2133
void parallel_for(const Range &range, const Body &body)
Definition: threads_none.h:73
const MeshBase & get_mesh() const
Definition: system.h:2033
void iota(ForwardIter first, ForwardIter last, T value)
Definition: utility.h:57
StoredRange< MeshBase::const_element_iterator, const Elem * > ConstElemRange
Definition: elem_range.h:34
void enforce_adjoint_constraints_exactly(NumericVector< Number > &v, unsigned int q) const
processor_id_type n_processors() const
virtual element_iterator active_local_elements_begin()=0
virtual void close()=0
virtual void set(const numeric_index_type i, const T value)=0
unsigned int n_vars() const
Definition: system.h:2105
processor_id_type processor_id() const
const DofMap & get_dof_map() const
Definition: system.h:2049
uint8_t dof_id_type
Definition: id_types.h:64
const FEType & type() const
Definition: variable.h:119
void enforce_constraints_exactly(const System &system, NumericVector< Number > *v=nullptr, bool homogeneous=false) const

◆ project_vector() [3/5]

void libMesh::System::project_vector ( ValueFunctionPointer  fptr,
GradientFunctionPointer  gptr,
const Parameters parameters,
NumericVector< Number > &  new_vector,
int  is_adjoint = -1 
) const
inherited

Projects arbitrary functions onto a vector of degree of freedom values for the current system. 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.

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

Definition at line 836 of file system_projection.C.

841 {
842  WrappedFunction<Number> f(*this, fptr, &parameters);
843  WrappedFunction<Gradient> g(*this, gptr, &parameters);
844  this->project_vector(new_vector, &f, &g, is_adjoint);
845 }
void project_vector(NumericVector< Number > &new_vector, FunctionBase< Number > *f, FunctionBase< Gradient > *g=nullptr, int is_adjoint=-1) const

◆ project_vector() [4/5]

void libMesh::System::project_vector ( NumericVector< Number > &  vector,
int  is_adjoint = -1 
) const
protectedinherited

Projects the vector defined on the old mesh onto the new mesh.

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

Definition at line 212 of file system_projection.C.

References libMesh::NumericVector< T >::clone().

214 {
215  // Create a copy of the vector, which currently
216  // contains the old data.
217  std::unique_ptr<NumericVector<Number>>
218  old_vector (vector.clone());
219 
220  // Project the old vector to the new vector
221  this->project_vector (*old_vector, vector, is_adjoint);
222 }
virtual std::unique_ptr< NumericVector< T > > clone() const =0
void project_vector(NumericVector< Number > &new_vector, FunctionBase< Number > *f, FunctionBase< Gradient > *g=nullptr, int is_adjoint=-1) const

◆ project_vector() [5/5]

void libMesh::System::project_vector ( const NumericVector< Number > &  ,
NumericVector< Number > &  ,
int  is_adjoint = -1 
) const
protectedinherited

Projects the vector defined on the old mesh onto the new mesh. The original vector is unchanged and the new vector is passed through the second argument.

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

◆ projection_matrix()

void libMesh::System::projection_matrix ( SparseMatrix< Number > &  proj_mat) const
inherited

This method creates a projection matrix which corresponds to the operation of project_vector between old and new solution spaces.

Heterogeneous Dirichlet boundary conditions are not taken into account here; if this matrix is used for prolongation (mesh refinement) on a side with a heterogeneous BC, the newly created degrees of freedom on that side will still match the coarse grid approximation of the BC, not the fine grid approximation.

This method creates a projection matrix which corresponds to the operation of project_vector between old and new solution spaces.

Definition at line 730 of file system_projection.C.

References libMesh::Utility::iota(), n_vars, libMesh::Threads::parallel_for(), libMesh::SCALAR, libMesh::DofMap::SCALAR_dof_indices(), and libMesh::SparseMatrix< T >::set().

731 {
732  LOG_SCOPE ("projection_matrix()", "System");
733 
734  const unsigned int n_variables = this->n_vars();
735 
736  if (n_variables)
737  {
738  ConstElemRange active_local_elem_range
739  (this->get_mesh().active_local_elements_begin(),
740  this->get_mesh().active_local_elements_end());
741 
742  std::vector<unsigned int> vars(n_variables);
743  std::iota(vars.begin(), vars.end(), 0);
744 
745  // Use a typedef to make the calling sequence for parallel_for() a bit more readable
746  typedef OldSolutionCoefs<Real, &FEMContext::point_value> OldSolutionValueCoefs;
747  typedef OldSolutionCoefs<RealGradient, &FEMContext::point_gradient> OldSolutionGradientCoefs;
748 
749  typedef
750  GenericProjector<OldSolutionValueCoefs,
751  OldSolutionGradientCoefs,
752  DynamicSparseNumberArray<Real,dof_id_type>,
753  MatrixFillAction<Real, Number> > ProjMatFiller;
754 
755  OldSolutionValueCoefs f(*this);
756  OldSolutionGradientCoefs g(*this);
757  MatrixFillAction<Real, Number> setter(proj_mat);
758 
759  Threads::parallel_for (active_local_elem_range,
760  ProjMatFiller(*this, f, &g, setter, vars));
761 
762  // Set the SCALAR dof transfer entries too.
763  // Note: We assume that all SCALAR dofs are on the
764  // processor with highest ID
765  if (this->processor_id() == (this->n_processors()-1))
766  {
767  const DofMap & dof_map = this->get_dof_map();
768  for (unsigned int var=0; var<this->n_vars(); var++)
769  if (this->variable(var).type().family == SCALAR)
770  {
771  // We can just map SCALAR dofs directly across
772  std::vector<dof_id_type> new_SCALAR_indices, old_SCALAR_indices;
773  dof_map.SCALAR_dof_indices (new_SCALAR_indices, var, false);
774  dof_map.SCALAR_dof_indices (old_SCALAR_indices, var, true);
775  const unsigned int new_n_dofs =
776  cast_int<unsigned int>(new_SCALAR_indices.size());
777 
778  for (unsigned int i=0; i<new_n_dofs; i++)
779  {
780  proj_mat.set( new_SCALAR_indices[i],
781  old_SCALAR_indices[i], 1);
782  }
783  }
784  }
785  }
786 }
FEFamily family
Definition: fe_type.h:204
const Variable & variable(unsigned int var) const
Definition: system.h:2133
void parallel_for(const Range &range, const Body &body)
Definition: threads_none.h:73
const MeshBase & get_mesh() const
Definition: system.h:2033
void iota(ForwardIter first, ForwardIter last, T value)
Definition: utility.h:57
StoredRange< MeshBase::const_element_iterator, const Elem * > ConstElemRange
Definition: elem_range.h:34
virtual void set(const numeric_index_type i, const numeric_index_type j, const T value)=0
processor_id_type n_processors() const
unsigned int n_vars() const
Definition: system.h:2105
processor_id_type processor_id() const
const DofMap & get_dof_map() const
Definition: system.h:2049
const FEType & type() const
Definition: variable.h:119

◆ prolong_vectors()

void libMesh::System::prolong_vectors ( )
virtualinherited

Prolong vectors after the mesh has refined

Definition at line 380 of file system.C.

References libMesh::System::restrict_vectors().

Referenced by libMesh::EquationSystems::reinit_solutions().

381 {
382 #ifdef LIBMESH_ENABLE_AMR
383  // Currently project_vector handles both restriction and prolongation
384  this->restrict_vectors();
385 #endif
386 }
virtual void restrict_vectors()
Definition: system.C:324

◆ qoi_parameter_hessian()

void libMesh::ImplicitSystem::qoi_parameter_hessian ( const QoISet qoi_indices,
const ParameterVector parameters,
SensitivityData hessian 
)
overridevirtualinherited

For each of the system's quantities of interest q in qoi[qoi_indices], and for a vector of parameters p, the parameter sensitivity Hessian H_ij is defined as H_ij = (d^2 q)/(d p_i d p_j) This Hessian is the output of this method, where for each q_i, H_jk is stored in hessian.second_derivative(i,j,k).

Note that in some cases only current_local_solution is used during assembly, and, therefore, if solution has been altered without update() being called, then the user must call update() before calling this function.

Reimplemented from libMesh::System.

Definition at line 1102 of file implicit_system.C.

References libMesh::ImplicitSystem::adjoint_solve(), libMesh::SensitivityData::allocate_hessian_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_adjoint_solution(), libMesh::System::get_sensitivity_solution(), libMesh::QoISet::has_index(), libMesh::System::is_adjoint_already_solved(), libMesh::ImplicitSystem::matrix, libMesh::System::n_qois(), libMesh::System::qoi, libMesh::Real, libMesh::ExplicitSystem::rhs, libMesh::SensitivityData::second_derivative(), libMesh::ImplicitSystem::sensitivity_solve(), libMesh::ParameterVector::size(), libMesh::System::solution, libMesh::TOLERANCE, libMesh::System::update(), and libMesh::SparseMatrix< T >::vector_mult().

1105 {
1106  // We currently get partial derivatives via finite differencing
1107  const Real delta_p = TOLERANCE;
1108 
1109  ParameterVector & parameters =
1110  const_cast<ParameterVector &>(parameters_in);
1111 
1112  // We'll use one temporary vector for matrix-vector-vector products
1113  std::unique_ptr<NumericVector<Number>> tempvec = this->solution->zero_clone();
1114 
1115  // And another temporary vector to hold a copy of the true solution
1116  // so we can safely perturb this->solution.
1117  std::unique_ptr<NumericVector<Number>> oldsolution = this->solution->clone();
1118 
1119  const unsigned int Np = cast_int<unsigned int>
1120  (parameters.size());
1121  const unsigned int Nq = this->n_qois();
1122 
1123  // For each quantity of interest q, the parameter sensitivity
1124  // Hessian is defined as q''_{kl} = {d^2 q}/{d p_k d p_l}.
1125  //
1126  // We calculate it from values and partial derivatives of the
1127  // quantity of interest function Q, solution u, adjoint solution z,
1128  // and residual R, as:
1129  //
1130  // q''_{kl} =
1131  // Q''_{kl} + Q''_{uk}(u)*u'_l + Q''_{ul}(u) * u'_k +
1132  // Q''_{uu}(u)*u'_k*u'_l -
1133  // R''_{kl}(u,z) -
1134  // R''_{uk}(u,z)*u'_l - R''_{ul}(u,z)*u'_k -
1135  // R''_{uu}(u,z)*u'_k*u'_l
1136  //
1137  // See the adjoints model document for more details.
1138 
1139  // We first do an adjoint solve to get z for each quantity of
1140  // interest
1141  // if we havent already or dont have an initial condition for the adjoint
1142  if (!this->is_adjoint_already_solved())
1143  {
1144  this->adjoint_solve(qoi_indices);
1145  }
1146 
1147  // And a sensitivity solve to get u_k for each parameter
1148  this->sensitivity_solve(parameters);
1149 
1150  // Get ready to fill in second derivatives:
1151  sensitivities.allocate_hessian_data(qoi_indices, *this, parameters);
1152 
1153  for (unsigned int k=0; k != Np; ++k)
1154  {
1155  Number old_parameterk = *parameters[k];
1156 
1157  // The Hessian is symmetric, so we just calculate the lower
1158  // triangle and the diagonal, and we get the upper triangle from
1159  // the transpose of the lower
1160 
1161  for (unsigned int l=0; l != k+1; ++l)
1162  {
1163  // The second partial derivatives with respect to parameters
1164  // are all calculated via a central finite difference
1165  // stencil:
1166  // F''_{kl} ~= (F(p+dp*e_k+dp*e_l) - F(p+dp*e_k-dp*e_l) -
1167  // F(p-dp*e_k+dp*e_l) + F(p-dp*e_k-dp*e_l))/(4*dp^2)
1168  // We will add Q''_{kl}(u) and subtract R''_{kl}(u,z) at the
1169  // same time.
1170  //
1171  // We have to be careful with the perturbations to handle
1172  // the k=l case
1173 
1174  Number old_parameterl = *parameters[l];
1175 
1176  *parameters[k] += delta_p;
1177  *parameters[l] += delta_p;
1178  this->assemble_qoi(qoi_indices);
1179  this->assembly(true, false, true);
1180  this->rhs->close();
1181  std::vector<Number> partial2q_term = this->qoi;
1182  std::vector<Number> partial2R_term(this->n_qois());
1183  for (unsigned int i=0; i != Nq; ++i)
1184  if (qoi_indices.has_index(i))
1185  partial2R_term[i] = this->rhs->dot(this->get_adjoint_solution(i));
1186 
1187  *parameters[l] -= 2.*delta_p;
1188  this->assemble_qoi(qoi_indices);
1189  this->assembly(true, false, true);
1190  this->rhs->close();
1191  for (unsigned int i=0; i != Nq; ++i)
1192  if (qoi_indices.has_index(i))
1193  {
1194  partial2q_term[i] -= this->qoi[i];
1195  partial2R_term[i] -= this->rhs->dot(this->get_adjoint_solution(i));
1196  }
1197 
1198  *parameters[k] -= 2.*delta_p;
1199  this->assemble_qoi(qoi_indices);
1200  this->assembly(true, false, true);
1201  this->rhs->close();
1202  for (unsigned int i=0; i != Nq; ++i)
1203  if (qoi_indices.has_index(i))
1204  {
1205  partial2q_term[i] += this->qoi[i];
1206  partial2R_term[i] += this->rhs->dot(this->get_adjoint_solution(i));
1207  }
1208 
1209  *parameters[l] += 2.*delta_p;
1210  this->assemble_qoi(qoi_indices);
1211  this->assembly(true, false, true);
1212  this->rhs->close();
1213  for (unsigned int i=0; i != Nq; ++i)
1214  if (qoi_indices.has_index(i))
1215  {
1216  partial2q_term[i] -= this->qoi[i];
1217  partial2R_term[i] -= this->rhs->dot(this->get_adjoint_solution(i));
1218  partial2q_term[i] /= (4. * delta_p * delta_p);
1219  partial2R_term[i] /= (4. * delta_p * delta_p);
1220  }
1221 
1222  for (unsigned int i=0; i != Nq; ++i)
1223  if (qoi_indices.has_index(i))
1224  {
1225  Number current_terms = partial2q_term[i] - partial2R_term[i];
1226  sensitivities.second_derivative(i,k,l) += current_terms;
1227  if (k != l)
1228  sensitivities.second_derivative(i,l,k) += current_terms;
1229  }
1230 
1231  // Don't leave the parameters perturbed
1232  *parameters[l] = old_parameterl;
1233  *parameters[k] = old_parameterk;
1234  }
1235 
1236  // We get (partial q / partial u) and
1237  // (partial R / partial u) from the user, but centrally
1238  // difference to get q_uk and R_uk terms:
1239  // (partial^2 q / partial u partial k)
1240  // q_uk*u'_l = (q_u(p+dp*e_k)*u'_l - q_u(p-dp*e_k)*u'_l)/(2*dp)
1241  // R_uk*z*u'_l = (R_u(p+dp*e_k)*z*u'_l - R_u(p-dp*e_k)*z*u'_l)/(2*dp)
1242  //
1243  // To avoid creating Nq temporary vectors, we add these
1244  // subterms to the sensitivities output one by one.
1245  //
1246  // FIXME: this is probably a bad order of operations for
1247  // controlling floating point error.
1248 
1249  *parameters[k] = old_parameterk + delta_p;
1250  this->assembly(false, true);
1251  this->matrix->close();
1252  this->assemble_qoi_derivative(qoi_indices,
1253  /* include_liftfunc = */ true,
1254  /* apply_constraints = */ false);
1255 
1256  for (unsigned int l=0; l != Np; ++l)
1257  {
1258  this->matrix->vector_mult(*tempvec, this->get_sensitivity_solution(l));
1259  for (unsigned int i=0; i != Nq; ++i)
1260  if (qoi_indices.has_index(i))
1261  {
1262  this->get_adjoint_rhs(i).close();
1263  Number current_terms =
1264  (this->get_adjoint_rhs(i).dot(this->get_sensitivity_solution(l)) -
1265  tempvec->dot(this->get_adjoint_solution(i))) / (2.*delta_p);
1266  sensitivities.second_derivative(i,k,l) += current_terms;
1267 
1268  // We use the _uk terms twice; symmetry lets us reuse
1269  // these calculations for the _ul terms.
1270 
1271  sensitivities.second_derivative(i,l,k) += current_terms;
1272  }
1273  }
1274 
1275  *parameters[k] = old_parameterk - delta_p;
1276  this->assembly(false, true);
1277  this->matrix->close();
1278  this->assemble_qoi_derivative(qoi_indices,
1279  /* include_liftfunc = */ true,
1280  /* apply_constraints = */ false);
1281 
1282  for (unsigned int l=0; l != Np; ++l)
1283  {
1284  this->matrix->vector_mult(*tempvec, this->get_sensitivity_solution(l));
1285  for (unsigned int i=0; i != Nq; ++i)
1286  if (qoi_indices.has_index(i))
1287  {
1288  this->get_adjoint_rhs(i).close();
1289  Number current_terms =
1290  (-this->get_adjoint_rhs(i).dot(this->get_sensitivity_solution(l)) +
1291  tempvec->dot(this->get_adjoint_solution(i))) / (2.*delta_p);
1292  sensitivities.second_derivative(i,k,l) += current_terms;
1293 
1294  // We use the _uk terms twice; symmetry lets us reuse
1295  // these calculations for the _ul terms.
1296 
1297  sensitivities.second_derivative(i,l,k) += current_terms;
1298  }
1299  }
1300 
1301  // Don't leave the parameter perturbed
1302  *parameters[k] = old_parameterk;
1303 
1304  // Our last remaining terms are -R_uu(u,z)*u_k*u_l and
1305  // Q_uu(u)*u_k*u_l
1306  //
1307  // We take directional central finite differences of R_u and Q_u
1308  // to approximate these terms, e.g.:
1309  //
1310  // Q_uu(u)*u_k ~= (Q_u(u+dp*u_k) - Q_u(u-dp*u_k))/(2*dp)
1311 
1312  *this->solution = this->get_sensitivity_solution(k);
1313  *this->solution *= delta_p;
1314  *this->solution += *oldsolution;
1315 
1316  // We've modified solution, so we need to update before calling
1317  // assembly since assembly may only use current_local_solution
1318  this->update();
1319  this->assembly(false, true);
1320  this->matrix->close();
1321  this->assemble_qoi_derivative(qoi_indices,
1322  /* include_liftfunc = */ true,
1323  /* apply_constraints = */ false);
1324 
1325  // The Hessian is symmetric, so we just calculate the lower
1326  // triangle and the diagonal, and we get the upper triangle from
1327  // the transpose of the lower
1328  //
1329  // Note that, because we took the directional finite difference
1330  // with respect to k and not l, we've added an O(delta_p^2)
1331  // error to any permutational symmetry in the Hessian...
1332  for (unsigned int l=0; l != k+1; ++l)
1333  {
1334  this->matrix->vector_mult(*tempvec, this->get_sensitivity_solution(l));
1335  for (unsigned int i=0; i != Nq; ++i)
1336  if (qoi_indices.has_index(i))
1337  {
1338  this->get_adjoint_rhs(i).close();
1339  Number current_terms =
1340  (this->get_adjoint_rhs(i).dot(this->get_sensitivity_solution(l)) -
1341  tempvec->dot(this->get_adjoint_solution(i))) / (2.*delta_p);
1342  sensitivities.second_derivative(i,k,l) += current_terms;
1343  if (k != l)
1344  sensitivities.second_derivative(i,l,k) += current_terms;
1345  }
1346  }
1347 
1348  *this->solution = this->get_sensitivity_solution(k);
1349  *this->solution *= -delta_p;
1350  *this->solution += *oldsolution;
1351 
1352  // We've modified solution, so we need to update before calling
1353  // assembly since assembly may only use current_local_solution
1354  this->update();
1355  this->assembly(false, true);
1356  this->matrix->close();
1357  this->assemble_qoi_derivative(qoi_indices,
1358  /* include_liftfunc = */ true,
1359  /* apply_constraints = */ false);
1360 
1361  for (unsigned int l=0; l != k+1; ++l)
1362  {
1363  this->matrix->vector_mult(*tempvec, this->get_sensitivity_solution(l));
1364  for (unsigned int i=0; i != Nq; ++i)
1365  if (qoi_indices.has_index(i))
1366  {
1367  this->get_adjoint_rhs(i).close();
1368  Number current_terms =
1369  (-this->get_adjoint_rhs(i).dot(this->get_sensitivity_solution(l)) +
1370  tempvec->dot(this->get_adjoint_solution(i))) / (2.*delta_p);
1371  sensitivities.second_derivative(i,k,l) += current_terms;
1372  if (k != l)
1373  sensitivities.second_derivative(i,l,k) += current_terms;
1374  }
1375  }
1376 
1377  // Don't leave the solution perturbed
1378  *this->solution = *oldsolution;
1379  }
1380 
1381  // All parameters have been reset.
1382  // Don't leave the qoi or system changed - principle of least
1383  // surprise.
1384  // We've modified solution, so we need to update before calling
1385  // assembly since assembly may only use current_local_solution
1386  this->update();
1387  this->assembly(true, true);
1388  this->rhs->close();
1389  this->matrix->close();
1390  this->assemble_qoi(qoi_indices);
1391 }
void vector_mult(NumericVector< T > &dest, const NumericVector< T > &arg) const
unsigned int n_qois() const
Definition: system.h:2278
NumericVector< Number > & get_sensitivity_solution(unsigned int i=0)
Definition: system.C:916
NumericVector< Number > * rhs
virtual std::pair< unsigned int, Real > sensitivity_solve(const ParameterVector &parameters) override
static const Real TOLERANCE
virtual T dot(const NumericVector< T > &v) const =0
virtual std::pair< unsigned int, Real > adjoint_solve(const QoISet &qoi_indices=QoISet()) override
virtual void assembly(bool, bool, bool=false, bool=false)
std::vector< Number > qoi
Definition: system.h:1558
std::unique_ptr< NumericVector< Number > > solution
Definition: system.h:1523
bool is_adjoint_already_solved() const
Definition: system.h:388
virtual void close()=0
virtual void update()
Definition: system.C:408
virtual void close()=0
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
SparseMatrix< Number > * matrix
virtual void assemble_qoi(const QoISet &qoi_indices=QoISet()) override
virtual void assemble_qoi_derivative(const QoISet &qoi_indices=QoISet(), bool include_liftfunc=true, bool apply_constraints=true) override
NumericVector< Number > & get_adjoint_solution(unsigned int i=0)
Definition: system.C:969
NumericVector< Number > & get_adjoint_rhs(unsigned int i=0)
Definition: system.C:1031

◆ qoi_parameter_hessian_vector_product()

void libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product ( const QoISet qoi_indices,
const ParameterVector parameters,
const ParameterVector vector,
SensitivityData product 
)
overridevirtualinherited

For each of the system's quantities of interest q in qoi[qoi_indices], and for a vector of parameters p, the parameter sensitivity Hessian H_ij is defined as H_ij = (d^2 q)/(d p_i d p_j) The Hessian-vector product, for a vector v_k in parameter space, is S_j = H_jk v_k This product is the output of this method, where for each q_i, S_j is stored in sensitivities[i][j].

