libMesh::RBSCMConstruction Class Reference

This class is part of the rbOOmit framework. More...

#include <rb_scm_construction.h>

Inheritance diagram for libMesh::RBSCMConstruction:

Public Types
typedef RBSCMConstruction	sys_type
	The type of system. More...
typedef RBConstructionBase< CondensedEigenSystem >	Parent
	The type of the parent. More...
typedef Number(*	ValueFunctionPointer) (const Point &p, const Parameters &Parameters, const std::string &sys_name, const std::string &unknown_name)
	Projects arbitrary functions onto the current solution. More...
typedef Gradient(*	GradientFunctionPointer) (const Point &p, const Parameters &parameters, const std::string &sys_name, const std::string &unknown_name)
typedef std::map< std::string, std::unique_ptr< NumericVector< Number > >, std::less<> >::iterator	vectors_iterator
	Vector iterator typedefs. More...
typedef std::map< std::string, std::unique_ptr< NumericVector< Number > >, std::less<> >::const_iterator	const_vectors_iterator
typedef std::map< std::string, std::unique_ptr< SparseMatrix< Number > >, std::less<> >::iterator	matrices_iterator
	Matrix iterator typedefs. More...
typedef std::map< std::string, std::unique_ptr< SparseMatrix< Number > >, std::less<> >::const_iterator	const_matrices_iterator

Public Member Functions
	RBSCMConstruction (EquationSystems &es, const std::string &name_in, const unsigned int number_in)
	Constructor. More...
	RBSCMConstruction (RBSCMConstruction &&)=default
	Special functions. More...
	RBSCMConstruction (const RBSCMConstruction &)=delete
RBSCMConstruction &	operator= (const RBSCMConstruction &)=delete
RBSCMConstruction &	operator= (RBSCMConstruction &&)=delete
virtual	~RBSCMConstruction ()
virtual void	clear () override
	Clear all the data structures associated with the system. More...
void	set_rb_scm_evaluation (RBSCMEvaluation &rb_scm_eval_in)
	Set the RBSCMEvaluation object. More...
RBSCMEvaluation &	get_rb_scm_evaluation ()
	Get a reference to the RBSCMEvaluation object. More...
RBThetaExpansion &	get_rb_theta_expansion ()
	Get a reference to the RBThetaExpansion object. More...
virtual void	resize_SCM_vectors ()
	Clear and resize the SCM data vectors. More...
virtual void	process_parameters_file (const std::string &parameters_filename)
	Read in the parameters from file specified by parameters_filename and set the this system's member variables accordingly. More...
virtual void	print_info ()
	Print out info that describes the current setup of this RBSCMConstruction. More...
virtual void	set_eigensolver_properties (int)
	This function is called before truth eigensolves in compute_SCM_bounding_box and evaluate_stability_constant. More...
void	set_RB_system_name (const std::string &new_name)
	Set the name of the associated RB system — we need this to load the (symmetrized) affine operators. More...
Real	get_SCM_training_tolerance () const
	Get/set SCM_training_tolerance: tolerance for SCM greedy. More...
void	set_SCM_training_tolerance (Real SCM_training_tolerance_in)
virtual void	perform_SCM_greedy ()
	Perform the SCM greedy algorithm to develop a lower bound over the training set. More...
virtual void	attach_deflation_space ()
	Attach the deflation space defined by the specified vector, can be useful in solving constrained eigenvalue problems. More...
sys_type &	system ()
void	set_quiet_mode (bool quiet_mode_in)
	Set the quiet_mode flag. More...
bool	is_quiet () const
	Is the system in quiet mode? More...
void	set_normalize_solution_snapshots (bool value)
	Set the boolean option that indicates if we normalization solution snapshots or not. More...
numeric_index_type	get_n_training_samples () const
	Get the number of global training samples. More...
numeric_index_type	get_local_n_training_samples () const
	Get the total number of training samples local to this processor. More...
numeric_index_type	get_first_local_training_index () const
	Get the first local index of the training parameters. More...
numeric_index_type	get_last_local_training_index () const
	Get the last local index of the training parameters. More...
virtual void	initialize_training_parameters (const RBParameters &mu_min, const RBParameters &mu_max, const unsigned int n_global_training_samples, const std::map< std::string, bool > &log_param_scale, const bool deterministic=true)
	Initialize the parameter ranges and indicate whether deterministic or random training parameters should be used and whether or not we want the parameters to be scaled logarithmically. More...
virtual void	load_training_set (const std::map< std::string, std::vector< RBParameter >> &new_training_set)
	Overwrite the training parameters with new_training_set. More...
void	set_training_parameter_values (const std::string &param_name, const std::vector< RBParameter > &values)
	Overwrite the local training samples for param_name using values. More...
void	broadcast_parameters (const unsigned int proc_id)
	Broadcasts parameters from processor proc_id to all processors. More...
void	set_training_random_seed (int seed)
	Set the seed that is used to randomly generate training parameters. More...
void	set_deterministic_training_parameter_name (const std::string &name)
	In some cases we only want to allow discrete parameter values, instead of parameters that may take any value in a specified interval. More...
const std::string &	get_deterministic_training_parameter_name () const
	Get the name of the parameter that we will generate deterministic training parameters for. More...
void	initialize_condensed_dofs (const std::set< dof_id_type > &global_condensed_dofs_set=std::set< dof_id_type >())
	Loop over the dofs on each processor to initialize the list of non-condensed dofs. More...
dof_id_type	n_global_non_condensed_dofs () const
virtual void	solve () override
	Override to solve the condensed eigenproblem with the dofs in local_non_condensed_dofs_vector stripped out of the system matrices on each processor. More...
virtual std::pair< Real, Real >	get_eigenpair (dof_id_type i) override
	Override get_eigenpair() to retrieve the eigenpair for the condensed eigensolve. More...
bool	has_condensed_matrix_A () const
bool	has_condensed_matrix_B () const
bool	has_condensed_precond_matrix () const
SparseMatrix< Number > &	get_condensed_matrix_A ()
SparseMatrix< Number > &	get_condensed_matrix_B ()
SparseMatrix< Number > &	get_condensed_precond_matrix ()
void	copy_sub_to_super (const NumericVector< Number > &sub, NumericVector< Number > &super)
	Copy a logically sub-vector into a super-vector. More...
void	copy_super_to_sub (NumericVector< Number > &super, NumericVector< Number > &sub)
	Copy a logically super-vector into a sub-vector. More...
void	copy_super_to_sub (const SparseMatrix< Number > &super, SparseMatrix< Number > &sub)
	Copy a logically super-matrix into a sub-matrix. More...
void	dont_create_submatrices_in_solve ()
	Instructs not to create the condensed submatrices from the global matrices right before the solve. More...
void	initialize_condensed_matrices ()
	Initializes the condensed matrices. More...
bool	have_condensed_dofs () const
virtual void	reinit () override
	Reinitializes the member data fields associated with the system, so that, e.g., assemble() may be used. More...
virtual std::pair< Real, Real >	get_eigenvalue (dof_id_type i)
virtual std::string	system_type () const override
unsigned int	get_n_converged () const
unsigned int	get_n_iterations () const
void	set_eigenproblem_type (EigenProblemType ept)
	Sets the type of the current eigen problem. More...
EigenProblemType	get_eigenproblem_type () const
void	set_initial_space (NumericVector< Number > &initial_space_in)
	Sets an initial eigen vector. More...
bool	generalized () const
bool	use_shell_matrices () const
void	use_shell_matrices (bool use_shell_matrices)
	Set a flag to use shell matrices. More...
bool	use_shell_precond_matrix () const
void	use_shell_precond_matrix (bool use_shell_precond_matrix)
	Set a flag to use a shell preconditioning matrix. More...
const SparseMatrix< Number > &	get_matrix_A () const
SparseMatrix< Number > &	get_matrix_A ()
const SparseMatrix< Number > &	get_matrix_B () const
SparseMatrix< Number > &	get_matrix_B ()
const SparseMatrix< Number > &	get_precond_matrix () const
SparseMatrix< Number > &	get_precond_matrix ()
const ShellMatrix< Number > &	get_shell_matrix_A () const
ShellMatrix< Number > &	get_shell_matrix_A ()
const ShellMatrix< Number > &	get_shell_matrix_B () const
ShellMatrix< Number > &	get_shell_matrix_B ()
const ShellMatrix< Number > &	get_shell_precond_matrix () const
ShellMatrix< Number > &	get_shell_precond_matrix ()
const EigenSolver< Number > &	get_eigen_solver () const
EigenSolver< Number > &	get_eigen_solver ()
bool	has_matrix_A () const
bool	has_matrix_B () const
bool	has_precond_matrix () const
bool	has_shell_matrix_A () const
bool	has_shell_matrix_B () const
bool	has_shell_precond_matrix () const
void	init ()
	Initializes degrees of freedom on the current mesh. More...
virtual void	reinit_constraints ()
	Reinitializes the constraints for this system. More...
virtual void	reinit_mesh ()
	Reinitializes the system with a new mesh. More...
bool	is_initialized () const
virtual void	update ()
	Update the local values to reflect the solution on neighboring processors. More...
virtual void	assemble ()
	Prepares matrix and _dof_map for matrix assembly. More...
virtual void	assemble_qoi (const QoISet &qoi_indices=QoISet())
	Calls user qoi function. More...
virtual void	assemble_qoi_derivative (const QoISet &qoi_indices=QoISet(), bool include_liftfunc=true, bool apply_constraints=true)
	Calls user qoi derivative function. More...
virtual void	assemble_residual_derivatives (const ParameterVector &parameters)
	Calls residual parameter derivative function. More...
virtual void	restrict_solve_to (const SystemSubset *subset, const SubsetSolveMode subset_solve_mode=SUBSET_ZERO)
	After calling this method, any solve will be restricted to the given subdomain. More...
virtual std::pair< unsigned int, Real >	sensitivity_solve (const ParameterVector &parameters)
	Solves the sensitivity system, for the provided parameters. More...
virtual std::pair< unsigned int, Real >	weighted_sensitivity_solve (const ParameterVector &parameters, const ParameterVector &weights)
	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. More...
virtual std::pair< unsigned int, Real >	adjoint_solve (const QoISet &qoi_indices=QoISet())
	Solves the adjoint system, for the specified qoi indices, or for every qoi if qoi_indices is nullptr. More...
virtual std::pair< unsigned int, Real >	weighted_sensitivity_adjoint_solve (const ParameterVector &parameters, const ParameterVector &weights, const QoISet &qoi_indices=QoISet())
	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. More...
bool	is_adjoint_already_solved () const
	Accessor for the adjoint_already_solved boolean. More...
void	set_adjoint_already_solved (bool setting)
	Setter for the adjoint_already_solved boolean. More...
virtual void	qoi_parameter_sensitivity (const QoISet &qoi_indices, const ParameterVector &parameters, SensitivityData &sensitivities)
	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]. More...
virtual void	adjoint_qoi_parameter_sensitivity (const QoISet &qoi_indices, const ParameterVector &parameters, SensitivityData &sensitivities)
	Solves for parameter sensitivities using the adjoint method. More...
virtual void	forward_qoi_parameter_sensitivity (const QoISet &qoi_indices, const ParameterVector &parameters, SensitivityData &sensitivities)
	Solves for parameter sensitivities using the forward method. More...
virtual void	qoi_parameter_hessian (const QoISet &qoi_indices, const ParameterVector &parameters, SensitivityData &hessian)
	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). More...
virtual void	qoi_parameter_hessian_vector_product (const QoISet &qoi_indices, const ParameterVector &parameters, const ParameterVector &vector, SensitivityData &product)
	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]. More...
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
	Projects arbitrary functions onto the current solution. More...
void	project_solution (FEMFunctionBase< Number > *f, FEMFunctionBase< Gradient > *g=nullptr) const
	Projects arbitrary functions onto the current solution. More...
void	project_solution (ValueFunctionPointer fptr, GradientFunctionPointer gptr, const Parameters &parameters) const
	This method projects an arbitrary function onto the solution via L2 projections and nodal interpolations on each element. More...
void	project_vector (NumericVector< Number > &new_vector, FunctionBase< Number > *f, FunctionBase< Gradient > *g=nullptr, int is_adjoint=-1) const
	Projects arbitrary functions onto a vector of degree of freedom values for the current system. More...
void	project_vector (NumericVector< Number > &new_vector, FEMFunctionBase< Number > *f, FEMFunctionBase< Gradient > *g=nullptr, int is_adjoint=-1) const
	Projects arbitrary functions onto a vector of degree of freedom values for the current system. More...
void	project_vector (ValueFunctionPointer fptr, GradientFunctionPointer gptr, const Parameters &parameters, NumericVector< Number > &new_vector, int is_adjoint=-1) const
	Projects arbitrary functions onto a vector of degree of freedom values for the current system. More...
void	boundary_project_solution (const std::set< boundary_id_type > &b, const std::vector< unsigned int > &variables, FunctionBase< Number > *f, FunctionBase< Gradient > *g=nullptr)
	Projects arbitrary boundary functions onto a vector of degree of freedom values for the current system. More...
void	boundary_project_solution (const std::set< boundary_id_type > &b, const std::vector< unsigned int > &variables, ValueFunctionPointer fptr, GradientFunctionPointer gptr, const Parameters &parameters)
	Projects arbitrary boundary functions onto a vector of degree of freedom values for the current system. More...
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
	Projects arbitrary boundary functions onto a vector of degree of freedom values for the current system. More...
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
	Projects arbitrary boundary functions onto a vector of degree of freedom values for the current system. More...
unsigned int	number () const
void	update_global_solution (std::vector< Number > &global_soln) const
	Fill the input vector global_soln so that it contains the global solution on all processors. More...
void	update_global_solution (std::vector< Number > &global_soln, const processor_id_type dest_proc) const
	Fill the input vector global_soln so that it contains the global solution on processor dest_proc. More...
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 ()
	Activates the system. More...
void	deactivate ()
	Deactivates the system. More...
void	set_basic_system_only ()
	Sets the system to be "basic only": i.e. More...
vectors_iterator	vectors_begin ()
	Beginning of vectors container. More...
const_vectors_iterator	vectors_begin () const
	Beginning of vectors container. More...
vectors_iterator	vectors_end ()
	End of vectors container. More...
const_vectors_iterator	vectors_end () const
	End of vectors container. More...
matrices_iterator	matrices_begin ()
	Beginning of matrices container. More...
const_matrices_iterator	matrices_begin () const
	Beginning of matrices container. More...
matrices_iterator	matrices_end ()
	End of matrices container. More...
const_matrices_iterator	matrices_end () const
	End of matrices container. More...
NumericVector< Number > &	add_vector (std::string_view vec_name, const bool projections=true, const ParallelType type=PARALLEL)
	Adds the additional vector vec_name to this system. More...
void	remove_vector (std::string_view vec_name)
	Removes the additional vector vec_name from this system. More...
bool &	project_solution_on_reinit (void)
	Tells the System whether or not to project the solution vector onto new grids when the system is reinitialized. More...
bool	have_vector (std::string_view vec_name) const
const NumericVector< Number > *	request_vector (std::string_view vec_name) const
NumericVector< Number > *	request_vector (std::string_view 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 (std::string_view vec_name) const
NumericVector< Number > &	get_vector (std::string_view 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)
	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. More...
int	vector_is_adjoint (std::string_view vec_name) const
void	set_vector_preservation (const std::string &vec_name, bool preserve)
	Allows one to set the boolean controlling whether the vector identified by vec_name should be "preserved": projected to new meshes, saved, etc. More...
bool	vector_preservation (std::string_view 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_matrices () 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 (std::string_view var, const FEType &type, const std::set< subdomain_id_type > *const active_subdomains=nullptr)
	Adds the variable var to the list of variables for this system. More...
unsigned int	add_variable (std::string_view var, const Order order=FIRST, const FEFamily=LAGRANGE, const std::set< subdomain_id_type > *const active_subdomains=nullptr)
	Adds the variable var to the list of variables for this system. More...
unsigned int	add_variables (const std::vector< std::string > &vars, const FEType &type, const std::set< subdomain_id_type > *const active_subdomains=nullptr)
	Adds the variable var to the list of variables for this system. More...
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)
	Adds the variable var to the list of variables for this system. More...
const Variable &	variable (unsigned int var) const
	Return a constant reference to Variable var. More...
const VariableGroup &	variable_group (unsigned int vg) const
	Return a constant reference to VariableGroup vg. More...
bool	has_variable (std::string_view var) const
const std::string &	variable_name (const unsigned int i) const
unsigned int	variable_number (std::string_view var) const
void	get_all_variable_numbers (std::vector< unsigned int > &all_variable_numbers) const
	Fills all_variable_numbers with all the variable numbers for the variables that have been added to this system. More...
unsigned int	variable_scalar_number (std::string_view 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 (std::string_view var) const
bool	identify_variable_groups () const
void	identify_variable_groups (const bool)
	Toggle automatic VariableGroup identification. More...
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, std::string_view version, const bool read_header=true, const bool read_additional_data=true, const bool read_legacy_format=false)
	Reads the basic data header for this System. More...
void	read_legacy_data (Xdr &io, const bool read_additional_data=true)
	Reads additional data, namely vectors, for this System. More...
template<typename ValType >
void	read_serialized_data (Xdr &io, const bool read_additional_data=true)
	Reads additional data, namely vectors, for this System. More...
void	read_serialized_data (Xdr &io, const bool read_additional_data=true)
	Non-templated version for backward compatibility. More...
template<typename InValType >
std::size_t	read_serialized_vectors (Xdr &io, const std::vector< NumericVector< Number > *> &vectors) const
	Read a number of identically distributed vectors. More...
std::size_t	read_serialized_vectors (Xdr &io, const std::vector< NumericVector< Number > *> &vectors) const
	Non-templated version for backward compatibility. More...
template<typename InValType >
void	read_parallel_data (Xdr &io, const bool read_additional_data)
	Reads additional data, namely vectors, for this System. More...
void	read_parallel_data (Xdr &io, const bool read_additional_data)
	Non-templated version for backward compatibility. More...
void	write_header (Xdr &io, std::string_view version, const bool write_additional_data) const
	Writes the basic data header for this System. More...
void	write_serialized_data (Xdr &io, const bool write_additional_data=true) const
	Writes additional data, namely vectors, for this System. More...
std::size_t	write_serialized_vectors (Xdr &io, const std::vector< const NumericVector< Number > *> &vectors) const
	Serialize & write a number of identically distributed vectors. More...
void	write_parallel_data (Xdr &io, const bool write_additional_data) const
	Writes additional data, namely vectors, for this System. More...
std::string	get_info () const
void	attach_init_function (void fptr(EquationSystems &es, const std::string &name))
	Register a user function to use in initializing the system. More...
void	attach_init_object (Initialization &init)
	Register a user class to use to initialize the system. More...
void	attach_assemble_function (void fptr(EquationSystems &es, const std::string &name))
	Register a user function to use in assembling the system matrix and RHS. More...
void	attach_assemble_object (Assembly &assemble)
	Register a user object to use in assembling the system matrix and RHS. More...
void	attach_constraint_function (void fptr(EquationSystems &es, const std::string &name))
	Register a user function for imposing constraints. More...
void	attach_constraint_object (Constraint &constrain)
	Register a user object for imposing constraints. More...
bool	has_constraint_object () const
Constraint &	get_constraint_object ()
	Return the user object for imposing constraints. More...
void	attach_QOI_function (void fptr(EquationSystems &es, const std::string &name, const QoISet &qoi_indices))
	Register a user function for evaluating the quantities of interest, whose values should be placed in System::qoi. More...
void	attach_QOI_object (QOI &qoi)
	Register a user object for evaluating the quantities of interest, whose values should be placed in System::qoi. More...
void	attach_QOI_derivative (void fptr(EquationSystems &es, const std::string &name, const QoISet &qoi_indices, bool include_liftfunc, bool apply_constraints))
	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. More...
void	attach_QOI_derivative_object (QOIDerivative &qoi_derivative)
	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. More...
virtual void	user_initialization ()
	Calls user's attached initialization function, or is overridden by the user in derived classes. More...
virtual void	user_assembly ()
	Calls user's attached assembly function, or is overridden by the user in derived classes. More...
virtual void	user_constrain ()
	Calls user's attached constraint function, or is overridden by the user in derived classes. More...
virtual void	user_QOI (const QoISet &qoi_indices)
	Calls user's attached quantity of interest function, or is overridden by the user in derived classes. More...
virtual void	user_QOI_derivative (const QoISet &qoi_indices=QoISet(), bool include_liftfunc=true, bool apply_constraints=true)
	Calls user's attached quantity of interest derivative function, or is overridden by the user in derived classes. More...
virtual void	re_update ()
	Re-update the local values when the mesh has changed. More...
virtual void	restrict_vectors ()
	Restrict vectors after the mesh has coarsened. More...
virtual void	prolong_vectors ()
	Prolong vectors after the mesh has refined. More...
virtual void	disable_cache ()
	Avoids use of any cached data that might affect any solve result. More...
Number	current_solution (const dof_id_type global_dof_number) const
unsigned int	n_qois () const
	Number of currently active quantities of interest. More...
void	init_qois (unsigned int n_qois)
	Accessors for qoi and qoi_error_estimates vectors. More...
void	set_qoi (unsigned int qoi_index, Number qoi_value)
void	set_qoi (std::vector< Number > new_qoi)
Number	get_qoi_value (unsigned int qoi_index) const
std::vector< Number >	get_qoi_values () const
	Returns a copy of qoi, not a reference. More...
void	set_qoi_error_estimate (unsigned int qoi_index, Number qoi_error_estimate)
Number	get_qoi_error_estimate_value (unsigned int qoi_index) const
Number	point_value (unsigned int var, const Point &p, const bool insist_on_success=true, const NumericVector< Number > *sol=nullptr) const
Number	point_value (unsigned int var, const Point &p, const Elem &e, const NumericVector< Number > *sol=nullptr) const
Number	point_value (unsigned int var, const Point &p, const Elem *e) const
	Calls the version of point_value() which takes a reference. More...
Number	point_value (unsigned int var, const Point &p, const NumericVector< Number > *sol) const
	Calls the parallel version of point_value(). More...
Gradient	point_gradient (unsigned int var, const Point &p, const bool insist_on_success=true, const NumericVector< Number > *sol=nullptr) const
Gradient	point_gradient (unsigned int var, const Point &p, const Elem &e, const NumericVector< Number > *sol=nullptr) const
Gradient	point_gradient (unsigned int var, const Point &p, const Elem *e) const
	Calls the version of point_gradient() which takes a reference. More...
Gradient	point_gradient (unsigned int var, const Point &p, const NumericVector< Number > *sol) const
	Calls the parallel version of point_gradient(). More...
Tensor	point_hessian (unsigned int var, const Point &p, const bool insist_on_success=true, const NumericVector< Number > *sol=nullptr) const
Tensor	point_hessian (unsigned int var, const Point &p, const Elem &e, const NumericVector< Number > *sol=nullptr) const
Tensor	point_hessian (unsigned int var, const Point &p, const Elem *e) const
	Calls the version of point_hessian() which takes a reference. More...
Tensor	point_hessian (unsigned int var, const Point &p, const NumericVector< Number > *sol) const
	Calls the parallel version of point_hessian(). More...
void	local_dof_indices (const unsigned int var, std::set< dof_id_type > &var_indices) const
	Fills the std::set with the degrees of freedom on the local processor corresponding the the variable number passed in. More...
void	zero_variable (NumericVector< Number > &v, unsigned int var_num) const
	Zeroes all dofs in v that correspond to variable number var_num. More...
bool	get_project_with_constraints ()
	Setter and getter functions for project_with_constraints boolean. More...
void	set_project_with_constraints (bool _project_with_constraints)
bool &	hide_output ()
void	projection_matrix (SparseMatrix< Number > &proj_mat) const
	This method creates a projection matrix which corresponds to the operation of project_vector between old and new solution spaces. More...
SparseMatrix< Number > &	add_matrix (std::string_view mat_name, ParallelType type=PARALLEL, MatrixBuildType mat_build_type=MatrixBuildType::AUTOMATIC)
	Adds the additional matrix mat_name to this system. More...
template<template< typename > class>
SparseMatrix< Number > &	add_matrix (std::string_view mat_name, ParallelType=PARALLEL)
	Adds the additional matrix mat_name to this system. More...
SparseMatrix< Number > &	add_matrix (std::string_view mat_name, std::unique_ptr< SparseMatrix< Number >> matrix, ParallelType type=PARALLEL)
	Adds the additional matrix mat_name to this system. More...
void	remove_matrix (std::string_view mat_name)
	Removes the additional matrix mat_name from this system. More...
bool	have_matrix (std::string_view mat_name) const
const SparseMatrix< Number > *	request_matrix (std::string_view mat_name) const
SparseMatrix< Number > *	request_matrix (std::string_view mat_name)
const SparseMatrix< Number > &	get_matrix (std::string_view mat_name) const
SparseMatrix< Number > &	get_matrix (std::string_view mat_name)
void	prefer_hash_table_matrix_assembly (bool preference)
	Sets whether to use hash table matrix assembly if the matrix sub-classes support it. More...
void	prefix_with_name (bool value)
	Instructs this system to prefix solve options with its name for solvers that leverage prefixes. More...
bool	prefix_with_name () const
std::string	prefix () const
virtual void	create_static_condensation ()
	Request that static condensation be performed for this system. More...
bool	has_static_condensation () const
const Parallel::Communicator &	comm () const
processor_id_type	n_processors () const
processor_id_type	processor_id () const
void	initialize_parameters (const RBParameters &mu_min_in, const RBParameters &mu_max_in, const std::map< std::string, std::vector< Real >> &discrete_parameter_values)
	Initialize the parameter ranges and set current_parameters. More...
void	initialize_parameters (const RBParametrized &rb_parametrized)
	Initialize the parameter ranges and set current_parameters. More...
unsigned int	get_n_params () const
	Get the number of parameters. More...
unsigned int	get_n_continuous_params () const
	Get the number of continuous parameters. More...
unsigned int	get_n_discrete_params () const
	Get the number of discrete parameters. More...
std::set< std::string >	get_parameter_names () const
	Get a set that stores the parameter names. More...
const RBParameters &	get_parameters () const
	Get the current parameters. More...
bool	set_parameters (const RBParameters &params)
	Set the current parameters to params The parameters are checked for validity; an error is thrown if the number of parameters or samples is different than expected. More...
const RBParameters &	get_parameters_min () const
	Get an RBParameters object that specifies the minimum allowable value for each parameter. More...
const RBParameters &	get_parameters_max () const
	Get an RBParameters object that specifies the maximum allowable value for each parameter. More...
Real	get_parameter_min (const std::string &param_name) const
	Get minimum allowable value of parameter param_name. More...
Real	get_parameter_max (const std::string &param_name) const
	Get maximum allowable value of parameter param_name. More...
void	print_parameters () const
	Print the current parameters. More...
void	write_parameter_data_to_files (const std::string &continuous_param_file_name, const std::string &discrete_param_file_name, const bool write_binary_data)
	Write out the parameter ranges to files. More...
void	read_parameter_data_from_files (const std::string &continuous_param_file_name, const std::string &discrete_param_file_name, const bool read_binary_data)
	Read in the parameter ranges from files. More...
bool	is_discrete_parameter (const std::string &mu_name) const
	Is parameter mu_name discrete? More...
const std::map< std::string, std::vector< Real > > &	get_discrete_parameter_values () const
	Get a const reference to the discrete parameter values. More...
void	print_discrete_parameter_values () const
	Print out all the discrete parameter values. More...

Static Public Member Functions
static std::pair< std::size_t, std::size_t >	generate_training_parameters_random (const Parallel::Communicator &communicator, const std::map< std::string, bool > &log_param_scale, std::map< std::string, std::vector< RBParameter >> &local_training_parameters_in, const unsigned int n_global_training_samples_in, const RBParameters &min_parameters, const RBParameters &max_parameters, const int training_parameters_random_seed=-1, const bool serial_training_set=false)
	Static helper function for generating a randomized set of parameters. More...
static std::pair< std::size_t, std::size_t >	generate_training_parameters_deterministic (const Parallel::Communicator &communicator, const std::map< std::string, bool > &log_param_scale, std::map< std::string, std::vector< RBParameter >> &local_training_parameters_in, const unsigned int n_global_training_samples_in, const RBParameters &min_parameters, const RBParameters &max_parameters, const bool serial_training_set=false)
	Static helper function for generating a deterministic set of parameters. More...
static std::string	get_info ()
	Gets a string containing the reference information. More...
static std::string	get_info ()
	Gets a string containing the reference information. More...
static void	print_info (std::ostream &out_stream=libMesh::out)
	Prints the reference information, by default to libMesh::out. More...
static void	print_info (std::ostream &out_stream=libMesh::out)
	Prints the reference information, by default to libMesh::out. More...
static unsigned int	n_objects ()
	Prints the number of outstanding (created, but not yet destroyed) objects. More...
static unsigned int	n_objects ()
	Prints the number of outstanding (created, but not yet destroyed) objects. More...
static void	enable_print_counter_info ()
	Methods to enable/disable the reference counter output from print_info() More...
static void	enable_print_counter_info ()
	Methods to enable/disable the reference counter output from print_info() More...
static void	disable_print_counter_info ()
static void	disable_print_counter_info ()
static Real	get_closest_value (Real value, const std::vector< Real > &list_of_values)

Public Attributes
SparseMatrix< Number > *	condensed_matrix_A
	The (condensed) system matrix for standard eigenvalue problems. More...
SparseMatrix< Number > *	condensed_matrix_B
	A second (condensed) system matrix for generalized eigenvalue problems. More...
std::vector< dof_id_type >	local_non_condensed_dofs_vector
	Vector storing the local dof indices that will not be condensed. More...
SparseMatrix< Number > *	matrix_A
	The system matrix for standard eigenvalue problems. More...
SparseMatrix< Number > *	matrix_B
	A second system matrix for generalized eigenvalue problems. More...
std::unique_ptr< ShellMatrix< Number > >	shell_matrix_A
	The system shell matrix for standard eigenvalue problems. More...
std::unique_ptr< ShellMatrix< Number > >	shell_matrix_B
	A second system shell matrix for generalized eigenvalue problems. More...
SparseMatrix< Number > *	precond_matrix
	A preconditioning matrix. More...
std::unique_ptr< ShellMatrix< Number > >	shell_precond_matrix
	A preconditioning shell matrix. More...
std::unique_ptr< EigenSolver< Number > >	eigen_solver
	The EigenSolver, defining which interface, i.e solver package to use. More...
Parameters	parameters
	Parameters for the system. If a parameter is not provided, it should be retrieved from the EquationSystems. More...
bool	assemble_before_solve
	Flag which tells the system to whether or not to call the user assembly function during each call to solve(). More...
bool	use_fixed_solution
	A boolean to be set to true by systems using elem_fixed_solution, for optional use by e.g. More...
int	extra_quadrature_order
	A member int that can be employed to indicate increased or reduced quadrature order. More...
std::unique_ptr< NumericVector< Number > >	solution
	Data structure to hold solution values. More...
std::unique_ptr< NumericVector< Number > >	current_local_solution
	All the values I need to compute my contribution to the simulation at hand. More...
Real	time
	For time-dependent problems, this is the time t at the beginning of the current timestep. More...
bool	verbose_mode
	Public boolean to toggle verbose mode. More...

