#include <continuation_system.h>

Inheritance diagram for libMesh::ContinuationSystem:

[legend]

Public Types
enum	Predictor { Euler, AB2, Invalid_Predictor }

typedef ContinuationSystem	sys_type

typedef FEMSystem	Parent

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

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

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

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

virtual	~ContinuationSystem ()

virtual void	clear () override

virtual void	solve () override

void	continuation_solve ()

void	advance_arcstep ()

void	set_max_arclength_stepsize (Real maxds)

void	save_current_solution ()

virtual void	assembly (bool get_residual, bool get_jacobian, bool apply_heterogeneous_constraints=false, bool apply_no_constraints=false) override

void	mesh_position_get ()

void	mesh_position_set ()

virtual std::unique_ptr< DiffContext >	build_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	reinit () override

virtual void	assemble () override

virtual LinearSolver< Number > *	get_linear_solver () const override

virtual std::pair< unsigned int, Real >	get_linear_solve_parameters () const override

virtual void	release_linear_solver (LinearSolver< Number > *) const override

virtual std::pair< unsigned int, Real >	adjoint_solve (const QoISet &qoi_indices=QoISet()) override

virtual std::unique_ptr< DifferentiablePhysics >	clone_physics () override

virtual std::unique_ptr< DifferentiableQoI >	clone () override

const DifferentiablePhysics *	get_physics () const

DifferentiablePhysics *	get_physics ()

void	attach_physics (DifferentiablePhysics *physics_in)

void	swap_physics (DifferentiablePhysics *&swap_physics)

const DifferentiableQoI *	get_qoi () const

DifferentiableQoI *	get_qoi ()

void	attach_qoi (DifferentiableQoI *qoi_in)

void	set_time_solver (std::unique_ptr< TimeSolver > _time_solver)

TimeSolver &	get_time_solver ()

const TimeSolver &	get_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_type &	system ()

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, Real >	sensitivity_solve (const ParameterVector &parameters) override

virtual std::pair< unsigned int, Real >	weighted_sensitivity_solve (const ParameterVector &parameters, const ParameterVector &weights) override

virtual std::pair< unsigned int, Real >	weighted_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 MeshBase &	get_mesh () const

MeshBase &	get_mesh ()

const DofMap &	get_dof_map () const

DofMap &	get_dof_map ()

const EquationSystems &	get_equation_systems () const

EquationSystems &	get_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 Variable &	variable (unsigned int var) const

const VariableGroup &	variable_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 FEType &	variable_type (const unsigned int i) const

const FEType &	variable_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::Communicator &	comm () const

processor_id_type	n_processors () const

processor_id_type	processor_id () const

virtual void	clear_physics ()

virtual void	init_physics (const System &sys)

virtual bool	element_time_derivative (bool request_jacobian, DiffContext &)

virtual bool	element_constraint (bool request_jacobian, DiffContext &)

virtual bool	side_time_derivative (bool request_jacobian, DiffContext &)

virtual bool	side_constraint (bool request_jacobian, DiffContext &)

virtual bool	nonlocal_time_derivative (bool request_jacobian, DiffContext &)

virtual bool	nonlocal_constraint (bool request_jacobian, DiffContext &)

virtual void	time_evolving (unsigned int var)

virtual void	time_evolving (unsigned int var, unsigned int order)

bool	is_time_evolving (unsigned int var) const

virtual bool	eulerian_residual (bool request_jacobian, DiffContext &)

virtual bool	eulerian_residual (bool request_jacobian, DiffContext &context) override

virtual bool	mass_residual (bool request_jacobian, DiffContext &)

virtual bool	mass_residual (bool request_jacobian, DiffContext &) override

virtual bool	side_mass_residual (bool request_jacobian, DiffContext &)

virtual bool	nonlocal_mass_residual (bool request_jacobian, DiffContext &c)

virtual bool	damping_residual (bool request_jacobian, DiffContext &)

virtual bool	side_damping_residual (bool request_jacobian, DiffContext &)

virtual bool	nonlocal_damping_residual (bool request_jacobian, DiffContext &)

virtual void	set_mesh_system (System *sys)

const System *	get_mesh_system () const

System *	get_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)

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
Real *	continuation_parameter

bool	quiet

Real	continuation_parameter_tolerance

Real	solution_tolerance

Real	initial_newton_tolerance

Real	old_continuation_parameter

Real	min_continuation_parameter

Real	max_continuation_parameter

Real	Theta

Real	Theta_LOCA

unsigned int	n_backtrack_steps

unsigned int	n_arclength_reductions

Real	ds_min

Predictor	predictor

Real	newton_stepgrowth_aggressiveness

bool	newton_progress_check

bool	fe_reinit_during_postprocess

Real	numerical_jacobian_h

Real	verify_analytic_jacobians

std::unique_ptr< TimeSolver >	time_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< Number >	qoi

bool	compute_internal_sides

bool	assemble_qoi_sides

bool	assemble_qoi_internal_sides

bool	assemble_qoi_elements

Protected Types
enum	RHS_Mode { Residual, G_Lambda }

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

Protected Member Functions
virtual void	init_data () override

void	add_second_order_dot_vars ()

void	add_dot_var_dirichlet_bcs (unsigned int var_idx, unsigned int dot_var_idx)

virtual void	init_matrices ()

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

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

void	increment_constructor_count (const std::string &name)

void	increment_destructor_count (const std::string &name)

Protected Attributes
RHS_Mode	rhs_mode

DifferentiablePhysics *	_diff_physics

DifferentiableQoI *	diff_qoi

const Parallel::Communicator &	_communicator

System *	_mesh_sys

unsigned int	_mesh_x_var

unsigned int	_mesh_y_var

unsigned int	_mesh_z_var

std::vector< unsigned int >	_time_evolving

std::set< unsigned int >	_first_order_vars

std::set< unsigned int >	_second_order_vars

std::map< unsigned int, unsigned int >	_second_order_dot_vars

Static Protected Attributes
static Counts	_counts

static Threads::atomic< unsigned int >	_n_objects

static Threads::spin_mutex	_mutex

static bool	_enable_print_counter = true

Private Member Functions
void	initialize_tangent ()

void	solve_tangent ()

void	update_solution ()

void	set_Theta ()

void	set_Theta_LOCA ()

void	apply_predictor ()

Private Attributes
NumericVector< Number > *	du_ds

NumericVector< Number > *	previous_du_ds

NumericVector< Number > *	previous_u

NumericVector< Number > *	y

NumericVector< Number > *	y_old

NumericVector< Number > *	z

NumericVector< Number > *	delta_u

std::unique_ptr< LinearSolver< Number > >	linear_solver

bool	tangent_initialized

NewtonSolver *	newton_solver

Real	dlambda_ds

Real	ds

Real	ds_current

Real	previous_dlambda_ds

Real	previous_ds

unsigned int	newton_step

Detailed Description

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

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

Author: John W. Peterson

Date: 2007

Definition at line 55 of file continuation_system.h.

Member Typedef Documentation

◆ 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

typedef FEMSystem libMesh::ContinuationSystem::Parent

The type of the parent.

Definition at line 79 of file continuation_system.h.

◆ sys_type

typedef ContinuationSystem libMesh::ContinuationSystem::sys_type

The type of system.

Definition at line 74 of file continuation_system.h.

◆ TimeSolverResPtr

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

inherited

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.

Member Enumeration Documentation

◆ Predictor

enum libMesh::ContinuationSystem::Predictor

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

Enumerator
Euler	First-order Euler predictor
AB2	Second-order explicit Adams-Bashforth predictor
Invalid_Predictor	Invalid predictor

Definition at line 221 of file continuation_system.h.

                  {
     Euler,
 
     AB2,
 
     Invalid_Predictor
   };

◆ RHS_Mode

enum libMesh::ContinuationSystem::RHS_Mode

protected

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

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

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

Enumerator
Residual
G_Lambda

Definition at line 286 of file continuation_system.h.

286 {Residual,

287 G_Lambda};

libMesh::ContinuationSystem::Residual

Definition: continuation_system.h:286

libMesh::ContinuationSystem::G_Lambda

Definition: continuation_system.h:287

Constructor & Destructor Documentation

◆ ContinuationSystem()

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

Constructor. Optionally initializes required data structures.

Definition at line 29 of file continuation_system.C.

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

                                                                       :
   Parent(es, name_in, number_in),
   continuation_parameter(nullptr),
   quiet(true),
   continuation_parameter_tolerance(1.e-6),
   solution_tolerance(1.e-6),
   initial_newton_tolerance(0.01),
   old_continuation_parameter(0.),
   min_continuation_parameter(0.),
   max_continuation_parameter(0.),
   Theta(1.),
   Theta_LOCA(1.),
   n_backtrack_steps(5),
   n_arclength_reductions(5),
   ds_min(1.e-8),
   predictor(Euler),
   newton_stepgrowth_aggressiveness(1.),
   newton_progress_check(true),
   rhs_mode(Residual),
   linear_solver(LinearSolver<Number>::build(es.comm())),
   tangent_initialized(false),
   newton_solver(nullptr),
   dlambda_ds(0.707),
   ds(0.1),
   ds_current(0.1),
   previous_dlambda_ds(0.),
   previous_ds(0.),
   newton_step(0)
 {
   // Warn about using untested code
   libmesh_experimental();
 
   if (libMesh::on_command_line("--solver-system-names"))
     linear_solver->init((this->name()+"_").c_str());
   else
     linear_solver->init();
 }

◆ ~ContinuationSystem()

libMesh::ContinuationSystem::~ContinuationSystem ( )

virtual

Destructor.

Definition at line 72 of file continuation_system.C.

References clear().

 {
   this->clear();
 }

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.

 {
   _active = true;
 }

◆ 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.

 {
   return _active;
 }

◆ 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 libMesh::FEMSystem::assemble_qoi_derivative().

 {
   std::ostringstream adjoint_rhs_name;
   adjoint_rhs_name << "adjoint_rhs" << i;
 
   return this->add_vector(adjoint_rhs_name.str(), false);
 }

◆ 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().

 {
   std::ostringstream adjoint_name;
   adjoint_name << "adjoint_solution" << i;
 
   NumericVector<Number> & returnval = this->add_vector(adjoint_name.str());
   this->set_vector_as_adjoint(adjoint_name.str(), i);
   return returnval;
 }

◆ 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().

 {
   // We're assuming that there could be a lot more variables than
   // boundary conditions, so we search each of the boundary conditions
   // for this variable rather than looping over boundary conditions
   // in a separate loop and searching through all the variables.
   const DirichletBoundaries * all_dbcs =
     this->get_dof_map().get_dirichlet_boundaries();
 
   if (all_dbcs)
     {
       // We need to cache the DBCs to be added so that we add them
       // after looping over the existing DBCs. Otherwise, we're polluting
       // the thing we're looping over.
       std::vector<DirichletBoundary *> new_dbcs;
 
       for (const auto & dbc : *all_dbcs)
         {
           libmesh_assert(dbc);
 
           // Look for second order variable in the current
           // DirichletBoundary object
           std::vector<unsigned int>::const_iterator dbc_var_it =
             std::find( dbc->variables.begin(), dbc->variables.end(), var_idx );
 
           // If we found it, then we also need to add it's corresponding
           // "dot" variable to a DirichletBoundary
           std::vector<unsigned int> vars_to_add;
           if (dbc_var_it != dbc->variables.end())
             vars_to_add.push_back(dot_var_idx);
 
           if (!vars_to_add.empty())
             {
               // We need to check if the boundary condition is time-dependent.
               // Currently, we cannot automatically differentiate w.r.t. time
               // so if the user supplies a time-dependent Dirichlet BC, then
               // we can't automatically support the Dirichlet BC for the
               // "velocity" boundary condition, so we error. Otherwise,
               // the "velocity boundary condition will just be zero.
               bool is_time_evolving_bc = false;
               if (dbc->f)
                 is_time_evolving_bc = dbc->f->is_time_dependent();
               else if (dbc->f_fem)
                 // We it's a FEMFunctionBase object, it will be implicitly
                 // time-dependent since it is assumed to depend on the solution.
                 is_time_evolving_bc = true;
               else
                 libmesh_error_msg("Could not find valid boundary function!");
 
               if (is_time_evolving_bc)
                 libmesh_error_msg("Cannot currently support time-dependent Dirichlet BC for dot variables!");
 
 
               DirichletBoundary * new_dbc;
 
               if (dbc->f)
                 {
                   ZeroFunction<Number> zf;
 
                   new_dbc = new DirichletBoundary(dbc->b, vars_to_add, zf);
                 }
               else
                 libmesh_error();
 
               new_dbcs.push_back(new_dbc);
             }
         }
 
       // Let the DofMap make its own deep copy of the DirichletBC objects and delete our copy.
       for (const auto & dbc : new_dbcs)
         {
           this->get_dof_map().add_dirichlet_boundary(*dbc);
           delete dbc;
         }
 
     } // if (all_dbcs)
 }

◆ 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().

 {
   // only add matrices before initializing...
   if (!_can_add_matrices)
     libmesh_error_msg("ERROR: Too late.  Cannot add matrices to the system after initialization"
                       << "\n any more.  You should have done this earlier.");
 
   // Return the matrix if it is already there.
   if (this->have_matrix(mat_name))
     return *(_matrices[mat_name]);
 
   // Otherwise build the matrix and return it.
   SparseMatrix<Number> * buf = SparseMatrix<Number>::build(this->comm()).release();
   _matrices.insert (std::make_pair (mat_name, buf));
 
   return *buf;
 }

◆ 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().

 {
   const std::set<unsigned int> & second_order_vars = this->get_second_order_vars();
   if (!second_order_vars.empty())
     {
       for (const auto & var_id : second_order_vars)
         {
           const Variable & var = this->variable(var_id);
           std::string new_var_name = std::string("dot_")+var.name();
 
           unsigned int v_var_idx;
 
           if (var.active_subdomains().empty())
             v_var_idx = this->add_variable( new_var_name, var.type() );
           else
             v_var_idx = this->add_variable( new_var_name, var.type(), &var.active_subdomains() );
 
           _second_order_dot_vars.insert(std::pair<unsigned int, unsigned int>(var_id, v_var_idx));
 
           // The new velocities are time evolving variables of first order
           this->time_evolving( v_var_idx, 1 );
 
           // And if there are any boundary conditions set on the second order
           // variable, we also need to set it on its velocity variable.
           this->add_dot_var_dirichlet_bcs(var_id, v_var_idx);
         }
     }
 }

◆ 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().

 {
   std::ostringstream sensitivity_rhs_name;
   sensitivity_rhs_name << "sensitivity_rhs" << i;
 
   return this->add_vector(sensitivity_rhs_name.str(), false);
 }

◆ 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().

 {
   std::ostringstream sensitivity_name;
   sensitivity_name << "sensitivity_solution" << i;
 
   return this->add_vector(sensitivity_name.str());
 }

◆ 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().

 {
   libmesh_assert(!this->is_initialized());
 
   // Make sure the variable isn't there already
   // or if it is, that it's the type we want
   for (unsigned int v=0; v<this->n_vars(); v++)
     if (this->variable_name(v) == var)
       {
         if (this->variable_type(v) == type)
           return _variables[v].number();
 
         libmesh_error_msg("ERROR: incompatible variable " << var << " has already been added for this system!");
       }
 
   // Optimize for VariableGroups here - if the user is adding multiple
   // variables of the same FEType and subdomain restriction, catch
   // that here and add them as members of the same VariableGroup.
   //
   // start by setting this flag to whatever the user has requested
   // and then consider the conditions which should negate it.
   bool should_be_in_vg = this->identify_variable_groups();
 
   // No variable groups, nothing to add to
   if (!this->n_variable_groups())
     should_be_in_vg = false;
 
   else
     {
       VariableGroup & vg(_variable_groups.back());
 
       // get a pointer to their subdomain restriction, if any.
       const std::set<subdomain_id_type> * const
         their_active_subdomains (vg.implicitly_active() ?
                                  nullptr : &vg.active_subdomains());
 
       // Different types?
       if (vg.type() != type)
         should_be_in_vg = false;
 
       // they are restricted, we aren't?
       if (their_active_subdomains && !active_subdomains)
         should_be_in_vg = false;
 
       // they aren't restricted, we are?
       if (!their_active_subdomains && active_subdomains)
         should_be_in_vg = false;
 
       if (their_active_subdomains && active_subdomains)
         // restricted to different sets?
         if (*their_active_subdomains != *active_subdomains)
           should_be_in_vg = false;
 
       // OK, after all that, append the variable to the vg if none of the conditions
       // were violated
       if (should_be_in_vg)
         {
           const unsigned short curr_n_vars = cast_int<unsigned short>
             (this->n_vars());
 
           vg.append (var);
 
           _variables.push_back(vg(vg.n_variables()-1));
           _variable_numbers[var] = curr_n_vars;
           return curr_n_vars;
         }
     }
 
   // otherwise, fall back to adding a single variable group
   return this->add_variables (std::vector<std::string>(1, var),
                               type,
                               active_subdomains);
 }

◆ 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().

 {
   return this->add_variable(var,
                             FEType(order, family),
                             active_subdomains);
 }

◆ 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().

 {
   libmesh_assert(!this->is_initialized());
 
   // Make sure the variable isn't there already
   // or if it is, that it's the type we want
   for (std::size_t ov=0; ov<vars.size(); ov++)
     for (unsigned int v=0; v<this->n_vars(); v++)
       if (this->variable_name(v) == vars[ov])
         {
           if (this->variable_type(v) == type)
             return _variables[v].number();
 
           libmesh_error_msg("ERROR: incompatible variable " << vars[ov] << " has already been added for this system!");
         }
 
   const unsigned short curr_n_vars = cast_int<unsigned short>
     (this->n_vars());
 
   const unsigned int next_first_component = this->n_components();
 
   // Add the variable group to the list
   _variable_groups.push_back((active_subdomains == nullptr) ?
                              VariableGroup(this, vars, curr_n_vars,
                                            next_first_component, type) :
                              VariableGroup(this, vars, curr_n_vars,
                                            next_first_component, type, *active_subdomains));
 
   const VariableGroup & vg (_variable_groups.back());
 
   // Add each component of the group individually
   for (auto v : IntRange<unsigned int>(0, vars.size()))
     {
       _variables.push_back (vg(v));
       _variable_numbers[vars[v]] = cast_int<unsigned short>
         (curr_n_vars+v);
     }
 
   libmesh_assert_equal_to ((curr_n_vars+vars.size()), this->n_vars());
 
   // BSK - Defer this now to System::init_data() so we can detect
   // VariableGroups 12/28/2012
   // // Add the variable group to the _dof_map
   // _dof_map->add_variable_group (vg);
 
   // Return the number of the new variable
   return cast_int<unsigned int>(curr_n_vars+vars.size()-1);
 }

◆ 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().

 {
   return this->add_variables(vars,
                              FEType(order, family),
                              active_subdomains);
 }

◆ 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(), 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().

 {
   // Return the vector if it is already there.
   if (this->have_vector(vec_name))
     return *(_vectors[vec_name]);
 
   // Otherwise build the vector
   NumericVector<Number> * buf = NumericVector<Number>::build(this->comm()).release();
   _vectors.insert (std::make_pair (vec_name, buf));
   _vector_projections.insert (std::make_pair (vec_name, projections));
 
   _vector_types.insert (std::make_pair (vec_name, type));
 
   // Vectors are primal by default
   _vector_is_adjoint.insert (std::make_pair (vec_name, -1));
 
   // Initialize it if necessary
   if (_is_initialized)
     {
       if (type == GHOSTED)
         {
 #ifdef LIBMESH_ENABLE_GHOSTED
           buf->init (this->n_dofs(), this->n_local_dofs(),
                      _dof_map->get_send_list(), false,
                      GHOSTED);
 #else
           libmesh_error_msg("Cannot initialize ghosted vectors when they are not enabled.");
 #endif
         }
       else
         buf->init (this->n_dofs(), this->n_local_dofs(), false, type);
     }
 
   return *buf;
 }

◆ 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().

 {
   std::ostringstream adjoint_name;
   adjoint_name << "weighted_sensitivity_adjoint_solution" << i;
 
   NumericVector<Number> & returnval = this->add_vector(adjoint_name.str());
   this->set_vector_as_adjoint(adjoint_name.str(), i);
   return returnval;
 }

◆ 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().

 {
   return this->add_vector("weighted_sensitivity_solution");
 }

◆ 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.

 {
   ParameterVector & parameters =
     const_cast<ParameterVector &>(parameters_in);
 
   const unsigned int Np = cast_int<unsigned int>
     (parameters.size());
   const unsigned int Nq = this->n_qois();
 
   // An introduction to the problem:
   //
   // Residual R(u(p),p) = 0
   // partial R / partial u = J = system matrix
   //
   // This implies that:
   // d/dp(R) = 0
   // (partial R / partial p) +
   // (partial R / partial u) * (partial u / partial p) = 0
 
   // We first do an adjoint solve:
   // J^T * z = (partial q / partial u)
   // if we havent already or dont have an initial condition for the adjoint
   if (!this->is_adjoint_already_solved())
     {
       this->adjoint_solve(qoi_indices);
     }
 
   this->assemble_residual_derivatives(parameters_in);
 
   // Get ready to fill in sensitivities:
   sensitivities.allocate_data(qoi_indices, *this, parameters);
 
   // We use the identities:
   // dq/dp = (partial q / partial p) + (partial q / partial u) *
   //         (partial u / partial p)
   // dq/dp = (partial q / partial p) + (J^T * z) *
   //         (partial u / partial p)
   // dq/dp = (partial q / partial p) + z * J *
   //         (partial u / partial p)
 
   // Leading to our final formula:
   // dq/dp = (partial q / partial p) - z * (partial R / partial p)
 
   // In the case of adjoints with heterogenous Dirichlet boundary
   // function phi, where
   // q :=  S(u) - R(u,phi)
   // the final formula works out to:
   // dq/dp = (partial S / partial p) - z * (partial R / partial p)
   // Because we currently have no direct access to
   // (partial S / partial p), we use the identity
   // (partial S / partial p) = (partial q / partial p) +
   //                           phi * (partial R / partial p)
   // to derive an equivalent equation:
   // dq/dp = (partial q / partial p) - (z-phi) * (partial R / partial p)
 
   // Since z-phi degrees of freedom are zero for constrained indices,
   // we can use the same constrained -(partial R / partial p) that we
   // use for forward sensitivity solves, taking into account the
   // differing sign convention.
   //
   // Since that vector is constrained, its constrained indices are
   // zero, so its product with phi is zero, so we can neglect the
   // evaluation of phi terms.
 
   for (unsigned int j=0; j != Np; ++j)
     {
       // We currently get partial derivatives via central differencing
 
       // (partial q / partial p) ~= (q(p+dp)-q(p-dp))/(2*dp)
       // (partial R / partial p) ~= (rhs(p+dp) - rhs(p-dp))/(2*dp)
 
       Number old_parameter = *parameters[j];
 
       const Real delta_p =
         TOLERANCE * std::max(std::abs(old_parameter), 1e-3);
 
       *parameters[j] = old_parameter - delta_p;
       this->assemble_qoi(qoi_indices);
       std::vector<Number> qoi_minus = this->qoi;
 
       NumericVector<Number> & neg_partialR_partialp = this->get_sensitivity_rhs(j);
 
       *parameters[j] = old_parameter + delta_p;
       this->assemble_qoi(qoi_indices);
       std::vector<Number> & qoi_plus = this->qoi;
 
       std::vector<Number> partialq_partialp(Nq, 0);
       for (unsigned int i=0; i != Nq; ++i)
         if (qoi_indices.has_index(i))
           partialq_partialp[i] = (qoi_plus[i] - qoi_minus[i]) / (2.*delta_p);
 
       // Don't leave the parameter changed
       *parameters[j] = old_parameter;
 
       for (unsigned int i=0; i != Nq; ++i)
         if (qoi_indices.has_index(i))
           sensitivities[i][j] = partialq_partialp[i] +
             neg_partialR_partialp.dot(this->get_adjoint_solution(i));
     }
 
   // All parameters have been reset.
   // Reset the original qoi.
 
   this->assemble_qoi(qoi_indices);
 }

◆ 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().

 {
   // Get the time solver object associated with the system, and tell it that
   // we are solving the adjoint problem
   this->get_time_solver().set_is_adjoint(true);
 
   return this->ImplicitSystem::adjoint_solve(qoi_indices);
 }

◆ advance_arcstep()

void libMesh::ContinuationSystem::advance_arcstep ( )

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

Definition at line 936 of file continuation_system.C.

References solve_tangent(), and update_solution().

 {
   // Solve for the updated tangent du1/ds, d(lambda1)/ds
   solve_tangent();
 
   // Advance the solution and the parameter to the next value.
   update_solution();
 }

◆ apply_predictor()

void libMesh::ContinuationSystem::apply_predictor ( )

private

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

Definition at line 1375 of file continuation_system.C.

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

Referenced by continuation_solve(), and update_solution().

 {
   if (predictor == Euler)
     {
       // 1.) Euler Predictor
       // Predict next the solution
       solution->add(ds_current, *du_ds);
       solution->close();
 
       // Predict next parameter value
       *continuation_parameter += ds_current*dlambda_ds;
     }
 
 
   else if (predictor == AB2)
     {
       // 2.) 2nd-order explicit AB predictor
       libmesh_assert_not_equal_to (previous_ds, 0.0);
       const Real stepratio = ds_current/previous_ds;
 
       // Build up next solution value.
       solution->add( 0.5*ds_current*(2.+stepratio), *du_ds);
       solution->add(-0.5*ds_current*stepratio     , *previous_du_ds);
       solution->close();
 
       // Next parameter value
       *continuation_parameter +=
         0.5*ds_current*((2.+stepratio)*dlambda_ds -
                         stepratio*previous_dlambda_ds);
     }
 
   else
     libmesh_error_msg("Unknown predictor!");
 }

◆ 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().

 {
   this->assembly(true, true);
 }

◆ assemble_qoi()

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

overridevirtualinherited

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().

 {
   LOG_SCOPE("assemble_qoi()", "FEMSystem");
 
   const MeshBase & mesh = this->get_mesh();
 
   this->update();
 
   const unsigned int Nq = this->n_qois();
 
   // the quantity of interest is assumed to be a sum of element and
   // side terms
   for (unsigned int i=0; i != Nq; ++i)
     if (qoi_indices.has_index(i))
       qoi[i] = 0;
 
   // Create a non-temporary qoi_contributions object, so we can query
   // its results after the reduction
   QoIContributions qoi_contributions(*this, *(this->diff_qoi), qoi_indices);
 
   // Loop over every active mesh element on this processor
   Threads::parallel_reduce(elem_range.reset(mesh.active_local_elements_begin(),
                                             mesh.active_local_elements_end()),
                            qoi_contributions);
 
   this->diff_qoi->parallel_op( this->comm(), this->qoi, qoi_contributions.qoi, qoi_indices );
 }

◆ assemble_qoi_derivative()

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

overridevirtualinherited

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().

 {
   LOG_SCOPE("assemble_qoi_derivative()", "FEMSystem");
 
   const MeshBase & mesh = this->get_mesh();
 
   this->update();
 
   // The quantity of interest derivative assembly accumulates on
   // initially zero vectors
   for (unsigned int i=0; i != this->n_qois(); ++i)
     if (qoi_indices.has_index(i))
       this->add_adjoint_rhs(i).zero();
 
   // Loop over every active mesh element on this processor
   Threads::parallel_for (elem_range.reset(mesh.active_local_elements_begin(),
                                           mesh.active_local_elements_end()),
                          QoIDerivativeContributions(*this, qoi_indices,
                                                     *(this->diff_qoi),
                                                     include_liftfunc,
                                                     apply_constraints));
 
   for (unsigned int i=0; i != this->n_qois(); ++i)
     if (qoi_indices.has_index(i))
       this->diff_qoi->finalize_derivative(this->get_adjoint_rhs(i),i);
 }

◆ 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().

 {
   ParameterVector & parameters =
     const_cast<ParameterVector &>(parameters_in);
 
   const unsigned int Np = cast_int<unsigned int>
     (parameters.size());
 
   for (unsigned int p=0; p != Np; ++p)
     {
       NumericVector<Number> & sensitivity_rhs = this->add_sensitivity_rhs(p);
 
       // Approximate -(partial R / partial p) by
       // (R(p-dp) - R(p+dp)) / (2*dp)
 
       Number old_parameter = *parameters[p];
 
       const Real delta_p =
         TOLERANCE * std::max(std::abs(old_parameter), 1e-3);
 
       *parameters[p] -= delta_p;
 
       //      this->assembly(true, false, true);
       this->assembly(true, false, false);
       this->rhs->close();
       sensitivity_rhs = *this->rhs;
 
       *parameters[p] = old_parameter + delta_p;
 
       //      this->assembly(true, false, true);
       this->assembly(true, false, false);
       this->rhs->close();
 
       sensitivity_rhs -= *this->rhs;
       sensitivity_rhs /= (2*delta_p);
       sensitivity_rhs.close();
 
       *parameters[p] = old_parameter;
     }
 }

◆ assembly()

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

overridevirtualinherited

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

Referenced by continuation_solve(), and solve_tangent().

 {
   libmesh_assert(get_residual || get_jacobian);
 
   // Log residual and jacobian and combined performance separately
 #ifdef LIBMESH_ENABLE_PERFORMANCE_LOGGING
   const char * log_name;
   if (get_residual && get_jacobian)
     log_name = "assembly()";
   else if (get_residual)
     log_name = "assembly(get_residual)";
   else
     log_name = "assembly(get_jacobian)";
 
   LOG_SCOPE(log_name, "FEMSystem");
 #endif
 
   const MeshBase & mesh = this->get_mesh();
 
   if (print_solution_norms)
     {
       this->solution->close();
 
       std::streamsize old_precision = libMesh::out.precision();
       libMesh::out.precision(16);
       libMesh::out << "|U| = "
                    << this->solution->l1_norm()
                    << std::endl;
       libMesh::out.precision(old_precision);
     }
   if (print_solutions)
     {
       std::streamsize old_precision = libMesh::out.precision();
       libMesh::out.precision(16);
       libMesh::out << "U = [" << *(this->solution)
                    << "];" << std::endl;
       libMesh::out.precision(old_precision);
     }
 
   // Is this definitely necessary? [RHS]
   // Yes. [RHS 2012]
   if (get_jacobian)
     matrix->zero();
   if (get_residual)
     rhs->zero();
 
   // Stupid C++ lets you set *Real* verify_analytic_jacobians = true!
   if (verify_analytic_jacobians > 0.5)
     {
       libMesh::err << "WARNING!  verify_analytic_jacobians was set "
                    << "to absurdly large value of "
                    << verify_analytic_jacobians << std::endl;
       libMesh::err << "Resetting to 1e-6!" << std::endl;
       verify_analytic_jacobians = 1e-6;
     }
 
   // In time-dependent problems, the nonlinear function we're trying
   // to solve at each timestep may depend on the particular solver
   // we're using
   libmesh_assert(time_solver.get());
 
   // Build the residual and jacobian contributions on every active
   // mesh element on this processor
   Threads::parallel_for
     (elem_range.reset(mesh.active_local_elements_begin(),
                       mesh.active_local_elements_end()),
      AssemblyContributions(*this, get_residual, get_jacobian,
                            apply_heterogeneous_constraints,
                            apply_no_constraints));
 
   // Check and see if we have SCALAR variables
   bool have_scalar = false;
   for (unsigned int i=0; i != this->n_variable_groups(); ++i)
     {
       if (this->variable_group(i).type().family == SCALAR)
         {
           have_scalar = true;
           break;
         }
     }
 
   // SCALAR dofs are stored on the last processor, so we'll evaluate
   // their equation terms there and only if we have a SCALAR variable
   if (this->processor_id() == (this->n_processors()-1) && have_scalar)
     {
       std::unique_ptr<DiffContext> con = this->build_context();
       FEMContext & _femcontext = cast_ref<FEMContext &>(*con);
       this->init_context(_femcontext);
       _femcontext.pre_fe_reinit(*this, nullptr);
 
       bool jacobian_computed =
         this->time_solver->nonlocal_residual(get_jacobian, _femcontext);
 
       // Nonlocal residuals are likely to be length 0, in which case we
       // don't need to do any more.  And we shouldn't try to do any
       // more; lots of DenseVector/DenseMatrix code assumes rank>0.
       if (_femcontext.get_elem_residual().size())
         {
           // Compute a numeric jacobian if we have to
           if (get_jacobian && !jacobian_computed)
             {
               // Make sure we didn't compute a jacobian and lie about it
               libmesh_assert_equal_to (_femcontext.get_elem_jacobian().l1_norm(), 0.0);
               // Logging of numerical jacobians is done separately
               this->numerical_nonlocal_jacobian(_femcontext);
             }
 
           // Compute a numeric jacobian if we're asked to verify the
           // analytic jacobian we got
           if (get_jacobian && jacobian_computed &&
               this->verify_analytic_jacobians != 0.0)
             {
               DenseMatrix<Number> analytic_jacobian(_femcontext.get_elem_jacobian());
 
               _femcontext.get_elem_jacobian().zero();
               // Logging of numerical jacobians is done separately
               this->numerical_nonlocal_jacobian(_femcontext);
 
               Real analytic_norm = analytic_jacobian.l1_norm();
               Real numerical_norm = _femcontext.get_elem_jacobian().l1_norm();
 
               // If we can continue, we'll probably prefer the analytic jacobian
               analytic_jacobian.swap(_femcontext.get_elem_jacobian());
 
               // The matrix "analytic_jacobian" will now hold the error matrix
               analytic_jacobian.add(-1.0, _femcontext.get_elem_jacobian());
               Real error_norm = analytic_jacobian.l1_norm();
 
               Real relative_error = error_norm /
                 std::max(analytic_norm, numerical_norm);
 
               if (relative_error > this->verify_analytic_jacobians)
                 {
                   libMesh::err << "Relative error " << relative_error
                                << " detected in analytic jacobian on nonlocal dofs!"
                                << std::endl;
 
                   std::streamsize old_precision = libMesh::out.precision();
                   libMesh::out.precision(16);
                   libMesh::out << "J_analytic nonlocal = "
                                << _femcontext.get_elem_jacobian() << std::endl;
                   analytic_jacobian.add(1.0, _femcontext.get_elem_jacobian());
                   libMesh::out << "J_numeric nonlocal = "
                                << analytic_jacobian << std::endl;
 
                   libMesh::out.precision(old_precision);
 
                   libmesh_error_msg("Relative error too large, exiting!");
                 }
             }
 
           add_element_system
             (*this, get_residual, get_jacobian,
              apply_heterogeneous_constraints, apply_no_constraints, _femcontext);
         }
     }
 
   if (get_residual && (print_residual_norms || print_residuals))
     this->rhs->close();
   if (get_residual && print_residual_norms)
     {
       std::streamsize old_precision = libMesh::out.precision();
       libMesh::out.precision(16);
       libMesh::out << "|F| = " << this->rhs->l1_norm() << std::endl;
       libMesh::out.precision(old_precision);
     }
   if (get_residual && print_residuals)
     {
       std::streamsize old_precision = libMesh::out.precision();
       libMesh::out.precision(16);
       libMesh::out << "F = [" << *(this->rhs) << "];" << std::endl;
       libMesh::out.precision(old_precision);
     }
 
   if (get_jacobian && (print_jacobian_norms || print_jacobians))
     this->matrix->close();
   if (get_jacobian && print_jacobian_norms)
     {
       std::streamsize old_precision = libMesh::out.precision();
       libMesh::out.precision(16);
       libMesh::out << "|J| = " << this->matrix->l1_norm() << std::endl;
       libMesh::out.precision(old_precision);
     }
   if (get_jacobian && print_jacobians)
     {
       std::streamsize old_precision = libMesh::out.precision();
       libMesh::out.precision(16);
       libMesh::out << "J = [" << *(this->matrix) << "];" << std::endl;
       libMesh::out.precision(old_precision);
     }
 }

◆ 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.