Reimplemented from libMesh::System.

Definition at line 897 of file implicit_system.C.

References libMesh::ImplicitSystem::adjoint_solve(), 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::ParameterVector::deep_copy(), libMesh::NumericVector< T >::dot(), libMesh::System::get_adjoint_rhs(), libMesh::System::get_adjoint_solution(), libMesh::System::get_weighted_sensitivity_adjoint_solution(), libMesh::System::get_weighted_sensitivity_solution(), libMesh::QoISet::has_index(), libMesh::System::is_adjoint_already_solved(), libMesh::ImplicitSystem::matrix, libMesh::System::n_qois(), libMesh::System::qoi, libMesh::Real, libMesh::ExplicitSystem::rhs, libMesh::ParameterVector::size(), libMesh::System::solution, libMesh::TOLERANCE, libMesh::ParameterVector::value_copy(), libMesh::SparseMatrix< T >::vector_mult(), libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve(), and libMesh::ImplicitSystem::weighted_sensitivity_solve().

901 {
902  // We currently get partial derivatives via finite differencing
903  const Real delta_p = TOLERANCE;
904 
905  ParameterVector & parameters =
906  const_cast<ParameterVector &>(parameters_in);
907 
908  // We'll use a single temporary vector for matrix-vector-vector products
909  std::unique_ptr<NumericVector<Number>> tempvec = this->solution->zero_clone();
910 
911  const unsigned int Np = cast_int<unsigned int>
912  (parameters.size());
913  const unsigned int Nq = this->n_qois();
914 
915  // For each quantity of interest q, the parameter sensitivity
916  // Hessian is defined as q''_{kl} = {d^2 q}/{d p_k d p_l}.
917  // Given a vector of parameter perturbation weights w_l, this
918  // function evaluates the hessian-vector product sum_l(q''_{kl}*w_l)
919  //
920  // We calculate it from values and partial derivatives of the
921  // quantity of interest function Q, solution u, adjoint solution z,
922  // parameter sensitivity adjoint solutions z^l, and residual R, as:
923  //
924  // sum_l(q''_{kl}*w_l) =
925  // sum_l(w_l * Q''_{kl}) + Q''_{uk}(u)*(sum_l(w_l u'_l)) -
926  // R'_k(u, sum_l(w_l*z^l)) - R'_{uk}(u,z)*(sum_l(w_l u'_l) -
927  // sum_l(w_l*R''_{kl}(u,z))
928  //
929  // See the adjoints model document for more details.
930 
931  // We first do an adjoint solve to get z for each quantity of
932  // interest
933  // if we havent already or dont have an initial condition for the adjoint
934  if (!this->is_adjoint_already_solved())
935  {
936  this->adjoint_solve(qoi_indices);
937  }
938 
939  // Get ready to fill in sensitivities:
940  sensitivities.allocate_data(qoi_indices, *this, parameters);
941 
942  // We can't solve for all the solution sensitivities u'_l or for all
943  // of the parameter sensitivity adjoint solutions z^l without
944  // requiring O(Nq*Np) linear solves. So we'll solve directly for their
945  // weighted sum - this is just O(Nq) solves.
946 
947  // First solve for sum_l(w_l u'_l).
948  this->weighted_sensitivity_solve(parameters, vector);
949 
950  // Then solve for sum_l(w_l z^l).
951  this->weighted_sensitivity_adjoint_solve(parameters, vector, qoi_indices);
952 
953  for (unsigned int k=0; k != Np; ++k)
954  {
955  // We approximate sum_l(w_l * Q''_{kl}) with a central
956  // differencing perturbation:
957  // sum_l(w_l * Q''_{kl}) ~=
958  // (Q(p + dp*w_l*e_l + dp*e_k) - Q(p - dp*w_l*e_l + dp*e_k) -
959  // Q(p + dp*w_l*e_l - dp*e_k) + Q(p - dp*w_l*e_l - dp*e_k))/(4*dp^2)
960 
961  // The sum(w_l*R''_kl) term requires the same sort of perturbation,
962  // and so we subtract it in at the same time:
963  // sum_l(w_l * R''_{kl}) ~=
964  // (R(p + dp*w_l*e_l + dp*e_k) - R(p - dp*w_l*e_l + dp*e_k) -
965  // R(p + dp*w_l*e_l - dp*e_k) + R(p - dp*w_l*e_l - dp*e_k))/(4*dp^2)
966 
967  ParameterVector oldparameters, parameterperturbation;
968  parameters.deep_copy(oldparameters);
969  vector.deep_copy(parameterperturbation);
970  parameterperturbation *= delta_p;
971  parameters += parameterperturbation;
972 
973  Number old_parameter = *parameters[k];
974 
975  *parameters[k] = old_parameter + delta_p;
976  this->assemble_qoi(qoi_indices);
977  this->assembly(true, false, true);
978  this->rhs->close();
979  std::vector<Number> partial2q_term = this->qoi;
980  std::vector<Number> partial2R_term(this->n_qois());
981  for (unsigned int i=0; i != Nq; ++i)
982  if (qoi_indices.has_index(i))
983  partial2R_term[i] = this->rhs->dot(this->get_adjoint_solution(i));
984 
985  *parameters[k] = old_parameter - delta_p;
986  this->assemble_qoi(qoi_indices);
987  this->assembly(true, false, true);
988  this->rhs->close();
989  for (unsigned int i=0; i != Nq; ++i)
990  if (qoi_indices.has_index(i))
991  {
992  partial2q_term[i] -= this->qoi[i];
993  partial2R_term[i] -= this->rhs->dot(this->get_adjoint_solution(i));
994  }
995 
996  oldparameters.value_copy(parameters);
997  parameterperturbation *= -1.0;
998  parameters += parameterperturbation;
999 
1000  // Re-center old_parameter, which may be affected by vector
1001  old_parameter = *parameters[k];
1002 
1003  *parameters[k] = old_parameter + delta_p;
1004  this->assemble_qoi(qoi_indices);
1005  this->assembly(true, false, true);
1006  this->rhs->close();
1007  for (unsigned int i=0; i != Nq; ++i)
1008  if (qoi_indices.has_index(i))
1009  {
1010  partial2q_term[i] -= this->qoi[i];
1011  partial2R_term[i] -= this->rhs->dot(this->get_adjoint_solution(i));
1012  }
1013 
1014  *parameters[k] = old_parameter - delta_p;
1015  this->assemble_qoi(qoi_indices);
1016  this->assembly(true, false, true);
1017  this->rhs->close();
1018  for (unsigned int i=0; i != Nq; ++i)
1019  if (qoi_indices.has_index(i))
1020  {
1021  partial2q_term[i] += this->qoi[i];
1022  partial2R_term[i] += this->rhs->dot(this->get_adjoint_solution(i));
1023  }
1024 
1025  for (unsigned int i=0; i != Nq; ++i)
1026  if (qoi_indices.has_index(i))
1027  {
1028  partial2q_term[i] /= (4. * delta_p * delta_p);
1029  partial2R_term[i] /= (4. * delta_p * delta_p);
1030  }
1031 
1032  for (unsigned int i=0; i != Nq; ++i)
1033  if (qoi_indices.has_index(i))
1034  sensitivities[i][k] = partial2q_term[i] - partial2R_term[i];
1035 
1036  // We get (partial q / partial u), R, and
1037  // (partial R / partial u) from the user, but centrally
1038  // difference to get q_uk, R_k, and R_uk terms:
1039  // (partial R / partial k)
1040  // R_k*sum(w_l*z^l) = (R(p+dp*e_k)*sum(w_l*z^l) - R(p-dp*e_k)*sum(w_l*z^l))/(2*dp)
1041  // (partial^2 q / partial u partial k)
1042  // q_uk = (q_u(p+dp*e_k) - q_u(p-dp*e_k))/(2*dp)
1043  // (partial^2 R / partial u partial k)
1044  // R_uk*z*sum(w_l*u'_l) = (R_u(p+dp*e_k)*z*sum(w_l*u'_l) - R_u(p-dp*e_k)*z*sum(w_l*u'_l))/(2*dp)
1045 
1046  // To avoid creating Nq temporary vectors for q_uk or R_uk, we add
1047  // subterms to the sensitivities output one by one.
1048  //
1049  // FIXME: this is probably a bad order of operations for
1050  // controlling floating point error.
1051 
1052  *parameters[k] = old_parameter + delta_p;
1053  this->assembly(true, true);
1054  this->rhs->close();
1055  this->matrix->close();
1056  this->assemble_qoi_derivative(qoi_indices,
1057  /* include_liftfunc = */ true,
1058  /* apply_constraints = */ false);
1059 
1060  this->matrix->vector_mult(*tempvec, this->get_weighted_sensitivity_solution());
1061 
1062  for (unsigned int i=0; i != Nq; ++i)
1063  if (qoi_indices.has_index(i))
1064  {
1065  this->get_adjoint_rhs(i).close();
1066  sensitivities[i][k] += (this->get_adjoint_rhs(i).dot(this->get_weighted_sensitivity_solution()) -
1068  this->get_adjoint_solution(i).dot(*tempvec)) / (2.*delta_p);
1069  }
1070 
1071  *parameters[k] = old_parameter - delta_p;
1072  this->assembly(true, true);
1073  this->rhs->close();
1074  this->matrix->close();
1075  this->assemble_qoi_derivative(qoi_indices,
1076  /* include_liftfunc = */ true,
1077  /* apply_constraints = */ false);
1078 
1079  this->matrix->vector_mult(*tempvec, this->get_weighted_sensitivity_solution());
1080 
1081  for (unsigned int i=0; i != Nq; ++i)
1082  if (qoi_indices.has_index(i))
1083  {
1084  this->get_adjoint_rhs(i).close();
1085  sensitivities[i][k] += (-this->get_adjoint_rhs(i).dot(this->get_weighted_sensitivity_solution()) +
1087  this->get_adjoint_solution(i).dot(*tempvec)) / (2.*delta_p);
1088  }
1089  }
1090 
1091  // All parameters have been reset.
1092  // Don't leave the qoi or system changed - principle of least
1093  // surprise.
1094  this->assembly(true, true);
1095  this->rhs->close();
1096  this->matrix->close();
1097  this->assemble_qoi(qoi_indices);
1098 }
void vector_mult(NumericVector< T > &dest, const NumericVector< T > &arg) const
unsigned int n_qois() const
Definition: system.h:2278
virtual std::pair< unsigned int, Real > weighted_sensitivity_solve(const ParameterVector &parameters, const ParameterVector &weights) override
NumericVector< Number > * rhs
static const Real TOLERANCE
virtual T dot(const NumericVector< T > &v) const =0
virtual std::pair< unsigned int, Real > adjoint_solve(const QoISet &qoi_indices=QoISet()) override
NumericVector< Number > & get_weighted_sensitivity_solution()
Definition: system.C:943
virtual void assembly(bool, bool, bool=false, bool=false)
std::vector< Number > qoi
Definition: system.h:1558
std::unique_ptr< NumericVector< Number > > solution
Definition: system.h:1523
bool is_adjoint_already_solved() const
Definition: system.h:388
virtual void close()=0
virtual void close()=0
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
SparseMatrix< Number > * matrix
virtual void assemble_qoi(const QoISet &qoi_indices=QoISet()) override
virtual void assemble_qoi_derivative(const QoISet &qoi_indices=QoISet(), bool include_liftfunc=true, bool apply_constraints=true) override
NumericVector< Number > & get_adjoint_solution(unsigned int i=0)
Definition: system.C:969
virtual std::pair< unsigned int, Real > weighted_sensitivity_adjoint_solve(const ParameterVector &parameters, const ParameterVector &weights, const QoISet &qoi_indices=QoISet()) override
NumericVector< Number > & get_weighted_sensitivity_adjoint_solution(unsigned int i=0)
Definition: system.C:1001
NumericVector< Number > & get_adjoint_rhs(unsigned int i=0)
Definition: system.C:1031

◆ qoi_parameter_sensitivity()

void libMesh::System::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].

Note
parameters is a const vector, not a vector-of-const; parameter values in this vector need to be mutable for finite differencing to work.

Automatically chooses the forward method for problems with more quantities of interest than parameters, or the adjoint method otherwise.

This method is only usable in derived classes which override an implementation.

Definition at line 498 of file system.C.

References libMesh::System::adjoint_qoi_parameter_sensitivity(), libMesh::System::forward_qoi_parameter_sensitivity(), libMesh::ParameterVector::size(), and libMesh::QoISet::size().

501 {
502  // Forward sensitivities are more efficient for Nq > Np
503  if (qoi_indices.size(*this) > parameters.size())
504  forward_qoi_parameter_sensitivity(qoi_indices, parameters, sensitivities);
505  // Adjoint sensitivities are more efficient for Np > Nq,
506  // and an adjoint may be more reusable than a forward
507  // solution sensitivity in the Np == Nq case.
508  else
509  adjoint_qoi_parameter_sensitivity(qoi_indices, parameters, sensitivities);
510 }
virtual void forward_qoi_parameter_sensitivity(const QoISet &qoi_indices, const ParameterVector &parameters, SensitivityData &sensitivities)
Definition: system.h:2325
virtual void adjoint_qoi_parameter_sensitivity(const QoISet &qoi_indices, const ParameterVector &parameters, SensitivityData &sensitivities)
Definition: system.h:2316

◆ re_update()

void libMesh::System::re_update ( )
virtualinherited

Re-update the local values when the mesh has changed. This method takes the data updated by update() and makes it up-to-date on the current mesh.

Reimplemented in libMesh::TransientSystem< RBConstruction >.

Definition at line 429 of file system.C.

References libMesh::System::current_local_solution, libMesh::System::get_dof_map(), libMesh::DofMap::get_send_list(), libMesh::System::n_vars(), and libMesh::System::solution.

430 {
431  parallel_object_only();
432 
433  // If this system is empty... don't do anything!
434  if (!this->n_vars())
435  return;
436 
437  const std::vector<dof_id_type> & send_list = this->get_dof_map().get_send_list ();
438 
439  // Check sizes
440  libmesh_assert_equal_to (current_local_solution->size(), solution->size());
441  // Not true with ghosted vectors
442  // libmesh_assert_equal_to (current_local_solution->local_size(), solution->size());
443  // libmesh_assert (!send_list.empty());
444  libmesh_assert_less_equal (send_list.size(), solution->size());
445 
446  // Create current_local_solution from solution. This will
447  // put a local copy of solution into current_local_solution.
448  solution->localize (*current_local_solution, send_list);
449 }
std::unique_ptr< NumericVector< Number > > solution
Definition: system.h:1523
std::unique_ptr< NumericVector< Number > > current_local_solution
Definition: system.h:1535
unsigned int n_vars() const
Definition: system.h:2105
const DofMap & get_dof_map() const
Definition: system.h:2049
const std::vector< dof_id_type > & get_send_list() const
Definition: dof_map.h:450

◆ read_header()

void libMesh::System::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 
)
inherited

Reads the basic data header for this System.

Definition at line 115 of file system_io.C.

References libMesh::System::_additional_data_written, libMesh::System::_written_var_indices, libMesh::System::add_variable(), libMesh::System::add_vector(), libMesh::Parallel::Communicator::broadcast(), libMesh::System::clear(), libMesh::ParallelObject::comm(), libMesh::Xdr::data(), libMesh::FEType::family, libMesh::System::get_mesh(), libMesh::OrderWrapper::get_order(), libMesh::FEType::inf_map, libMesh::MeshBase::mesh_dimension(), libMesh::MONOMIAL, libMesh::on_command_line(), libMesh::FEType::order, libMesh::out, libMesh::ParallelObject::processor_id(), libMesh::FEType::radial_family, libMesh::FEType::radial_order, libMesh::Xdr::reading(), libMesh::System::variable_number(), libMesh::Xdr::version(), and libMesh::XYZ.

Referenced by libMesh::EquationSystems::_read_impl().

120 {
121  // This method implements the input of a
122  // System object, embedded in the output of
123  // an EquationSystems<T_sys>. This warrants some
124  // documentation. The output file essentially
125  // consists of 5 sections:
126  //
127  // for this system
128  //
129  // 5.) The number of variables in the system (unsigned int)
130  //
131  // for each variable in the system
132  //
133  // 6.) The name of the variable (string)
134  //
135  // 6.1.) Variable subdomains
136  //
137  // 7.) Combined in an FEType:
138  // - The approximation order(s) of the variable
139  // (Order Enum, cast to int/s)
140  // - The finite element family/ies of the variable
141  // (FEFamily Enum, cast to int/s)
142  //
143  // end variable loop
144  //
145  // 8.) The number of additional vectors (unsigned int),
146  //
147  // for each additional vector in the system object
148  //
149  // 9.) the name of the additional vector (string)
150  //
151  // end system
152  libmesh_assert (io.reading());
153 
154  // Possibly clear data structures and start from scratch.
155  if (read_header_in)
156  this->clear ();
157 
158  // Figure out if we need to read infinite element information.
159  // This will be true if the version string contains " with infinite elements"
160  const bool read_ifem_info =
161  (version.rfind(" with infinite elements") < version.size()) ||
162  libMesh::on_command_line ("--read-ifem-systems");
163 
164 
165  {
166  // 5.)
167  // Read the number of variables in the system
168  unsigned int nv=0;
169  if (this->processor_id() == 0)
170  io.data (nv);
171  this->comm().broadcast(nv);
172 
173  _written_var_indices.clear();
174  _written_var_indices.resize(nv, 0);
175 
176  for (unsigned int var=0; var<nv; var++)
177  {
178  // 6.)
179  // Read the name of the var-th variable
180  std::string var_name;
181  if (this->processor_id() == 0)
182  io.data (var_name);
183  this->comm().broadcast(var_name);
184 
185  // 6.1.)
186  std::set<subdomain_id_type> domains;
187  if (io.version() >= LIBMESH_VERSION_ID(0,7,2))
188  {
189  std::vector<subdomain_id_type> domain_array;
190  if (this->processor_id() == 0)
191  io.data (domain_array);
192  for (const auto & id : domain_array)
193  domains.insert(id);
194  }
195  this->comm().broadcast(domains);
196 
197  // 7.)
198  // Read the approximation order(s) of the var-th variable
199  int order=0;
200  if (this->processor_id() == 0)
201  io.data (order);
202  this->comm().broadcast(order);
203 
204 
205  // do the same for infinite element radial_order
206  int rad_order=0;
207  if (read_ifem_info)
208  {
209  if (this->processor_id() == 0)
210  io.data(rad_order);
211  this->comm().broadcast(rad_order);
212  }
213 
214  // Read the finite element type of the var-th variable
215  int fam=0;
216  if (this->processor_id() == 0)
217  io.data (fam);
218  this->comm().broadcast(fam);
219  FEType type;
220  type.order = static_cast<Order>(order);
221  type.family = static_cast<FEFamily>(fam);
222 
223  // Check for incompatibilities. The shape function indexing was
224  // changed for the monomial and xyz finite element families to
225  // simplify extension to arbitrary p. The consequence is that
226  // old restart files will not be read correctly. This is expected
227  // to be an unlikely occurence, but catch it anyway.
228  if (read_legacy_format)
229  if ((type.family == MONOMIAL || type.family == XYZ) &&
230  ((type.order.get_order() > 2 && this->get_mesh().mesh_dimension() == 2) ||
231  (type.order.get_order() > 1 && this->get_mesh().mesh_dimension() == 3)))
232  {
233  libmesh_here();
234  libMesh::out << "*****************************************************************\n"
235  << "* WARNING: reading a potentially incompatible restart file!!! *\n"
236  << "* contact libmesh-users@lists.sourceforge.net for more details *\n"
237  << "*****************************************************************"
238  << std::endl;
239  }
240 
241  // Read additional information for infinite elements
242  int radial_fam=0;
243  int i_map=0;
244  if (read_ifem_info)
245  {
246  if (this->processor_id() == 0)
247  io.data (radial_fam);
248  this->comm().broadcast(radial_fam);
249  if (this->processor_id() == 0)
250  io.data (i_map);
251  this->comm().broadcast(i_map);
252  }
253 
254 #ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
255 
256  type.radial_order = static_cast<Order>(rad_order);
257  type.radial_family = static_cast<FEFamily>(radial_fam);
258  type.inf_map = static_cast<InfMapType>(i_map);
259 
260 #endif
261 
262  if (read_header_in)
263  {
264  if (domains.empty())
265  _written_var_indices[var] = this->add_variable (var_name, type);
266  else
267  _written_var_indices[var] = this->add_variable (var_name, type, &domains);
268  }
269  else
270  _written_var_indices[var] = this->variable_number(var_name);
271  }
272  }
273 
274  // 8.)
275  // Read the number of additional vectors.
276  unsigned int nvecs=0;
277  if (this->processor_id() == 0)
278  io.data (nvecs);
279  this->comm().broadcast(nvecs);
280 
281  // If nvecs > 0, this means that write_additional_data
282  // was true when this file was written. We will need to
283  // make use of this fact later.
284  this->_additional_data_written = nvecs;
285 
286  for (unsigned int vec=0; vec<nvecs; vec++)
287  {
288  // 9.)
289  // Read the name of the vec-th additional vector
290  std::string vec_name;
291  if (this->processor_id() == 0)
292  io.data (vec_name);
293  this->comm().broadcast(vec_name);
294 
295  if (read_additional_data)
296  {
297  // Systems now can handle adding post-initialization vectors
298  // libmesh_assert(this->_can_add_vectors);
299  // Some systems may have added their own vectors already
300  // libmesh_assert_equal_to (this->_vectors.count(vec_name), 0);
301 
302  this->add_vector(vec_name);
303  }
304  }
305 }
virtual void clear()
Definition: system.C:205
const Parallel::Communicator & comm() const
const MeshBase & get_mesh() const
Definition: system.h:2033
NumericVector< Number > & add_vector(const std::string &vec_name, const bool projections=true, const ParallelType type=PARALLEL)
Definition: system.C:661
unsigned short int variable_number(const std::string &var) const
Definition: system.C:1243
unsigned int _additional_data_written
Definition: system.h:1984
unsigned int mesh_dimension() const
Definition: mesh_base.C:126
bool on_command_line(std::string arg)
Definition: libmesh.C:876
unsigned int add_variable(const std::string &var, const FEType &type, const std::set< subdomain_id_type > *const active_subdomains=nullptr)
Definition: system.C:1081
processor_id_type processor_id() const
OStreamProxy out(std::cout)
void broadcast(T &data, const unsigned int root_id=0) const
std::vector< unsigned int > _written_var_indices
Definition: system.h:1996

◆ read_legacy_data()

void libMesh::System::read_legacy_data ( Xdr io,
const bool  read_additional_data = true 
)
inherited

Reads additional data, namely vectors, for this System.