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

Protected Member Functions
virtual void	add_scaled_symm_Aq (unsigned int q_a, Number scalar)
	Add the scaled symmetrized affine matrix from the associated RBSystem to matrix_A. More...
virtual void	load_matrix_B ()
	Copy over the matrix to store in matrix_B, usually this is the mass or inner-product matrix, but needs to be implemented in subclass. More...
virtual void	compute_SCM_bounding_box ()
	Compute the SCM bounding box. More...
virtual void	evaluate_stability_constant ()
	Compute the stability constant for current_parameters by solving a generalized eigenvalue problem over the truth space. More...
virtual void	enrich_C_J (unsigned int new_C_J_index)
	Enrich C_J by adding the element of SCM_training_samples that has the largest gap between alpha_LB and alpha_LB. More...
virtual std::pair< unsigned int, Real >	compute_SCM_bounds_on_training_set ()
	Compute upper and lower bounds for each SCM training point. More...
Number	B_inner_product (const NumericVector< Number > &v, const NumericVector< Number > &w) const
	Compute the inner product between two vectors using the system's matrix_B. More...
Number	Aq_inner_product (unsigned int q, const NumericVector< Number > &v, const NumericVector< Number > &w)
	Compute the inner product between two vectors using matrix Aq. More...
virtual Real	SCM_greedy_error_indicator (Real LB, Real UB)
	Helper function which provides an error indicator to be used in the SCM greedy. More...
virtual void	init_data ()
	Initializes the member data fields associated with the system, so that, e.g., assemble() may be used. More...
RBParameters	get_params_from_training_set (unsigned int global_index)
	Return the RBParameters in index global_index of the global training set. More...
void	set_params_from_training_set (unsigned int global_index)
	Set parameters to the RBParameters stored in index global_index of the global training set. More...
virtual void	set_params_from_training_set_and_broadcast (unsigned int global_index)
	Load the specified training parameter and then broadcast to all processors. More...
virtual void	add_matrices () override
	Adds the necessary matrices and shell matrices. More...
virtual void	init_matrices () override
	Initializes the matrices associated with the system. More...
void	set_n_converged (unsigned int nconv)
	Set the _n_converged_eigenpairs member, useful for subclasses of EigenSystem. More...
void	set_n_iterations (unsigned int its)
	Set the _n_iterations member, useful for subclasses of EigenSystem. More...
void	solve_helper (SparseMatrix< Number > *const A, SparseMatrix< Number > *const B, SparseMatrix< Number > *const P)
void	project_vector (NumericVector< Number > &, int is_adjoint=-1) const
	Projects the vector defined on the old mesh onto the new mesh. More...
void	project_vector (const NumericVector< Number > &, NumericVector< Number > &, int is_adjoint=-1) const
	Projects the vector defined on the old mesh onto the new mesh. More...
bool	can_add_matrices () const
void	solve_for_unconstrained_dofs (NumericVector< Number > &, int is_adjoint=-1) const
void	increment_constructor_count (const std::string &name) noexcept
	Increments the construction counter. More...
void	increment_constructor_count (const std::string &name) noexcept
	Increments the construction counter. More...
void	increment_destructor_count (const std::string &name) noexcept
	Increments the destruction counter. More...
void	increment_destructor_count (const std::string &name) noexcept
	Increments the destruction counter. More...

Static Protected Member Functions
static void	get_global_max_error_pair (const Parallel::Communicator &communicator, std::pair< numeric_index_type, Real > &error_pair)
	Static function to return the error pair (index,error) that is corresponds to the largest error on all processors. More...

Protected Attributes
Real	SCM_training_tolerance
	Tolerance which controls when to terminate the SCM Greedy. More...
std::string	RB_system_name
	The name of the associated RB system. More...
bool	quiet_mode
	Flag to indicate whether we print out extra information during the Offline stage. More...
bool	serial_training_set
	This boolean flag indicates whether or not the training set should be the same on all processors. More...
bool	_normalize_solution_snapshots
	Set this boolean to true if we want to normalize solution snapshots used in training to have norm of 1. More...
std::unique_ptr< NumericVector< Number > >	inner_product_storage_vector
	We keep an extra temporary vector that is useful for performing inner products (avoids unnecessary memory allocation/deallocation). More...
const Parallel::Communicator &	_communicator

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

Private Attributes
RBSCMEvaluation *	rb_scm_eval
	The current RBSCMEvaluation object we are using to perform the Evaluation stage of the SCM. More...

Detailed Description

This class is part of the rbOOmit framework.

RBSCMConstruction implements the the Successive Constraint Method (SCM) for computing rigorous lower bounds for stability constants.

Author

David J. Knezevic

Date

2009

Definition at line 53 of file rb_scm_construction.h.

Member Typedef Documentation

const_matrices_iterator

typedef std::map<std::string, std::unique_ptr<SparseMatrix<Number> >, std::less<> >::const_iterator libMesh::System::const_matrices_iterator

inherited

Definition at line 784 of file system.h.

const_vectors_iterator

typedef std::map<std::string, std::unique_ptr<NumericVector<Number> >, std::less<> >::const_iterator libMesh::System::const_vectors_iterator

inherited

Definition at line 758 of file system.h.

Counts [1/2]

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

protectedinherited

Data structure to log the information.

The log is identified by the class name.

Definition at line 119 of file reference_counter.h.

Counts [2/2]

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

protectedinherited

Data structure to log the information.

The log is identified by the class name.

Definition at line 119 of file reference_counter.h.

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 541 of file system.h.

matrices_iterator

typedef std::map<std::string, std::unique_ptr<SparseMatrix<Number> >, std::less<> >::iterator libMesh::System::matrices_iterator

inherited

Matrix iterator typedefs.

Definition at line 783 of file system.h.

Parent

typedef RBConstructionBase<CondensedEigenSystem> libMesh::RBSCMConstruction::Parent

The type of the parent.

Definition at line 84 of file rb_scm_construction.h.

sys_type

typedef RBSCMConstruction libMesh::RBSCMConstruction::sys_type

The type of system.

Definition at line 79 of file rb_scm_construction.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 537 of file system.h.

vectors_iterator

typedef std::map<std::string, std::unique_ptr<NumericVector<Number> >, std::less<> >::iterator libMesh::System::vectors_iterator

inherited

Vector iterator typedefs.

Definition at line 757 of file system.h.

Constructor & Destructor Documentation

RBSCMConstruction() [1/3]

libMesh::RBSCMConstruction::RBSCMConstruction	(	EquationSystems &	es,
		const std::string &	name_in,
		const unsigned int	number_in
	)

Constructor.

Optionally initializes required data structures.

Definition at line 47 of file rb_scm_construction.C.

References libMesh::System::assemble_before_solve, libMesh::GHEP, and libMesh::EigenSystem::set_eigenproblem_type().

  : Parent(es, name_in, number_in),
    SCM_training_tolerance(0.5),
    RB_system_name(""),
    rb_scm_eval(nullptr)
{

  // set assemble_before_solve flag to false
  // so that we control matrix assembly.
  assemble_before_solve = false;

  // We symmetrize all operators hence use symmetric solvers
  set_eigenproblem_type(GHEP);

}

RBSCMConstruction() [2/3]

libMesh::RBSCMConstruction::RBSCMConstruction ( RBSCMConstruction &&  )

default

Special functions.

• This class has the same restrictions/defaults as its base class.
• Destructor is defaulted out-of-line

RBSCMConstruction() [3/3]

libMesh::RBSCMConstruction::RBSCMConstruction ( const RBSCMConstruction &  )

delete

~RBSCMConstruction()

libMesh::RBSCMConstruction::~RBSCMConstruction ( )

virtualdefault

Member Function Documentation

activate()

void libMesh::System::activate ( )

inlineinherited

Activates the system.

Only active systems are solved.

Definition at line 2398 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 2390 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 1297 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 1233 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_matrices()

void libMesh::CondensedEigenSystem::add_matrices ( )

overrideprotectedvirtualinherited

Adds the necessary matrices and shell matrices.

Reimplemented from libMesh::EigenSystem.

Definition at line 155 of file condensed_eigen_system.C.

References libMesh::CondensedEigenSystem::_condensed_matrix_A, libMesh::CondensedEigenSystem::_condensed_matrix_B, libMesh::CondensedEigenSystem::_condensed_precond_matrix, libMesh::EigenSystem::add_matrices(), libMesh::SparseMatrix< T >::build(), libMesh::ParallelObject::comm(), libMesh::CondensedEigenSystem::set_raw_pointers(), libMesh::EigenSystem::use_shell_matrices(), and libMesh::EigenSystem::use_shell_precond_matrix().

{
  Parent::add_matrices();

  if (!this->use_shell_matrices())
  {
    if (!_condensed_matrix_A)
      _condensed_matrix_A = SparseMatrix<Number>::build(this->comm());
    if (!_condensed_matrix_B)
      _condensed_matrix_B = SparseMatrix<Number>::build(this->comm());

    // When not using shell matrices we use A for P as well so we don't need to add P
  }
  // we *are* using shell matrices but we might not be using a shell matrix for P
  else if (!this->use_shell_precond_matrix())
  {
    if (!_condensed_precond_matrix)
      _condensed_precond_matrix = SparseMatrix<Number>::build(this->comm());
  }

#ifdef LIBMESH_ENABLE_DEPRECATED
  set_raw_pointers();
#endif
}

add_matrix() [1/3]

SparseMatrix< Number > & libMesh::System::add_matrix ( std::string_view  mat_name, ParallelType  type = PARALLEL, MatrixBuildType  mat_build_type = MatrixBuildType::AUTOMATIC  )

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 main/system matrix, then all the additional matrices, if existent, have to be initialized by the user, too.

This non-template method will add a derived matrix type corresponding to the solver package. If the user wishes to specify the matrix type to add, use the templated add_matrix method instead

Parameters

mat_name	A name for the matrix
type	The serial/parallel/ghosted type of the matrix
mat_build_type	The matrix type to build

Definition at line 1010 of file system.C.

References libMesh::System::_matrices, libMesh::System::_matrix_types, libMesh::SparseMatrix< T >::build(), libMesh::ParallelObject::comm(), libMesh::default_solver_package(), libMesh::DIAGONAL, libMesh::System::get_dof_map(), libMesh::System::get_mesh(), libMesh::DofMap::get_static_condensation(), libMesh::System::has_static_condensation(), libMesh::if(), libMesh::System::late_matrix_init(), and libMesh::libmesh_assert().

Referenced by libMesh::ImplicitSystem::add_matrices(), libMesh::EigenSystem::add_matrices(), alternative_fe_assembly(), libMesh::ClawSystem::assemble_boundary_condition_matrices(), libMesh::ImplicitSystem::create_static_condensation_system_matrix(), form_matrixA(), libMesh::EigenTimeSolver::init(), main(), and libMesh::NewmarkSystem::NewmarkSystem().

{
  parallel_object_only();

  libmesh_assert(this->comm().verify(std::string(mat_name)));
  libmesh_assert(this->comm().verify(int(type)));
  libmesh_assert(this->comm().verify(int(mat_build_type)));

  // Return the matrix if it is already there.
  if (auto it = this->_matrices.find(mat_name);
      it != this->_matrices.end())
    return *it->second;

  // Otherwise build the matrix to return.
  std::unique_ptr<SparseMatrix<Number>> matrix;
  if (this->has_static_condensation())
    {
      if (mat_build_type == MatrixBuildType::DIAGONAL)
        libmesh_error_msg(
            "We do not currently support static condensation of the diagonal matrix type");
      matrix = std::make_unique<StaticCondensation>(this->get_mesh(),
                                                    *this,
                                                    this->get_dof_map(),
                                                    this->get_dof_map().get_static_condensation());
    }
  else
    matrix = SparseMatrix<Number>::build(this->comm(), libMesh::default_solver_package());
  auto & mat = *matrix;

  _matrices.emplace(mat_name, std::move(matrix));

  _matrix_types.emplace(mat_name, type);

  // Initialize it first if we've already initialized the others.
  this->late_matrix_init(mat, type);

  return mat;
}

add_matrix() [2/3]

template<template< typename > class MatrixType>

SparseMatrix< Number > & libMesh::System::add_matrix ( std::string_view  mat_name, ParallelType  type = PARALLEL  )

inlineinherited

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 main/system matrix, then all the additional matrices, if existent, have to be initialized by the user, too.

This method will create add a derived matrix of type MatrixType<Number>. One can use the non-templated add_matrix method to add a matrix corresponding to the default solver package

Parameters

mat_name	A name for the matrix
type	The serial/parallel/ghosted type of the matrix

Definition at line 2707 of file system.h.

References libMesh::System::_matrices, libMesh::System::_matrix_types, and libMesh::System::late_matrix_init().

{
  // Return the matrix if it is already there.
  auto it = this->_matrices.find(mat_name);
  if (it != this->_matrices.end())
    return *it->second;

  // Otherwise build the matrix to return.
  auto pr = _matrices.emplace(mat_name, std::make_unique<MatrixType<Number>>(this->comm()));
  _matrix_types.emplace(mat_name, type);

  SparseMatrix<Number> & mat = *(pr.first->second);

  // Initialize it first if we've already initialized the others.
  this->late_matrix_init(mat, type);

  return mat;
}

add_matrix() [3/3]

SparseMatrix< Number > & libMesh::System::add_matrix ( std::string_view  mat_name, std::unique_ptr< SparseMatrix< Number >>  matrix, ParallelType  type = PARALLEL  )

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 main/system matrix, then all the additional matrices, if existent, have to be initialized by the user, too.

Parameters

mat_name	A name for the matrix
matrix	The matrix we are handing over the System for ownership
type	The serial/parallel/ghosted type of the matrix

Definition at line 1053 of file system.C.

References libMesh::System::_matrices, libMesh::System::_matrix_types, libMesh::ParallelObject::comm(), libMesh::System::late_matrix_init(), and libMesh::libmesh_assert().

{
  parallel_object_only();

  libmesh_assert(this->comm().verify(std::string(mat_name)));
  libmesh_assert(this->comm().verify(int(type)));

  auto [it, inserted] = _matrices.emplace(mat_name, std::move(matrix));
  libmesh_error_msg_if(!inserted,
                       "Tried to add '" << mat_name << "' but the matrix already exists");

  _matrix_types.emplace(mat_name, type);

  SparseMatrix<Number> & mat = *(it->second);

  // Initialize it first if we've already initialized the others.
  this->late_matrix_init(mat, type);

  return mat;
}

add_scaled_symm_Aq()

void libMesh::RBSCMConstruction::add_scaled_symm_Aq ( unsigned int  q_a, Number  scalar  )

protectedvirtual

Add the scaled symmetrized affine matrix from the associated RBSystem to matrix_A.

Definition at line 204 of file rb_scm_construction.C.

References libMesh::RBConstruction::add_scaled_Aq(), libMesh::System::get_equation_systems(), libMesh::EigenSystem::get_matrix_A(), libMesh::EquationSystems::get_system(), and RB_system_name.

Referenced by Aq_inner_product(), compute_SCM_bounding_box(), and evaluate_stability_constant().

{
  LOG_SCOPE("add_scaled_symm_Aq()", "RBSCMConstruction");
  // Load the operators from the RBConstruction
  EquationSystems & es = this->get_equation_systems();
  RBConstruction & rb_system = es.get_system<RBConstruction>(RB_system_name);
  rb_system.add_scaled_Aq(scalar, q_a, &get_matrix_A(), true);
}

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 1327 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 1182 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 ( std::string_view  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.

If active_subdomains is either nullptr (the default) or points to an empty set, then it will be assumed that var has no subdomain restrictions

Returns

The index number for the new variable.

Definition at line 1357 of file system.C.

References libMesh::System::_variable_groups, libMesh::System::_variable_numbers, libMesh::System::_variables, libMesh::Variable::active_subdomains(), libMesh::System::add_variables(), libMesh::ParallelObject::comm(), libMesh::System::identify_variable_groups(), libMesh::Variable::implicitly_active(), libMesh::System::is_initialized(), libMesh::libmesh_assert(), libMesh::make_range(), libMesh::System::n_variable_groups(), libMesh::System::n_vars(), libMesh::System::variable(), libMesh::System::variable_name(), and libMesh::System::variable_type().

Referenced by libMesh::DifferentiableSystem::add_second_order_dot_vars(), libMesh::System::add_variable(), assemble_and_solve(), OverlappingTestBase::init(), SolidSystem::init_data(), CurlCurlSystem::init_data(), SimpleEIMConstruction::init_data(), libMesh::VariationalSmootherSystem::init_data(), libMesh::AdvectionSystem::init_data(), HeatSystem::init_data(), SimpleRBConstruction::init_data(), NonManifoldCouplingTestBase::init_es(), main(), libMesh::ErrorVector::plot_error(), libMesh::System::read_header(), RationalMapTest< elem_type >::setUp(), SlitMeshRefinedSystemTest::setUp(), FETestBase< order, family, elem_type, 1 >::setUp(), WriteVecAndScalar::setupTests(), SystemsTest::simpleSetup(), MultiEvaluablePredTest::test(), ConstraintOperatorTest::test1DCoarseningNewNodes(), ConstraintOperatorTest::test1DCoarseningOperator(), MeshfunctionDFEM::test_mesh_function_dfem(), MeshfunctionDFEM::test_mesh_function_dfem_grad(), MeshFunctionTest::test_p_level(), MeshFunctionTest::test_subdomain_id_sets(), SystemsTest::testAssemblyWithDgFemContext(), DofMapTest::testBadElemFECombo(), EquationSystemsTest::testBadVarNames(), SystemsTest::testBlockRestrictedVarNDofs(), SystemsTest::testBoundaryProjectCube(), DofMapTest::testConstraintLoopDetection(), MeshInputTest::testCopyElementSolutionImpl(), MeshInputTest::testCopyElementVectorImpl(), MeshInputTest::testCopyNodalSolutionImpl(), ConstraintOperatorTest::testCoreform(), DefaultCouplingTest::testCoupling(), PointNeighborCouplingTest::testCoupling(), SystemsTest::testDofCouplingWithVarGroups(), DofMapTest::testDofOwner(), MeshInputTest::testDynaReadPatch(), MeshInputTest::testExodusWriteElementDataFromDiscontinuousNodalData(), MeshAssignTest::testMeshMoveAssign(), PeriodicBCTest::testPeriodicBC(), EquationSystemsTest::testPostInitAddElem(), EquationSystemsTest::testPostInitAddRealSystem(), SystemsTest::testProjectCubeWithMeshFunction(), MeshInputTest::testProjectionRegression(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), SystemsTest::testProjectMatrix3D(), InfFERadialTest::testRefinement(), EquationSystemsTest::testRefineThenReinitPreserveFlags(), EquationSystemsTest::testReinitWithNodeElem(), EquationSystemsTest::testRepartitionThenReinit(), EquationSystemsTest::testSelectivePRefine(), SystemsTest::testSetSystemParameterOverEquationSystem(), BoundaryInfoTest::testShellFaceConstraints(), MeshInputTest::testSingleElementImpl(), WriteVecAndScalar::testWriteExodus(), and WriteVecAndScalar::testWriteNemesis().

{
  parallel_object_only();  // Not strictly needed, but the only safe way to keep in sync

  libmesh_assert(this->comm().verify(std::string(var)));
  libmesh_assert(this->comm().verify(type));
  libmesh_assert(this->comm().verify((active_subdomains == nullptr)));

  if (active_subdomains)
    libmesh_assert(this->comm().verify(active_subdomains->size()));

  // Make sure the variable isn't there already
  // or if it is, that it's the type we want
  for (auto v : make_range(this->n_vars()))
    if (this->variable_name(v) == var)
      {
        if (this->variable_type(v) == type)
          {
            // Check whether the existing variable's active subdomains also matches
            // the incoming variable's active subdomains. If they don't match, then
            // either it is an error by the user or the user is trying to change the
            // subdomain restriction after the variable has already been added, which
            // is not supported.
            const Variable & existing_var = this->variable(v);

            // Check whether active_subdomains is not provided/empty and the existing_var is implicitly_active()
            bool check1 = (!active_subdomains || active_subdomains->empty()) && existing_var.implicitly_active();

            // Check if the provided active_subdomains is equal to the existing_var's active_subdomains
            bool check2 = (active_subdomains && (*active_subdomains == existing_var.active_subdomains()));

            // If either of these checks passed, then we already have this variable
            if (check1 || check2)
              return _variables[v].number();
          }

        libmesh_error_msg("ERROR: incompatible variable " << var << " has already been added for this system!");
      }

  libmesh_assert(!this->is_initialized());

  if (this->n_variable_groups())
    {
      // 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();

      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 || (active_subdomains && active_subdomains->empty())))
        should_be_in_vg = false;

      // they aren't restricted, we are?
      if (!their_active_subdomains && (active_subdomains && !active_subdomains->empty()))
        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 int curr_n_vars = this->n_vars();

          std::string varstr(var);

          _variable_numbers[varstr] = curr_n_vars;
          vg.append (std::move(varstr));
          _variables.push_back(vg(vg.n_variables()-1));

          return curr_n_vars;
        }
    }

  // otherwise, fall back to adding a single variable group
  return this->add_variables (std::vector<std::string>(1, std::string(var)),
                              type,
                              active_subdomains);
}

add_variable() [2/2]

unsigned int libMesh::System::add_variable ( std::string_view  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. If active_subdomains is either nullptr (the default) or points to an empty set, then it will be assumed that var has no subdomain restrictions

Definition at line 1459 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.

If active_subdomains is either nullptr (the default) or points to an empty set, then it will be assumed that var has no subdomain restrictions

Returns

The index number for the new variable.

Definition at line 1471 of file system.C.

References libMesh::System::_variable_groups, libMesh::System::_variable_numbers, libMesh::System::_variables, libMesh::ParallelObject::comm(), libMesh::System::identify_variable_groups(), libMesh::System::is_initialized(), libMesh::libmesh_assert(), libMesh::make_range(), libMesh::System::n_components(), libMesh::System::n_variable_groups(), libMesh::System::n_vars(), libMesh::System::variable_name(), and libMesh::System::variable_type().

Referenced by libMesh::System::add_variable(), libMesh::System::add_variables(), and SystemsTest::test100KVariables().

{
  parallel_object_only();  // Not strictly needed, but the only safe way to keep in sync

  libmesh_assert(!this->is_initialized());

  libmesh_assert(this->comm().verify(vars.size()));
  libmesh_assert(this->comm().verify(type));
  libmesh_assert(this->comm().verify((active_subdomains == nullptr)));

  if (active_subdomains)
    libmesh_assert(this->comm().verify(active_subdomains->size()));

  // Make sure the variable isn't there already
  // or if it is, that it's the type we want
  for (auto ovar : vars)
    {
      libmesh_assert(this->comm().verify(ovar));

      for (auto v : make_range(this->n_vars()))
        if (this->variable_name(v) == ovar)
          {
            if (this->variable_type(v) == type)
              return _variables[v].number();

            libmesh_error_msg("ERROR: incompatible variable " << ovar << " has already been added for this system!");
          }
    }

  if (this->n_variable_groups())
    {
      // 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();

      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 || (active_subdomains && active_subdomains->empty())))
        should_be_in_vg = false;

      // they aren't restricted, we are?
      if (!their_active_subdomains && (active_subdomains && !active_subdomains->empty()))
        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;

      // If after all that none of the conditions were violated,
      // append the variables to the vg and we're done
      if (should_be_in_vg)
        {
          unsigned int curr_n_vars = this->n_vars();

          for (auto ovar : vars)
            {
              curr_n_vars = this->n_vars();

              vg.append (ovar);

              _variables.push_back(vg(vg.n_variables()-1));
              _variable_numbers[ovar] = curr_n_vars;
            }
          return curr_n_vars;
        }
    }

  const unsigned int curr_n_vars = this->n_vars();

  const unsigned int next_first_component = this->n_components();

  // We weren't able to add to an existing variable group, so
  // add a new 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 : make_range(vars.size()))
    {
      _variables.push_back (vg(v));
      _variable_numbers[vars[v]] = 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. If active_subdomains is either nullptr (the default) or points to an empty set, then it will be assumed that var has no subdomain restrictions

Definition at line 1590 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 ( std::string_view  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

If the vector already exists, the existing vector is returned. after any upgrade to the projections or type has been made. We only handle upgrades (projections false->true, or type PARALLEL->GHOSTED) in this fashion, not downgrades, on the theory that if two codes have differing needs we want to support the union of those needs, not the intersection. Downgrades can only be accomplished manually, via set_vector_preservation() or by setting a vector type() and re-initializing.

Definition at line 768 of file system.C.

References libMesh::System::_dof_map, libMesh::System::_is_initialized, libMesh::System::_vector_is_adjoint, libMesh::System::_vector_projections, libMesh::System::_vectors, libMesh::NumericVector< T >::build(), libMesh::NumericVector< T >::close(), libMesh::NumericVector< T >::closed(), libMesh::ParallelObject::comm(), libMesh::default_solver_package(), libMesh::GHOSTED, libMesh::NumericVector< T >::initialized(), libMesh::libmesh_assert(), libMesh::System::n_dofs(), libMesh::System::n_local_dofs(), libMesh::ParallelObject::n_processors(), libMesh::PARALLEL, libMesh::SERIAL, libMesh::NumericVector< T >::set_type(), libMesh::NumericVector< T >::swap(), and libMesh::NumericVector< T >::type().

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(), alternative_fe_assembly(), libMesh::AdjointRefinementEstimator::estimate_error(), fe_assembly(), form_functionA(), form_functionB(), libMesh::SecondOrderUnsteadySolver::init(), libMesh::UnsteadySolver::init(), libMesh::UnsteadySolver::init_adjoints(), libMesh::TimeSolver::init_adjoints(), libMesh::OptimizationSystem::init_data(), libMesh::ContinuationSystem::init_data(), main(), libMesh::NewmarkSystem::NewmarkSystem(), libMesh::System::read_header(), libMesh::FrequencySystem::set_frequencies(), libMesh::FrequencySystem::set_frequencies_by_range(), libMesh::FrequencySystem::set_frequencies_by_steps(), SystemsTest::testAddVectorProjChange(), SystemsTest::testAddVectorTypeChange(), SystemsTest::testPostInitAddVector(), and SystemsTest::testPostInitAddVectorTypeChange().

{
  parallel_object_only();

  libmesh_assert(this->comm().verify(std::string(vec_name)));
  libmesh_assert(this->comm().verify(int(type)));
  libmesh_assert(this->comm().verify(projections));

  // Return the vector if it is already there.
  if (auto it = this->_vectors.find(vec_name);
      it != this->_vectors.end())
    {
      // If the projection setting has *upgraded*, change it.
      if (projections) // only do expensive lookup if needed
        libmesh_map_find(_vector_projections, vec_name) = projections;

      NumericVector<Number> & vec = *it->second;

      // If we're in serial, our vectors are effectively SERIAL, so
      // we'll ignore any type setting.  If we're in parallel, we
      // might have a type change to deal with.

      if (this->n_processors() > 1)
        {
          // If the type setting has changed in a way we can't
          // perceive as an upgrade or a downgrade, scream.
          libmesh_assert_equal_to(type == SERIAL,
                                  vec.type() == SERIAL);

          // If the type setting has *upgraded*, change it.
          if (type == GHOSTED && vec.type() == PARALLEL)
            {
              // A *really* late upgrade is expensive, but better not
              // to risk zeroing data.
              if (vec.initialized())
                {
                  if (!vec.closed())
                    vec.close();

                  // Ideally we'd move parallel coefficients and then
                  // add ghosted coefficients, but copy and swap is
                  // simpler.  If anyone actually ever uses this case
                  // for real we can look into optimizing it.
                  auto new_vec = NumericVector<Number>::build(this->comm());
#ifdef LIBMESH_ENABLE_GHOSTED
                  new_vec->init (this->n_dofs(), this->n_local_dofs(),
                                 _dof_map->get_send_list(), /*fast=*/false,
                                 GHOSTED);
#else
                  libmesh_error_msg("Cannot initialize ghosted vectors when they are not enabled.");
#endif

                  *new_vec = vec;
                  vec.swap(*new_vec);
                }
              else
                // The PARALLEL vec is not yet initialized, so we can
                // just "upgrade" it to GHOSTED.
                vec.set_type(type);
            }
        }

      // Any upgrades are done; we're happy here.
      return vec;
    }

  // Otherwise, build the vector. The following emplace() is
  // guaranteed to succeed because, if we made it here, we don't
  // already have a vector named "vec_name". We pass the user's
  // requested ParallelType directly to NumericVector::build() so
  // that, even if the vector is not initialized now, it will get the
  // right type when it is initialized later.
  auto pr =
    _vectors.emplace(vec_name,
                     NumericVector<Number>::build(this->comm(),
                                                  libMesh::default_solver_package(),
                                                  type));
  auto buf = pr.first->second.get();
  _vector_projections.emplace(vec_name, projections);

  // Vectors are primal by default
  _vector_is_adjoint.emplace(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(), /*fast=*/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 1265 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 1212 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::System::adjoint_qoi_parameter_sensitivity ( const QoISet &  qoi_indices, const ParameterVector &  parameters, SensitivityData &  sensitivities  )

inlinevirtualinherited

Solves for parameter sensitivities using the adjoint method.

This method is only implemented in some derived classes.

Reimplemented in libMesh::ImplicitSystem.

Definition at line 2663 of file system.h.

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

{
  libmesh_not_implemented();
}

adjoint_solve()

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

inlinevirtualinherited

Solves the adjoint system, for the specified qoi indices, or for every qoi if qoi_indices is nullptr.

Must be overridden in derived systems.

Returns

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

This method is only implemented in some derived classes.

Reimplemented in libMesh::ImplicitSystem, and libMesh::DifferentiableSystem.

Definition at line 2647 of file system.h.

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), and libMesh::AdjointResidualErrorEstimator::estimate_error().

{
  libmesh_not_implemented();
}

Aq_inner_product()

Number libMesh::RBSCMConstruction::Aq_inner_product ( unsigned int  q, const NumericVector< Number > &  v, const NumericVector< Number > &  w  )

protected

Compute the inner product between two vectors using matrix Aq.

Definition at line 405 of file rb_scm_construction.C.

References add_scaled_symm_Aq(), libMesh::NumericVector< T >::dot(), get_rb_theta_expansion(), libMesh::RBConstructionBase< CondensedEigenSystem >::inner_product_storage_vector, libMesh::EigenSystem::matrix_A, libMesh::SparseMatrix< T >::vector_mult(), and libMesh::SparseMatrix< T >::zero().

Referenced by evaluate_stability_constant().

{
  libmesh_error_msg_if(q >= get_rb_theta_expansion().get_n_A_terms(),
                       "Error: We must have q < Q_a in Aq_inner_product.");

  matrix_A->zero();
  add_scaled_symm_Aq(q, 1.);
  matrix_A->vector_mult(*inner_product_storage_vector, w);

  return v.dot(*inner_product_storage_vector);
}

assemble()

void libMesh::System::assemble ( )

virtualinherited

Prepares matrix and _dof_map for matrix assembly.