 {
   libmesh_assert(fptr);
 
   if (_assemble_system_object != nullptr)
     {
       libmesh_here();
       libMesh::out << "WARNING:  Cannot specify both assembly function and object!"
                    << std::endl;
 
       _assemble_system_object = nullptr;
     }
 
   _assemble_system_function = fptr;
 }

◆ 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.

 {
   if (_assemble_system_function != nullptr)
     {
       libmesh_here();
       libMesh::out << "WARNING:  Cannot specify both assembly object and function!"
                    << std::endl;
 
       _assemble_system_function = nullptr;
     }
 
   _assemble_system_object = &assemble_in;
 }

◆ 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.

 {
   libmesh_assert(fptr);
 
   if (_constrain_system_object != nullptr)
     {
       libmesh_here();
       libMesh::out << "WARNING:  Cannot specify both constraint function and object!"
                    << std::endl;
 
       _constrain_system_object = nullptr;
     }
 
   _constrain_system_function = fptr;
 }

◆ 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.

 {
   if (_constrain_system_function != nullptr)
     {
       libmesh_here();
       libMesh::out << "WARNING:  Cannot specify both constraint object and function!"
                    << std::endl;
 
       _constrain_system_function = nullptr;
     }
 
   _constrain_system_object = &constrain;
 }

◆ 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.

 {
   libmesh_assert(fptr);
 
   if (_init_system_object != nullptr)
     {
       libmesh_here();
       libMesh::out << "WARNING:  Cannot specify both initialization function and object!"
                    << std::endl;
 
       _init_system_object = nullptr;
     }
 
   _init_system_function = fptr;
 }

◆ 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.

 {
   if (_init_system_function != nullptr)
     {
       libmesh_here();
       libMesh::out << "WARNING:  Cannot specify both initialization object and function!"
                    << std::endl;
 
       _init_system_function = nullptr;
     }
 
   _init_system_object = &init_in;
 }

◆ 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);}

libMesh::DifferentiableSystem::_diff_physics

DifferentiablePhysics * _diff_physics

Definition: diff_system.h:371

libMesh::DifferentiablePhysics::init_physics

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.

   { this->diff_qoi = (qoi_in->clone()).release();
     // User needs to resize qoi system qoi accordingly
     this->diff_qoi->init_qoi( this->qoi );}

◆ 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.

 {
   libmesh_assert(fptr);
 
   if (_qoi_evaluate_derivative_object != nullptr)
     {
       libmesh_here();
       libMesh::out << "WARNING:  Cannot specify both QOI derivative function and object!"
                    << std::endl;
 
       _qoi_evaluate_derivative_object = nullptr;
     }
 
   _qoi_evaluate_derivative_function = fptr;
 }

◆ 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.

 {
   if (_qoi_evaluate_derivative_function != nullptr)
     {
       libmesh_here();
       libMesh::out << "WARNING:  Cannot specify both QOI derivative object and function!"
                    << std::endl;
 
       _qoi_evaluate_derivative_function = nullptr;
     }
 
   _qoi_evaluate_derivative_object = &qoi_derivative;
 }

◆ 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.

 {
   libmesh_assert(fptr);
 
   if (_qoi_evaluate_object != nullptr)
     {
       libmesh_here();
       libMesh::out << "WARNING:  Cannot specify both QOI function and object!"
                    << std::endl;
 
       _qoi_evaluate_object = nullptr;
     }
 
   _qoi_evaluate_function = fptr;
 }

◆ 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.

 {
   if (_qoi_evaluate_function != nullptr)
     {
       libmesh_here();
       libMesh::out << "WARNING:  Cannot specify both QOI object and function!"
                    << std::endl;
 
       _qoi_evaluate_function = nullptr;
     }
 
   _qoi_evaluate_object = &qoi_in;
 }

◆ 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.

 {
   this->boundary_project_vector(b, variables, *solution, f, g);
 
   solution->localize(*current_local_solution);
 }

◆ 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.

 {
   WrappedFunction<Number> f(*this, fptr, &parameters);
   WrappedFunction<Gradient> g(*this, gptr, &parameters);
   this->boundary_project_solution(b, variables, &f, &g);
 }

◆ 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().

 {
   LOG_SCOPE ("boundary_project_vector()", "System");
 
   Threads::parallel_for
     (ConstElemRange (this->get_mesh().active_local_elements_begin(),
                      this->get_mesh().active_local_elements_end() ),
      BoundaryProjectSolution(b, variables, *this, f, g,
                              this->get_equation_systems().parameters,
                              new_vector)
      );
 
   // We don't do SCALAR dofs when just projecting the boundary, so
   // we're done here.
 
   new_vector.close();
 
 #ifdef LIBMESH_ENABLE_CONSTRAINTS
   if (is_adjoint == -1)
     this->get_dof_map().enforce_constraints_exactly(*this, &new_vector);
   else if (is_adjoint >= 0)
     this->get_dof_map().enforce_adjoint_constraints_exactly(new_vector,
                                                             is_adjoint);
 #endif
 }

◆ 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.

 {
   WrappedFunction<Number> f(*this, fptr, &parameters);
   WrappedFunction<Gradient> g(*this, gptr, &parameters);
   this->boundary_project_vector(b, variables, new_vector, &f, &g,
                                 is_adjoint);
 }

◆ build_context()

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

overridevirtualinherited

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

 {
   FEMContext * fc = new FEMContext(*this);
 
   DifferentiablePhysics * phys = this->get_physics();
 
   libmesh_assert (phys);
 
   // If we are solving a moving mesh problem, tell that to the Context
   fc->set_mesh_system(phys->get_mesh_system());
   fc->set_mesh_x_var(phys->get_mesh_x_var());
   fc->set_mesh_y_var(phys->get_mesh_y_var());
   fc->set_mesh_z_var(phys->get_mesh_z_var());
 
   fc->set_deltat_pointer( &deltat );
 
   // If we are solving the adjoint problem, tell that to the Context
   fc->is_adjoint() = this->get_time_solver().is_adjoint();
 
   return std::unique_ptr<DiffContext>(fc);
 }

◆ 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().

 {
   //short circuit to save time
   if (norm_type == DISCRETE_L1 ||
       norm_type == DISCRETE_L2 ||
       norm_type == DISCRETE_L_INF)
     return discrete_var_norm(v,var,norm_type);
 
   // Not a discrete norm
   std::vector<FEMNormType> norms(this->n_vars(), L2);
   std::vector<Real> weights(this->n_vars(), 0.0);
   norms[var] = norm_type;
   weights[var] = 1.0;
   Real val = this->calculate_norm(v, SystemNorm(norms, weights), skip_dimensions);
   return val;
 }

◆ 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().

 {
   // This function must be run on all processors at once
   parallel_object_only();
 
   LOG_SCOPE ("calculate_norm()", "System");
 
   // Zero the norm before summation
   Real v_norm = 0.;
 
   if (norm.is_discrete())
     {
       //Check to see if all weights are 1.0 and all types are equal
       FEMNormType norm_type0 = norm.type(0);
       unsigned int check_var = 0;
       for (; check_var != this->n_vars(); ++check_var)
         if ((norm.weight(check_var) != 1.0) || (norm.type(check_var) != norm_type0))
           break;
 
       //All weights were 1.0 so just do the full vector discrete norm
       if (check_var == this->n_vars())
         {
           if (norm_type0 == DISCRETE_L1)
             return v.l1_norm();
           if (norm_type0 == DISCRETE_L2)
             return v.l2_norm();
           if (norm_type0 == DISCRETE_L_INF)
             return v.linfty_norm();
           else
             libmesh_error_msg("Invalid norm_type0 = " << norm_type0);
         }
 
       for (unsigned int var=0; var != this->n_vars(); ++var)
         {
           // Skip any variables we don't need to integrate
           if (norm.weight(var) == 0.0)
             continue;
 
           v_norm += norm.weight(var) * discrete_var_norm(v, var, norm.type(var));
         }
 
       return v_norm;
     }
 
   // Localize the potentially parallel vector
   std::unique_ptr<NumericVector<Number>> local_v = NumericVector<Number>::build(this->comm());
   local_v->init(v.size(), true, SERIAL);
   v.localize (*local_v, _dof_map->get_send_list());
 
   // I'm not sure how best to mix Hilbert norms on some variables (for
   // which we'll want to square then sum then square root) with norms
   // like L_inf (for which we'll just want to take an absolute value
   // and then sum).
   bool using_hilbert_norm = true,
     using_nonhilbert_norm = true;
 
   // Loop over all variables
   for (unsigned int var=0; var != this->n_vars(); ++var)
     {
       // Skip any variables we don't need to integrate
       Real norm_weight_sq = norm.weight_sq(var);
       if (norm_weight_sq == 0.0)
         continue;
       Real norm_weight = norm.weight(var);
 
       // Check for unimplemented norms (rather than just returning 0).
       FEMNormType norm_type = norm.type(var);
       if ((norm_type==H1) ||
           (norm_type==H2) ||
           (norm_type==L2) ||
           (norm_type==H1_SEMINORM) ||
           (norm_type==H2_SEMINORM))
         {
           if (!using_hilbert_norm)
             libmesh_not_implemented();
           using_nonhilbert_norm = false;
         }
       else if ((norm_type==L1) ||
                (norm_type==L_INF) ||
                (norm_type==W1_INF_SEMINORM) ||
                (norm_type==W2_INF_SEMINORM))
         {
           if (!using_nonhilbert_norm)
             libmesh_not_implemented();
           using_hilbert_norm = false;
         }
       else
         libmesh_not_implemented();
 
       const FEType & fe_type = this->get_dof_map().variable_type(var);
 
       // Allow space for dims 0-3, even if we don't use them all
       std::vector<std::unique_ptr<FEBase>> fe_ptrs(4);
       std::vector<std::unique_ptr<QBase>> q_rules(4);
 
       const std::set<unsigned char> & elem_dims = _mesh.elem_dimensions();
 
       // Prepare finite elements for each dimension present in the mesh
       for (const auto & dim : elem_dims)
         {
           if (skip_dimensions && skip_dimensions->find(dim) != skip_dimensions->end())
             continue;
 
           // Construct quadrature and finite element objects
           q_rules[dim] = fe_type.default_quadrature_rule (dim);
           fe_ptrs[dim] = FEBase::build(dim, fe_type);
 
           // Attach quadrature rule to FE object
           fe_ptrs[dim]->attach_quadrature_rule (q_rules[dim].get());
         }
 
       std::vector<dof_id_type> dof_indices;
 
       // Begin the loop over the elements
       for (const auto & elem : this->get_mesh().active_local_element_ptr_range())
         {
           const unsigned int dim = elem->dim();
 
 #ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
 
           // One way for implementing this would be to exchange the fe with the FEInterface- class.
           // However, it needs to be discussed whether integral-norms make sense for infinite elements.
           // or in which sense they could make sense.
           if (elem->infinite() )
             libmesh_not_implemented();
 
 #endif
 
           if (skip_dimensions && skip_dimensions->find(dim) != skip_dimensions->end())
             continue;
 
           FEBase * fe = fe_ptrs[dim].get();
           QBase * qrule = q_rules[dim].get();
           libmesh_assert(fe);
           libmesh_assert(qrule);
 
           const std::vector<Real> &               JxW = fe->get_JxW();
           const std::vector<std::vector<Real>> * phi = nullptr;
           if (norm_type == H1 ||
               norm_type == H2 ||
               norm_type == L2 ||
               norm_type == L1 ||
               norm_type == L_INF)
             phi = &(fe->get_phi());
 
           const std::vector<std::vector<RealGradient>> * dphi = nullptr;
           if (norm_type == H1 ||
               norm_type == H2 ||
               norm_type == H1_SEMINORM ||
               norm_type == W1_INF_SEMINORM)
             dphi = &(fe->get_dphi());
 #ifdef LIBMESH_ENABLE_SECOND_DERIVATIVES
           const std::vector<std::vector<RealTensor>> *   d2phi = nullptr;
           if (norm_type == H2 ||
               norm_type == H2_SEMINORM ||
               norm_type == W2_INF_SEMINORM)
             d2phi = &(fe->get_d2phi());
 #endif
 
           fe->reinit (elem);
 
           this->get_dof_map().dof_indices (elem, dof_indices, var);
 
           const unsigned int n_qp = qrule->n_points();
 
           const unsigned int n_sf = cast_int<unsigned int>
             (dof_indices.size());
 
           // Begin the loop over the Quadrature points.
           for (unsigned int qp=0; qp<n_qp; qp++)
             {
               if (norm_type == L1)
                 {
                   Number u_h = 0.;
                   for (unsigned int i=0; i != n_sf; ++i)
                     u_h += (*phi)[i][qp] * (*local_v)(dof_indices[i]);
                   v_norm += norm_weight *
                     JxW[qp] * std::abs(u_h);
                 }
 
               if (norm_type == L_INF)
                 {
                   Number u_h = 0.;
                   for (unsigned int i=0; i != n_sf; ++i)
                     u_h += (*phi)[i][qp] * (*local_v)(dof_indices[i]);
                   v_norm = std::max(v_norm, norm_weight * std::abs(u_h));
                 }
 
               if (norm_type == H1 ||
                   norm_type == H2 ||
                   norm_type == L2)
                 {
                   Number u_h = 0.;
                   for (unsigned int i=0; i != n_sf; ++i)
                     u_h += (*phi)[i][qp] * (*local_v)(dof_indices[i]);
                   v_norm += norm_weight_sq *
                     JxW[qp] * TensorTools::norm_sq(u_h);
                 }
 
               if (norm_type == H1 ||
                   norm_type == H2 ||
                   norm_type == H1_SEMINORM)
                 {
                   Gradient grad_u_h;
                   for (unsigned int i=0; i != n_sf; ++i)
                     grad_u_h.add_scaled((*dphi)[i][qp], (*local_v)(dof_indices[i]));
                   v_norm += norm_weight_sq *
                     JxW[qp] * grad_u_h.norm_sq();
                 }
 
               if (norm_type == W1_INF_SEMINORM)
                 {
                   Gradient grad_u_h;
                   for (unsigned int i=0; i != n_sf; ++i)
                     grad_u_h.add_scaled((*dphi)[i][qp], (*local_v)(dof_indices[i]));
                   v_norm = std::max(v_norm, norm_weight * grad_u_h.norm());
                 }
 
 #ifdef LIBMESH_ENABLE_SECOND_DERIVATIVES
               if (norm_type == H2 ||
                   norm_type == H2_SEMINORM)
                 {
                   Tensor hess_u_h;
                   for (unsigned int i=0; i != n_sf; ++i)
                     hess_u_h.add_scaled((*d2phi)[i][qp], (*local_v)(dof_indices[i]));
                   v_norm += norm_weight_sq *
                     JxW[qp] * hess_u_h.norm_sq();
                 }
 
               if (norm_type == W2_INF_SEMINORM)
                 {
                   Tensor hess_u_h;
                   for (unsigned int i=0; i != n_sf; ++i)
                     hess_u_h.add_scaled((*d2phi)[i][qp], (*local_v)(dof_indices[i]));
                   v_norm = std::max(v_norm, norm_weight * hess_u_h.norm());
                 }
 #endif
             }
         }
     }
 
   if (using_hilbert_norm)
     {
       this->comm().sum(v_norm);
       v_norm = std::sqrt(v_norm);
     }
   else
     {
       this->comm().max(v_norm);
     }
 
   return v_norm;
 }

◆ clear()

void libMesh::ContinuationSystem::clear ( )

overridevirtual

Clear all the data structures associated with the system.

Reimplemented from libMesh::DifferentiableSystem.

Definition at line 80 of file continuation_system.C.

References libMesh::DifferentiableSystem::clear().

Referenced by ~ContinuationSystem().

 {
   // FIXME: Do anything here, e.g. zero vectors, etc?
 
   // Call the Parent's clear function
   Parent::clear();
 }

◆ 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().

   {
     libmesh_not_implemented();
     // dummy
     return std::unique_ptr<DifferentiableQoI>(this);
   }

◆ 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.

   {
     libmesh_not_implemented();
     // dummy
     return std::unique_ptr<DifferentiablePhysics>(this);
   }

◆ 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.

90 { return _communicator; }

libMesh::ParallelObject::_communicator

const Parallel::Communicator & _communicator

Definition: parallel_object.h:107

◆ 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().

 {
   // we do not care for matrices, but for vectors
   libmesh_assert (_is_initialized);
   libmesh_assert (other_system._is_initialized);
 
   if (verbose)
     {
       libMesh::out << "  Systems \"" << _sys_name << "\"" << std::endl;
       libMesh::out << "   comparing matrices not supported." << std::endl;
       libMesh::out << "   comparing names...";
     }
 
   // compare the name: 0 means identical
   const int name_result = _sys_name.compare(other_system.name());
   if (verbose)
     {
       if (name_result == 0)
         libMesh::out << " identical." << std::endl;
       else
         libMesh::out << "  names not identical." << std::endl;
       libMesh::out << "   comparing solution vector...";
     }
 
 
   // compare the solution: -1 means identical
   const int solu_result = solution->compare (*other_system.solution.get(),
                                              threshold);
 
   if (verbose)
     {
       if (solu_result == -1)
         libMesh::out << " identical up to threshold." << std::endl;
       else
         libMesh::out << "  first difference occurred at index = "
                      << solu_result << "." << std::endl;
     }
 
 
   // safety check, whether we handle at least the same number
   // of vectors
   std::vector<int> ov_result;
 
   if (this->n_vectors() != other_system.n_vectors())
     {
       if (verbose)
         {
           libMesh::out << "   Fatal difference. This system handles "
                        << this->n_vectors() << " add'l vectors," << std::endl
                        << "   while the other system handles "
                        << other_system.n_vectors()
                        << " add'l vectors." << std::endl
                        << "   Aborting comparison." << std::endl;
         }
       return false;
     }
   else if (this->n_vectors() == 0)
     {
       // there are no additional vectors...
       ov_result.clear ();
     }
   else
     {
       // compare other vectors
       for (auto & pr : _vectors)
         {
           if (verbose)
             libMesh::out << "   comparing vector \""
                          << pr.first << "\" ...";
 
           // assume they have the same name
           const NumericVector<Number> & other_system_vector =
             other_system.get_vector(pr.first);
 
           ov_result.push_back(pr.second->compare (other_system_vector,
                                                   threshold));
 
           if (verbose)
             {
               if (ov_result[ov_result.size()-1] == -1)
                 libMesh::out << " identical up to threshold." << std::endl;
               else
                 libMesh::out << " first difference occurred at" << std::endl
                              << "   index = " << ov_result[ov_result.size()-1] << "." << std::endl;
             }
         }
     } // finished comparing additional vectors
 
 
   bool overall_result;
 
   // sum up the results
   if ((name_result==0) && (solu_result==-1))
     {
       if (ov_result.size()==0)
         overall_result = true;
       else
         {
           bool ov_identical;
           unsigned int n    = 0;
           do
             {
               ov_identical = (ov_result[n]==-1);
               n++;
             }
           while (ov_identical && n<ov_result.size());
           overall_result = ov_identical;
         }
     }
   else
     overall_result = false;
 
   if (verbose)
     {
       libMesh::out << "   finished comparisons, ";
       if (overall_result)
         libMesh::out << "found no differences." << std::endl << std::endl;
       else
         libMesh::out << "found differences." << std::endl << std::endl;
     }
 
   return overall_result;
 }

◆ continuation_solve()

void libMesh::ContinuationSystem::continuation_solve ( )

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

Definition at line 358 of file continuation_system.C.

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

 {
   // Be sure the user has set the continuation parameter pointer
   if (!continuation_parameter)
     libmesh_error_msg("You must set the continuation_parameter pointer " \
                       << "to a member variable of the derived class, preferably in the " \
                       << "Derived class's init_data function.  This is how the ContinuationSystem " \
                       << "updates the continuation parameter.");
 
   // Use extra precision for all the numbers printed in this function.
   std::streamsize old_precision = libMesh::out.precision();
   libMesh::out.precision(16);
   libMesh::out.setf(std::ios_base::scientific);
 
   // We can't start solving the augmented PDE system unless the tangent
   // vectors have been initialized.  This only needs to occur once.
   if (!tangent_initialized)
     initialize_tangent();
 
   // Save the old value of -du/dlambda.  This will be used after the Newton iterations
   // to compute the angle between previous tangent vectors.  This cosine of this angle is
   //
   // tau := abs( (du/d(lambda)_i , du/d(lambda)_{i-1}) / (||du/d(lambda)_i|| * ||du/d(lambda)_{i-1}||) )
   //
   // The scaling factor tau (which should vary between 0 and 1) is used to shrink the step-size ds
   // when we are approaching a turning point.  Note that it can only shrink the step size.
   *y_old = *y;
 
   // Set pointer to underlying Newton solver
   if (!newton_solver)
     newton_solver = cast_ptr<NewtonSolver *> (this->time_solver->diff_solver().get());
 
   // A pair for catching return values from linear system solves.
   std::pair<unsigned int, Real> rval;
 
   // Convergence flag for the entire arcstep
   bool arcstep_converged = false;
 
   // Begin loop over arcstep reductions.
   for (unsigned int ns=0; ns<n_arclength_reductions; ++ns)
     {
       if (!quiet)
         {
           libMesh::out << "Current arclength stepsize, ds_current=" << ds_current << std::endl;
           libMesh::out << "Current parameter value, lambda=" << *continuation_parameter << std::endl;
         }
 
       // Upon exit from the nonlinear loop, the newton_converged flag
       // will tell us the convergence status of Newton's method.
       bool newton_converged = false;
 
       // The nonlinear residual before *any* nonlinear steps have been taken.
       Real nonlinear_residual_firststep = 0.;
 
       // The nonlinear residual from the current "k" Newton step, before the Newton step
       Real nonlinear_residual_beforestep = 0.;
 
       // The nonlinear residual from the current "k" Newton step, after the Newton step
       Real nonlinear_residual_afterstep = 0.;
 
       // The linear solver tolerance, can be updated dynamically at each Newton step.
       Real current_linear_tolerance = 0.;
 
       // The nonlinear loop
       for (newton_step=0; newton_step<newton_solver->max_nonlinear_iterations; ++newton_step)
         {
           libMesh::out << "\n === Starting Newton step " << newton_step << " ===" << std::endl;
 
           // Set the linear system solver tolerance
           //   // 1.) Set the current linear tolerance based as a multiple of the current residual of the system.
           //   const Real residual_multiple = 1.e-4;
           //   Real current_linear_tolerance = residual_multiple*nonlinear_residual_beforestep;
 
           //   // But if the current residual isn't small, don't let the solver exit with zero iterations!
           //   if (current_linear_tolerance > 1.)
           //     current_linear_tolerance = residual_multiple;
 
           // 2.) Set the current linear tolerance based on the method based on technique of Eisenstat & Walker.
           if (newton_step==0)
             {
               // At first step, only try reducing the residual by a small amount
               current_linear_tolerance = initial_newton_tolerance;//0.01;
             }
 
           else
             {
               // The new tolerance is based on the ratio of the most recent tolerances
               const Real alp=0.5*(1.+std::sqrt(5.));
               const Real gam=0.9;
 
               libmesh_assert_not_equal_to (nonlinear_residual_beforestep, 0.0);
               libmesh_assert_not_equal_to (nonlinear_residual_afterstep, 0.0);
 
               current_linear_tolerance = std::min(gam*std::pow(nonlinear_residual_afterstep/nonlinear_residual_beforestep, alp),
                                                   current_linear_tolerance*current_linear_tolerance
                                                   );
 
               // Don't let it get ridiculously small!!
               if (current_linear_tolerance < 1.e-12)
                 current_linear_tolerance = 1.e-12;
             }
 
           if (!quiet)
             libMesh::out << "Using current_linear_tolerance=" << current_linear_tolerance << std::endl;
 
 
           // Assemble the residual (and Jacobian).
           rhs_mode = Residual;
           assembly(true,   // Residual
                    true); // Jacobian
           rhs->close();
 
           // Save the current nonlinear residual.  We don't need to recompute the residual unless
           // this is the first step, since it was already computed as part of the convergence check
           // at the end of the last loop iteration.
           if (newton_step==0)
             {
               nonlinear_residual_beforestep = rhs->l2_norm();
 
               // Store the residual before any steps have been taken.  This will *not*
               // be updated at each step, and can be used to see if any progress has
               // been made from the initial residual at later steps.
               nonlinear_residual_firststep = nonlinear_residual_beforestep;
 
               const Real old_norm_u = solution->l2_norm();
               libMesh::out << "  (before step) ||R||_{L2} = " << nonlinear_residual_beforestep << std::endl;
               libMesh::out << "  (before step) ||R||_{L2}/||u|| = " << nonlinear_residual_beforestep / old_norm_u << std::endl;
 
               // In rare cases (very small arcsteps), it's possible that the residual is
               // already below our absolute linear tolerance.
               if (nonlinear_residual_beforestep  < solution_tolerance)
                 {
                   if (!quiet)
                     libMesh::out << "Initial guess satisfied linear tolerance, exiting with zero Newton iterations!" << std::endl;
 
                   // Since we go straight from here to the solve of the next tangent, we
                   // have to close the matrix before it can be assembled again.
                   matrix->close();
                   newton_converged=true;
                   break; // out of Newton iterations, with newton_converged=true
                 }
             }
 
           else
             {
               nonlinear_residual_beforestep = nonlinear_residual_afterstep;
             }
 
 
           // Solve the linear system G_u*z = G
           // Initial guess?
           z->zero(); // It seems to be extremely important to zero z here, otherwise the solver quits early.
           z->close();
 
           // It's possible that we have selected the current_linear_tolerance so large that
           // a guess of z=zero yields a linear system residual |Az + R| small enough that the
           // linear solver exits in zero iterations.  If this happens, we will reduce the
           // current_linear_tolerance until the linear solver does at least 1 iteration.
           do
             {
               rval =
                 linear_solver->solve(*matrix,
                                      *z,
                                      *rhs,
                                      //1.e-12,
                                      current_linear_tolerance,
                                      newton_solver->max_linear_iterations);   // max linear iterations
 
               if (rval.first==0)
                 {
                   if (newton_step==0)
                     {
                       libMesh::out << "Repeating initial solve with smaller linear tolerance!" << std::endl;
                       current_linear_tolerance *= initial_newton_tolerance; // reduce the linear tolerance to force the solver to do some work
                     }
                   else
                     // We shouldn't get here ... it means the linear solver did no work on a Newton
                     // step other than the first one.  If this happens, we need to think more about our
                     // tolerance selection.
                     libmesh_error_msg("Linear solver did no work!");
                 }
 
             } while (rval.first==0);
 
 
           if (!quiet)
             libMesh::out << "  G_u*z = G solver converged at step "
                          << rval.first
                          << " linear tolerance = "
                          << rval.second
                          << "."
                          << std::endl;
 
           // Sometimes (I am not sure why) the linear solver exits after zero iterations.
           // Perhaps it is hitting PETSc's divergence tolerance dtol???  If this occurs,
           // we should break out of the Newton iteration loop because nothing further is
           // going to happen...  Of course if the tolerance is already small enough after
           // zero iterations (how can this happen?!) we should not quit.
           if ((rval.first == 0) && (rval.second > current_linear_tolerance*nonlinear_residual_beforestep))
             {
               if (!quiet)
                 libMesh::out << "Linear solver exited in zero iterations!" << std::endl;
 
               // Try to find out the reason for convergence/divergence
               linear_solver->print_converged_reason();
 
               break; // out of Newton iterations
             }
 
           // Note: need to scale z by -1 since our code always solves Jx=R
           // instead of Jx=-R.
           z->scale(-1.);
           z->close();
 
 
 
 
 
 
           // Assemble the G_Lambda vector, skip residual.
           rhs_mode = G_Lambda;
 
           // Assemble both rhs and Jacobian
           assembly(true,  // Residual
                    false); // Jacobian
 
           // Not sure if this is really necessary
           rhs->close();
           const Real yrhsnorm=rhs->l2_norm();
           if (yrhsnorm == 0.0)
             libmesh_error_msg("||G_Lambda|| = 0");
 
           // We select a tolerance for the y-system which is based on the inexact Newton
           // tolerance but scaled by an extra term proportional to the RHS (which is not -> 0 in this case)
           const Real ysystemtol=current_linear_tolerance*(nonlinear_residual_beforestep/yrhsnorm);
           if (!quiet)
             libMesh::out << "ysystemtol=" << ysystemtol << std::endl;
 
           // Solve G_u*y = G_{\lambda}
           // FIXME: Initial guess?  This is really a solve for -du/dlambda so we could try
           // initializing it with the latest approximation to that... du/dlambda ~ du/ds * ds/dlambda
           //*y = *solution;
           //y->add(-1., *previous_u);
           //y->scale(-1. / (*continuation_parameter - old_continuation_parameter)); // Be careful of divide by zero...
           //y->close();
 
           //  const unsigned int max_attempts=1;
           // unsigned int attempt=0;
           //   do
           //     {
           //       if (!quiet)
           // libMesh::out << "Trying to solve tangent system, attempt " << attempt << std::endl;
 
           rval =
             linear_solver->solve(*matrix,
                                  *y,
                                  *rhs,
                                  //1.e-12,
                                  ysystemtol,
                                  newton_solver->max_linear_iterations);   // max linear iterations
 
           if (!quiet)
             libMesh::out << "  G_u*y = G_{lambda} solver converged at step "
                          << rval.first
                          << ", linear tolerance = "
                          << rval.second
                          << "."
                          << std::endl;
 
           // Sometimes (I am not sure why) the linear solver exits after zero iterations.
           // Perhaps it is hitting PETSc's divergence tolerance dtol???  If this occurs,
           // we should break out of the Newton iteration loop because nothing further is
           // going to happen...
           if ((rval.first == 0) && (rval.second > ysystemtol))
             {
               if (!quiet)
                 libMesh::out << "Linear solver exited in zero iterations!" << std::endl;
 
               break; // out of Newton iterations
             }
 
           //       ++attempt;
           //     } while ((attempt<max_attempts) && (rval.first==newton_solver->max_linear_iterations));
 
 
 
 
 
           // Compute N, the residual of the arclength constraint eqn.
           // Note 1: N(u,lambda,s) := (u-u_{old}, du_ds) + (lambda-lambda_{old}, dlambda_ds) - _ds
           // We temporarily use the delta_u vector as a temporary vector for this calculation.
           *delta_u = *solution;
           delta_u->add(-1., *previous_u);
 
           // First part of the arclength constraint
           const Number N1 = Theta_LOCA*Theta_LOCA*Theta*delta_u->dot(*du_ds);
           const Number N2 = ((*continuation_parameter) - old_continuation_parameter)*dlambda_ds;
           const Number N3 = ds_current;
 
           if (!quiet)
             {
               libMesh::out << "  N1=" << N1 << std::endl;
               libMesh::out << "  N2=" << N2 << std::endl;
               libMesh::out << "  N3=" << N3 << std::endl;
             }
 