Deprecated:
The ability to read XDR data files in the old (aka "legacy") XDR format has been deprecated for many years, this capability may soon disappear altogether.

Definition at line 310 of file system_io.C.

References libMesh::System::_additional_data_written, libMesh::System::_vectors, libMesh::System::_written_var_indices, libMesh::Parallel::Communicator::broadcast(), libMesh::ParallelObject::comm(), libMesh::Xdr::data(), libMesh::System::get_mesh(), libMesh::DofObject::invalid_id, libMesh::System::n_dofs(), libMesh::System::n_vars(), libMesh::System::number(), libMesh::ParallelObject::processor_id(), libMesh::Xdr::reading(), libMesh::System::solution, and libMesh::zero.

312 {
313  libmesh_deprecated();
314 
315  // This method implements the output of the vectors
316  // contained in this System object, embedded in the
317  // output of an EquationSystems<T_sys>.
318  //
319  // 10.) The global solution vector, re-ordered to be node-major
320  // (More on this later.)
321  //
322  // for each additional vector in the object
323  //
324  // 11.) The global additional vector, re-ordered to be
325  // node-major (More on this later.)
326  libmesh_assert (io.reading());
327 
328  // read and reordering buffers
329  std::vector<Number> global_vector;
330  std::vector<Number> reordered_vector;
331 
332  // 10.)
333  // Read and set the solution vector
334  {
335  if (this->processor_id() == 0)
336  io.data (global_vector);
337  this->comm().broadcast(global_vector);
338 
339  // Remember that the stored vector is node-major.
340  // We need to put it into whatever application-specific
341  // ordering we may have using the dof_map.
342  reordered_vector.resize(global_vector.size());
343 
344  //libMesh::out << "global_vector.size()=" << global_vector.size() << std::endl;
345  //libMesh::out << "this->n_dofs()=" << this->n_dofs() << std::endl;
346 
347  libmesh_assert_equal_to (global_vector.size(), this->n_dofs());
348 
349  dof_id_type cnt=0;
350 
351  const unsigned int sys = this->number();
352  const unsigned int nv = cast_int<unsigned int>
353  (this->_written_var_indices.size());
354  libmesh_assert_less_equal (nv, this->n_vars());
355 
356  for (unsigned int data_var=0; data_var<nv; data_var++)
357  {
358  const unsigned int var = _written_var_indices[data_var];
359 
360  // First reorder the nodal DOF values
361  for (auto & node : this->get_mesh().node_ptr_range())
362  for (unsigned int index=0; index<node->n_comp(sys,var); index++)
363  {
364  libmesh_assert_not_equal_to (node->dof_number(sys, var, index),
366 
367  libmesh_assert_less (cnt, global_vector.size());
368 
369  reordered_vector[node->dof_number(sys, var, index)] =
370  global_vector[cnt++];
371  }
372 
373  // Then reorder the element DOF values
374  for (auto & elem : this->get_mesh().active_element_ptr_range())
375  for (unsigned int index=0; index<elem->n_comp(sys,var); index++)
376  {
377  libmesh_assert_not_equal_to (elem->dof_number(sys, var, index),
379 
380  libmesh_assert_less (cnt, global_vector.size());
381 
382  reordered_vector[elem->dof_number(sys, var, index)] =
383  global_vector[cnt++];
384  }
385  }
386 
387  *(this->solution) = reordered_vector;
388  }
389 
390  // For each additional vector, simply go through the list.
391  // ONLY attempt to do this IF additional data was actually
392  // written to the file for this system (controlled by the
393  // _additional_data_written flag).
394  if (this->_additional_data_written)
395  {
396  const std::size_t nvecs = this->_vectors.size();
397 
398  // If the number of additional vectors written is non-zero, and
399  // the number of additional vectors we have is non-zero, and
400  // they don't match, then something is wrong and we can't be
401  // sure we're reading data into the correct places.
402  if (read_additional_data && nvecs &&
403  nvecs != this->_additional_data_written)
404  libmesh_error_msg
405  ("Additional vectors in file do not match system");
406 
407  std::map<std::string, NumericVector<Number> *>::iterator
408  pos = this->_vectors.begin();
409 
410  for (std::size_t i = 0; i != this->_additional_data_written; ++i)
411  {
412  // 11.)
413  // Read the values of the vec-th additional vector.
414  // Prior do _not_ clear, but fill with zero, since the
415  // additional vectors _have_ to have the same size
416  // as the solution vector
417  std::fill (global_vector.begin(), global_vector.end(), libMesh::zero);
418 
419  if (this->processor_id() == 0)
420  io.data (global_vector);
421 
422  // If read_additional_data==true and we have additional vectors,
423  // then we will keep this vector data; otherwise we are going to
424  // throw it away.
425  if (read_additional_data && nvecs)
426  {
427  this->comm().broadcast(global_vector);
428 
429  // Remember that the stored vector is node-major.
430  // We need to put it into whatever application-specific
431  // ordering we may have using the dof_map.
432  std::fill (reordered_vector.begin(),
433  reordered_vector.end(),
434  libMesh::zero);
435 
436  reordered_vector.resize(global_vector.size());
437 
438  libmesh_assert_equal_to (global_vector.size(), this->n_dofs());
439 
440  dof_id_type cnt=0;
441 
442  const unsigned int sys = this->number();
443  const unsigned int nv = cast_int<unsigned int>
444  (this->_written_var_indices.size());
445  libmesh_assert_less_equal (nv, this->n_vars());
446 
447  for (unsigned int data_var=0; data_var<nv; data_var++)
448  {
449  const unsigned int var = _written_var_indices[data_var];
450  // First reorder the nodal DOF values
451  for (auto & node : this->get_mesh().node_ptr_range())
452  for (unsigned int index=0; index<node->n_comp(sys,var); index++)
453  {
454  libmesh_assert_not_equal_to (node->dof_number(sys, var, index),
456 
457  libmesh_assert_less (cnt, global_vector.size());
458 
459  reordered_vector[node->dof_number(sys, var, index)] =
460  global_vector[cnt++];
461  }
462 
463  // Then reorder the element DOF values
464  for (auto & elem : this->get_mesh().active_element_ptr_range())
465  for (unsigned int index=0; index<elem->n_comp(sys,var); index++)
466  {
467  libmesh_assert_not_equal_to (elem->dof_number(sys, var, index),
469 
470  libmesh_assert_less (cnt, global_vector.size());
471 
472  reordered_vector[elem->dof_number(sys, var, index)] =
473  global_vector[cnt++];
474  }
475  }
476 
477  // use the overloaded operator=(std::vector) to assign the values
478  *(pos->second) = reordered_vector;
479  }
480 
481  // If we've got vectors then we need to be iterating through
482  // those too
483  if (pos != this->_vectors.end())
484  ++pos;
485  }
486  } // end if (_additional_data_written)
487 }
const Parallel::Communicator & comm() const
const Number zero
Definition: libmesh.h:239
const MeshBase & get_mesh() const
Definition: system.h:2033
dof_id_type n_dofs() const
Definition: system.C:150
unsigned int number() const
Definition: system.h:2025
std::unique_ptr< NumericVector< Number > > solution
Definition: system.h:1523
static const dof_id_type invalid_id
Definition: dof_object.h:347
unsigned int _additional_data_written
Definition: system.h:1984
std::map< std::string, NumericVector< Number > *> _vectors
Definition: system.h:1935
unsigned int n_vars() const
Definition: system.h:2105
processor_id_type processor_id() const
void broadcast(T &data, const unsigned int root_id=0) const
std::vector< unsigned int > _written_var_indices
Definition: system.h:1996
uint8_t dof_id_type
Definition: id_types.h:64

◆ read_parallel_data() [1/2]

template<typename InValType >
void libMesh::System::read_parallel_data ( Xdr io,
const bool  read_additional_data 
)
inherited

Reads additional data, namely vectors, for this System. This method may safely be called on a distributed-memory mesh. This method will read an individual file for each processor in the simulation where the local solution components for that processor are stored.

This method implements the output of the vectors contained in this System object, embedded in the output of an EquationSystems<T_sys>.

9.) The global solution vector, re-ordered to be node-major (More on this later.)

for each additional vector in the object

10.) The global additional vector, re-ordered to be node-major (More on this later.)

Note that the actual IO is handled through the Xdr class (to be renamed later?) which provides a uniform interface to both the XDR (eXternal Data Representation) interface and standard ASCII output. Thus this one section of code will read XDR or ASCII files with no changes.

Definition at line 493 of file system_io.C.

References libMesh::System::_additional_data_written, libMesh::System::_vectors, libMesh::System::_written_var_indices, libMesh::Xdr::data(), libMesh::FEType::family, libMesh::System::get_dof_map(), libMesh::System::get_mesh(), libMesh::DofObject::invalid_id, libMesh::Xdr::is_open(), libMesh::ParallelObject::n_processors(), libMesh::System::n_vars(), libMesh::System::number(), libMesh::ParallelObject::processor_id(), libMesh::Xdr::reading(), libMesh::SCALAR, libMesh::DofMap::SCALAR_dof_indices(), libMesh::System::solution, libMesh::Variable::type(), and libMesh::System::variable().

495 {
515  // PerfLog pl("IO Performance",false);
516  // pl.push("read_parallel_data");
517  dof_id_type total_read_size = 0;
518 
519  libmesh_assert (io.reading());
520  libmesh_assert (io.is_open());
521 
522  // build the ordered nodes and element maps.
523  // when writing/reading parallel files we need to iterate
524  // over our nodes/elements in order of increasing global id().
525  // however, this is not guaranteed to be ordering we obtain
526  // by using the node_iterators/element_iterators directly.
527  // so build a set, sorted by id(), that provides the ordering.
528  // further, for memory economy build the set but then transfer
529  // its contents to vectors, which will be sorted.
530  std::vector<const DofObject *> ordered_nodes, ordered_elements;
531  {
532  std::set<const DofObject *, CompareDofObjectsByID>
533  ordered_nodes_set (this->get_mesh().local_nodes_begin(),
534  this->get_mesh().local_nodes_end());
535 
536  ordered_nodes.insert(ordered_nodes.end(),
537  ordered_nodes_set.begin(),
538  ordered_nodes_set.end());
539  }
540  {
541  std::set<const DofObject *, CompareDofObjectsByID>
542  ordered_elements_set (this->get_mesh().local_elements_begin(),
543  this->get_mesh().local_elements_end());
544 
545  ordered_elements.insert(ordered_elements.end(),
546  ordered_elements_set.begin(),
547  ordered_elements_set.end());
548  }
549 
550  // std::vector<Number> io_buffer;
551  std::vector<InValType> io_buffer;
552 
553  // 9.)
554  //
555  // Actually read the solution components
556  // for the ith system to disk
557  io.data(io_buffer);
558 
559  total_read_size += cast_int<dof_id_type>(io_buffer.size());
560 
561  const unsigned int sys_num = this->number();
562  const unsigned int nv = cast_int<unsigned int>
563  (this->_written_var_indices.size());
564  libmesh_assert_less_equal (nv, this->n_vars());
565 
566  dof_id_type cnt=0;
567 
568  // Loop over each non-SCALAR variable and each node, and read out the value.
569  for (unsigned int data_var=0; data_var<nv; data_var++)
570  {
571  const unsigned int var = _written_var_indices[data_var];
572  if (this->variable(var).type().family != SCALAR)
573  {
574  // First read the node DOF values
575  for (const auto & node : ordered_nodes)
576  for (unsigned int comp=0; comp<node->n_comp(sys_num, var); comp++)
577  {
578  libmesh_assert_not_equal_to (node->dof_number(sys_num, var, comp),
580  libmesh_assert_less (cnt, io_buffer.size());
581  this->solution->set(node->dof_number(sys_num, var, comp), io_buffer[cnt++]);
582  }
583 
584  // Then read the element DOF values
585  for (const auto & elem : ordered_elements)
586  for (unsigned int comp=0; comp<elem->n_comp(sys_num, var); comp++)
587  {
588  libmesh_assert_not_equal_to (elem->dof_number(sys_num, var, comp),
590  libmesh_assert_less (cnt, io_buffer.size());
591  this->solution->set(elem->dof_number(sys_num, var, comp), io_buffer[cnt++]);
592  }
593  }
594  }
595 
596  // Finally, read the SCALAR variables on the last processor
597  for (unsigned int data_var=0; data_var<nv; data_var++)
598  {
599  const unsigned int var = _written_var_indices[data_var];
600  if (this->variable(var).type().family == SCALAR)
601  {
602  if (this->processor_id() == (this->n_processors()-1))
603  {
604  const DofMap & dof_map = this->get_dof_map();
605  std::vector<dof_id_type> SCALAR_dofs;
606  dof_map.SCALAR_dof_indices(SCALAR_dofs, var);
607 
608  for (std::size_t i=0; i<SCALAR_dofs.size(); i++)
609  this->solution->set(SCALAR_dofs[i], io_buffer[cnt++]);
610  }
611  }
612  }
613 
614  // And we're done setting solution entries
615  this->solution->close();
616 
617  // For each additional vector, simply go through the list.
618  // ONLY attempt to do this IF additional data was actually
619  // written to the file for this system (controlled by the
620  // _additional_data_written flag).
621  if (this->_additional_data_written)
622  {
623  const std::size_t nvecs = this->_vectors.size();
624 
625  // If the number of additional vectors written is non-zero, and
626  // the number of additional vectors we have is non-zero, and
627  // they don't match, then something is wrong and we can't be
628  // sure we're reading data into the correct places.
629  if (read_additional_data && nvecs &&
630  nvecs != this->_additional_data_written)
631  libmesh_error_msg
632  ("Additional vectors in file do not match system");
633 
634  std::map<std::string, NumericVector<Number> *>::const_iterator
635  pos = _vectors.begin();
636 
637  for (std::size_t i = 0; i != this->_additional_data_written; ++i)
638  {
639  cnt=0;
640  io_buffer.clear();
641 
642  // 10.)
643  //
644  // Actually read the additional vector components
645  // for the ith system from disk
646  io.data(io_buffer);
647 
648  total_read_size += cast_int<dof_id_type>(io_buffer.size());
649 
650  // If read_additional_data==true and we have additional vectors,
651  // then we will keep this vector data; otherwise we are going to
652  // throw it away.
653  if (read_additional_data && nvecs)
654  {
655  // Loop over each non-SCALAR variable and each node, and read out the value.
656  for (unsigned int data_var=0; data_var<nv; data_var++)
657  {
658  const unsigned int var = _written_var_indices[data_var];
659  if (this->variable(var).type().family != SCALAR)
660  {
661  // First read the node DOF values
662  for (const auto & node : ordered_nodes)
663  for (unsigned int comp=0; comp<node->n_comp(sys_num, var); comp++)
664  {
665  libmesh_assert_not_equal_to (node->dof_number(sys_num, var, comp),
667  libmesh_assert_less (cnt, io_buffer.size());
668  pos->second->set(node->dof_number(sys_num, var, comp), io_buffer[cnt++]);
669  }
670 
671  // Then read the element DOF values
672  for (const auto & elem : ordered_elements)
673  for (unsigned int comp=0; comp<elem->n_comp(sys_num, var); comp++)
674  {
675  libmesh_assert_not_equal_to (elem->dof_number(sys_num, var, comp),
677  libmesh_assert_less (cnt, io_buffer.size());
678  pos->second->set(elem->dof_number(sys_num, var, comp), io_buffer[cnt++]);
679  }
680  }
681  }
682 
683  // Finally, read the SCALAR variables on the last processor
684  for (unsigned int data_var=0; data_var<nv; data_var++)
685  {
686  const unsigned int var = _written_var_indices[data_var];
687  if (this->variable(var).type().family == SCALAR)
688  {
689  if (this->processor_id() == (this->n_processors()-1))
690  {
691  const DofMap & dof_map = this->get_dof_map();
692  std::vector<dof_id_type> SCALAR_dofs;
693  dof_map.SCALAR_dof_indices(SCALAR_dofs, var);
694 
695  for (std::size_t sd=0; sd<SCALAR_dofs.size(); sd++)
696  pos->second->set(SCALAR_dofs[sd], io_buffer[cnt++]);
697  }
698  }
699  }
700 
701  // And we're done setting entries for this variable
702  pos->second->close();
703  }
704 
705  // If we've got vectors then we need to be iterating through
706  // those too
707  if (pos != this->_vectors.end())
708  ++pos;
709  }
710  }
711 
712  // const Real
713  // dt = pl.get_elapsed_time(),
714  // rate = total_read_size*sizeof(Number)/dt;
715 
716  // libMesh::err << "Read " << total_read_size << " \"Number\" values\n"
717  // << " Elapsed time = " << dt << '\n'
718  // << " Rate = " << rate/1.e6 << "(MB/sec)\n\n";
719 
720  // pl.pop("read_parallel_data");
721 }
FEFamily family
Definition: fe_type.h:204
const Variable & variable(unsigned int var) const
Definition: system.h:2133
const MeshBase & get_mesh() const
Definition: system.h:2033
processor_id_type n_processors() const
unsigned int number() const
Definition: system.h:2025
std::unique_ptr< NumericVector< Number > > solution
Definition: system.h:1523
static const dof_id_type invalid_id
Definition: dof_object.h:347
unsigned int _additional_data_written
Definition: system.h:1984
std::map< std::string, NumericVector< Number > *> _vectors
Definition: system.h:1935
unsigned int n_vars() const
Definition: system.h:2105
processor_id_type processor_id() const
const DofMap & get_dof_map() const
Definition: system.h:2049
std::vector< unsigned int > _written_var_indices
Definition: system.h:1996
uint8_t dof_id_type
Definition: id_types.h:64
const FEType & type() const
Definition: variable.h:119

◆ read_parallel_data() [2/2]

template void libMesh::System::read_parallel_data< Real > ( Xdr io,
const bool  read_additional_data 
)
inlineinherited

Non-templated version for backward compatibility.

Reads additional data, namely vectors, for this System. This method may safely be called on a distributed-memory mesh. This method will read an individual file for each processor in the simulation where the local solution components for that processor are stored.

Definition at line 1299 of file system.h.

1301  { read_parallel_data<Number>(io, read_additional_data); }

◆ read_serialized_data() [1/2]

template<typename InValType >
void libMesh::System::read_serialized_data ( Xdr io,
const bool  read_additional_data = true 
)
inherited

Reads additional data, namely vectors, for this System. This method may safely be called on a distributed-memory mesh.

Definition at line 725 of file system_io.C.

References libMesh::System::_additional_data_written, libMesh::System::_vectors, libMesh::ParallelObject::processor_id(), and libMesh::System::solution.