Does not actually assemble anything. For matrix assembly, use the assemble() in derived classes. Should be overridden in derived classes.

Reimplemented in libMesh::LinearImplicitSystem, libMesh::DifferentiableSystem, libMesh::ImplicitSystem, libMesh::FrequencySystem, and libMesh::NewmarkSystem.

Definition at line 566 of file system.C.

References libMesh::System::user_assembly().

Referenced by libMesh::ImplicitSystem::assemble(), libMesh::EigenSystem::solve(), libMesh::CondensedEigenSystem::solve(), and libMesh::ExplicitSystem::solve().

{
  // Log how long the user's assembly code takes
  LOG_SCOPE("assemble()", "System");

  // Call the user-specified assembly function
  this->user_assembly();
}

assemble_qoi()

void libMesh::System::assemble_qoi ( const QoISet &  qoi_indices = QoISet() )

virtualinherited

Calls user qoi function.

Can be overridden in derived classes.

Reimplemented in libMesh::FEMSystem, and libMesh::ExplicitSystem.

Definition at line 577 of file system.C.

References libMesh::System::user_QOI().

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

{
  // Log how long the user's assembly code takes
  LOG_SCOPE("assemble_qoi()", "System");

  // Call the user-specified quantity of interest function
  this->user_QOI(qoi_indices);
}

assemble_qoi_derivative()

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

virtualinherited

Calls user qoi derivative function.

Can be overridden in derived classes.

Reimplemented in libMesh::FEMSystem, and libMesh::ExplicitSystem.

Definition at line 588 of file system.C.

References libMesh::System::user_QOI_derivative().

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

{
  // Log how long the user's assembly code takes
  LOG_SCOPE("assemble_qoi_derivative()", "System");

  // Call the user-specified quantity of interest function
  this->user_QOI_derivative(qoi_indices, include_liftfunc,
                            apply_constraints);
}

assemble_residual_derivatives()

void libMesh::System::assemble_residual_derivatives ( const ParameterVector &  parameters )

inlinevirtualinherited

Calls residual parameter derivative function.

Library subclasses use finite differences by default.

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

This method is only implemented in some derived classes.

Reimplemented in libMesh::ImplicitSystem.

Definition at line 2612 of file system.h.

{
  libmesh_not_implemented();
}

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 2161 of file system.C.

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

Referenced by assemble_and_solve(), main(), ConstraintOperatorTest::test1DCoarseningNewNodes(), ConstraintOperatorTest::test1DCoarseningOperator(), SystemsTest::testAssemblyWithDgFemContext(), ConstraintOperatorTest::testCoreform(), SystemsTest::testDofCouplingWithVarGroups(), and PeriodicBCTest::testPeriodicBC().

{
  libmesh_assert(fptr);

  if (_assemble_system_object != nullptr)
    {
      libmesh_warning("WARNING:  Cannot specify both assembly function and object!");

      _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 2178 of file system.C.

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

Referenced by main().

{
  if (_assemble_system_function != nullptr)
    {
      libmesh_warning("WARNING:  Cannot specify both assembly object and function!");

      _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 2192 of file system.C.

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

{
  libmesh_assert(fptr);

  if (_constrain_system_object != nullptr)
    {
      libmesh_warning("WARNING:  Cannot specify both constraint function and object!");

      _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 2209 of file system.C.

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

Referenced by libMesh::VariationalMeshSmoother::smooth(), and DofMapTest::testConstraintLoopDetection().

{
  if (_constrain_system_function != nullptr)
    {
      libmesh_warning("WARNING:  Cannot specify both constraint object and function!");

      _constrain_system_function = nullptr;
    }

  _constrain_system_object = &constrain;
}

attach_deflation_space()

virtual void libMesh::RBSCMConstruction::attach_deflation_space ( )

inlinevirtual

Attach the deflation space defined by the specified vector, can be useful in solving constrained eigenvalue problems.

This function is called at the start of perform_SCM_greedy and by default is does nothing. Override in subclass to attach a specific vector.

Definition at line 162 of file rb_scm_construction.h.

Referenced by perform_SCM_greedy().

{}

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 2130 of file system.C.

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

Referenced by main().

{
  libmesh_assert(fptr);

  if (_init_system_object != nullptr)
    {
      libmesh_warning("WARNING:  Cannot specify both initialization function and object!");

      _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 2147 of file system.C.

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

{
  if (_init_system_function != nullptr)
    {
      libmesh_warning("WARNING:  Cannot specify both initialization object and function!");

      _init_system_function = nullptr;
    }

  _init_system_object = &init_in;
}

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 2266 of file system.C.

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

{
  libmesh_assert(fptr);

  if (_qoi_evaluate_derivative_object != nullptr)
    {
      libmesh_warning("WARNING:  Cannot specify both QOI derivative function and object!");

      _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 2283 of file system.C.

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

{
  if (_qoi_evaluate_derivative_function != nullptr)
    {
      libmesh_warning("WARNING:  Cannot specify both QOI derivative object and function!");

      _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 2234 of file system.C.

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

{
  libmesh_assert(fptr);

  if (_qoi_evaluate_object != nullptr)
    {
      libmesh_warning("WARNING:  Cannot specify both QOI function and object!");

      _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 2252 of file system.C.

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

{
  if (_qoi_evaluate_function != nullptr)
    {
      libmesh_warning("WARNING:  Cannot specify both QOI object and function!");

      _qoi_evaluate_function = nullptr;
    }

  _qoi_evaluate_object = &qoi_in;
}

B_inner_product()

Number libMesh::RBSCMConstruction::B_inner_product ( const NumericVector< Number > &  v, const NumericVector< Number > &  w  ) const

protected

Compute the inner product between two vectors using the system's matrix_B.

Definition at line 397 of file rb_scm_construction.C.

References libMesh::NumericVector< T >::dot(), libMesh::RBConstructionBase< CondensedEigenSystem >::inner_product_storage_vector, libMesh::EigenSystem::matrix_B, and libMesh::SparseMatrix< T >::vector_mult().

Referenced by evaluate_stability_constant().

{
  matrix_B->vector_mult(*inner_product_storage_vector, w);

  return v.dot(*inner_product_storage_vector);
}

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.

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

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.

Definition at line 1253 of file system_projection.C.

Referenced by SystemsTest::testBoundaryProjectCube().

{
  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.

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

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.

Definition at line 1236 of file system_projection.C.

References fptr(), and gptr().

{
  WrappedFunction<Number> f(*this, fptr, &function_parameters);
  WrappedFunction<Gradient> g(*this, gptr, &function_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.

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

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.

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

Definition at line 1289 of file system_projection.C.

References libMesh::NumericVector< T >::close(), libMesh::libmesh_ignore(), 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);
#else
  libmesh_ignore(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.

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

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.

Definition at line 1271 of file system_projection.C.

References fptr(), and gptr().

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

broadcast_parameters()

void libMesh::RBConstructionBase< CondensedEigenSystem >::broadcast_parameters ( const unsigned int  proc_id )

inherited

Broadcasts parameters from processor proc_id to all processors.

This broadcasts the RBParameters object from .get_parameters(), and then sets it on all processors with .set_parameters().

Definition at line 720 of file rb_construction_base.C.

References libMesh::make_range(), libMesh::RBParameters::n_parameters(), libMesh::RBParameters::n_samples(), and libMesh::MeshTools::Subdivision::next.

{
  libmesh_assert_less (proc_id, this->n_processors());

  // create a copy of the current parameters
  RBParameters current_parameters = get_parameters();
  libmesh_error_msg_if(current_parameters.n_samples()!=1,
      "Only single-sample RBParameter objects can be broadcast.");

  // Serialize the current_parameters to current_parameters_vector in order to broadcast.
  // We handle multiple samples and vector values.
  // However, the vector values are assumed to remain the same size across samples.
  const std::size_t nparams = current_parameters.n_parameters();
  const std::size_t nsamples = current_parameters.n_samples();

  // First we get the sizes of all the parameter value vectors.
  std::vector<std::size_t> param_value_sizes;
  param_value_sizes.reserve(nparams);
  for (const auto & pr : current_parameters)
    param_value_sizes.push_back(pr.second[0].size());

  // Broadcast the sizes vector and reserve memory.
  this->comm().broadcast(param_value_sizes, proc_id);
  std::size_t buffsize = std::accumulate(param_value_sizes.cbegin(), param_value_sizes.cend(), 0ul);
  std::vector<Real> serialized_parameters;
  serialized_parameters.reserve(buffsize);

  // Then we serialize the parameters/sample/value vectors into a single vector.
  for (const auto & pr : current_parameters)
    {
      for (const auto sample_idx : make_range(nsamples))
        serialized_parameters.insert(serialized_parameters.end(),
                                     pr.second[sample_idx].cbegin(),
                                     pr.second[sample_idx].cend());
    }

  // Do the broadcasts.
  this->comm().broadcast(serialized_parameters, proc_id);

  // Deserialize into the copy of the RBParameters object.
  std::size_t param_idx = 0;
  auto val_idx = serialized_parameters.cbegin();
  for (const auto & pr : current_parameters)
    {
      const std::size_t param_value_size = param_value_sizes[param_idx];
      for (const auto sample_idx: make_range(nsamples))
        {
          auto end_val_idx = std::next(val_idx,param_value_size);
          RBParameter sample_val(val_idx, end_val_idx);
          current_parameters.set_value(pr.first, sample_idx, sample_val);
          val_idx = end_val_idx;
        }
      ++param_idx;
    }

  // Overwrite the parameters globally.
  set_parameters(current_parameters);
}

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 1724 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::TwostepTimeSolver::adjoint_solve(), libMesh::AdaptiveTimeSolver::calculate_norm(), libMesh::UnsteadySolver::du(), main(), output_norms(), ConstraintOperatorTest::testCoreform(), and MeshInputTest::testProjectionRegression().

{
  //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 1746 of file system.C.

References libMesh::System::_dof_map, libMesh::System::_mesh, libMesh::FEGenericBase< OutputType >::build(), libMesh::NumericVector< T >::build(), libMesh::ParallelObject::comm(), libMesh::FEType::default_quadrature_rule(), dim, libMesh::DISCRETE_L1, libMesh::DISCRETE_L2, libMesh::DISCRETE_L_INF, libMesh::System::discrete_var_norm(), libMesh::DofMap::dof_indices(), libMesh::MeshBase::elem_dimensions(), libMesh::Utility::enum_to_string(), libMesh::FEInterface::field_type(), libMesh::System::get_dof_map(), libMesh::System::get_mesh(), libMesh::GHOSTED, libMesh::H1, libMesh::H1_SEMINORM, libMesh::H2, libMesh::H2_SEMINORM, libMesh::L1, libMesh::NumericVector< T >::l1_norm(), libMesh::L2, libMesh::NumericVector< T >::l2_norm(), libMesh::L_INF, libMesh::libmesh_assert(), libMesh::NumericVector< T >::linfty_norm(), libMesh::NumericVector< T >::local_size(), libMesh::NumericVector< T >::localize(), libMesh::make_range(), TIMPI::Communicator::max(), libMesh::System::n_vars(), libMesh::TensorTools::norm(), libMesh::TensorTools::norm_sq(), libMesh::Real, libMesh::NumericVector< T >::size(), TIMPI::Communicator::sum(), libMesh::TYPE_SCALAR, libMesh::TYPE_VECTOR, libMesh::DofMap::variable_type(), libMesh::W1_INF_SEMINORM, libMesh::W2_INF_SEMINORM, and libMesh::SystemNorm::weight().

{
  // 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, check_end = this->n_vars();
      for (; check_var != check_end; ++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 = " << Utility::enum_to_string(norm_type0));
        }

      for (auto var : make_range(this->n_vars()))
        {
          // 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(), v.local_size(), _dof_map->get_send_list(),
                true, GHOSTED);
  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 (auto var : make_range(this->n_vars()))
    {
      // 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, and for both scalar and vector
      // elements, even if we don't use them all
      std::vector<std::unique_ptr<FEBase>> fe_ptrs(4);
      std::vector<std::unique_ptr<FEVectorBase>> vec_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);

          const FEFieldType field_type = FEInterface::field_type(fe_type);
          if (field_type == TYPE_SCALAR)
            {
              fe_ptrs[dim] = FEBase::build(dim, fe_type);
              fe_ptrs[dim]->attach_quadrature_rule (q_rules[dim].get());
            }
          else
            {
              vec_fe_ptrs[dim] = FEVectorBase::build(dim, fe_type);
              vec_fe_ptrs[dim]->attach_quadrature_rule (q_rules[dim].get());
              libmesh_assert_equal_to(field_type, TYPE_VECTOR);
            }

        }

      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();

          // 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();

          if (skip_dimensions && skip_dimensions->find(dim) != skip_dimensions->end())
            continue;

          QBase * qrule = q_rules[dim].get();
          libmesh_assert(qrule);

          this->get_dof_map().dof_indices (elem, dof_indices, var);

          auto element_calculation = [&dof_indices, &elem,
               norm_type, norm_weight, norm_weight_sq, &qrule,
               &local_v, &v_norm](auto & fe) {
          typedef typename std::remove_reference<decltype(fe)>::type::OutputShape OutputShape;
          typedef typename TensorTools::MakeNumber<OutputShape>::type OutputNumberShape;
          typedef typename std::remove_reference<decltype(fe)>::type::OutputGradient OutputGradient;
          typedef typename TensorTools::MakeNumber<OutputGradient>::type OutputNumberGradient;

          const std::vector<Real> &                     JxW = fe.get_JxW();
          const std::vector<std::vector<OutputShape>> * 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<OutputGradient>> * 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
          typedef typename std::remove_reference<decltype(fe)>::type::OutputTensor OutputTensor;

          const std::vector<std::vector<OutputTensor>> *  d2phi = nullptr;
          if (norm_type == H2 ||
              norm_type == H2_SEMINORM ||
              norm_type == W2_INF_SEMINORM)
            d2phi = &(fe.get_d2phi());
#endif

          fe.reinit (elem);

          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)
                {
                  OutputNumberShape 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] * TensorTools::norm(u_h);
                }

              if (norm_type == L_INF)
                {
                  OutputNumberShape 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 * TensorTools::norm(u_h));
                }

              if (norm_type == H1 ||
                  norm_type == H2 ||
                  norm_type == L2)
                {
                  OutputNumberShape 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)
                {
                  OutputNumberGradient 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)
                {
                  OutputNumberGradient 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
              typedef typename TensorTools::MakeNumber<OutputTensor>::type OutputNumberTensor;

              if (norm_type == H2 ||
                  norm_type == H2_SEMINORM)
                {
                  OutputNumberTensor 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)
                {
                  OutputNumberTensor 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
            }
          };

          FEBase * scalar_fe = fe_ptrs[dim].get();
          FEVectorBase * vec_fe = vec_fe_ptrs[dim].get();

          if (scalar_fe)
            {
              libmesh_assert(!vec_fe);
              element_calculation(*scalar_fe);
            }

          if (vec_fe)
            {
              libmesh_assert(!scalar_fe);
              element_calculation(*vec_fe);
            }
        }
    }

  if (using_hilbert_norm)
    {
      this->comm().sum(v_norm);
      v_norm = std::sqrt(v_norm);
    }
  else
    {
      this->comm().max(v_norm);
    }

  return v_norm;
}

can_add_matrices()

bool libMesh::System::can_add_matrices ( ) const

inlineprotectedinherited

Returns

Whether or not matrices can still be added without expensive per-matrix initialization.

Definition at line 1975 of file system.h.

References libMesh::System::_matrices_initialized.

Referenced by libMesh::EigenSystem::set_eigenproblem_type().

{ return !_matrices_initialized; }

clear()

void libMesh::RBSCMConstruction::clear ( )

overridevirtual

Clear all the data structures associated with the system.

Reimplemented from libMesh::RBConstructionBase< CondensedEigenSystem >.

Definition at line 67 of file rb_scm_construction.C.

References libMesh::RBConstructionBase< CondensedEigenSystem >::clear().

{
  Parent::clear();
}

comm()

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

inlineinherited

Returns

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

Definition at line 97 of file parallel_object.h.

References libMesh::ParallelObject::_communicator.

Referenced by libMesh::__libmesh_petsc_diff_solver_jacobian(), libMesh::__libmesh_petsc_diff_solver_monitor(), libMesh::__libmesh_petsc_diff_solver_residual(), libMesh::__libmesh_tao_equality_constraints(), libMesh::__libmesh_tao_equality_constraints_jacobian(), libMesh::__libmesh_tao_gradient(), libMesh::__libmesh_tao_hessian(), libMesh::__libmesh_tao_inequality_constraints(), libMesh::__libmesh_tao_inequality_constraints_jacobian(), libMesh::__libmesh_tao_objective(), libMesh::MeshRefinement::_coarsen_elements(), libMesh::ExactSolution::_compute_error(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::Partitioner::_find_global_index_by_pid_map(), libMesh::BoundaryInfo::_find_id_maps(), libMesh::PetscLinearSolver< Number >::_petsc_shell_matrix_get_diagonal(), libMesh::SlepcEigenSolver< libMesh::Number >::_petsc_shell_matrix_get_diagonal(), libMesh::PetscLinearSolver< Number >::_petsc_shell_matrix_mult(), libMesh::SlepcEigenSolver< libMesh::Number >::_petsc_shell_matrix_mult(), libMesh::PetscLinearSolver< Number >::_petsc_shell_matrix_mult_add(), libMesh::MeshRefinement::_refine_elements(), libMesh::MeshRefinement::_smooth_flags(), libMesh::DofMap::add_constraints_to_send_list(), add_cube_convex_hull_to_mesh(), libMesh::PetscDMWrapper::add_dofs_helper(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::TransientRBConstruction::add_IC_to_RB_space(), libMesh::RBEIMEvaluation::add_interpolation_data(), libMesh::CondensedEigenSystem::add_matrices(), libMesh::EigenSystem::add_matrices(), libMesh::System::add_matrix(), libMesh::RBConstruction::add_scaled_matrix_and_vector(), libMesh::System::add_variable(), libMesh::System::add_variables(), libMesh::System::add_vector(), libMesh::MeshTools::Modification::all_tri(), libMesh::LaplaceMeshSmoother::allgather_graph(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::TransientRBConstruction::allocate_data_structures(), libMesh::RBConstruction::allocate_data_structures(), libMesh::TransientRBConstruction::assemble_affine_expansion(), libMesh::AdvectionSystem::assemble_claw_rhs(), libMesh::FEMSystem::assemble_qoi(), libMesh::Nemesis_IO::assert_symmetric_cmaps(), libMesh::MeshCommunication::assign_global_indices(), libMesh::Partitioner::assign_partitioning(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::Partitioner::build_graph(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::PetscDMWrapper::build_section(), libMesh::PetscDMWrapper::build_sf(), libMesh::MeshBase::cache_elem_data(), libMesh::System::calculate_norm(), libMesh::DofMap::check_dirichlet_bcid_consistency(), libMesh::RBConstruction::compute_Fq_representor_innerprods(), libMesh::RBConstruction::compute_max_error_bound(), libMesh::Nemesis_IO_Helper::compute_num_global_elem_blocks(), libMesh::Nemesis_IO_Helper::compute_num_global_nodesets(), libMesh::Nemesis_IO_Helper::compute_num_global_sidesets(), libMesh::RBConstruction::compute_output_dual_innerprods(), libMesh::RBConstruction::compute_residual_dual_norm_slow(), compute_SCM_bounds_on_training_set(), libMesh::DofMap::computed_sparsity_already(), libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), libMesh::ContinuationSystem::ContinuationSystem(), libMesh::MeshBase::copy_constraint_rows(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::CondensedEigenSystem::copy_super_to_sub(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::MeshTools::create_bounding_box(), libMesh::DofMap::create_dof_constraints(), libMesh::MeshTools::create_nodal_bounding_box(), libMesh::MeshRefinement::create_parent_error_vector(), libMesh::MeshTools::create_processor_bounding_box(), libMesh::MeshTools::create_subdomain_bounding_box(), libMesh::PetscMatrix< T >::create_submatrix_nosort(), create_wrapped_function(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::RBEIMEvaluation::distribute_bfs(), DMlibMeshFunction(), DMlibMeshJacobian(), DMlibMeshSetSystem_libMesh(), DMVariableBounds_libMesh(), libMesh::DTKSolutionTransfer::DTKSolutionTransfer(), libMesh::MeshRefinement::eliminate_unrefined_patches(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_interiors(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_nodes(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_sides(), libMesh::TransientRBConstruction::enrich_RB_space(), libMesh::EpetraVector< T >::EpetraVector(), AssembleOptimization::equality_constraints(), libMesh::PatchRecoveryErrorEstimator::estimate_error(), libMesh::WeightedPatchRecoveryErrorEstimator::estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::MeshRefinement::flag_elements_by_elem_fraction(), libMesh::MeshRefinement::flag_elements_by_error_fraction(), libMesh::MeshRefinement::flag_elements_by_error_tolerance(), libMesh::MeshRefinement::flag_elements_by_mean_stddev(), libMesh::MeshRefinement::flag_elements_by_nelem_target(), libMesh::RBEIMEvaluation::gather_bfs(), libMesh::DofMap::gather_constraints(), libMesh::MeshfreeInterpolation::gather_remote_data(), libMesh::CondensedEigenSystem::get_eigenpair(), libMesh::RBEIMEvaluation::get_eim_basis_function_node_value(), libMesh::RBEIMEvaluation::get_eim_basis_function_side_value(), libMesh::RBEIMEvaluation::get_eim_basis_function_value(), libMesh::MeshBase::get_info(), libMesh::System::get_info(), libMesh::DofMap::get_info(), libMesh::RBEIMEvaluation::get_interior_basis_functions_as_vecs(), libMesh::ImplicitSystem::get_linear_solver(), libMesh::RBEIMConstruction::get_max_abs_value(), libMesh::RBEIMConstruction::get_node_max_abs_value(), libMesh::RBEIMEvaluation::get_parametrized_function_node_value(), libMesh::RBEIMEvaluation::get_parametrized_function_side_value(), libMesh::RBEIMEvaluation::get_parametrized_function_value(), libMesh::RBEIMConstruction::get_random_point(), AssembleOptimization::inequality_constraints(), AssembleOptimization::inequality_constraints_jacobian(), libMesh::LocationMap< T >::init(), libMesh::TimeSolver::init(), libMesh::StaticCondensation::init(), libMesh::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_and_attach_petscdm(), libMesh::AdvectionSystem::init_data(), libMesh::ClawSystem::init_data(), libMesh::PetscDMWrapper::init_petscdm(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::OptimizationSystem::initialize_equality_constraints_storage(), libMesh::OptimizationSystem::initialize_inequality_constraints_storage(), libMesh::RBEIMConstruction::initialize_parametrized_functions_in_training_set(), libMesh::RBEIMConstruction::inner_product(), integrate_function(), libMesh::MeshTools::libmesh_assert_consistent_distributed(), libMesh::MeshTools::libmesh_assert_consistent_distributed_nodes(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_equal_connectivity(), libMesh::MeshTools::libmesh_assert_equal_points(), libMesh::MeshTools::libmesh_assert_parallel_consistent_new_node_procids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_topology_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_valid_boundary_ids(), libMesh::MeshTools::libmesh_assert_valid_constraint_rows(), libMesh::MeshTools::libmesh_assert_valid_dof_ids(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_flags(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_object_ids(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_p_levels(), libMesh::MeshTools::libmesh_assert_valid_refinement_flags(), libMesh::MeshTools::libmesh_assert_valid_unique_ids(), libMesh::libmesh_petsc_linesearch_shellfunc(), libMesh::libmesh_petsc_preconditioner_apply(), libMesh::libmesh_petsc_recalculate_monitor(), libMesh::libmesh_petsc_snes_fd_residual(), libMesh::libmesh_petsc_snes_jacobian(), libMesh::libmesh_petsc_snes_mffd_interface(), libMesh::libmesh_petsc_snes_mffd_residual(), libMesh::libmesh_petsc_snes_postcheck(), libMesh::libmesh_petsc_snes_precheck(), libMesh::libmesh_petsc_snes_residual(), libMesh::libmesh_petsc_snes_residual_helper(), libMesh::MeshRefinement::limit_level_mismatch_at_edge(), libMesh::MeshRefinement::limit_level_mismatch_at_node(), libMesh::MeshRefinement::limit_overrefined_boundary(), libMesh::MeshRefinement::limit_underrefined_boundary(), libMesh::LinearImplicitSystem::LinearImplicitSystem(), main(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshCommunication::make_elems_parallel_consistent(), libMesh::MeshRefinement::make_flags_parallel_consistent(), libMesh::MeshCommunication::make_new_node_proc_ids_parallel_consistent(), libMesh::MeshCommunication::make_new_nodes_parallel_consistent(), libMesh::MeshCommunication::make_node_bcids_parallel_consistent(), libMesh::MeshCommunication::make_node_ids_parallel_consistent(), libMesh::MeshCommunication::make_node_proc_ids_parallel_consistent(), libMesh::MeshCommunication::make_node_unique_ids_parallel_consistent(), libMesh::MeshCommunication::make_nodes_parallel_consistent(), libMesh::MeshCommunication::make_p_levels_parallel_consistent(), libMesh::MeshRefinement::make_refinement_compatible(), libMesh::TransientRBConstruction::mass_matrix_scaled_matvec(), libMesh::FEMSystem::mesh_position_set(), libMesh::TriangulatorInterface::MeshedHole::MeshedHole(), LinearElasticityWithContact::move_mesh(), libMesh::DistributedMesh::n_active_elem(), libMesh::MeshTools::n_active_levels(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::MeshTools::n_connected_components(), libMesh::DofMap::n_constrained_dofs(), libMesh::MeshBase::n_constraint_rows(), libMesh::DofMap::n_dofs(), libMesh::DofMap::n_dofs_per_processor(), libMesh::BoundaryInfo::n_edge_conds(), libMesh::CondensedEigenSystem::n_global_non_condensed_dofs(), libMesh::MeshTools::n_levels(), MixedOrderTest::n_neighbor_links(), libMesh::BoundaryInfo::n_nodeset_conds(), libMesh::SparsityPattern::Build::n_nonzeros(), libMesh::MeshTools::n_p_levels(), libMesh::BoundaryInfo::n_shellface_conds(), libMesh::RBEIMEvaluation::node_distribute_bfs(), libMesh::RBEIMEvaluation::node_gather_bfs(), libMesh::RBEIMConstruction::node_inner_product(), libMesh::MeshBase::operator==(), libMesh::DistributedMesh::parallel_max_elem_id(), libMesh::DistributedMesh::parallel_max_node_id(), libMesh::ReplicatedMesh::parallel_max_unique_id(), libMesh::DistributedMesh::parallel_max_unique_id(), libMesh::DistributedMesh::parallel_n_elem(), libMesh::DistributedMesh::parallel_n_nodes(), libMesh::SparsityPattern::Build::parallel_sync(), libMesh::BoundaryInfo::parallel_sync_node_ids(), libMesh::BoundaryInfo::parallel_sync_side_ids(), libMesh::MeshTools::paranoid_n_levels(), libMesh::Partitioner::partition(), libMesh::Partitioner::partition_unpartitioned_elements(), libMesh::petsc_auto_fieldsplit(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::MeshBase::prepare_for_use(), libMesh::MeshBase::print_constraint_rows(), libMesh::DofMap::print_dof_constraints(), libMesh::DofMap::process_mesh_constraint_rows(), libMesh::Partitioner::processor_pairs_to_interface_nodes(), libMesh::InterMeshProjection::project_system_vectors(), FEMParameters::read(), libMesh::Nemesis_IO::read(), libMesh::XdrIO::read(), libMesh::EquationSystems::read(), libMesh::ExodusII_IO::read_header(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::System::read_header(), libMesh::RBEIMEvaluation::read_in_interior_basis_functions(), libMesh::RBEIMEvaluation::read_in_node_basis_functions(), libMesh::RBEIMEvaluation::read_in_side_basis_functions(), libMesh::RBEvaluation::read_in_vectors_from_multiple_files(), libMesh::System::read_legacy_data(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), libMesh::System::read_SCALAR_dofs(), libMesh::XdrIO::read_serialized_bc_names(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::System::read_serialized_vector(), libMesh::Nemesis_IO_Helper::read_var_names_impl(), libMesh::MeshBase::recalculate_n_partitions(), libMesh::MeshRefinement::refine_and_coarsen_elements(), libMesh::SimplexRefiner::refine_via_edges(), libMesh::StaticCondensationDofMap::reinit(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::DistributedMesh::renumber_nodes_and_elements(), LinearElasticityWithContact::residual_and_jacobian(), OverlappingAlgebraicGhostingTest::run_ghosting_test(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), scale_mesh_and_plot(), libMesh::DofMap::scatter_constraints(), libMesh::CheckpointIO::select_split_config(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::send_and_insert_dof_values(), libMesh::TransientRBConstruction::set_error_temporal_data(), libMesh::Partitioner::set_interface_node_processor_ids_BFS(), libMesh::Partitioner::set_interface_node_processor_ids_linear(), libMesh::Partitioner::set_interface_node_processor_ids_petscpartitioner(), libMesh::Partitioner::set_node_processor_ids(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::Partitioner::set_parent_processor_ids(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::PetscDiffSolver::setup_petsc_data(), libMesh::RBEIMEvaluation::side_distribute_bfs(), libMesh::RBEIMEvaluation::side_gather_bfs(), libMesh::RBEIMConstruction::side_inner_product(), libMesh::Partitioner::single_partition(), libMesh::LaplaceMeshSmoother::smooth(), libMesh::VariationalMeshSmoother::smooth(), libMesh::ClawSystem::solve_conservation_law(), libMesh::split_mesh(), libMesh::RBEIMConstruction::store_eim_solutions_for_training_set(), libMesh::MeshBase::subdomain_ids(), libMesh::BoundaryInfo::sync(), ConstraintOperatorTest::test1DCoarseningNewNodes(), ConstraintOperatorTest::test1DCoarseningOperator(), libMesh::MeshRefinement::test_level_one(), MeshfunctionDFEM::test_mesh_function_dfem(), MeshfunctionDFEM::test_mesh_function_dfem_grad(), MeshFunctionTest::test_p_level(), libMesh::MeshRefinement::test_unflagged(), DofMapTest::testBadElemFECombo(), SystemsTest::testBlockRestrictedVarNDofs(), BoundaryInfoTest::testBoundaryOnChildrenErrors(), VolumeTest::testC0PolygonMethods(), VolumeTest::testC0PolyhedronMethods(), ConstraintOperatorTest::testCoreform(), ConnectedComponentsTest::testEdge(), MeshInputTest::testExodusIGASidesets(), MeshTriangulationTest::testFoundCenters(), PointLocatorTest::testLocator(), BoundaryInfoTest::testMesh(), PointLocatorTest::testPlanar(), MeshTriangulationTest::testPoly2TriRefinementBase(), SystemsTest::testProjectCubeWithMeshFunction(), BoundaryInfoTest::testRenumber(), CheckpointIOTest::testSplitter(), MeshInputTest::testTetgenIO(), MeshTriangulationTest::testTriangulatorInterp(), MeshTriangulationTest::testTriangulatorMeshedHoles(), MeshTriangulationTest::testTriangulatorRoundHole(), libMesh::MeshTools::total_weight(), libMesh::RBConstruction::train_reduced_basis_with_POD(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::MeshfreeSolutionTransfer::transfer(), libMesh::Poly2TriTriangulator::triangulate(), libMesh::TransientRBConstruction::truth_assembly(), libMesh::RBConstruction::truth_assembly(), libMesh::MeshRefinement::uniformly_coarsen(), update_current_local_solution(), libMesh::TransientRBConstruction::update_RB_initial_condition_all_N(), libMesh::TransientRBConstruction::update_RB_system_matrices(), libMesh::RBConstruction::update_RB_system_matrices(), libMesh::TransientRBConstruction::update_residual_terms(), libMesh::RBConstruction::update_residual_terms(), libMesh::MeshTools::volume(), libMesh::STLIO::write(), libMesh::NameBasedIO::write(), libMesh::XdrIO::write(), libMesh::VTKIO::write_nodal_data(), libMesh::RBEIMEvaluation::write_out_interior_basis_functions(), libMesh::RBEIMEvaluation::write_out_node_basis_functions(), libMesh::RBEIMEvaluation::write_out_side_basis_functions(), libMesh::RBEvaluation::write_out_vectors(), libMesh::TransientRBConstruction::write_riesz_representors_to_files(), libMesh::RBConstruction::write_riesz_representors_to_files(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), libMesh::XdrIO::write_serialized_nodesets(), libMesh::RBDataSerialization::RBEvaluationSerialization::write_to_file(), libMesh::RBDataSerialization::TransientRBEvaluationSerialization::write_to_file(), libMesh::RBDataSerialization::RBEIMEvaluationSerialization::write_to_file(), and libMesh::RBDataSerialization::RBSCMEvaluationSerialization::write_to_file().