           // The arclength constraint value
           const Number N = N1+N2-N3;
 
           if (!quiet)
             libMesh::out << "  N=" << N << std::endl;
 
           const Number duds_dot_z = du_ds->dot(*z);
           const Number duds_dot_y = du_ds->dot(*y);
 
           //libMesh::out << "duds_dot_z=" << duds_dot_z << std::endl;
           //libMesh::out << "duds_dot_y=" << duds_dot_y << std::endl;
           //libMesh::out << "dlambda_ds=" << dlambda_ds << std::endl;
 
           const Number delta_lambda_numerator   = -(N          + Theta_LOCA*Theta_LOCA*Theta*duds_dot_z);
           const Number delta_lambda_denominator =  (dlambda_ds - Theta_LOCA*Theta_LOCA*Theta*duds_dot_y);
 
           libmesh_assert_not_equal_to (delta_lambda_denominator, 0.0);
 
           // Now, we are ready to compute the step delta_lambda
           const Number delta_lambda_comp = delta_lambda_numerator /
             delta_lambda_denominator;
           // Lambda is real-valued
           const Real delta_lambda = libmesh_real(delta_lambda_comp);
 
           // Knowing delta_lambda, we are ready to update delta_u
           // delta_u = z - delta_lambda*y
           delta_u->zero();
           delta_u->add(1., *z);
           delta_u->add(-delta_lambda, *y);
           delta_u->close();
 
           // Update the system solution and the continuation parameter.
           solution->add(1., *delta_u);
           solution->close();
           *continuation_parameter += delta_lambda;
 
           // Did the Newton step actually reduce the residual?
           rhs_mode = Residual;
           assembly(true,   // Residual
                    false); // Jacobian
           rhs->close();
           nonlinear_residual_afterstep = rhs->l2_norm();
 
 
           // In a "normal" Newton step, ||du||/||R|| > 1 since the most recent
           // step is where you "just were" and the current residual is where
           // you are now.  It can occur that ||du||/||R|| < 1, but these are
           // likely not good cases to attempt backtracking (?).
           const Real norm_du_norm_R = delta_u->l2_norm() / nonlinear_residual_afterstep;
           if (!quiet)
             libMesh::out << "  norm_du_norm_R=" << norm_du_norm_R << std::endl;
 
 
           // Factor to decrease the stepsize by for backtracking
           Real newton_stepfactor = 1.;
 
           const bool attempt_backtracking =
             (nonlinear_residual_afterstep > solution_tolerance)
             && (nonlinear_residual_afterstep > nonlinear_residual_beforestep)
             && (n_backtrack_steps>0)
             && (norm_du_norm_R > 1.)
             ;
 
           // If residual is not reduced, do Newton back tracking.
           if (attempt_backtracking)
             {
               if (!quiet)
                 libMesh::out << "Newton step did not reduce residual." << std::endl;
 
               // back off the previous step.
               solution->add(-1., *delta_u);
               solution->close();
               *continuation_parameter -= delta_lambda;
 
               // Backtracking: start cutting the Newton stepsize by halves until
               // the new residual is actually smaller...
               for (unsigned int backtrack_step=0; backtrack_step<n_backtrack_steps; ++backtrack_step)
                 {
                   newton_stepfactor *= 0.5;
 
                   if (!quiet)
                     libMesh::out << "Shrinking step size by " << newton_stepfactor << std::endl;
 
                   // Take fractional step
                   solution->add(newton_stepfactor, *delta_u);
                   solution->close();
                   *continuation_parameter += newton_stepfactor*delta_lambda;
 
                   rhs_mode = Residual;
                   assembly(true,   // Residual
                            false); // Jacobian
                   rhs->close();
                   nonlinear_residual_afterstep = rhs->l2_norm();
 
                   if (!quiet)
                     libMesh::out << "At shrink step "
                                  << backtrack_step
                                  << ", nonlinear_residual_afterstep="
                                  << nonlinear_residual_afterstep
                                  << std::endl;
 
                   if (nonlinear_residual_afterstep < nonlinear_residual_beforestep)
                     {
                       if (!quiet)
                         libMesh::out << "Backtracking succeeded!" << std::endl;
 
                       break; // out of backtracking loop
                     }
 
                   else
                     {
                       // Back off that step
                       solution->add(-newton_stepfactor, *delta_u);
                       solution->close();
                       *continuation_parameter -= newton_stepfactor*delta_lambda;
                     }
 
                   // Save a copy of the solution from before the Newton step.
                   //std::unique_ptr<NumericVector<Number>> prior_iterate = solution->clone();
                 }
             } // end if (attempte_backtracking)
 
 
           // If we tried backtracking but the residual is still not reduced, print message.
           if ((attempt_backtracking) && (nonlinear_residual_afterstep > nonlinear_residual_beforestep))
             {
               //libMesh::err << "Backtracking failed." << std::endl;
               libMesh::out << "Backtracking failed." << std::endl;
 
               // 1.) Quit, exit program.
               //libmesh_error_msg("Backtracking failed!");
 
               // 2.) Continue with last newton_stepfactor
               if (newton_step<3)
                 {
                   solution->add(newton_stepfactor, *delta_u);
                   solution->close();
                   *continuation_parameter += newton_stepfactor*delta_lambda;
                   if (!quiet)
                     libMesh::out << "Backtracking could not reduce residual ... continuing anyway!" << std::endl;
                 }
 
               // 3.) Break out of Newton iteration loop with newton_converged = false,
               //     reduce the arclength stepsize, and try again.
               else
                 {
                   break; // out of Newton iteration loop, with newton_converged=false
                 }
             }
 
           // Another type of convergence check: suppose the residual has not been reduced
           // from its initial value after half of the allowed Newton steps have occurred.
           // In our experience, this typically means that it isn't going to converge and
           // we could probably save time by dropping out of the Newton iteration loop and
           // trying a smaller arcstep.
           if (this->newton_progress_check)
             {
               if ((nonlinear_residual_afterstep > nonlinear_residual_firststep) &&
                   (newton_step+1 > static_cast<unsigned int>(0.5*newton_solver->max_nonlinear_iterations)))
                 {
                   libMesh::out << "Progress check failed: the current residual: "
                                << nonlinear_residual_afterstep
                                << ", is\n"
                                << "larger than the initial residual, and half of the allowed\n"
                                << "number of Newton iterations have elapsed.\n"
                                << "Exiting Newton iterations with converged==false." << std::endl;
 
                   break; // out of Newton iteration loop, newton_converged = false
                 }
             }
 
           // Safety check: Check the current continuation parameter against user-provided min-allowable parameter value
           if (*continuation_parameter < min_continuation_parameter)
             {
               libMesh::out << "Continuation parameter fell below min-allowable value." << std::endl;
               break; // out of Newton iteration loop, newton_converged = false
             }
 
           // Safety check: Check the current continuation parameter against user-provided max-allowable parameter value
           if ( (max_continuation_parameter != 0.0) &&
                (*continuation_parameter > max_continuation_parameter) )
             {
               libMesh::out << "Current continuation parameter value: "
                            << *continuation_parameter
                            << " exceeded max-allowable value."
                            << std::endl;
               break; // out of Newton iteration loop, newton_converged = false
             }
 
 
           // Check the convergence of the parameter and the solution.  If they are small
           // enough, we can break out of the Newton iteration loop.
           const Real norm_delta_u = delta_u->l2_norm();
           const Real norm_u = solution->l2_norm();
           libMesh::out << "  delta_lambda                   = " << delta_lambda << std::endl;
           libMesh::out << "  newton_stepfactor*delta_lambda = " << newton_stepfactor*delta_lambda << std::endl;
           libMesh::out << "  lambda_current                 = " << *continuation_parameter << std::endl;
           libMesh::out << "  ||delta_u||                    = " << norm_delta_u << std::endl;
           libMesh::out << "  ||delta_u||/||u||              = " << norm_delta_u / norm_u << std::endl;
 
 
           // Evaluate the residual at the current Newton iterate.  We don't want to detect
           // convergence due to a small Newton step when the residual is still not small.
           rhs_mode = Residual;
           assembly(true,   // Residual
                    false); // Jacobian
           rhs->close();
           const Real norm_residual = rhs->l2_norm();
           libMesh::out << "  ||R||_{L2} = " << norm_residual << std::endl;
           libMesh::out << "  ||R||_{L2}/||u|| = " << norm_residual / norm_u << std::endl;
 
 
           // FIXME: The norm_delta_u tolerance (at least) should be relative.
           // It doesn't make sense to converge a solution whose size is ~ 10^5 to
           // a tolerance of 1.e-6.  Oh, and we should also probably check the
           // (relative) size of the residual as well, instead of just the step.
           if ((std::abs(delta_lambda) < continuation_parameter_tolerance) &&
               //(norm_delta_u       < solution_tolerance)               && // This is a *very* strict criterion we can probably skip
               (norm_residual      < solution_tolerance))
             {
               if (!quiet)
                 libMesh::out << "Newton iterations converged!" << std::endl;
 
               newton_converged = true;
               break; // out of Newton iterations
             }
         } // end nonlinear loop
 
       if (!newton_converged)
         {
           libMesh::out << "Newton iterations of augmented system did not converge!" << std::endl;
 
           // Reduce ds_current, recompute the solution and parameter, and continue to next
           // arcstep, if there is one.
           ds_current *= 0.5;
 
           // Go back to previous solution and parameter value.
           *solution = *previous_u;
           *continuation_parameter = old_continuation_parameter;
 
           // Compute new predictor with smaller ds
           apply_predictor();
         }
       else
         {
           // Set step convergence and break out
           arcstep_converged=true;
           break; // out of arclength reduction loop
         }
 
     } // end loop over arclength reductions
 
   // Check for convergence of the whole arcstep.  If not converged at this
   // point, we have no choice but to quit.
   if (!arcstep_converged)
     libmesh_error_msg("Arcstep failed to converge after max number of reductions! Exiting...");
 
   // Print converged solution control parameter and max value.
   libMesh::out << "lambda_current=" << *continuation_parameter << std::endl;
   //libMesh::out << "u_max=" << solution->max() << std::endl;
 
   // Reset old stream precision and flags.
   libMesh::out.precision(old_precision);
   libMesh::out.unsetf(std::ios_base::scientific);
 
   // Note: we don't want to go on to the next guess yet, since the user may
   // want to post-process this data.  It's up to the user to call advance_arcstep()
   // when they are ready to go on.
 }

◆ current_solution()

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

inherited

Returns: The current solution for the specified global DOF.

Definition at line 194 of file system.C.

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

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

 {
   // Check the sizes
   libmesh_assert_less (global_dof_number, _dof_map->n_dofs());
   libmesh_assert_less (global_dof_number, current_local_solution->size());
 
   return (*current_local_solution)(global_dof_number);
 }

◆ 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().

                                                 {
     return request_jacobian;
   }

◆ 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.

 {
   _active = false;
 }

◆ 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().

                                     {
   this->assemble_before_solve = true;
   this->get_linear_solver()->reuse_preconditioner(false);
 }

◆ 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().

 {
   _enable_print_counter = false;
   return;
 }

◆ 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().

                                                   {
     return request_jacobian;
   }

◆ 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().

                                                        {
     return request_jacobian;
   }

◆ 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.

 {
   _enable_print_counter = true;
   return;
 }

◆ 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.

                                                  {
     return request_jacobian;
   }

◆ 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 libMesh::FEMSystem::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.

 {
   ParameterVector & parameters =
     const_cast<ParameterVector &>(parameters_in);
 
   const unsigned int Np = cast_int<unsigned int>
     (parameters.size());
   const unsigned int Nq = this->n_qois();
 
   // An introduction to the problem:
   //
   // Residual R(u(p),p) = 0
   // partial R / partial u = J = system matrix
   //
   // This implies that:
   // d/dp(R) = 0
   // (partial R / partial p) +
   // (partial R / partial u) * (partial u / partial p) = 0
 
   // We first solve for (partial u / partial p) for each parameter:
   // J * (partial u / partial p) = - (partial R / partial p)
 
   this->sensitivity_solve(parameters);
 
   // Get ready to fill in sensitivities:
   sensitivities.allocate_data(qoi_indices, *this, parameters);
 
   // We use the identity:
   // dq/dp = (partial q / partial p) + (partial q / partial u) *
   //         (partial u / partial p)
 
   // We get (partial q / partial u) from the user
   this->assemble_qoi_derivative(qoi_indices,
                                 /* include_liftfunc = */ true,
                                 /* apply_constraints = */ false);
 
   // We don't need these to be closed() in this function, but libMesh
   // standard practice is to have them closed() by the time the
   // function exits
   for (unsigned int i=0; i != this->n_qois(); ++i)
     if (qoi_indices.has_index(i))
       this->get_adjoint_rhs(i).close();
 
   for (unsigned int j=0; j != Np; ++j)
     {
       // We currently get partial derivatives via central differencing
 
       // (partial q / partial p) ~= (q(p+dp)-q(p-dp))/(2*dp)
 
       Number old_parameter = *parameters[j];
 
       const Real delta_p =
         TOLERANCE * std::max(std::abs(old_parameter), 1e-3);
 
       *parameters[j] = old_parameter - delta_p;
       this->assemble_qoi(qoi_indices);
       std::vector<Number> qoi_minus = this->qoi;
 
       *parameters[j] = old_parameter + delta_p;
       this->assemble_qoi(qoi_indices);
       std::vector<Number> & qoi_plus = this->qoi;
 
       std::vector<Number> partialq_partialp(Nq, 0);
       for (unsigned int i=0; i != Nq; ++i)
         if (qoi_indices.has_index(i))
           partialq_partialp[i] = (qoi_plus[i] - qoi_minus[i]) / (2.*delta_p);
 
       // Don't leave the parameter changed
       *parameters[j] = old_parameter;
 
       for (unsigned int i=0; i != Nq; ++i)
         if (qoi_indices.has_index(i))
           sensitivities[i][j] = partialq_partialp[i] +
             this->get_adjoint_rhs(i).dot(this->get_sensitivity_solution(j));
     }
 
   // All parameters have been reset.
   // We didn't cache the original rhs or matrix for memory reasons,
   // but we can restore them to a state consistent solution -
   // principle of least surprise.
   this->assembly(true, true);
   this->rhs->close();
   this->matrix->close();
   this->assemble_qoi(qoi_indices);
 }

◆ 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().

 {
   std::ostringstream adjoint_rhs_name;
   adjoint_rhs_name << "adjoint_rhs" << i;
 
   return this->get_vector(adjoint_rhs_name.str());
 }

◆ 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().

 {
   std::ostringstream adjoint_rhs_name;
   adjoint_rhs_name << "adjoint_rhs" << i;
 
   return this->get_vector(adjoint_rhs_name.str());
 }

◆ 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().

 {
   std::ostringstream adjoint_name;
   adjoint_name << "adjoint_solution" << i;
 
   return this->get_vector(adjoint_name.str());
 }

◆ 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().

 {
   std::ostringstream adjoint_name;
   adjoint_name << "adjoint_solution" << i;
 
   return this->get_vector(adjoint_name.str());
 }

◆ 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().

 {
   all_variable_numbers.resize(n_vars());
 
   // Make sure the variable exists
   std::map<std::string, unsigned short int>::const_iterator
     it = _variable_numbers.begin();
   std::map<std::string, unsigned short int>::const_iterator
     it_end = _variable_numbers.end();
 
   unsigned int count = 0;
   for ( ; it != it_end; ++it)
     {
       all_variable_numbers[count] = it->second;
       count++;
     }
 }

◆ 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.

 {
   return *_dof_map;
 }

◆ 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.

 {
   return *_dof_map;
 }

◆ get_equation_systems() [1/2]

const EquationSystems& libMesh::System::get_equation_systems ( ) const

inlineinherited

Returns: A constant reference to this system's parent EquationSystems object.

Definition at line 712 of file system.h.

References libMesh::System::_equation_systems.

712 { return _equation_systems; }

libMesh::System::_equation_systems

EquationSystems & _equation_systems

Definition: system.h:1890

◆ 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; }

libMesh::System::_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; }

libMesh::DifferentiablePhysics::_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().

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

◆ 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.

 {
   std::ostringstream oss;
 
 
   const std::string & sys_name = this->name();
 
   oss << "   System #"  << this->number() << ", \"" << sys_name << "\"\n"
       << "    Type \""  << this->system_type() << "\"\n"
       << "    Variables=";
 
   for (unsigned int vg=0; vg<this->n_variable_groups(); vg++)
     {
       const VariableGroup & vg_description (this->variable_group(vg));
 
       if (vg_description.n_variables() > 1) oss << "{ ";
       for (unsigned int vn=0; vn<vg_description.n_variables(); vn++)
         oss << "\"" << vg_description.name(vn) << "\" ";
       if (vg_description.n_variables() > 1) oss << "} ";
     }
 
   oss << '\n';
 
   oss << "    Finite Element Types=";
 #ifndef LIBMESH_ENABLE_INFINITE_ELEMENTS
   for (unsigned int vg=0; vg<this->n_variable_groups(); vg++)
     oss << "\""
         << Utility::enum_to_string<FEFamily>(this->get_dof_map().variable_group(vg).type().family)
         << "\" ";
 #else
   for (unsigned int vg=0; vg<this->n_variable_groups(); vg++)
     {
       oss << "\""
           << Utility::enum_to_string<FEFamily>(this->get_dof_map().variable_group(vg).type().family)
           << "\", \""
           << Utility::enum_to_string<FEFamily>(this->get_dof_map().variable_group(vg).type().radial_family)
           << "\" ";
     }
 
   oss << '\n' << "    Infinite Element Mapping=";
   for (unsigned int vg=0; vg<this->n_variable_groups(); vg++)
     oss << "\""
         << Utility::enum_to_string<InfMapType>(this->get_dof_map().variable_group(vg).type().inf_map)
         << "\" ";
 #endif
 
   oss << '\n';
 
   oss << "    Approximation Orders=";
   for (unsigned int vg=0; vg<this->n_variable_groups(); vg++)
     {
 #ifndef LIBMESH_ENABLE_INFINITE_ELEMENTS
       oss << "\""
           << Utility::enum_to_string<Order>(this->get_dof_map().variable_group(vg).type().order)
           << "\" ";
 #else
       oss << "\""
           << Utility::enum_to_string<Order>(this->get_dof_map().variable_group(vg).type().order)
           << "\", \""
           << Utility::enum_to_string<Order>(this->get_dof_map().variable_group(vg).type().radial_order)
           << "\" ";
 #endif
     }
 
   oss << '\n';
 
   oss << "    n_dofs()="             << this->n_dofs()             << '\n';
   oss << "    n_local_dofs()="       << this->n_local_dofs()       << '\n';
 #ifdef LIBMESH_ENABLE_CONSTRAINTS
   oss << "    n_constrained_dofs()=" << this->n_constrained_dofs() << '\n';
   oss << "    n_local_constrained_dofs()=" << this->n_local_constrained_dofs() << '\n';
 #endif
 
   oss << "    " << "n_vectors()="  << this->n_vectors()  << '\n';
   oss << "    " << "n_matrices()="  << this->n_matrices()  << '\n';
   //   oss << "    " << "n_additional_matrices()=" << this->n_additional_matrices() << '\n';
 
   oss << this->get_dof_map().get_info();
 
   return oss.str();
 }

◆ 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.

 {
   libmesh_assert(time_solver.get());
   libmesh_assert_equal_to (&(time_solver->system()), this);
   return std::make_pair(this->time_solver->diff_solver()->max_linear_iterations,
                         this->time_solver->diff_solver()->relative_residual_tolerance);
 }

◆ 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.

 {
   libmesh_assert(time_solver.get());
   libmesh_assert_equal_to (&(time_solver->system()), this);
   return this->time_solver->linear_solver().get();
 }

◆ 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().

 {
   // Make sure the matrix exists
   const_matrices_iterator pos = _matrices.find (mat_name);
 
   if (pos == _matrices.end())
     libmesh_error_msg("ERROR: matrix " << mat_name << " does not exist in this system!");
 
   return *(pos->second);
 }

◆ 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.

 {
   // Make sure the matrix exists
   matrices_iterator pos = _matrices.find (mat_name);
 
   if (pos == _matrices.end())
     libmesh_error_msg("ERROR: matrix " << mat_name << " does not exist in this system!");
 
   return *(pos->second);
 }

◆ 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.

 {
   return _mesh;
 }

◆ 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.

 {
   return _mesh;
 }

◆ 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 libMesh::FEMSystem::build_context().

 {
   return _mesh_sys;
 }

◆ 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.

 {
   return _mesh_sys;
 }

◆ 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 libMesh::FEMSystem::build_context().

 {
   return _mesh_x_var;
 }

◆ 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 libMesh::FEMSystem::build_context().

 {
   return _mesh_y_var;
 }

◆ 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 libMesh::FEMSystem::build_context().

 {
   return _mesh_z_var;
 }

◆ get_physics() [1/2]

const DifferentiablePhysics* libMesh::DifferentiableSystem::get_physics ( ) const

inlineinherited

Returns: A const reference to a DifferentiablePhysics object.

Note: If no external Physics object is attached, the default is this.

Definition at line 182 of file diff_system.h.

References libMesh::DifferentiableSystem::_diff_physics.

Referenced by libMesh::EulerSolver::_general_residual(), libMesh::Euler2Solver::_general_residual(), libMesh::SteadySolver::_general_residual(), libMesh::NewmarkSolver::_general_residual(), libMesh::FEMSystem::build_context(), libMesh::EulerSolver::element_residual(), libMesh::Euler2Solver::element_residual(), libMesh::EigenTimeSolver::element_residual(), libMesh::FEMSystem::init_context(), libMesh::EigenTimeSolver::nonlocal_residual(), and libMesh::EigenTimeSolver::side_residual().

183 { return this->_diff_physics; }

libMesh::DifferentiableSystem::_diff_physics

DifferentiablePhysics * _diff_physics

Definition: diff_system.h:371

◆ 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; }

libMesh::DifferentiableSystem::_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; }

libMesh::DifferentiableSystem::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; }

libMesh::DifferentiableSystem::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().

 {
   // For SteadySolver or SecondOrderUnsteadySolvers, we just give back var
   unsigned int dot_var = var;
 
   if (!time_solver->is_steady())
     {
       const UnsteadySolver & unsteady_solver =
         cast_ref<const UnsteadySolver &>(*(time_solver.get()));
 
       if (unsteady_solver.time_order() == 1)
         dot_var = this->_second_order_dot_vars.find(var)->second;
     }
 
   return dot_var;
 }

◆ get_second_order_vars()

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

inlineinherited

Returns: The set of second order in time variable indices. May be empty.

Definition at line 530 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_second_order_vars.

Referenced by libMesh::DifferentiableSystem::add_second_order_dot_vars(), libMesh::DiffContext::DiffContext(), libMesh::Euler2Solver::element_residual(), libMesh::DifferentiableSystem::have_second_order_scalar_vars(), and libMesh::FEMContext::pre_fe_reinit().

531 { return _second_order_vars; }

libMesh::DifferentiablePhysics::_second_order_vars

std::set< unsigned int > _second_order_vars

Definition: diff_physics.h:564

◆ 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().

 {
   std::ostringstream sensitivity_rhs_name;
   sensitivity_rhs_name << "sensitivity_rhs" << i;
 
   return this->get_vector(sensitivity_rhs_name.str());
 }

◆ 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().

 {
   std::ostringstream sensitivity_rhs_name;
   sensitivity_rhs_name << "sensitivity_rhs" << i;
 
   return this->get_vector(sensitivity_rhs_name.str());
 }

◆ 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().

 {
   std::ostringstream sensitivity_name;
   sensitivity_name << "sensitivity_solution" << i;
 
   return this->get_vector(sensitivity_name.str());
 }

◆ 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().

 {
   std::ostringstream sensitivity_name;
   sensitivity_name << "sensitivity_solution" << i;
 
   return this->get_vector(sensitivity_name.str());
 }

◆ 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(), libMesh::FEMSystem::build_context(), libMesh::DiffContext::DiffContext(), libMesh::FEMSystem::postprocess(), libMesh::FEMContext::pre_fe_reinit(), and libMesh::DifferentiableSystem::solve().

 {
   libmesh_assert(time_solver.get());
   libmesh_assert_equal_to (&(time_solver->system()), this);
   return *time_solver;
 }

◆ 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.

 {
   libmesh_assert(time_solver.get());
   libmesh_assert_equal_to (&(time_solver->system()), this);
   return *time_solver;
 }

◆ 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().

 {
   // Make sure the vector exists
   const_vectors_iterator pos = _vectors.find(vec_name);
 
   if (pos == _vectors.end())
     libmesh_error_msg("ERROR: vector " << vec_name << " does not exist in this system!");
 
   return *(pos->second);
 }

◆ 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.

 {
   // Make sure the vector exists
   vectors_iterator pos = _vectors.find(vec_name);
 
   if (pos == _vectors.end())
     libmesh_error_msg("ERROR: vector " << vec_name << " does not exist in this system!");
 
   return *(pos->second);
 }

◆ 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().

 {
   const_vectors_iterator v = vectors_begin();
   const_vectors_iterator v_end = vectors_end();
   unsigned int num = 0;
   while ((num<vec_num) && (v!=v_end))
     {
       num++;
       ++v;
     }
   libmesh_assert (v != v_end);
   return *(v->second);
 }

◆ 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().

 {
   vectors_iterator v = vectors_begin();
   vectors_iterator v_end = vectors_end();
   unsigned int num = 0;
   while ((num<vec_num) && (v!=v_end))
     {
       num++;
       ++v;
     }
   libmesh_assert (v != v_end);
   return *(v->second);
 }

◆ 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().

 {
   std::ostringstream adjoint_name;
   adjoint_name << "weighted_sensitivity_adjoint_solution" << i;
 
   return this->get_vector(adjoint_name.str());
 }

◆ 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().

 {
   std::ostringstream adjoint_name;
   adjoint_name << "weighted_sensitivity_adjoint_solution" << i;
 
   return this->get_vector(adjoint_name.str());
 }

◆ 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().

 {
   return this->get_vector("weighted_sensitivity_solution");
 }

◆ 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().

 {
   return this->get_vector("weighted_sensitivity_solution");
 }

◆ 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().

 {
   return _variable_numbers.count(var);
 }

◆ 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().

 {
   bool have_first_order_scalar_vars = false;
 
   if (this->have_first_order_vars())
     for (const auto & var : this->get_first_order_vars())
       if (this->variable(var).type().family == SCALAR)
         have_first_order_scalar_vars = true;
 
   return have_first_order_scalar_vars;
 }

◆ 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(); }

libMesh::DifferentiablePhysics::_first_order_vars

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().

 {
   return (_matrices.count(mat_name));
 }

◆ 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().

 {
   bool have_second_order_scalar_vars = false;
 
   if (this->have_second_order_vars())
     for (const auto & var : this->get_second_order_vars())
       if (this->variable(var).type().family == SCALAR)
         have_second_order_scalar_vars = true;
 
   return have_second_order_scalar_vars;
 }

◆ have_second_order_vars()

bool libMesh::DifferentiablePhysics::have_second_order_vars ( ) const

inlineinherited

Definition at line 524 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_second_order_vars.

Referenced by libMesh::EulerSolver::element_residual(), and libMesh::DifferentiableSystem::have_second_order_scalar_vars().

525 { return !_second_order_vars.empty(); }

libMesh::DifferentiablePhysics::_second_order_vars

std::set< unsigned int > _second_order_vars

Definition: diff_physics.h:564

◆ 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().

 {
   return (_vectors.count(vec_name));
 }

◆ 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; }

libMesh::System::_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().

 {
   return _identify_variable_groups;
 }

◆ 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.

 {
   _identify_variable_groups = ivg;
 }

◆ 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().

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

◆ 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().

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

◆ 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().

 {
   // Calling init() twice on the same system currently works evil
   // magic, whether done directly or via EquationSystems::read()
   libmesh_assert(!this->is_initialized());
 
   // First initialize any required data:
   // either only the basic System data
   if (_basic_system_only)
     System::init_data();
   // or all the derived class' data too
   else
     this->init_data();
 
   // If no variables have been added to this system
   // don't do anything
   if (!this->n_vars())
     return;
 
   // Then call the user-provided initialization function
   this->user_initialization();
 }

◆ init_context()

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

overridevirtualinherited

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

 {
   // Parent::init_context(c);  // may be a good idea in derived classes
 
   // Although we do this in DiffSystem::build_context() and
   // FEMSystem::build_context() as well, we do it here just to be
   // extra sure that the deltat pointer gets set.  Since the
   // intended behavior is for classes derived from FEMSystem to
   // call Parent::init_context() in their own init_context()
   // overloads, we can ensure that those classes get the correct
   // deltat pointers even if they have different build_context()
   // overloads.
   c.set_deltat_pointer ( &deltat );
 
   FEMContext & context = cast_ref<FEMContext &>(c);
 
   // Make sure we're prepared to do mass integration
   for (unsigned int var = 0; var != this->n_vars(); ++var)
     if (this->get_physics()->is_time_evolving(var))
       {
         // Request shape functions based on FEType
         switch( FEInterface::field_type( this->variable_type(var) ) )
           {
           case( TYPE_SCALAR ):
             {
               FEBase * elem_fe = nullptr;
               context.get_element_fe(var, elem_fe);
               elem_fe->get_JxW();
               elem_fe->get_phi();
             }
             break;
           case( TYPE_VECTOR ):
             {
               FEGenericBase<RealGradient> * elem_fe = nullptr;
               context.get_element_fe(var, elem_fe);
               elem_fe->get_JxW();
               elem_fe->get_phi();
             }
             break;
           default:
             libmesh_error_msg("Unrecognized field type!");
           }
       }
 }

◆ init_data()

void libMesh::ContinuationSystem::init_data ( )

overrideprotectedvirtual

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

Reimplemented from libMesh::FEMSystem.

Definition at line 90 of file continuation_system.C.

References libMesh::System::add_vector(), delta_u, du_ds, libMesh::FEMSystem::init_data(), previous_du_ds, previous_u, y, y_old, and z.

 {
   // Add a vector which stores the tangent "du/ds" to the system and save its pointer.
   du_ds = &(add_vector("du_ds"));
 
   // Add a vector which stores the tangent "du/ds" to the system and save its pointer.
   previous_du_ds = &(add_vector("previous_du_ds"));
 
   // Add a vector to keep track of the previous nonlinear solution
   // at the old value of lambda.
   previous_u = &(add_vector("previous_u"));
 
   // Add a vector to keep track of the temporary solution "y" of Ay=G_{\lambda}.
   y = &(add_vector("y"));
 
   // Add a vector to keep track of the "old value" of "y" which is the solution of Ay=G_{\lambda}.
   y_old = &(add_vector("y_old"));
 
   // Add a vector to keep track of the temporary solution "z" of Az=-G.
   z = &(add_vector("z"));
 
   // Add a vector to keep track of the Newton update during the constrained PDE solves.
   delta_u = &(add_vector("delta_u"));
 
   // Call the Parent's initialization routine.
   Parent::init_data();
 }

◆ 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().

 {
   libmesh_assert(matrix);
 
   // Check for quick return in case the system matrix
   // (and by extension all the matrices) has already
   // been initialized
   if (matrix->initialized())
     return;
 
   // Get a reference to the DofMap
   DofMap & dof_map = this->get_dof_map();
 
   // no chance to add other matrices
   _can_add_matrices = false;
 
   // Tell the matrices about the dof map, and vice versa
   for (auto & pr : _matrices)
     {
       SparseMatrix<Number> & m = *(pr.second);
       libmesh_assert (!m.initialized());
 
       // We want to allow repeated init() on systems, but we don't
       // want to attach the same matrix to the DofMap twice
       if (!dof_map.is_attached(m))
         dof_map.attach_matrix (m);
     }
 
   // Compute the sparsity pattern for the current
   // mesh and DOF distribution.  This also updates
   // additional matrices, \p DofMap now knows them
   dof_map.compute_sparsity (this->get_mesh());
 
   // Initialize matrices
   for (auto & pr : _matrices)
     pr.second->init ();
 
   // Set the additional matrices to 0.
   for (auto & pr : _matrices)
     pr.second->zero ();
 }

◆ 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 {}

◆ initialize_tangent()

void libMesh::ContinuationSystem::initialize_tangent ( )

private

Before starting arclength continuation, we need at least 2 prior solutions (both solution and u_previous should be filled with meaningful values) And we need to initialize the tangent vector. This only needs to be called once.

Definition at line 131 of file continuation_system.C.

References libMesh::NumericVector< T >::add(), libMesh::NumericVector< T >::close(), continuation_parameter, dlambda_ds, ds_current, du_ds, libMesh::NumericVector< T >::l2_norm(), old_continuation_parameter, libMesh::out, previous_u, quiet, libMesh::Real, libMesh::NumericVector< T >::scale(), set_Theta(), libMesh::System::solution, solve_tangent(), tangent_initialized, Theta, Theta_LOCA, update_solution(), and y.

Referenced by continuation_solve().

 {
   // Be sure the tangent was not already initialized.
   libmesh_assert (!tangent_initialized);
 
   // Compute delta_s_zero, the initial arclength traveled during the
   // first step.  Here we assume that previous_u and lambda_old store
   // the previous solution and control parameter.  You may need to
   // read in an old solution (or solve the non-continuation system)
   // first and call save_current_solution() before getting here.
 