727 {
728  // This method implements the input of the vectors
729  // contained in this System object, embedded in the
730  // output of an EquationSystems<T_sys>.
731  //
732  // 10.) The global solution vector, re-ordered to be node-major
733  // (More on this later.)
734  //
735  // for each additional vector in the object
736  //
737  // 11.) The global additional vector, re-ordered to be
738  // node-major (More on this later.)
739  parallel_object_only();
740  std::string comment;
741 
742  // PerfLog pl("IO Performance",false);
743  // pl.push("read_serialized_data");
744  // std::size_t total_read_size = 0;
745 
746  // 10.)
747  // Read the global solution vector
748  {
749  // total_read_size +=
750  this->read_serialized_vector<InValType>(io, this->solution.get());
751 
752  // get the comment
753  if (this->processor_id() == 0)
754  io.comment (comment);
755  }
756 
757  // 11.)
758  // Only read additional vectors if data is available, and only use
759  // that data to fill our vectors if the user requested it.
760  if (this->_additional_data_written)
761  {
762  const std::size_t nvecs = this->_vectors.size();
763 
764  // If the number of additional vectors written is non-zero, and
765  // the number of additional vectors we have is non-zero, and
766  // they don't match, then we can't read additional vectors
767  // and be sure we're reading data into the correct places.
768  if (read_additional_data && nvecs &&
769  nvecs != this->_additional_data_written)
770  libmesh_error_msg
771  ("Additional vectors in file do not match system");
772 
773  std::map<std::string, NumericVector<Number> *>::const_iterator
774  pos = _vectors.begin();
775 
776  for (std::size_t i = 0; i != this->_additional_data_written; ++i)
777  {
778  // Read data, but only put it into a vector if we've been
779  // asked to and if we have a corresponding vector to read.
780 
781  // total_read_size +=
782  this->read_serialized_vector<InValType>
783  (io, (read_additional_data && nvecs) ? pos->second : nullptr);
784 
785  // get the comment
786  if (this->processor_id() == 0)
787  io.comment (comment);
788 
789 
790  // If we've got vectors then we need to be iterating through
791  // those too
792  if (pos != this->_vectors.end())
793  ++pos;
794  }
795  }
796 
797  // const Real
798  // dt = pl.get_elapsed_time(),
799  // rate = total_read_size*sizeof(Number)/dt;
800 
801  // libMesh::out << "Read " << total_read_size << " \"Number\" values\n"
802  // << " Elapsed time = " << dt << '\n'
803  // << " Rate = " << rate/1.e6 << "(MB/sec)\n\n";
804 
805  // pl.pop("read_serialized_data");
806 }
std::unique_ptr< NumericVector< Number > > solution
Definition: system.h:1523
unsigned int _additional_data_written
Definition: system.h:1984
std::map< std::string, NumericVector< Number > *> _vectors
Definition: system.h:1935
processor_id_type processor_id() const

◆ read_serialized_data() [2/2]

template void libMesh::System::read_serialized_data< Real > ( Xdr io,
const bool  read_additional_data = true 
)
inlineinherited

Non-templated version for backward compatibility.

Reads additional data, namely vectors, for this System. This method may safely be called on a distributed-memory mesh.

Definition at line 1257 of file system.h.

1259  { read_serialized_data<Number>(io, read_additional_data); }

◆ read_serialized_vectors() [1/2]

template<typename InValType >
std::size_t libMesh::System::read_serialized_vectors ( Xdr io,
const std::vector< NumericVector< Number > *> &  vectors 
) const
inherited

Read a number of identically distributed vectors. This method allows for optimization for the multiple vector case by only communicating the metadata once.

Definition at line 2203 of file system_io.C.

References libMesh::Xdr::data(), libMesh::FEType::family, libMesh::System::get_mesh(), libMesh::MeshBase::n_elem(), libMesh::MeshTools::n_elem(), n_nodes, libMesh::MeshBase::n_nodes(), libMesh::System::n_vars(), libMesh::ParallelObject::processor_id(), libMesh::System::read_SCALAR_dofs(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::Xdr::reading(), libMesh::SCALAR, libMesh::Variable::type(), and libMesh::System::variable().

2205 {
2206  parallel_object_only();
2207 
2208  // Error checking
2209  // #ifndef NDEBUG
2210  // // In parallel we better be reading a parallel vector -- if not
2211  // // we will not set all of its components below!!
2212  // if (this->n_processors() > 1)
2213  // {
2214  // libmesh_assert (vec.type() == PARALLEL ||
2215  // vec.type() == GHOSTED);
2216  // }
2217  // #endif
2218 
2219  libmesh_assert (io.reading());
2220 
2221  if (this->processor_id() == 0)
2222  {
2223  // sizes
2224  unsigned int num_vecs=0;
2225  dof_id_type vector_length=0;
2226 
2227  // Get the number of vectors
2228  io.data(num_vecs);
2229  // Get the buffer size
2230  io.data(vector_length);
2231 
2232  libmesh_assert_equal_to (num_vecs, vectors.size());
2233 
2234  if (num_vecs != 0)
2235  {
2236  libmesh_assert_not_equal_to (vectors[0], 0);
2237  libmesh_assert_equal_to (vectors[0]->size(), vector_length);
2238  }
2239  }
2240 
2241  // no need to actually communicate these.
2242  // this->comm().broadcast(num_vecs);
2243  // this->comm().broadcast(vector_length);
2244 
2245  // Cache these - they are not free!
2246  const dof_id_type
2247  n_nodes = this->get_mesh().n_nodes(),
2248  n_elem = this->get_mesh().n_elem();
2249 
2250  std::size_t read_length = 0;
2251 
2252  //---------------------------------
2253  // Collect the values for all nodes
2254  read_length +=
2255  this->read_serialized_blocked_dof_objects (n_nodes,
2256  this->get_mesh().local_nodes_begin(),
2257  this->get_mesh().local_nodes_end(),
2258  InValType(),
2259  io,
2260  vectors);
2261 
2262  //------------------------------------
2263  // Collect the values for all elements
2264  read_length +=
2266  this->get_mesh().local_elements_begin(),
2267  this->get_mesh().local_elements_end(),
2268  InValType(),
2269  io,
2270  vectors);
2271 
2272  //-------------------------------------------
2273  // Finally loop over all the SCALAR variables
2274  for (std::size_t vec=0; vec<vectors.size(); vec++)
2275  for (unsigned int var=0; var<this->n_vars(); var++)
2276  if (this->variable(var).type().family == SCALAR)
2277  {
2278  libmesh_assert_not_equal_to (vectors[vec], 0);
2279 
2280  read_length +=
2281  this->read_SCALAR_dofs (var, io, vectors[vec]);
2282  }
2283 
2284  //---------------------------------------
2285  // last step - must close all the vectors
2286  for (std::size_t vec=0; vec<vectors.size(); vec++)
2287  {
2288  libmesh_assert_not_equal_to (vectors[vec], 0);
2289  vectors[vec]->close();
2290  }
2291 
2292  return read_length;
2293 }
FEFamily family
Definition: fe_type.h:204
const Variable & variable(unsigned int var) const
Definition: system.h:2133
dof_id_type n_elem(const MeshBase::const_element_iterator &begin, const MeshBase::const_element_iterator &end)
Definition: mesh_tools.C:702
std::size_t read_serialized_blocked_dof_objects(const dof_id_type n_objects, const iterator_type begin, const iterator_type end, const InValType dummy, Xdr &io, const std::vector< NumericVector< Number > *> &vecs, const unsigned int var_to_read=libMesh::invalid_uint) const
Definition: system_io.C:811
const MeshBase & get_mesh() const
Definition: system.h:2033
const dof_id_type n_nodes
Definition: tecplot_io.C:68
unsigned int read_SCALAR_dofs(const unsigned int var, Xdr &io, NumericVector< Number > *vec) const
Definition: system_io.C:1121
unsigned int n_vars() const
Definition: system.h:2105
virtual dof_id_type n_elem() const =0
processor_id_type processor_id() const
virtual dof_id_type n_nodes() const =0
uint8_t dof_id_type
Definition: id_types.h:64
const FEType & type() const
Definition: variable.h:119

◆ read_serialized_vectors() [2/2]

template std::size_t libMesh::System::read_serialized_vectors< Real > ( Xdr io,
const std::vector< NumericVector< Number > *> &  vectors 
) const
inlineinherited

Non-templated version for backward compatibility.

Read a number of identically distributed vectors. This method allows for optimization for the multiple vector case by only communicating the metadata once.

Definition at line 1277 of file system.h.

1279  { return read_serialized_vectors<Number>(io, vectors); }

◆ reinit()

void libMesh::DifferentiableSystem::reinit ( )
overridevirtualinherited

Reinitializes the member data fields associated with the system, so that, e.g., assemble() may be used.

Reimplemented from libMesh::ImplicitSystem.

Definition at line 96 of file diff_system.C.

References libMesh::ImplicitSystem::reinit(), and libMesh::DifferentiableSystem::time_solver.

97 {
99 
100  libmesh_assert(time_solver.get());
101  libmesh_assert_equal_to (&(time_solver->system()), this);
102 
103  time_solver->reinit();
104 }
virtual void reinit() override
std::unique_ptr< TimeSolver > time_solver
Definition: diff_system.h:234

◆ reinit_constraints()

void libMesh::System::reinit_constraints ( )
virtualinherited

Reinitializes the constraints for this system.

Definition at line 397 of file system.C.

References libMesh::System::_mesh, libMesh::DofMap::create_dof_constraints(), libMesh::System::get_dof_map(), libMesh::DofMap::prepare_send_list(), libMesh::DofMap::process_constraints(), libMesh::System::time, and libMesh::System::user_constrain().

Referenced by libMesh::EquationSystems::allgather(), libMesh::System::init_data(), and libMesh::EquationSystems::reinit_solutions().

398 {
399 #ifdef LIBMESH_ENABLE_CONSTRAINTS
401  user_constrain();
403 #endif
405 }
void process_constraints(MeshBase &)
void create_dof_constraints(const MeshBase &, Real time=0)
void prepare_send_list()
Definition: dof_map.C:1639
virtual void user_constrain()
Definition: system.C:1946
const DofMap & get_dof_map() const
Definition: system.h:2049
MeshBase & _mesh
Definition: system.h:1896

◆ release_linear_solver()

void libMesh::DifferentiableSystem::release_linear_solver ( LinearSolver< Number > *  ) const
overridevirtualinherited

Releases a pointer to a linear solver acquired by this->get_linear_solver()

Reimplemented from libMesh::ImplicitSystem.

Definition at line 194 of file diff_system.C.

195 {
196 }

◆ remove_matrix()

void libMesh::ImplicitSystem::remove_matrix ( const std::string &  mat_name)
inherited

Removes the additional matrix mat_name from this system

Definition at line 222 of file implicit_system.C.

References libMesh::ImplicitSystem::_matrices.

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

223 {
224  matrices_iterator pos = _matrices.find (mat_name);
225 
226  //Return if the matrix does not exist
227  if (pos == _matrices.end())
228  return;
229 
230  delete pos->second;
231 
232  _matrices.erase(pos);
233 }
std::map< std::string, SparseMatrix< Number > * > _matrices
std::map< std::string, SparseMatrix< Number > * >::iterator matrices_iterator

◆ remove_vector()

void libMesh::System::remove_vector ( const std::string &  vec_name)
inherited

Removes the additional vector vec_name from this system

Definition at line 699 of file system.C.

References libMesh::System::_vector_is_adjoint, libMesh::System::_vector_projections, libMesh::System::_vector_types, and libMesh::System::_vectors.

700 {
701  vectors_iterator pos = _vectors.find(vec_name);
702 
703  //Return if the vector does not exist
704  if (pos == _vectors.end())
705  return;
706 
707  delete pos->second;
708 
709  _vectors.erase(pos);
710 
711  _vector_projections.erase(vec_name);
712  _vector_is_adjoint.erase(vec_name);
713  _vector_types.erase(vec_name);
714 }
std::map< std::string, ParallelType > _vector_types
Definition: system.h:1952
std::map< std::string, int > _vector_is_adjoint
Definition: system.h:1947
std::map< std::string, NumericVector< Number > * >::iterator vectors_iterator
Definition: system.h:748
std::map< std::string, NumericVector< Number > *> _vectors
Definition: system.h:1935
std::map< std::string, bool > _vector_projections
Definition: system.h:1941

◆ request_matrix() [1/2]

const SparseMatrix< Number > * libMesh::ImplicitSystem::request_matrix ( const std::string &  mat_name) const
inherited
Returns
A const pointer to this system's additional matrix named mat_name, or nullptr if no matrix by that name exists.

Definition at line 237 of file implicit_system.C.

References libMesh::ImplicitSystem::_matrices.

Referenced by libMesh::ImplicitSystem::sensitivity_solve(), libMesh::NewtonSolver::solve(), and libMesh::LinearImplicitSystem::solve().

238 {
239  // Make sure the matrix exists
240  const_matrices_iterator pos = _matrices.find (mat_name);
241 
242  if (pos == _matrices.end())
243  return nullptr;
244 
245  return pos->second;
246 }
std::map< std::string, SparseMatrix< Number > * > _matrices
std::map< std::string, SparseMatrix< Number > * >::const_iterator const_matrices_iterator

◆ request_matrix() [2/2]

SparseMatrix< Number > * libMesh::ImplicitSystem::request_matrix ( const std::string &  mat_name)
inherited
Returns
A writable pointer to this system's additional matrix named mat_name, or nullptr if no matrix by that name exists.

Definition at line 250 of file implicit_system.C.

References libMesh::ImplicitSystem::_matrices.

251 {
252  // Make sure the matrix exists
253  matrices_iterator pos = _matrices.find (mat_name);
254 
255  if (pos == _matrices.end())
256  return nullptr;
257 
258  return pos->second;
259 }
std::map< std::string, SparseMatrix< Number > * > _matrices
std::map< std::string, SparseMatrix< Number > * >::iterator matrices_iterator

◆ request_vector() [1/4]

const NumericVector< Number > * libMesh::System::request_vector ( const std::string &  vec_name) const
inherited
Returns
A const pointer to the vector if this System has a vector associated with the given name, nullptr otherwise.

Definition at line 716 of file system.C.

References libMesh::System::_vectors.

Referenced by libMesh::UniformRefinementEstimator::_estimate_error().

717 {
718  const_vectors_iterator pos = _vectors.find(vec_name);
719 
720  if (pos == _vectors.end())
721  return nullptr;
722 
723  return pos->second;
724 }
std::map< std::string, NumericVector< Number > * >::const_iterator const_vectors_iterator
Definition: system.h:749
std::map< std::string, NumericVector< Number > *> _vectors
Definition: system.h:1935

◆ request_vector() [2/4]

NumericVector< Number > * libMesh::System::request_vector ( const std::string &  vec_name)
inherited
Returns
A pointer to the vector if this System has a vector associated with the given name, nullptr otherwise.

Definition at line 728 of file system.C.

References libMesh::System::_vectors.

729 {
730  vectors_iterator pos = _vectors.find(vec_name);
731 
732  if (pos == _vectors.end())
733  return nullptr;
734 
735  return pos->second;
736 }
std::map< std::string, NumericVector< Number > * >::iterator vectors_iterator
Definition: system.h:748
std::map< std::string, NumericVector< Number > *> _vectors
Definition: system.h:1935

◆ request_vector() [3/4]

const NumericVector< Number > * libMesh::System::request_vector ( const unsigned int  vec_num) const
inherited
Returns
A const pointer to this system's additional vector number vec_num (where the vectors are counted starting with 0), or nullptr if the system has no such vector.

Definition at line 740 of file system.C.

References libMesh::System::vectors_begin(), and libMesh::System::vectors_end().

741 {
744  unsigned int num = 0;
745  while ((num<vec_num) && (v!=v_end))
746  {
747  num++;
748  ++v;
749  }
750  if (v==v_end)
751  return nullptr;
752  return v->second;
753 }
vectors_iterator vectors_end()
Definition: system.h:2257
std::map< std::string, NumericVector< Number > * >::const_iterator const_vectors_iterator
Definition: system.h:749
vectors_iterator vectors_begin()
Definition: system.h:2245

◆ request_vector() [4/4]

NumericVector< Number > * libMesh::System::request_vector ( const unsigned int  vec_num)
inherited
Returns
A writable pointer to this system's additional vector number vec_num (where the vectors are counted starting with 0), or nullptr if the system has no such vector.

Definition at line 757 of file system.C.

References libMesh::System::vectors_begin(), and libMesh::System::vectors_end().

758 {
760  vectors_iterator v_end = vectors_end();
761  unsigned int num = 0;
762  while ((num<vec_num) && (v!=v_end))
763  {
764  num++;
765  ++v;
766  }
767  if (v==v_end)
768  return nullptr;
769  return v->second;
770 }
vectors_iterator vectors_end()
Definition: system.h:2257
vectors_iterator vectors_begin()
Definition: system.h:2245
std::map< std::string, NumericVector< Number > * >::iterator vectors_iterator
Definition: system.h:748

◆ restrict_solve_to()

void libMesh::System::restrict_solve_to ( const SystemSubset subset,
const SubsetSolveMode  subset_solve_mode = SUBSET_ZERO 
)
virtualinherited

After calling this method, any solve will be restricted to the given subdomain. To disable this mode, call this method with subset being a nullptr.

Reimplemented in libMesh::LinearImplicitSystem.

Definition at line 453 of file system.C.

455 {
456  if (subset != nullptr)
457  libmesh_not_implemented();
458 }

◆ restrict_vectors()

void libMesh::System::restrict_vectors ( )
virtualinherited

Restrict vectors after the mesh has coarsened

Definition at line 324 of file system.C.

References libMesh::System::_dof_map, libMesh::System::_solution_projection, libMesh::System::_vector_projections, libMesh::System::_vector_types, libMesh::System::_vectors, libMesh::System::current_local_solution, libMesh::GHOSTED, libMesh::System::n_dofs(), libMesh::System::n_local_dofs(), libMesh::PARALLEL, libMesh::System::project_vector(), libMesh::System::solution, and libMesh::System::vector_is_adjoint().

Referenced by libMesh::System::prolong_vectors(), and libMesh::EquationSystems::reinit_solutions().

325 {
326 #ifdef LIBMESH_ENABLE_AMR
327  // Restrict the _vectors on the coarsened cells
328  for (auto & pr : _vectors)
329  {
330  NumericVector<Number> * v = pr.second;
331 
332  if (_vector_projections[pr.first])
333  {
334  this->project_vector (*v, this->vector_is_adjoint(pr.first));
335  }
336  else
337  {
338  ParallelType type = _vector_types[pr.first];
339 
340  if (type == GHOSTED)
341  {
342 #ifdef LIBMESH_ENABLE_GHOSTED
343  pr.second->init (this->n_dofs(), this->n_local_dofs(),
344  _dof_map->get_send_list(), false,
345  GHOSTED);
346 #else
347  libmesh_error_msg("Cannot initialize ghosted vectors when they are not enabled.");
348 #endif
349  }
350  else
351  pr.second->init (this->n_dofs(), this->n_local_dofs(), false, type);
352  }
353  }
354 
355  const std::vector<dof_id_type> & send_list = _dof_map->get_send_list ();
356 
357  // Restrict the solution on the coarsened cells
359  this->project_vector (*solution);
360  // Or at least make sure the solution vector is the correct size
361  else
362  solution->init (this->n_dofs(), this->n_local_dofs(), true, PARALLEL);
363 
364 #ifdef LIBMESH_ENABLE_GHOSTED
365  current_local_solution->init(this->n_dofs(),
366  this->n_local_dofs(), send_list,
367  false, GHOSTED);
368 #else
369  current_local_solution->init(this->n_dofs());
370 #endif
371 
373  solution->localize (*current_local_solution, send_list);
374 
375 #endif // LIBMESH_ENABLE_AMR
376 }
std::map< std::string, ParallelType > _vector_types
Definition: system.h:1952
int vector_is_adjoint(const std::string &vec_name) const
Definition: system.C:896
std::unique_ptr< DofMap > _dof_map
Definition: system.h:1884
dof_id_type n_local_dofs() const
Definition: system.C:187
dof_id_type n_dofs() const
Definition: system.C:150
std::unique_ptr< NumericVector< Number > > solution
Definition: system.h:1523
bool _solution_projection
Definition: system.h:1959
std::map< std::string, NumericVector< Number > *> _vectors
Definition: system.h:1935
std::map< std::string, bool > _vector_projections
Definition: system.h:1941
std::unique_ptr< NumericVector< Number > > current_local_solution
Definition: system.h:1535
void project_vector(NumericVector< Number > &new_vector, FunctionBase< Number > *f, FunctionBase< Gradient > *g=nullptr, int is_adjoint=-1) const

◆ sensitivity_solve()

std::pair< unsigned int, Real > libMesh::ImplicitSystem::sensitivity_solve ( const ParameterVector parameters)
overridevirtualinherited

Assembles & solves the linear system(s) (dR/du)*u_p = -dR/dp, for those parameters contained within parameters.

Returns
A pair with the total number of linear iterations performed and the (sum of the) final residual norms

Reimplemented from libMesh::System.

Definition at line 314 of file implicit_system.C.

References libMesh::System::add_sensitivity_solution(), libMesh::System::assemble_before_solve, libMesh::ImplicitSystem::assemble_residual_derivatives(), libMesh::ImplicitSystem::assembly(), libMesh::SparseMatrix< T >::close(), libMesh::DofMap::enforce_constraints_exactly(), libMesh::System::get_dof_map(), libMesh::ImplicitSystem::get_linear_solve_parameters(), libMesh::ImplicitSystem::get_linear_solver(), libMesh::System::get_sensitivity_rhs(), libMesh::System::get_sensitivity_solution(), libMesh::ImplicitSystem::matrix, libMesh::ImplicitSystem::release_linear_solver(), libMesh::ImplicitSystem::request_matrix(), libMesh::ParameterVector::size(), and libMesh::LinearSolver< T >::solve().

Referenced by libMesh::ImplicitSystem::forward_qoi_parameter_sensitivity(), and libMesh::ImplicitSystem::qoi_parameter_hessian().