  { return _communicator; }

compare()

bool libMesh::System::compare ( const System &  other_system, const Real  threshold, const bool  verbose  ) const

virtualinherited

Returns

true when the other system contains identical data, up to the given threshold. Outputs some diagnostic info when verbose is set.

Definition at line 618 of file system.C.

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

{
  // 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 & [vec_name, vec] : _vectors)
        {
          if (verbose)
            libMesh::out << "   comparing vector \""
                         << vec_name << "\" ...";

          // assume they have the same name
          const NumericVector<Number> & other_system_vector =
            other_system.get_vector(vec_name);

          ov_result.push_back(vec->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;
}

compute_SCM_bounding_box()

void libMesh::RBSCMConstruction::compute_SCM_bounding_box ( )

protectedvirtual

Compute the SCM bounding box.

Definition at line 287 of file rb_scm_construction.C.

References add_scaled_symm_Aq(), libMesh::RBSCMEvaluation::B_max, libMesh::RBSCMEvaluation::B_min, libMesh::EigenSystem::eigen_solver, libMesh::RBSCMEvaluation::get_B_max(), libMesh::RBSCMEvaluation::get_B_min(), libMesh::CondensedEigenSystem::get_eigenpair(), libMesh::RBThetaExpansion::get_n_A_terms(), libMesh::EigenSystem::get_n_converged(), get_rb_theta_expansion(), libMesh::LARGEST_REAL, libMesh::EigenSystem::matrix_A, libMesh::out, rb_scm_eval, libMesh::RBSCMEvaluation::set_B_max(), libMesh::RBSCMEvaluation::set_B_min(), set_eigensolver_properties(), libMesh::SMALLEST_REAL, libMesh::CondensedEigenSystem::solve(), libMesh::TOLERANCE, and libMesh::SparseMatrix< T >::zero().

Referenced by perform_SCM_greedy().

{
  LOG_SCOPE("compute_SCM_bounding_box()", "RBSCMConstruction");

  // Resize the bounding box vectors
  rb_scm_eval->B_min.resize(get_rb_theta_expansion().get_n_A_terms());
  rb_scm_eval->B_max.resize(get_rb_theta_expansion().get_n_A_terms());

  for (unsigned int q=0; q<get_rb_theta_expansion().get_n_A_terms(); q++)
    {
      matrix_A->zero();
      add_scaled_symm_Aq(q, 1.);

      // Compute B_min(q)
      eigen_solver->set_position_of_spectrum(SMALLEST_REAL);
      set_eigensolver_properties(q);

      solve();
      // TODO: Assert convergence for eigensolver

      unsigned int nconv = get_n_converged();
      if (nconv != 0)
        {
          std::pair<Real, Real> eval = get_eigenpair(0);

          // ensure that the eigenvalue is real
          libmesh_assert_less (eval.second, TOLERANCE);

          rb_scm_eval->set_B_min(q, eval.first);
          libMesh::out << std::endl << "B_min("<<q<<") = " << rb_scm_eval->get_B_min(q) << std::endl;
        }
      else
        libmesh_error_msg("Eigen solver for computing B_min did not converge");

      // Compute B_max(q)
      eigen_solver->set_position_of_spectrum(LARGEST_REAL);
      set_eigensolver_properties(q);

      solve();
      // TODO: Assert convergence for eigensolver

      nconv = get_n_converged();
      if (nconv != 0)
        {
          std::pair<Real, Real> eval = get_eigenpair(0);

          // ensure that the eigenvalue is real
          libmesh_assert_less (eval.second, TOLERANCE);

          rb_scm_eval->set_B_max(q,eval.first);
          libMesh::out << "B_max("<<q<<") = " << rb_scm_eval->get_B_max(q) << std::endl;
        }
      else
        libmesh_error_msg("Eigen solver for computing B_max did not converge");
    }
}

compute_SCM_bounds_on_training_set()

std::pair< unsigned int, Real > libMesh::RBSCMConstruction::compute_SCM_bounds_on_training_set ( )

protectedvirtual

Compute upper and lower bounds for each SCM training point.

Return a pair containing the maximum SCM error, and the index of the parameter in the training set at which the max error is achieved.

Definition at line 419 of file rb_scm_construction.C.

References libMesh::ParallelObject::comm(), libMesh::RBConstructionBase< CondensedEigenSystem >::get_first_local_training_index(), libMesh::RBConstructionBase< CondensedEigenSystem >::get_global_max_error_pair(), libMesh::RBConstructionBase< CondensedEigenSystem >::get_local_n_training_samples(), libMesh::RBParametrized::get_parameters(), libMesh::RBSCMEvaluation::get_SCM_LB(), libMesh::RBSCMEvaluation::get_SCM_UB(), rb_scm_eval, libMesh::Real, SCM_greedy_error_indicator(), libMesh::RBParametrized::set_parameters(), and libMesh::RBConstructionBase< CondensedEigenSystem >::set_params_from_training_set().

Referenced by perform_SCM_greedy().

{
  LOG_SCOPE("compute_SCM_bounds_on_training_set()", "RBSCMConstruction");

  // Now compute the maximum bound error over training_parameters
  unsigned int new_C_J_index = 0;
  Real max_SCM_error = 0.;

  numeric_index_type first_index = get_first_local_training_index();
  for (unsigned int i=0; i<get_local_n_training_samples(); i++)
    {
      set_params_from_training_set(first_index+i);
      rb_scm_eval->set_parameters( get_parameters() );
      Real LB = rb_scm_eval->get_SCM_LB();
      Real UB = rb_scm_eval->get_SCM_UB();

      Real error_i = SCM_greedy_error_indicator(LB, UB);

      if (error_i > max_SCM_error)
        {
          max_SCM_error = error_i;
          new_C_J_index = i;
        }
    }

  numeric_index_type global_index = first_index + new_C_J_index;
  std::pair<numeric_index_type,Real> error_pair(global_index, max_SCM_error);
  get_global_max_error_pair(this->comm(),error_pair);

  return error_pair;
}

copy_sub_to_super()

void libMesh::CondensedEigenSystem::copy_sub_to_super ( const NumericVector< Number > &  sub, NumericVector< Number > &  super  )

inherited

Copy a logically sub-vector into a super-vector.

The sub-vector local size should correspond to the size of our local_non_condensed_dofs_vector, e.g. the sub-vector should represent non-condensed degree of freedom. The super should contain both condensed and non-condensed dofs

Definition at line 299 of file condensed_eigen_system.C.

References libMesh::System::get_dof_map(), libMesh::NumericVector< T >::get_subvector(), libMesh::CondensedEigenSystem::local_non_condensed_dofs_vector, libMesh::NumericVector< T >::local_size(), libMesh::DofMap::n_local_constrained_dofs(), and libMesh::NumericVector< T >::restore_subvector().

Referenced by update_current_local_solution().

{
  libmesh_assert_equal_to(sub.local_size(), local_non_condensed_dofs_vector.size());
  libmesh_assert_equal_to(sub.local_size() + this->get_dof_map().n_local_constrained_dofs(),
                          super.local_size());
  auto super_sub_view = super.get_subvector(local_non_condensed_dofs_vector);
  *super_sub_view = sub;
  super.restore_subvector(std::move(super_sub_view), local_non_condensed_dofs_vector);
}

copy_super_to_sub() [1/2]

void libMesh::CondensedEigenSystem::copy_super_to_sub ( NumericVector< Number > &  super, NumericVector< Number > &  sub  )

inherited

Copy a logically super-vector into a sub-vector.

The super vector should represent all dofs, both condensed and non-condensed. The sub should contain only non-condensed dofs, e.g. its local size should match the size of our local_non_condensed_dofs_vector

Definition at line 311 of file condensed_eigen_system.C.

References libMesh::System::get_dof_map(), libMesh::NumericVector< T >::get_subvector(), libMesh::CondensedEigenSystem::local_non_condensed_dofs_vector, libMesh::NumericVector< T >::local_size(), libMesh::DofMap::n_local_constrained_dofs(), and libMesh::NumericVector< T >::restore_subvector().

{
  libmesh_assert_equal_to(sub.local_size(), local_non_condensed_dofs_vector.size());
  libmesh_assert_equal_to(sub.local_size() + this->get_dof_map().n_local_constrained_dofs(),
                          super.local_size());
  auto super_sub_view = super.get_subvector(local_non_condensed_dofs_vector);
  sub = *super_sub_view;
  super.restore_subvector(std::move(super_sub_view), local_non_condensed_dofs_vector);
}

copy_super_to_sub() [2/2]

void libMesh::CondensedEigenSystem::copy_super_to_sub ( const SparseMatrix< Number > &  super, SparseMatrix< Number > &  sub  )

inherited

Copy a logically super-matrix into a sub-matrix.

The super matrix should represent all dofs, both condensed and non-condensed. The sub should contain only non-condensed dofs, e.g. its local row ownership size should match the size of our local_non_condensed_dofs_vector

Definition at line 323 of file condensed_eigen_system.C.

References libMesh::SparseMatrix< T >::build(), libMesh::ParallelObject::comm(), libMesh::SparseMatrix< T >::create_submatrix(), libMesh::System::get_dof_map(), libMesh::SparseMatrix< T >::local_m(), libMesh::CondensedEigenSystem::local_non_condensed_dofs_vector, and libMesh::DofMap::n_local_constrained_dofs().

{
  parallel_object_only();

  libmesh_assert_equal_to(sub.local_m(), local_non_condensed_dofs_vector.size());
  libmesh_assert_equal_to(sub.local_m() + this->get_dof_map().n_local_constrained_dofs(),
                          super.local_m());
  auto super_sub_view = SparseMatrix<Number>::build(super.comm());
  super.create_submatrix(
      *super_sub_view, local_non_condensed_dofs_vector, local_non_condensed_dofs_vector);
  sub = *super_sub_view;
}

create_static_condensation()

void libMesh::System::create_static_condensation ( )

virtualinherited

Request that static condensation be performed for this system.

Reimplemented in libMesh::ImplicitSystem, libMesh::NonlinearImplicitSystem, and libMesh::LinearImplicitSystem.

Definition at line 2866 of file system.C.

References libMesh::DofMap::create_static_condensation(), libMesh::System::get_dof_map(), and libMesh::System::get_mesh().

Referenced by libMesh::ImplicitSystem::create_static_condensation(), and libMesh::System::System().

{
  this->get_dof_map().create_static_condensation(this->get_mesh(), *this);
}

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 165 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(), compute_stresses(), LinearElasticityWithContact::compute_stresses(), LinearElasticity::compute_stresses(), LargeDeformationElasticity::compute_stresses(), libMesh::ExactErrorEstimator::estimate_error(), main(), libMesh::WeightedPatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::PatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::HPCoarsenTest::select_refinement(), SolidSystem::side_time_derivative(), 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);
}

deactivate()

void libMesh::System::deactivate ( )

inlineinherited

Deactivates the system.

Only active systems are solved.

Definition at line 2406 of file system.h.

References libMesh::System::_active.

{
  _active = false;
}

disable_cache()

void libMesh::System::disable_cache ( )

inlinevirtualinherited

Avoids use of any cached data that might affect any solve result.

Should be overridden in derived systems.

Reimplemented in libMesh::ImplicitSystem.

Definition at line 2618 of file system.h.

References libMesh::System::assemble_before_solve.

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

{ assemble_before_solve = true; }

disable_print_counter_info() [1/2]

void libMesh::ReferenceCounter::disable_print_counter_info ( )

staticinherited

Definition at line 100 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

{
  _enable_print_counter = false;
  return;
}

disable_print_counter_info() [2/2]

void libMesh::ReferenceCounter::disable_print_counter_info ( )

staticinherited

Definition at line 100 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

{
  _enable_print_counter = false;
  return;
}

dont_create_submatrices_in_solve()

void libMesh::CondensedEigenSystem::dont_create_submatrices_in_solve ( )

inlineinherited

Instructs not to create the condensed submatrices from the global matrices right before the solve.

This API should be used when assembly occurs during callbacks during the solve, e.g. for a nonlinear eigen problem, solved with a Newton-based solver to determine the fundamental mode, in which function and matrix evalations are liable to change with every nonlinear iteration. Moreover, calling create_submatrix wipes away callbacks associated with the condensed matrix

Definition at line 169 of file condensed_eigen_system.h.

References libMesh::CondensedEigenSystem::_create_submatrices_in_solve.

{ _create_submatrices_in_solve = false; }

enable_print_counter_info() [1/2]

void libMesh::ReferenceCounter::enable_print_counter_info ( )

staticinherited

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

Definition at line 94 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

{
  _enable_print_counter = true;
  return;
}

enable_print_counter_info() [2/2]

void libMesh::ReferenceCounter::enable_print_counter_info ( )

staticinherited

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

Definition at line 94 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

{
  _enable_print_counter = true;
  return;
}

enrich_C_J()

void libMesh::RBSCMConstruction::enrich_C_J ( unsigned int  new_C_J_index )

protectedvirtual

Enrich C_J by adding the element of SCM_training_samples that has the largest gap between alpha_LB and alpha_LB.

Definition at line 451 of file rb_scm_construction.C.

References libMesh::RBSCMEvaluation::C_J, libMesh::RBSCMEvaluation::C_J_stability_vector, libMesh::RBParametrized::get_parameters(), get_rb_theta_expansion(), libMesh::RBParameters::get_value(), libMesh::out, rb_scm_eval, libMesh::RBSCMEvaluation::SCM_UB_vectors, and libMesh::RBConstructionBase< CondensedEigenSystem >::set_params_from_training_set_and_broadcast().

Referenced by perform_SCM_greedy().

{
  LOG_SCOPE("enrich_C_J()", "RBSCMConstruction");

  set_params_from_training_set_and_broadcast(new_C_J_index);

  rb_scm_eval->C_J.push_back(get_parameters());

  libMesh::out << std::endl << "SCM: Added mu = (";

  bool first = true;
  for (const auto & pr : get_parameters())
    {
      if (!first)
        libMesh::out << ",";
      const std::string & param_name = pr.first;
      RBParameters C_J_params = rb_scm_eval->C_J[rb_scm_eval->C_J.size()-1];
      libMesh::out << C_J_params.get_value(param_name);
      first = false;
    }
  libMesh::out << ")" << std::endl;

  // Finally, resize C_J_stability_vector and SCM_UB_vectors
  rb_scm_eval->C_J_stability_vector.push_back(0.);

  std::vector<Real> zero_vector(get_rb_theta_expansion().get_n_A_terms());
  rb_scm_eval->SCM_UB_vectors.push_back(zero_vector);
}

evaluate_stability_constant()

void libMesh::RBSCMConstruction::evaluate_stability_constant ( )

protectedvirtual

Compute the stability constant for current_parameters by solving a generalized eigenvalue problem over the truth space.

Definition at line 344 of file rb_scm_construction.C.

References add_scaled_symm_Aq(), Aq_inner_product(), B_inner_product(), libMesh::RBSCMEvaluation::C_J, libMesh::EigenSystem::eigen_solver, libMesh::RBSCMEvaluation::get_C_J_stability_constraint(), libMesh::CondensedEigenSystem::get_eigenpair(), libMesh::RBThetaExpansion::get_n_A_terms(), libMesh::EigenSystem::get_n_converged(), libMesh::RBParametrized::get_parameters(), get_rb_theta_expansion(), libMesh::libmesh_real(), libMesh::EigenSystem::matrix_A, libMesh::out, rb_scm_eval, libMesh::Real, libMesh::RBSCMEvaluation::set_C_J_stability_constraint(), set_eigensolver_properties(), libMesh::RBSCMEvaluation::set_SCM_UB_vector(), libMesh::SMALLEST_REAL, libMesh::System::solution, libMesh::CondensedEigenSystem::solve(), libMesh::TOLERANCE, and libMesh::SparseMatrix< T >::zero().

Referenced by perform_SCM_greedy().

{
  LOG_SCOPE("evaluate_stability_constant()", "RBSCMConstruction");

  // Get current index of C_J
  const unsigned int j = cast_int<unsigned int>(rb_scm_eval->C_J.size()-1);

  eigen_solver->set_position_of_spectrum(SMALLEST_REAL);

  // We assume B is set in system assembly
  // For coercive problems, B is set to the inner product matrix
  // For non-coercive time-dependent problems, B is set to the mass matrix

  // Set matrix A corresponding to mu_star
  matrix_A->zero();
  for (unsigned int q=0; q<get_rb_theta_expansion().get_n_A_terms(); q++)
    {
      add_scaled_symm_Aq(q, get_rb_theta_expansion().eval_A_theta(q,get_parameters()));
    }

  set_eigensolver_properties(-1);
  solve();
  // TODO: Assert convergence for eigensolver

  unsigned int nconv = get_n_converged();
  if (nconv != 0)
    {
      std::pair<Real, Real> eval = get_eigenpair(0);

      // ensure that the eigenvalue is real
      libmesh_assert_less (eval.second, TOLERANCE);

      // Store the coercivity constant corresponding to mu_star
      rb_scm_eval->set_C_J_stability_constraint(j,eval.first);
      libMesh::out << std::endl << "Stability constant for C_J("<<j<<") = "
                   << rb_scm_eval->get_C_J_stability_constraint(j) << std::endl << std::endl;

      // Compute and store the vector y = (y_1, \ldots, y_Q) for the
      // eigenvector currently stored in eigen_system.solution.
      // We use this later to compute the SCM upper bounds.
      Real norm_B2 = libmesh_real( B_inner_product(*solution, *solution) );

      for (unsigned int q=0; q<get_rb_theta_expansion().get_n_A_terms(); q++)
        {
          Real norm_Aq2 = libmesh_real( Aq_inner_product(q, *solution, *solution) );

          rb_scm_eval->set_SCM_UB_vector(j,q,norm_Aq2/norm_B2);
        }
    }
  else
    libmesh_error_msg("Error: Eigensolver did not converge in evaluate_stability_constant");
}

forward_qoi_parameter_sensitivity()

void libMesh::System::forward_qoi_parameter_sensitivity ( const QoISet &  qoi_indices, const ParameterVector &  parameters, SensitivityData &  sensitivities  )

inlinevirtualinherited

Solves for parameter sensitivities using the forward method.

This method is only implemented in some derived classes.

Reimplemented in libMesh::ImplicitSystem.

Definition at line 2672 of file system.h.

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

{
  libmesh_not_implemented();
}

generalized()

bool libMesh::EigenSystem::generalized ( ) const

inherited

Returns

true if the underlying problem is generalized , false otherwise.

Definition at line 325 of file eigen_system.C.

References libMesh::EigenSystem::_eigen_problem_type, libMesh::GHEP, libMesh::GHIEP, and libMesh::GNHEP.

Referenced by libMesh::EigenSystem::add_matrices(), libMesh::EigenSystem::get_matrix_B(), libMesh::EigenSystem::get_shell_matrix_B(), libMesh::CondensedEigenSystem::solve(), and libMesh::EigenSystem::solve_helper().

{
  return _eigen_problem_type == GNHEP ||
         _eigen_problem_type == GHEP ||
         _eigen_problem_type == GHIEP;
}

generate_training_parameters_deterministic()

std::pair< std::size_t, std::size_t > libMesh::RBConstructionBase< CondensedEigenSystem >::generate_training_parameters_deterministic ( const Parallel::Communicator &  communicator, const std::map< std::string, bool > &  log_param_scale, std::map< std::string, std::vector< RBParameter >> &  local_training_parameters_in, const unsigned int  n_global_training_samples_in, const RBParameters &  min_parameters, const RBParameters &  max_parameters, const bool  serial_training_set = false  )

staticinherited

Static helper function for generating a deterministic set of parameters.

Only works with 1 or 2 parameters (as defined by the lengths of min/max parameters vectors), otherwise throws an error. The parameter n_global_training_samples_in is the total number of parameters to generate, and they will be split across all the processors (unless serial_training_set=true) in the local_training_parameters_in map.

Returns

a pair of {first_local_index,last_local_index}

Definition at line 572 of file rb_construction_base.C.

References communicator, libMesh::RBParameters::get_value(), libMesh::RBParameters::n_parameters(), libMesh::Utility::pow(), and libMesh::Real.

{
  libmesh_assert_equal_to ( min_parameters.n_parameters(), max_parameters.n_parameters() );
  const unsigned int num_params = min_parameters.n_parameters();

  if (num_params == 0)
    return {0,0};

  if (num_params > 3)
    libmesh_not_implemented_msg("ERROR: Deterministic training sample generation "
                                "not implemented for more than three parameters.");

  // TODO - we don't support vector-data here yet. This would only apply in the case where
  //        min or max are vector-valued, and all the generated points need to stay within those ranges.
  //        But typically we expect that if we're calling this function, we only have 1 min and 1 max,
  //        so the generated values are single-valued as well. The .get_value() calls will throw an error
  //        if this is not the case.

  // Reinitialize training_parameters_in (but don't remove existing keys!)
  const auto &[n_local_training_samples, first_local_index] =
      calculate_n_local_samples_and_index(communicator, n_global_training_samples_in,
                                         serial_training_set);
  const auto last_local_index = first_local_index + n_local_training_samples;
  for (const auto & pr : min_parameters)
    local_training_parameters_in[pr.first] = std::vector<RBParameter>(n_local_training_samples);

  // n_training_samples_per_param has 3 entries, but entries after "num_params"
  // are unused so we just set their value to 1. We need to set it to 1 (rather
  // than 0) so that we don't skip the inner part of the triply-nested loop over
  // n_training_samples_per_param below.
  std::vector<unsigned int> n_training_samples_per_param(3);
  for (unsigned int param=0; param<3; param++)
    {
      if (param < num_params)
        {
          n_training_samples_per_param[param] =
            static_cast<unsigned int>( std::round(std::pow(static_cast<Real>(n_global_training_samples_in), 1./num_params)) );
        }
      else
        {
          n_training_samples_per_param[param] = 1;
        }
    }

  {
    // The current implementation assumes that we have the same number of
    // samples in each parameter, so we check that n_training_samples_in
    // is consistent with this assumption.
    unsigned int total_samples_check = 1;
    for (unsigned int n_samples : n_training_samples_per_param)
      {
        total_samples_check *= n_samples;
      }

    libmesh_error_msg_if(total_samples_check != n_global_training_samples_in,
                         "Error: Number of training samples = "
                         << n_global_training_samples_in
                         << " does not enable a uniform grid of samples with "
                         << num_params << " parameters. Try "
                         << total_samples_check << " samples instead?");
  }

  // First we make a list of training samples associated with each parameter,
  // then we take a tensor product to obtain the final set of training samples.
  std::vector<std::vector<Real>> training_samples_per_param(num_params);
  {
    unsigned int i = 0;
    for (const auto & pr : min_parameters)
      {
        const std::string & param_name = pr.first;
        const bool use_log_scaling = libmesh_map_find(log_param_scale, param_name);
        Real min_param = min_parameters.get_value(param_name);
        Real max_param = max_parameters.get_value(param_name);

        training_samples_per_param[i].resize(n_training_samples_per_param[i]);

        for (unsigned int j=0; j<n_training_samples_per_param[i]; j++)
          {
            // Generate log10 scaled training parameters
            if (use_log_scaling)
              {
                Real epsilon = 1.e-6; // Prevent rounding errors triggering asserts
                Real log_min   = std::log10(min_param + epsilon);
                Real log_range = std::log10( (max_param-epsilon) / (min_param+epsilon) );
                Real step_size = log_range /
                  std::max((unsigned int)1,(n_training_samples_per_param[i]-1));

                if (j<(n_training_samples_per_param[i]-1))
                  {
                    training_samples_per_param[i][j] = std::pow(10., log_min + j*step_size );
                  }
                else
                  {
                    // due to rounding error, the last parameter can be slightly
                    // bigger than max_parameters, hence snap back to the max
                    training_samples_per_param[i][j] = max_param;
                  }
              }
            else
              {
                // Generate linearly scaled training parameters
                Real step_size = (max_param - min_param) /
                  std::max((unsigned int)1,(n_training_samples_per_param[i]-1));
                training_samples_per_param[i][j] = j*step_size + min_param;
              }

          }
        i++;
      }
  }

  // Now load into training_samples_in
  {
    std::vector<unsigned int> indices(3);
    unsigned int index_count = 0;
    for (indices[0]=0; indices[0]<n_training_samples_per_param[0]; indices[0]++)
      {
        for (indices[1]=0; indices[1]<n_training_samples_per_param[1]; indices[1]++)
          {
            for (indices[2]=0; indices[2]<n_training_samples_per_param[2]; indices[2]++)
              {
                unsigned int param_count = 0;
                for (const auto & pr : min_parameters)
                  {
                    std::vector<RBParameter> & training_vector =
                      libmesh_map_find(local_training_parameters_in, pr.first);
                    if (first_local_index <= index_count && index_count < last_local_index)
                      training_vector[index_count - first_local_index] =
                        {training_samples_per_param[param_count][indices[param_count]]};

                    param_count++;
                  }
                index_count++;
              }
          }
      }
  }
  return {first_local_index, first_local_index+n_local_training_samples};
}

generate_training_parameters_random()

std::pair< std::size_t, std::size_t > libMesh::RBConstructionBase< CondensedEigenSystem >::generate_training_parameters_random ( const Parallel::Communicator &  communicator, const std::map< std::string, bool > &  log_param_scale, std::map< std::string, std::vector< RBParameter >> &  local_training_parameters_in, const unsigned int  n_global_training_samples_in, const RBParameters &  min_parameters, const RBParameters &  max_parameters, const int  training_parameters_random_seed = -1, const bool  serial_training_set = false  )

staticinherited

Static helper function for generating a randomized set of parameters.

The parameter n_global_training_samples_in is the total number of parameters to generate, and they will be split across all the processors (unless serial_training_set=true) in the local_training_parameters_in map.

Returns

a pair of {first_local_index,last_local_index}

Definition at line 472 of file rb_construction_base.C.

References communicator, libMesh::RBParameters::get_value(), libMesh::make_range(), libMesh::RBParameters::n_parameters(), libMesh::Utility::pow(), and libMesh::Real.

{
  const unsigned int num_params = min_parameters.n_parameters();
  libmesh_error_msg_if(num_params!=max_parameters.n_parameters(),
    "Number of parameters must be identical for min/max.");

  // Clear training_parameters_in
  local_training_parameters_in.clear();

  if (num_params == 0)
    return {0,0};

  if (training_parameters_random_seed < 0)
    {
      if (!serial_training_set)
        {
          // seed the random number generator with the system time
          // and the processor ID so that the seed is different
          // on different processors
          std::srand( static_cast<unsigned>( std::time(0)*(1+communicator.rank()) ));
        }
      else
        {
          // seed the random number generator with the system time
          // only so that the seed is the same on all processors
          //
          // Note that we broadcast the time on processor 0 to make
          // sure all processors agree.
          unsigned int current_time = static_cast<unsigned>( std::time(0) );
          communicator.broadcast(current_time, 0);
          std::srand(current_time);
        }
    }
  else
    {
      if (!serial_training_set)
        {
          // seed the random number generator with the provided value
          // and the processor ID so that the seed is different
          // on different processors
          std::srand( static_cast<unsigned>( training_parameters_random_seed*(1+communicator.rank()) ));
        }
      else
        {
          // seed the random number generator with the provided value
          // so that the seed is the same on all processors
          std::srand( static_cast<unsigned>( training_parameters_random_seed ));
        }
    }

  // TODO - we don't support vector-data here yet. This would only apply in the case where
  //        min or max are vector-valued, and all the generated points need to stay within those ranges.
  //        But typically we expect that if we're calling this function, we only have 1 min and 1 max,
  //        so the generated values are single-valued as well. The .get_value() calls will throw an error
  //        if this is not the case.

  // initialize training_parameters_in
  const auto & [n_local_training_samples, first_local_index] =
      calculate_n_local_samples_and_index(communicator, n_global_training_samples_in,
                                          serial_training_set);
  for (const auto & pr : min_parameters)
    local_training_parameters_in[pr.first] = std::vector<RBParameter>(n_local_training_samples);

  // finally, set the values
  for (auto & [param_name, sample_vector] : local_training_parameters_in)
    {
      for (auto i : make_range(n_local_training_samples))
        {
          Real random_number = static_cast<Real>(std::rand()) / RAND_MAX; // in range [0,1]

          // Generate log10 scaled training parameters
          if (libmesh_map_find(log_param_scale, param_name))
            {
              Real log_min   = std::log10(min_parameters.get_value(param_name));
              Real log_range = std::log10(max_parameters.get_value(param_name) / min_parameters.get_value(param_name));

              sample_vector[i] = {std::pow(Real(10.), log_min + random_number*log_range )};
            }
          // Generate linearly scaled training parameters
          else
            {
              sample_vector[i] = {
                  random_number * (max_parameters.get_value(param_name) -
                                   min_parameters.get_value(param_name)) +
                  min_parameters.get_value(param_name)};
            }
        }
    }
  return {first_local_index, first_local_index+n_local_training_samples};
}

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 1307 of file system.C.

References libMesh::System::get_vector().

Referenced by libMesh::ImplicitSystem::adjoint_solve(), libMesh::FEMSystem::assemble_qoi_derivative(), 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 1317 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 1245 of file system.C.

References libMesh::System::get_vector().