   // 1.) Compute delta_s_zero as ||u|| - ||u_old|| + ...
   // Compute norms of the current and previous solutions
   //   Real norm_u          = solution->l2_norm();
   //   Real norm_previous_u = previous_u->l2_norm();
 
   //   if (!quiet)
   //     {
   //       libMesh::out << "norm_u=" << norm_u << std::endl;
   //       libMesh::out << "norm_previous_u=" << norm_previous_u << std::endl;
   //     }
 
   //   if (norm_u == norm_previous_u)
   //     {
   //       libMesh::err << "Warning, it appears u and previous_u are the "
   //   << "same, are you sure this is correct?"
   //   << "It's possible you forgot to set one or the other..."
   //   << std::endl;
   //     }
 
   //   Real delta_s_zero = std::sqrt(
   //   (norm_u - norm_previous_u)*(norm_u - norm_previous_u) +
   //   (*continuation_parameter-old_continuation_parameter)*
   //   (*continuation_parameter-old_continuation_parameter)
   //   );
 
   //   // 2.) Compute delta_s_zero as ||u -u_old|| + ...
   //   *delta_u = *solution;
   //   delta_u->add(-1., *previous_u);
   //   delta_u->close();
   //   Real norm_delta_u = delta_u->l2_norm();
   //   Real norm_u          = solution->l2_norm();
   //   Real norm_previous_u = previous_u->l2_norm();
 
   //   // Scale norm_delta_u by the bigger of either norm_u or norm_previous_u
   //   norm_delta_u /= std::max(norm_u, norm_previous_u);
 
   //   if (!quiet)
   //     {
   //       libMesh::out << "norm_u=" << norm_u << std::endl;
   //       libMesh::out << "norm_previous_u=" << norm_previous_u << std::endl;
   //       //libMesh::out << "norm_delta_u=" << norm_delta_u << std::endl;
   //       libMesh::out << "norm_delta_u/max(|u|,|u_old|)=" << norm_delta_u << std::endl;
   //       libMesh::out << "|norm_u-norm_previous_u|=" << std::abs(norm_u - norm_previous_u) << std::endl;
   //     }
 
   //   const Real dlambda = *continuation_parameter-old_continuation_parameter;
 
   //   if (!quiet)
   //     libMesh::out << "dlambda=" << dlambda << std::endl;
 
   //   Real delta_s_zero = std::sqrt(
   //   (norm_delta_u*norm_delta_u) +
   //   (dlambda*dlambda)
   //   );
 
   //   if (!quiet)
   //     libMesh::out << "delta_s_zero=" << delta_s_zero << std::endl;
 
   // 1.) + 2.)
   //   // Now approximate the initial tangent d(lambda)/ds
   //   this->dlambda_ds = (*continuation_parameter-old_continuation_parameter) / delta_s_zero;
 
 
   //   // We can also approximate the deriv. wrt s by finite differences:
   //   // du/ds = (u1 - u0) / delta_s_zero.
   //   // FIXME: Use delta_u from above if we decide to keep that method.
   //   *du_ds = *solution;
   //   du_ds->add(-1., *previous_u);
   //   du_ds->scale(1./delta_s_zero);
   //   du_ds->close();
 
 
   // 3.) Treating (u-previous_u)/(lambda - lambda_old) as an approximation to du/d(lambda),
   // we follow the same technique as Carnes and Shadid.
   //   const Real dlambda = *continuation_parameter-old_continuation_parameter;
   //   libmesh_assert_greater (dlambda, 0.);
 
   //   // Use delta_u for temporary calculation of du/d(lambda)
   //   *delta_u = *solution;
   //   delta_u->add(-1., *previous_u);
   //   delta_u->scale(1. / dlambda);
   //   delta_u->close();
 
   //   // Determine initial normalization parameter
   //   const Real solution_size = std::max(solution->l2_norm(), previous_u->l2_norm());
   //   if (solution_size > 1.)
   //     {
   //       Theta = 1./solution_size;
 
   //       if (!quiet)
   // libMesh::out << "Setting Normalization Parameter Theta=" << Theta << std::endl;
   //     }
 
   //   // Compute d(lambda)/ds
   //   // The correct sign of d(lambda)/ds should be positive, since we assume that (lambda > lambda_old)
   //   // but we could always double-check that as well.
   //   Real norm_delta_u = delta_u->l2_norm();
   //   this->dlambda_ds = 1. / std::sqrt(1. + Theta*Theta*norm_delta_u*norm_delta_u);
 
   //   // Finally, compute du/ds = d(lambda)/ds * du/d(lambda)
   //   *du_ds = *delta_u;
   //   du_ds->scale(dlambda_ds);
   //   du_ds->close();
 
 
   // 4.) Use normalized arclength formula to estimate delta_s_zero
   //   // Determine initial normalization parameter
   //   set_Theta();
 
   //   // Compute (normalized) delta_s_zero
   //   *delta_u = *solution;
   //   delta_u->add(-1., *previous_u);
   //   delta_u->close();
   //   Real norm_delta_u = delta_u->l2_norm();
 
   //   const Real dlambda = *continuation_parameter-old_continuation_parameter;
 
   //   if (!quiet)
   //     libMesh::out << "dlambda=" << dlambda << std::endl;
 
   //   Real delta_s_zero = std::sqrt(
   //   (Theta_LOCA*Theta_LOCA*Theta*norm_delta_u*norm_delta_u) +
   //   (dlambda*dlambda)
   //   );
   //   *du_ds = *delta_u;
   //   du_ds->scale(1./delta_s_zero);
   //   dlambda_ds = dlambda / delta_s_zero;
 
   //   if (!quiet)
   //     {
   //       libMesh::out << "delta_s_zero=" << delta_s_zero << std::endl;
   //       libMesh::out << "initial d(lambda)/ds|_0 = " << dlambda_ds << std::endl;
   //       libMesh::out << "initial ||du_ds||_0 = " << du_ds->l2_norm() << std::endl;
   //     }
 
   //   // FIXME: Also store the initial finite-differenced approximation to -du/dlambda as y.
   //   // We stick to the convention of storing negative y, since that is what we typically
   //   // solve for anyway.
   //   *y = *delta_u;
   //   y->scale(-1./dlambda);
   //   y->close();
 
 
 
   // 5.) Assume dlambda/ds_0 ~ 1/sqrt(2) and determine the value of Theta_LOCA which
   // will satisfy this criterion
 
   // Initial change in parameter
   const Real dlambda = *continuation_parameter-old_continuation_parameter;
   libmesh_assert_not_equal_to (dlambda, 0.0);
 
   // Ideal initial value of dlambda_ds
   dlambda_ds = 1. / std::sqrt(2.);
   if (dlambda < 0.)
     dlambda_ds *= -1.;
 
   // This also implies the initial value of ds
   ds_current = dlambda / dlambda_ds;
 
   if (!quiet)
     libMesh::out << "Setting ds_current|_0=" << ds_current << std::endl;
 
   // Set y = -du/dlambda using finite difference approximation
   *y = *solution;
   y->add(-1., *previous_u);
   y->scale(-1./dlambda);
   y->close();
   const Real ynorm=y->l2_norm();
 
   // Finally, set the value of du_ds to be used in the upcoming
   // tangent calculation. du/ds = du/dlambda * dlambda/ds
   *du_ds = *y;
   du_ds->scale(-dlambda_ds);
   du_ds->close();
 
   // Determine additional solution normalization parameter
   // (Since we just set du/ds, it will be:  ||du||*||du/ds||)
   set_Theta();
 
   // The value of Theta_LOCA which makes dlambda_ds = 1/sqrt(2),
   // assuming our Theta = ||du||^2.
   // Theta_LOCA = std::abs(dlambda);
 
   // Assuming general Theta
   Theta_LOCA = std::sqrt(1./Theta/ynorm/ynorm);
 
 
   if (!quiet)
     {
       libMesh::out << "Setting initial Theta_LOCA = " << Theta_LOCA << std::endl;
       libMesh::out << "Theta_LOCA^2*Theta         = " << Theta_LOCA*Theta_LOCA*Theta << std::endl;
       libMesh::out << "initial d(lambda)/ds|_0    = " << dlambda_ds << std::endl;
       libMesh::out << "initial ||du_ds||_0        = " << du_ds->l2_norm() << std::endl;
     }
 
 
 
   // OK, we estimated the tangent at point u0.
   // Now, to estimate the tangent at point u1, we call the solve_tangent routine.
 
   // Set the flag which tells us the method has been initialized.
   tangent_initialized = true;
 
   solve_tangent();
 
   // Advance the solution and the parameter to the next value.
   update_solution();
 }

◆ is_adjoint_already_solved()

bool libMesh::System::is_adjoint_already_solved ( ) const

inlineinherited

Accessor for the adjoint_already_solved boolean

Definition at line 388 of file system.h.

References libMesh::System::adjoint_already_solved.

Referenced by libMesh::ImplicitSystem::adjoint_qoi_parameter_sensitivity(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::AdjointResidualErrorEstimator::estimate_error(), libMesh::ImplicitSystem::qoi_parameter_hessian(), and libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product().

389 { return adjoint_already_solved;}

libMesh::System::adjoint_already_solved

bool adjoint_already_solved

Definition: system.h:2003

◆ 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(); }

libMesh::DifferentiablePhysics::_first_order_vars

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().

 {
   return _is_initialized;
 }

◆ is_second_order_var()

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

inlineinherited

Definition at line 533 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_second_order_vars.

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

534 { return _second_order_vars.find(var) != _second_order_vars.end(); }

libMesh::DifferentiablePhysics::_second_order_vars

std::set< unsigned int > _second_order_vars

Definition: diff_physics.h:564

◆ 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 libMesh::FEMSystem::init_context().

   {
     libmesh_assert_less(var,_time_evolving.size());
     libmesh_assert( _time_evolving[var] == 0 ||
                     _time_evolving[var] == 1 ||
                     _time_evolving[var] == 2 );
     return _time_evolving[var];
   }

◆ 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().

 {
   // Make sure the set is clear
   var_indices.clear();
 
   std::vector<dof_id_type> dof_indices;
 
   const dof_id_type
     first_local = this->get_dof_map().first_dof(),
     end_local   = this->get_dof_map().end_dof();
 
   // Begin the loop over the elements
   for (const auto & elem : this->get_mesh().active_local_element_ptr_range())
     {
       this->get_dof_map().dof_indices (elem, dof_indices, var);
 
       for (std::size_t i=0; i<dof_indices.size(); i++)
         {
           dof_id_type dof = dof_indices[i];
 
           //If the dof is owned by the local processor
           if (first_local <= dof && dof < end_local)
             var_indices.insert(dof_indices[i]);
         }
     }
 
   // we may have missed assigning DOFs to nodes that we own
   // but to which we have no connected elements matching our
   // variable restriction criterion.  this will happen, for example,
   // if variable V is restricted to subdomain S.  We may not own
   // any elements which live in S, but we may own nodes which are
   // *connected* to elements which do.
   for (const auto & node : this->get_mesh().local_node_ptr_range())
     {
       libmesh_assert(node);
       this->get_dof_map().dof_indices (node, dof_indices, var);
       for (auto dof : dof_indices)
         if (first_local <= dof && dof < end_local)
           var_indices.insert(dof);
     }
 }

◆ 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().

                                              {
     return request_jacobian;
   }

◆ mesh_position_get()

void libMesh::FEMSystem::mesh_position_get ( )

inherited

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(), libMesh::FEMSystem::build_context(), libMesh::FEMContext::elem_position_get(), libMesh::DiffContext::get_dof_indices(), libMesh::DiffContext::get_elem_solution(), libMesh::System::get_mesh(), libMesh::FEMSystem::init_context(), libMesh::invalid_uint, mesh, libMesh::FEMContext::pre_fe_reinit(), libMesh::System::solution, and libMesh::System::update().

 {
   // This function makes no sense unless we've already picked out some
   // variable(s) to reflect mesh position coordinates
   if (!_mesh_sys)
     libmesh_error_msg("_mesh_sys was nullptr!");
 
   // We currently assume mesh variables are in our own system
   if (_mesh_sys != this)
     libmesh_not_implemented();
 
   // Loop over every active mesh element on this processor
   const MeshBase & mesh = this->get_mesh();
 
   std::unique_ptr<DiffContext> con = this->build_context();
   FEMContext & _femcontext = cast_ref<FEMContext &>(*con);
   this->init_context(_femcontext);
 
   // Get the solution's mesh variables from every element
   for (const auto & elem : mesh.active_local_element_ptr_range())
     {
       _femcontext.pre_fe_reinit(*this, elem);
 
       _femcontext.elem_position_get();
 
       if (_mesh_x_var != libMesh::invalid_uint)
         this->solution->insert(_femcontext.get_elem_solution(_mesh_x_var),
                                _femcontext.get_dof_indices(_mesh_x_var) );
       if (_mesh_y_var != libMesh::invalid_uint)
         this->solution->insert(_femcontext.get_elem_solution(_mesh_y_var),
                                _femcontext.get_dof_indices(_mesh_y_var));
       if (_mesh_z_var != libMesh::invalid_uint)
         this->solution->insert(_femcontext.get_elem_solution(_mesh_z_var),
                                _femcontext.get_dof_indices(_mesh_z_var));
     }
 
   this->solution->close();
 
   // And make sure the current_local_solution is up to date too
   this->System::update();
 }

◆ mesh_position_set()

void libMesh::FEMSystem::mesh_position_set ( )

inherited

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(), libMesh::FEMSystem::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(), libMesh::FEMSystem::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 libMesh::FEMSystem::solve().

 {
   // If we don't need to move the mesh, we're done
   if (_mesh_sys != this)
     return;
 
   MeshBase & mesh = this->get_mesh();
 
   std::unique_ptr<DiffContext> con = this->build_context();
   FEMContext & _femcontext = cast_ref<FEMContext &>(*con);
   this->init_context(_femcontext);
 
   // Move every mesh element we can
   for (const auto & elem : mesh.active_local_element_ptr_range())
     {
       // We need the algebraic data
       _femcontext.pre_fe_reinit(*this, elem);
       // And when asserts are on, we also need the FE so
       // we can assert that the mesh data is of the right type.
 #ifndef NDEBUG
       _femcontext.elem_fe_reinit();
 #endif
 
       // This code won't handle moving subactive elements
       libmesh_assert(!_femcontext.get_elem().has_children());
 
       _femcontext.elem_position_set(1.);
     }
 
   // We've now got positions set on all local nodes (and some
   // semilocal nodes); let's request positions for non-local nodes
   // from their processors.
 
   SyncNodalPositions sync_object(mesh);
   Parallel::sync_dofobject_data_by_id
     (this->comm(), mesh.nodes_begin(), mesh.nodes_end(), sync_object);
 }

◆ 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().

 {
   return this->n_dofs() - this->n_constrained_dofs();
 }

◆ 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().

 {
   if (_variables.empty())
     return 0;
 
   const Variable & last = _variables.back();
   return last.first_scalar_number() + last.n_components();
 }

◆ 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().

 {
 #ifdef LIBMESH_ENABLE_CONSTRAINTS
 
   return _dof_map->n_constrained_dofs();
 
 #else
 
   return 0;
 
 #endif
 }

◆ n_dofs()

dof_id_type libMesh::System::n_dofs ( ) const

inherited

Returns: The number of degrees of freedom in the system

Definition at line 150 of file system.C.

References libMesh::System::_dof_map.

Referenced by libMesh::System::add_vector(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::System::get_info(), libMesh::SecondOrderUnsteadySolver::init_data(), libMesh::UnsteadySolver::init_data(), libMesh::System::init_data(), libMesh::OptimizationSystem::initialize_equality_constraints_storage(), libMesh::OptimizationSystem::initialize_inequality_constraints_storage(), libMesh::System::n_active_dofs(), libMesh::CondensedEigenSystem::n_global_non_condensed_dofs(), libMesh::FEMSystem::numerical_jacobian(), libMesh::System::read_legacy_data(), libMesh::SecondOrderUnsteadySolver::reinit(), libMesh::UnsteadySolver::reinit(), and libMesh::System::restrict_vectors().

 {
   return _dof_map->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().

 {
 #ifdef LIBMESH_ENABLE_CONSTRAINTS
 
   return _dof_map->n_local_constrained_dofs();
 
 #else
 
   return 0;
 
 #endif
 }

◆ n_local_dofs()

dof_id_type libMesh::System::n_local_dofs ( ) const

inherited

Returns: The number of degrees of freedom local to this processor

Definition at line 187 of file system.C.

References libMesh::System::_dof_map, and libMesh::ParallelObject::processor_id().

Referenced by libMesh::System::add_vector(), libMesh::PetscDMWrapper::build_section(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::System::get_info(), libMesh::SecondOrderUnsteadySolver::init_data(), libMesh::UnsteadySolver::init_data(), libMesh::System::init_data(), libMesh::OptimizationSystem::initialize_equality_constraints_storage(), libMesh::OptimizationSystem::initialize_inequality_constraints_storage(), libMesh::SecondOrderUnsteadySolver::reinit(), libMesh::UnsteadySolver::reinit(), and libMesh::System::restrict_vectors().

 {
   return _dof_map->n_dofs_on_processor (this->processor_id());
 }

◆ 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.

 {
   return cast_int<unsigned int>(_matrices.size());
 }

◆ 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; }

libMesh::ReferenceCounter::_n_objects

static Threads::atomic< unsigned int > _n_objects

Definition: reference_counter.h:130

◆ 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().

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

libMesh::Parallel::Communicator::size

processor_id_type size() const

Definition: communicator.h:175

libMesh::ParallelObject::_communicator

const Parallel::Communicator & _communicator

Definition: parallel_object.h:107

◆ n_qois()

unsigned int libMesh::System::n_qois ( ) const

inlineinherited

Number of currently active quantities of interest.

Definition at line 2278 of file system.h.

References libMesh::System::qoi.

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::ImplicitSystem::adjoint_qoi_parameter_sensitivity(), libMesh::ImplicitSystem::adjoint_solve(), libMesh::SensitivityData::allocate_data(), libMesh::SensitivityData::allocate_hessian_data(), libMesh::ExplicitSystem::assemble_qoi(), libMesh::FEMSystem::assemble_qoi(), libMesh::ExplicitSystem::assemble_qoi_derivative(), libMesh::FEMSystem::assemble_qoi_derivative(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::AdjointResidualErrorEstimator::estimate_error(), libMesh::ImplicitSystem::forward_qoi_parameter_sensitivity(), libMesh::FEMContext::pre_fe_reinit(), libMesh::ImplicitSystem::qoi_parameter_hessian(), libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product(), libMesh::QoISet::size(), and libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve().

 {
   return cast_int<unsigned int>(this->qoi.size());
 }

◆ 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(), libMesh::FEMSystem::assembly(), libMesh::System::get_info(), and libMesh::System::init_data().

 {
   return cast_int<unsigned int>(_variable_groups.size());
 }

◆ 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.

 {
   return cast_int<unsigned int>(_variables.size());
 }

◆ 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().

 {
   return cast_int<unsigned int>(_vectors.size());
 }

◆ name()

const std::string & libMesh::System::name ( ) const

inlineinherited

Returns: The system name.

Definition at line 2017 of file system.h.

References libMesh::System::_sys_name.

Referenced by libMesh::System::compare(), ContinuationSystem(), DMlibMeshSetUpName_Private(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::ExactSolution::ExactSolution(), libMesh::ExactErrorEstimator::find_squared_element_error(), libMesh::System::get_info(), libMesh::ImplicitSystem::get_linear_solver(), libMesh::NewtonSolver::init(), libMesh::TimeSolver::init_data(), libMesh::petsc_auto_fieldsplit(), libMesh::TimeSolver::reinit(), libMesh::PetscDiffSolver::setup_petsc_data(), libMesh::FrequencySystem::solve(), libMesh::LinearImplicitSystem::solve(), libMesh::NonlinearImplicitSystem::solve(), libMesh::System::user_assembly(), libMesh::System::user_constrain(), libMesh::System::user_initialization(), libMesh::System::user_QOI(), libMesh::System::user_QOI_derivative(), libMesh::System::write_header(), libMesh::System::write_parallel_data(), and libMesh::System::write_serialized_data().

 {
   return _sys_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().

                                                    {
     return request_jacobian;
   }

◆ 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().

                                                          {
     return request_jacobian;
   }

◆ 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().

                                                         {
     return request_jacobian;
   }

◆ number()

unsigned int libMesh::System::number ( ) const

inlineinherited

Returns: The system number.

Definition at line 2025 of file system.h.

References libMesh::System::_sys_number.

Referenced by libMesh::ExactSolution::_compute_error(), libMesh::PetscDMWrapper::add_dofs_helper(), libMesh::System::add_variable(), libMesh::System::add_variables(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ExactErrorEstimator::find_squared_element_error(), libMesh::System::get_info(), libMesh::System::read_legacy_data(), libMesh::System::read_parallel_data(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::HPCoarsenTest::select_refinement(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::System::write_parallel_data(), libMesh::System::write_serialized_blocked_dof_objects(), and libMesh::System::zero_variable().

 {
   return _sys_number;
 }

◆ numerical_elem_jacobian()

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

inherited

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 libMesh::FEMSystem::numerical_jacobian().

 {
   LOG_SCOPE("numerical_elem_jacobian()", "FEMSystem");
   this->numerical_jacobian(&TimeSolver::element_residual, context);
 }

◆ numerical_jacobian()

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

inherited

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(), libMesh::FEMSystem::numerical_jacobian_h, libMesh::FEMSystem::numerical_jacobian_h_for_var(), libMesh::Elem::point(), libMesh::Real, and libMesh::DenseVector< T >::zero().

Referenced by libMesh::FEMSystem::numerical_elem_jacobian(), libMesh::FEMSystem::numerical_nonlocal_jacobian(), and libMesh::FEMSystem::numerical_side_jacobian().

 {
   // Logging is done by numerical_elem_jacobian
   // or numerical_side_jacobian
 
   DenseVector<Number> original_residual(context.get_elem_residual());
   DenseVector<Number> backwards_residual(context.get_elem_residual());
   DenseMatrix<Number> numeric_jacobian(context.get_elem_jacobian());
 #ifdef DEBUG
   DenseMatrix<Number> old_jacobian(context.get_elem_jacobian());
 #endif
 
   Real numerical_point_h = 0.;
   if (_mesh_sys == this)
     numerical_point_h = numerical_jacobian_h * context.get_elem().hmin();
 
   const unsigned int n_dofs =
     cast_int<unsigned int>(context.get_dof_indices().size());
 
   for (unsigned int v = 0; v != context.n_vars(); ++v)
     {
       const Real my_h = this->numerical_jacobian_h_for_var(v);
 
       unsigned int j_offset = libMesh::invalid_uint;
 
       if (!context.get_dof_indices(v).empty())
         {
           for (auto i : IntRange<unsigned int>(0, n_dofs))
             if (context.get_dof_indices()[i] ==
                 context.get_dof_indices(v)[0])
               j_offset = i;
 
           libmesh_assert_not_equal_to(j_offset, libMesh::invalid_uint);
         }
 
       for (auto j : IntRange<unsigned int>(0, context.get_dof_indices(v).size()))
         {
           const unsigned int total_j = j + j_offset;
 
           // Take the "minus" side of a central differenced first derivative
           Number original_solution = context.get_elem_solution(v)(j);
           context.get_elem_solution(v)(j) -= my_h;
 
           // Make sure to catch any moving mesh terms
           Real * coord = nullptr;
           if (_mesh_sys == this)
             {
               if (_mesh_x_var == v)
                 coord = &(context.get_elem().point(j)(0));
               else if (_mesh_y_var == v)
                 coord = &(context.get_elem().point(j)(1));
               else if (_mesh_z_var == v)
                 coord = &(context.get_elem().point(j)(2));
             }
           if (coord)
             {
               // We have enough information to scale the perturbations
               // here appropriately
               context.get_elem_solution(v)(j) = original_solution - numerical_point_h;
               *coord = libmesh_real(context.get_elem_solution(v)(j));
             }
 
           context.get_elem_residual().zero();
           ((*time_solver).*(res))(false, context);
 #ifdef DEBUG
           libmesh_assert_equal_to (old_jacobian, context.get_elem_jacobian());
 #endif
           backwards_residual = context.get_elem_residual();
 
           // Take the "plus" side of a central differenced first derivative
           context.get_elem_solution(v)(j) = original_solution + my_h;
           if (coord)
             {
               context.get_elem_solution()(j) = original_solution + numerical_point_h;
               *coord = libmesh_real(context.get_elem_solution(v)(j));
             }
           context.get_elem_residual().zero();
           ((*time_solver).*(res))(false, context);
 #ifdef DEBUG
           libmesh_assert_equal_to (old_jacobian, context.get_elem_jacobian());
 #endif
 
           context.get_elem_solution(v)(j) = original_solution;
           if (coord)
             {
               *coord = libmesh_real(context.get_elem_solution(v)(j));
               for (auto i : IntRange<unsigned int>(0, n_dofs))
                 {
                   numeric_jacobian(i,total_j) =
                     (context.get_elem_residual()(i) - backwards_residual(i)) /
                     2. / numerical_point_h;
                 }
             }
           else
             {
               for (auto i : IntRange<unsigned int>(0, n_dofs))
                 {
                   numeric_jacobian(i,total_j) =
                     (context.get_elem_residual()(i) - backwards_residual(i)) /
                     2. / my_h;
                 }
             }
         }
     }
 
   context.get_elem_residual() = original_residual;
   context.get_elem_jacobian() = numeric_jacobian;
 }

◆ numerical_jacobian_h_for_var()

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

inlineinherited

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 libMesh::FEMSystem::_numerical_jacobian_h_for_var, libMesh::FEMSystem::numerical_jacobian_h, and libMesh::Real.

Referenced by libMesh::FEMSystem::numerical_jacobian().

 {
   if ((var_num >= _numerical_jacobian_h_for_var.size()) ||
       _numerical_jacobian_h_for_var[var_num] == Real(0))
     return numerical_jacobian_h;
 
   return _numerical_jacobian_h_for_var[var_num];
 }

◆ numerical_nonlocal_jacobian()

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

inherited

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 libMesh::FEMSystem::numerical_jacobian().

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

 {
   LOG_SCOPE("numerical_nonlocal_jacobian()", "FEMSystem");
   this->numerical_jacobian(&TimeSolver::nonlocal_residual, context);
 }

◆ numerical_side_jacobian()

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

inherited

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

 {
   LOG_SCOPE("numerical_side_jacobian()", "FEMSystem");
   this->numerical_jacobian(&TimeSolver::side_residual, context);
 }

◆ 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 libMesh::FEMSystem::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().

 {
   // This function must be called on every processor; there's no
   // telling where in the partition p falls.
   parallel_object_only();
 
   // And every processor had better agree about which point we're
   // looking for
 #ifndef NDEBUG
   libmesh_assert(this->comm().verify(p(0)));
 #if LIBMESH_DIM > 1
   libmesh_assert(this->comm().verify(p(1)));
 #endif
 #if LIBMESH_DIM > 2
   libmesh_assert(this->comm().verify(p(2)));
 #endif
 #endif // NDEBUG
 
   // Get a reference to the mesh object associated with the system object that calls this function
   const MeshBase & mesh = this->get_mesh();
 
   // Use an existing PointLocator or create a new one
   std::unique_ptr<PointLocatorBase> locator_ptr = mesh.sub_point_locator();
   PointLocatorBase & locator = *locator_ptr;
 
   if (!insist_on_success || !mesh.is_serial())
     locator.enable_out_of_mesh_mode();
 
   // Get a pointer to the element that contains P
   const Elem * e = locator(p);
 
   Gradient grad_u;
 
   if (e && this->get_dof_map().is_evaluable(*e, var))
     grad_u = point_gradient(var, p, *e);
 
   // If I have an element containing p, then let's let everyone know
   processor_id_type lowest_owner =
     (e && (e->processor_id() == this->processor_id())) ?
     this->processor_id() : this->n_processors();
   this->comm().min(lowest_owner);
 
   // Everybody should get their value from a processor that was able
   // to compute it.
   // If nobody admits owning the point, we may have a problem.
   if (lowest_owner != this->n_processors())
     this->comm().broadcast(grad_u, lowest_owner);
   else
     libmesh_assert(!insist_on_success);
 
   return grad_u;
 }

◆ 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().

 {
   // Ensuring that the given point is really in the element is an
   // expensive assert, but as long as debugging is turned on we might
   // as well try to catch a particularly nasty potential error
   libmesh_assert (e.contains_point(p));
 
 #ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
   if (e.infinite())
     libmesh_not_implemented();
 #endif
 
   // Get the dof map to get the proper indices for our computation
   const DofMap & dof_map = this->get_dof_map();
 
   // Make sure we can evaluate on this element.
   libmesh_assert (dof_map.is_evaluable(e, var));
 
   // Need dof_indices for phi[i][j]
   std::vector<dof_id_type> dof_indices;
 
   // Fill in the dof_indices for our element
   dof_map.dof_indices (&e, dof_indices, var);
 
   // Get the no of dofs associated with this point
   const unsigned int num_dofs = cast_int<unsigned int>
     (dof_indices.size());
 
   FEType fe_type = dof_map.variable_type(var);
 
   // Build a FE again so we can calculate u(p)
   std::unique_ptr<FEBase> fe (FEBase::build(e.dim(), fe_type));
 
   // Map the physical co-ordinates to the master co-ordinates using the inverse_map from fe_interface.h
   // Build a vector of point co-ordinates to send to reinit
   std::vector<Point> coor(1, FEInterface::inverse_map(e.dim(), fe_type, &e, p));
 
   // Get the values of the shape function derivatives
   const std::vector<std::vector<RealGradient>> &  dphi = fe->get_dphi();
 
   // Reinitialize the element and compute the shape function values at coor
   fe->reinit (&e, &coor);
 
   // Get ready to accumulate a gradient
   Gradient grad_u;
 
   for (unsigned int l=0; l<num_dofs; l++)
     {
       grad_u.add_scaled (dphi[l][0], this->current_solution (dof_indices[l]));
     }
 
   return grad_u;
 }

◆ 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().

 {
   libmesh_assert(e);
   return this->point_gradient(var, p, *e);
 }

◆ 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().

 {
   // This function must be called on every processor; there's no
   // telling where in the partition p falls.
   parallel_object_only();
 
   // And every processor had better agree about which point we're
   // looking for
 #ifndef NDEBUG
   libmesh_assert(this->comm().verify(p(0)));
 #if LIBMESH_DIM > 1
   libmesh_assert(this->comm().verify(p(1)));
 #endif
 #if LIBMESH_DIM > 2
   libmesh_assert(this->comm().verify(p(2)));
 #endif
 #endif // NDEBUG
 
   // Get a reference to the mesh object associated with the system object that calls this function
   const MeshBase & mesh = this->get_mesh();
 
   // Use an existing PointLocator or create a new one
   std::unique_ptr<PointLocatorBase> locator_ptr = mesh.sub_point_locator();
   PointLocatorBase & locator = *locator_ptr;
 
   if (!insist_on_success || !mesh.is_serial())
     locator.enable_out_of_mesh_mode();
 
   // Get a pointer to the element that contains P
   const Elem * e = locator(p);
 
   Tensor hess_u;
 
   if (e && this->get_dof_map().is_evaluable(*e, var))
     hess_u = point_hessian(var, p, *e);
 
   // If I have an element containing p, then let's let everyone know
   processor_id_type lowest_owner =
     (e && (e->processor_id() == this->processor_id())) ?
     this->processor_id() : this->n_processors();
   this->comm().min(lowest_owner);
 
   // Everybody should get their value from a processor that was able
   // to compute it.
   // If nobody admits owning the point, we may have a problem.
   if (lowest_owner != this->n_processors())
     this->comm().broadcast(hess_u, lowest_owner);
   else
     libmesh_assert(!insist_on_success);
 
   return hess_u;
 }

◆ 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().

 {
   // Ensuring that the given point is really in the element is an
   // expensive assert, but as long as debugging is turned on we might
   // as well try to catch a particularly nasty potential error
   libmesh_assert (e.contains_point(p));
 
 #ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
   if (e.infinite())
     libmesh_not_implemented();
 #endif
 
   // Get the dof map to get the proper indices for our computation
   const DofMap & dof_map = this->get_dof_map();
 
   // Make sure we can evaluate on this element.
   libmesh_assert (dof_map.is_evaluable(e, var));
 
   // Need dof_indices for phi[i][j]
   std::vector<dof_id_type> dof_indices;
 
   // Fill in the dof_indices for our element
   dof_map.dof_indices (&e, dof_indices, var);
 
   // Get the no of dofs associated with this point
   const unsigned int num_dofs = cast_int<unsigned int>
     (dof_indices.size());
 
   FEType fe_type = dof_map.variable_type(var);
 
   // Build a FE again so we can calculate u(p)
   std::unique_ptr<FEBase> fe (FEBase::build(e.dim(), fe_type));
 
   // Map the physical co-ordinates to the master co-ordinates using the inverse_map from fe_interface.h
   // Build a vector of point co-ordinates to send to reinit
   std::vector<Point> coor(1, FEInterface::inverse_map(e.dim(), fe_type, &e, p));
 
   // Get the values of the shape function derivatives
   const std::vector<std::vector<RealTensor>> &  d2phi = fe->get_d2phi();
 
   // Reinitialize the element and compute the shape function values at coor
   fe->reinit (&e, &coor);
 
   // Get ready to accumulate a hessian
   Tensor hess_u;
 
   for (unsigned int l=0; l<num_dofs; l++)
     {
       hess_u.add_scaled (d2phi[l][0], this->current_solution (dof_indices[l]));
     }
 
   return hess_u;
 }

◆ 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().