315 {
316  // Log how long the linear solve takes.
317  LOG_SCOPE("sensitivity_solve()", "ImplicitSystem");
318 
319  // The forward system should now already be solved.
320  // Now assemble the corresponding sensitivity system.
321 
322  if (this->assemble_before_solve)
323  {
324  // Build the Jacobian
325  this->assembly(false, true);
326  this->matrix->close();
327 
328  // Reset and build the RHS from the residual derivatives
329  this->assemble_residual_derivatives(parameters);
330  }
331 
332  // The sensitivity problem is linear
333  LinearSolver<Number> * linear_solver = this->get_linear_solver();
334 
335  // Our iteration counts and residuals will be sums of the individual
336  // results
337  std::pair<unsigned int, Real> solver_params =
339  std::pair<unsigned int, Real> totalrval = std::make_pair(0,0.0);
340 
341  // Solve the linear system.
342  SparseMatrix<Number> * pc = this->request_matrix("Preconditioner");
343  for (auto p : IntRange<unsigned int>(0, parameters.size()))
344  {
345  std::pair<unsigned int, Real> rval =
346  linear_solver->solve (*matrix, pc,
347  this->add_sensitivity_solution(p),
348  this->get_sensitivity_rhs(p),
349  solver_params.second,
350  solver_params.first);
351 
352  totalrval.first += rval.first;
353  totalrval.second += rval.second;
354  }
355 
356  // The linear solver may not have fit our constraints exactly
357 #ifdef LIBMESH_ENABLE_CONSTRAINTS
358  for (auto p : IntRange<unsigned int>(0, parameters.size()))
360  (*this, &this->get_sensitivity_solution(p),
361  /* homogeneous = */ true);
362 #endif
363 
364  this->release_linear_solver(linear_solver);
365 
366  return totalrval;
367 }
virtual std::pair< unsigned int, Real > get_linear_solve_parameters() const
NumericVector< Number > & get_sensitivity_solution(unsigned int i=0)
Definition: system.C:916
NumericVector< Number > & get_sensitivity_rhs(unsigned int i=0)
Definition: system.C:1061
virtual LinearSolver< Number > * get_linear_solver() const
virtual void release_linear_solver(LinearSolver< Number > *) const
virtual void assembly(bool, bool, bool=false, bool=false)
const SparseMatrix< Number > * request_matrix(const std::string &mat_name) const
virtual void close()=0
SparseMatrix< Number > * matrix
virtual void assemble_residual_derivatives(const ParameterVector &parameters) override
NumericVector< Number > & add_sensitivity_solution(unsigned int i=0)
Definition: system.C:906
bool assemble_before_solve
Definition: system.h:1477
const DofMap & get_dof_map() const
Definition: system.h:2049
void enforce_constraints_exactly(const System &system, NumericVector< Number > *v=nullptr, bool homogeneous=false) const

◆ set_adjoint_already_solved()

void libMesh::System::set_adjoint_already_solved ( bool  setting)
inlineinherited

Setter for the adjoint_already_solved boolean

Definition at line 394 of file system.h.

References libMesh::System::adjoint_already_solved.

395  { adjoint_already_solved = setting;}
bool adjoint_already_solved
Definition: system.h:2003

◆ set_basic_system_only()

void libMesh::System::set_basic_system_only ( )
inlineinherited

Sets the system to be "basic only": i.e. advanced system components such as ImplicitSystem matrices may not be initialized. This is useful for efficiency in certain utility programs that never use System::solve(). This method must be called after the System or derived class is created but before it is initialized; e.g. from within EquationSystems::read()

Definition at line 2097 of file system.h.

References libMesh::System::_basic_system_only.

Referenced by libMesh::EquationSystems::_read_impl().

2098 {
2099  _basic_system_only = true;
2100 }
bool _basic_system_only
Definition: system.h:1965

◆ set_mesh_system()

void libMesh::DifferentiablePhysics::set_mesh_system ( System sys)
inlinevirtualinherited

Tells the DifferentiablePhysics that system sys contains the isoparametric Lagrangian variables which correspond to the coordinates of mesh nodes, in problems where the mesh itself is expected to move in time.

The system with mesh coordinate data (which may be this system itself, for fully coupled moving mesh problems) is currently assumed to have new (end of time step) mesh coordinates stored in solution, old (beginning of time step) mesh coordinates stored in _old_nonlinear_solution, and constant velocity motion during each time step.

Activating this function ensures that local (but not neighbor!) element geometry is correctly repositioned when evaluating element residuals.

Currently sys must be *this for a tightly coupled moving mesh problem or nullptr to stop mesh movement; loosely coupled moving mesh problems are not implemented.

This code is experimental. "Trust but verify, and not in that order"

Definition at line 580 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_mesh_sys.

581 {
582  // For now we assume that we're doing fully coupled mesh motion
583  // if (sys && sys != this)
584  // libmesh_not_implemented();
585 
586  // For the foreseeable future we'll assume that we keep these
587  // Systems in the same EquationSystems
588  // libmesh_assert_equal_to (&this->get_equation_systems(),
589  // &sys->get_equation_systems());
590 
591  // And for the immediate future this code may not even work
592  libmesh_experimental();
593 
594  _mesh_sys = sys;
595 }

◆ set_mesh_x_var()

void libMesh::DifferentiablePhysics::set_mesh_x_var ( unsigned int  var)
inlinevirtualinherited

Tells the DifferentiablePhysics that variable var from the mesh system should be used to update the x coordinate of mesh nodes, in problems where the mesh itself is expected to move in time.

The system with mesh coordinate data (which may be this system itself, for fully coupled moving mesh problems) is currently assumed to have new (end of time step) mesh coordinates stored in solution, old (beginning of time step) mesh coordinates stored in _old_nonlinear_solution, and constant velocity motion during each time step.

Activating this function ensures that local (but not neighbor!) element geometry is correctly repositioned when evaluating element residuals.

Definition at line 600 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_mesh_x_var.

601 {
602  _mesh_x_var = var;
603 }

◆ set_mesh_y_var()

void libMesh::DifferentiablePhysics::set_mesh_y_var ( unsigned int  var)
inlinevirtualinherited

Tells the DifferentiablePhysics that variable var from the mesh system should be used to update the y coordinate of mesh nodes.

Definition at line 608 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_mesh_y_var.

609 {
610  _mesh_y_var = var;
611 }

◆ set_mesh_z_var()

void libMesh::DifferentiablePhysics::set_mesh_z_var ( unsigned int  var)
inlinevirtualinherited

Tells the DifferentiablePhysics that variable var from the mesh system should be used to update the z coordinate of mesh nodes.

Definition at line 616 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_mesh_z_var.

617 {
618  _mesh_z_var = var;
619 }

◆ set_numerical_jacobian_h_for_var()

void libMesh::FEMSystem::set_numerical_jacobian_h_for_var ( unsigned int  var_num,
Real  new_h 
)
inline

Definition at line 269 of file fem_system.h.

References _numerical_jacobian_h_for_var, and libMesh::Real.

271 {
272  if (_numerical_jacobian_h_for_var.size() <= var_num)
273  _numerical_jacobian_h_for_var.resize(var_num+1,Real(0));
274 
275  libmesh_assert_greater(new_h, 0);
276 
277  _numerical_jacobian_h_for_var[var_num] = new_h;
278 }
std::vector< Real > _numerical_jacobian_h_for_var
Definition: fem_system.h:252
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real

◆ set_time_solver()

void libMesh::DifferentiableSystem::set_time_solver ( std::unique_ptr< TimeSolver _time_solver)
inlineinherited

Sets the time_solver FIXME: This code is a little dangerous as it transfers ownership from the TimeSolver creator to this class. The user must no longer access his original TimeSolver object after calling this function.

Definition at line 242 of file diff_system.h.

References libMesh::DifferentiableSystem::time_solver.

243  {
244  time_solver.reset(_time_solver.release());
245  }
std::unique_ptr< TimeSolver > time_solver
Definition: diff_system.h:234

◆ set_vector_as_adjoint()

void libMesh::System::set_vector_as_adjoint ( const std::string &  vec_name,
int  qoi_num 
)
inherited

Allows one to set the QoI index controlling whether the vector identified by vec_name represents a solution from the adjoint (qoi_num >= 0) or primal (qoi_num == -1) space. This becomes significant if those spaces have differing heterogeneous Dirichlet constraints.

qoi_num == -2 can be used to indicate a vector which should not be affected by constraints during projection operations.

Definition at line 885 of file system.C.

References libMesh::System::_vector_is_adjoint.

Referenced by libMesh::System::add_adjoint_solution(), and libMesh::System::add_weighted_sensitivity_adjoint_solution().

887 {
888  // We reserve -1 for vectors which get primal constraints, -2 for
889  // vectors which get no constraints
890  libmesh_assert_greater_equal(qoi_num, -2);
891  _vector_is_adjoint[vec_name] = qoi_num;
892 }
std::map< std::string, int > _vector_is_adjoint
Definition: system.h:1947

◆ set_vector_preservation()

void libMesh::System::set_vector_preservation ( const std::string &  vec_name,
bool  preserve 
)
inherited

Allows one to set the boolean controlling whether the vector identified by vec_name should be "preserved": projected to new meshes, saved, etc.

Definition at line 867 of file system.C.

References libMesh::System::_vector_projections.

869 {
870  _vector_projections[vec_name] = preserve;
871 }
std::map< std::string, bool > _vector_projections
Definition: system.h:1941

◆ side_constraint()

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

Adds the constraint contribution on side of 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 depending on the boundary conditions.

To implement a weak form of the constraint 0 = G(u), the user should examine u = elem_solution and add (G(u), phi_i) boundary integral contributions to elem_residual in side_constraint().

Definition at line 191 of file diff_physics.h.

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

192  {
193  return request_jacobian;
194  }

◆ side_damping_residual()

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

Subtracts a damping vector contribution on side of elem from 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.

For most problems, the default implementation of "do nothing" is correct; users with boundary conditions including first time derivatives may need to reimplement this themselves.

Definition at line 391 of file diff_physics.h.

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

392  {
393  return request_jacobian;
394  }

◆ side_mass_residual()

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

Subtracts a mass vector contribution on side of elem from 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.

For most problems, the default implementation of "do nothing" is correct; users with boundary conditions including time derivatives may need to reimplement this themselves.

Definition at line 335 of file diff_physics.h.

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

336  {
337  return request_jacobian;
338  }

◆ side_postprocess()

virtual void libMesh::DifferentiableSystem::side_postprocess ( DiffContext )
inlinevirtualinherited

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

Definition at line 288 of file diff_system.h.

288 {}

◆ side_qoi()

virtual void libMesh::DifferentiableQoI::side_qoi ( DiffContext ,
const QoISet  
)
inlinevirtualinherited

Does any work that needs to be done on side of 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 131 of file diff_qoi.h.

133  {}

◆ side_qoi_derivative()

virtual void libMesh::DifferentiableQoI::side_qoi_derivative ( DiffContext ,
const QoISet  
)
inlinevirtualinherited

Does any work that needs to be done on side of 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 143 of file diff_qoi.h.

145  {}

◆ side_time_derivative()

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

Adds the time derivative contribution on side of 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 depending on the boundary conditions.

To implement a weak form of the source term du/dt = F(u) on sides, such as might arise in a flux boundary condition, the user should examine u = elem_solution and add (F(u), phi_i) boundary integral contributions to elem_residual in side_constraint().

Definition at line 171 of file diff_physics.h.

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

172  {
173  return request_jacobian;
174  }

◆ solve()

void libMesh::FEMSystem::solve ( )
overridevirtual

Invokes the solver associated with the system. For steady state solvers, this will find a root x where F(x) = 0. For transient solvers, this will integrate dx/dt = F(x).

For moving mesh systems, this also translates the mesh to the solution position.

Reimplemented from libMesh::DifferentiableSystem.

Reimplemented in libMesh::ContinuationSystem.

Definition at line 1050 of file fem_system.C.

References mesh_position_set(), and libMesh::DifferentiableSystem::solve().

1051 {
1052  // We are solving the primal problem
1053  Parent::solve();
1054 
1055  // On a moving mesh we want the mesh to reflect the new solution
1056  this->mesh_position_set();
1057 }
void mesh_position_set()
Definition: fem_system.C:1061
virtual void solve() override
Definition: diff_system.C:152

◆ swap_physics()

void libMesh::DifferentiableSystem::swap_physics ( DifferentiablePhysics *&  swap_physics)
inherited

Swap current physics object with external object

Definition at line 349 of file diff_system.C.

References libMesh::DifferentiableSystem::_diff_physics, and swap().

350 {
352 }
void swap_physics(DifferentiablePhysics *&swap_physics)
Definition: diff_system.C:349
DifferentiablePhysics * _diff_physics
Definition: diff_system.h:371
void swap(Iterator &lhs, Iterator &rhs)

◆ system()

sys_type& libMesh::ImplicitSystem::system ( )
inlineinherited
Returns
A reference to *this.

Definition at line 81 of file implicit_system.h.

81 { return *this; }

◆ system_type()

virtual std::string libMesh::ImplicitSystem::system_type ( ) const
inlineoverridevirtualinherited
Returns
"Implicit". Helps in identifying the system type in an equation system file.

Reimplemented from libMesh::ExplicitSystem.

Reimplemented in libMesh::OptimizationSystem, libMesh::NonlinearImplicitSystem, libMesh::LinearImplicitSystem, libMesh::RBConstruction, libMesh::FrequencySystem, libMesh::NewmarkSystem, and libMesh::TransientSystem< RBConstruction >.

Definition at line 117 of file implicit_system.h.

117 { return "Implicit"; }

◆ thread_join()

virtual void libMesh::DifferentiableQoI::thread_join ( std::vector< Number > &  qoi,
const std::vector< Number > &  other_qoi,
const QoISet qoi_indices 
)
virtualinherited

Method to combine thread-local qois. By default, simply sums thread qois.

◆ time_evolving() [1/2]

virtual void libMesh::DifferentiablePhysics::time_evolving ( unsigned int  var)
inlinevirtualinherited

Tells the DiffSystem that variable var is evolving with respect to time. In general, the user's init() function should call time_evolving() for any variables which behave like du/dt = F(u), and should not call time_evolving() for any variables which behave like 0 = G(u).

Most derived systems will not have to reimplement this function; however any system which reimplements mass_residual() may have to reimplement time_evolving() to prepare data structures.

Deprecated:
Instead, use the time_evolving override and specify the order-in-time of the variable, either 1 or 2. This method assumes the variable is first order for backward compatibility.

Definition at line 249 of file diff_physics.h.

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

250  {
251  libmesh_deprecated();
252  this->time_evolving(var,1);
253  }
virtual void time_evolving(unsigned int var)
Definition: diff_physics.h:249

◆ time_evolving() [2/2]

virtual void libMesh::DifferentiablePhysics::time_evolving ( unsigned int  var,
unsigned int  order 
)
virtualinherited

Tells the DiffSystem that variable var is evolving with respect to time. In general, the user's init() function should call time_evolving() with order 1 for any variables which behave like du/dt = F(u), with order 2 for any variables that behave like d^2u/dt^2 = F(u), and should not call time_evolving() for any variables which behave like 0 = G(u).

Most derived systems will not have to reimplement this function; however any system which reimplements mass_residual() may have to reimplement time_evolving() to prepare data structures.

◆ update()

void libMesh::System::update ( )
virtualinherited

Update the local values to reflect the solution on neighboring processors.

Definition at line 408 of file system.C.

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

Referenced by libMesh::__libmesh_petsc_diff_solver_jacobian(), libMesh::__libmesh_petsc_diff_solver_residual(), libMesh::UniformRefinementEstimator::_estimate_error(), assemble_qoi(), assemble_qoi_derivative(), libMesh::NonlinearImplicitSystem::assembly(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::NewmarkSolver::compute_initial_accel(), libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::GMVIO::copy_nodal_solution(), DMlibMeshFunction(), DMlibMeshJacobian(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::CondensedEigenSystem::get_eigenpair(), libMesh::libmesh_petsc_snes_jacobian(), libMesh::libmesh_petsc_snes_residual_helper(), libMesh::NewtonSolver::line_search(), mesh_position_get(), postprocess(), libMesh::ImplicitSystem::qoi_parameter_hessian(), libMesh::NewtonSolver::solve(), libMesh::ExplicitSystem::solve(), libMesh::LinearImplicitSystem::solve(), libMesh::NonlinearImplicitSystem::solve(), and libMesh::OptimizationSystem::solve().

409 {
410  libmesh_assert(solution->closed());
411 
412  const std::vector<dof_id_type> & send_list = _dof_map->get_send_list ();
413 
414  // Check sizes
415  libmesh_assert_equal_to (current_local_solution->size(), solution->size());
416  // More processors than elements => empty send_list
417  // libmesh_assert (!send_list.empty());
418  libmesh_assert_less_equal (send_list.size(), solution->size());
419 
420  // Create current_local_solution from solution. This will
421  // put a local copy of solution into current_local_solution.
422  // Only the necessary values (specified by the send_list)
423  // are copied to minimize communication
424  solution->localize (*current_local_solution, send_list);
425 }
std::unique_ptr< DofMap > _dof_map
Definition: system.h:1884
std::unique_ptr< NumericVector< Number > > solution
Definition: system.h:1523
std::unique_ptr< NumericVector< Number > > current_local_solution
Definition: system.h:1535

◆ update_global_solution() [1/2]

void libMesh::System::update_global_solution ( std::vector< Number > &  global_soln) const
inherited

Fill the input vector global_soln so that it contains the global solution on all processors. Requires communication with all other processors.

Definition at line 642 of file system.C.

References libMesh::System::solution.

Referenced by libMesh::ExactSolution::_compute_error(), libMesh::EquationSystems::build_discontinuous_solution_vector(), and libMesh::ExactErrorEstimator::estimate_error().

643 {
644  global_soln.resize (solution->size());
645 
646  solution->localize (global_soln);
647 }
std::unique_ptr< NumericVector< Number > > solution
Definition: system.h:1523

◆ update_global_solution() [2/2]

void libMesh::System::update_global_solution ( std::vector< Number > &  global_soln,
const processor_id_type  dest_proc 
) const
inherited

Fill the input vector global_soln so that it contains the global solution on processor dest_proc. Requires communication with all other processors.

Definition at line 651 of file system.C.

References libMesh::System::solution.

653 {
654  global_soln.resize (solution->size());
655 
656  solution->localize_to_one (global_soln, dest_proc);
657 }
std::unique_ptr< NumericVector< Number > > solution
Definition: system.h:1523

◆ user_assembly()

void libMesh::System::user_assembly ( )
virtualinherited

Calls user's attached assembly function, or is overridden by the user in derived classes.

Definition at line 1932 of file system.C.

References libMesh::System::_assemble_system_function, libMesh::System::_assemble_system_object, libMesh::System::_equation_systems, libMesh::System::Assembly::assemble(), and libMesh::System::name().

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

1933 {
1934  // Call the user-provided assembly function,
1935  // if it was provided
1936  if (_assemble_system_function != nullptr)
1938 
1939  // ...or the user-provided assembly object.
1940  else if (_assemble_system_object != nullptr)
1942 }
Assembly * _assemble_system_object
Definition: system.h:1841
virtual void assemble()=0
EquationSystems & _equation_systems
Definition: system.h:1890
const std::string & name() const
Definition: system.h:2017
void(* _assemble_system_function)(EquationSystems &es, const std::string &name)
Definition: system.h:1835

◆ user_constrain()

void libMesh::System::user_constrain ( )
virtualinherited

Calls user's attached constraint function, or is overridden by the user in derived classes.

Definition at line 1946 of file system.C.

References libMesh::System::_constrain_system_function, libMesh::System::_constrain_system_object, libMesh::System::_equation_systems, libMesh::System::Constraint::constrain(), and libMesh::System::name().

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

1947 {
1948  // Call the user-provided constraint function,
1949  // if it was provided
1950  if (_constrain_system_function!= nullptr)
1952 
1953  // ...or the user-provided constraint object.
1954  else if (_constrain_system_object != nullptr)
1956 }
void(* _constrain_system_function)(EquationSystems &es, const std::string &name)
Definition: system.h:1846
Constraint * _constrain_system_object
Definition: system.h:1852
EquationSystems & _equation_systems
Definition: system.h:1890
virtual void constrain()=0
const std::string & name() const
Definition: system.h:2017

◆ user_initialization()

void libMesh::System::user_initialization ( )
virtualinherited

Calls user's attached initialization function, or is overridden by the user in derived classes.

Definition at line 1918 of file system.C.

References libMesh::System::_equation_systems, libMesh::System::_init_system_function, libMesh::System::_init_system_object, libMesh::System::Initialization::initialize(), and libMesh::System::name().

Referenced by libMesh::System::init(), and libMesh::NewmarkSystem::initial_conditions().

1919 {
1920  // Call the user-provided initialization function,
1921  // if it was provided
1922  if (_init_system_function != nullptr)
1923  this->_init_system_function (_equation_systems, this->name());
1924 
1925  // ...or the user-provided initialization object.
1926  else if (_init_system_object != nullptr)
1928 }
Initialization * _init_system_object
Definition: system.h:1830
void(* _init_system_function)(EquationSystems &es, const std::string &name)
Definition: system.h:1824
EquationSystems & _equation_systems
Definition: system.h:1890
const std::string & name() const
Definition: system.h:2017

◆ user_QOI()

void libMesh::System::user_QOI ( const QoISet qoi_indices)
virtualinherited

Calls user's attached quantity of interest function, or is overridden by the user in derived classes.

Definition at line 1960 of file system.C.

References libMesh::System::_equation_systems, libMesh::System::_qoi_evaluate_function, libMesh::System::_qoi_evaluate_object, libMesh::System::name(), and libMesh::System::QOI::qoi().