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::AdaptiveTimeSolver::adjoint_advance_timestep(), libMesh::UnsteadySolver::adjoint_advance_timestep(), libMesh::TwostepTimeSolver::adjoint_solve(), libMesh::ImplicitSystem::adjoint_solve(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::AdjointResidualErrorEstimator::estimate_error(), HeatSystem::init_context(), libMesh::Euler2Solver::integrate_adjoint_refinement_error_estimate(), libMesh::EulerSolver::integrate_adjoint_refinement_error_estimate(), main(), libMesh::ImplicitSystem::qoi_parameter_hessian(), libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product(), libMesh::FileSolutionHistory::retrieve(), 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 1255 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 1617 of file system.C.

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

Referenced by MeshfunctionDFEM::test_mesh_function_dfem(), MeshfunctionDFEM::test_mesh_function_dfem_grad(), and SystemsTest::testProjectCubeWithMeshFunction().

{
  all_variable_numbers.resize(n_vars());

  unsigned int count = 0;
  for (auto vn : _variable_numbers)
    all_variable_numbers[count++] = vn.second;
}

get_closest_value()

Real libMesh::RBParametrized::get_closest_value ( Real  value, const std::vector< Real > &  list_of_values  )

staticinherited

Returns

The closest entry to value from list_of_values.

Definition at line 446 of file rb_parametrized.C.

References distance(), libMesh::Real, and value.

Referenced by libMesh::RBParametrized::is_value_in_list().

{
  libmesh_error_msg_if(list_of_values.empty(), "Error: list_of_values is empty.");

  Real min_distance = std::numeric_limits<Real>::max();
  Real closest_val = 0.;
  for (const auto & current_value : list_of_values)
    {
      Real distance = std::abs(value - current_value);
      if (distance < min_distance)
        {
          min_distance = distance;
          closest_val = current_value;
        }
    }

  return closest_val;
}

get_condensed_matrix_A()

SparseMatrix< Number > & libMesh::CondensedEigenSystem::get_condensed_matrix_A ( )

inherited

Returns

The system matrix used for standard eigenvalue problems

Definition at line 280 of file condensed_eigen_system.C.

References libMesh::CondensedEigenSystem::_condensed_matrix_A, and libMesh::libmesh_assert().

Referenced by libMesh::CondensedEigenSystem::initialize_condensed_matrices().

{
  libmesh_assert(_condensed_matrix_A);
  return *_condensed_matrix_A;
}

get_condensed_matrix_B()

SparseMatrix< Number > & libMesh::CondensedEigenSystem::get_condensed_matrix_B ( )

inherited

Returns

The second system matrix used for generalized eigenvalue problems.

Definition at line 286 of file condensed_eigen_system.C.

References libMesh::CondensedEigenSystem::_condensed_matrix_B, and libMesh::libmesh_assert().

Referenced by libMesh::CondensedEigenSystem::initialize_condensed_matrices().

{
  libmesh_assert(_condensed_matrix_B);
  return *_condensed_matrix_B;
}

get_condensed_precond_matrix()

SparseMatrix< Number > & libMesh::CondensedEigenSystem::get_condensed_precond_matrix ( )

inherited

Returns

The condensed preconditioning matrix

Definition at line 292 of file condensed_eigen_system.C.

References libMesh::CondensedEigenSystem::_condensed_precond_matrix, and libMesh::libmesh_assert().

Referenced by libMesh::CondensedEigenSystem::initialize_condensed_matrices().

{
  libmesh_assert(_condensed_precond_matrix);
  return *_condensed_precond_matrix;
}

get_constraint_object()

System::Constraint & libMesh::System::get_constraint_object ( )

inherited

Return the user object for imposing constraints.

Definition at line 2226 of file system.C.

References libMesh::System::_constrain_system_object.

{
  libmesh_assert_msg(_constrain_system_object,"No constraint object available.");
  return *_constrain_system_object;
}

get_deterministic_training_parameter_name()

const std::string& libMesh::RBConstructionBase< CondensedEigenSystem >::get_deterministic_training_parameter_name ( ) const

inherited

Get the name of the parameter that we will generate deterministic training parameters for.

get_discrete_parameter_values()

const std::map< std::string, std::vector< Real > > & libMesh::RBParametrized::get_discrete_parameter_values ( ) const

inherited

Get a const reference to the discrete parameter values.

Definition at line 373 of file rb_parametrized.C.

References libMesh::RBParametrized::_discrete_parameter_values, and libMesh::RBParametrized::parameters_initialized.

Referenced by libMesh::RBDataSerialization::add_parameter_ranges_to_builder(), libMesh::RBParametrized::check_if_valid_params(), libMesh::RBParametrized::get_n_discrete_params(), libMesh::RBParametrized::initialize_parameters(), libMesh::RBParametrized::print_discrete_parameter_values(), and libMesh::RBParametrized::write_discrete_parameter_values_to_file().

{
  libmesh_error_msg_if(!parameters_initialized, "Error: parameters not initialized in RBParametrized::get_discrete_parameter_values");

  return _discrete_parameter_values;
}

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 2374 of file system.h.

References libMesh::System::_dof_map.

Referenced by libMesh::__libmesh_petsc_diff_solver_jacobian(), libMesh::__libmesh_petsc_diff_solver_residual(), libMesh::ExactSolution::_compute_error(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::DifferentiableSystem::add_dot_var_dirichlet_bcs(), libMesh::System::add_matrix(), libMesh::HPCoarsenTest::add_projection(), libMesh::RBConstruction::add_scaled_matrix_and_vector(), libMesh::AdaptiveTimeSolver::adjoint_advance_timestep(), libMesh::UnsteadySolver::adjoint_advance_timestep(), libMesh::ImplicitSystem::adjoint_solve(), libMesh::NewmarkSolver::advance_timestep(), libMesh::AdaptiveTimeSolver::advance_timestep(), libMesh::UnsteadySolver::advance_timestep(), libMesh::EquationSystems::allgather(), libMesh::TransientRBConstruction::allocate_data_structures(), libMesh::RBConstruction::allocate_data_structures(), alternative_fe_assembly(), assemble(), LinearElasticity::assemble(), assemble_1D(), AssembleOptimization::assemble_A_and_F(), libMesh::ClawSystem::assemble_advection_matrices(), assemble_and_solve(), libMesh::ClawSystem::assemble_avg_coupling_matrices(), assemble_biharmonic(), libMesh::ClawSystem::assemble_boundary_condition_matrices(), assemble_divgrad(), assemble_elasticity(), assemble_ellipticdg(), assemble_func(), assemble_graddiv(), assemble_helmholtz(), libMesh::ClawSystem::assemble_jump_coupling_matrix(), assemble_laplace(), assemble_mass(), libMesh::ClawSystem::assemble_mass_matrix(), assemble_matrices(), assemble_matrix_and_rhs(), assemble_poisson(), assemble_SchroedingerEquation(), assemble_shell(), assemble_stokes(), assemble_wave(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::PetscDMWrapper::build_sf(), libMesh::System::calculate_norm(), compute_jacobian(), compute_residual(), compute_stresses(), LinearElasticityWithContact::compute_stresses(), LinearElasticity::compute_stresses(), LargeDeformationElasticity::compute_stresses(), libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), MyConstraint::constrain(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::Nemesis_IO::copy_elemental_solution(), libMesh::Nemesis_IO::copy_nodal_solution(), libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::Nemesis_IO::copy_scalar_solution(), libMesh::CondensedEigenSystem::copy_sub_to_super(), libMesh::CondensedEigenSystem::copy_super_to_sub(), libMesh::System::create_static_condensation(), libMesh::ImplicitSystem::create_static_condensation_system_matrix(), create_wrapped_function(), DMCreateDomainDecomposition_libMesh(), DMCreateFieldDecomposition_libMesh(), DMlibMeshFunction(), DMlibMeshJacobian(), DMlibMeshSetSystem_libMesh(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), fe_assembly(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::SubFunctor::find_dofs_to_send(), libMesh::VariationalSmootherConstraint::fix_node(), form_functionA(), form_functionB(), form_matrixA(), libMesh::CondensedEigenSystem::get_eigenpair(), libMesh::System::get_info(), libMesh::System::has_static_condensation(), libMesh::SystemSubsetBySubdomain::init(), libMesh::SecondOrderUnsteadySolver::init_data(), libMesh::UnsteadySolver::init_data(), HeatSystem::init_data(), SimpleRBConstruction::init_data(), libMesh::ClawSystem::init_data(), LaplaceSystem::init_dirichlet_bcs(), NonManifoldCouplingTestBase::init_es(), libMesh::FEMContext::init_internal_data(), libMesh::EigenSystem::init_matrices(), libMesh::System::init_matrices(), libMesh::PetscDMWrapper::init_petscdm(), libMesh::CondensedEigenSystem::initialize_condensed_dofs(), libMesh::OptimizationSystem::initialize_equality_constraints_storage(), libMesh::OptimizationSystem::initialize_inequality_constraints_storage(), LaplaceYoung::jacobian(), LargeDeformationElasticity::jacobian(), libMesh::System::late_matrix_init(), 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::System::local_dof_indices(), AssembleOptimization::lower_and_upper_bounds(), main(), libMesh::DofMap::max_constraint_error(), LinearElasticityWithContact::move_mesh(), libMesh::DGFEMContext::neighbor_side_fe_reinit(), libMesh::UnsteadySolver::old_nonlinear_solution(), libMesh::SecondOrderUnsteadySolver::old_solution_accel(), libMesh::SecondOrderUnsteadySolver::old_solution_rate(), libMesh::WeightedPatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::PatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::ProjectSides::operator()(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::ProjectInteriors::operator()(), perform_SCM_greedy(), periodic_bc_test_poisson(), libMesh::petsc_auto_fieldsplit(), libMesh::ErrorVector::plot_error(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::FEMContext::pre_fe_reinit(), libMesh::InterMeshProjection::project_system_vectors(), libMesh::System::re_update(), libMesh::System::read_parallel_data(), libMesh::System::read_SCALAR_dofs(), libMesh::SecondOrderUnsteadySolver::reinit(), libMesh::UnsteadySolver::reinit(), libMesh::System::reinit(), libMesh::System::reinit_constraints(), libMesh::EquationSystems::reinit_solutions(), LaplaceYoung::residual(), LargeDeformationElasticity::residual(), LinearElasticityWithContact::residual_and_jacobian(), libMesh::UnsteadySolver::retrieve_timestep(), OverlappingAlgebraicGhostingTest::run_ghosting_test(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), libMesh::HPCoarsenTest::select_refinement(), libMesh::ImplicitSystem::sensitivity_solve(), libMesh::RBConstruction::set_context_solution_vec(), libMesh::PetscDMWrapper::set_point_range_in_section(), set_system_parameters(), SlitMeshRefinedSystemTest::setUp(), FETestBase< order, family, elem_type, 1 >::setUp(), SolidSystem::side_time_derivative(), libMesh::NewtonSolver::solve(), libMesh::PetscDiffSolver::solve(), libMesh::EigenSystem::solve(), libMesh::RBConstruction::solve_for_matrix_and_rhs(), SystemsTest::test100KVariables(), ConstraintOperatorTest::test1DCoarseningNewNodes(), ConstraintOperatorTest::test1DCoarseningOperator(), MeshfunctionDFEM::test_mesh_function_dfem(), MeshfunctionDFEM::test_mesh_function_dfem_grad(), MeshFunctionTest::test_p_level(), MeshFunctionTest::test_subdomain_id_sets(), SystemsTest::testBlockRestrictedVarNDofs(), DofMapTest::testConstraintLoopDetection(), DefaultCouplingTest::testCoupling(), PointNeighborCouplingTest::testCoupling(), EquationSystemsTest::testDisableDefaultGhosting(), SystemsTest::testDofCouplingWithVarGroups(), DofMapTest::testDofOwner(), MeshInputTest::testDynaReadPatch(), MeshInputTest::testExodusWriteElementDataFromDiscontinuousNodalData(), MeshAssignTest::testMeshMoveAssign(), PeriodicBCTest::testPeriodicBC(), SystemsTest::testPostInitAddVectorTypeChange(), SystemsTest::testProjectCubeWithMeshFunction(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), SystemsTest::testProjectMatrix3D(), InfFERadialTest::testRefinement(), EquationSystemsTest::testSelectivePRefine(), BoundaryInfoTest::testShellFaceConstraints(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::BoundaryVolumeSolutionTransfer::transfer_boundary_volume(), libMesh::UnsteadySolver::update(), update_current_local_solution(), NonManifoldGhostingFunctorTest::verify_send_list_entries_helper(), libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve(), libMesh::ImplicitSystem::weighted_sensitivity_solve(), libMesh::Nemesis_IO_Helper::write_nodal_solution(), libMesh::System::write_parallel_data(), libMesh::EnsightIO::write_scalar_ascii(), libMesh::System::write_SCALAR_dofs(), libMesh::EnsightIO::write_vector_ascii(), and libMesh::RBConstruction::zero_constrained_dofs_on_vector().

{
  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 2382 of file system.h.

References libMesh::System::_dof_map.

{
  return *_dof_map;
}

get_eigen_solver() [1/2]

const EigenSolver< Number > & libMesh::EigenSystem::get_eigen_solver ( ) const

inherited

Returns

A const reference to the EigenSolver.

Definition at line 482 of file eigen_system.C.

References libMesh::EigenSystem::eigen_solver, and libMesh::libmesh_assert().

Referenced by main().

{
  libmesh_assert(eigen_solver);
  return *eigen_solver;
}

get_eigen_solver() [2/2]

EigenSolver< Number > & libMesh::EigenSystem::get_eigen_solver ( )

inherited

Returns

A reference to the EigenSolver.

Definition at line 489 of file eigen_system.C.

References libMesh::EigenSystem::eigen_solver, and libMesh::libmesh_assert().

{
  libmesh_assert(eigen_solver);
  return *eigen_solver;
}

get_eigenpair()

std::pair< Real, Real > libMesh::CondensedEigenSystem::get_eigenpair ( dof_id_type  i )

overridevirtualinherited

Override get_eigenpair() to retrieve the eigenpair for the condensed eigensolve.

We only set the non-condensed entries of the solution vector (the condensed entries are set to zero by default).

Reimplemented from libMesh::EigenSystem.

Definition at line 234 of file condensed_eigen_system.C.

References libMesh::CondensedEigenSystem::_have_condensed_dofs, libMesh::NumericVector< T >::build(), libMesh::ParallelObject::comm(), libMesh::EigenSystem::eigen_solver, libMesh::DofMap::enforce_constraints_exactly(), libMesh::System::get_dof_map(), libMesh::EigenSystem::get_eigenpair(), libMesh::libmesh_assert(), libMesh::CondensedEigenSystem::local_non_condensed_dofs_vector, libMesh::make_range(), libMesh::PARALLEL, libMesh::System::solution, TIMPI::Communicator::sum(), and libMesh::System::update().

Referenced by compute_SCM_bounding_box(), evaluate_stability_constant(), and main().

{
  LOG_SCOPE("get_eigenpair()", "CondensedEigenSystem");

  // If we haven't initialized any condensed dofs,
  // just use the default eigen_system
  if (!_have_condensed_dofs)
    return Parent::get_eigenpair(i);

  // If we reach here, then there should be some non-condensed dofs
  libmesh_assert(!local_non_condensed_dofs_vector.empty());

  // This function assumes that condensed_solve has just been called.
  // If this is not the case, then we will trip an asset in get_eigenpair
  std::unique_ptr<NumericVector<Number>> temp = NumericVector<Number>::build(this->comm());
  const dof_id_type n_local =
    cast_int<dof_id_type>(local_non_condensed_dofs_vector.size());
  dof_id_type n       = n_local;
  this->comm().sum(n);

  temp->init (n, n_local, false, PARALLEL);

  std::pair<Real, Real> eval = eigen_solver->get_eigenpair (i, *temp);

  // Now map temp to solution. Loop over local entries of local_non_condensed_dofs_vector
  libmesh_assert(this->comm().verify(this->solution->closed()));
  if (!this->solution->closed())
    this->solution->close();
  this->solution->zero();
  for (auto j : make_range(n_local))
    {
      const dof_id_type index = local_non_condensed_dofs_vector[j];
      solution->set(index,(*temp)(temp->first_local_index()+j));
    }

  // Enforcing constraints requires creating a ghosted version of the solution, which requires the
  // solution be assembled
  solution->close();
  get_dof_map().enforce_constraints_exactly(*this);
  this->update();

  return eval;
}

get_eigenproblem_type()

EigenProblemType libMesh::EigenSystem::get_eigenproblem_type ( ) const

inlineinherited

Returns

The eigen problem type.

Definition at line 145 of file eigen_system.h.

References libMesh::EigenSystem::_eigen_problem_type.

{return _eigen_problem_type;}

get_eigenvalue()

std::pair< Real, Real > libMesh::EigenSystem::get_eigenvalue ( dof_id_type  i )

virtualinherited

Returns

Real and imaginary part of the ith eigenvalue but does not copy the respective eigen vector to the solution vector.

Definition at line 314 of file eigen_system.C.

References libMesh::EigenSystem::eigen_solver.

{
  return eigen_solver->get_eigenvalue (i);
}

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 721 of file system.h.

References libMesh::System::_equation_systems.

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), add_scaled_symm_Aq(), libMesh::NewmarkSystem::clear(), libMesh::FrequencySystem::clear_all(), compute_jacobian(), compute_residual(), LinearElasticityWithContact::compute_stresses(), SolidSystem::element_time_derivative(), libMesh::RBConstruction::enrich_basis_from_rhs_terms(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::AdjointResidualErrorEstimator::estimate_error(), libMesh::ExactErrorEstimator::find_squared_element_error(), libMesh::ImplicitSystem::get_linear_solve_parameters(), SolidSystem::init_data(), HeatSystem::init_data(), libMesh::FrequencySystem::init_data(), LaplaceYoung::jacobian(), load_matrix_B(), LinearElasticityWithContact::move_mesh(), libMesh::FrequencySystem::n_frequencies(), perform_SCM_greedy(), libMesh::System::point_gradient(), libMesh::System::point_value(), libMesh::InterMeshProjection::project_system_vectors(), libMesh::StaticCondensationDofMap::reinit(), LaplaceYoung::residual(), LinearElasticityWithContact::residual_and_jacobian(), libMesh::FileHistoryData::retrieve_adjoint_solution(), libMesh::FileHistoryData::retrieve_primal_solution(), libMesh::FileHistoryData::rewrite_stored_solution(), SolidSystem::save_initial_mesh(), libMesh::FrequencySystem::set_current_frequency(), libMesh::FrequencySystem::set_frequencies(), libMesh::FrequencySystem::set_frequencies_by_range(), libMesh::FrequencySystem::set_frequencies_by_steps(), libMesh::NewmarkSystem::set_newmark_parameters(), libMesh::NonlinearImplicitSystem::set_solver_parameters(), SolidSystem::side_time_derivative(), libMesh::EigenSystem::solve(), libMesh::CondensedEigenSystem::solve(), libMesh::FrequencySystem::solve(), libMesh::ClawSystem::solve_conservation_law(), libMesh::RBConstruction::solve_for_matrix_and_rhs(), libMesh::EigenSystem::solve_helper(), libMesh::FileHistoryData::store_adjoint_solution(), libMesh::FileHistoryData::store_initial_solution(), libMesh::FileHistoryData::store_primal_solution(), MeshFunctionTest::test_p_level(), MeshFunctionTest::test_subdomain_id_sets(), MeshAssignTest::testMeshMoveAssign(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::DirectSolutionTransfer::transfer(), libMesh::MeshfreeSolutionTransfer::transfer(), libMesh::DTKSolutionTransfer::transfer(), libMesh::TransientRBConstruction::truth_solve(), libMesh::RBConstruction::truth_solve(), and libMesh::WrappedFunction< Output >::WrappedFunction().

{ return _equation_systems; }

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 726 of file system.h.

References libMesh::System::_equation_systems.

{ return _equation_systems; }

get_first_local_training_index()

numeric_index_type libMesh::RBConstructionBase< CondensedEigenSystem >::get_first_local_training_index ( ) const

inherited

Get the first local index of the training parameters.

Definition at line 191 of file rb_construction_base.C.

Referenced by compute_SCM_bounds_on_training_set().

{
  libmesh_error_msg_if(!_training_parameters_initialized,
                       "Error: training parameters must first be initialized.");

  // First we check if there are no parameters here, and in that case we
  // return 0 for a serial training set and comm().rank() for a parallel
  // training set. This is consistent with get_n_training_samples(), and
  // avoids accessing training_parameters.begin() when training_parameters
  // is empty.
  if (_training_parameters.empty())
    {
      if (serial_training_set)
        return 0;
      else
        return this->comm().rank();
    }

  return _first_local_index;
}

get_global_max_error_pair()

void libMesh::RBConstructionBase< CondensedEigenSystem >::get_global_max_error_pair ( const Parallel::Communicator &  communicator, std::pair< numeric_index_type, Real > &  error_pair  )

staticprotectedinherited

Static function to return the error pair (index,error) that is corresponds to the largest error on all processors.

Definition at line 134 of file rb_construction_base.C.

References communicator.

Referenced by compute_SCM_bounds_on_training_set().

{
  // Set error_pair.second to the maximum global value and also
  // find which processor contains the maximum value
  unsigned int proc_ID_index;
  communicator.maxloc(error_pair.second, proc_ID_index);

  // Then broadcast error_pair.first from proc_ID_index
  communicator.broadcast(error_pair.first, proc_ID_index);
}

get_info() [1/3]

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 & [name, cd] : _counts)
    oss << "| " << name << " reference count information:\n"
        << "|  Creations:    " << cd.first    << '\n'
        << "|  Destructions: " << cd.second << '\n';

  oss << " ---------------------------------------------------------------------------- \n";

  return oss.str();

#else

  return "";

#endif
}

get_info() [2/3]

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 & [name, cd] : _counts)
    oss << "| " << name << " reference count information:\n"
        << "|  Creations:    " << cd.first    << '\n'
        << "|  Destructions: " << cd.second << '\n';

  oss << " ---------------------------------------------------------------------------- \n";

  return oss.str();

#else

  return "";

#endif
}

get_info() [3/3]

std::string libMesh::System::get_info ( ) const

inherited

Returns

A string containing information about the system.

Definition at line 2040 of file system.C.

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

{
  std::ostringstream oss;


  const std::string & sys_name = this->name();

  oss << "   System #"  << this->number() << ", \"" << sys_name << "\"\n"
      << "    Type \""  << this->system_type() << "\"\n"
      << "    Variables=";

  for (auto vg : make_range(this->n_variable_groups()))
    {
      const VariableGroup & vg_description (this->variable_group(vg));

      if (vg_description.n_variables() > 1) oss << "{ ";
      for (auto vn : make_range(vg_description.n_variables()))
        oss << "\"" << vg_description.name(vn) << "\" ";
      if (vg_description.n_variables() > 1) oss << "} ";
    }

  oss << '\n';

  oss << "    Finite Element Types=";
#ifndef LIBMESH_ENABLE_INFINITE_ELEMENTS
  for (auto vg : make_range(this->n_variable_groups()))
    oss << "\""
        << Utility::enum_to_string<FEFamily>(this->get_dof_map().variable_group(vg).type().family)
        << "\" ";
#else
  for (auto vg : make_range(this->n_variable_groups()))
    {
      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 (auto vg : make_range(this->n_variable_groups()))
    oss << "\""
        << Utility::enum_to_string<InfMapType>(this->get_dof_map().variable_group(vg).type().inf_map)
        << "\" ";
#endif

  oss << '\n';

  oss << "    Approximation Orders=";
  for (auto vg : make_range(this->n_variable_groups()))
    {
#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';
  dof_id_type local_dofs = this->n_local_dofs();
  oss << "    n_local_dofs()="       << local_dofs                 << '\n';
  this->comm().max(local_dofs);
  oss << "    max(n_local_dofs())="       << 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';
  dof_id_type local_unconstrained_dofs = this->n_local_dofs() - this->n_local_constrained_dofs();
  this->comm().max(local_unconstrained_dofs);
  oss << "    max(local unconstrained dofs)=" << local_unconstrained_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_last_local_training_index()

numeric_index_type libMesh::RBConstructionBase< CondensedEigenSystem >::get_last_local_training_index ( ) const

inherited

Get the last local index of the training parameters.

Definition at line 213 of file rb_construction_base.C.

{
  libmesh_error_msg_if(!_training_parameters_initialized,
                       "Error: training parameters must first be initialized.");

  if (_training_parameters.empty())
    return 0;

  return _first_local_index + _n_local_training_samples;
}

get_local_n_training_samples()

numeric_index_type libMesh::RBConstructionBase< CondensedEigenSystem >::get_local_n_training_samples ( ) const

inherited

Get the total number of training samples local to this processor.

Definition at line 175 of file rb_construction_base.C.

Referenced by compute_SCM_bounds_on_training_set().

{
  libmesh_error_msg_if(!_training_parameters_initialized,
                       "Error: training parameters must first be initialized.");

  // First we check if there are no parameters here, and in that case we
  // return 1 for both serial and parallel training sets. This is consistent
  // with get_n_training_samples(), and avoids accessing
  // training_parameters.begin() when training_parameters is empty.
  if (_training_parameters.empty())
    return 1;

  return _n_local_training_samples;
}

get_matrix() [1/2]

const SparseMatrix< Number > & libMesh::System::get_matrix ( std::string_view  mat_name ) const

inherited

Returns

A const reference to this system's matrix named mat_name.

Definition at line 1124 of file system.C.

References libMesh::System::_matrices.

Referenced by add_M_C_K_helmholtz(), assemble(), assemble_helmholtz(), assemble_poisson(), libMesh::NewmarkSystem::compute_matrix(), libMesh::ImplicitSystem::get_system_matrix(), main(), libMesh::EigenTimeSolver::solve(), and libMesh::NewmarkSystem::update_rhs().

{
  return *libmesh_map_find(_matrices, mat_name);
}

get_matrix() [2/2]

SparseMatrix< Number > & libMesh::System::get_matrix ( std::string_view  mat_name )

inherited

Returns

A writable reference to this system's matrix named mat_name.

Definition at line 1131 of file system.C.

References libMesh::System::_matrices.

{
  return *libmesh_map_find(_matrices, mat_name);
}

get_matrix_A() [1/2]

const SparseMatrix< Number > & libMesh::EigenSystem::get_matrix_A ( ) const

inherited

Returns

A const reference to the system matrix used for standard eigenvalue problems.

This matrix should only be available (and therefore this should only be called) if !_use_shell_matrices.

Definition at line 333 of file eigen_system.C.

References libMesh::EigenSystem::_use_shell_matrices, libMesh::EigenSystem::has_matrix_A(), libMesh::libmesh_assert(), and libMesh::EigenSystem::matrix_A.

Referenced by add_scaled_symm_Aq(), assemble_mass(), assemble_matrices(), and assemble_SchroedingerEquation().

{
  libmesh_assert(matrix_A);
  libmesh_assert(!_use_shell_matrices);
  libmesh_assert(has_matrix_A());
  return *matrix_A;
}

get_matrix_A() [2/2]

SparseMatrix< Number > & libMesh::EigenSystem::get_matrix_A ( )

inherited

Returns

A reference to the system matrix used for standard eigenvalue problems.

This matrix should only be available (and therefore this should only be called) if !_use_shell_matrices.

Definition at line 342 of file eigen_system.C.

References libMesh::EigenSystem::_use_shell_matrices, libMesh::EigenSystem::has_matrix_A(), libMesh::libmesh_assert(), and libMesh::EigenSystem::matrix_A.

{
  libmesh_assert(matrix_A);
  libmesh_assert(!_use_shell_matrices);
  libmesh_assert(has_matrix_A());
  return *matrix_A;
}

get_matrix_B() [1/2]

const SparseMatrix< Number > & libMesh::EigenSystem::get_matrix_B ( ) const

inherited

Returns

A const reference to the system matrix used for generalized eigenvalue problems

This matrix should only be available (and therefore this should only be called) if !_use_shell_matrices and generalized().

Definition at line 351 of file eigen_system.C.

References libMesh::EigenSystem::_use_shell_matrices, libMesh::EigenSystem::generalized(), libMesh::EigenSystem::has_matrix_B(), libMesh::libmesh_assert(), and libMesh::EigenSystem::matrix_B.

Referenced by assemble_mass(), assemble_matrices(), and assemble_SchroedingerEquation().

{
  libmesh_assert(matrix_B);
  libmesh_assert(!_use_shell_matrices);
  libmesh_assert(generalized());
  libmesh_assert(has_matrix_B());
  return *matrix_B;
}

get_matrix_B() [2/2]

SparseMatrix< Number > & libMesh::EigenSystem::get_matrix_B ( )

inherited

Returns

A const reference to the system matrix used for generalized eigenvalue problems

This matrix should only be available (and therefore this should only be called) if !_use_shell_matrices and generalized().

Definition at line 361 of file eigen_system.C.

References libMesh::EigenSystem::_use_shell_matrices, libMesh::EigenSystem::generalized(), libMesh::EigenSystem::has_matrix_B(), libMesh::libmesh_assert(), and libMesh::EigenSystem::matrix_B.

{
  libmesh_assert(matrix_B);
  libmesh_assert(!_use_shell_matrices);
  libmesh_assert(generalized());
  libmesh_assert(has_matrix_B());
  return *matrix_B;
}

get_mesh() [1/2]

const MeshBase & libMesh::System::get_mesh ( ) const

inlineinherited

Returns

A constant reference to this systems's _mesh.

Definition at line 2358 of file system.h.

References libMesh::System::_mesh.