 {
   libmesh_assert(e);
   return this->point_hessian(var, p, *e);
 }

◆ 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().

 {
   // This function must be called on every processor; there's no
   // telling where in the partition p falls.
   parallel_object_only();
 
   // And every processor had better agree about which point we're
   // looking for
 #ifndef NDEBUG
   libmesh_assert(this->comm().verify(p(0)));
 #if LIBMESH_DIM > 1
   libmesh_assert(this->comm().verify(p(1)));
 #endif
 #if LIBMESH_DIM > 2
   libmesh_assert(this->comm().verify(p(2)));
 #endif
 #endif // NDEBUG
 
   // Get a reference to the mesh object associated with the system object that calls this function
   const MeshBase & mesh = this->get_mesh();
 
   // Use an existing PointLocator or create a new one
   std::unique_ptr<PointLocatorBase> locator_ptr = mesh.sub_point_locator();
   PointLocatorBase & locator = *locator_ptr;
 
   if (!insist_on_success || !mesh.is_serial())
     locator.enable_out_of_mesh_mode();
 
   // Get a pointer to the element that contains P
   const Elem * e = locator(p);
 
   Number u = 0;
 
   if (e && this->get_dof_map().is_evaluable(*e, var))
     u = point_value(var, p, *e);
 
   // If I have an element containing p, then let's let everyone know
   processor_id_type lowest_owner =
     (e && (e->processor_id() == this->processor_id())) ?
     this->processor_id() : this->n_processors();
   this->comm().min(lowest_owner);
 
   // Everybody should get their value from a processor that was able
   // to compute it.
   // If nobody admits owning the point, we have a problem.
   if (lowest_owner != this->n_processors())
     this->comm().broadcast(u, lowest_owner);
   else
     libmesh_assert(!insist_on_success);
 
   return u;
 }

◆ 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().

 {
   // Ensuring that the given point is really in the element is an
   // expensive assert, but as long as debugging is turned on we might
   // as well try to catch a particularly nasty potential error
   libmesh_assert (e.contains_point(p));
 
   // Get the dof map to get the proper indices for our computation
   const DofMap & dof_map = this->get_dof_map();
 
   // Make sure we can evaluate on this element.
   libmesh_assert (dof_map.is_evaluable(e, var));
 
   // Need dof_indices for phi[i][j]
   std::vector<dof_id_type> dof_indices;
 
   // Fill in the dof_indices for our element
   dof_map.dof_indices (&e, dof_indices, var);
 
   // Get the no of dofs associated with this point
   const unsigned int num_dofs = cast_int<unsigned int>
     (dof_indices.size());
 
   FEType fe_type = dof_map.variable_type(var);
 
   // Map the physical co-ordinates to the master co-ordinates using the inverse_map from fe_interface.h.
   Point coor = FEInterface::inverse_map(e.dim(), fe_type, &e, p);
 
   // get the shape function value via the FEInterface to also handle the case
   // of infinite elements correcly, the shape function is not fe->phi().
   FEComputeData fe_data(this->get_equation_systems(), coor);
   FEInterface::compute_data(e.dim(), fe_type, &e, fe_data);
 
   // Get ready to accumulate a value
   Number u = 0;
 
   for (unsigned int l=0; l<num_dofs; l++)
     {
       u += fe_data.shape[l]*this->current_solution (dof_indices[l]);
     }
 
   return u;
 }

◆ 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().

 {
   libmesh_assert(e);
   return this->point_value(var, p, *e);
 }

◆ postprocess()

void libMesh::FEMSystem::postprocess ( )

overridevirtualinherited

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().

 {
   LOG_SCOPE("postprocess()", "FEMSystem");
 
   const MeshBase & mesh = this->get_mesh();
 
   this->update();
 
   // Get the time solver object associated with the system, and tell it that
   // we are not solving the adjoint problem
   this->get_time_solver().set_is_adjoint(false);
 
   // Loop over every active mesh element on this processor
   Threads::parallel_for (elem_range.reset(mesh.active_local_elements_begin(),
                                           mesh.active_local_elements_end()),
                          PostprocessContributions(*this));
 }

◆ 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().

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

◆ processor_id()

processor_id_type libMesh::ParallelObject::processor_id ( ) const

inlineinherited

Returns: The rank of this processor in the group.

Definition at line 101 of file parallel_object.h.

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

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

libMesh::ParallelObject::_communicator

const Parallel::Communicator & _communicator

Definition: parallel_object.h:107

libMesh::Parallel::Communicator::rank

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.

 {
   this->project_vector(*solution, f, g);
 
   solution->localize(*current_local_solution, _dof_map->get_send_list());
 }

◆ 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.

 {
   this->project_vector(*solution, f, g);
 
   solution->localize(*current_local_solution, _dof_map->get_send_list());
 }

◆ 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.

 {
   WrappedFunction<Number> f(*this, fptr, &parameters);
   WrappedFunction<Gradient> g(*this, gptr, &parameters);
   this->project_solution(&f, &g);
 }

◆ 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; }

libMesh::System::_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().

 {
   LOG_SCOPE ("project_vector(FunctionBase)", "System");
 
   libmesh_assert(f);
 
   WrappedFunctor<Number> f_fem(*f);
 
   if (g)
     {
       WrappedFunctor<Gradient> g_fem(*g);
 
       this->project_vector(new_vector, &f_fem, &g_fem, is_adjoint);
     }
   else
     this->project_vector(new_vector, &f_fem, nullptr, is_adjoint);
 }

◆ 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().

 {
   LOG_SCOPE ("project_fem_vector()", "System");
 
   libmesh_assert (f);
 
   ConstElemRange active_local_range
     (this->get_mesh().active_local_elements_begin(),
      this->get_mesh().active_local_elements_end() );
 
   VectorSetAction<Number> setter(new_vector);
 
   const unsigned int n_variables = this->n_vars();
 
   std::vector<unsigned int> vars(n_variables);
   std::iota(vars.begin(), vars.end(), 0);
 
   // Use a typedef to make the calling sequence for parallel_for() a bit more readable
   typedef
     GenericProjector<FEMFunctionWrapper<Number>, FEMFunctionWrapper<Gradient>,
                      Number, VectorSetAction<Number>> FEMProjector;
 
   FEMFunctionWrapper<Number> fw(*f);
 
   if (g)
     {
       FEMFunctionWrapper<Gradient> gw(*g);
 
       Threads::parallel_for
         (active_local_range,
          FEMProjector(*this, fw, &gw, setter, vars));
     }
   else
     Threads::parallel_for
       (active_local_range,
        FEMProjector(*this, fw, nullptr, setter, vars));
 
   // Also, load values into the SCALAR dofs
   // Note: We assume that all SCALAR dofs are on the
   // processor with highest ID
   if (this->processor_id() == (this->n_processors()-1))
     {
       // FIXME: Do we want to first check for SCALAR vars before building this? [PB]
       FEMContext context( *this );
 
       const DofMap & dof_map = this->get_dof_map();
       for (unsigned int var=0; var<this->n_vars(); var++)
         if (this->variable(var).type().family == SCALAR)
           {
             // FIXME: We reinit with an arbitrary element in case the user
             //        doesn't override FEMFunctionBase::component. Is there
             //        any use case we're missing? [PB]
             Elem * el = const_cast<Elem *>(*(this->get_mesh().active_local_elements_begin()));
             context.pre_fe_reinit(*this, el);
 
             std::vector<dof_id_type> SCALAR_indices;
             dof_map.SCALAR_dof_indices (SCALAR_indices, var);
             const unsigned int n_SCALAR_dofs =
               cast_int<unsigned int>(SCALAR_indices.size());
 
             for (unsigned int i=0; i<n_SCALAR_dofs; i++)
               {
                 const dof_id_type global_index = SCALAR_indices[i];
                 const unsigned int component_index =
                   this->variable_scalar_number(var,i);
 
                 new_vector.set(global_index, f->component(context, component_index, Point(), this->time));
               }
           }
     }
 
   new_vector.close();
 
 #ifdef LIBMESH_ENABLE_CONSTRAINTS
   if (is_adjoint == -1)
     this->get_dof_map().enforce_constraints_exactly(*this, &new_vector);
   else if (is_adjoint >= 0)
     this->get_dof_map().enforce_adjoint_constraints_exactly(new_vector,
                                                             is_adjoint);
 #endif
 }

◆ 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.

 {
   WrappedFunction<Number> f(*this, fptr, &parameters);
   WrappedFunction<Gradient> g(*this, gptr, &parameters);
   this->project_vector(new_vector, &f, &g, is_adjoint);
 }

◆ 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().

 {
   // Create a copy of the vector, which currently
   // contains the old data.
   std::unique_ptr<NumericVector<Number>>
     old_vector (vector.clone());
 
   // Project the old vector to the new vector
   this->project_vector (*old_vector, vector, is_adjoint);
 }

◆ 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().

 {
   LOG_SCOPE ("projection_matrix()", "System");
 
   const unsigned int n_variables = this->n_vars();
 
   if (n_variables)
     {
       ConstElemRange active_local_elem_range
         (this->get_mesh().active_local_elements_begin(),
          this->get_mesh().active_local_elements_end());
 
       std::vector<unsigned int> vars(n_variables);
       std::iota(vars.begin(), vars.end(), 0);
 
       // Use a typedef to make the calling sequence for parallel_for() a bit more readable
       typedef OldSolutionCoefs<Real, &FEMContext::point_value> OldSolutionValueCoefs;
       typedef OldSolutionCoefs<RealGradient, &FEMContext::point_gradient> OldSolutionGradientCoefs;
 
       typedef
         GenericProjector<OldSolutionValueCoefs,
                          OldSolutionGradientCoefs,
                          DynamicSparseNumberArray<Real,dof_id_type>,
                          MatrixFillAction<Real, Number> > ProjMatFiller;
 
       OldSolutionValueCoefs    f(*this);
       OldSolutionGradientCoefs g(*this);
       MatrixFillAction<Real, Number> setter(proj_mat);
 
       Threads::parallel_for (active_local_elem_range,
                              ProjMatFiller(*this, f, &g, setter, vars));
 
       // Set the SCALAR dof transfer entries too.
       // Note: We assume that all SCALAR dofs are on the
       // processor with highest ID
       if (this->processor_id() == (this->n_processors()-1))
         {
           const DofMap & dof_map = this->get_dof_map();
           for (unsigned int var=0; var<this->n_vars(); var++)
             if (this->variable(var).type().family == SCALAR)
               {
                 // We can just map SCALAR dofs directly across
                 std::vector<dof_id_type> new_SCALAR_indices, old_SCALAR_indices;
                 dof_map.SCALAR_dof_indices (new_SCALAR_indices, var, false);
                 dof_map.SCALAR_dof_indices (old_SCALAR_indices, var, true);
                 const unsigned int new_n_dofs =
                   cast_int<unsigned int>(new_SCALAR_indices.size());
 
                 for (unsigned int i=0; i<new_n_dofs; i++)
                   {
                     proj_mat.set( new_SCALAR_indices[i],
                                   old_SCALAR_indices[i], 1);
                   }
               }
         }
     }
 }

◆ 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().

 {
 #ifdef LIBMESH_ENABLE_AMR
   // Currently project_vector handles both restriction and prolongation
   this->restrict_vectors();
 #endif
 }

◆ 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().

 {
   // We currently get partial derivatives via finite differencing
   const Real delta_p = TOLERANCE;
 
   ParameterVector & parameters =
     const_cast<ParameterVector &>(parameters_in);
 
   // We'll use one temporary vector for matrix-vector-vector products
   std::unique_ptr<NumericVector<Number>> tempvec = this->solution->zero_clone();
 
   // And another temporary vector to hold a copy of the true solution
   // so we can safely perturb this->solution.
   std::unique_ptr<NumericVector<Number>> oldsolution = this->solution->clone();
 
   const unsigned int Np = cast_int<unsigned int>
     (parameters.size());
   const unsigned int Nq = this->n_qois();
 
   // For each quantity of interest q, the parameter sensitivity
   // Hessian is defined as q''_{kl} = {d^2 q}/{d p_k d p_l}.
   //
   // We calculate it from values and partial derivatives of the
   // quantity of interest function Q, solution u, adjoint solution z,
   // and residual R, as:
   //
   // q''_{kl} =
   // Q''_{kl} + Q''_{uk}(u)*u'_l + Q''_{ul}(u) * u'_k +
   // Q''_{uu}(u)*u'_k*u'_l -
   // R''_{kl}(u,z) -
   // R''_{uk}(u,z)*u'_l - R''_{ul}(u,z)*u'_k -
   // R''_{uu}(u,z)*u'_k*u'_l
   //
   // See the adjoints model document for more details.
 
   // We first do an adjoint solve to get z for each quantity of
   // interest
   // if we havent already or dont have an initial condition for the adjoint
   if (!this->is_adjoint_already_solved())
     {
       this->adjoint_solve(qoi_indices);
     }
 
   // And a sensitivity solve to get u_k for each parameter
   this->sensitivity_solve(parameters);
 
   // Get ready to fill in second derivatives:
   sensitivities.allocate_hessian_data(qoi_indices, *this, parameters);
 
   for (unsigned int k=0; k != Np; ++k)
     {
       Number old_parameterk = *parameters[k];
 
       // The Hessian is symmetric, so we just calculate the lower
       // triangle and the diagonal, and we get the upper triangle from
       // the transpose of the lower
 
       for (unsigned int l=0; l != k+1; ++l)
         {
           // The second partial derivatives with respect to parameters
           // are all calculated via a central finite difference
           // stencil:
           // F''_{kl} ~= (F(p+dp*e_k+dp*e_l) - F(p+dp*e_k-dp*e_l) -
           //              F(p-dp*e_k+dp*e_l) + F(p-dp*e_k-dp*e_l))/(4*dp^2)
           // We will add Q''_{kl}(u) and subtract R''_{kl}(u,z) at the
           // same time.
           //
           // We have to be careful with the perturbations to handle
           // the k=l case
 
           Number old_parameterl = *parameters[l];
 
           *parameters[k] += delta_p;
           *parameters[l] += delta_p;
           this->assemble_qoi(qoi_indices);
           this->assembly(true, false, true);
           this->rhs->close();
           std::vector<Number> partial2q_term = this->qoi;
           std::vector<Number> partial2R_term(this->n_qois());
           for (unsigned int i=0; i != Nq; ++i)
             if (qoi_indices.has_index(i))
               partial2R_term[i] = this->rhs->dot(this->get_adjoint_solution(i));
 
           *parameters[l] -= 2.*delta_p;
           this->assemble_qoi(qoi_indices);
           this->assembly(true, false, true);
           this->rhs->close();
           for (unsigned int i=0; i != Nq; ++i)
             if (qoi_indices.has_index(i))
               {
                 partial2q_term[i] -= this->qoi[i];
                 partial2R_term[i] -= this->rhs->dot(this->get_adjoint_solution(i));
               }
 
           *parameters[k] -= 2.*delta_p;
           this->assemble_qoi(qoi_indices);
           this->assembly(true, false, true);
           this->rhs->close();
           for (unsigned int i=0; i != Nq; ++i)
             if (qoi_indices.has_index(i))
               {
                 partial2q_term[i] += this->qoi[i];
                 partial2R_term[i] += this->rhs->dot(this->get_adjoint_solution(i));
               }
 
           *parameters[l] += 2.*delta_p;
           this->assemble_qoi(qoi_indices);
           this->assembly(true, false, true);
           this->rhs->close();
           for (unsigned int i=0; i != Nq; ++i)
             if (qoi_indices.has_index(i))
               {
                 partial2q_term[i] -= this->qoi[i];
                 partial2R_term[i] -= this->rhs->dot(this->get_adjoint_solution(i));
                 partial2q_term[i] /= (4. * delta_p * delta_p);
                 partial2R_term[i] /= (4. * delta_p * delta_p);
               }
 
           for (unsigned int i=0; i != Nq; ++i)
             if (qoi_indices.has_index(i))
               {
                 Number current_terms = partial2q_term[i] - partial2R_term[i];
                 sensitivities.second_derivative(i,k,l) += current_terms;
                 if (k != l)
                   sensitivities.second_derivative(i,l,k) += current_terms;
               }
 
           // Don't leave the parameters perturbed
           *parameters[l] = old_parameterl;
           *parameters[k] = old_parameterk;
         }
 
       // We get (partial q / partial u) and
       // (partial R / partial u) from the user, but centrally
       // difference to get q_uk and R_uk terms:
       // (partial^2 q / partial u partial k)
       // q_uk*u'_l = (q_u(p+dp*e_k)*u'_l - q_u(p-dp*e_k)*u'_l)/(2*dp)
       // 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)
       //
       // To avoid creating Nq temporary vectors, we add these
       // subterms to the sensitivities output one by one.
       //
       // FIXME: this is probably a bad order of operations for
       // controlling floating point error.
 
       *parameters[k] = old_parameterk + delta_p;
       this->assembly(false, true);
       this->matrix->close();
       this->assemble_qoi_derivative(qoi_indices,
                                     /* include_liftfunc = */ true,
                                     /* apply_constraints = */ false);
 
       for (unsigned int l=0; l != Np; ++l)
         {
           this->matrix->vector_mult(*tempvec, this->get_sensitivity_solution(l));
           for (unsigned int i=0; i != Nq; ++i)
             if (qoi_indices.has_index(i))
               {
                 this->get_adjoint_rhs(i).close();
                 Number current_terms =
                   (this->get_adjoint_rhs(i).dot(this->get_sensitivity_solution(l)) -
                    tempvec->dot(this->get_adjoint_solution(i))) / (2.*delta_p);
                 sensitivities.second_derivative(i,k,l) += current_terms;
 
                 // We use the _uk terms twice; symmetry lets us reuse
                 // these calculations for the _ul terms.
 
                 sensitivities.second_derivative(i,l,k) += current_terms;
               }
         }
 
       *parameters[k] = old_parameterk - delta_p;
       this->assembly(false, true);
       this->matrix->close();
       this->assemble_qoi_derivative(qoi_indices,
                                     /* include_liftfunc = */ true,
                                     /* apply_constraints = */ false);
 
       for (unsigned int l=0; l != Np; ++l)
         {
           this->matrix->vector_mult(*tempvec, this->get_sensitivity_solution(l));
           for (unsigned int i=0; i != Nq; ++i)
             if (qoi_indices.has_index(i))
               {
                 this->get_adjoint_rhs(i).close();
                 Number current_terms =
                   (-this->get_adjoint_rhs(i).dot(this->get_sensitivity_solution(l)) +
                    tempvec->dot(this->get_adjoint_solution(i))) / (2.*delta_p);
                 sensitivities.second_derivative(i,k,l) += current_terms;
 
                 // We use the _uk terms twice; symmetry lets us reuse
                 // these calculations for the _ul terms.
 
                 sensitivities.second_derivative(i,l,k) += current_terms;
               }
         }
 
       // Don't leave the parameter perturbed
       *parameters[k] = old_parameterk;
 
       // Our last remaining terms are -R_uu(u,z)*u_k*u_l and
       // Q_uu(u)*u_k*u_l
       //
       // We take directional central finite differences of R_u and Q_u
       // to approximate these terms, e.g.:
       //
       // Q_uu(u)*u_k ~= (Q_u(u+dp*u_k) - Q_u(u-dp*u_k))/(2*dp)
 
       *this->solution = this->get_sensitivity_solution(k);
       *this->solution *= delta_p;
       *this->solution += *oldsolution;
 
       // We've modified solution, so we need to update before calling
       // assembly since assembly may only use current_local_solution
       this->update();
       this->assembly(false, true);
       this->matrix->close();
       this->assemble_qoi_derivative(qoi_indices,
                                     /* include_liftfunc = */ true,
                                     /* apply_constraints = */ false);
 
       // The Hessian is symmetric, so we just calculate the lower
       // triangle and the diagonal, and we get the upper triangle from
       // the transpose of the lower
       //
       // Note that, because we took the directional finite difference
       // with respect to k and not l, we've added an O(delta_p^2)
       // error to any permutational symmetry in the Hessian...
       for (unsigned int l=0; l != k+1; ++l)
         {
           this->matrix->vector_mult(*tempvec, this->get_sensitivity_solution(l));
           for (unsigned int i=0; i != Nq; ++i)
             if (qoi_indices.has_index(i))
               {
                 this->get_adjoint_rhs(i).close();
                 Number current_terms =
                   (this->get_adjoint_rhs(i).dot(this->get_sensitivity_solution(l)) -
                    tempvec->dot(this->get_adjoint_solution(i))) / (2.*delta_p);
                 sensitivities.second_derivative(i,k,l) += current_terms;
                 if (k != l)
                   sensitivities.second_derivative(i,l,k) += current_terms;
               }
         }
 
       *this->solution = this->get_sensitivity_solution(k);
       *this->solution *= -delta_p;
       *this->solution += *oldsolution;
 
       // We've modified solution, so we need to update before calling
       // assembly since assembly may only use current_local_solution
       this->update();
       this->assembly(false, true);
       this->matrix->close();
       this->assemble_qoi_derivative(qoi_indices,
                                     /* include_liftfunc = */ true,
                                     /* apply_constraints = */ false);
 
       for (unsigned int l=0; l != k+1; ++l)
         {
           this->matrix->vector_mult(*tempvec, this->get_sensitivity_solution(l));
           for (unsigned int i=0; i != Nq; ++i)
             if (qoi_indices.has_index(i))
               {
                 this->get_adjoint_rhs(i).close();
                 Number current_terms =
                   (-this->get_adjoint_rhs(i).dot(this->get_sensitivity_solution(l)) +
                    tempvec->dot(this->get_adjoint_solution(i))) / (2.*delta_p);
                 sensitivities.second_derivative(i,k,l) += current_terms;
                 if (k != l)
                   sensitivities.second_derivative(i,l,k) += current_terms;
               }
         }
 
       // Don't leave the solution perturbed
       *this->solution = *oldsolution;
     }
 
   // All parameters have been reset.
   // Don't leave the qoi or system changed - principle of least
   // surprise.
   // We've modified solution, so we need to update before calling
   // assembly since assembly may only use current_local_solution
   this->update();
   this->assembly(true, true);
   this->rhs->close();
   this->matrix->close();
   this->assemble_qoi(qoi_indices);
 }

◆ 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().

 {
   // We currently get partial derivatives via finite differencing
   const Real delta_p = TOLERANCE;
 
   ParameterVector & parameters =
     const_cast<ParameterVector &>(parameters_in);
 
   // We'll use a single temporary vector for matrix-vector-vector products
   std::unique_ptr<NumericVector<Number>> tempvec = this->solution->zero_clone();
 
   const unsigned int Np = cast_int<unsigned int>
     (parameters.size());
   const unsigned int Nq = this->n_qois();
 
   // For each quantity of interest q, the parameter sensitivity
   // Hessian is defined as q''_{kl} = {d^2 q}/{d p_k d p_l}.
   // Given a vector of parameter perturbation weights w_l, this
   // function evaluates the hessian-vector product sum_l(q''_{kl}*w_l)
   //
   // We calculate it from values and partial derivatives of the
   // quantity of interest function Q, solution u, adjoint solution z,
   // parameter sensitivity adjoint solutions z^l, and residual R, as:
   //
   // sum_l(q''_{kl}*w_l) =
   // sum_l(w_l * Q''_{kl}) + Q''_{uk}(u)*(sum_l(w_l u'_l)) -
   // R'_k(u, sum_l(w_l*z^l)) - R'_{uk}(u,z)*(sum_l(w_l u'_l) -
   // sum_l(w_l*R''_{kl}(u,z))
   //
   // See the adjoints model document for more details.
 
   // We first do an adjoint solve to get z for each quantity of
   // interest
   // if we havent already or dont have an initial condition for the adjoint
   if (!this->is_adjoint_already_solved())
     {
       this->adjoint_solve(qoi_indices);
     }
 
   // Get ready to fill in sensitivities:
   sensitivities.allocate_data(qoi_indices, *this, parameters);
 
   // We can't solve for all the solution sensitivities u'_l or for all
   // of the parameter sensitivity adjoint solutions z^l without
   // requiring O(Nq*Np) linear solves.  So we'll solve directly for their
   // weighted sum - this is just O(Nq) solves.
 
   // First solve for sum_l(w_l u'_l).
   this->weighted_sensitivity_solve(parameters, vector);
 
   // Then solve for sum_l(w_l z^l).
   this->weighted_sensitivity_adjoint_solve(parameters, vector, qoi_indices);
 
   for (unsigned int k=0; k != Np; ++k)
     {
       // We approximate sum_l(w_l * Q''_{kl}) with a central
       // differencing perturbation:
       // sum_l(w_l * Q''_{kl}) ~=
       // (Q(p + dp*w_l*e_l + dp*e_k) - Q(p - dp*w_l*e_l + dp*e_k) -
       // Q(p + dp*w_l*e_l - dp*e_k) + Q(p - dp*w_l*e_l - dp*e_k))/(4*dp^2)
 
       // The sum(w_l*R''_kl) term requires the same sort of perturbation,
       // and so we subtract it in at the same time:
       // sum_l(w_l * R''_{kl}) ~=
       // (R(p + dp*w_l*e_l + dp*e_k) - R(p - dp*w_l*e_l + dp*e_k) -
       // R(p + dp*w_l*e_l - dp*e_k) + R(p - dp*w_l*e_l - dp*e_k))/(4*dp^2)
 
       ParameterVector oldparameters, parameterperturbation;
       parameters.deep_copy(oldparameters);
       vector.deep_copy(parameterperturbation);
       parameterperturbation *= delta_p;
       parameters += parameterperturbation;
 
       Number old_parameter = *parameters[k];
 
       *parameters[k] = old_parameter + delta_p;
       this->assemble_qoi(qoi_indices);
       this->assembly(true, false, true);
       this->rhs->close();
       std::vector<Number> partial2q_term = this->qoi;
       std::vector<Number> partial2R_term(this->n_qois());
       for (unsigned int i=0; i != Nq; ++i)
         if (qoi_indices.has_index(i))
           partial2R_term[i] = this->rhs->dot(this->get_adjoint_solution(i));
 
       *parameters[k] = old_parameter - delta_p;
       this->assemble_qoi(qoi_indices);
       this->assembly(true, false, true);
       this->rhs->close();
       for (unsigned int i=0; i != Nq; ++i)
         if (qoi_indices.has_index(i))
           {
             partial2q_term[i] -= this->qoi[i];
             partial2R_term[i] -= this->rhs->dot(this->get_adjoint_solution(i));
           }
 
       oldparameters.value_copy(parameters);
       parameterperturbation *= -1.0;
       parameters += parameterperturbation;
 
       // Re-center old_parameter, which may be affected by vector
       old_parameter = *parameters[k];
 
       *parameters[k] = old_parameter + delta_p;
       this->assemble_qoi(qoi_indices);
       this->assembly(true, false, true);
       this->rhs->close();
       for (unsigned int i=0; i != Nq; ++i)
         if (qoi_indices.has_index(i))
           {
             partial2q_term[i] -= this->qoi[i];
             partial2R_term[i] -= this->rhs->dot(this->get_adjoint_solution(i));
           }
 
       *parameters[k] = old_parameter - delta_p;
       this->assemble_qoi(qoi_indices);
       this->assembly(true, false, true);
       this->rhs->close();
       for (unsigned int i=0; i != Nq; ++i)
         if (qoi_indices.has_index(i))
           {
             partial2q_term[i] += this->qoi[i];
             partial2R_term[i] += this->rhs->dot(this->get_adjoint_solution(i));
           }
 
       for (unsigned int i=0; i != Nq; ++i)
         if (qoi_indices.has_index(i))
           {
             partial2q_term[i] /= (4. * delta_p * delta_p);
             partial2R_term[i] /= (4. * delta_p * delta_p);
           }
 
       for (unsigned int i=0; i != Nq; ++i)
         if (qoi_indices.has_index(i))
           sensitivities[i][k] = partial2q_term[i] - partial2R_term[i];
 
       // We get (partial q / partial u), R, and
       // (partial R / partial u) from the user, but centrally
       // difference to get q_uk, R_k, and R_uk terms:
       // (partial R / partial k)
       // 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)
       // (partial^2 q / partial u partial k)
       // q_uk = (q_u(p+dp*e_k) - q_u(p-dp*e_k))/(2*dp)
       // (partial^2 R / partial u partial k)
       // 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)
 
       // To avoid creating Nq temporary vectors for q_uk or R_uk, we add
       // subterms to the sensitivities output one by one.
       //
       // FIXME: this is probably a bad order of operations for
       // controlling floating point error.
 
       *parameters[k] = old_parameter + delta_p;
       this->assembly(true, true);
       this->rhs->close();
       this->matrix->close();
       this->assemble_qoi_derivative(qoi_indices,
                                     /* include_liftfunc = */ true,
                                     /* apply_constraints = */ false);
 
       this->matrix->vector_mult(*tempvec, this->get_weighted_sensitivity_solution());
 
       for (unsigned int i=0; i != Nq; ++i)
         if (qoi_indices.has_index(i))
           {
             this->get_adjoint_rhs(i).close();
             sensitivities[i][k] += (this->get_adjoint_rhs(i).dot(this->get_weighted_sensitivity_solution()) -
                                     this->rhs->dot(this->get_weighted_sensitivity_adjoint_solution(i)) -
                                     this->get_adjoint_solution(i).dot(*tempvec)) / (2.*delta_p);
           }
 
       *parameters[k] = old_parameter - delta_p;
       this->assembly(true, true);
       this->rhs->close();
       this->matrix->close();
       this->assemble_qoi_derivative(qoi_indices,
                                     /* include_liftfunc = */ true,
                                     /* apply_constraints = */ false);
 
       this->matrix->vector_mult(*tempvec, this->get_weighted_sensitivity_solution());
 
       for (unsigned int i=0; i != Nq; ++i)
         if (qoi_indices.has_index(i))
           {
             this->get_adjoint_rhs(i).close();
             sensitivities[i][k] += (-this->get_adjoint_rhs(i).dot(this->get_weighted_sensitivity_solution()) +
                                     this->rhs->dot(this->get_weighted_sensitivity_adjoint_solution(i)) +
                                     this->get_adjoint_solution(i).dot(*tempvec)) / (2.*delta_p);
           }
     }
 
   // All parameters have been reset.
   // Don't leave the qoi or system changed - principle of least
   // surprise.
   this->assembly(true, true);
   this->rhs->close();
   this->matrix->close();
   this->assemble_qoi(qoi_indices);
 }

◆ 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().

 {
   // Forward sensitivities are more efficient for Nq > Np
   if (qoi_indices.size(*this) > parameters.size())
     forward_qoi_parameter_sensitivity(qoi_indices, parameters, sensitivities);
   // Adjoint sensitivities are more efficient for Np > Nq,
   // and an adjoint may be more reusable than a forward
   // solution sensitivity in the Np == Nq case.
   else
     adjoint_qoi_parameter_sensitivity(qoi_indices, parameters, sensitivities);
 }

◆ 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.

 {
   parallel_object_only();
 
   // If this system is empty... don't do anything!
   if (!this->n_vars())
     return;
 
   const std::vector<dof_id_type> & send_list = this->get_dof_map().get_send_list ();
 
   // Check sizes
   libmesh_assert_equal_to (current_local_solution->size(), solution->size());
   // Not true with ghosted vectors
   // libmesh_assert_equal_to (current_local_solution->local_size(), solution->size());
   // libmesh_assert (!send_list.empty());
   libmesh_assert_less_equal (send_list.size(), solution->size());
 
   // Create current_local_solution from solution.  This will
   // put a local copy of solution into current_local_solution.
   solution->localize (*current_local_solution, send_list);
 }

◆ 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().