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

1961 {
1962  // Call the user-provided quantity of interest function,
1963  // if it was provided
1964  if (_qoi_evaluate_function != nullptr)
1965  this->_qoi_evaluate_function(_equation_systems, this->name(), qoi_indices);
1966 
1967  // ...or the user-provided QOI function object.
1968  else if (_qoi_evaluate_object != nullptr)
1969  this->_qoi_evaluate_object->qoi(qoi_indices);
1970 }
void(* _qoi_evaluate_function)(EquationSystems &es, const std::string &name, const QoISet &qoi_indices)
Definition: system.h:1857
virtual void qoi(const QoISet &qoi_indices)=0
QOI * _qoi_evaluate_object
Definition: system.h:1864
EquationSystems & _equation_systems
Definition: system.h:1890
const std::string & name() const
Definition: system.h:2017

◆ user_QOI_derivative()

void libMesh::System::user_QOI_derivative ( const QoISet qoi_indices = QoISet(),
bool  include_liftfunc = true,
bool  apply_constraints = true 
)
virtualinherited

Calls user's attached quantity of interest derivative function, or is overridden by the user in derived classes.

Definition at line 1974 of file system.C.

References libMesh::System::_equation_systems, libMesh::System::_qoi_evaluate_derivative_function, libMesh::System::_qoi_evaluate_derivative_object, libMesh::System::name(), and libMesh::System::QOIDerivative::qoi_derivative().

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

1977 {
1978  // Call the user-provided quantity of interest derivative,
1979  // if it was provided
1980  if (_qoi_evaluate_derivative_function != nullptr)
1982  (_equation_systems, this->name(), qoi_indices, include_liftfunc,
1983  apply_constraints);
1984 
1985  // ...or the user-provided QOI derivative function object.
1986  else if (_qoi_evaluate_derivative_object != nullptr)
1988  (qoi_indices, include_liftfunc, apply_constraints);
1989 }
QOIDerivative * _qoi_evaluate_derivative_object
Definition: system.h:1878
virtual void qoi_derivative(const QoISet &qoi_indices, bool include_liftfunc, bool apply_constraints)=0
EquationSystems & _equation_systems
Definition: system.h:1890
const std::string & name() const
Definition: system.h:2017
void(* _qoi_evaluate_derivative_function)(EquationSystems &es, const std::string &name, const QoISet &qoi_indices, bool include_liftfunc, bool apply_constraints)
Definition: system.h:1869

◆ variable()

◆ variable_group()

const VariableGroup & libMesh::System::variable_group ( unsigned int  vg) const
inlineinherited

Return a constant reference to VariableGroup vg.

Definition at line 2143 of file system.h.

References libMesh::System::_variable_groups.

Referenced by assembly(), and libMesh::System::get_info().

2144 {
2145  libmesh_assert_less (vg, _variable_groups.size());
2146 
2147  return _variable_groups[vg];
2148 }
std::vector< VariableGroup > _variable_groups
Definition: system.h:1916

◆ variable_name()

const std::string & libMesh::System::variable_name ( const unsigned int  i) const
inlineinherited

◆ variable_number()

unsigned short int libMesh::System::variable_number ( const std::string &  var) const
inherited
Returns
The variable number associated with the user-specified variable named var.

Definition at line 1243 of file system.C.

References libMesh::System::_variable_numbers, and libMesh::System::_variables.

Referenced by libMesh::ExactSolution::_compute_error(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::GMVIO::copy_nodal_solution(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::ExactErrorEstimator::find_squared_element_error(), libMesh::System::read_header(), libMesh::System::variable_scalar_number(), libMesh::System::variable_type(), libMesh::EnsightIO::write_scalar_ascii(), and libMesh::EnsightIO::write_vector_ascii().

1244 {
1245  // Make sure the variable exists
1246  std::map<std::string, unsigned short int>::const_iterator
1247  pos = _variable_numbers.find(var);
1248 
1249  if (pos == _variable_numbers.end())
1250  libmesh_error_msg("ERROR: variable " << var << " does not exist in this system!");
1251 
1252  libmesh_assert_equal_to (_variables[pos->second].name(), var);
1253 
1254  return pos->second;
1255 }
std::map< std::string, unsigned short int > _variable_numbers
Definition: system.h:1922
std::vector< Variable > _variables
Definition: system.h:1911

◆ variable_scalar_number() [1/2]

unsigned int libMesh::System::variable_scalar_number ( const std::string &  var,
unsigned int  component 
) const
inlineinherited
Returns
An index, starting from 0 for the first component of the first variable, and incrementing for each component of each (potentially vector-valued) variable in the system in order. For systems with only scalar-valued variables, this will be the same as variable_number(var)

Irony: currently our only non-scalar-valued variable type is SCALAR.

Definition at line 2164 of file system.h.

References libMesh::System::variable_number().

Referenced by libMesh::ExactSolution::_compute_error(), and libMesh::ExactErrorEstimator::find_squared_element_error().

2166 {
2167  return variable_scalar_number(this->variable_number(var), component);
2168 }
unsigned int variable_scalar_number(const std::string &var, unsigned int component) const
Definition: system.h:2164
unsigned short int variable_number(const std::string &var) const
Definition: system.C:1243

◆ variable_scalar_number() [2/2]

unsigned int libMesh::System::variable_scalar_number ( unsigned int  var_num,
unsigned int  component 
) const
inlineinherited
Returns
An index, starting from 0 for the first component of the first variable, and incrementing for each component of each (potentially vector-valued) variable in the system in order. For systems with only scalar-valued variables, this will be the same as var_num

Irony: currently our only non-scalar-valued variable type is SCALAR.

Definition at line 2174 of file system.h.

References libMesh::System::_variables.

2176 {
2177  return _variables[var_num].first_scalar_number() + component;
2178 }
std::vector< Variable > _variables
Definition: system.h:1911

◆ variable_type() [1/2]

◆ variable_type() [2/2]

const FEType & libMesh::System::variable_type ( const std::string &  var) const
inlineinherited
Returns
The finite element type for variable var.

Definition at line 2193 of file system.h.

References libMesh::System::_variables, and libMesh::System::variable_number().

2194 {
2195  return _variables[this->variable_number(var)].type();
2196 }
std::vector< Variable > _variables
Definition: system.h:1911
unsigned short int variable_number(const std::string &var) const
Definition: system.C:1243

◆ vector_is_adjoint()

int libMesh::System::vector_is_adjoint ( const std::string &  vec_name) const
inherited
Returns
The integer describing whether the vector identified by vec_name represents a solution from an adjoint (non-negative) or the primal (-1) space.

Definition at line 896 of file system.C.

References libMesh::System::_vector_is_adjoint.

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

897 {
898  libmesh_assert(_vector_is_adjoint.find(vec_name) !=
899  _vector_is_adjoint.end());
900 
901  return _vector_is_adjoint.find(vec_name)->second;
902 }
std::map< std::string, int > _vector_is_adjoint
Definition: system.h:1947

◆ vector_name() [1/2]

const std::string & libMesh::System::vector_name ( const unsigned int  vec_num) const
inherited
Returns
The name of this system's additional vector number vec_num (where the vectors are counted starting with 0).

Definition at line 832 of file system.C.

References libMesh::System::vectors_begin(), and libMesh::System::vectors_end().

833 {
836  unsigned int num = 0;
837  while ((num<vec_num) && (v!=v_end))
838  {
839  num++;
840  ++v;
841  }
842  libmesh_assert (v != v_end);
843  return v->first;
844 }
vectors_iterator vectors_end()
Definition: system.h:2257
std::map< std::string, NumericVector< Number > * >::const_iterator const_vectors_iterator
Definition: system.h:749
vectors_iterator vectors_begin()
Definition: system.h:2245

◆ vector_name() [2/2]

const std::string & libMesh::System::vector_name ( const NumericVector< Number > &  vec_reference) const
inherited
Returns
The name of a system vector, given a reference to that vector

Definition at line 846 of file system.C.

References libMesh::System::vectors_begin(), and libMesh::System::vectors_end().

847 {
850 
851  for (; v != v_end; ++v)
852  {
853  // Check if the current vector is the one whose name we want
854  if (&vec_reference == v->second)
855  break; // exit loop if it is
856  }
857 
858  // Before returning, make sure we didnt loop till the end and not find any match
859  libmesh_assert (v != v_end);
860 
861  // Return the string associated with the current vector
862  return v->first;
863 }
vectors_iterator vectors_end()
Definition: system.h:2257
std::map< std::string, NumericVector< Number > * >::const_iterator const_vectors_iterator
Definition: system.h:749
vectors_iterator vectors_begin()
Definition: system.h:2245

◆ vector_preservation()

bool libMesh::System::vector_preservation ( const std::string &  vec_name) const
inherited
Returns
The boolean describing whether the vector identified by vec_name should be "preserved": projected to new meshes, saved, etc.

Definition at line 875 of file system.C.

References libMesh::System::_vector_projections.

Referenced by libMesh::MemorySolutionHistory::store().

876 {
877  if (_vector_projections.find(vec_name) == _vector_projections.end())
878  return false;
879 
880  return _vector_projections.find(vec_name)->second;
881 }
std::map< std::string, bool > _vector_projections
Definition: system.h:1941

◆ vectors_begin() [1/2]

System::vectors_iterator libMesh::System::vectors_begin ( )
inlineinherited

Beginning of vectors container

Definition at line 2245 of file system.h.

References libMesh::System::_vectors.

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::System::get_vector(), libMesh::System::request_vector(), libMesh::MemorySolutionHistory::store(), and libMesh::System::vector_name().

2246 {
2247  return _vectors.begin();
2248 }
std::map< std::string, NumericVector< Number > *> _vectors
Definition: system.h:1935

◆ vectors_begin() [2/2]

System::const_vectors_iterator libMesh::System::vectors_begin ( ) const
inlineinherited

Beginning of vectors container

Definition at line 2251 of file system.h.

References libMesh::System::_vectors.

2252 {
2253  return _vectors.begin();
2254 }
std::map< std::string, NumericVector< Number > *> _vectors
Definition: system.h:1935

◆ vectors_end() [1/2]

System::vectors_iterator libMesh::System::vectors_end ( )
inlineinherited

◆ vectors_end() [2/2]

System::const_vectors_iterator libMesh::System::vectors_end ( ) const
inlineinherited

End of vectors container

Definition at line 2263 of file system.h.

References libMesh::System::_vectors.

2264 {
2265  return _vectors.end();
2266 }
std::map< std::string, NumericVector< Number > *> _vectors
Definition: system.h:1935

◆ weighted_sensitivity_adjoint_solve()

std::pair< unsigned int, Real > libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve ( const ParameterVector parameters,
const ParameterVector weights,
const QoISet qoi_indices = QoISet() 
)
overridevirtualinherited

Assembles & solves the linear system(s) (dR/du)^T*z_w = sum(w_p*(d^2q/dudp - d^2R/dudp*z)), for those parameters p contained within parameters, weighted by the values w_p found within weights.

Assumes that adjoint_solve has already calculated z for each qoi in qoi_indices.

Returns
A pair with the total number of linear iterations performed and the (sum of the) final residual norms

Reimplemented from libMesh::System.

Definition at line 425 of file implicit_system.C.

References libMesh::System::add_weighted_sensitivity_adjoint_solution(), libMesh::ExplicitSystem::assemble_qoi_derivative(), libMesh::ImplicitSystem::assembly(), libMesh::NumericVector< T >::close(), libMesh::SparseMatrix< T >::close(), libMesh::ParameterVector::deep_copy(), libMesh::DofMap::enforce_constraints_exactly(), libMesh::System::get_adjoint_rhs(), libMesh::System::get_adjoint_solution(), libMesh::System::get_dof_map(), libMesh::ImplicitSystem::get_linear_solve_parameters(), libMesh::ImplicitSystem::get_linear_solver(), libMesh::SparseMatrix< T >::get_transpose(), libMesh::System::get_weighted_sensitivity_adjoint_solution(), libMesh::DofMap::has_adjoint_dirichlet_boundaries(), libMesh::QoISet::has_index(), libMesh::ImplicitSystem::matrix, libMesh::System::n_qois(), libMesh::Real, libMesh::ImplicitSystem::release_linear_solver(), libMesh::ExplicitSystem::rhs, libMesh::LinearSolver< T >::solve(), libMesh::TOLERANCE, libMesh::ParameterVector::value_copy(), libMesh::SparseMatrix< T >::vector_mult_add(), and libMesh::NumericVector< T >::zero_clone().

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

428 {
429  // Log how long the linear solve takes.
430  LOG_SCOPE("weighted_sensitivity_adjoint_solve()", "ImplicitSystem");
431 
432  // We currently get partial derivatives via central differencing
433  const Real delta_p = TOLERANCE;
434 
435  ParameterVector & parameters =
436  const_cast<ParameterVector &>(parameters_in);
437 
438  // The forward system should now already be solved.
439  // The adjoint system should now already be solved.
440  // Now we're assembling a weighted sum of adjoint-adjoint systems:
441  //
442  // dR/du (u, sum_l(w_l*z^l)) = sum_l(w_l*(Q''_ul - R''_ul (u, z)))
443 
444  // FIXME: The derivation here does not yet take adjoint boundary
445  // conditions into account.
446  for (unsigned int i=0; i != this->n_qois(); ++i)
447  if (qoi_indices.has_index(i))
448  libmesh_assert(!this->get_dof_map().has_adjoint_dirichlet_boundaries(i));
449 
450  // We'll assemble the rhs first, because the R'' term will require
451  // perturbing the jacobian
452 
453  // We'll use temporary rhs vectors, because we haven't (yet) found
454  // any good reasons why users might want to save these:
455 
456  std::vector<std::unique_ptr<NumericVector<Number>>> temprhs(this->n_qois());
457  for (unsigned int i=0; i != this->n_qois(); ++i)
458  if (qoi_indices.has_index(i))
459  temprhs[i] = this->rhs->zero_clone();
460 
461  // We approximate the _l partial derivatives via a central
462  // differencing perturbation in the w_l direction:
463  //
464  // sum_l(w_l*v_l) ~= (v(p + dp*w_l*e_l) - v(p - dp*w_l*e_l))/(2*dp)
465 
466  // PETSc doesn't implement SGEMX, so neither does NumericVector,
467  // so we want to avoid calculating f -= R'*z. We'll thus evaluate
468  // the above equation by first adding -v(p+dp...), then multiplying
469  // the intermediate result vectors by -1, then adding -v(p-dp...),
470  // then finally dividing by 2*dp.
471 
472  ParameterVector oldparameters, parameterperturbation;
473  parameters.deep_copy(oldparameters);
474  weights.deep_copy(parameterperturbation);
475  parameterperturbation *= delta_p;
476  parameters += parameterperturbation;
477 
478  this->assembly(false, true);
479  this->matrix->close();
480 
481  // Take the discrete adjoint, so that we can calculate R_u(u,z) with
482  // a matrix-vector product of R_u and z.
484 
485  this->assemble_qoi_derivative(qoi_indices,
486  /* include_liftfunc = */ false,
487  /* apply_constraints = */ true);
488  for (unsigned int i=0; i != this->n_qois(); ++i)
489  if (qoi_indices.has_index(i))
490  {
491  this->get_adjoint_rhs(i).close();
492  *(temprhs[i]) -= this->get_adjoint_rhs(i);
493  this->matrix->vector_mult_add(*(temprhs[i]), this->get_adjoint_solution(i));
494  *(temprhs[i]) *= -1.0;
495  }
496 
497  oldparameters.value_copy(parameters);
498  parameterperturbation *= -1.0;
499  parameters += parameterperturbation;
500 
501  this->assembly(false, true);
502  this->matrix->close();
504 
505  this->assemble_qoi_derivative(qoi_indices,
506  /* include_liftfunc = */ false,
507  /* apply_constraints = */ true);
508  for (unsigned int i=0; i != this->n_qois(); ++i)
509  if (qoi_indices.has_index(i))
510  {
511  this->get_adjoint_rhs(i).close();
512  *(temprhs[i]) -= this->get_adjoint_rhs(i);
513  this->matrix->vector_mult_add(*(temprhs[i]), this->get_adjoint_solution(i));
514  *(temprhs[i]) /= (2.0*delta_p);
515  }
516 
517  // Finally, assemble the jacobian at the non-perturbed parameter
518  // values. Ignore assemble_before_solve; if we had a good
519  // non-perturbed matrix before we've already overwritten it.
520  oldparameters.value_copy(parameters);
521 
522  // if (this->assemble_before_solve)
523  {
524  // Build the Jacobian
525  this->assembly(false, true);
526  this->matrix->close();
527 
528  // Take the discrete adjoint
530  }
531 
532  // The weighted adjoint-adjoint problem is linear
533  LinearSolver<Number> * linear_solver = this->get_linear_solver();
534 
535  // Our iteration counts and residuals will be sums of the individual
536  // results
537  std::pair<unsigned int, Real> solver_params =
539  std::pair<unsigned int, Real> totalrval = std::make_pair(0,0.0);
540 
541  for (unsigned int i=0; i != this->n_qois(); ++i)
542  if (qoi_indices.has_index(i))
543  {
544  const std::pair<unsigned int, Real> rval =
545  linear_solver->solve (*matrix, this->add_weighted_sensitivity_adjoint_solution(i),
546  *(temprhs[i]),
547  solver_params.second,
548  solver_params.first);
549 
550  totalrval.first += rval.first;
551  totalrval.second += rval.second;
552  }
553 
554  this->release_linear_solver(linear_solver);
555 
556  // The linear solver may not have fit our constraints exactly
557 #ifdef LIBMESH_ENABLE_CONSTRAINTS
558  for (unsigned int i=0; i != this->n_qois(); ++i)
559  if (qoi_indices.has_index(i))
562  /* homogeneous = */ true);
563 #endif
564 
565  return totalrval;
566 }
virtual std::pair< unsigned int, Real > get_linear_solve_parameters() const
unsigned int n_qois() const
Definition: system.h:2278
virtual std::unique_ptr< NumericVector< T > > zero_clone() const =0
NumericVector< Number > * rhs
virtual LinearSolver< Number > * get_linear_solver() const
static const Real TOLERANCE
virtual void release_linear_solver(LinearSolver< Number > *) const
NumericVector< Number > & add_weighted_sensitivity_adjoint_solution(unsigned int i=0)
Definition: system.C:989
virtual void assembly(bool, bool, bool=false, bool=false)
bool has_adjoint_dirichlet_boundaries(unsigned int q) const
virtual void close()=0
virtual void close()=0
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
void vector_mult_add(NumericVector< T > &dest, const NumericVector< T > &arg) const
SparseMatrix< Number > * matrix
virtual void get_transpose(SparseMatrix< T > &dest) const =0
virtual void assemble_qoi_derivative(const QoISet &qoi_indices=QoISet(), bool include_liftfunc=true, bool apply_constraints=true) override
NumericVector< Number > & get_adjoint_solution(unsigned int i=0)
Definition: system.C:969
const DofMap & get_dof_map() const
Definition: system.h:2049
NumericVector< Number > & get_weighted_sensitivity_adjoint_solution(unsigned int i=0)
Definition: system.C:1001
void enforce_constraints_exactly(const System &system, NumericVector< Number > *v=nullptr, bool homogeneous=false) const
NumericVector< Number > & get_adjoint_rhs(unsigned int i=0)
Definition: system.C:1031

◆ weighted_sensitivity_solve()

std::pair< unsigned int, Real > libMesh::ImplicitSystem::weighted_sensitivity_solve ( const ParameterVector parameters,
const ParameterVector weights 
)
overridevirtualinherited

Assembles & solves the linear system(s) (dR/du)*u_w = sum(w_p*-dR/dp), for those parameters p contained within parameters weighted by the values w_p found within weights.

Returns
A pair with the total number of linear iterations performed and the (sum of the) final residual norms

Reimplemented from libMesh::System.

Definition at line 571 of file implicit_system.C.

References libMesh::System::add_weighted_sensitivity_solution(), libMesh::ImplicitSystem::assembly(), libMesh::NumericVector< T >::clone(), libMesh::NumericVector< T >::close(), libMesh::SparseMatrix< T >::close(), libMesh::ParameterVector::deep_copy(), libMesh::DofMap::enforce_constraints_exactly(), libMesh::System::get_dof_map(), libMesh::ImplicitSystem::get_linear_solve_parameters(), libMesh::ImplicitSystem::get_linear_solver(), libMesh::System::get_weighted_sensitivity_solution(), libMesh::ImplicitSystem::matrix, libMesh::Real, libMesh::ImplicitSystem::release_linear_solver(), libMesh::ExplicitSystem::rhs, libMesh::LinearSolver< T >::solve(), libMesh::TOLERANCE, and libMesh::ParameterVector::value_copy().