Referenced by libMesh::ExactSolution::_compute_error(), LinearElasticityWithContact::add_contact_edge_elements(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::System::add_matrix(), libMesh::HPCoarsenTest::add_projection(), libMesh::RBConstruction::add_scaled_matrix_and_vector(), AssembleOptimization::assemble_A_and_F(), libMesh::ClawSystem::assemble_advection_matrices(), libMesh::ClawSystem::assemble_avg_coupling_matrices(), libMesh::ClawSystem::assemble_boundary_condition_matrices(), libMesh::ClawSystem::assemble_jump_coupling_matrix(), libMesh::ClawSystem::assemble_mass_matrix(), libMesh::FEMSystem::assemble_qoi(), libMesh::FEMSystem::assemble_qoi_derivative(), libMesh::VariationalSmootherSystem::assembly(), libMesh::FEMSystem::assembly(), AssemblyA0::boundary_assembly(), AssemblyA1::boundary_assembly(), AssemblyF0::boundary_assembly(), AssemblyF1::boundary_assembly(), AssemblyA2::boundary_assembly(), AssemblyF2::boundary_assembly(), libMesh::System::calculate_norm(), libMesh::VariationalSmootherSystem::compute_element_reference_volume(), compute_jacobian(), compute_residual(), LinearElasticityWithContact::compute_stresses(), libMesh::VariationalSmootherConstraint::constrain(), libMesh::System::create_static_condensation(), libMesh::ImplicitSystem::create_static_condensation_system_matrix(), libMesh::RBEIMEvaluation::distribute_bfs(), DMCreateDomainDecomposition_libMesh(), DMCreateFieldDecomposition_libMesh(), DMlibMeshSetSystem_libMesh(), SolidSystem::element_time_derivative(), HeatSystem::element_time_derivative(), libMesh::RBConstruction::enrich_basis_from_rhs_terms(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_interiors(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_sides(), libMesh::PatchRecoveryErrorEstimator::estimate_error(), libMesh::WeightedPatchRecoveryErrorEstimator::estimate_error(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::AdjointResidualErrorEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::SubFunctor::find_dofs_to_send(), libMesh::VariationalSmootherConstraint::fix_node(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::GenericProjector(), LinearElasticityWithContact::get_least_and_max_gap_function(), libMesh::SystemSubsetBySubdomain::init(), libMesh::RBEIMConstruction::init_context(), SolidSystem::init_data(), libMesh::VariationalSmootherSystem::init_data(), libMesh::System::init_data(), libMesh::System::init_matrices(), libMesh::PetscDMWrapper::init_petscdm(), LinearElasticityWithContact::initialize_contact_load_paths(), libMesh::RBEIMConstruction::initialize_qp_data(), libMesh::System::local_dof_indices(), libMesh::DofMap::max_constraint_error(), libMesh::FEMSystem::mesh_position_get(), libMesh::FEMSystem::mesh_position_set(), LinearElasticityWithContact::move_mesh(), libMesh::System::n_components(), libMesh::RBEIMEvaluation::node_distribute_bfs(), libMesh::WeightedPatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::PatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::ProjectVertices::operator()(), libMesh::petsc_auto_fieldsplit(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::FEMSystem::postprocess(), libMesh::RBParametrizedFunction::preevaluate_parametrized_function_on_mesh(), libMesh::RBParametrizedFunction::preevaluate_parametrized_function_on_mesh_sides(), libMesh::System::read_header(), libMesh::RBEvaluation::read_in_vectors_from_multiple_files(), libMesh::System::read_legacy_data(), libMesh::System::read_parallel_data(), libMesh::System::read_serialized_vector(), libMesh::System::read_serialized_vectors(), libMesh::System::reinit(), LinearElasticityWithContact::residual_and_jacobian(), OverlappingAlgebraicGhostingTest::run_ghosting_test(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), SolidSystem::save_initial_mesh(), libMesh::HPSingularity::select_refinement(), libMesh::HPCoarsenTest::select_refinement(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::RBEIMEvaluation::side_distribute_bfs(), SolidSystem::side_time_derivative(), libMesh::PetscDiffSolver::solve(), libMesh::ClawSystem::solve_conservation_law(), MeshAssignTest::testMeshMoveAssign(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::BoundaryVolumeSolutionTransfer::transfer(), libMesh::BoundaryVolumeSolutionTransfer::transfer_boundary_volume(), libMesh::BoundaryVolumeSolutionTransfer::transfer_volume_boundary(), libMesh::TransientRBConstruction::truth_solve(), libMesh::RBConstruction::truth_solve(), libMesh::System::write_header(), libMesh::RBEvaluation::write_out_vectors(), libMesh::System::write_parallel_data(), libMesh::System::write_serialized_vector(), libMesh::System::write_serialized_vectors(), and libMesh::System::zero_variable().

{
  return _mesh;
}

get_mesh() [2/2]

MeshBase & libMesh::System::get_mesh ( )

inlineinherited

Returns

A reference to this systems's _mesh.

Definition at line 2366 of file system.h.

References libMesh::System::_mesh.

{
  return _mesh;
}

get_n_continuous_params()

unsigned int libMesh::RBParametrized::get_n_continuous_params ( ) const

inherited

Get the number of continuous parameters.

Definition at line 112 of file rb_parametrized.C.

References libMesh::RBParametrized::get_n_discrete_params(), libMesh::RBParametrized::get_n_params(), libMesh::libmesh_assert(), and libMesh::RBParametrized::parameters_initialized.

Referenced by libMesh::RBDataSerialization::add_parameter_ranges_to_builder(), and libMesh::RBParametrized::write_parameter_ranges_to_file().

{
  libmesh_error_msg_if(!parameters_initialized, "Error: parameters not initialized in RBParametrized::get_n_continuous_params");

  libmesh_assert(get_n_params() >= get_n_discrete_params());

  return static_cast<unsigned int>(get_n_params() - get_n_discrete_params());
}

get_n_converged()

unsigned int libMesh::EigenSystem::get_n_converged ( ) const

inlineinherited

Returns

The number of converged eigenpairs.

Definition at line 130 of file eigen_system.h.

References libMesh::EigenSystem::_n_converged_eigenpairs.

Referenced by compute_SCM_bounding_box(), evaluate_stability_constant(), and main().

{return _n_converged_eigenpairs;}

get_n_discrete_params()

unsigned int libMesh::RBParametrized::get_n_discrete_params ( ) const

inherited

Get the number of discrete parameters.

Definition at line 121 of file rb_parametrized.C.

References libMesh::RBParametrized::get_discrete_parameter_values(), and libMesh::RBParametrized::parameters_initialized.

Referenced by libMesh::RBDataSerialization::add_parameter_ranges_to_builder(), libMesh::RBParametrized::get_n_continuous_params(), and libMesh::RBParametrized::write_discrete_parameter_values_to_file().

{
  libmesh_error_msg_if(!parameters_initialized, "Error: parameters not initialized in RBParametrized::get_n_discrete_params");

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

get_n_iterations()

unsigned int libMesh::EigenSystem::get_n_iterations ( ) const

inlineinherited

Returns

The number of eigen solver iterations.

Definition at line 135 of file eigen_system.h.

References libMesh::EigenSystem::_n_iterations.

{return _n_iterations;}

get_n_params()

unsigned int libMesh::RBParametrized::get_n_params ( ) const

inherited

Get the number of parameters.

Definition at line 103 of file rb_parametrized.C.

References libMesh::RBParameters::n_parameters(), libMesh::RBParametrized::parameters_initialized, libMesh::RBParametrized::parameters_max, and libMesh::RBParametrized::parameters_min.

Referenced by libMesh::RBParametrized::check_if_valid_params(), libMesh::RBEIMConstruction::compute_max_eim_error(), libMesh::RBConstruction::compute_max_error_bound(), libMesh::RBParametrized::get_n_continuous_params(), print_info(), libMesh::RBEIMConstruction::print_info(), libMesh::RBConstruction::print_info(), libMesh::RBEIMEvaluation::set_eim_error_indicator_active(), and libMesh::RBConstruction::train_reduced_basis_with_POD().

{
  libmesh_error_msg_if(!parameters_initialized, "Error: parameters not initialized in RBParametrized::get_n_params");

  libmesh_assert_equal_to ( parameters_min.n_parameters(), parameters_max.n_parameters() );

  return parameters_min.n_parameters();
}

get_n_training_samples()

numeric_index_type libMesh::RBConstructionBase< CondensedEigenSystem >::get_n_training_samples ( ) const

inherited

Get the number of global training samples.

Definition at line 153 of file rb_construction_base.C.

Referenced by print_info().

{
  libmesh_error_msg_if(!_training_parameters_initialized,
                       "Error: training parameters must first be initialized.");

  // First we check if there are no parameters here, and in that case we
  // return 1 since a single training sample is sufficient to generate an
  // RB approximation if there are no parameters. Note that in parallel,
  // and when we don't have a serial training set, set return comm().size()
  // so that each processor is assigned a single (empty) training sample.
  if (_training_parameters.empty())
    {
      if (serial_training_set)
        return 1;
      else
        return this->comm().size();
    }

  return _n_global_training_samples;
}

get_parameter_max()

Real libMesh::RBParametrized::get_parameter_max ( const std::string &  param_name ) const

inherited

Get maximum allowable value of parameter param_name.

Definition at line 185 of file rb_parametrized.C.

References libMesh::RBParameters::get_value(), libMesh::RBParametrized::parameters_initialized, and libMesh::RBParametrized::parameters_max.

Referenced by libMesh::RBParametrized::check_if_valid_params(), print_info(), libMesh::RBEIMConstruction::print_info(), and libMesh::RBConstruction::print_info().

{
  libmesh_error_msg_if(!parameters_initialized, "Error: parameters not initialized in RBParametrized::get_parameter_max");

  return parameters_max.get_value(param_name);
}

get_parameter_min()

Real libMesh::RBParametrized::get_parameter_min ( const std::string &  param_name ) const

inherited

Get minimum allowable value of parameter param_name.

Definition at line 178 of file rb_parametrized.C.

References libMesh::RBParameters::get_value(), libMesh::RBParametrized::parameters_initialized, and libMesh::RBParametrized::parameters_min.

Referenced by libMesh::RBParametrized::check_if_valid_params(), print_info(), libMesh::RBEIMConstruction::print_info(), and libMesh::RBConstruction::print_info().

{
  libmesh_error_msg_if(!parameters_initialized, "Error: parameters not initialized in RBParametrized::get_parameter_min");

  return parameters_min.get_value(param_name);
}

get_parameter_names()

std::set< std::string > libMesh::RBParametrized::get_parameter_names ( ) const

inherited

Get a set that stores the parameter names.

Deprecated:

to avoid making it too easy to create copies that in most circumstances aren't needed. If this functionality really is required, call get_parameters_min().get_parameters_map() and loop over the keys directly.

Definition at line 130 of file rb_parametrized.C.

References libMesh::RBParametrized::parameters_initialized, and libMesh::RBParametrized::parameters_min.

{
  libmesh_deprecated();
  libmesh_error_msg_if(!parameters_initialized, "Error: parameters not initialized in RBParametrized::get_parameter_names");

  std::set<std::string> parameter_names;
  for (const auto & pr : parameters_min)
    parameter_names.insert(pr.first);

  return parameter_names;
}

get_parameters()

const RBParameters & libMesh::RBParametrized::get_parameters ( ) const

inherited

Get the current parameters.

Definition at line 157 of file rb_parametrized.C.

References libMesh::RBParametrized::parameters, and libMesh::RBParametrized::parameters_initialized.

Referenced by libMesh::TransientRBConstruction::add_scaled_mass_matrix(), libMesh::TransientRBEvaluation::cache_online_residual_terms(), libMesh::RBEvaluation::compute_residual_dual_norm(), compute_SCM_bounds_on_training_set(), enrich_C_J(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_interiors(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_nodes(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_sides(), libMesh::RBEvaluation::eval_output_dual_norm(), evaluate_stability_constant(), libMesh::RBConstruction::get_RB_error_bound(), libMesh::RBSCMEvaluation::get_SCM_LB(), libMesh::RBSCMEvaluation::get_SCM_UB(), SimpleRBEvaluation::get_stability_lower_bound(), libMesh::RBConstruction::greedy_termination_test(), libMesh::RBEIMConstruction::initialize_parametrized_functions_in_training_set(), libMesh::RBSCMEvaluation::legacy_read_offline_data_from_files(), libMesh::TransientRBConstruction::mass_matrix_scaled_matvec(), libMesh::RBConstruction::preevaluate_thetas(), print_info(), libMesh::RBEIMConstruction::print_info(), libMesh::RBConstruction::print_info(), libMesh::RBParametrized::print_parameters(), process_parameters_file(), libMesh::TransientRBEvaluation::rb_solve(), libMesh::RBEvaluation::rb_solve(), libMesh::RBSCMEvaluation::save_current_parameters(), libMesh::RBEIMConstruction::train_eim_approximation_with_greedy(), libMesh::RBEIMConstruction::train_eim_approximation_with_POD(), libMesh::TransientRBConstruction::truth_assembly(), libMesh::RBConstruction::truth_assembly(), libMesh::TransientRBConstruction::truth_solve(), libMesh::RBConstruction::truth_solve(), libMesh::TransientRBEvaluation::uncached_compute_residual_dual_norm(), and libMesh::RBConstruction::update_greedy_param_list().

{
  libmesh_error_msg_if(!parameters_initialized, "Error: parameters not initialized in RBParametrized::get_parameters");

  return parameters;
}

get_parameters_max()

const RBParameters & libMesh::RBParametrized::get_parameters_max ( ) const

inherited

Get an RBParameters object that specifies the maximum allowable value for each parameter.

Definition at line 171 of file rb_parametrized.C.

References libMesh::RBParametrized::parameters_initialized, and libMesh::RBParametrized::parameters_max.

Referenced by libMesh::RBDataSerialization::add_parameter_ranges_to_builder(), libMesh::RBParametrized::initialize_parameters(), process_parameters_file(), libMesh::RBEIMConstruction::set_rb_construction_parameters(), libMesh::RBConstruction::set_rb_construction_parameters(), and libMesh::RBParametrized::write_parameter_ranges_to_file().

{
  libmesh_error_msg_if(!parameters_initialized, "Error: parameters not initialized in RBParametrized::get_parameters_max");

  return parameters_max;
}

get_parameters_min()

const RBParameters & libMesh::RBParametrized::get_parameters_min ( ) const

inherited

Get an RBParameters object that specifies the minimum allowable value for each parameter.

Definition at line 164 of file rb_parametrized.C.

References libMesh::RBParametrized::parameters_initialized, and libMesh::RBParametrized::parameters_min.

Referenced by libMesh::RBDataSerialization::add_parameter_ranges_to_builder(), libMesh::RBParametrized::initialize_parameters(), process_parameters_file(), libMesh::RBEIMConstruction::set_rb_construction_parameters(), libMesh::RBConstruction::set_rb_construction_parameters(), and libMesh::RBParametrized::write_parameter_ranges_to_file().

{
  libmesh_error_msg_if(!parameters_initialized, "Error: parameters not initialized in RBParametrized::get_parameters_min");

  return parameters_min;
}

get_params_from_training_set()

RBParameters libMesh::RBConstructionBase< CondensedEigenSystem >::get_params_from_training_set ( unsigned int  global_index )

protectedinherited

Return the RBParameters in index global_index of the global training set.

Why do we use an index here? RBParameters supports loading the full sample set. This seems probably unnecessary now to load individually. Maybe it's a memory issue?

Definition at line 231 of file rb_construction_base.C.

References libMesh::as_range(), libMesh::MeshTools::Generation::Private::idx(), libMesh::index_range(), libMesh::RBParameters::set_extra_value(), and libMesh::RBParameters::set_value().

{
  libmesh_error_msg_if(!_training_parameters_initialized,
                       "Error: training parameters must first be initialized.");

  // If the _training_parameters are empty, return an empty RBParameters.
  // Otherwise, create a new RBParameters object from the single sample requested.
  RBParameters params;
  if (!_training_parameters.empty())
    {
      libmesh_error_msg_if((global_index < this->get_first_local_training_index()) ||
                           (global_index >= this->get_last_local_training_index()),
                           "Error: index "
                           << global_index
                           << " must be within range: "
                           << this->get_first_local_training_index()
                           << " - "
                           << this->get_last_local_training_index());

      const numeric_index_type local_index = global_index - get_first_local_training_index();
      for (const auto & [param_name, sample_vector] : _training_parameters)
        params.set_value(param_name, sample_vector[local_index]);

      // Copy all extra values into the new RBParameters.
      // We assume that the samples may be indexed differently for extra parameters,
      // so we don't just copy the local_index value.
      const auto & mine = get_parameters();
      for (const auto & [key, extra_sample_vector] :
           as_range(mine.extra_begin(), mine.extra_end()))
        {
          for (const auto idx : index_range(extra_sample_vector))
            params.set_extra_value(key, idx, extra_sample_vector[idx]);
        }
    }

  return params;
}

get_precond_matrix() [1/2]

const SparseMatrix< Number > & libMesh::EigenSystem::get_precond_matrix ( ) const

inherited

Returns

A const reference to the preconditioning matrix.

This matrix should only be available (and therefore this should only be called) if !_use_shell_matrices.

Definition at line 371 of file eigen_system.C.

References libMesh::EigenSystem::_use_shell_matrices, libMesh::EigenSystem::_use_shell_precond_matrix, libMesh::EigenSystem::has_precond_matrix(), libMesh::libmesh_assert(), and libMesh::EigenSystem::precond_matrix.

{
  libmesh_assert(precond_matrix);
  libmesh_assert(_use_shell_matrices);
  libmesh_assert(!_use_shell_precond_matrix);
  libmesh_assert(has_precond_matrix());
  return *precond_matrix;
}

get_precond_matrix() [2/2]

SparseMatrix< Number > & libMesh::EigenSystem::get_precond_matrix ( )

inherited

Returns

A reference to the preconditioning matrix.

This matrix should only be available (and therefore this should only be called) if !_use_shell_matrices.

Definition at line 381 of file eigen_system.C.

References libMesh::EigenSystem::_use_shell_matrices, libMesh::EigenSystem::_use_shell_precond_matrix, libMesh::EigenSystem::has_precond_matrix(), libMesh::libmesh_assert(), and libMesh::EigenSystem::precond_matrix.

{
  libmesh_assert(precond_matrix);
  libmesh_assert(_use_shell_matrices);
  libmesh_assert(!_use_shell_precond_matrix);
  libmesh_assert(has_precond_matrix());
  return *precond_matrix;
}

get_project_with_constraints()

bool libMesh::System::get_project_with_constraints ( )

inlineinherited

Setter and getter functions for project_with_constraints boolean.

Definition at line 1795 of file system.h.

References libMesh::System::project_with_constraints.

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

  {
    return project_with_constraints;
  }

get_qoi_error_estimate_value()

Number libMesh::System::get_qoi_error_estimate_value ( unsigned int  qoi_index ) const

inherited

Definition at line 2413 of file system.C.

References libMesh::libmesh_assert(), and libMesh::System::qoi_error_estimates.

Referenced by libMesh::TwostepTimeSolver::integrate_adjoint_refinement_error_estimate(), and main().

{
  libmesh_assert(qoi_index < qoi_error_estimates.size());
  return qoi_error_estimates[qoi_index];
}

get_qoi_value()

Number libMesh::System::get_qoi_value ( unsigned int  qoi_index ) const

inherited

Definition at line 2386 of file system.C.

References libMesh::libmesh_assert(), and libMesh::System::qoi.

Referenced by libMesh::Euler2Solver::integrate_qoi_timestep(), libMesh::TwostepTimeSolver::integrate_qoi_timestep(), libMesh::EulerSolver::integrate_qoi_timestep(), main(), libMesh::ImplicitSystem::qoi_parameter_hessian(), and libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product().

{
  libmesh_assert(qoi_index < qoi.size());
  return qoi[qoi_index];
}

get_qoi_values()

std::vector< Number > libMesh::System::get_qoi_values ( ) const

inherited

Returns a copy of qoi, not a reference.

Definition at line 2393 of file system.C.

References libMesh::System::qoi.

Referenced by libMesh::ImplicitSystem::adjoint_qoi_parameter_sensitivity(), libMesh::FEMSystem::assemble_qoi(), libMesh::ImplicitSystem::forward_qoi_parameter_sensitivity(), libMesh::ImplicitSystem::qoi_parameter_hessian(), and libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product().

{
  return this->qoi;
}

get_rb_scm_evaluation()

RBSCMEvaluation & libMesh::RBSCMConstruction::get_rb_scm_evaluation

(

)

Get a reference to the RBSCMEvaluation object.

Definition at line 77 of file rb_scm_construction.C.

References rb_scm_eval.

Referenced by get_rb_theta_expansion().

{
  libmesh_error_msg_if(!rb_scm_eval, "Error: RBSCMEvaluation object hasn't been initialized yet");

  return *rb_scm_eval;
}

get_rb_theta_expansion()

RBThetaExpansion & libMesh::RBSCMConstruction::get_rb_theta_expansion

(

)

Get a reference to the RBThetaExpansion object.

Definition at line 84 of file rb_scm_construction.C.

References get_rb_scm_evaluation(), and libMesh::RBSCMEvaluation::get_rb_theta_expansion().

Referenced by Aq_inner_product(), compute_SCM_bounding_box(), enrich_C_J(), evaluate_stability_constant(), print_info(), and resize_SCM_vectors().

{
  return get_rb_scm_evaluation().get_rb_theta_expansion();
}

get_SCM_training_tolerance()

Real libMesh::RBSCMConstruction::get_SCM_training_tolerance ( ) const

inline

Get/set SCM_training_tolerance: tolerance for SCM greedy.

Definition at line 145 of file rb_scm_construction.h.

References SCM_training_tolerance.

Referenced by print_info().

{ return SCM_training_tolerance; }

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 1337 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 1347 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 1192 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 1202 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_shell_matrix_A() [1/2]

const ShellMatrix< Number > & libMesh::EigenSystem::get_shell_matrix_A ( ) const

inherited

Returns

A const reference to the system shell matrix used for standard eigenvalue problems.

This matrix should only be available (and therefore this should only be called) if _use_shell_matrices.

Definition at line 391 of file eigen_system.C.

References libMesh::EigenSystem::_use_shell_matrices, libMesh::EigenSystem::has_shell_matrix_A(), libMesh::libmesh_assert(), and libMesh::EigenSystem::shell_matrix_A.

{
  libmesh_assert(_use_shell_matrices);
  libmesh_assert(has_shell_matrix_A());
  return *shell_matrix_A;
}

get_shell_matrix_A() [2/2]

ShellMatrix< Number > & libMesh::EigenSystem::get_shell_matrix_A ( )

inherited

Returns

A reference to the system shell matrix used for standard eigenvalue problems.

This matrix should only be available (and therefore this should only be called) if _use_shell_matrices.

Definition at line 399 of file eigen_system.C.

References libMesh::EigenSystem::_use_shell_matrices, libMesh::EigenSystem::has_shell_matrix_A(), libMesh::libmesh_assert(), and libMesh::EigenSystem::shell_matrix_A.

{
  libmesh_assert(_use_shell_matrices);
  libmesh_assert(has_shell_matrix_A());
  return *shell_matrix_A;
}

get_shell_matrix_B() [1/2]

const ShellMatrix< Number > & libMesh::EigenSystem::get_shell_matrix_B ( ) const

inherited

Returns

A const reference to the system shell matrix used for generalized eigenvalue problems.

This matrix should only be available (and therefore this should only be called) if _use_shell_matrices and generalized().

Definition at line 407 of file eigen_system.C.

References libMesh::EigenSystem::_use_shell_matrices, libMesh::EigenSystem::generalized(), libMesh::EigenSystem::has_shell_matrix_B(), libMesh::libmesh_assert(), and libMesh::EigenSystem::shell_matrix_B.

{
  libmesh_assert(_use_shell_matrices);
  libmesh_assert(generalized());
  libmesh_assert(has_shell_matrix_B());
  return *shell_matrix_B;
}

get_shell_matrix_B() [2/2]

ShellMatrix< Number > & libMesh::EigenSystem::get_shell_matrix_B ( )

inherited

Returns

A reference to the system shell matrix used for generalized eigenvalue problems.

This matrix should only be available (and therefore this should only be called) if _use_shell_matrices and generalized().

Definition at line 416 of file eigen_system.C.

References libMesh::EigenSystem::_use_shell_matrices, libMesh::EigenSystem::generalized(), libMesh::EigenSystem::has_shell_matrix_B(), libMesh::libmesh_assert(), and libMesh::EigenSystem::shell_matrix_B.

{
  libmesh_assert(_use_shell_matrices);
  libmesh_assert(generalized());
  libmesh_assert(has_shell_matrix_B());
  return *shell_matrix_B;
}

get_shell_precond_matrix() [1/2]

const ShellMatrix< Number > & libMesh::EigenSystem::get_shell_precond_matrix ( ) const

inherited

Returns

A const reference to the system shell matrix used for preconditioning.

Definition at line 425 of file eigen_system.C.

References libMesh::EigenSystem::_use_shell_matrices, libMesh::EigenSystem::_use_shell_precond_matrix, libMesh::EigenSystem::has_shell_precond_matrix(), libMesh::libmesh_assert(), and libMesh::EigenSystem::shell_precond_matrix.

{
  libmesh_assert(_use_shell_matrices);
  libmesh_assert(_use_shell_precond_matrix);
  libmesh_assert(has_shell_precond_matrix());
  return *shell_precond_matrix;
}

get_shell_precond_matrix() [2/2]

ShellMatrix< Number > & libMesh::EigenSystem::get_shell_precond_matrix ( )

inherited

Returns

A reference to the system shell matrix used for preconditioning.

Definition at line 434 of file eigen_system.C.

References libMesh::EigenSystem::_use_shell_matrices, libMesh::EigenSystem::_use_shell_precond_matrix, libMesh::EigenSystem::has_shell_precond_matrix(), libMesh::libmesh_assert(), and libMesh::EigenSystem::shell_precond_matrix.

{
  libmesh_assert(_use_shell_matrices);
  libmesh_assert(_use_shell_precond_matrix);
  libmesh_assert(has_shell_precond_matrix());
  return *shell_precond_matrix;
}

get_vector() [1/4]

const NumericVector< Number > & libMesh::System::get_vector ( std::string_view  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 943 of file system.C.

References libMesh::System::_vectors.

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), add_M_C_K_helmholtz(), libMesh::AdaptiveTimeSolver::adjoint_advance_timestep(), libMesh::UnsteadySolver::adjoint_advance_timestep(), libMesh::NewmarkSolver::advance_timestep(), libMesh::AdaptiveTimeSolver::advance_timestep(), libMesh::UnsteadySolver::advance_timestep(), apply_initial(), assemble(), 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(), AssembleOptimization::lower_and_upper_bounds(), main(), libMesh::NewmarkSolver::project_initial_accel(), libMesh::SecondOrderUnsteadySolver::project_initial_rate(), libMesh::InterMeshProjection::project_system_vectors(), libMesh::SecondOrderUnsteadySolver::reinit(), libMesh::UnsteadySolver::reinit(), libMesh::FileSolutionHistory::retrieve(), libMesh::UnsteadySolver::retrieve_timestep(), libMesh::MemoryHistoryData::retrieve_vectors(), libMesh::TwostepTimeSolver::solve(), libMesh::FrequencySystem::solve(), libMesh::UnsteadySolver::update(), libMesh::NewmarkSystem::update_rhs(), and libMesh::NewmarkSystem::update_u_v_a().

{
  return *(libmesh_map_find(_vectors, vec_name));
}

get_vector() [2/4]

NumericVector< Number > & libMesh::System::get_vector ( std::string_view  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 950 of file system.C.

References libMesh::System::_vectors.

{
  return *(libmesh_map_find(_vectors, vec_name));
}

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 957 of file system.C.

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

{
  // If we don't have that many vectors, throw an error
  libmesh_assert_less(vec_num, _vectors.size());

  // Otherwise return a reference to the vec_num'th vector
  auto it = vectors_begin();
  std::advance(it, vec_num);
  return *(it->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 970 of file system.C.

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

{
  // If we don't have that many vectors, throw an error
  libmesh_assert_less(vec_num, _vectors.size());

  // Otherwise return a reference to the vec_num'th vector
  auto it = vectors_begin();
  std::advance(it, vec_num);
  return *(it->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 1277 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 1287 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 1219 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 1226 of file system.C.

References libMesh::System::get_vector().

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

has_condensed_matrix_A()

bool libMesh::CondensedEigenSystem::has_condensed_matrix_A ( ) const

inlineinherited

Definition at line 121 of file condensed_eigen_system.h.

References libMesh::CondensedEigenSystem::_condensed_matrix_A.

Referenced by libMesh::CondensedEigenSystem::initialize_condensed_matrices().

{ return _condensed_matrix_A.get(); }

has_condensed_matrix_B()

bool libMesh::CondensedEigenSystem::has_condensed_matrix_B ( ) const

inlineinherited

Definition at line 122 of file condensed_eigen_system.h.

References libMesh::CondensedEigenSystem::_condensed_matrix_B.

Referenced by libMesh::CondensedEigenSystem::initialize_condensed_matrices().

{ return _condensed_matrix_B.get(); }

has_condensed_precond_matrix()

bool libMesh::CondensedEigenSystem::has_condensed_precond_matrix ( ) const

inlineinherited

Definition at line 123 of file condensed_eigen_system.h.

References libMesh::CondensedEigenSystem::_condensed_precond_matrix.

Referenced by libMesh::CondensedEigenSystem::initialize_condensed_matrices().

{ return _condensed_precond_matrix.get(); }

has_constraint_object()

bool libMesh::System::has_constraint_object ( ) const

inherited

Returns

true if there is a user-defined constraint object attached to this object, false otherwise. Calling System:: get_constraint_object() when there is no user-defined constraint object attached leads to either undefined behavior (dereferencing a nullptr) or an assert (in dbg mode) so you should call this function first unless you are sure there is a user-defined constraint object attached.

Definition at line 2221 of file system.C.

References libMesh::System::_constrain_system_object.

{
  return _constrain_system_object != nullptr;
}

has_matrix_A()

bool libMesh::EigenSystem::has_matrix_A ( ) const

inherited

Returns

Whether or not the system has matrix A

Definition at line 443 of file eigen_system.C.

References libMesh::EigenSystem::matrix_A, and libMesh::System::request_matrix().

Referenced by libMesh::EigenSystem::get_matrix_A().

{
  libmesh_assert_equal_to(request_matrix("Eigen Matrix A"), matrix_A);
  return matrix_A;
}

has_matrix_B()

bool libMesh::EigenSystem::has_matrix_B ( ) const

inherited

Returns

Whether or not the system has matrix B

Definition at line 450 of file eigen_system.C.

References libMesh::EigenSystem::matrix_B, and libMesh::System::request_matrix().

Referenced by libMesh::EigenSystem::get_matrix_B().

{
  libmesh_assert_equal_to(request_matrix("Eigen Matrix B"), matrix_B);
  return matrix_B;
}

has_precond_matrix()

bool libMesh::EigenSystem::has_precond_matrix ( ) const

inherited

Returns

Whether or not the system has the non-shell preconditioning matrix

Definition at line 457 of file eigen_system.C.

References libMesh::EigenSystem::precond_matrix, and libMesh::System::request_matrix().

Referenced by libMesh::EigenSystem::get_precond_matrix().

{
  libmesh_assert_equal_to(request_matrix("Eigen Preconditioner"), precond_matrix);
  return precond_matrix;
}

has_shell_matrix_A()

bool libMesh::EigenSystem::has_shell_matrix_A ( ) const

inherited

Returns

Whether or not the system has the shell matrix A

Definition at line 464 of file eigen_system.C.

References libMesh::EigenSystem::shell_matrix_A.

Referenced by libMesh::EigenSystem::get_shell_matrix_A().

{
  return shell_matrix_A.get();
}

has_shell_matrix_B()

bool libMesh::EigenSystem::has_shell_matrix_B ( ) const

inherited

Returns

Whether or not the system has the shell matrix B

Definition at line 470 of file eigen_system.C.

References libMesh::EigenSystem::shell_matrix_B.

Referenced by libMesh::EigenSystem::get_shell_matrix_B().

{
  return shell_matrix_B.get();
}

has_shell_precond_matrix()

bool libMesh::EigenSystem::has_shell_precond_matrix ( ) const

inherited

Returns

Whether or not the system has the shell preconditioning matrix

Definition at line 476 of file eigen_system.C.

References libMesh::EigenSystem::shell_precond_matrix.

Referenced by libMesh::EigenSystem::get_shell_precond_matrix().