 {
   // This method implements the input of a
   // System object, embedded in the output of
   // an EquationSystems<T_sys>.  This warrants some
   // documentation.  The output file essentially
   // 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.) Variable subdomains
   //
   //     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
   libmesh_assert (io.reading());
 
   // Possibly clear data structures and start from scratch.
   if (read_header_in)
     this->clear ();
 
   // Figure out if we need to read infinite element information.
   // This will be true if the version string contains " with infinite elements"
   const bool read_ifem_info =
     (version.rfind(" with infinite elements") < version.size()) ||
     libMesh::on_command_line ("--read-ifem-systems");
 
 
   {
     // 5.)
     // Read the number of variables in the system
     unsigned int nv=0;
     if (this->processor_id() == 0)
       io.data (nv);
     this->comm().broadcast(nv);
 
     _written_var_indices.clear();
     _written_var_indices.resize(nv, 0);
 
     for (unsigned int var=0; var<nv; var++)
       {
         // 6.)
         // Read the name of the var-th variable
         std::string var_name;
         if (this->processor_id() == 0)
           io.data (var_name);
         this->comm().broadcast(var_name);
 
         // 6.1.)
         std::set<subdomain_id_type> domains;
         if (io.version() >= LIBMESH_VERSION_ID(0,7,2))
           {
             std::vector<subdomain_id_type> domain_array;
             if (this->processor_id() == 0)
               io.data (domain_array);
             for (const auto & id : domain_array)
               domains.insert(id);
           }
         this->comm().broadcast(domains);
 
         // 7.)
         // Read the approximation order(s) of the var-th variable
         int order=0;
         if (this->processor_id() == 0)
           io.data (order);
         this->comm().broadcast(order);
 
 
         // do the same for infinite element radial_order
         int rad_order=0;
         if (read_ifem_info)
           {
             if (this->processor_id() == 0)
               io.data(rad_order);
             this->comm().broadcast(rad_order);
           }
 
         // Read the finite element type of the var-th variable
         int fam=0;
         if (this->processor_id() == 0)
           io.data (fam);
         this->comm().broadcast(fam);
         FEType type;
         type.order  = static_cast<Order>(order);
         type.family = static_cast<FEFamily>(fam);
 
         // Check for incompatibilities.  The shape function indexing was
         // changed for the monomial and xyz finite element families to
         // simplify extension to arbitrary p.  The consequence is that
         // old restart files will not be read correctly.  This is expected
         // to be an unlikely occurence, but catch it anyway.
         if (read_legacy_format)
           if ((type.family == MONOMIAL || type.family == XYZ) &&
               ((type.order.get_order() > 2 && this->get_mesh().mesh_dimension() == 2) ||
                (type.order.get_order() > 1 && this->get_mesh().mesh_dimension() == 3)))
             {
               libmesh_here();
               libMesh::out << "*****************************************************************\n"
                            << "* WARNING: reading a potentially incompatible restart file!!!   *\n"
                            << "*  contact libmesh-users@lists.sourceforge.net for more details *\n"
                            << "*****************************************************************"
                            << std::endl;
             }
 
         // Read additional information for infinite elements
         int radial_fam=0;
         int i_map=0;
         if (read_ifem_info)
           {
             if (this->processor_id() == 0)
               io.data (radial_fam);
             this->comm().broadcast(radial_fam);
             if (this->processor_id() == 0)
               io.data (i_map);
             this->comm().broadcast(i_map);
           }
 
 #ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
 
         type.radial_order  = static_cast<Order>(rad_order);
         type.radial_family = static_cast<FEFamily>(radial_fam);
         type.inf_map       = static_cast<InfMapType>(i_map);
 
 #endif
 
         if (read_header_in)
           {
             if (domains.empty())
               _written_var_indices[var] = this->add_variable (var_name, type);
             else
               _written_var_indices[var] = this->add_variable (var_name, type, &domains);
           }
         else
           _written_var_indices[var] = this->variable_number(var_name);
       }
   }
 
   // 8.)
   // Read the number of additional vectors.
   unsigned int nvecs=0;
   if (this->processor_id() == 0)
     io.data (nvecs);
   this->comm().broadcast(nvecs);
 
   // If nvecs > 0, this means that write_additional_data
   // was true when this file was written.  We will need to
   // make use of this fact later.
   this->_additional_data_written = nvecs;
 
   for (unsigned int vec=0; vec<nvecs; vec++)
     {
       // 9.)
       // Read the name of the vec-th additional vector
       std::string vec_name;
       if (this->processor_id() == 0)
         io.data (vec_name);
       this->comm().broadcast(vec_name);
 
       if (read_additional_data)
         {
           // Systems now can handle adding post-initialization vectors
           //  libmesh_assert(this->_can_add_vectors);
           // Some systems may have added their own vectors already
           //  libmesh_assert_equal_to (this->_vectors.count(vec_name), 0);
 
           this->add_vector(vec_name);
         }
     }
 }

◆ 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.

 {
   libmesh_deprecated();
 
   // This method implements the output of the vectors
   // contained in this System object, embedded in the
   // output of an EquationSystems<T_sys>.
   //
   //   10.) The global solution vector, re-ordered to be node-major
   //       (More on this later.)
   //
   //      for each additional vector in the object
   //
   //      11.) The global additional vector, re-ordered to be
   //           node-major (More on this later.)
   libmesh_assert (io.reading());
 
   // read and reordering buffers
   std::vector<Number> global_vector;
   std::vector<Number> reordered_vector;
 
   // 10.)
   // Read and set the solution vector
   {
     if (this->processor_id() == 0)
       io.data (global_vector);
     this->comm().broadcast(global_vector);
 
     // Remember that the stored vector is node-major.
     // We need to put it into whatever application-specific
     // ordering we may have using the dof_map.
     reordered_vector.resize(global_vector.size());
 
     //libMesh::out << "global_vector.size()=" << global_vector.size() << std::endl;
     //libMesh::out << "this->n_dofs()=" << this->n_dofs() << std::endl;
 
     libmesh_assert_equal_to (global_vector.size(), this->n_dofs());
 
     dof_id_type cnt=0;
 
     const unsigned int sys = this->number();
     const unsigned int nv  = cast_int<unsigned int>
       (this->_written_var_indices.size());
     libmesh_assert_less_equal (nv, this->n_vars());
 
     for (unsigned int data_var=0; data_var<nv; data_var++)
       {
         const unsigned int var = _written_var_indices[data_var];
 
         // First reorder the nodal DOF values
         for (auto & node : this->get_mesh().node_ptr_range())
           for (unsigned int index=0; index<node->n_comp(sys,var); index++)
             {
               libmesh_assert_not_equal_to (node->dof_number(sys, var, index),
                                            DofObject::invalid_id);
 
               libmesh_assert_less (cnt, global_vector.size());
 
               reordered_vector[node->dof_number(sys, var, index)] =
                 global_vector[cnt++];
             }
 
         // Then reorder the element DOF values
         for (auto & elem : this->get_mesh().active_element_ptr_range())
           for (unsigned int index=0; index<elem->n_comp(sys,var); index++)
             {
               libmesh_assert_not_equal_to (elem->dof_number(sys, var, index),
                                            DofObject::invalid_id);
 
               libmesh_assert_less (cnt, global_vector.size());
 
               reordered_vector[elem->dof_number(sys, var, index)] =
                 global_vector[cnt++];
             }
       }
 
     *(this->solution) = reordered_vector;
   }
 
   // For each additional vector, simply go through the list.
   // ONLY attempt to do this IF additional data was actually
   // written to the file for this system (controlled by the
   // _additional_data_written flag).
   if (this->_additional_data_written)
     {
       const std::size_t nvecs = this->_vectors.size();
 
       // If the number of additional vectors written is non-zero, and
       // the number of additional vectors we have is non-zero, and
       // they don't match, then something is wrong and we can't be
       // sure we're reading data into the correct places.
       if (read_additional_data && nvecs &&
           nvecs != this->_additional_data_written)
         libmesh_error_msg
           ("Additional vectors in file do not match system");
 
       std::map<std::string, NumericVector<Number> *>::iterator
         pos = this->_vectors.begin();
 
       for (std::size_t i = 0; i != this->_additional_data_written; ++i)
         {
           // 11.)
           // Read the values of the vec-th additional vector.
           // Prior do _not_ clear, but fill with zero, since the
           // additional vectors _have_ to have the same size
           // as the solution vector
           std::fill (global_vector.begin(), global_vector.end(), libMesh::zero);
 
           if (this->processor_id() == 0)
             io.data (global_vector);
 
           // If read_additional_data==true and we have additional vectors,
           // then we will keep this vector data; otherwise we are going to
           // throw it away.
           if (read_additional_data && nvecs)
             {
               this->comm().broadcast(global_vector);
 
               // Remember that the stored vector is node-major.
               // We need to put it into whatever application-specific
               // ordering we may have using the dof_map.
               std::fill (reordered_vector.begin(),
                          reordered_vector.end(),
                          libMesh::zero);
 
               reordered_vector.resize(global_vector.size());
 
               libmesh_assert_equal_to (global_vector.size(), this->n_dofs());
 
               dof_id_type cnt=0;
 
               const unsigned int sys = this->number();
               const unsigned int nv  = cast_int<unsigned int>
                 (this->_written_var_indices.size());
               libmesh_assert_less_equal (nv, this->n_vars());
 
               for (unsigned int data_var=0; data_var<nv; data_var++)
                 {
                   const unsigned int var = _written_var_indices[data_var];
                   // First reorder the nodal DOF values
                   for (auto & node : this->get_mesh().node_ptr_range())
                     for (unsigned int index=0; index<node->n_comp(sys,var); index++)
                       {
                         libmesh_assert_not_equal_to (node->dof_number(sys, var, index),
                                                      DofObject::invalid_id);
 
                         libmesh_assert_less (cnt, global_vector.size());
 
                         reordered_vector[node->dof_number(sys, var, index)] =
                           global_vector[cnt++];
                       }
 
                   // Then reorder the element DOF values
                   for (auto & elem : this->get_mesh().active_element_ptr_range())
                     for (unsigned int index=0; index<elem->n_comp(sys,var); index++)
                       {
                         libmesh_assert_not_equal_to (elem->dof_number(sys, var, index),
                                                      DofObject::invalid_id);
 
                         libmesh_assert_less (cnt, global_vector.size());
 
                         reordered_vector[elem->dof_number(sys, var, index)] =
                           global_vector[cnt++];
                       }
                 }
 
               // use the overloaded operator=(std::vector) to assign the values
               *(pos->second) = reordered_vector;
             }
 
           // If we've got vectors then we need to be iterating through
           // those too
           if (pos != this->_vectors.end())
             ++pos;
         }
     } // end if (_additional_data_written)
 }

◆ 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().

 {
   // PerfLog pl("IO Performance",false);
   // pl.push("read_parallel_data");
   dof_id_type total_read_size = 0;
 
   libmesh_assert (io.reading());
   libmesh_assert (io.is_open());
 
   // build the ordered nodes and element maps.
   // when writing/reading parallel files we need to iterate
   // over our nodes/elements in order of increasing global id().
   // however, this is not guaranteed to be ordering we obtain
   // by using the node_iterators/element_iterators directly.
   // so build a set, sorted by id(), that provides the ordering.
   // further, for memory economy build the set but then transfer
   // its contents to vectors, which will be sorted.
   std::vector<const DofObject *> ordered_nodes, ordered_elements;
   {
     std::set<const DofObject *, CompareDofObjectsByID>
       ordered_nodes_set (this->get_mesh().local_nodes_begin(),
                          this->get_mesh().local_nodes_end());
 
     ordered_nodes.insert(ordered_nodes.end(),
                          ordered_nodes_set.begin(),
                          ordered_nodes_set.end());
   }
   {
     std::set<const DofObject *, CompareDofObjectsByID>
       ordered_elements_set (this->get_mesh().local_elements_begin(),
                             this->get_mesh().local_elements_end());
 
     ordered_elements.insert(ordered_elements.end(),
                             ordered_elements_set.begin(),
                             ordered_elements_set.end());
   }
 
   //  std::vector<Number> io_buffer;
   std::vector<InValType> io_buffer;
 
   // 9.)
   //
   // Actually read the solution components
   // for the ith system to disk
   io.data(io_buffer);
 
   total_read_size += cast_int<dof_id_type>(io_buffer.size());
 
   const unsigned int sys_num = this->number();
   const unsigned int nv      = cast_int<unsigned int>
     (this->_written_var_indices.size());
   libmesh_assert_less_equal (nv, this->n_vars());
 
   dof_id_type cnt=0;
 
   // Loop over each non-SCALAR variable and each node, and read out the value.
   for (unsigned int data_var=0; data_var<nv; data_var++)
     {
       const unsigned int var = _written_var_indices[data_var];
       if (this->variable(var).type().family != SCALAR)
         {
           // First read the node DOF values
           for (const auto & node : ordered_nodes)
             for (unsigned int comp=0; comp<node->n_comp(sys_num, var); comp++)
               {
                 libmesh_assert_not_equal_to (node->dof_number(sys_num, var, comp),
                                              DofObject::invalid_id);
                 libmesh_assert_less (cnt, io_buffer.size());
                 this->solution->set(node->dof_number(sys_num, var, comp), io_buffer[cnt++]);
               }
 
           // Then read the element DOF values
           for (const auto & elem : ordered_elements)
             for (unsigned int comp=0; comp<elem->n_comp(sys_num, var); comp++)
               {
                 libmesh_assert_not_equal_to (elem->dof_number(sys_num, var, comp),
                                              DofObject::invalid_id);
                 libmesh_assert_less (cnt, io_buffer.size());
                 this->solution->set(elem->dof_number(sys_num, var, comp), io_buffer[cnt++]);
               }
         }
     }
 
   // Finally, read the SCALAR variables on the last processor
   for (unsigned int data_var=0; data_var<nv; data_var++)
     {
       const unsigned int var = _written_var_indices[data_var];
       if (this->variable(var).type().family == SCALAR)
         {
           if (this->processor_id() == (this->n_processors()-1))
             {
               const DofMap & dof_map = this->get_dof_map();
               std::vector<dof_id_type> SCALAR_dofs;
               dof_map.SCALAR_dof_indices(SCALAR_dofs, var);
 
               for (std::size_t i=0; i<SCALAR_dofs.size(); i++)
                 this->solution->set(SCALAR_dofs[i], io_buffer[cnt++]);
             }
         }
     }
 
   // And we're done setting solution entries
   this->solution->close();
 
   // For each additional vector, simply go through the list.
   // ONLY attempt to do this IF additional data was actually
   // written to the file for this system (controlled by the
   // _additional_data_written flag).
   if (this->_additional_data_written)
     {
       const std::size_t nvecs = this->_vectors.size();
 
       // If the number of additional vectors written is non-zero, and
       // the number of additional vectors we have is non-zero, and
       // they don't match, then something is wrong and we can't be
       // sure we're reading data into the correct places.
       if (read_additional_data && nvecs &&
           nvecs != this->_additional_data_written)
         libmesh_error_msg
           ("Additional vectors in file do not match system");
 
       std::map<std::string, NumericVector<Number> *>::const_iterator
         pos = _vectors.begin();
 
       for (std::size_t i = 0; i != this->_additional_data_written; ++i)
         {
           cnt=0;
           io_buffer.clear();
 
           // 10.)
           //
           // Actually read the additional vector components
           // for the ith system from disk
           io.data(io_buffer);
 
           total_read_size += cast_int<dof_id_type>(io_buffer.size());
 
           // If read_additional_data==true and we have additional vectors,
           // then we will keep this vector data; otherwise we are going to
           // throw it away.
           if (read_additional_data && nvecs)
             {
               // Loop over each non-SCALAR variable and each node, and read out the value.
               for (unsigned int data_var=0; data_var<nv; data_var++)
                 {
                   const unsigned int var = _written_var_indices[data_var];
                   if (this->variable(var).type().family != SCALAR)
                     {
                       // First read the node DOF values
                       for (const auto & node : ordered_nodes)
                         for (unsigned int comp=0; comp<node->n_comp(sys_num, var); comp++)
                           {
                             libmesh_assert_not_equal_to (node->dof_number(sys_num, var, comp),
                                                          DofObject::invalid_id);
                             libmesh_assert_less (cnt, io_buffer.size());
                             pos->second->set(node->dof_number(sys_num, var, comp), io_buffer[cnt++]);
                           }
 
                       // Then read the element DOF values
                       for (const auto & elem : ordered_elements)
                         for (unsigned int comp=0; comp<elem->n_comp(sys_num, var); comp++)
                           {
                             libmesh_assert_not_equal_to (elem->dof_number(sys_num, var, comp),
                                                          DofObject::invalid_id);
                             libmesh_assert_less (cnt, io_buffer.size());
                             pos->second->set(elem->dof_number(sys_num, var, comp), io_buffer[cnt++]);
                           }
                     }
                 }
 
               // Finally, read the SCALAR variables on the last processor
               for (unsigned int data_var=0; data_var<nv; data_var++)
                 {
                   const unsigned int var = _written_var_indices[data_var];
                   if (this->variable(var).type().family == SCALAR)
                     {
                       if (this->processor_id() == (this->n_processors()-1))
                         {
                           const DofMap & dof_map = this->get_dof_map();
                           std::vector<dof_id_type> SCALAR_dofs;
                           dof_map.SCALAR_dof_indices(SCALAR_dofs, var);
 
                           for (std::size_t sd=0; sd<SCALAR_dofs.size(); sd++)
                             pos->second->set(SCALAR_dofs[sd], io_buffer[cnt++]);
                         }
                     }
                 }
 
               // And we're done setting entries for this variable
               pos->second->close();
             }
 
           // If we've got vectors then we need to be iterating through
           // those too
           if (pos != this->_vectors.end())
             ++pos;
         }
     }
 
   // const Real
   //   dt   = pl.get_elapsed_time(),
   //   rate = total_read_size*sizeof(Number)/dt;
 
   // libMesh::err << "Read " << total_read_size << " \"Number\" values\n"
   //     << " Elapsed time = " << dt << '\n'
   //     << " Rate = " << rate/1.e6 << "(MB/sec)\n\n";
 
   // pl.pop("read_parallel_data");
 }

◆ 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.

 {
   // This method implements the input of the vectors
   // contained in this System object, embedded in the
   // output of an EquationSystems<T_sys>.
   //
   //   10.) The global solution vector, re-ordered to be node-major
   //       (More on this later.)
   //
   //      for each additional vector in the object
   //
   //      11.) The global additional vector, re-ordered to be
   //          node-major (More on this later.)
   parallel_object_only();
   std::string comment;
 
   // PerfLog pl("IO Performance",false);
   // pl.push("read_serialized_data");
   // std::size_t total_read_size = 0;
 
   // 10.)
   // Read the global solution vector
   {
     // total_read_size +=
     this->read_serialized_vector<InValType>(io, this->solution.get());
 
     // get the comment
     if (this->processor_id() == 0)
       io.comment (comment);
   }
 
   // 11.)
   // Only read additional vectors if data is available, and only use
   // that data to fill our vectors if the user requested it.
   if (this->_additional_data_written)
     {
       const std::size_t nvecs = this->_vectors.size();
 
       // If the number of additional vectors written is non-zero, and
       // the number of additional vectors we have is non-zero, and
       // they don't match, then we can't read additional vectors
       // and be sure we're reading data into the correct places.
       if (read_additional_data && nvecs &&
           nvecs != this->_additional_data_written)
         libmesh_error_msg
           ("Additional vectors in file do not match system");
 
       std::map<std::string, NumericVector<Number> *>::const_iterator
         pos = _vectors.begin();
 
       for (std::size_t i = 0; i != this->_additional_data_written; ++i)
         {
           // Read data, but only put it into a vector if we've been
           // asked to and if we have a corresponding vector to read.
 
           // total_read_size +=
           this->read_serialized_vector<InValType>
             (io, (read_additional_data && nvecs) ? pos->second : nullptr);
 
           // get the comment
           if (this->processor_id() == 0)
             io.comment (comment);
 
 
           // If we've got vectors then we need to be iterating through
           // those too
           if (pos != this->_vectors.end())
             ++pos;
         }
     }
 
   // const Real
   //   dt   = pl.get_elapsed_time(),
   //   rate = total_read_size*sizeof(Number)/dt;
 
   // libMesh::out << "Read " << total_read_size << " \"Number\" values\n"
   //     << " Elapsed time = " << dt << '\n'
   //     << " Rate = " << rate/1.e6 << "(MB/sec)\n\n";
 
   // pl.pop("read_serialized_data");
 }

◆ 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().

 {
   parallel_object_only();
 
   // Error checking
   // #ifndef NDEBUG
   //   // In parallel we better be reading a parallel vector -- if not
   //   // we will not set all of its components below!!
   //   if (this->n_processors() > 1)
   //     {
   //       libmesh_assert (vec.type() == PARALLEL ||
   //       vec.type() == GHOSTED);
   //     }
   // #endif
 
   libmesh_assert (io.reading());
 
   if (this->processor_id() == 0)
     {
       // sizes
       unsigned int num_vecs=0;
       dof_id_type vector_length=0;
 
       // Get the number of vectors
       io.data(num_vecs);
       // Get the buffer size
       io.data(vector_length);
 
       libmesh_assert_equal_to (num_vecs, vectors.size());
 
       if (num_vecs != 0)
         {
           libmesh_assert_not_equal_to (vectors[0], 0);
           libmesh_assert_equal_to     (vectors[0]->size(), vector_length);
         }
     }
 
   // no need to actually communicate these.
   // this->comm().broadcast(num_vecs);
   // this->comm().broadcast(vector_length);
 
   // Cache these - they are not free!
   const dof_id_type
     n_nodes = this->get_mesh().n_nodes(),
     n_elem  = this->get_mesh().n_elem();
 
   std::size_t read_length = 0;
 
   //---------------------------------
   // Collect the values for all nodes
   read_length +=
     this->read_serialized_blocked_dof_objects (n_nodes,
                                                this->get_mesh().local_nodes_begin(),
                                                this->get_mesh().local_nodes_end(),
                                                InValType(),
                                                io,
                                                vectors);
 
   //------------------------------------
   // Collect the values for all elements
   read_length +=
     this->read_serialized_blocked_dof_objects (n_elem,
                                                this->get_mesh().local_elements_begin(),
                                                this->get_mesh().local_elements_end(),
                                                InValType(),
                                                io,
                                                vectors);
 
   //-------------------------------------------
   // Finally loop over all the SCALAR variables
   for (std::size_t vec=0; vec<vectors.size(); vec++)
     for (unsigned int var=0; var<this->n_vars(); var++)
       if (this->variable(var).type().family == SCALAR)
         {
           libmesh_assert_not_equal_to (vectors[vec], 0);
 
           read_length +=
             this->read_SCALAR_dofs (var, io, vectors[vec]);
         }
 
   //---------------------------------------
   // last step - must close all the vectors
   for (std::size_t vec=0; vec<vectors.size(); vec++)
     {
       libmesh_assert_not_equal_to (vectors[vec], 0);
       vectors[vec]->close();
     }
 
   return read_length;
 }

◆ 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.

 {
   Parent::reinit();
 
   libmesh_assert(time_solver.get());
   libmesh_assert_equal_to (&(time_solver->system()), this);
 
   time_solver->reinit();
 }

◆ 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().

 {
 #ifdef LIBMESH_ENABLE_CONSTRAINTS
   get_dof_map().create_dof_constraints(_mesh, this->time);
   user_constrain();
   get_dof_map().process_constraints(_mesh);
 #endif
   get_dof_map().prepare_send_list();
 }

◆ 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().

 {
   matrices_iterator pos = _matrices.find (mat_name);
 
   //Return if the matrix does not exist
   if (pos == _matrices.end())
     return;
 
   delete pos->second;
 
   _matrices.erase(pos);
 }

◆ 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.

 {
   vectors_iterator pos = _vectors.find(vec_name);
 
   //Return if the vector does not exist
   if (pos == _vectors.end())
     return;
 
   delete pos->second;
 
   _vectors.erase(pos);
 
   _vector_projections.erase(vec_name);
   _vector_is_adjoint.erase(vec_name);
   _vector_types.erase(vec_name);
 }

◆ 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().

 {
   // Make sure the matrix exists
   const_matrices_iterator pos = _matrices.find (mat_name);
 
   if (pos == _matrices.end())
     return nullptr;
 
   return pos->second;
 }

◆ 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.

 {
   // Make sure the matrix exists
   matrices_iterator pos = _matrices.find (mat_name);
 
   if (pos == _matrices.end())
     return nullptr;
 
   return pos->second;
 }

◆ 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().

 {
   const_vectors_iterator pos = _vectors.find(vec_name);
 
   if (pos == _vectors.end())
     return nullptr;
 
   return pos->second;
 }

◆ 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.

 {
   vectors_iterator pos = _vectors.find(vec_name);
 
   if (pos == _vectors.end())
     return nullptr;
 
   return pos->second;
 }

◆ 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().

 {
   const_vectors_iterator v = vectors_begin();
   const_vectors_iterator v_end = vectors_end();
   unsigned int num = 0;
   while ((num<vec_num) && (v!=v_end))
     {
       num++;
       ++v;
     }
   if (v==v_end)
     return nullptr;
   return v->second;
 }

◆ 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().

 {
   vectors_iterator v = vectors_begin();
   vectors_iterator v_end = vectors_end();
   unsigned int num = 0;
   while ((num<vec_num) && (v!=v_end))
     {
       num++;
       ++v;
     }
   if (v==v_end)
     return nullptr;
   return v->second;
 }

◆ 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.

 {
   if (subset != nullptr)
     libmesh_not_implemented();
 }

◆ 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().

 {
 #ifdef LIBMESH_ENABLE_AMR
   // Restrict the _vectors on the coarsened cells
   for (auto & pr : _vectors)
     {
       NumericVector<Number> * v = pr.second;
 
       if (_vector_projections[pr.first])
         {
           this->project_vector (*v, this->vector_is_adjoint(pr.first));
         }
       else
         {
           ParallelType type = _vector_types[pr.first];
 
           if (type == GHOSTED)
             {
 #ifdef LIBMESH_ENABLE_GHOSTED
               pr.second->init (this->n_dofs(), this->n_local_dofs(),
                                _dof_map->get_send_list(), false,
                                GHOSTED);
 #else
               libmesh_error_msg("Cannot initialize ghosted vectors when they are not enabled.");
 #endif
             }
           else
             pr.second->init (this->n_dofs(), this->n_local_dofs(), false, type);
         }
     }
 
   const std::vector<dof_id_type> & send_list = _dof_map->get_send_list ();
 
   // Restrict the solution on the coarsened cells
   if (_solution_projection)
     this->project_vector (*solution);
   // Or at least make sure the solution vector is the correct size
   else
     solution->init (this->n_dofs(), this->n_local_dofs(), true, PARALLEL);
 
 #ifdef LIBMESH_ENABLE_GHOSTED
   current_local_solution->init(this->n_dofs(),
                                this->n_local_dofs(), send_list,
                                false, GHOSTED);
 #else
   current_local_solution->init(this->n_dofs());
 #endif
 
   if (_solution_projection)
     solution->localize (*current_local_solution, send_list);
 
 #endif // LIBMESH_ENABLE_AMR
 }

◆ save_current_solution()

void libMesh::ContinuationSystem::save_current_solution ( )

Stores the current solution and continuation parameter (as "previous_u" and "old_continuation_parameter") for later referral. You may need to call this e.g. after the first regular solve, in order to store the first solution, before computing a second solution and beginning arclength continuation.

Definition at line 1364 of file continuation_system.C.

References continuation_parameter, old_continuation_parameter, previous_u, and libMesh::System::solution.

Referenced by update_solution().

 {
   // Save the old solution vector
   *previous_u = *solution;
 
   // Save the old value of lambda
   old_continuation_parameter = *continuation_parameter;
 }

◆ 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().

 {
   // Log how long the linear solve takes.
   LOG_SCOPE("sensitivity_solve()", "ImplicitSystem");
 
   // The forward system should now already be solved.
   // Now assemble the corresponding sensitivity system.
 
   if (this->assemble_before_solve)
     {
       // Build the Jacobian
       this->assembly(false, true);
       this->matrix->close();
 
       // Reset and build the RHS from the residual derivatives
       this->assemble_residual_derivatives(parameters);
     }
 
   // The sensitivity problem is linear
   LinearSolver<Number> * linear_solver = this->get_linear_solver();
 
   // Our iteration counts and residuals will be sums of the individual
   // results
   std::pair<unsigned int, Real> solver_params =
     this->get_linear_solve_parameters();
   std::pair<unsigned int, Real> totalrval = std::make_pair(0,0.0);
 
   // Solve the linear system.
   SparseMatrix<Number> * pc = this->request_matrix("Preconditioner");
   for (auto p : IntRange<unsigned int>(0, parameters.size()))
     {
       std::pair<unsigned int, Real> rval =
         linear_solver->solve (*matrix, pc,
                               this->add_sensitivity_solution(p),
                               this->get_sensitivity_rhs(p),
                               solver_params.second,
                               solver_params.first);
 
       totalrval.first  += rval.first;
       totalrval.second += rval.second;
     }
 
   // The linear solver may not have fit our constraints exactly
 #ifdef LIBMESH_ENABLE_CONSTRAINTS
   for (auto p : IntRange<unsigned int>(0, parameters.size()))
     this->get_dof_map().enforce_constraints_exactly
       (*this, &this->get_sensitivity_solution(p),
        /* homogeneous = */ true);
 #endif
 
   this->release_linear_solver(linear_solver);
 
   return totalrval;
 }

◆ 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;}

libMesh::System::adjoint_already_solved

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().

 {
   _basic_system_only = true;
 }

◆ set_max_arclength_stepsize()

void libMesh::ContinuationSystem::set_max_arclength_stepsize ( Real maxds )

inline

Sets (initializes) the max-allowable ds value and the current ds value. Call this before beginning arclength continuation. The default max stepsize is 0.1

Definition at line 128 of file continuation_system.h.

References ds, and ds_current.

128 { ds=maxds; ds_current=maxds; }

libMesh::ContinuationSystem::ds

Real ds

Definition: continuation_system.h:403

libMesh::ContinuationSystem::ds_current

Real ds_current

Definition: continuation_system.h:409

◆ 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.

 {
   // For now we assume that we're doing fully coupled mesh motion
   //  if (sys && sys != this)
   //    libmesh_not_implemented();
 
   // For the foreseeable future we'll assume that we keep these
   // Systems in the same EquationSystems
   // libmesh_assert_equal_to (&this->get_equation_systems(),
   //                          &sys->get_equation_systems());
 
   // And for the immediate future this code may not even work
   libmesh_experimental();
 
   _mesh_sys = sys;
 }

◆ 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.

 {
   _mesh_x_var = var;
 }

◆ 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.

 {
   _mesh_y_var = var;
 }

◆ 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.

 {
   _mesh_z_var = var;
 }

◆ set_numerical_jacobian_h_for_var()

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

inlineinherited

Definition at line 269 of file fem_system.h.

References libMesh::FEMSystem::_numerical_jacobian_h_for_var, and libMesh::Real.

 {
   if (_numerical_jacobian_h_for_var.size() <= var_num)
     _numerical_jacobian_h_for_var.resize(var_num+1,Real(0));
 
   libmesh_assert_greater(new_h, 0);
 
   _numerical_jacobian_h_for_var[var_num] = new_h;
 }

◆ set_Theta()

void libMesh::ContinuationSystem::set_Theta ( )

private

A centralized function for setting the normalization parameter theta

Definition at line 1065 of file continuation_system.C.

References libMesh::out, quiet, and Theta.

Referenced by initialize_tangent(), and update_solution().

 {
   // // Use the norm of the latest solution, squared.
   //const Real normu = solution->l2_norm();
   //libmesh_assert_not_equal_to (normu, 0.0);
   //Theta = 1./normu/normu;
 
   // // 1.) Use the norm of du, squared
   //   *delta_u = *solution;
   //   delta_u->add(-1, *previous_u);
   //   delta_u->close();
   //   const Real normdu = delta_u->l2_norm();
 
   //   if (normdu < 1.) // don't divide by zero or make a huge scaling parameter.
   //     Theta = 1.;
   //   else
   //     Theta = 1./normdu/normdu;
 
   // 2.) Use 1.0, i.e. don't scale
   Theta=1.;
 
   // 3.) Use a formula which attempts to make the "solution triangle" isosceles.
   //   libmesh_assert_less (std::abs(dlambda_ds), 1.);
 
   //   *delta_u = *solution;
   //   delta_u->add(-1, *previous_u);
   //   delta_u->close();
   //   const Real normdu = delta_u->l2_norm();
 
   //   Theta = std::sqrt(1. - dlambda_ds*dlambda_ds) / normdu * tau * ds;
 
 
   //   // 4.) Use the norm of du and the norm of du/ds
   //   *delta_u = *solution;
   //   delta_u->add(-1, *previous_u);
   //   delta_u->close();
   //   const Real normdu   = delta_u->l2_norm();
   //   du_ds->close();
   //   const Real normduds = du_ds->l2_norm();
 
   //   if (normduds < 1.e-12)
   //     {
   //       libMesh::out << "Setting initial Theta= 1./normdu/normdu" << std::endl;
   //       libMesh::out << "normdu=" << normdu << std::endl;
 
   //       // Don't use this scaling if the solution delta is already O(1)
   //       if (normdu > 1.)
   // Theta = 1./normdu/normdu;
   //       else
   // Theta = 1.;
   //     }
   //   else
   //     {
   //       libMesh::out << "Setting Theta= 1./normdu/normduds" << std::endl;
   //       libMesh::out << "normdu=" << normdu << std::endl;
   //       libMesh::out << "normduds=" << normduds << std::endl;
 
   //       // Don't use this scaling if the solution delta is already O(1)
   //       if ((normdu>1.) || (normduds>1.))
   // Theta = 1./normdu/normduds;
   //       else
   // Theta = 1.;
   //     }
 
   if (!quiet)
     libMesh::out << "Setting Normalization Parameter Theta=" << Theta << std::endl;
 }

◆ set_Theta_LOCA()

void libMesh::ContinuationSystem::set_Theta_LOCA ( )

private

A centralized function for setting the other normalization parameter, i.e. the one suggested by the LOCA developers.

Definition at line 1135 of file continuation_system.C.

References std::abs(), dlambda_ds, libMesh::out, quiet, and Theta_LOCA.

Referenced by update_solution().