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

573 {
574  // Log how long the linear solve takes.
575  LOG_SCOPE("weighted_sensitivity_solve()", "ImplicitSystem");
576 
577  // We currently get partial derivatives via central differencing
578  const Real delta_p = TOLERANCE;
579 
580  ParameterVector & parameters =
581  const_cast<ParameterVector &>(parameters_in);
582 
583  // The forward system should now already be solved.
584 
585  // Now we're assembling a weighted sum of sensitivity systems:
586  //
587  // dR/du (u, v)(sum(w_l*u'_l)) = -sum_l(w_l*R'_l (u, v)) forall v
588 
589  // We'll assemble the rhs first, because the R' term will require
590  // perturbing the system, and some applications may not be able to
591  // assemble a perturbed residual without simultaneously constructing
592  // a perturbed jacobian.
593 
594  // We approximate the _l partial derivatives via a central
595  // differencing perturbation in the w_l direction:
596  //
597  // sum_l(w_l*v_l) ~= (v(p + dp*w_l*e_l) - v(p - dp*w_l*e_l))/(2*dp)
598 
599  ParameterVector oldparameters, parameterperturbation;
600  parameters.deep_copy(oldparameters);
601  weights.deep_copy(parameterperturbation);
602  parameterperturbation *= delta_p;
603  parameters += parameterperturbation;
604 
605  this->assembly(true, false, true);
606  this->rhs->close();
607 
608  std::unique_ptr<NumericVector<Number>> temprhs = this->rhs->clone();
609 
610  oldparameters.value_copy(parameters);
611  parameterperturbation *= -1.0;
612  parameters += parameterperturbation;
613 
614  this->assembly(true, false, true);
615  this->rhs->close();
616 
617  *temprhs -= *(this->rhs);
618  *temprhs /= (2.0*delta_p);
619 
620  // Finally, assemble the jacobian at the non-perturbed parameter
621  // values
622  oldparameters.value_copy(parameters);
623 
624  // Build the Jacobian
625  this->assembly(false, true);
626  this->matrix->close();
627 
628  // The weighted sensitivity problem is linear
629  LinearSolver<Number> * linear_solver = this->get_linear_solver();
630 
631  std::pair<unsigned int, Real> solver_params =
633 
634  const std::pair<unsigned int, Real> rval =
635  linear_solver->solve (*matrix, this->add_weighted_sensitivity_solution(),
636  *temprhs,
637  solver_params.second,
638  solver_params.first);
639 
640  this->release_linear_solver(linear_solver);
641 
642  // The linear solver may not have fit our constraints exactly
643 #ifdef LIBMESH_ENABLE_CONSTRAINTS
645  (*this, &this->get_weighted_sensitivity_solution(),
646  /* homogeneous = */ true);
647 #endif
648 
649  return rval;
650 }
virtual std::pair< unsigned int, Real > get_linear_solve_parameters() const
NumericVector< Number > * rhs
virtual std::unique_ptr< NumericVector< T > > clone() const =0
virtual LinearSolver< Number > * get_linear_solver() const
static const Real TOLERANCE
NumericVector< Number > & add_weighted_sensitivity_solution()
Definition: system.C:936
NumericVector< Number > & get_weighted_sensitivity_solution()
Definition: system.C:943
virtual void release_linear_solver(LinearSolver< Number > *) const
virtual void assembly(bool, bool, bool=false, bool=false)
virtual void close()=0
virtual void close()=0
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
SparseMatrix< Number > * matrix
const DofMap & get_dof_map() const
Definition: system.h:2049
void enforce_constraints_exactly(const System &system, NumericVector< Number > *v=nullptr, bool homogeneous=false) const

◆ write_header()

void libMesh::System::write_header ( Xdr io,
const std::string &  version,
const bool  write_additional_data 
) const
inherited

Writes the basic data header for this System.

This method implements the output of a System object, embedded in the output of an EquationSystems<T_sys>. This warrants some documentation. The output of this part consists of 5 sections:

for this system

5.) The number of variables in the system (unsigned int)

for each variable in the system

6.) The name of the variable (string)

6.1.) subdomain where the variable lives

7.) Combined in an FEType:

  • The approximation order(s) of the variable (Order Enum, cast to int/s)
  • The finite element family/ies of the variable (FEFamily Enum, cast to int/s)

end variable loop

8.) The number of additional vectors (unsigned int),

for each additional vector in the system object

9.) the name of the additional vector (string)

end system

Definition at line 1299 of file system_io.C.

References libMesh::System::_vectors, libMesh::Variable::active_subdomains(), libMesh::Xdr::data(), libMesh::FEType::family, libMesh::System::get_mesh(), libMesh::FEType::inf_map, libMesh::System::n_vars(), libMesh::System::n_vectors(), libMesh::System::name(), libMesh::FEType::order, libMesh::ParallelObject::processor_id(), libMesh::FEType::radial_family, libMesh::FEType::radial_order, libMesh::System::variable(), libMesh::System::variable_name(), libMesh::System::variable_type(), and libMesh::Xdr::writing().

1302 {
1336  libmesh_assert (io.writing());
1337 
1338 
1339  // Only write the header information
1340  // if we are processor 0.
1341  if (this->get_mesh().processor_id() != 0)
1342  return;
1343 
1344  std::string comment;
1345  char buf[80];
1346 
1347  // 5.)
1348  // Write the number of variables in the system
1349 
1350  {
1351  // set up the comment
1352  comment = "# No. of Variables in System \"";
1353  comment += this->name();
1354  comment += "\"";
1355 
1356  unsigned int nv = this->n_vars();
1357  io.data (nv, comment.c_str());
1358  }
1359 
1360 
1361  for (unsigned int var=0; var<this->n_vars(); var++)
1362  {
1363  // 6.)
1364  // Write the name of the var-th variable
1365  {
1366  // set up the comment
1367  comment = "# Name, Variable No. ";
1368  std::sprintf(buf, "%u", var);
1369  comment += buf;
1370  comment += ", System \"";
1371  comment += this->name();
1372  comment += "\"";
1373 
1374  std::string var_name = this->variable_name(var);
1375  io.data (var_name, comment.c_str());
1376  }
1377 
1378  // 6.1.) Variable subdomains
1379  {
1380  // set up the comment
1381  comment = "# Subdomains, Variable \"";
1382  std::sprintf(buf, "%s", this->variable_name(var).c_str());
1383  comment += buf;
1384  comment += "\", System \"";
1385  comment += this->name();
1386  comment += "\"";
1387 
1388  const std::set<subdomain_id_type> & domains = this->variable(var).active_subdomains();
1389  std::vector<subdomain_id_type> domain_array;
1390  domain_array.assign(domains.begin(), domains.end());
1391  io.data (domain_array, comment.c_str());
1392  }
1393 
1394  // 7.)
1395  // Write the approximation order of the var-th variable
1396  // in this system
1397  {
1398  // set up the comment
1399  comment = "# Approximation Order, Variable \"";
1400  std::sprintf(buf, "%s", this->variable_name(var).c_str());
1401  comment += buf;
1402  comment += "\", System \"";
1403  comment += this->name();
1404  comment += "\"";
1405 
1406  int order = static_cast<int>(this->variable_type(var).order);
1407  io.data (order, comment.c_str());
1408  }
1409 
1410 
1411 #ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
1412 
1413  // do the same for radial_order
1414  {
1415  comment = "# Radial Approximation Order, Variable \"";
1416  std::sprintf(buf, "%s", this->variable_name(var).c_str());
1417  comment += buf;
1418  comment += "\", System \"";
1419  comment += this->name();
1420  comment += "\"";
1421 
1422  int rad_order = static_cast<int>(this->variable_type(var).radial_order);
1423  io.data (rad_order, comment.c_str());
1424  }
1425 
1426 #endif
1427 
1428  // Write the Finite Element type of the var-th variable
1429  // in this System
1430  {
1431  // set up the comment
1432  comment = "# FE Family, Variable \"";
1433  std::sprintf(buf, "%s", this->variable_name(var).c_str());
1434  comment += buf;
1435  comment += "\", System \"";
1436  comment += this->name();
1437  comment += "\"";
1438 
1439  const FEType & type = this->variable_type(var);
1440  int fam = static_cast<int>(type.family);
1441  io.data (fam, comment.c_str());
1442 
1443 #ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
1444 
1445  comment = "# Radial FE Family, Variable \"";
1446  std::sprintf(buf, "%s", this->variable_name(var).c_str());
1447  comment += buf;
1448  comment += "\", System \"";
1449  comment += this->name();
1450  comment += "\"";
1451 
1452  int radial_fam = static_cast<int>(type.radial_family);
1453  io.data (radial_fam, comment.c_str());
1454 
1455  comment = "# Infinite Mapping Type, Variable \"";
1456  std::sprintf(buf, "%s", this->variable_name(var).c_str());
1457  comment += buf;
1458  comment += "\", System \"";
1459  comment += this->name();
1460  comment += "\"";
1461 
1462  int i_map = static_cast<int>(type.inf_map);
1463  io.data (i_map, comment.c_str());
1464 #endif
1465  }
1466  } // end of the variable loop
1467 
1468  // 8.)
1469  // Write the number of additional vectors in the System.
1470  // If write_additional_data==false, then write zero for
1471  // the number of additional vectors.
1472  {
1473  {
1474  // set up the comment
1475  comment = "# No. of Additional Vectors, System \"";
1476  comment += this->name();
1477  comment += "\"";
1478 
1479  unsigned int nvecs = write_additional_data ? this->n_vectors () : 0;
1480  io.data (nvecs, comment.c_str());
1481  }
1482 
1483  if (write_additional_data)
1484  {
1485  unsigned int cnt=0;
1486  for (const auto & pr : _vectors)
1487  {
1488  // 9.)
1489  // write the name of the cnt-th additional vector
1490  comment = "# Name of ";
1491  std::sprintf(buf, "%d", cnt++);
1492  comment += buf;
1493  comment += "th vector";
1494  std::string vec_name = pr.first;
1495 
1496  io.data (vec_name, comment.c_str());
1497  }
1498  }
1499  }
1500 }
const Variable & variable(unsigned int var) const
Definition: system.h:2133
OrderWrapper radial_order
Definition: fe_type.h:237
OrderWrapper order
Definition: fe_type.h:198
const MeshBase & get_mesh() const
Definition: system.h:2033
const std::set< subdomain_id_type > & active_subdomains() const
Definition: variable.h:150
unsigned int n_vectors() const
Definition: system.h:2233
const std::string & variable_name(const unsigned int i) const
Definition: system.h:2153
const FEType & variable_type(const unsigned int i) const
Definition: system.h:2183
std::map< std::string, NumericVector< Number > *> _vectors
Definition: system.h:1935
const std::string & name() const
Definition: system.h:2017
unsigned int n_vars() const
Definition: system.h:2105
processor_id_type processor_id() const

◆ write_parallel_data()

void libMesh::System::write_parallel_data ( Xdr io,
const bool  write_additional_data 
) const
inherited

Writes additional data, namely vectors, for this System. This method may safely be called on a distributed-memory mesh. This method will create an individual file for each processor in the simulation where the local solution components for that processor will be stored.

This method implements the output of the vectors contained in this System object, embedded in the output of an EquationSystems<T_sys>.

9.) The global solution vector, re-ordered to be node-major (More on this later.)

for each additional vector in the object

10.) The global additional vector, re-ordered to be node-major (More on this later.)

Note that the actual IO is handled through the Xdr class (to be renamed later?) which provides a uniform interface to both the XDR (eXternal Data Representation) interface and standard ASCII output. Thus this one section of code will read XDR or ASCII files with no changes.

Definition at line 1504 of file system_io.C.

References libMesh::System::_vectors, libMesh::Xdr::data(), libMesh::FEType::family, libMesh::System::get_dof_map(), libMesh::System::get_mesh(), libMesh::DofObject::invalid_id, libMesh::ParallelObject::n_processors(), libMesh::System::n_vars(), libMesh::System::name(), libMesh::System::number(), libMesh::ParallelObject::processor_id(), libMesh::SCALAR, libMesh::DofMap::SCALAR_dof_indices(), libMesh::System::solution, libMesh::Variable::type(), libMesh::System::variable(), and libMesh::Xdr::writing().

1506 {
1526  // PerfLog pl("IO Performance",false);
1527  // pl.push("write_parallel_data");
1528  // std::size_t total_written_size = 0;
1529 
1530  std::string comment;
1531 
1532  libmesh_assert (io.writing());
1533 
1534  std::vector<Number> io_buffer; io_buffer.reserve(this->solution->local_size());
1535 
1536  // build the ordered nodes and element maps.
1537  // when writing/reading parallel files we need to iterate
1538  // over our nodes/elements in order of increasing global id().
1539  // however, this is not guaranteed to be ordering we obtain
1540  // by using the node_iterators/element_iterators directly.
1541  // so build a set, sorted by id(), that provides the ordering.
1542  // further, for memory economy build the set but then transfer
1543  // its contents to vectors, which will be sorted.
1544  std::vector<const DofObject *> ordered_nodes, ordered_elements;
1545  {
1546  std::set<const DofObject *, CompareDofObjectsByID>
1547  ordered_nodes_set (this->get_mesh().local_nodes_begin(),
1548  this->get_mesh().local_nodes_end());
1549 
1550  ordered_nodes.insert(ordered_nodes.end(),
1551  ordered_nodes_set.begin(),
1552  ordered_nodes_set.end());
1553  }
1554  {
1555  std::set<const DofObject *, CompareDofObjectsByID>
1556  ordered_elements_set (this->get_mesh().local_elements_begin(),
1557  this->get_mesh().local_elements_end());
1558 
1559  ordered_elements.insert(ordered_elements.end(),
1560  ordered_elements_set.begin(),
1561  ordered_elements_set.end());
1562  }
1563 
1564  const unsigned int sys_num = this->number();
1565  const unsigned int nv = this->n_vars();
1566 
1567  // Loop over each non-SCALAR variable and each node, and write out the value.
1568  for (unsigned int var=0; var<nv; var++)
1569  if (this->variable(var).type().family != SCALAR)
1570  {
1571  // First write the node DOF values
1572  for (const auto & node : ordered_nodes)
1573  for (unsigned int comp=0; comp<node->n_comp(sys_num, var); comp++)
1574  {
1575  libmesh_assert_not_equal_to (node->dof_number(sys_num, var, comp),
1577 
1578  io_buffer.push_back((*this->solution)(node->dof_number(sys_num, var, comp)));
1579  }
1580 
1581  // Then write the element DOF values
1582  for (const auto & elem : ordered_elements)
1583  for (unsigned int comp=0; comp<elem->n_comp(sys_num, var); comp++)
1584  {
1585  libmesh_assert_not_equal_to (elem->dof_number(sys_num, var, comp),
1587 
1588  io_buffer.push_back((*this->solution)(elem->dof_number(sys_num, var, comp)));
1589  }
1590  }
1591 
1592  // Finally, write the SCALAR data on the last processor
1593  for (unsigned int var=0; var<this->n_vars(); var++)
1594  if (this->variable(var).type().family == SCALAR)
1595  {
1596  if (this->processor_id() == (this->n_processors()-1))
1597  {
1598  const DofMap & dof_map = this->get_dof_map();
1599  std::vector<dof_id_type> SCALAR_dofs;
1600  dof_map.SCALAR_dof_indices(SCALAR_dofs, var);
1601 
1602  for (std::size_t i=0; i<SCALAR_dofs.size(); i++)
1603  io_buffer.push_back((*this->solution)(SCALAR_dofs[i]));
1604  }
1605  }
1606 
1607  // 9.)
1608  //
1609  // Actually write the reordered solution vector
1610  // for the ith system to disk
1611 
1612  // set up the comment
1613  {
1614  comment = "# System \"";
1615  comment += this->name();
1616  comment += "\" Solution Vector";
1617  }
1618 
1619  io.data (io_buffer, comment.c_str());
1620 
1621  // total_written_size += io_buffer.size();
1622 
1623  // Only write additional vectors if wanted
1624  if (write_additional_data)
1625  {
1626  for (auto & pr : _vectors)
1627  {
1628  io_buffer.clear();
1629  io_buffer.reserve(pr.second->local_size());
1630 
1631  // Loop over each non-SCALAR variable and each node, and write out the value.
1632  for (unsigned int var=0; var<nv; var++)
1633  if (this->variable(var).type().family != SCALAR)
1634  {
1635  // First write the node DOF values
1636  for (const auto & node : ordered_nodes)
1637  for (unsigned int comp=0; comp<node->n_comp(sys_num, var); comp++)
1638  {
1639  libmesh_assert_not_equal_to (node->dof_number(sys_num, var, comp),
1641 
1642  io_buffer.push_back((*pr.second)(node->dof_number(sys_num, var, comp)));
1643  }
1644 
1645  // Then write the element DOF values
1646  for (const auto & elem : ordered_elements)
1647  for (unsigned int comp=0; comp<elem->n_comp(sys_num, var); comp++)
1648  {
1649  libmesh_assert_not_equal_to (elem->dof_number(sys_num, var, comp),
1651 
1652  io_buffer.push_back((*pr.second)(elem->dof_number(sys_num, var, comp)));
1653  }
1654  }
1655 
1656  // Finally, write the SCALAR data on the last processor
1657  for (unsigned int var=0; var<this->n_vars(); var++)
1658  if (this->variable(var).type().family == SCALAR)
1659  {
1660  if (this->processor_id() == (this->n_processors()-1))
1661  {
1662  const DofMap & dof_map = this->get_dof_map();
1663  std::vector<dof_id_type> SCALAR_dofs;
1664  dof_map.SCALAR_dof_indices(SCALAR_dofs, var);
1665 
1666  for (std::size_t i=0; i<SCALAR_dofs.size(); i++)
1667  io_buffer.push_back((*pr.second)(SCALAR_dofs[i]));
1668  }
1669  }
1670 
1671  // 10.)
1672  //
1673  // Actually write the reordered additional vector
1674  // for this system to disk
1675 
1676  // set up the comment
1677  {
1678  comment = "# System \"";
1679  comment += this->name();
1680  comment += "\" Additional Vector \"";
1681  comment += pr.first;
1682  comment += "\"";
1683  }
1684 
1685  io.data (io_buffer, comment.c_str());
1686 
1687  // total_written_size += io_buffer.size();
1688  }
1689  }
1690 
1691  // const Real
1692  // dt = pl.get_elapsed_time(),
1693  // rate = total_written_size*sizeof(Number)/dt;
1694 
1695  // libMesh::err << "Write " << total_written_size << " \"Number\" values\n"
1696  // << " Elapsed time = " << dt << '\n'
1697  // << " Rate = " << rate/1.e6 << "(MB/sec)\n\n";
1698 
1699  // pl.pop("write_parallel_data");
1700 }
FEFamily family
Definition: fe_type.h:204
const Variable & variable(unsigned int var) const
Definition: system.h:2133
const MeshBase & get_mesh() const
Definition: system.h:2033
processor_id_type n_processors() const
unsigned int number() const
Definition: system.h:2025
std::unique_ptr< NumericVector< Number > > solution
Definition: system.h:1523
static const dof_id_type invalid_id
Definition: dof_object.h:347
std::map< std::string, NumericVector< Number > *> _vectors
Definition: system.h:1935
const std::string & name() const
Definition: system.h:2017
unsigned int n_vars() const
Definition: system.h:2105
processor_id_type processor_id() const
const DofMap & get_dof_map() const
Definition: system.h:2049
const FEType & type() const
Definition: variable.h:119

◆ write_serialized_data()

void libMesh::System::write_serialized_data ( Xdr io,
const bool  write_additional_data = true 
) const
inherited

Writes additional data, namely vectors, for this System. This method may safely be called on a distributed-memory mesh.

This method implements the output of the vectors contained in this System object, embedded in the output of an EquationSystems<T_sys>.

9.) The global solution vector, re-ordered to be node-major (More on this later.)

for each additional vector in the object

10.) The global additional vector, re-ordered to be node-major (More on this later.)

Definition at line 1704 of file system_io.C.

References libMesh::System::_vectors, libMesh::Xdr::comment(), libMesh::System::name(), libMesh::ParallelObject::processor_id(), libMesh::System::solution, and libMesh::System::write_serialized_vector().

1706 {
1720  parallel_object_only();
1721  std::string comment;
1722 
1723  // PerfLog pl("IO Performance",false);
1724  // pl.push("write_serialized_data");
1725  // std::size_t total_written_size = 0;
1726 
1727  // total_written_size +=
1728  this->write_serialized_vector(io, *this->solution);
1729 
1730  // set up the comment
1731  if (this->processor_id() == 0)
1732  {
1733  comment = "# System \"";
1734  comment += this->name();
1735  comment += "\" Solution Vector";
1736 
1737  io.comment (comment);
1738  }
1739 
1740  // Only write additional vectors if wanted
1741  if (write_additional_data)
1742  {
1743  std::map<std::string, NumericVector<Number> *>::const_iterator
1744  pos = _vectors.begin();
1745 
1746  for (; pos != this->_vectors.end(); ++pos)
1747  {
1748  // total_written_size +=
1749  this->write_serialized_vector(io, *pos->second);
1750 
1751  // set up the comment
1752  if (this->processor_id() == 0)
1753  {
1754  comment = "# System \"";
1755  comment += this->name();
1756  comment += "\" Additional Vector \"";
1757  comment += pos->first;
1758  comment += "\"";
1759  io.comment (comment);
1760  }
1761  }
1762  }
1763 
1764  // const Real
1765  // dt = pl.get_elapsed_time(),
1766  // rate = total_written_size*sizeof(Number)/dt;
1767 
1768  // libMesh::out << "Write " << total_written_size << " \"Number\" values\n"
1769  // << " Elapsed time = " << dt << '\n'
1770  // << " Rate = " << rate/1.e6 << "(MB/sec)\n\n";
1771 
1772  // pl.pop("write_serialized_data");
1773 
1774 
1775 
1776 
1777  // // test the new method
1778  // {
1779  // std::vector<std::string> names;
1780  // std::vector<NumericVector<Number> *> vectors_to_write;
1781 
1782  // names.push_back("Solution Vector");
1783  // vectors_to_write.push_back(this->solution.get());
1784 
1785  // // Only write additional vectors if wanted
1786  // if (write_additional_data)
1787  // {
1788  // std::map<std::string, NumericVector<Number> *>::const_iterator
1789  // pos = _vectors.begin();
1790 
1791  // for (; pos != this->_vectors.end(); ++pos)
1792  // {
1793  // names.push_back("Additional Vector " + pos->first);
1794  // vectors_to_write.push_back(pos->second);
1795  // }
1796  // }
1797 
1798  // total_written_size =
1799  // this->write_serialized_vectors (io, names, vectors_to_write);
1800 
1801  // const Real
1802  // dt2 = pl.get_elapsed_time(),
1803  // rate2 = total_written_size*sizeof(Number)/(dt2-dt);
1804 
1805  // libMesh::out << "Write (new) " << total_written_size << " \"Number\" values\n"
1806  // << " Elapsed time = " << (dt2-dt) << '\n'
1807  // << " Rate = " << rate2/1.e6 << "(MB/sec)\n\n";
1808 
1809  // }
1810 }
std::unique_ptr< NumericVector< Number > > solution
Definition: system.h:1523
std::map< std::string, NumericVector< Number > *> _vectors
Definition: system.h:1935
const std::string & name() const
Definition: system.h:2017
processor_id_type processor_id() const
dof_id_type write_serialized_vector(Xdr &io, const NumericVector< Number > &vec) const
Definition: system_io.C:2156

◆ write_serialized_vectors()

std::size_t libMesh::System::write_serialized_vectors ( Xdr io,
const std::vector< const NumericVector< Number > *> &  vectors 
) const
inherited

Serialize & write a number of identically distributed vectors. This method allows for optimization for the multiple vector case by only communicating the metadata once.