{
  return shell_precond_matrix.get();
}

has_static_condensation()

bool libMesh::System::has_static_condensation ( ) const

inherited

Returns

Whether this system will be statically condensed

Definition at line 2871 of file system.C.

References libMesh::System::get_dof_map(), and libMesh::DofMap::has_static_condensation().

Referenced by libMesh::System::add_matrix(), assemble_poisson(), libMesh::ImplicitSystem::ImplicitSystem(), libMesh::LinearImplicitSystem::LinearImplicitSystem(), and libMesh::NonlinearImplicitSystem::NonlinearImplicitSystem().

{
  return this->get_dof_map().has_static_condensation();
}

has_variable()

bool libMesh::System::has_variable ( std::string_view  var ) const

inherited

Returns

true if a variable named var exists in this System

Definition at line 1602 of file system.C.

References libMesh::System::_variable_numbers.

Referenced by libMesh::GMVIO::copy_nodal_solution(), and main().

{
  return _variable_numbers.count(var);
}

have_condensed_dofs()

bool libMesh::CondensedEigenSystem::have_condensed_dofs ( ) const

inlineinherited

Returns

Whether there are condensed degrees of freedom

Definition at line 205 of file condensed_eigen_system.h.

References libMesh::CondensedEigenSystem::_condensed_dofs_initialized, libMesh::CondensedEigenSystem::_have_condensed_dofs, and libMesh::libmesh_assert().

  { libmesh_assert(_condensed_dofs_initialized); return _have_condensed_dofs; }

have_matrix()

bool libMesh::System::have_matrix ( std::string_view  mat_name ) const

inlineinherited

Returns

true if this System has a matrix associated with the given name, false otherwise.

Definition at line 1891 of file system.h.

References libMesh::System::_matrices.

Referenced by libMesh::EigenTimeSolver::init().

{ return _matrices.count(mat_name); }

have_vector()

bool libMesh::System::have_vector ( std::string_view  vec_name ) const

inlineinherited

Returns

true if this System has a vector associated with the given name, false otherwise.

Definition at line 2550 of file system.h.

References libMesh::System::_vectors.

{
  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 1810 of file system.h.

References libMesh::System::_hide_output.

{ return _hide_output; }

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 2526 of file system.h.

References libMesh::System::_identify_variable_groups.

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

{
  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 2534 of file system.h.

References libMesh::System::_identify_variable_groups.

{
  _identify_variable_groups = ivg;
}

increment_constructor_count() [1/2]

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

inlineprotectednoexceptinherited

Increments the construction counter.

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

Definition at line 183 of file reference_counter.h.

References libMesh::err, libMesh::BasicOStreamProxy< charT, traits >::get(), libMesh::Quality::name(), and libMesh::Threads::spin_mtx.

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

{
  libmesh_try
  {
    Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
    std::pair<unsigned int, unsigned int> & p = _counts[name];
    p.first++;
  }
  libmesh_catch (...)
  {
    auto stream = libMesh::err.get();
    stream->exceptions(stream->goodbit); // stream must not throw
    libMesh::err << "Encountered unrecoverable error while calling "
                 << "ReferenceCounter::increment_constructor_count() "
                 << "for a(n) " << name << " object." << std::endl;
    std::terminate();
  }
}

increment_constructor_count() [2/2]

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

inlineprotectednoexceptinherited

Increments the construction counter.

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

Definition at line 183 of file reference_counter.h.

References libMesh::err, libMesh::BasicOStreamProxy< charT, traits >::get(), libMesh::Quality::name(), and libMesh::Threads::spin_mtx.

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

{
  libmesh_try
  {
    Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
    std::pair<unsigned int, unsigned int> & p = _counts[name];
    p.first++;
  }
  libmesh_catch (...)
  {
    auto stream = libMesh::err.get();
    stream->exceptions(stream->goodbit); // stream must not throw
    libMesh::err << "Encountered unrecoverable error while calling "
                 << "ReferenceCounter::increment_constructor_count() "
                 << "for a(n) " << name << " object." << std::endl;
    std::terminate();
  }
}

increment_destructor_count() [1/2]

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

inlineprotectednoexceptinherited

Increments the destruction counter.

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

Definition at line 207 of file reference_counter.h.

References libMesh::err, libMesh::BasicOStreamProxy< charT, traits >::get(), libMesh::Quality::name(), and libMesh::Threads::spin_mtx.

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

{
  libmesh_try
  {
    Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
    std::pair<unsigned int, unsigned int> & p = _counts[name];
    p.second++;
  }
  libmesh_catch (...)
  {
    auto stream = libMesh::err.get();
    stream->exceptions(stream->goodbit); // stream must not throw
    libMesh::err << "Encountered unrecoverable error while calling "
                 << "ReferenceCounter::increment_destructor_count() "
                 << "for a(n) " << name << " object." << std::endl;
    std::terminate();
  }
}

increment_destructor_count() [2/2]

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

inlineprotectednoexceptinherited

Increments the destruction counter.

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

Definition at line 207 of file reference_counter.h.

References libMesh::err, libMesh::BasicOStreamProxy< charT, traits >::get(), libMesh::Quality::name(), and libMesh::Threads::spin_mtx.

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

{
  libmesh_try
  {
    Threads::spin_mutex::scoped_lock lock(Threads::spin_mtx);
    std::pair<unsigned int, unsigned int> & p = _counts[name];
    p.second++;
  }
  libmesh_catch (...)
  {
    auto stream = libMesh::err.get();
    stream->exceptions(stream->goodbit); // stream must not throw
    libMesh::err << "Encountered unrecoverable error while calling "
                 << "ReferenceCounter::increment_destructor_count() "
                 << "for a(n) " << name << " object." << std::endl;
    std::terminate();
  }
}

init()

void libMesh::System::init ( )

inherited

Initializes degrees of freedom on the current mesh.

Sets the

Definition at line 197 of file system.C.

References libMesh::System::is_initialized(), libMesh::libmesh_assert(), and libMesh::System::reinit_mesh().

Referenced by libMesh::StaticCondensationDofMap::reinit().

{
  // Calling init() twice on the same system currently works evil
  // magic, whether done directly or via EquationSystems::read()
  libmesh_assert(!this->is_initialized());

  this->reinit_mesh();
}

init_data()

void libMesh::RBConstructionBase< CondensedEigenSystem >::init_data ( )

protectedvirtualinherited

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

Reimplemented from libMesh::System.

Definition at line 123 of file rb_construction_base.C.

References libMesh::PARALLEL.

{
  Base::init_data();

  // Initialize the inner product storage vector, which is useful for
  // storing intermediate results when evaluating inner products
  inner_product_storage_vector = NumericVector<Number>::build(this->comm());
  inner_product_storage_vector->init (this->n_dofs(), this->n_local_dofs(), false, PARALLEL);
}

init_matrices()

void libMesh::EigenSystem::init_matrices ( )

overrideprotectedvirtualinherited

Initializes the matrices associated with the system.

Reimplemented from libMesh::System.

Definition at line 158 of file eigen_system.C.

References libMesh::System::condense_constrained_dofs(), libMesh::System::get_dof_map(), libMesh::System::init_matrices(), libMesh::EigenSystem::shell_matrix_A, libMesh::EigenSystem::shell_matrix_B, and libMesh::EigenSystem::shell_precond_matrix.

{
  Parent::init_matrices();

  const bool condense_constraints = condense_constrained_dofs();
  if (shell_matrix_A)
    {
      shell_matrix_A->attach_dof_map(this->get_dof_map());
      if (condense_constraints)
        shell_matrix_A->omit_constrained_dofs();
      shell_matrix_A->init();
    }

  if (shell_matrix_B)
    {
      shell_matrix_B->attach_dof_map(this->get_dof_map());
      if (condense_constraints)
        shell_matrix_B->omit_constrained_dofs();
      shell_matrix_B->init();
    }

  if (shell_precond_matrix)
    {
      shell_precond_matrix->attach_dof_map(this->get_dof_map());
      if (condense_constraints)
        shell_precond_matrix->omit_constrained_dofs();
      shell_precond_matrix->init();
    }
}

init_qois()

void libMesh::System::init_qois ( unsigned int  n_qois )

inherited

Accessors for qoi and qoi_error_estimates vectors.

Definition at line 2371 of file system.C.

References libMesh::System::n_qois(), libMesh::System::qoi, and libMesh::System::qoi_error_estimates.

Referenced by CoupledSystemQoI::init_qoi_count(), LaplaceQoI::init_qoi_count(), and main().

{
  qoi.resize(n_qois);
  qoi_error_estimates.resize(n_qois);
}

initialize_condensed_dofs()

void libMesh::CondensedEigenSystem::initialize_condensed_dofs ( const std::set< dof_id_type > &  global_condensed_dofs_set = std::set<dof_id_type>() )

inherited

Loop over the dofs on each processor to initialize the list of non-condensed dofs.

These are the dofs in the system that are not contained in global_dirichlet_dofs_set and are not subject to constraints due to adaptive mesh hanging nodes, periodic boundary conditions, or Dirichlet boundary conditions.

Most users will not need to use the global_condensed_dofs_set argument; simply call initialize_condensed_dofs() after any time the EquationSystems (and therefore its constraint equations) gets initialized or reinitialized.

Definition at line 49 of file condensed_eigen_system.C.

References libMesh::CondensedEigenSystem::_condensed_dofs_initialized, libMesh::CondensedEigenSystem::_have_condensed_dofs, libMesh::DofMapBase::end_dof(), libMesh::DofMapBase::first_dof(), libMesh::System::get_dof_map(), libMesh::DofMap::is_constrained_dof(), libMesh::CondensedEigenSystem::local_non_condensed_dofs_vector, libMesh::make_range(), and libMesh::DofMap::n_constrained_dofs().

Referenced by libMesh::CondensedEigenSystem::initialize_condensed_matrices(), main(), and perform_SCM_greedy().

{
  const DofMap & dof_map = this->get_dof_map();
  if (global_dirichlet_dofs_set.empty() && !dof_map.n_constrained_dofs())
    {
      _have_condensed_dofs = false;
      _condensed_dofs_initialized = true;
      return;
    }

  // First, put all unconstrained local dofs into non_dirichlet_dofs_set
  std::set<dof_id_type> local_non_condensed_dofs_set;
  for (auto i : make_range(dof_map.first_dof(), dof_map.end_dof()))
#if LIBMESH_ENABLE_CONSTRAINTS
    if (!dof_map.is_constrained_dof(i))
#endif
      local_non_condensed_dofs_set.insert(i);

  // Now erase the condensed dofs
  for (const auto dof : global_dirichlet_dofs_set)
    if ((dof_map.first_dof() <= dof) && (dof < dof_map.end_dof()))
      local_non_condensed_dofs_set.erase(dof);

  // Finally, move local_non_condensed_dofs_set over to a vector for convenience in solve()
  this->local_non_condensed_dofs_vector.clear();

  for (const auto dof : local_non_condensed_dofs_set)
    this->local_non_condensed_dofs_vector.push_back(dof);

  _have_condensed_dofs = true;
  _condensed_dofs_initialized = true;
}

initialize_condensed_matrices()

void libMesh::CondensedEigenSystem::initialize_condensed_matrices ( )

inherited

Initializes the condensed matrices.

This API should be used if the condensed matrices will be assembled during the solve as opposed to pre-solve

Definition at line 90 of file condensed_eigen_system.C.

References libMesh::ParallelObject::_communicator, libMesh::CondensedEigenSystem::_condensed_dofs_initialized, libMesh::CondensedEigenSystem::_have_condensed_dofs, libMesh::SparseMatrix< T >::close(), libMesh::CondensedEigenSystem::get_condensed_matrix_A(), libMesh::CondensedEigenSystem::get_condensed_matrix_B(), libMesh::CondensedEigenSystem::get_condensed_precond_matrix(), libMesh::CondensedEigenSystem::has_condensed_matrix_A(), libMesh::CondensedEigenSystem::has_condensed_matrix_B(), libMesh::CondensedEigenSystem::has_condensed_precond_matrix(), libMesh::SparseMatrix< T >::init(), libMesh::CondensedEigenSystem::initialize_condensed_dofs(), libMesh::CondensedEigenSystem::local_non_condensed_dofs_vector, and TIMPI::Communicator::sum().

{
  if (!_condensed_dofs_initialized)
    this->initialize_condensed_dofs();

  if (!_have_condensed_dofs)
    return;

  const auto m = cast_int<numeric_index_type>(this->local_non_condensed_dofs_vector.size());
  auto M = m;
  _communicator.sum(M);
  if (this->has_condensed_matrix_A())
  {
    this->get_condensed_matrix_A().init(M, M, m, m);
    // A bit ludicrously MatCopy requires the matrix being copied to to be assembled
    this->get_condensed_matrix_A().close();
  }
  if (this->has_condensed_matrix_B())
  {
    this->get_condensed_matrix_B().init(M, M, m, m);
    this->get_condensed_matrix_B().close();
  }
  if (this->has_condensed_precond_matrix())
  {
    this->get_condensed_precond_matrix().init(M, M, m, m);
    this->get_condensed_precond_matrix().close();
  }
}

initialize_parameters() [1/2]

void libMesh::RBParametrized::initialize_parameters ( const RBParameters &  mu_min_in, const RBParameters &  mu_max_in, const std::map< std::string, std::vector< Real >> &  discrete_parameter_values  )

inherited

Initialize the parameter ranges and set current_parameters.

Parameter ranges are inclusive. The input min/max RBParameters should have exactly 1 sample each. Vector-valued samples are not currently supported for the min/max parameters or for discrete parameters.

Definition at line 53 of file rb_parametrized.C.

References libMesh::RBParametrized::_discrete_parameter_values, libMesh::RBParameters::begin_serialized(), libMesh::RBParameters::end_serialized(), libMesh::RBParameters::n_parameters(), libMesh::RBParameters::n_samples(), libMesh::Quality::name(), libMesh::RBParametrized::parameters_initialized, libMesh::RBParametrized::parameters_max, libMesh::RBParametrized::parameters_min, libMesh::Real, libMesh::RBParametrized::set_parameters(), and libMesh::RBParameters::set_value().

Referenced by libMesh::RBConstruction::enrich_basis_from_rhs_terms(), libMesh::RBParametrized::initialize_parameters(), libMesh::RBDataDeserialization::load_parameter_ranges(), perform_SCM_greedy(), process_parameters_file(), libMesh::RBParametrized::read_parameter_data_from_files(), libMesh::RBEIMConstruction::set_rb_construction_parameters(), libMesh::RBConstruction::set_rb_construction_parameters(), RBParametersTest::testRBParametrized(), libMesh::RBEIMConstruction::train_eim_approximation_with_greedy(), libMesh::RBEIMConstruction::train_eim_approximation_with_POD(), libMesh::RBConstruction::train_reduced_basis_with_greedy(), and libMesh::RBConstruction::train_reduced_basis_with_POD().

{
  // Check that the min/max vectors have the same size.
  libmesh_error_msg_if(mu_min_in.n_parameters() != mu_max_in.n_parameters(),
                       "Error: Invalid mu_min/mu_max in initialize_parameters(), different number of parameters.");
  libmesh_error_msg_if(mu_min_in.n_samples() != 1 ||
                       mu_max_in.n_samples() != 1,
                       "Error: Invalid mu_min/mu_max in initialize_parameters(), only 1 sample supported.");

  // Ensure all the values are valid for min and max.
  auto pr_min = mu_min_in.begin_serialized();
  auto pr_max = mu_max_in.begin_serialized();
  for (; pr_min != mu_min_in.end_serialized(); ++pr_min, ++pr_max)
    libmesh_error_msg_if((*pr_min).second > (*pr_max).second,
                         "Error: Invalid mu_min/mu_max in RBParameters constructor.");

  parameters_min = mu_min_in;
  parameters_max = mu_max_in;

  // Add in min/max values due to the discrete parameters
  for (const auto & [name, vals] : discrete_parameter_values)
    {
      libmesh_error_msg_if(vals.empty(), "Error: List of discrete parameters for " << name << " is empty.");

      Real min_val = *std::min_element(vals.begin(), vals.end());
      Real max_val = *std::max_element(vals.begin(), vals.end());

      libmesh_assert_less_equal(min_val, max_val);

      parameters_min.set_value(name, min_val);
      parameters_max.set_value(name, max_val);
    }

    _discrete_parameter_values = discrete_parameter_values;

  parameters_initialized = true;

  // Initialize the current parameters to parameters_min
  set_parameters(parameters_min);
}

initialize_parameters() [2/2]

void libMesh::RBParametrized::initialize_parameters ( const RBParametrized &  rb_parametrized )

inherited

Initialize the parameter ranges and set current_parameters.

Definition at line 96 of file rb_parametrized.C.

References libMesh::RBParametrized::get_discrete_parameter_values(), libMesh::RBParametrized::get_parameters_max(), libMesh::RBParametrized::get_parameters_min(), and libMesh::RBParametrized::initialize_parameters().

{
  initialize_parameters(rb_parametrized.get_parameters_min(),
                        rb_parametrized.get_parameters_max(),
                        rb_parametrized.get_discrete_parameter_values());
}

initialize_training_parameters()

void libMesh::RBConstructionBase< CondensedEigenSystem >::initialize_training_parameters ( const RBParameters &  mu_min, const RBParameters &  mu_max, const unsigned int  n_global_training_samples, const std::map< std::string, bool > &  log_param_scale, const bool  deterministic = true  )

virtualinherited

Initialize the parameter ranges and indicate whether deterministic or random training parameters should be used and whether or not we want the parameters to be scaled logarithmically.

n_global_training_samples is the total number of samples to generate, which will be distributed across all the processors.

Definition at line 292 of file rb_construction_base.C.

References libMesh::index_range(), libMesh::out, and libMesh::Real.

Referenced by process_parameters_file().

{
  if (!is_quiet())
    {
      // Print out some info about the training set initialization
      libMesh::out << "Initializing training parameters with "
                  << (deterministic ? "deterministic " : "random " )
                  << "training set..." << std::endl;

      for (const auto & pr : log_param_scale)
        libMesh::out << "Parameter "
                     << pr.first
                     << ": log scaling = "
                     << pr.second
                     << std::endl;

      libMesh::out << std::endl;
    }

  if (deterministic)
    {
      const auto [first_local_index, last_local_index] =
        generate_training_parameters_deterministic(this->comm(),
                                                   log_param_scale,
                                                   _training_parameters,
                                                   n_global_training_samples,
                                                   mu_min,
                                                   mu_max,
                                                   serial_training_set);
      _first_local_index = first_local_index;
      _n_local_training_samples = last_local_index-first_local_index;
    }
  else
    {
      // Generate random training samples for all parameters
      const auto [first_local_index, last_local_index] =
        generate_training_parameters_random(this->comm(),
                                            log_param_scale,
                                            _training_parameters,
                                            n_global_training_samples,
                                            mu_min,
                                            mu_max,
                                            this->_training_parameters_random_seed,
                                            serial_training_set);
      _first_local_index = first_local_index;
      _n_local_training_samples = last_local_index-first_local_index;
    }
  _n_global_training_samples = _n_local_training_samples;

  if (!serial_training_set)
    this->comm().sum(_n_global_training_samples);

  // For each parameter that only allows discrete values, we "snap" to the nearest
  // allowable discrete value
  if (get_n_discrete_params() > 0)
    {
      for (auto & [param_name, sample_vector] : _training_parameters)
        {
          if (is_discrete_parameter(param_name))
            {
              const std::vector<Real> & discrete_values =
                libmesh_map_find(get_discrete_parameter_values(), param_name);

              for (const auto sample_idx : index_range(sample_vector))
                {
                  // Round all values to the closest discrete value.
                  std::vector<Real> discretized_vector(sample_vector[sample_idx].size());
                  std::transform(sample_vector[sample_idx].cbegin(),
                                 sample_vector[sample_idx].cend(),
                                 discretized_vector.begin(),
                                 [&discrete_values](const Real & val) {
                                   return get_closest_value(val, discrete_values);
                                 });
                  sample_vector[sample_idx] = discretized_vector;
                }
            }
        }
    }

  _training_parameters_initialized = true;
}

is_adjoint_already_solved()

bool libMesh::System::is_adjoint_already_solved ( ) const

inlineinherited

Accessor for the adjoint_already_solved boolean.

Definition at line 409 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().

  { return adjoint_already_solved;}

is_discrete_parameter()

bool libMesh::RBParametrized::is_discrete_parameter ( const std::string &  mu_name ) const

inherited

Is parameter mu_name discrete?

Definition at line 365 of file rb_parametrized.C.

References libMesh::RBParametrized::_discrete_parameter_values, and libMesh::RBParametrized::parameters_initialized.

Referenced by libMesh::RBDataSerialization::add_parameter_ranges_to_builder(), libMesh::RBEIMConstruction::print_info(), libMesh::RBConstruction::print_info(), and libMesh::RBParametrized::write_parameter_ranges_to_file().

{
  libmesh_error_msg_if(!parameters_initialized,
                       "Error: parameters not initialized in RBParametrized::is_discrete_parameter");

  return _discrete_parameter_values.count(mu_name);
}

is_initialized()

bool libMesh::System::is_initialized ( ) const

inlineinherited

Returns

true iff this system has been initialized.

Definition at line 2414 of file system.h.

References libMesh::System::_is_initialized.

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

{
  return _is_initialized;
}

is_quiet()

bool libMesh::RBConstructionBase< CondensedEigenSystem >::is_quiet ( ) const

inlineinherited

Is the system in quiet mode?

Definition at line 106 of file rb_construction_base.h.

References libMesh::RBConstructionBase< Base >::quiet_mode.

  { return this->quiet_mode; }

load_matrix_B()

void libMesh::RBSCMConstruction::load_matrix_B ( )

protectedvirtual

Copy over the matrix to store in matrix_B, usually this is the mass or inner-product matrix, but needs to be implemented in subclass.

Definition at line 213 of file rb_scm_construction.C.

References libMesh::SparseMatrix< T >::add(), libMesh::SparseMatrix< T >::close(), libMesh::System::get_equation_systems(), libMesh::RBConstruction::get_inner_product_matrix(), libMesh::EquationSystems::get_system(), libMesh::EigenSystem::matrix_B, RB_system_name, and libMesh::SparseMatrix< T >::zero().

Referenced by perform_SCM_greedy().

{
  // Load the operators from the RBConstruction
  EquationSystems & es = this->get_equation_systems();
  RBConstruction & rb_system = es.get_system<RBConstruction>(RB_system_name);

  matrix_B->zero();
  matrix_B->close();
  matrix_B->add(1.,*rb_system.get_inner_product_matrix());
}

load_training_set()

void libMesh::RBConstructionBase< CondensedEigenSystem >::load_training_set ( const std::map< std::string, std::vector< RBParameter >> &  new_training_set )

virtualinherited

Overwrite the training parameters with new_training_set.

This training set is assumed to contain only the samples local to this processor.

Definition at line 379 of file rb_construction_base.C.

References libMesh::libmesh_assert(), and libMesh::make_range().

{
  // Make sure we're running this on all processors at the same time
  libmesh_parallel_only(this->comm());

  // First, make sure that an initial training set has already been generated
  libmesh_error_msg_if(!_training_parameters_initialized,
                       "Error: load_training_set cannot be used to initialize parameters");

  // Make sure that the training set has the correct number of parameters
  const unsigned int n_params = get_n_params();
  libmesh_error_msg_if(new_training_set.size() > n_params,
                       "Error: new_training_set should not have more than get_n_params() parameters.");

  // Check that (new_training_set.size() == get_n_params()) is the same on all processes so that
  // we go into the same branch of the "if" statement below on all processes.
  const bool size_matches = (new_training_set.size() == n_params);
  libmesh_assert(this->comm().verify(size_matches));

  if (size_matches)
    {
      // If new_training_set stores values for all parameters, then we overwrite
      // _training_parameters with new_training_set.

      // Get the number of local and global training parameters
      _first_local_index = 0;
      _n_local_training_samples =
        cast_int<numeric_index_type>(new_training_set.begin()->second.size());
      _n_global_training_samples = _n_local_training_samples;

      if (!serial_training_set)
        {
          this->comm().sum(_n_global_training_samples);

          // Set the first/last indices.
          std::vector<numeric_index_type> local_sizes (this->n_processors(), 0);
          local_sizes[this->processor_id()] = _n_local_training_samples;
          this->comm().sum(local_sizes);

          // first_local_index is the sum of local_sizes
          // for all processor ids less than ours
          for (auto p : make_range(this->processor_id()))
            _first_local_index += local_sizes[p];
        }

      // Ensure that the parameters are the same.
      for (const auto & pr : _training_parameters)
        libmesh_error_msg_if(!new_training_set.count(pr.first),
                             "Parameters must be identical in order to overwrite dataset.");

      // Copy the values from the new_training_set to the internal training_parameters.
      _training_parameters = new_training_set;
    }
  else
    {
      // If new_training_set stores values for a subset of the parameters, then we keep the
      // length of training_parameters unchanged and overwrite the entries of the specified
      // parameters from new_training_set. Note that we repeatedly loop over new_training_set
      // to fill up the entire length of the sample_vector.
      for (auto & [param_name, sample_vector]: _training_parameters)
        {
          if (new_training_set.count(param_name))
            {
              for (const auto i : make_range(get_local_n_training_samples()))
                {
                  const unsigned int num_new_samples = libmesh_map_find(new_training_set,param_name).size();
                  libmesh_error_msg_if (num_new_samples==0, "new_training_set set should not be empty");

                  const unsigned int new_training_set_index = i % num_new_samples;
                  sample_vector[i] = libmesh_map_find(new_training_set,param_name)[new_training_set_index];
                }
            }
        }
    }
}

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 1627 of file system.C.

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

Referenced by libMesh::System::discrete_var_norm(), SystemsTest::testBlockRestrictedVarNDofs(), and libMesh::DirectSolutionTransfer::transfer().

{
  // 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 (dof_id_type dof : dof_indices)
        //If the dof is owned by the local processor
        if (first_local <= dof && dof < end_local)
          var_indices.insert(dof);
    }

  // 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);
    }
}

matrices_begin() [1/2]

System::matrices_iterator libMesh::System::matrices_begin ( )

inlineinherited

Beginning of matrices container.

Definition at line 2588 of file system.h.

References libMesh::System::_matrices.

{
  return _matrices.begin();
}

matrices_begin() [2/2]

System::const_matrices_iterator libMesh::System::matrices_begin ( ) const

inlineinherited

Beginning of matrices container.

Definition at line 2594 of file system.h.

References libMesh::System::_matrices.

{
  return _matrices.begin();
}

matrices_end() [1/2]

System::matrices_iterator libMesh::System::matrices_end ( )

inlineinherited

End of matrices container.

Definition at line 2600 of file system.h.

References libMesh::System::_matrices.

{
  return _matrices.end();
}

matrices_end() [2/2]

System::const_matrices_iterator libMesh::System::matrices_end ( ) const

inlineinherited

End of matrices container.

Definition at line 2606 of file system.h.

References libMesh::System::_matrices.

{
  return _matrices.end();
}

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 2542 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 2446 of file system.h.

References libMesh::System::_variables, libMesh::Variable::first_scalar_number(), libMesh::System::get_mesh(), 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(this->get_mesh());
}

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 128 of file system.C.

References libMesh::System::_dof_map.

Referenced by form_functionA(), form_functionB(), form_matrixA(), libMesh::System::get_info(), libMesh::System::n_active_dofs(), libMesh::EigenSystem::solve(), and BoundaryInfoTest::testShellFaceConstraints().

{
#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 121 of file system.C.

References libMesh::System::_dof_map.

Referenced by libMesh::TransientRBConstruction::add_IC_to_RB_space(), libMesh::System::add_vector(), libMesh::TransientRBConstruction::allocate_data_structures(), libMesh::RBConstruction::allocate_data_structures(), libMesh::TransientRBConstruction::assemble_affine_expansion(), libMesh::ClawSystem::assemble_avg_coupling_matrices(), libMesh::ClawSystem::assemble_boundary_condition_matrices(), libMesh::AdvectionSystem::assemble_claw_rhs(), libMesh::ClawSystem::assemble_jump_coupling_matrix(), libMesh::RBConstruction::compute_Fq_representor_innerprods(), libMesh::RBConstruction::compute_output_dual_innerprods(), libMesh::RBConstruction::compute_residual_dual_norm_slow(), libMesh::TransientRBConstruction::enrich_RB_space(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::System::get_info(), libMesh::SecondOrderUnsteadySolver::init_data(), libMesh::AdvectionSystem::init_data(), libMesh::UnsteadySolver::init_data(), libMesh::System::init_data(), libMesh::OptimizationSystem::initialize_equality_constraints_storage(), libMesh::OptimizationSystem::initialize_inequality_constraints_storage(), main(), libMesh::TransientRBConstruction::mass_matrix_scaled_matvec(), libMesh::System::n_active_dofs(), libMesh::CondensedEigenSystem::n_global_non_condensed_dofs(), libMesh::FEMSystem::numerical_jacobian(), perform_SCM_greedy(), libMesh::RBEvaluation::read_in_vectors_from_multiple_files(), libMesh::System::read_legacy_data(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), libMesh::SecondOrderUnsteadySolver::reinit(), libMesh::UnsteadySolver::reinit(), libMesh::System::restrict_vectors(), OverlappingAlgebraicGhostingTest::run_ghosting_test(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), libMesh::TransientRBConstruction::set_error_temporal_data(), libMesh::ClawSystem::solve_conservation_law(), SystemsTest::test100KVariables(), MeshfunctionDFEM::test_mesh_function_dfem(), MeshfunctionDFEM::test_mesh_function_dfem_grad(), MeshFunctionTest::test_p_level(), SystemsTest::testPostInitAddVector(), SystemsTest::testPostInitAddVectorTypeChange(), SystemsTest::testProjectCubeWithMeshFunction(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), SystemsTest::testProjectMatrix3D(), libMesh::RBConstruction::train_reduced_basis_with_POD(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::TransientRBConstruction::truth_assembly(), libMesh::RBConstruction::truth_assembly(), libMesh::TransientRBConstruction::update_RB_initial_condition_all_N(), libMesh::TransientRBConstruction::update_RB_system_matrices(), libMesh::RBConstruction::update_RB_system_matrices(), libMesh::TransientRBConstruction::update_residual_terms(), and libMesh::RBConstruction::update_residual_terms().

{
  return _dof_map->n_dofs();
}

n_global_non_condensed_dofs()

dof_id_type libMesh::CondensedEigenSystem::n_global_non_condensed_dofs ( ) const

inherited

Returns

The global number of non-condensed dofs in the system.

Definition at line 119 of file condensed_eigen_system.C.

References libMesh::CondensedEigenSystem::_have_condensed_dofs, libMesh::ParallelObject::comm(), libMesh::CondensedEigenSystem::local_non_condensed_dofs_vector, libMesh::System::n_dofs(), and TIMPI::Communicator::sum().

{
  if (!_have_condensed_dofs)
    return this->n_dofs();
  else
    {
      dof_id_type n_global_non_condensed_dofs =
        cast_int<dof_id_type>(local_non_condensed_dofs_vector.size());
      this->comm().sum(n_global_non_condensed_dofs);

      return n_global_non_condensed_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 143 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 158 of file system.C.