 {
   // We also recompute the LOCA normalization parameter based on the
   // most recently computed value of dlambda_ds
   // if (!quiet)
   //   libMesh::out << "(Theta_LOCA) dlambda_ds=" << dlambda_ds << std::endl;
 
   // Formula makes no sense if |dlambda_ds| > 1
   libmesh_assert_less (std::abs(dlambda_ds), 1.);
 
   // 1.) Attempt to implement the method in LOCA paper
   //   const Real g = 1./std::sqrt(2.); // "desired" dlambda_ds
 
   //   // According to the LOCA people, we only renormalize for
   //   // when |dlambda_ds| exceeds some pre-selected maximum (which they take to be zero, btw).
   //   if (std::abs(dlambda_ds) > .9)
   //     {
   //       // Note the *= ... This is updating the previous value of Theta_LOCA
   //       // Note: The LOCA people actually use Theta_LOCA^2 to normalize their arclength constraint.
   //       Theta_LOCA *= std::abs( (dlambda_ds/g)*std::sqrt( (1.-g*g) / (1.-dlambda_ds*dlambda_ds) ) );
 
   //       // Suggested max-allowable value for Theta_LOCA
   //       if (Theta_LOCA > 1.e8)
   // {
   //   Theta_LOCA = 1.e8;
 
   //   if (!quiet)
   //     libMesh::out << "max Theta_LOCA=" << Theta_LOCA << " has been selected." << std::endl;
   // }
   //     }
   //   else
   //     Theta_LOCA=1.0;
 
   // 2.) FIXME: Should we do *= or just =?  This function is of dlambda_ds is
   //  < 1,  |dlambda_ds| < 1/sqrt(2) ~~ .7071
   //  > 1,  |dlambda_ds| > 1/sqrt(2) ~~ .7071
   Theta_LOCA *= std::abs( dlambda_ds / std::sqrt( (1.-dlambda_ds*dlambda_ds) ) );
 
   // Suggested max-allowable value for Theta_LOCA.  I've never come close
   // to this value in my code.
   if (Theta_LOCA > 1.e8)
     {
       Theta_LOCA = 1.e8;
 
       if (!quiet)
         libMesh::out << "max Theta_LOCA=" << Theta_LOCA << " has been selected." << std::endl;
     }
 
   // 3.) Use 1.0, i.e. don't scale
   //Theta_LOCA=1.0;
 
   if (!quiet)
     libMesh::out << "Setting Theta_LOCA=" << Theta_LOCA << std::endl;
 }

◆ 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.

   {
     time_solver.reset(_time_solver.release());
   }

◆ 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().

 {
   // We reserve -1 for vectors which get primal constraints, -2 for
   // vectors which get no constraints
   libmesh_assert_greater_equal(qoi_num, -2);
   _vector_is_adjoint[vec_name] = qoi_num;
 }

◆ 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.

 {
   _vector_projections[vec_name] = preserve;
 }

◆ 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().

                                                {
     return request_jacobian;
   }

◆ 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().

                                                      {
     return request_jacobian;
   }

◆ 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().

                                                   {
     return request_jacobian;
   }

◆ 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().

                                                     {
     return request_jacobian;
   }

◆ solve()

void libMesh::ContinuationSystem::solve ( )

overridevirtual

Perform a standard "solve" of the system, without doing continuation.

Reimplemented from libMesh::FEMSystem.

Definition at line 121 of file continuation_system.C.

References Residual, rhs_mode, and libMesh::DifferentiableSystem::solve().

 {
   // Set the Residual RHS mode, and call the normal solve routine.
   rhs_mode      = Residual;
   DifferentiableSystem::solve();
 }

◆ solve_tangent()

void libMesh::ContinuationSystem::solve_tangent ( )

private

Special solve algorithm for solving the tangent system.

Definition at line 956 of file continuation_system.C.

References libMesh::NumericVector< T >::add(), libMesh::FEMSystem::assembly(), libMesh::NumericVector< T >::close(), continuation_parameter, delta_u, dlambda_ds, libMesh::NumericVector< T >::dot(), du_ds, G_Lambda, libMesh::NumericVector< T >::l2_norm(), libMesh::libmesh_real(), linear_solver, libMesh::ImplicitSystem::matrix, libMesh::DiffSolver::max_linear_iterations, newton_solver, old_continuation_parameter, libMesh::out, previous_dlambda_ds, previous_du_ds, previous_u, quiet, libMesh::Real, libMesh::ExplicitSystem::rhs, rhs_mode, libMesh::NumericVector< T >::scale(), libMesh::System::solution, tangent_initialized, Theta, Theta_LOCA, libMesh::DifferentiableSystem::time_solver, y, and libMesh::NumericVector< T >::zero().

Referenced by advance_arcstep(), and initialize_tangent().

 {
   // We shouldn't call this unless the current tangent already makes sense.
   libmesh_assert (tangent_initialized);
 
   // Set pointer to underlying Newton solver
   if (!newton_solver)
     newton_solver =
       cast_ptr<NewtonSolver *> (this->time_solver->diff_solver().get());
 
   // Assemble the system matrix AND rhs, with rhs = G_{\lambda}
   this->rhs_mode = G_Lambda;
 
   // Assemble Residual and Jacobian
   this->assembly(true,   // Residual
                  true); // Jacobian
 
   // Not sure if this is really necessary
   rhs->close();
 
   // Solve G_u*y =  G_{\lambda}
   std::pair<unsigned int, Real> rval =
     linear_solver->solve(*matrix,
                          *y,
                          *rhs,
                          1.e-12, // relative linear tolerance
                          2*newton_solver->max_linear_iterations);   // max linear iterations
 
   // FIXME: If this doesn't converge at all, the new tangent vector is
   // going to be really bad...
 
   if (!quiet)
     libMesh::out << "G_u*y = G_{lambda} solver converged at step "
                  << rval.first
                  << " linear tolerance = "
                  << rval.second
                  << "."
                  << std::endl;
 
   // Save old solution and parameter tangents for possible use in higher-order
   // predictor schemes.
   previous_dlambda_ds = dlambda_ds;
   *previous_du_ds     = *du_ds;
 
 
   // 1.) Previous, probably wrong, technique!
   //   // Solve for the updated d(lambda)/ds
   //   // denom = N_{lambda}   - (du_ds)^t y
   //   //       = d(lambda)/ds - (du_ds)^t y
   //   Real denom = dlambda_ds - du_ds->dot(*y);
 
   //   //libMesh::out << "denom=" << denom << std::endl;
   //   libmesh_assert_not_equal_to (denom, 0.0);
 
   //   dlambda_ds = 1.0 / denom;
 
 
   //   if (!quiet)
   //     libMesh::out << "dlambda_ds=" << dlambda_ds << std::endl;
 
   //   // Compute the updated value of du/ds = -_dlambda_ds * y
   //   du_ds->zero();
   //   du_ds->add(-dlambda_ds, *y);
   //   du_ds->close();
 
 
   // 2.) From Brian Carnes' paper...
   // According to Carnes, y comes from solving G_u * y = -G_{\lambda}
   y->scale(-1.);
   const Real ynorm = y->l2_norm();
   dlambda_ds = 1. / std::sqrt(1. + Theta_LOCA*Theta_LOCA*Theta*ynorm*ynorm);
 
   // Determine the correct sign for dlambda_ds.
 
   // We will use delta_u to temporarily compute this sign.
   *delta_u = *solution;
   delta_u->add(-1., *previous_u);
   delta_u->close();
 
   const Real sgn_dlambda_ds =
     libmesh_real(Theta_LOCA*Theta_LOCA*Theta*y->dot(*delta_u) +
                  (*continuation_parameter-old_continuation_parameter));
 
   if (sgn_dlambda_ds < 0.)
     {
       if (!quiet)
         libMesh::out << "dlambda_ds is negative." << std::endl;
 
       dlambda_ds *= -1.;
     }
 
   // Finally, set the new tangent vector, du/ds = dlambda/ds * y.
   du_ds->zero();
   du_ds->add(dlambda_ds, *y);
   du_ds->close();
 
   if (!quiet)
     {
       libMesh::out << "d(lambda)/ds = " << dlambda_ds << std::endl;
       libMesh::out << "||du_ds||    = " << du_ds->l2_norm() << std::endl;
     }
 
   // Our next solve expects y ~ -du/dlambda, so scale it back by -1 again now.
   y->scale(-1.);
   y->close();
 }

◆ 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().

 {
   std::swap(this->_diff_physics, swap_physics);
 }

◆ 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().

   {
     libmesh_deprecated();
     this->time_evolving(var,1);
   }

◆ 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(), libMesh::FEMSystem::assemble_qoi(), libMesh::FEMSystem::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(), libMesh::FEMSystem::mesh_position_get(), libMesh::FEMSystem::postprocess(), libMesh::ImplicitSystem::qoi_parameter_hessian(), libMesh::NewtonSolver::solve(), libMesh::ExplicitSystem::solve(), libMesh::LinearImplicitSystem::solve(), libMesh::NonlinearImplicitSystem::solve(), and libMesh::OptimizationSystem::solve().

 {
   libmesh_assert(solution->closed());
 
   const std::vector<dof_id_type> & send_list = _dof_map->get_send_list ();
 
   // Check sizes
   libmesh_assert_equal_to (current_local_solution->size(), solution->size());
   // More processors than elements => empty send_list
   //  libmesh_assert (!send_list.empty());
   libmesh_assert_less_equal (send_list.size(), solution->size());
 
   // Create current_local_solution from solution.  This will
   // put a local copy of solution into current_local_solution.
   // Only the necessary values (specified by the send_list)
   // are copied to minimize communication
   solution->localize (*current_local_solution, send_list);
 }

◆ 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().

 {
   global_soln.resize (solution->size());
 
   solution->localize (global_soln);
 }

◆ 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.

 {
   global_soln.resize        (solution->size());
 
   solution->localize_to_one (global_soln, dest_proc);
 }

◆ update_solution()

void libMesh::ContinuationSystem::update_solution ( )

private

This function (which assumes the most recent tangent vector has been computed) updates the solution and the control parameter with the initial guess for the next point on the continuation path.

Definition at line 1192 of file continuation_system.C.

References std::abs(), libMesh::NumericVector< T >::add(), apply_predictor(), libMesh::NumericVector< T >::close(), continuation_parameter, delta_u, libMesh::NumericVector< T >::dot(), ds, ds_current, ds_min, libMesh::NumericVector< T >::l2_norm(), libMesh::DiffSolver::max_nonlinear_iterations, newton_solver, newton_step, newton_stepgrowth_aggressiveness, old_continuation_parameter, libMesh::out, libMesh::BasicOStreamProxy< charT, traits >::precision(), previous_ds, previous_u, quiet, libMesh::Real, save_current_solution(), set_Theta(), set_Theta_LOCA(), libMesh::BasicOStreamProxy< charT, traits >::setf(), libMesh::System::solution, tangent_initialized, Theta, Theta_LOCA, libMesh::BasicOStreamProxy< charT, traits >::unsetf(), y, and y_old.

Referenced by advance_arcstep(), and initialize_tangent().

 {
   // Set some stream formatting flags
   std::streamsize old_precision = libMesh::out.precision();
   libMesh::out.precision(16);
   libMesh::out.setf(std::ios_base::scientific);
 
   // We must have a tangent that makes sense before we can update the solution.
   libmesh_assert (tangent_initialized);
 
   // Compute tau, the stepsize scaling parameter which attempts to
   // reduce ds when the angle between the most recent two tangent
   // vectors becomes large.  tau is actually the (absolute value of
   // the) cosine of the angle between these two vectors... so if tau ~
   // 0 the angle is ~ 90 degrees, while if tau ~ 1 the angle is ~ 0
   // degrees.
   y_old->close();
   y->close();
   const Real yoldnorm = y_old->l2_norm();
   const Real ynorm = y->l2_norm();
   const Number yoldy = y_old->dot(*y);
   const Real yold_over_y = yoldnorm/ynorm;
 
   if (!quiet)
     {
       libMesh::out << "yoldnorm=" << yoldnorm << std::endl;
       libMesh::out << "ynorm="    << ynorm << std::endl;
       libMesh::out << "yoldy="    << yoldy << std::endl;
       libMesh::out << "yoldnorm/ynorm=" << yoldnorm/ynorm << std::endl;
     }
 
   // Save the current value of ds before updating it
   previous_ds = ds_current;
 
   // // 1.) Cosine method (for some reason this always predicts the angle is ~0)
   // // Don't try dividing by zero
   // if ((yoldnorm > 1.e-12) && (ynorm > 1.e-12))
   //   tau = std::abs(yoldy) / yoldnorm  / ynorm;
   // else
   //   tau = 1.;
 
   // // 2.) Relative size of old and new du/dlambda method with cutoff of 0.9
   // if ((yold_over_y < 0.9) && (yold_over_y > 1.e-6))
   //   tau = yold_over_y;
   // else
   //   tau = 1.;
 
   // 3.) Grow (or shrink) the arclength stepsize by the ratio of du/dlambda, but do not
   // exceed the user-specified value of ds.
   if (yold_over_y > 1.e-6)
     {
       // // 1.) Scale current ds by the ratio of successive tangents.
       //       ds_current *= yold_over_y;
       //       if (ds_current > ds)
       // ds_current = ds;
 
       // 2.) Technique 1 tends to shrink the step fairly well (and even if it doesn't
       // get very small, we still have step reduction) but it seems to grow the step
       // very slowly.  Another possible technique is step-doubling:
       //       if (yold_over_y > 1.)
       //       ds_current *= 2.;
       //       else
       // ds_current *= yold_over_y;
 
       // 3.) Technique 2 may over-zealous when we are also using the Newton stepgrowth
       // factor.  For technique 3 we multiply by yold_over_y unless yold_over_y > 2
       // in which case we use 2.
       //       if (yold_over_y > 2.)
       // ds_current *= 2.;
       //       else
       // ds_current *= yold_over_y;
 
       // 4.) Double-or-halve.  We double the arc-step if the ratio of successive tangents
       // is larger than 'double_threshold', halve it if it is less than 'halve_threshold'
       const Real double_threshold = 0.5;
       const Real halve_threshold  = 0.5;
       if (yold_over_y > double_threshold)
         ds_current *= 2.;
       else if (yold_over_y < halve_threshold)
         ds_current *= 0.5;
 
 
       // Also possibly use the number of Newton iterations required to compute the previous
       // step (relative to the maximum-allowed number of Newton iterations) to grow the step.
       if (newton_stepgrowth_aggressiveness > 0.)
         {
           libmesh_assert(newton_solver);
           const unsigned int Nmax = newton_solver->max_nonlinear_iterations;
 
           // // The LOCA Newton step growth technique (note: only grows step length)
           // const Real stepratio = static_cast<Real>(Nmax-(newton_step+1))/static_cast<Real>(Nmax-1.);
           // const Real newtonstep_growthfactor = 1. + newton_stepgrowth_aggressiveness*stepratio*stepratio;
 
           // The "Nopt/N" method, may grow or shrink the step.  Assume Nopt=Nmax/2.
           const Real newtonstep_growthfactor =
             newton_stepgrowth_aggressiveness * 0.5 *
             static_cast<Real>(Nmax) / static_cast<Real>(newton_step+1);
 
           if (!quiet)
             libMesh::out << "newtonstep_growthfactor=" << newtonstep_growthfactor << std::endl;
 
           ds_current *= newtonstep_growthfactor;
         }
     }
 
 
   // Don't let the stepsize get above the user's maximum-allowed stepsize.
   if (ds_current > ds)
     ds_current = ds;
 
   // Check also for a minimum allowed stepsize.
   if (ds_current < ds_min)
     {
       libMesh::out << "Enforcing minimum-allowed arclength stepsize of " << ds_min << std::endl;
       ds_current = ds_min;
     }
 
   if (!quiet)
     {
       libMesh::out << "Current step size: ds_current=" << ds_current << std::endl;
     }
 
   // Recompute scaling factor Theta for
   // the current solution before updating.
   set_Theta();
 
   // Also, recompute the LOCA scaling factor, which attempts to
   // maintain a reasonable value of dlambda/ds
   set_Theta_LOCA();
 
   libMesh::out << "Theta*Theta_LOCA^2=" << Theta*Theta_LOCA*Theta_LOCA << std::endl;
 
   // Based on the asymptotic singular behavior of du/dlambda near simple turning points,
   // we can compute a single parameter which may suggest that we are close to a singularity.
   *delta_u = *solution;
   delta_u->add(-1, *previous_u);
   delta_u->close();
   const Real normdu   = delta_u->l2_norm();
   const Real C = (std::log (Theta_LOCA*normdu) /
                   std::log (std::abs(*continuation_parameter-old_continuation_parameter))) - 1.0;
   if (!quiet)
     libMesh::out << "C=" << C << std::endl;
 
   // Save the current value of u and lambda before updating.
   save_current_solution();
 
   if (!quiet)
     {
       libMesh::out << "Updating the solution with the tangent guess." << std::endl;
       libMesh::out << "||u_old||=" << this->solution->l2_norm() << std::endl;
       libMesh::out << "lambda_old=" << *continuation_parameter << std::endl;
     }
 
   // Since we solved for the tangent vector, now we can compute an
   // initial guess for the new solution, and an initial guess for the
   // new value of lambda.
   apply_predictor();
 
   if (!quiet)
     {
       libMesh::out << "||u_new||=" << this->solution->l2_norm() << std::endl;
       libMesh::out << "lambda_new=" << *continuation_parameter << std::endl;
     }
 
   // Unset previous stream flags
   libMesh::out.precision(old_precision);
   libMesh::out.unsetf(std::ios_base::scientific);
 }

◆ 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().

 {
   // Call the user-provided assembly function,
   // if it was provided
   if (_assemble_system_function != nullptr)
     this->_assemble_system_function (_equation_systems, this->name());
 
   // ...or the user-provided assembly object.
   else if (_assemble_system_object != nullptr)
     this->_assemble_system_object->assemble();
 }

◆ 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().

 {
   // Call the user-provided constraint function,
   // if it was provided
   if (_constrain_system_function!= nullptr)
     this->_constrain_system_function(_equation_systems, this->name());
 
   // ...or the user-provided constraint object.
   else if (_constrain_system_object != nullptr)
     this->_constrain_system_object->constrain();
 }

◆ 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().

 {
   // Call the user-provided initialization function,
   // if it was provided
   if (_init_system_function != nullptr)
     this->_init_system_function (_equation_systems, this->name());
 
   // ...or the user-provided initialization object.
   else if (_init_system_object != nullptr)
     this->_init_system_object->initialize();
 }

◆ 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().

 {
   // Call the user-provided quantity of interest function,
   // if it was provided
   if (_qoi_evaluate_function != nullptr)
     this->_qoi_evaluate_function(_equation_systems, this->name(), qoi_indices);
 
   // ...or the user-provided QOI function object.
   else if (_qoi_evaluate_object != nullptr)
     this->_qoi_evaluate_object->qoi(qoi_indices);
 }

◆ 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().

 {
   // Call the user-provided quantity of interest derivative,
   // if it was provided
   if (_qoi_evaluate_derivative_function != nullptr)
     this->_qoi_evaluate_derivative_function
       (_equation_systems, this->name(), qoi_indices, include_liftfunc,
        apply_constraints);
 
   // ...or the user-provided QOI derivative function object.
   else if (_qoi_evaluate_derivative_object != nullptr)
     this->_qoi_evaluate_derivative_object->qoi_derivative
       (qoi_indices, include_liftfunc, apply_constraints);
 }

◆ variable()

const Variable & libMesh::System::variable ( unsigned int var ) const

inlineinherited

Return a constant reference to Variable var.

Definition at line 2133 of file system.h.

References libMesh::System::_variables.

Referenced by libMesh::ExactSolution::_compute_error(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::DifferentiableSystem::add_second_order_dot_vars(), libMesh::EquationSystems::build_discontinuous_solution_vector(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::FirstOrderUnsteadySolver::compute_second_order_eqns(), libMesh::DifferentiableSystem::have_first_order_scalar_vars(), libMesh::DifferentiableSystem::have_second_order_scalar_vars(), libMesh::System::read_parallel_data(), libMesh::System::read_SCALAR_dofs(), libMesh::System::read_serialized_vector(), libMesh::System::read_serialized_vectors(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::System::write_header(), libMesh::System::write_parallel_data(), libMesh::System::write_serialized_vector(), and libMesh::System::write_serialized_vectors().

 {
   libmesh_assert_less (i, _variables.size());
 
   return _variables[i];
 }

◆ 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 libMesh::FEMSystem::assembly(), and libMesh::System::get_info().

 {
   libmesh_assert_less (vg, _variable_groups.size());
 
   return _variable_groups[vg];
 }

◆ variable_name()

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

inlineinherited

Returns: The name of variable i.

Definition at line 2153 of file system.h.

References libMesh::System::_variables.

Referenced by libMesh::System::add_variable(), libMesh::System::add_variables(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::PetscDMWrapper::build_section(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::ExactSolution::ExactSolution(), libMesh::petsc_auto_fieldsplit(), and libMesh::System::write_header().

 {
   libmesh_assert_less (i, _variables.size());
 
   return _variables[i].name();
 }

◆ 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().

 {
   // Make sure the variable exists
   std::map<std::string, unsigned short int>::const_iterator
     pos = _variable_numbers.find(var);
 
   if (pos == _variable_numbers.end())
     libmesh_error_msg("ERROR: variable " << var << " does not exist in this system!");
 
   libmesh_assert_equal_to (_variables[pos->second].name(), var);
 
   return pos->second;
 }

◆ 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().

 {
   return variable_scalar_number(this->variable_number(var), component);
 }

◆ 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.

 {
   return _variables[var_num].first_scalar_number() + component;
 }

◆ variable_type() [1/2]

const FEType & libMesh::System::variable_type ( const unsigned int i ) const

inlineinherited

Returns: The finite element type variable number i.

Definition at line 2183 of file system.h.

References libMesh::System::_variables.

Referenced by 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::ExodusII_IO::copy_elemental_solution(), libMesh::GMVIO::copy_nodal_solution(), libMesh::DGFEMContext::DGFEMContext(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::FEMSystem::init_context(), libMesh::FEMContext::init_internal_data(), libMesh::System::write_header(), libMesh::EnsightIO::write_scalar_ascii(), and libMesh::EnsightIO::write_vector_ascii().

 {
   libmesh_assert_less (i, _variables.size());
 
   return _variables[i].type();
 }

◆ 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().

 {
   return _variables[this->variable_number(var)].type();
 }

◆ 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().

 {
   libmesh_assert(_vector_is_adjoint.find(vec_name) !=
                  _vector_is_adjoint.end());
 
   return _vector_is_adjoint.find(vec_name)->second;
 }

◆ 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().

 {
   const_vectors_iterator v = vectors_begin();
   const_vectors_iterator v_end = vectors_end();
   unsigned int num = 0;
   while ((num<vec_num) && (v!=v_end))
     {
       num++;
       ++v;
     }
   libmesh_assert (v != v_end);
   return v->first;
 }

◆ 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().

 {
   const_vectors_iterator v = vectors_begin();
   const_vectors_iterator v_end = vectors_end();
 
   for (; v != v_end; ++v)
     {
       // Check if the current vector is the one whose name we want
       if (&vec_reference == v->second)
         break; // exit loop if it is
     }
 
   // Before returning, make sure we didnt loop till the end and not find any match
   libmesh_assert (v != v_end);
 
   // Return the string associated with the current vector
   return v->first;
 }

◆ 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().

 {
   if (_vector_projections.find(vec_name) == _vector_projections.end())
     return false;
 
   return _vector_projections.find(vec_name)->second;
 }

◆ 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().

 {
   return _vectors.begin();
 }

◆ 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.

 {
   return _vectors.begin();
 }

◆ vectors_end() [1/2]

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

inlineinherited

End of vectors container

Definition at line 2257 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().

 {
   return _vectors.end();
 }

◆ 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.

 {
   return _vectors.end();
 }

◆ 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().

 {
   // Log how long the linear solve takes.
   LOG_SCOPE("weighted_sensitivity_adjoint_solve()", "ImplicitSystem");
 
   // We currently get partial derivatives via central differencing
   const Real delta_p = TOLERANCE;
 
   ParameterVector & parameters =
     const_cast<ParameterVector &>(parameters_in);
 
   // The forward system should now already be solved.
   // The adjoint system should now already be solved.
   // Now we're assembling a weighted sum of adjoint-adjoint systems:
   //
   // dR/du (u, sum_l(w_l*z^l)) = sum_l(w_l*(Q''_ul - R''_ul (u, z)))
 
   // FIXME: The derivation here does not yet take adjoint boundary
   // conditions into account.
   for (unsigned int i=0; i != this->n_qois(); ++i)
     if (qoi_indices.has_index(i))
       libmesh_assert(!this->get_dof_map().has_adjoint_dirichlet_boundaries(i));
 
   // We'll assemble the rhs first, because the R'' term will require
   // perturbing the jacobian
 
   // We'll use temporary rhs vectors, because we haven't (yet) found
   // any good reasons why users might want to save these:
 
   std::vector<std::unique_ptr<NumericVector<Number>>> temprhs(this->n_qois());
   for (unsigned int i=0; i != this->n_qois(); ++i)
     if (qoi_indices.has_index(i))
       temprhs[i] = this->rhs->zero_clone();
 
   // We approximate the _l partial derivatives via a central
   // differencing perturbation in the w_l direction:
   //
   // sum_l(w_l*v_l) ~= (v(p + dp*w_l*e_l) - v(p - dp*w_l*e_l))/(2*dp)
 
   // PETSc doesn't implement SGEMX, so neither does NumericVector,
   // so we want to avoid calculating f -= R'*z.  We'll thus evaluate
   // the above equation by first adding -v(p+dp...), then multiplying
   // the intermediate result vectors by -1, then adding -v(p-dp...),
   // then finally dividing by 2*dp.
 
   ParameterVector oldparameters, parameterperturbation;
   parameters.deep_copy(oldparameters);
   weights.deep_copy(parameterperturbation);
   parameterperturbation *= delta_p;
   parameters += parameterperturbation;
 
   this->assembly(false, true);
   this->matrix->close();
 
   // Take the discrete adjoint, so that we can calculate R_u(u,z) with
   // a matrix-vector product of R_u and z.
   matrix->get_transpose(*matrix);
 
   this->assemble_qoi_derivative(qoi_indices,
                                 /* include_liftfunc = */ false,
                                 /* apply_constraints = */ true);
   for (unsigned int i=0; i != this->n_qois(); ++i)
     if (qoi_indices.has_index(i))
       {
         this->get_adjoint_rhs(i).close();
         *(temprhs[i]) -= this->get_adjoint_rhs(i);
         this->matrix->vector_mult_add(*(temprhs[i]), this->get_adjoint_solution(i));
         *(temprhs[i]) *= -1.0;
       }
 
   oldparameters.value_copy(parameters);
   parameterperturbation *= -1.0;
   parameters += parameterperturbation;
 
   this->assembly(false, true);
   this->matrix->close();
   matrix->get_transpose(*matrix);
 
   this->assemble_qoi_derivative(qoi_indices,
                                 /* include_liftfunc = */ false,
                                 /* apply_constraints = */ true);
   for (unsigned int i=0; i != this->n_qois(); ++i)
     if (qoi_indices.has_index(i))
       {
         this->get_adjoint_rhs(i).close();
         *(temprhs[i]) -= this->get_adjoint_rhs(i);
         this->matrix->vector_mult_add(*(temprhs[i]), this->get_adjoint_solution(i));
         *(temprhs[i]) /= (2.0*delta_p);
       }
 
   // Finally, assemble the jacobian at the non-perturbed parameter
   // values.  Ignore assemble_before_solve; if we had a good
   // non-perturbed matrix before we've already overwritten it.
   oldparameters.value_copy(parameters);
 
   // if (this->assemble_before_solve)
   {
     // Build the Jacobian
     this->assembly(false, true);
     this->matrix->close();
 
     // Take the discrete adjoint
     matrix->get_transpose(*matrix);
   }
 
   // The weighted adjoint-adjoint problem is linear
   LinearSolver<Number> * linear_solver = this->get_linear_solver();
 
   // Our iteration counts and residuals will be sums of the individual
   // results
   std::pair<unsigned int, Real> solver_params =
     this->get_linear_solve_parameters();
   std::pair<unsigned int, Real> totalrval = std::make_pair(0,0.0);
 
   for (unsigned int i=0; i != this->n_qois(); ++i)
     if (qoi_indices.has_index(i))
       {
         const std::pair<unsigned int, Real> rval =
           linear_solver->solve (*matrix, this->add_weighted_sensitivity_adjoint_solution(i),
                                 *(temprhs[i]),
                                 solver_params.second,
                                 solver_params.first);
 
         totalrval.first  += rval.first;
         totalrval.second += rval.second;
       }
 
   this->release_linear_solver(linear_solver);
 
   // The linear solver may not have fit our constraints exactly
 #ifdef LIBMESH_ENABLE_CONSTRAINTS
   for (unsigned int i=0; i != this->n_qois(); ++i)
     if (qoi_indices.has_index(i))
       this->get_dof_map().enforce_constraints_exactly
         (*this, &this->get_weighted_sensitivity_adjoint_solution(i),
          /* homogeneous = */ true);
 #endif
 
   return totalrval;
 }

◆ 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().

 {
   // Log how long the linear solve takes.
   LOG_SCOPE("weighted_sensitivity_solve()", "ImplicitSystem");
 
   // We currently get partial derivatives via central differencing
   const Real delta_p = TOLERANCE;
 
   ParameterVector & parameters =
     const_cast<ParameterVector &>(parameters_in);
 
   // The forward system should now already be solved.
 
   // Now we're assembling a weighted sum of sensitivity systems:
   //
   // dR/du (u, v)(sum(w_l*u'_l)) = -sum_l(w_l*R'_l (u, v)) forall v
 
   // We'll assemble the rhs first, because the R' term will require
   // perturbing the system, and some applications may not be able to
   // assemble a perturbed residual without simultaneously constructing
   // a perturbed jacobian.
 
   // We approximate the _l partial derivatives via a central
   // differencing perturbation in the w_l direction:
   //
   // sum_l(w_l*v_l) ~= (v(p + dp*w_l*e_l) - v(p - dp*w_l*e_l))/(2*dp)
 
   ParameterVector oldparameters, parameterperturbation;
   parameters.deep_copy(oldparameters);
   weights.deep_copy(parameterperturbation);
   parameterperturbation *= delta_p;
   parameters += parameterperturbation;
 
   this->assembly(true, false, true);
   this->rhs->close();
 
   std::unique_ptr<NumericVector<Number>> temprhs = this->rhs->clone();
 
   oldparameters.value_copy(parameters);
   parameterperturbation *= -1.0;
   parameters += parameterperturbation;
 
   this->assembly(true, false, true);
   this->rhs->close();
 
   *temprhs -= *(this->rhs);
   *temprhs /= (2.0*delta_p);
 
   // Finally, assemble the jacobian at the non-perturbed parameter
   // values
   oldparameters.value_copy(parameters);
 
   // Build the Jacobian
   this->assembly(false, true);
   this->matrix->close();
 
   // The weighted sensitivity problem is linear
   LinearSolver<Number> * linear_solver = this->get_linear_solver();
 
   std::pair<unsigned int, Real> solver_params =
     this->get_linear_solve_parameters();
 
   const std::pair<unsigned int, Real> rval =
     linear_solver->solve (*matrix, this->add_weighted_sensitivity_solution(),
                           *temprhs,
                           solver_params.second,
                           solver_params.first);
 
   this->release_linear_solver(linear_solver);
 
   // The linear solver may not have fit our constraints exactly
 #ifdef LIBMESH_ENABLE_CONSTRAINTS
   this->get_dof_map().enforce_constraints_exactly
     (*this, &this->get_weighted_sensitivity_solution(),
      /* homogeneous = */ true);
 #endif
 
   return rval;
 }

◆ 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().

 {
   libmesh_assert (io.writing());
 
 
   // Only write the header information
   // if we are processor 0.
   if (this->get_mesh().processor_id() != 0)
     return;
 
   std::string comment;
   char buf[80];
 
   // 5.)
   // Write the number of variables in the system
 
   {
     // set up the comment
     comment = "# No. of Variables in System \"";
     comment += this->name();
     comment += "\"";
 
     unsigned int nv = this->n_vars();
     io.data (nv, comment.c_str());
   }
 
 
   for (unsigned int var=0; var<this->n_vars(); var++)
     {
       // 6.)
       // Write the name of the var-th variable
       {
         // set up the comment
         comment  = "#   Name, Variable No. ";
         std::sprintf(buf, "%u", var);
         comment += buf;
         comment += ", System \"";
         comment += this->name();
         comment += "\"";
 
         std::string var_name = this->variable_name(var);
         io.data (var_name, comment.c_str());
       }
 
       // 6.1.) Variable subdomains
       {
         // set up the comment
         comment  = "#     Subdomains, Variable \"";
         std::sprintf(buf, "%s", this->variable_name(var).c_str());
         comment += buf;
         comment += "\", System \"";
         comment += this->name();
         comment += "\"";
 
         const std::set<subdomain_id_type> & domains = this->variable(var).active_subdomains();
         std::vector<subdomain_id_type> domain_array;
         domain_array.assign(domains.begin(), domains.end());
         io.data (domain_array, comment.c_str());
       }
 
       // 7.)
       // Write the approximation order of the var-th variable
       // in this system
       {
         // set up the comment
         comment = "#     Approximation Order, Variable \"";
         std::sprintf(buf, "%s", this->variable_name(var).c_str());
         comment += buf;
         comment += "\", System \"";
         comment += this->name();
         comment += "\"";
 
         int order = static_cast<int>(this->variable_type(var).order);
         io.data (order, comment.c_str());
       }
 
 
 #ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
 
       // do the same for radial_order
       {
         comment = "#     Radial Approximation Order, Variable \"";
         std::sprintf(buf, "%s", this->variable_name(var).c_str());
         comment += buf;
         comment += "\", System \"";
         comment += this->name();
         comment += "\"";
 
         int rad_order = static_cast<int>(this->variable_type(var).radial_order);
         io.data (rad_order, comment.c_str());
       }
 
 #endif
 
       // Write the Finite Element type of the var-th variable
       // in this System
       {
         // set up the comment
         comment = "#     FE Family, Variable \"";
         std::sprintf(buf, "%s", this->variable_name(var).c_str());
         comment += buf;
         comment += "\", System \"";
         comment += this->name();
         comment += "\"";
 
         const FEType & type = this->variable_type(var);
         int fam = static_cast<int>(type.family);
         io.data (fam, comment.c_str());
 
 #ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
 
         comment = "#     Radial FE Family, Variable \"";
         std::sprintf(buf, "%s", this->variable_name(var).c_str());
         comment += buf;
         comment += "\", System \"";
         comment += this->name();
         comment += "\"";
 
         int radial_fam = static_cast<int>(type.radial_family);
         io.data (radial_fam, comment.c_str());
 
         comment = "#     Infinite Mapping Type, Variable \"";
         std::sprintf(buf, "%s", this->variable_name(var).c_str());
         comment += buf;
         comment += "\", System \"";
         comment += this->name();
         comment += "\"";
 
         int i_map = static_cast<int>(type.inf_map);
         io.data (i_map, comment.c_str());
 #endif
       }
     } // end of the variable loop
 
   // 8.)
   // Write the number of additional vectors in the System.
   // If write_additional_data==false, then write zero for
   // the number of additional vectors.
   {
     {
       // set up the comment
       comment = "# No. of Additional Vectors, System \"";
       comment += this->name();
       comment += "\"";
 
       unsigned int nvecs = write_additional_data ? this->n_vectors () : 0;
       io.data (nvecs, comment.c_str());
     }
 
     if (write_additional_data)
       {
         unsigned int cnt=0;
         for (const auto & pr : _vectors)
           {
             // 9.)
             // write the name of the cnt-th additional vector
             comment =  "# Name of ";
             std::sprintf(buf, "%d", cnt++);
             comment += buf;
             comment += "th vector";
             std::string vec_name = pr.first;
 
             io.data (vec_name, comment.c_str());
           }
       }
   }
 }

◆ 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().