Definition at line 2297 of file system_io.C.

References libMesh::Xdr::data(), libMesh::FEType::family, libMesh::System::get_mesh(), libMesh::MeshBase::n_elem(), libMesh::MeshTools::n_elem(), n_nodes, libMesh::MeshBase::n_nodes(), libMesh::System::n_vars(), libMesh::ParallelObject::processor_id(), libMesh::SCALAR, libMesh::Variable::type(), libMesh::System::variable(), libMesh::System::write_SCALAR_dofs(), libMesh::System::write_serialized_blocked_dof_objects(), and libMesh::Xdr::writing().

2299 {
2300  parallel_object_only();
2301 
2302  libmesh_assert (io.writing());
2303 
2304  // Cache these - they are not free!
2305  const dof_id_type
2306  n_nodes = this->get_mesh().n_nodes(),
2307  n_elem = this->get_mesh().n_elem();
2308 
2309  std::size_t written_length = 0;
2310 
2311  if (this->processor_id() == 0)
2312  {
2313  unsigned int
2314  n_vec = cast_int<unsigned int>(vectors.size());
2315  dof_id_type
2316  vec_size = vectors.empty() ? 0 : vectors[0]->size();
2317  // Set the number of vectors
2318  io.data(n_vec, "# number of vectors");
2319  // Set the buffer size
2320  io.data(vec_size, "# vector length");
2321  }
2322 
2323  //---------------------------------
2324  // Collect the values for all nodes
2325  written_length +=
2326  this->write_serialized_blocked_dof_objects (vectors,
2327  n_nodes,
2328  this->get_mesh().local_nodes_begin(),
2329  this->get_mesh().local_nodes_end(),
2330  io);
2331 
2332  //------------------------------------
2333  // Collect the values for all elements
2334  written_length +=
2335  this->write_serialized_blocked_dof_objects (vectors,
2336  n_elem,
2337  this->get_mesh().local_elements_begin(),
2338  this->get_mesh().local_elements_end(),
2339  io);
2340 
2341  //-------------------------------------------
2342  // Finally loop over all the SCALAR variables
2343  for (std::size_t vec=0; vec<vectors.size(); vec++)
2344  for (unsigned int var=0; var<this->n_vars(); var++)
2345  if (this->variable(var).type().family == SCALAR)
2346  {
2347  libmesh_assert_not_equal_to (vectors[vec], 0);
2348 
2349  written_length +=
2350  this->write_SCALAR_dofs (*vectors[vec], var, io);
2351  }
2352 
2353  return written_length;
2354 }
FEFamily family
Definition: fe_type.h:204
const Variable & variable(unsigned int var) const
Definition: system.h:2133
dof_id_type n_elem(const MeshBase::const_element_iterator &begin, const MeshBase::const_element_iterator &end)
Definition: mesh_tools.C:702
unsigned int write_SCALAR_dofs(const NumericVector< Number > &vec, const unsigned int var, Xdr &io) const
Definition: system_io.C:2101
const MeshBase & get_mesh() const
Definition: system.h:2033
const dof_id_type n_nodes
Definition: tecplot_io.C:68
unsigned int n_vars() const
Definition: system.h:2105
virtual dof_id_type n_elem() const =0
processor_id_type processor_id() const
virtual dof_id_type n_nodes() const =0
std::size_t write_serialized_blocked_dof_objects(const std::vector< const NumericVector< Number > *> &vecs, const dof_id_type n_objects, const iterator_type begin, const iterator_type end, Xdr &io, const unsigned int var_to_write=libMesh::invalid_uint) const
Definition: system_io.C:1815
uint8_t dof_id_type
Definition: id_types.h:64
const FEType & type() const
Definition: variable.h:119

◆ zero_variable()

void libMesh::System::zero_variable ( NumericVector< Number > &  v,
unsigned int  var_num 
) const
inherited

Zeroes all dofs in v that correspond to variable number var_num.

Definition at line 1322 of file system.C.

References libMesh::System::get_mesh(), mesh, libMesh::System::n_vars(), libMesh::System::number(), and libMesh::NumericVector< T >::set().

1324 {
1325  /* Make sure the call makes sense. */
1326  libmesh_assert_less (var_num, this->n_vars());
1327 
1328  /* Get a reference to the mesh. */
1329  const MeshBase & mesh = this->get_mesh();
1330 
1331  /* Check which system we are. */
1332  const unsigned int sys_num = this->number();
1333 
1334  // Loop over nodes.
1335  for (const auto & node : mesh.local_node_ptr_range())
1336  {
1337  unsigned int n_comp = node->n_comp(sys_num,var_num);
1338  for (unsigned int i=0; i<n_comp; i++)
1339  {
1340  const dof_id_type index = node->dof_number(sys_num,var_num,i);
1341  v.set(index,0.0);
1342  }
1343  }
1344 
1345  // Loop over elements.
1346  for (const auto & elem : mesh.active_local_element_ptr_range())
1347  {
1348  unsigned int n_comp = elem->n_comp(sys_num,var_num);
1349  for (unsigned int i=0; i<n_comp; i++)
1350  {
1351  const dof_id_type index = elem->dof_number(sys_num,var_num,i);
1352  v.set(index,0.0);
1353  }
1354  }
1355 }
MeshBase & mesh
const MeshBase & get_mesh() const
Definition: system.h:2033
unsigned int number() const
Definition: system.h:2025
virtual void set(const numeric_index_type i, const T value)=0
unsigned int n_vars() const
Definition: system.h:2105
uint8_t dof_id_type
Definition: id_types.h:64

Member Data Documentation

◆ _communicator

◆ _counts

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

◆ _diff_physics

DifferentiablePhysics* libMesh::DifferentiableSystem::_diff_physics
protectedinherited

Pointer to object to use for physics assembly evaluations. Defaults to this for backwards compatibility; in the future users should create separate physics objects.

Definition at line 371 of file diff_system.h.

Referenced by libMesh::DifferentiableSystem::attach_physics(), libMesh::DifferentiableSystem::clear(), libMesh::DifferentiableSystem::get_physics(), libMesh::DifferentiableSystem::init_data(), libMesh::DifferentiableSystem::swap_physics(), and libMesh::DifferentiableSystem::~DifferentiableSystem().

◆ _enable_print_counter

bool libMesh::ReferenceCounter::_enable_print_counter = true
staticprotectedinherited

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

Definition at line 141 of file reference_counter.h.

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

◆ _first_order_vars

std::set<unsigned int> libMesh::DifferentiablePhysics::_first_order_vars
protectedinherited

◆ _mesh_sys

System* libMesh::DifferentiablePhysics::_mesh_sys
protectedinherited

◆ _mesh_x_var

unsigned int libMesh::DifferentiablePhysics::_mesh_x_var
protectedinherited

Variables from which to acquire moving mesh information

Definition at line 547 of file diff_physics.h.

Referenced by libMesh::DifferentiablePhysics::get_mesh_x_var(), mesh_position_get(), numerical_jacobian(), and libMesh::DifferentiablePhysics::set_mesh_x_var().

◆ _mesh_y_var

unsigned int libMesh::DifferentiablePhysics::_mesh_y_var
protectedinherited

◆ _mesh_z_var

unsigned int libMesh::DifferentiablePhysics::_mesh_z_var
protectedinherited

◆ _mutex

Threads::spin_mutex libMesh::ReferenceCounter::_mutex
staticprotectedinherited

Mutual exclusion object to enable thread-safe reference counting.

Definition at line 135 of file reference_counter.h.

◆ _n_objects

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

The number of objects. Print the reference count information when the number returns to 0.

Definition at line 130 of file reference_counter.h.

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

◆ _numerical_jacobian_h_for_var

std::vector<Real> libMesh::FEMSystem::_numerical_jacobian_h_for_var
private

Definition at line 252 of file fem_system.h.

Referenced by numerical_jacobian_h_for_var(), and set_numerical_jacobian_h_for_var().

◆ _second_order_dot_vars

std::map<unsigned int,unsigned int> libMesh::DifferentiablePhysics::_second_order_dot_vars
protectedinherited

If the user adds any second order variables, then we need to also cache the map to their corresponding dot variable that will be added by this TimeSolver class.

Definition at line 571 of file diff_physics.h.

Referenced by libMesh::DifferentiableSystem::add_second_order_dot_vars(), and libMesh::DifferentiableSystem::get_second_order_dot_var().

◆ _second_order_vars

std::set<unsigned int> libMesh::DifferentiablePhysics::_second_order_vars
protectedinherited

◆ _time_evolving

std::vector<unsigned int> libMesh::DifferentiablePhysics::_time_evolving
protectedinherited

Stores unsigned int to tell us which variables are evolving as first order in time (1), second order in time (2), or are not time evolving (0).

Definition at line 554 of file diff_physics.h.

Referenced by libMesh::DifferentiablePhysics::is_time_evolving().

◆ assemble_before_solve

bool libMesh::System::assemble_before_solve
inherited

Flag which tells the system to whether or not to call the user assembly function during each call to solve(). By default, every call to solve() begins with a call to the user assemble, so this flag is true. (For explicit systems, "solving" the system occurs during the assembly step, so this flag is always true for explicit systems.)

You will only want to set this to false if you need direct control over when the system is assembled, and are willing to track the state of its assembly yourself. An example of such a case is an implicit system with multiple right hand sides. In this instance, a single assembly would likely be followed with multiple calls to solve.

The frequency system and Newmark system have their own versions of this flag, called _finished_assemble, which might be able to be replaced with this more general concept.

Definition at line 1477 of file system.h.

Referenced by libMesh::ImplicitSystem::adjoint_solve(), libMesh::ImplicitSystem::disable_cache(), libMesh::System::disable_cache(), libMesh::ImplicitSystem::sensitivity_solve(), libMesh::CondensedEigenSystem::solve(), libMesh::EigenSystem::solve(), and libMesh::LinearImplicitSystem::solve().

◆ assemble_qoi_elements

bool libMesh::DifferentiableQoI::assemble_qoi_elements
inherited

If assemble_qoi_elements is false (it is true by default), the assembly loop for a quantity of interest or its derivatives will skip computing on mesh elements, and will only compute on mesh sides.

Definition at line 99 of file diff_qoi.h.

◆ assemble_qoi_internal_sides

bool libMesh::DifferentiableQoI::assemble_qoi_internal_sides
inherited

If assemble_qoi_internal_sides is true (it is false by default), the assembly loop for a quantity of interest or its derivatives will loop over element sides which do not fall on domain boundaries.

Definition at line 91 of file diff_qoi.h.

◆ assemble_qoi_sides

bool libMesh::DifferentiableQoI::assemble_qoi_sides
inherited

If assemble_qoi_sides is true (it is false by default), the assembly loop for a quantity of interest or its derivatives will loop over domain boundary sides. To add domain interior sides, also set assemble_qoi_internal_sides to true.

Definition at line 83 of file diff_qoi.h.

◆ compute_internal_sides

bool libMesh::DifferentiablePhysics::compute_internal_sides
inherited

compute_internal_sides is false by default, indicating that side_* computations will only be done on boundary sides. If compute_internal_sides is true, computations will be done on sides between elements as well.

Definition at line 153 of file diff_physics.h.

◆ current_local_solution

std::unique_ptr<NumericVector<Number> > libMesh::System::current_local_solution
inherited

All the values I need to compute my contribution to the simulation at hand. Think of this as the current solution with any ghost values needed from other processors. This vector is necessarily larger than the solution vector in the case of a parallel simulation. The update() member is used to synchronize the contents of the solution and current_local_solution vectors.

Definition at line 1535 of file system.h.

Referenced by libMesh::__libmesh_petsc_diff_solver_jacobian(), libMesh::__libmesh_petsc_diff_solver_residual(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::NonlinearImplicitSystem::assembly(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::System::clear(), libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), libMesh::System::current_solution(), DMlibMeshFunction(), DMlibMeshJacobian(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::System::init_data(), libMesh::libmesh_petsc_snes_fd_residual(), libMesh::libmesh_petsc_snes_jacobian(), libMesh::libmesh_petsc_snes_mffd_residual(), libMesh::libmesh_petsc_snes_residual(), libMesh::libmesh_petsc_snes_residual_helper(), libMesh::FEMContext::pre_fe_reinit(), libMesh::System::re_update(), libMesh::System::reinit(), libMesh::System::restrict_vectors(), and libMesh::System::update().

◆ deltat

◆ diff_qoi

DifferentiableQoI* libMesh::DifferentiableSystem::diff_qoi
protectedinherited

Pointer to object to use for quantity of interest assembly evaluations. Defaults to this for backwards compatibility; in the future users should create separate physics objects.

Definition at line 378 of file diff_system.h.

Referenced by assemble_qoi(), assemble_qoi_derivative(), libMesh::DifferentiableSystem::attach_qoi(), libMesh::DifferentiableSystem::clear(), libMesh::DifferentiableSystem::get_qoi(), and libMesh::DifferentiableSystem::~DifferentiableSystem().

◆ extra_quadrature_order

int libMesh::System::extra_quadrature_order
inherited

A member int that can be employed to indicate increased or reduced quadrature order.

Note
For FEMSystem users, by default, when calling the user-defined residual functions, the FEMSystem will first set up an appropriate FEType::default_quadrature_rule() object for performing the integration. This rule will integrate elements of order up to 2*p+1 exactly (where p is the sum of the base FEType and local p refinement levels), but if additional (or reduced) quadrature accuracy is desired then this extra_quadrature_order (default 0) will be added.

Definition at line 1508 of file system.h.

◆ fe_reinit_during_postprocess

bool libMesh::FEMSystem::fe_reinit_during_postprocess

If fe_reinit_during_postprocess is true (it is true by default), FE objects will be reinit()ed with their default quadrature rules. If false, FE objects will need to be reinit()ed by the user or will be in an undefined state.

Definition at line 170 of file fem_system.h.

◆ matrix

◆ numerical_jacobian_h

Real libMesh::FEMSystem::numerical_jacobian_h

If calculating numeric jacobians is required, the FEMSystem will perturb each solution vector entry by numerical_jacobian_h when calculating finite differences. This defaults to the libMesh TOLERANCE but can be set manually.

For ALE terms, the FEMSystem will perturb each mesh point in an element by numerical_jacobian_h * Elem::hmin()

Definition at line 181 of file fem_system.h.

Referenced by numerical_jacobian(), and numerical_jacobian_h_for_var().

◆ postprocess_sides

bool libMesh::DifferentiableSystem::postprocess_sides
inherited

If postprocess_sides is true (it is false by default), the postprocessing loop will loop over all sides as well as all elements.

Definition at line 315 of file diff_system.h.

◆ print_element_jacobians

bool libMesh::DifferentiableSystem::print_element_jacobians
inherited

Set print_element_jacobians to true to print each J_elem contribution.

Definition at line 362 of file diff_system.h.

◆ print_element_residuals

bool libMesh::DifferentiableSystem::print_element_residuals
inherited

Set print_element_residuals to true to print each R_elem contribution.

Definition at line 357 of file diff_system.h.

◆ print_element_solutions

bool libMesh::DifferentiableSystem::print_element_solutions
inherited

Set print_element_solutions to true to print each U_elem input.

Definition at line 352 of file diff_system.h.

◆ print_jacobian_norms

bool libMesh::DifferentiableSystem::print_jacobian_norms
inherited

Set print_jacobian_norms to true to print |J| whenever it is assembled.

Definition at line 342 of file diff_system.h.

Referenced by assembly().

◆ print_jacobians

bool libMesh::DifferentiableSystem::print_jacobians
inherited

Set print_jacobians to true to print J whenever it is assembled.

Definition at line 347 of file diff_system.h.

Referenced by assembly().

◆ print_residual_norms

bool libMesh::DifferentiableSystem::print_residual_norms
inherited

Set print_residual_norms to true to print |F| whenever it is assembled.

Definition at line 332 of file diff_system.h.

Referenced by assembly().

◆ print_residuals

bool libMesh::DifferentiableSystem::print_residuals
inherited

Set print_residuals to true to print F whenever it is assembled.

Definition at line 337 of file diff_system.h.

Referenced by assembly().

◆ print_solution_norms

bool libMesh::DifferentiableSystem::print_solution_norms
inherited

Set print_residual_norms to true to print |U| whenever it is used in an assembly() call

Definition at line 321 of file diff_system.h.

Referenced by assembly().

◆ print_solutions

bool libMesh::DifferentiableSystem::print_solutions
inherited

Set print_solutions to true to print U whenever it is used in an assembly() call

Definition at line 327 of file diff_system.h.

Referenced by assembly().

◆ qoi

std::vector<Number> libMesh::System::qoi
inherited

◆ rhs

◆ solution

std::unique_ptr<NumericVector<Number> > libMesh::System::solution
inherited

Data structure to hold solution values.

Definition at line 1523 of file system.h.

Referenced by libMesh::__libmesh_petsc_diff_solver_jacobian(), libMesh::__libmesh_petsc_diff_solver_residual(), libMesh::ExactSolution::_compute_error(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::NewmarkSolver::advance_timestep(), libMesh::AdaptiveTimeSolver::advance_timestep(), libMesh::UnsteadySolver::advance_timestep(), libMesh::ContinuationSystem::apply_predictor(), assembly(), libMesh::LinearImplicitSystem::assembly(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::System::clear(), libMesh::System::compare(), libMesh::NewmarkSolver::compute_initial_accel(), libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), libMesh::ContinuationSystem::continuation_solve(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::GMVIO::copy_nodal_solution(), DMCreateGlobalVector_libMesh(), DMlibMeshFunction(), DMlibMeshJacobian(), libMesh::UnsteadySolver::du(), libMesh::DofMap::enforce_constraints_exactly(), libMesh::WeightedPatchRecoveryErrorEstimator::estimate_error(), libMesh::PatchRecoveryErrorEstimator::estimate_error(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::AdjointResidualErrorEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::CondensedEigenSystem::get_eigenpair(), libMesh::EigenSystem::get_eigenpair(), libMesh::System::init_data(), libMesh::ContinuationSystem::initialize_tangent(), libMesh::libmesh_petsc_snes_jacobian(), libMesh::libmesh_petsc_snes_postcheck(), libMesh::libmesh_petsc_snes_residual_helper(), libMesh::DofMap::max_constraint_error(), mesh_position_get(), libMesh::ErrorVector::plot_error(), libMesh::ImplicitSystem::qoi_parameter_hessian(), libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product(), libMesh::System::re_update(), libMesh::System::read_legacy_data(), libMesh::System::read_parallel_data(), libMesh::System::read_serialized_data(), libMesh::System::reinit(), libMesh::System::restrict_vectors(), libMesh::MemorySolutionHistory::retrieve(), libMesh::ContinuationSystem::save_current_solution(), libMesh::TwostepTimeSolver::solve(), libMesh::NewtonSolver::solve(), libMesh::PetscDiffSolver::solve(), libMesh::FrequencySystem::solve(), libMesh::LinearImplicitSystem::solve(), libMesh::NonlinearImplicitSystem::solve(), libMesh::ContinuationSystem::solve_tangent(), libMesh::MemorySolutionHistory::store(), libMesh::System::update(), libMesh::System::update_global_solution(), libMesh::ContinuationSystem::update_solution(), libMesh::NewmarkSystem::update_u_v_a(), libMesh::System::write_parallel_data(), and libMesh::System::write_serialized_data().

◆ time

◆ time_solver

◆ use_fixed_solution

bool libMesh::System::use_fixed_solution
inherited

A boolean to be set to true by systems using elem_fixed_solution, for optional use by e.g. stabilized methods. False by default.

Note
For FEMSystem users, if this variable is set to true, it must be before init_data() is called.

Definition at line 1493 of file system.h.

Referenced by libMesh::EulerSolver::_general_residual(), libMesh::Euler2Solver::_general_residual(), libMesh::SteadySolver::_general_residual(), libMesh::NewmarkSolver::_general_residual(), libMesh::DifferentiableSystem::clear(), libMesh::DiffContext::DiffContext(), and libMesh::FEMContext::pre_fe_reinit().

◆ verify_analytic_jacobians

Real libMesh::FEMSystem::verify_analytic_jacobians

If verify_analytic_jacobian is equal to zero (as it is by default), no numeric jacobians will be calculated unless an overridden element_time_derivative(), element_constraint(), side_time_derivative(), or side_constraint() function cannot provide an analytic jacobian upon request.

If verify_analytic_jacobian is equal to the positive value tol, then any time a full analytic element jacobian can be calculated it will be tested against a numerical jacobian on the same element, and the program will abort if the relative error (in matrix l1 norms) exceeds tol.

Definition at line 209 of file fem_system.h.

Referenced by assembly().

◆ zero_out_matrix_and_rhs

bool libMesh::ImplicitSystem::zero_out_matrix_and_rhs
inherited

By default, the system will zero out the matrix and the right hand side. If this flag is false, it is the responsibility of the client code to take care of setting these to zero before assembly begins

Definition at line 380 of file implicit_system.h.

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


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