 {
   // PerfLog pl("IO Performance",false);
   // pl.push("write_parallel_data");
   // std::size_t total_written_size = 0;
 
   std::string comment;
 
   libmesh_assert (io.writing());
 
   std::vector<Number> io_buffer; io_buffer.reserve(this->solution->local_size());
 
   // build the ordered nodes and element maps.
   // when writing/reading parallel files we need to iterate
   // over our nodes/elements in order of increasing global id().
   // however, this is not guaranteed to be ordering we obtain
   // by using the node_iterators/element_iterators directly.
   // so build a set, sorted by id(), that provides the ordering.
   // further, for memory economy build the set but then transfer
   // its contents to vectors, which will be sorted.
   std::vector<const DofObject *> ordered_nodes, ordered_elements;
   {
     std::set<const DofObject *, CompareDofObjectsByID>
       ordered_nodes_set (this->get_mesh().local_nodes_begin(),
                          this->get_mesh().local_nodes_end());
 
     ordered_nodes.insert(ordered_nodes.end(),
                          ordered_nodes_set.begin(),
                          ordered_nodes_set.end());
   }
   {
     std::set<const DofObject *, CompareDofObjectsByID>
       ordered_elements_set (this->get_mesh().local_elements_begin(),
                             this->get_mesh().local_elements_end());
 
     ordered_elements.insert(ordered_elements.end(),
                             ordered_elements_set.begin(),
                             ordered_elements_set.end());
   }
 
   const unsigned int sys_num = this->number();
   const unsigned int nv      = this->n_vars();
 
   // Loop over each non-SCALAR variable and each node, and write out the value.
   for (unsigned int var=0; var<nv; var++)
     if (this->variable(var).type().family != SCALAR)
       {
         // First write the node DOF values
         for (const auto & node : ordered_nodes)
           for (unsigned int comp=0; comp<node->n_comp(sys_num, var); comp++)
             {
               libmesh_assert_not_equal_to (node->dof_number(sys_num, var, comp),
                                            DofObject::invalid_id);
 
               io_buffer.push_back((*this->solution)(node->dof_number(sys_num, var, comp)));
             }
 
         // Then write the element DOF values
         for (const auto & elem : ordered_elements)
           for (unsigned int comp=0; comp<elem->n_comp(sys_num, var); comp++)
             {
               libmesh_assert_not_equal_to (elem->dof_number(sys_num, var, comp),
                                            DofObject::invalid_id);
 
               io_buffer.push_back((*this->solution)(elem->dof_number(sys_num, var, comp)));
             }
       }
 
   // Finally, write the SCALAR data on the last processor
   for (unsigned int var=0; var<this->n_vars(); var++)
     if (this->variable(var).type().family == SCALAR)
       {
         if (this->processor_id() == (this->n_processors()-1))
           {
             const DofMap & dof_map = this->get_dof_map();
             std::vector<dof_id_type> SCALAR_dofs;
             dof_map.SCALAR_dof_indices(SCALAR_dofs, var);
 
             for (std::size_t i=0; i<SCALAR_dofs.size(); i++)
               io_buffer.push_back((*this->solution)(SCALAR_dofs[i]));
           }
       }
 
   // 9.)
   //
   // Actually write the reordered solution vector
   // for the ith system to disk
 
   // set up the comment
   {
     comment = "# System \"";
     comment += this->name();
     comment += "\" Solution Vector";
   }
 
   io.data (io_buffer, comment.c_str());
 
   // total_written_size += io_buffer.size();
 
   // Only write additional vectors if wanted
   if (write_additional_data)
     {
       for (auto & pr : _vectors)
         {
           io_buffer.clear();
           io_buffer.reserve(pr.second->local_size());
 
           // Loop over each non-SCALAR variable and each node, and write out the value.
           for (unsigned int var=0; var<nv; var++)
             if (this->variable(var).type().family != SCALAR)
               {
                 // First write the node DOF values
                 for (const auto & node : ordered_nodes)
                   for (unsigned int comp=0; comp<node->n_comp(sys_num, var); comp++)
                     {
                       libmesh_assert_not_equal_to (node->dof_number(sys_num, var, comp),
                                                    DofObject::invalid_id);
 
                       io_buffer.push_back((*pr.second)(node->dof_number(sys_num, var, comp)));
                     }
 
                 // Then write the element DOF values
                 for (const auto & elem : ordered_elements)
                   for (unsigned int comp=0; comp<elem->n_comp(sys_num, var); comp++)
                     {
                       libmesh_assert_not_equal_to (elem->dof_number(sys_num, var, comp),
                                                    DofObject::invalid_id);
 
                       io_buffer.push_back((*pr.second)(elem->dof_number(sys_num, var, comp)));
                     }
               }
 
           // Finally, write the SCALAR data on the last processor
           for (unsigned int var=0; var<this->n_vars(); var++)
             if (this->variable(var).type().family == SCALAR)
               {
                 if (this->processor_id() == (this->n_processors()-1))
                   {
                     const DofMap & dof_map = this->get_dof_map();
                     std::vector<dof_id_type> SCALAR_dofs;
                     dof_map.SCALAR_dof_indices(SCALAR_dofs, var);
 
                     for (std::size_t i=0; i<SCALAR_dofs.size(); i++)
                       io_buffer.push_back((*pr.second)(SCALAR_dofs[i]));
                   }
               }
 
           // 10.)
           //
           // Actually write the reordered additional vector
           // for this system to disk
 
           // set up the comment
           {
             comment = "# System \"";
             comment += this->name();
             comment += "\" Additional Vector \"";
             comment += pr.first;
             comment += "\"";
           }
 
           io.data (io_buffer, comment.c_str());
 
           // total_written_size += io_buffer.size();
         }
     }
 
   // const Real
   //   dt   = pl.get_elapsed_time(),
   //   rate = total_written_size*sizeof(Number)/dt;
 
   // libMesh::err << "Write " << total_written_size << " \"Number\" values\n"
   //     << " Elapsed time = " << dt << '\n'
   //     << " Rate = " << rate/1.e6 << "(MB/sec)\n\n";
 
   // pl.pop("write_parallel_data");
 }

◆ 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().

 {
   parallel_object_only();
   std::string comment;
 
   // PerfLog pl("IO Performance",false);
   // pl.push("write_serialized_data");
   // std::size_t total_written_size = 0;
 
   // total_written_size +=
   this->write_serialized_vector(io, *this->solution);
 
   // set up the comment
   if (this->processor_id() == 0)
     {
       comment = "# System \"";
       comment += this->name();
       comment += "\" Solution Vector";
 
       io.comment (comment);
     }
 
   // Only write additional vectors if wanted
   if (write_additional_data)
     {
       std::map<std::string, NumericVector<Number> *>::const_iterator
         pos = _vectors.begin();
 
       for (; pos != this->_vectors.end(); ++pos)
         {
           // total_written_size +=
           this->write_serialized_vector(io, *pos->second);
 
           // set up the comment
           if (this->processor_id() == 0)
             {
               comment = "# System \"";
               comment += this->name();
               comment += "\" Additional Vector \"";
               comment += pos->first;
               comment += "\"";
               io.comment (comment);
             }
         }
     }
 
   // const Real
   //   dt   = pl.get_elapsed_time(),
   //   rate = total_written_size*sizeof(Number)/dt;
 
   // libMesh::out << "Write " << total_written_size << " \"Number\" values\n"
   //     << " Elapsed time = " << dt << '\n'
   //     << " Rate = " << rate/1.e6 << "(MB/sec)\n\n";
 
   // pl.pop("write_serialized_data");
 
 
 
 
   // // test the new method
   // {
   //   std::vector<std::string> names;
   //   std::vector<NumericVector<Number> *> vectors_to_write;
 
   //   names.push_back("Solution Vector");
   //   vectors_to_write.push_back(this->solution.get());
 
   //   // Only write additional vectors if wanted
   //   if (write_additional_data)
   //     {
   // std::map<std::string, NumericVector<Number> *>::const_iterator
   //   pos = _vectors.begin();
 
   // for (; pos != this->_vectors.end(); ++pos)
   //   {
   //     names.push_back("Additional Vector " + pos->first);
   //     vectors_to_write.push_back(pos->second);
   //   }
   //     }
 
   //   total_written_size =
   //     this->write_serialized_vectors (io, names, vectors_to_write);
 
   //   const Real
   //     dt2   = pl.get_elapsed_time(),
   //     rate2 = total_written_size*sizeof(Number)/(dt2-dt);
 
   //   libMesh::out << "Write (new) " << total_written_size << " \"Number\" values\n"
   //       << " Elapsed time = " << (dt2-dt) << '\n'
   //       << " Rate = " << rate2/1.e6 << "(MB/sec)\n\n";
 
   // }
 }

◆ 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().

 {
   parallel_object_only();
 
   libmesh_assert (io.writing());
 
   // Cache these - they are not free!
   const dof_id_type
     n_nodes       = this->get_mesh().n_nodes(),
     n_elem        = this->get_mesh().n_elem();
 
   std::size_t written_length = 0;
 
   if (this->processor_id() == 0)
     {
       unsigned int
         n_vec    = cast_int<unsigned int>(vectors.size());
       dof_id_type
         vec_size = vectors.empty() ? 0 : vectors[0]->size();
       // Set the number of vectors
       io.data(n_vec, "# number of vectors");
       // Set the buffer size
       io.data(vec_size, "# vector length");
     }
 
   //---------------------------------
   // Collect the values for all nodes
   written_length +=
     this->write_serialized_blocked_dof_objects (vectors,
                                                 n_nodes,
                                                 this->get_mesh().local_nodes_begin(),
                                                 this->get_mesh().local_nodes_end(),
                                                 io);
 
   //------------------------------------
   // Collect the values for all elements
   written_length +=
     this->write_serialized_blocked_dof_objects (vectors,
                                                 n_elem,
                                                 this->get_mesh().local_elements_begin(),
                                                 this->get_mesh().local_elements_end(),
                                                 io);
 
   //-------------------------------------------
   // Finally loop over all the SCALAR variables
   for (std::size_t vec=0; vec<vectors.size(); vec++)
     for (unsigned int var=0; var<this->n_vars(); var++)
       if (this->variable(var).type().family == SCALAR)
         {
           libmesh_assert_not_equal_to (vectors[vec], 0);
 
           written_length +=
             this->write_SCALAR_dofs (*vectors[vec], var, io);
         }
 
   return written_length;
 }

◆ 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().

 {
   /* Make sure the call makes sense.  */
   libmesh_assert_less (var_num, this->n_vars());
 
   /* Get a reference to the mesh.  */
   const MeshBase & mesh = this->get_mesh();
 
   /* Check which system we are.  */
   const unsigned int sys_num = this->number();
 
   // Loop over nodes.
   for (const auto & node : mesh.local_node_ptr_range())
     {
       unsigned int n_comp = node->n_comp(sys_num,var_num);
       for (unsigned int i=0; i<n_comp; i++)
         {
           const dof_id_type index = node->dof_number(sys_num,var_num,i);
           v.set(index,0.0);
         }
     }
 
   // Loop over elements.
   for (const auto & elem : mesh.active_local_element_ptr_range())
     {
       unsigned int n_comp = elem->n_comp(sys_num,var_num);
       for (unsigned int i=0; i<n_comp; i++)
         {
           const dof_id_type index = elem->dof_number(sys_num,var_num,i);
           v.set(index,0.0);
         }
     }
 }

Member Data Documentation

◆ _communicator

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

protectedinherited

Definition at line 107 of file parallel_object.h.

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

◆ _counts

ReferenceCounter::Counts libMesh::ReferenceCounter::_counts

staticprotectedinherited

Actually holds the data.

Definition at line 122 of file reference_counter.h.

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

◆ _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

Variable indices for those variables that are first order in time.

Definition at line 559 of file diff_physics.h.

Referenced by libMesh::DifferentiablePhysics::get_first_order_vars(), libMesh::DifferentiablePhysics::have_first_order_vars(), and libMesh::DifferentiablePhysics::is_first_order_var().

◆ _mesh_sys

System* libMesh::DifferentiablePhysics::_mesh_sys

protectedinherited

System from which to acquire moving mesh information

Definition at line 542 of file diff_physics.h.

Referenced by libMesh::DifferentiablePhysics::get_mesh_system(), libMesh::FEMSystem::mesh_position_get(), libMesh::FEMSystem::mesh_position_set(), libMesh::FEMSystem::numerical_jacobian(), and libMesh::DifferentiablePhysics::set_mesh_system().

◆ _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(), libMesh::FEMSystem::mesh_position_get(), libMesh::FEMSystem::numerical_jacobian(), and libMesh::DifferentiablePhysics::set_mesh_x_var().

◆ _mesh_y_var

unsigned int libMesh::DifferentiablePhysics::_mesh_y_var

protectedinherited

Definition at line 547 of file diff_physics.h.

Referenced by libMesh::DifferentiablePhysics::get_mesh_y_var(), libMesh::FEMSystem::mesh_position_get(), libMesh::FEMSystem::numerical_jacobian(), and libMesh::DifferentiablePhysics::set_mesh_y_var().

◆ _mesh_z_var

unsigned int libMesh::DifferentiablePhysics::_mesh_z_var

protectedinherited

Definition at line 547 of file diff_physics.h.

Referenced by libMesh::DifferentiablePhysics::get_mesh_z_var(), libMesh::FEMSystem::mesh_position_get(), libMesh::FEMSystem::numerical_jacobian(), and libMesh::DifferentiablePhysics::set_mesh_z_var().

◆ _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().

◆ _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

Variable indices for those variables that are second order in time.

Definition at line 564 of file diff_physics.h.

Referenced by libMesh::DifferentiablePhysics::get_second_order_vars(), libMesh::DifferentiablePhysics::have_second_order_vars(), and libMesh::DifferentiablePhysics::is_second_order_var().

◆ _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.

◆ continuation_parameter

Real* libMesh::ContinuationSystem::continuation_parameter

The continuation parameter must be a member variable of the derived class, and the "continuation_parameter" pointer defined here must be a pointer to that variable. This is how the continuation system updates the derived class's continuation parameter.

Also sometimes referred to as "lambda" in the code comments.

Definition at line 115 of file continuation_system.h.

Referenced by apply_predictor(), continuation_solve(), initialize_tangent(), save_current_solution(), solve_tangent(), and update_solution().

◆ continuation_parameter_tolerance

Real libMesh::ContinuationSystem::continuation_parameter_tolerance

How tightly should the Newton iterations attempt to converge delta_lambda. Defaults to 1.e-6.

Definition at line 134 of file continuation_system.h.

Referenced by continuation_solve().

◆ 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().

◆ delta_u

NumericVector<Number>* libMesh::ContinuationSystem::delta_u

private

Temporary vector "delta u" ... the Newton step update in our custom augmented PDE solve.

Definition at line 370 of file continuation_system.h.

Referenced by continuation_solve(), init_data(), solve_tangent(), and update_solution().

◆ deltat

Real libMesh::DifferentiableSystem::deltat

inherited

For time-dependent problems, this is the amount delta t to advance the solution in time.

Definition at line 261 of file diff_system.h.

Referenced by libMesh::EulerSolver::_general_residual(), libMesh::Euler2Solver::_general_residual(), libMesh::NewmarkSolver::_general_residual(), libMesh::UnsteadySolver::adjoint_advance_timestep(), libMesh::NewmarkSolver::advance_timestep(), libMesh::UnsteadySolver::advance_timestep(), libMesh::FEMSystem::build_context(), libMesh::DifferentiableSystem::build_context(), libMesh::FEMSystem::init_context(), libMesh::TwostepTimeSolver::solve(), and libMesh::UnsteadySolver::solve().

◆ 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 libMesh::FEMSystem::assemble_qoi(), libMesh::FEMSystem::assemble_qoi_derivative(), libMesh::DifferentiableSystem::attach_qoi(), libMesh::DifferentiableSystem::clear(), libMesh::DifferentiableSystem::get_qoi(), and libMesh::DifferentiableSystem::~DifferentiableSystem().

◆ dlambda_ds

Real libMesh::ContinuationSystem::dlambda_ds

private

The most recent value of the derivative of the continuation parameter with respect to s. We use "lambda" here for shortness of notation, lambda always refers to the continuation parameter.

Definition at line 396 of file continuation_system.h.

Referenced by apply_predictor(), continuation_solve(), initialize_tangent(), set_Theta_LOCA(), and solve_tangent().

◆ ds

Real libMesh::ContinuationSystem::ds

private

The initial arclength stepsize, selected by the user. This is the max-allowable arclength stepsize, but the algorithm may frequently reduce ds near turning points.

Definition at line 403 of file continuation_system.h.

Referenced by set_max_arclength_stepsize(), and update_solution().

◆ ds_current

Real libMesh::ContinuationSystem::ds_current

private

Value of stepsize currently in use. Will not exceed user-provided maximum arclength stepsize ds.

Definition at line 409 of file continuation_system.h.

Referenced by apply_predictor(), continuation_solve(), initialize_tangent(), set_max_arclength_stepsize(), and update_solution().

◆ ds_min

Real libMesh::ContinuationSystem::ds_min

The minimum-allowed steplength, defaults to 1.e-8.

Definition at line 214 of file continuation_system.h.

Referenced by update_solution().

◆ du_ds

NumericVector<Number>* libMesh::ContinuationSystem::du_ds

private

Extra work vectors used by the continuation algorithm. These are added to the system by the init_data() routine.

The "solution" tangent vector du/ds.

Definition at line 338 of file continuation_system.h.

Referenced by apply_predictor(), continuation_solve(), init_data(), initialize_tangent(), and solve_tangent().

◆ 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

inherited

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.

◆ initial_newton_tolerance

Real libMesh::ContinuationSystem::initial_newton_tolerance

How much to try to reduce the residual by at the first (inexact) Newton step. This is frequently something large like 1/2 in an inexact Newton method, to prevent oversolving.

Definition at line 147 of file continuation_system.h.

Referenced by continuation_solve().

◆ linear_solver

std::unique_ptr<LinearSolver<Number> > libMesh::ContinuationSystem::linear_solver

private

We maintain our own linear solver interface, for solving custom systems of equations and/or things which do not require a full-blown NewtonSolver.

Definition at line 377 of file continuation_system.h.

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

◆ matrix

SparseMatrix<Number>* libMesh::ImplicitSystem::matrix

inherited

The system matrix. Implicit systems are characterized by the need to solve the linear system Ax=b. This is the system matrix A.

Definition at line 373 of file implicit_system.h.

◆ max_continuation_parameter

Real libMesh::ContinuationSystem::max_continuation_parameter

The maximum-allowable value of the continuation parameter. The Newton iterations will quit if the continuation parameter goes above this value. If this value is zero, there is no maximum value for the continuation parameter.

Definition at line 174 of file continuation_system.h.

Referenced by continuation_solve().

◆ min_continuation_parameter

Real libMesh::ContinuationSystem::min_continuation_parameter

The minimum-allowable value of the continuation parameter. The Newton iterations will quit if the continuation parameter falls below this value.

Definition at line 167 of file continuation_system.h.

Referenced by continuation_solve().

◆ n_arclength_reductions

unsigned int libMesh::ContinuationSystem::n_arclength_reductions

Number of arclength reductions to try when Newton fails to reduce the residual. For each arclength reduction, the arcstep size is cut in half.

Definition at line 209 of file continuation_system.h.

Referenced by continuation_solve().

◆ n_backtrack_steps

unsigned int libMesh::ContinuationSystem::n_backtrack_steps

Another scaling parameter suggested by the LOCA people. This one attempts to shrink the stepsize ds whenever the angle between the previous two tangent vectors gets large. Number of (Newton) backtracking steps to attempt if a Newton step does not reduce the residual. This is backtracking within a single Newton step, if you want to try a smaller arcstep, set n_arclength_reductions > 0.

Definition at line 202 of file continuation_system.h.

Referenced by continuation_solve().

◆ newton_progress_check

bool libMesh::ContinuationSystem::newton_progress_check

True by default, the Newton progress check allows the Newton loop to exit if half the allowed iterations have elapsed without a reduction in the initial residual. In our experience this usually means the Newton steps are going to fail eventually and we could save some time by quitting early.

Definition at line 256 of file continuation_system.h.

Referenced by continuation_solve().

◆ newton_solver

NewtonSolver* libMesh::ContinuationSystem::newton_solver

private

A pointer to the underlying Newton solver used by the DiffSystem. From this pointer, we can get access to all the parameters and options which are available to the "normal" Newton solver.

Definition at line 389 of file continuation_system.h.

Referenced by continuation_solve(), solve_tangent(), and update_solution().

◆ newton_step

unsigned int libMesh::ContinuationSystem::newton_step

private

Loop counter for nonlinear (Newton) iteration loop.

Definition at line 424 of file continuation_system.h.

Referenced by continuation_solve(), and update_solution().

◆ newton_stepgrowth_aggressiveness

Real libMesh::ContinuationSystem::newton_stepgrowth_aggressiveness

A measure of how rapidly one should attempt to grow the arclength stepsize based on the number of Newton iterations required to solve the problem. Default value is 1.0, if set to zero, will not try to grow or shrink the arclength stepsize based on the number of Newton iterations required.

Definition at line 247 of file continuation_system.h.

Referenced by update_solution().

◆ numerical_jacobian_h

Real libMesh::FEMSystem::numerical_jacobian_h

inherited

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 libMesh::FEMSystem::numerical_jacobian(), and libMesh::FEMSystem::numerical_jacobian_h_for_var().

◆ old_continuation_parameter

Real libMesh::ContinuationSystem::old_continuation_parameter

The system also keeps track of the old value of the continuation parameter.

Definition at line 161 of file continuation_system.h.

Referenced by continuation_solve(), initialize_tangent(), save_current_solution(), solve_tangent(), and update_solution().

◆ 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.

◆ predictor

Predictor libMesh::ContinuationSystem::predictor

Definition at line 238 of file continuation_system.h.

Referenced by apply_predictor().

◆ previous_dlambda_ds

Real libMesh::ContinuationSystem::previous_dlambda_ds

private

The old parameter tangent value.

Definition at line 414 of file continuation_system.h.

Referenced by apply_predictor(), and solve_tangent().

◆ previous_ds

Real libMesh::ContinuationSystem::previous_ds

private

The previous arcstep length used.

Definition at line 419 of file continuation_system.h.

Referenced by apply_predictor(), and update_solution().

◆ previous_du_ds

NumericVector<Number>* libMesh::ContinuationSystem::previous_du_ds

private

The value of du_ds from the previous solution

Definition at line 343 of file continuation_system.h.

Referenced by apply_predictor(), init_data(), and solve_tangent().

◆ previous_u

NumericVector<Number>* libMesh::ContinuationSystem::previous_u

private

The solution at the previous value of the continuation variable.

Definition at line 348 of file continuation_system.h.

Referenced by continuation_solve(), init_data(), initialize_tangent(), save_current_solution(), solve_tangent(), and update_solution().

◆ 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 libMesh::FEMSystem::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 libMesh::FEMSystem::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 libMesh::FEMSystem::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 libMesh::FEMSystem::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 libMesh::FEMSystem::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 libMesh::FEMSystem::assembly().

◆ qoi

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

inherited

Values of the quantities of interest. This vector needs to be both resized and filled by the user before any quantity of interest assembly is done and before any sensitivities are calculated.

Definition at line 1558 of file system.h.

Referenced by libMesh::ImplicitSystem::adjoint_qoi_parameter_sensitivity(), libMesh::ExplicitSystem::assemble_qoi(), libMesh::FEMSystem::assemble_qoi(), libMesh::DifferentiableSystem::attach_qoi(), libMesh::DiffContext::DiffContext(), libMesh::ImplicitSystem::forward_qoi_parameter_sensitivity(), libMesh::System::n_qois(), libMesh::ImplicitSystem::qoi_parameter_hessian(), and libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product().

◆ quiet

bool libMesh::ContinuationSystem::quiet

If quiet==false, the System prints extra information about what it is doing.

Definition at line 121 of file continuation_system.h.

Referenced by continuation_solve(), initialize_tangent(), set_Theta(), set_Theta_LOCA(), solve_tangent(), and update_solution().

◆ rhs

NumericVector<Number>* libMesh::ExplicitSystem::rhs

inherited

The system matrix. Implicit systems are characterized by the need to solve the linear system Ax=b. This is the right-hand-side vector b.

Definition at line 114 of file explicit_system.h.

Referenced by libMesh::__libmesh_petsc_diff_solver_residual(), libMesh::ExplicitSystem::add_system_rhs(), libMesh::ImplicitSystem::assemble(), libMesh::ImplicitSystem::assemble_residual_derivatives(), libMesh::FEMSystem::assembly(), libMesh::LinearImplicitSystem::assembly(), libMesh::NonlinearImplicitSystem::assembly(), libMesh::Problem_Interface::computeF(), continuation_solve(), DMlibMeshFunction(), libMesh::ImplicitSystem::forward_qoi_parameter_sensitivity(), libMesh::NewtonSolver::line_search(), libMesh::ImplicitSystem::qoi_parameter_hessian(), libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product(), libMesh::NewtonSolver::solve(), libMesh::PetscDiffSolver::solve(), libMesh::FrequencySystem::solve(), libMesh::LinearImplicitSystem::solve(), libMesh::NonlinearImplicitSystem::solve(), solve_tangent(), libMesh::NewmarkSystem::update_rhs(), libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve(), and libMesh::ImplicitSystem::weighted_sensitivity_solve().

◆ rhs_mode

RHS_Mode libMesh::ContinuationSystem::rhs_mode

protected

Definition at line 289 of file continuation_system.h.

Referenced by continuation_solve(), solve(), and solve_tangent().

◆ solution

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

inherited

Data structure to hold solution values.

Definition at line 1523 of file system.h.

◆ solution_tolerance

Real libMesh::ContinuationSystem::solution_tolerance

How tightly should the Newton iterations attempt to converge ||delta_u|| Defaults to 1.e-6.

Definition at line 140 of file continuation_system.h.

Referenced by continuation_solve().

◆ tangent_initialized

bool libMesh::ContinuationSystem::tangent_initialized

private

False until initialize_tangent() is called

Definition at line 382 of file continuation_system.h.

Referenced by continuation_solve(), initialize_tangent(), solve_tangent(), and update_solution().

◆ Theta

Real libMesh::ContinuationSystem::Theta

Arclength normalization parameter. Defaults to 1.0 (no normalization). Used to ensure that one term in the arclength constraint equation does not wash out all the others.

Definition at line 181 of file continuation_system.h.

Referenced by continuation_solve(), initialize_tangent(), set_Theta(), solve_tangent(), and update_solution().

◆ Theta_LOCA

Real libMesh::ContinuationSystem::Theta_LOCA

Another normalization parameter, which is described in the LOCA manual. This one is designed to maintain a relatively "fixed" value of d(lambda)/ds. It is initially 1.0 and is updated after each solve.

Definition at line 188 of file continuation_system.h.

Referenced by continuation_solve(), initialize_tangent(), set_Theta_LOCA(), solve_tangent(), and update_solution().

◆ time

Real libMesh::System::time

inherited

For time-dependent problems, this is the time t at the beginning of the current timestep.

Note: For DifferentiableSystem users: do not access this time during an assembly! Use the DiffContext::time value instead to get correct results.

Definition at line 1545 of file system.h.

Referenced by libMesh::UnsteadySolver::adjoint_advance_timestep(), libMesh::AdaptiveTimeSolver::advance_timestep(), libMesh::UnsteadySolver::advance_timestep(), libMesh::ExactErrorEstimator::find_squared_element_error(), libMesh::MemorySolutionHistory::find_stored_entry(), libMesh::WeightedPatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::System::reinit_constraints(), libMesh::MemorySolutionHistory::retrieve(), libMesh::TwostepTimeSolver::solve(), and libMesh::MemorySolutionHistory::store().

◆ time_solver

std::unique_ptr<TimeSolver> libMesh::DifferentiableSystem::time_solver

inherited

A pointer to the solver object we're going to use. This must be instantiated by the user before solving!

Definition at line 234 of file diff_system.h.

Referenced by libMesh::FEMSystem::assembly(), continuation_solve(), libMesh::DifferentiableSystem::get_linear_solve_parameters(), libMesh::DifferentiableSystem::get_linear_solver(), libMesh::DifferentiableSystem::get_second_order_dot_var(), libMesh::DifferentiableSystem::get_time_solver(), libMesh::DifferentiableSystem::init_data(), libMesh::DifferentiableSystem::reinit(), libMesh::DifferentiableSystem::set_time_solver(), libMesh::DifferentiableSystem::solve(), and solve_tangent().

◆ 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

inherited

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 libMesh::FEMSystem::assembly().

◆ y

NumericVector<Number>* libMesh::ContinuationSystem::y

private

Temporary vector "y" ... stores -du/dlambda, the solution of $Ay=G_{\lambda}$ .

Definition at line 353 of file continuation_system.h.

Referenced by continuation_solve(), init_data(), initialize_tangent(), solve_tangent(), and update_solution().

◆ y_old

NumericVector<Number>* libMesh::ContinuationSystem::y_old

private

Temporary vector "y_old" ... stores the previous value of -du/dlambda, which is the solution of $Ay=G_{\lambda}$ .

Definition at line 359 of file continuation_system.h.

Referenced by continuation_solve(), init_data(), and update_solution().

◆ z

NumericVector<Number>* libMesh::ContinuationSystem::z

private

Temporary vector "z" ... the solution of $ Az = -G $

Definition at line 364 of file continuation_system.h.

Referenced by continuation_solve(), and init_data().

◆ 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:

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Types

Protected Member Functions

Protected Attributes

Static Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ const_matrices_iterator

◆ const_vectors_iterator

◆ Counts

◆ GradientFunctionPointer

◆ matrices_iterator

◆ Parent

◆ sys_type

◆ TimeSolverResPtr

◆ ValueFunctionPointer

◆ vectors_iterator

Member Enumeration Documentation

◆ Predictor

◆ RHS_Mode

Constructor & Destructor Documentation

◆ ContinuationSystem()

◆ ~ContinuationSystem()

Member Function Documentation

◆ _eulerian_time_deriv()

◆ activate()

◆ active()

◆ add_adjoint_rhs()

◆ add_adjoint_solution()

◆ add_dot_var_dirichlet_bcs()

◆ add_matrix()

◆ add_second_order_dot_vars()

◆ add_sensitivity_rhs()

◆ add_sensitivity_solution()

◆ add_variable() [1/2]

◆ add_variable() [2/2]

◆ add_variables() [1/2]

◆ add_variables() [2/2]

◆ add_vector()

◆ add_weighted_sensitivity_adjoint_solution()

◆ add_weighted_sensitivity_solution()

◆ adjoint_qoi_parameter_sensitivity()

◆ adjoint_solve()

◆ advance_arcstep()

◆ apply_predictor()

◆ assemble()

◆ assemble_qoi()

◆ assemble_qoi_derivative()

◆ assemble_residual_derivatives()

◆ assembly()

◆ attach_assemble_function()

◆ attach_assemble_object()

◆ attach_constraint_function()

◆ attach_constraint_object()

◆ attach_init_function()

◆ attach_init_object()

◆ attach_physics()

◆ attach_qoi()

◆ attach_QOI_derivative()

◆ attach_QOI_derivative_object()

◆ attach_QOI_function()

◆ attach_QOI_object()

◆ boundary_project_solution() [1/2]

◆ boundary_project_solution() [2/2]

◆ boundary_project_vector() [1/2]

◆ boundary_project_vector() [2/2]

◆ build_context()

◆ calculate_norm() [1/2]

◆ calculate_norm() [2/2]

◆ clear()

◆ clear_physics()

◆ clear_qoi()

◆ clone()

◆ clone_physics()

◆ comm()