References libMesh::System::_dof_map.

Referenced by libMesh::TransientRBConstruction::add_IC_to_RB_space(), libMesh::System::add_vector(), libMesh::TransientRBConstruction::allocate_data_structures(), libMesh::RBConstruction::allocate_data_structures(), libMesh::TransientRBConstruction::assemble_affine_expansion(), libMesh::AdvectionSystem::assemble_claw_rhs(), libMesh::PetscDMWrapper::build_section(), libMesh::RBConstruction::compute_Fq_representor_innerprods(), libMesh::RBConstruction::compute_output_dual_innerprods(), libMesh::RBConstruction::compute_residual_dual_norm_slow(), libMesh::TransientRBConstruction::enrich_RB_space(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::System::get_info(), libMesh::SecondOrderUnsteadySolver::init_data(), libMesh::AdvectionSystem::init_data(), libMesh::UnsteadySolver::init_data(), libMesh::System::init_data(), libMesh::OptimizationSystem::initialize_equality_constraints_storage(), libMesh::OptimizationSystem::initialize_inequality_constraints_storage(), main(), libMesh::TransientRBConstruction::mass_matrix_scaled_matvec(), libMesh::RBEvaluation::read_in_vectors_from_multiple_files(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), libMesh::SecondOrderUnsteadySolver::reinit(), libMesh::UnsteadySolver::reinit(), libMesh::System::restrict_vectors(), OverlappingAlgebraicGhostingTest::run_ghosting_test(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), libMesh::TransientRBConstruction::set_error_temporal_data(), libMesh::ClawSystem::solve_conservation_law(), MeshFunctionTest::test_p_level(), libMesh::RBConstruction::train_reduced_basis_with_POD(), libMesh::TransientRBConstruction::truth_assembly(), libMesh::RBConstruction::truth_assembly(), libMesh::TransientRBConstruction::update_RB_initial_condition_all_N(), libMesh::TransientRBConstruction::update_RB_system_matrices(), libMesh::RBConstruction::update_RB_system_matrices(), libMesh::TransientRBConstruction::update_residual_terms(), and libMesh::RBConstruction::update_residual_terms().

{
  return _dof_map->n_local_dofs();
}

n_matrices()

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

inlineinherited

Returns

The number of matrices handled by this system. This is the size of the _matrices map

Definition at line 2699 of file system.h.

References libMesh::System::_matrices.

Referenced by libMesh::ImplicitSystem::add_matrices(), and libMesh::System::get_info().

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

n_objects() [1/2]

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

inlinestaticinherited

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

Definition at line 85 of file reference_counter.h.

References libMesh::ReferenceCounter::_n_objects.

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

  { return _n_objects; }

n_objects() [2/2]

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

inlinestaticinherited

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

Definition at line 85 of file reference_counter.h.

References libMesh::ReferenceCounter::_n_objects.

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

  { return _n_objects; }

n_processors()

processor_id_type libMesh::ParallelObject::n_processors ( ) const

inlineinherited

Returns

The number of processors in the group.

Definition at line 103 of file parallel_object.h.

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

Referenced by libMesh::Partitioner::_find_global_index_by_pid_map(), libMesh::BoundaryInfo::_find_id_maps(), libMesh::DofMap::add_constraints_to_send_list(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::DistributedMesh::add_elem(), libMesh::DofMap::add_neighbors_to_send_list(), libMesh::DistributedMesh::add_node(), libMesh::System::add_vector(), libMesh::LaplaceMeshSmoother::allgather_graph(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::FEMSystem::assembly(), libMesh::Nemesis_IO::assert_symmetric_cmaps(), libMesh::Partitioner::assign_partitioning(), libMesh::AztecLinearSolver< T >::AztecLinearSolver(), libMesh::Partitioner::build_graph(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::DistributedMesh::clear(), libMesh::DistributedMesh::clear_elems(), libMesh::Nemesis_IO_Helper::compute_border_node_ids(), libMesh::Nemesis_IO_Helper::construct_nemesis_filename(), libMesh::UnstructuredMesh::copy_nodes_and_elements(), libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::Nemesis_IO::copy_scalar_solution(), libMesh::UnstructuredMesh::create_pid_mesh(), libMesh::MeshTools::create_processor_bounding_box(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_scalar_dofs(), libMesh::DistributedMesh::DistributedMesh(), libMesh::EnsightIO::EnsightIO(), libMesh::RBEIMEvaluation::gather_bfs(), libMesh::MeshBase::get_info(), libMesh::StaticCondensation::init(), libMesh::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_petscdm(), libMesh::Nemesis_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::DistributedMesh::insert_elem(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_new_node_procids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_topology_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_valid_boundary_ids(), libMesh::MeshTools::libmesh_assert_valid_dof_ids(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::MeshTools::libmesh_assert_valid_refinement_flags(), libMesh::DofMap::local_variable_indices(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshBase::n_active_elem_on_proc(), libMesh::DofMap::n_dofs_per_processor(), libMesh::MeshBase::n_elem_on_proc(), libMesh::MeshBase::n_nodes_on_proc(), libMesh::RBEIMEvaluation::node_gather_bfs(), libMesh::Partitioner::partition(), libMesh::MeshBase::partition(), libMesh::Partitioner::partition_unpartitioned_elements(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::DofMap::prepare_send_list(), libMesh::MeshBase::print_constraint_rows(), libMesh::DofMap::print_dof_constraints(), libMesh::NameBasedIO::read(), libMesh::Nemesis_IO::read(), libMesh::CheckpointIO::read(), libMesh::CheckpointIO::read_connectivity(), libMesh::XdrIO::read_header(), libMesh::CheckpointIO::read_nodes(), libMesh::System::read_parallel_data(), libMesh::System::read_SCALAR_dofs(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::System::read_serialized_vector(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::Partitioner::repartition(), OverlappingFunctorTest::run_partitioner_test(), libMesh::DofMap::scatter_constraints(), libMesh::DistributedMesh::set_next_unique_id(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::PetscDMWrapper::set_point_range_in_section(), WriteVecAndScalar::setupTests(), libMesh::RBEIMEvaluation::side_gather_bfs(), DistributedMeshTest::testRemoteElemError(), CheckpointIOTest::testSplitter(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::DistributedMesh::update_parallel_id_counts(), libMesh::GMVIO::write_binary(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::ExodusII_IO_Helper::write_nodal_coordinates(), libMesh::VTKIO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data(), libMesh::System::write_parallel_data(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), and libMesh::XdrIO::write_serialized_nodesets().

  {
    processor_id_type returnval =
      cast_int<processor_id_type>(_communicator.size());
    libmesh_assert(returnval); // We never have an empty comm
    return returnval;
  }

n_qois()

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

inlineinherited

Number of currently active quantities of interest.

Definition at line 2621 of file system.h.

References libMesh::System::qoi, and libMesh::System::qoi_error_estimates.

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::AdaptiveTimeSolver::adjoint_advance_timestep(), libMesh::UnsteadySolver::adjoint_advance_timestep(), libMesh::ImplicitSystem::adjoint_qoi_parameter_sensitivity(), libMesh::TwostepTimeSolver::adjoint_solve(), 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::DiffContext::DiffContext(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::AdjointResidualErrorEstimator::estimate_error(), libMesh::FileSolutionHistory::FileSolutionHistory(), libMesh::ImplicitSystem::forward_qoi_parameter_sensitivity(), libMesh::UnsteadySolver::init_adjoints(), libMesh::TimeSolver::init_adjoints(), libMesh::System::init_qois(), libMesh::Euler2Solver::integrate_adjoint_refinement_error_estimate(), libMesh::TwostepTimeSolver::integrate_adjoint_refinement_error_estimate(), libMesh::EulerSolver::integrate_adjoint_refinement_error_estimate(), libMesh::Euler2Solver::integrate_qoi_timestep(), libMesh::TwostepTimeSolver::integrate_qoi_timestep(), libMesh::EulerSolver::integrate_qoi_timestep(), main(), libMesh::FEMContext::pre_fe_reinit(), libMesh::ImplicitSystem::qoi_parameter_hessian(), libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product(), libMesh::FileSolutionHistory::retrieve(), libMesh::QoISet::size(), libMesh::UnsteadySolver::UnsteadySolver(), and libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve().

{
#ifndef LIBMESH_ENABLE_DEPRECATED
  libmesh_assert_equal_to(this->qoi.size(), this->qoi_error_estimates.size());
#endif

  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 2438 of file system.h.

References libMesh::System::_variable_groups.

Referenced by libMesh::System::add_variable(), libMesh::System::add_variables(), 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 2430 of file system.h.

References libMesh::System::_variables.

Referenced by libMesh::ExactSolution::_compute_error(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::PetscDMWrapper::add_dofs_helper(), libMesh::DiffContext::add_localized_vector(), libMesh::RBConstruction::add_scaled_matrix_and_vector(), libMesh::System::add_variable(), libMesh::System::add_variables(), libMesh::TwostepTimeSolver::adjoint_solve(), libMesh::FEMContext::attach_quadrature_rules(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::PetscDMWrapper::build_section(), libMesh::System::calculate_norm(), compute_stresses(), LinearElasticityWithContact::compute_stresses(), LinearElasticity::compute_stresses(), LargeDeformationElasticity::compute_stresses(), libMesh::DGFEMContext::DGFEMContext(), libMesh::DiffContext::DiffContext(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::AdjointResidualErrorEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::ErrorEstimator::estimate_errors(), libMesh::ExactSolution::ExactSolution(), libMesh::FEMContext::find_hardest_fe_type(), libMesh::EquationSystems::find_variable_numbers(), libMesh::System::get_all_variable_numbers(), libMesh::FEMSystem::init_context(), libMesh::RBEIMConstruction::init_context(), libMesh::FEMContext::init_internal_data(), libMesh::PetscDMWrapper::init_petscdm(), libMesh::DifferentiablePhysics::init_physics(), AssemblyA0::interior_assembly(), AssemblyA1::interior_assembly(), AssemblyA2::interior_assembly(), InnerProductAssembly::interior_assembly(), main(), libMesh::WeightedPatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::PatchRecoveryErrorEstimator::EstimateError::operator()(), output_norms(), libMesh::petsc_auto_fieldsplit(), libMesh::FEMContext::pre_fe_reinit(), libMesh::InterMeshProjection::project_system_vectors(), libMesh::System::re_update(), libMesh::System::read_legacy_data(), libMesh::System::read_parallel_data(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::System::read_serialized_vector(), libMesh::System::read_serialized_vectors(), libMesh::System::reinit_mesh(), libMesh::HPCoarsenTest::select_refinement(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::SystemSubsetBySubdomain::set_var_nums(), OverlappingTestBase::setup_coupling_matrix(), SystemsTest::testDofCouplingWithVarGroups(), SlitMeshRefinedSystemTest::testRestart(), SlitMeshRefinedSystemTest::testSystem(), libMesh::System::write_header(), libMesh::System::write_parallel_data(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::System::write_serialized_vector(), libMesh::System::write_serialized_vectors(), and libMesh::System::zero_variable().

{
  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 2558 of file system.h.

References libMesh::System::_vectors.

Referenced by libMesh::ExplicitSystem::add_system_rhs(), libMesh::System::compare(), libMesh::System::get_info(), main(), libMesh::InterMeshProjection::project_system_vectors(), 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 2342 of file system.h.

References libMesh::System::_sys_name.

Referenced by libMesh::System::compare(), compute_jacobian(), compute_residual(), DMlibMeshSetUpName_Private(), libMesh::RBConstruction::enrich_basis_from_rhs_terms(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::ExactSolution::ExactSolution(), libMesh::ExactErrorEstimator::find_squared_element_error(), libMesh::System::get_info(), libMesh::NewtonSolver::init(), libMesh::StaticCondensation::init(), libMesh::TimeSolver::init_data(), libMesh::System::init_matrices(), main(), output_norms(), libMesh::petsc_auto_fieldsplit(), libMesh::System::prefix(), print_info(), libMesh::ClawSystem::print_info(), libMesh::RBEIMConstruction::print_info(), libMesh::RBConstruction::print_info(), libMesh::TimeSolver::reinit(), libMesh::PetscDiffSolver::setup_petsc_data(), libMesh::FrequencySystem::solve(), libMesh::RBConstruction::truth_solve(), libMesh::System::user_assembly(), libMesh::System::user_constrain(), libMesh::System::user_initialization(), libMesh::System::user_QOI(), libMesh::System::user_QOI_derivative(), libMesh::System::variable_number(), libMesh::System::write_header(), libMesh::System::write_parallel_data(), and libMesh::System::write_serialized_data().

{
  return _sys_name;
}

number()

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

inlineinherited

Returns

The system number.

Definition at line 2350 of file system.h.

References libMesh::System::_sys_number.

Referenced by libMesh::ExactSolution::_compute_error(), libMesh::PetscDMWrapper::add_dofs_helper(), assemble_matrix_and_rhs(), assemble_shell(), libMesh::VariationalSmootherSystem::assembly(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::Nemesis_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::Nemesis_IO::copy_nodal_solution(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ExactErrorEstimator::find_squared_element_error(), libMesh::EquationSystems::find_variable_numbers(), libMesh::VariationalSmootherConstraint::fix_node(), libMesh::System::get_info(), libMesh::VariationalSmootherSystem::init_data(), main(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::SortAndCopy::operator()(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::ProjectVertices::operator()(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::ProjectEdges::operator()(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::ProjectSides::operator()(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::ProjectInteriors::operator()(), libMesh::System::read_legacy_data(), libMesh::System::read_parallel_data(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::StaticCondensationDofMap::reinit(), LinearElasticityWithContact::residual_and_jacobian(), SolidSystem::save_initial_mesh(), libMesh::HPCoarsenTest::select_refinement(), libMesh::PetscDMWrapper::set_point_range_in_section(), MeshInputTest::testCopyElementVectorImpl(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::MeshfreeSolutionTransfer::transfer(), libMesh::BoundaryVolumeSolutionTransfer::transfer_boundary_volume(), libMesh::BoundaryVolumeSolutionTransfer::transfer_volume_boundary(), libMesh::DTKAdapter::update_variable_values(), libMesh::System::write_parallel_data(), libMesh::System::write_serialized_blocked_dof_objects(), and libMesh::System::zero_variable().

{
  return _sys_number;
}

operator=() [1/2]

RBSCMConstruction& libMesh::RBSCMConstruction::operator= ( const RBSCMConstruction &  )

delete

operator=() [2/2]

RBSCMConstruction& libMesh::RBSCMConstruction::operator= ( RBSCMConstruction &&  )

delete

perform_SCM_greedy()

void libMesh::RBSCMConstruction::perform_SCM_greedy ( )

virtual

Perform the SCM greedy algorithm to develop a lower bound over the training set.

Definition at line 224 of file rb_scm_construction.C.

References attach_deflation_space(), compute_SCM_bounding_box(), compute_SCM_bounds_on_training_set(), enrich_C_J(), evaluate_stability_constant(), libMesh::System::get_dof_map(), libMesh::System::get_equation_systems(), libMesh::EquationSystems::get_system(), libMesh::CondensedEigenSystem::initialize_condensed_dofs(), libMesh::RBParametrized::initialize_parameters(), libMesh::DofMap::is_constrained_dof(), load_matrix_B(), libMesh::System::n_dofs(), libMesh::out, rb_scm_eval, RB_system_name, and SCM_training_tolerance.

{
  LOG_SCOPE("perform_SCM_greedy()", "RBSCMConstruction");

  // initialize rb_scm_eval's parameters
  rb_scm_eval->initialize_parameters(*this);

#ifdef LIBMESH_ENABLE_CONSTRAINTS
  // Get a list of constrained dofs from rb_system
  std::set<dof_id_type> constrained_dofs_set;
  EquationSystems & es = this->get_equation_systems();
  RBConstruction & rb_system = es.get_system<RBConstruction>(RB_system_name);

  for (dof_id_type i=0; i<rb_system.n_dofs(); i++)
    {
      if (rb_system.get_dof_map().is_constrained_dof(i))
        {
          constrained_dofs_set.insert(i);
        }
    }

  // Use these constrained dofs to identify which dofs we want to "get rid of"
  // (i.e. condense) in our eigenproblems.
  this->initialize_condensed_dofs(constrained_dofs_set);
#endif // LIBMESH_ENABLE_CONSTRAINTS

  // Copy the inner product matrix over from rb_system to be used as matrix_B
  load_matrix_B();

  attach_deflation_space();

  compute_SCM_bounding_box();
  // This loads the new parameter into current_parameters
  enrich_C_J(0);

  unsigned int SCM_iter=0;
  while (true)
    {
      // matrix_A is reinitialized for the current parameters
      // on each call to evaluate_stability_constant
      evaluate_stability_constant();

      std::pair<unsigned int,Real> SCM_error_pair = compute_SCM_bounds_on_training_set();

      libMesh::out << "SCM iteration " << SCM_iter
                   << ", max_SCM_error = " << SCM_error_pair.second << std::endl;

      if (SCM_error_pair.second < SCM_training_tolerance)
        {
          libMesh::out << std::endl << "SCM tolerance of " << SCM_training_tolerance << " reached."
                       << std::endl << std::endl;
          break;
        }

      // If we need another SCM iteration, then enrich C_J
      enrich_C_J(SCM_error_pair.first);

      libMesh::out << std::endl << "-----------------------------------" << std::endl << std::endl;

      SCM_iter++;
    }
}

point_gradient() [1/4]

Gradient libMesh::System::point_gradient ( unsigned int  var, const Point &  p, const bool  insist_on_success = true, const NumericVector< Number > *  sol = nullptr  ) 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 2550 of file system.C.

References libMesh::Variable::active_subdomains(), TIMPI::Communicator::broadcast(), libMesh::ParallelObject::comm(), libMesh::PointLocatorBase::enable_out_of_mesh_mode(), libMesh::System::get_dof_map(), libMesh::System::get_mesh(), libMesh::libmesh_assert(), mesh, TIMPI::Communicator::min(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::processor_id(), libMesh::DofObject::processor_id(), and libMesh::System::variable().

Referenced by line_print(), and 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 an element that contains p and allows us to
  // evaluate var
  const std::set<subdomain_id_type> & raw_subdomains =
    this->variable(var).active_subdomains();
  const std::set<subdomain_id_type> * implicit_subdomains =
    raw_subdomains.empty() ? nullptr : &raw_subdomains;
  const Elem * e = locator(p, implicit_subdomains);

  Gradient grad_u;

  if (e && this->get_dof_map().is_evaluable(*e, var))
    grad_u = point_gradient(var, p, *e, sol);

  // 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() [2/4]

Gradient libMesh::System::point_gradient ( unsigned int  var, const Point &  p, const Elem &  e, const NumericVector< Number > *  sol = nullptr  ) 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 2612 of file system.C.

References libMesh::FEInterface::compute_data(), libMesh::Elem::contains_point(), libMesh::System::current_local_solution, dim, libMesh::Elem::dim(), libMesh::DofMap::dof_indices(), libMesh::FEComputeData::dshape, libMesh::FEComputeData::enable_derivative(), libMesh::System::get_dof_map(), libMesh::System::get_equation_systems(), libMesh::FEMap::inverse_map(), libMesh::DofMap::is_evaluable(), libMesh::libmesh_assert(), libMesh::FEComputeData::local_transform, 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));

  if (!sol)
    sol = this->current_local_solution.get();

  // Get the dof map to get the proper indices for our computation
  const DofMap & dof_map = this->get_dof_map();

  // write the element dimension into a separate variable.
  const unsigned int dim = e.dim();

  // 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
  Point coor = FEMap::inverse_map(dim, &e, p);

  // get the shape function value via the FEInterface to also handle the case
  // of infinite elements correctly, the shape function is not fe->phi().
  FEComputeData fe_data(this->get_equation_systems(), coor);
  fe_data.enable_derivative();
  FEInterface::compute_data(dim, fe_type, &e, fe_data);

  // Get ready to accumulate a gradient
  Gradient grad_u;

  for (unsigned int l=0; l<num_dofs; l++)
    {
      // Chartesian coordinates have always LIBMESH_DIM entries,
      // local coordinates have as many coordinates as the element has.
      for (std::size_t v=0; v<dim; v++)
        for (std::size_t xyz=0; xyz<LIBMESH_DIM; xyz++)
          {
            // FIXME: this needs better syntax: It is matrix-vector multiplication.
            grad_u(xyz) += fe_data.local_transform[v][xyz]
              * fe_data.dshape[l](v)
              * (*sol)(dof_indices[l]);
          }
    }

  return grad_u;
}

point_gradient() [3/4]

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 2677 of file system.C.

References libMesh::libmesh_assert(), and libMesh::System::point_gradient().

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

point_gradient() [4/4]

Gradient libMesh::System::point_gradient ( unsigned int  var, const Point &  p, const NumericVector< Number > *  sol  ) const

inherited

Calls the parallel version of point_gradient().

This function exists only to prevent people from accidentally calling the version of point_gradient() that has a boolean third argument, which would result in incorrect output.

Definition at line 2685 of file system.C.

References libMesh::System::point_gradient().

{
  return this->point_gradient(var, p, true, sol);
}

point_hessian() [1/4]

Tensor libMesh::System::point_hessian ( unsigned int  var, const Point &  p, const bool  insist_on_success = true, const NumericVector< Number > *  sol = nullptr  ) 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 2694 of file system.C.

References libMesh::Variable::active_subdomains(), TIMPI::Communicator::broadcast(), libMesh::ParallelObject::comm(), libMesh::PointLocatorBase::enable_out_of_mesh_mode(), libMesh::System::get_dof_map(), libMesh::System::get_mesh(), libMesh::libmesh_assert(), mesh, TIMPI::Communicator::min(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::processor_id(), libMesh::DofObject::processor_id(), and libMesh::System::variable().

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 an element that contains p and allows us to
  // evaluate var
  const std::set<subdomain_id_type> & raw_subdomains =
    this->variable(var).active_subdomains();
  const std::set<subdomain_id_type> * implicit_subdomains =
    raw_subdomains.empty() ? nullptr : &raw_subdomains;
  const Elem * e = locator(p, implicit_subdomains);

  Tensor hess_u;

  if (e && this->get_dof_map().is_evaluable(*e, var))
    hess_u = point_hessian(var, p, *e, sol);

  // 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() [2/4]

Tensor libMesh::System::point_hessian ( unsigned int  var, const Point &  p, const Elem &  e, const NumericVector< Number > *  sol = nullptr  ) 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 2755 of file system.C.

References libMesh::TypeTensor< T >::add_scaled(), libMesh::FEGenericBase< OutputType >::build(), libMesh::Elem::contains_point(), libMesh::System::current_local_solution, libMesh::Elem::dim(), libMesh::DofMap::dof_indices(), libMesh::System::get_dof_map(), libMesh::Elem::infinite(), libMesh::FEMap::inverse_map(), libMesh::DofMap::is_evaluable(), libMesh::libmesh_assert(), 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));

  if (!sol)
    sol = this->current_local_solution.get();

  if (e.infinite())
    libmesh_not_implemented();

  // 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
  // Build a vector of point co-ordinates to send to reinit
  std::vector<Point> coor(1, FEMap::inverse_map(e.dim(), &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], (*sol)(dof_indices[l]));
    }

  return hess_u;
}

point_hessian() [3/4]

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 2815 of file system.C.

References libMesh::libmesh_assert(), and libMesh::System::point_hessian().

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

point_hessian() [4/4]

Tensor libMesh::System::point_hessian ( unsigned int  var, const Point &  p, const NumericVector< Number > *  sol  ) const

inherited

Calls the parallel version of point_hessian().

This function exists only to prevent people from accidentally calling the version of point_hessian() that has a boolean third argument, which would result in incorrect output.

Definition at line 2823 of file system.C.

References libMesh::System::point_hessian().

{
  return this->point_hessian(var, p, true, sol);
}

point_value() [1/4]

Number libMesh::System::point_value ( unsigned int  var, const Point &  p, const bool  insist_on_success = true, const NumericVector< Number > *  sol = nullptr  ) 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, using the degree of freedom coefficients in sol (or in current_local_solution if sol is left null).

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 2421 of file system.C.

References libMesh::Variable::active_subdomains(), TIMPI::Communicator::broadcast(), libMesh::ParallelObject::comm(), libMesh::PointLocatorBase::enable_out_of_mesh_mode(), libMesh::System::get_dof_map(), libMesh::System::get_mesh(), libMesh::libmesh_assert(), mesh, TIMPI::Communicator::min(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::processor_id(), libMesh::DofObject::processor_id(), and libMesh::System::variable().

Referenced by line_print(), main(), libMesh::System::point_value(), MeshInputTest::testCopyElementSolutionImpl(), MeshInputTest::testCopyElementVectorImpl(), MeshInputTest::testCopyNodalSolutionImpl(), DefaultCouplingTest::testCoupling(), PointNeighborCouplingTest::testCoupling(), MeshInputTest::testExodusWriteElementDataFromDiscontinuousNodalData(), PeriodicBCTest::testPeriodicBC(), SystemsTest::testProjectCubeWithMeshFunction(), and EquationSystemsTest::testRepartitionThenReinit().

{
  // 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 an element that contains p and allows us to
  // evaluate var
  const std::set<subdomain_id_type> & raw_subdomains =
    this->variable(var).active_subdomains();
  const std::set<subdomain_id_type> * implicit_subdomains =
    raw_subdomains.empty() ? nullptr : &raw_subdomains;
  const Elem * e = locator(p, implicit_subdomains);

  Number u = 0;

  if (e && this->get_dof_map().is_evaluable(*e, var))
    u = point_value(var, p, *e, sol);

  // 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() [2/4]

Number libMesh::System::point_value ( unsigned int  var, const Point &  p, const Elem &  e, const NumericVector< Number > *  sol = nullptr  ) const

inherited

Returns

The value of the solution variable var at the physical point p contained in local Elem e, using the degree of freedom coefficients in sol (or in current_local_solution if sol is left null).

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 2482 of file system.C.

References libMesh::FEInterface::compute_data(), libMesh::Elem::contains_point(), libMesh::System::current_local_solution, libMesh::Elem::dim(), libMesh::DofMap::dof_indices(), libMesh::System::get_dof_map(), libMesh::System::get_equation_systems(), libMesh::FEMap::inverse_map(), libMesh::DofMap::is_evaluable(), libMesh::libmesh_assert(), 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));

  if (!sol)
    sol = this->current_local_solution.get();

  // 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
  Point coor = FEMap::inverse_map(e.dim(), &e, p);

  // get the shape function value via the FEInterface to also handle the case
  // of infinite elements correctly, 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] * (*sol)(dof_indices[l]);
    }

  return u;
}

point_value() [3/4]

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 2534 of file system.C.

References libMesh::libmesh_assert(), and libMesh::System::point_value().

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

point_value() [4/4]

Number libMesh::System::point_value ( unsigned int  var, const Point &  p, const NumericVector< Number > *  sol  ) const

inherited

Calls the parallel version of point_value().

This function exists only to prevent people from accidentally calling the version of point_value() that has a boolean third argument, which would result in incorrect output.

Definition at line 2542 of file system.C.

References libMesh::System::point_value().

{
  return this->point_value(var, p, true, sol);
}

prefer_hash_table_matrix_assembly()

void libMesh::System::prefer_hash_table_matrix_assembly ( bool  preference )

inlineinherited

Sets whether to use hash table matrix assembly if the matrix sub-classes support it.

Definition at line 2728 of file system.h.

References libMesh::System::_matrices_initialized, and libMesh::System::_prefer_hash_table_matrix_assembly.

Referenced by main().

{
  libmesh_error_msg_if(
      _matrices_initialized,
      "System::prefer_hash_table_matrix_assembly() should be called before matrices are initialized");
  _prefer_hash_table_matrix_assembly = preference;
}

prefix()

std::string libMesh::System::prefix ( ) const

inlineinherited

Returns

A prefix that may be applied to solver options. Note that this prefix is only used if prefix_with_name()

Definition at line 1938 of file system.h.

References libMesh::System::name().

Referenced by libMesh::ImplicitSystem::get_linear_solver(), libMesh::LinearImplicitSystem::solve(), and libMesh::NonlinearImplicitSystem::solve().

{ return this->name() + "_"; }

prefix_with_name() [1/2]

void libMesh::System::prefix_with_name ( bool  value )

inlineinherited

Instructs this system to prefix solve options with its name for solvers that leverage prefixes.

Definition at line 1927 of file system.h.

References libMesh::System::_prefix_with_name, and value.

{ _prefix_with_name = value; }

prefix_with_name() [2/2]

bool libMesh::System::prefix_with_name ( ) const

inlineinherited

Returns

Whether we are name prefixing

Definition at line 1932 of file system.h.

References libMesh::System::_prefix_with_name.

Referenced by libMesh::ContinuationSystem::ContinuationSystem(), libMesh::ImplicitSystem::get_linear_solver(), libMesh::LinearImplicitSystem::solve(), libMesh::NonlinearImplicitSystem::solve(), and libMesh::System::System().

{ return _prefix_with_name; }

print_discrete_parameter_values()

void libMesh::RBParametrized::print_discrete_parameter_values ( ) const

inherited

Print out all the discrete parameter values.

Definition at line 380 of file rb_parametrized.C.

References libMesh::RBParametrized::get_discrete_parameter_values(), libMesh::Quality::name(), libMesh::out, and value.

Referenced by print_info(), libMesh::RBEIMConstruction::print_info(), and libMesh::RBConstruction::print_info().

{
  for (const auto & [name, values] : get_discrete_parameter_values())
    {
      libMesh::out << "Discrete parameter " << name << ", values: ";

      for (const auto & value : values)
        libMesh::out << value << " ";
      libMesh::out << std::endl;
    }
}

print_info() [1/3]

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

staticinherited

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

Definition at line 81 of file reference_counter.C.

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

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

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

print_info() [2/3]

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

staticinherited

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

Definition at line 81 of file reference_counter.C.

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

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

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

print_info() [3/3]

void libMesh::RBSCMConstruction::print_info ( )

virtual

Print out info that describes the current setup of this RBSCMConstruction.

Definition at line 161 of file rb_scm_construction.C.

References libMesh::RBThetaExpansion::get_n_A_terms(), libMesh::RBParametrized::get_n_params(), libMesh::RBConstructionBase< CondensedEigenSystem >::get_n_training_samples(), libMesh::RBParametrized::get_parameter_max(), libMesh::RBParametrized::get_parameter_min(), libMesh::RBParametrized::get_parameters(), get_rb_theta_expansion(), get_SCM_training_tolerance(), libMesh::System::name(), libMesh::out, libMesh::RBParametrized::print_discrete_parameter_values(), and rb_scm_eval.

{
  // Print out info that describes the current setup
  libMesh::out << std::endl << "RBSCMConstruction parameters:" << std::endl;
  libMesh::out << "system name: " << this->name() << std::endl;
  libMesh::out << "SCM Greedy tolerance: " << get_SCM_training_tolerance() << std::endl;
  if (rb_scm_eval)
    {
      libMesh::out << "A_q operators attached: " << get_rb_theta_expansion().get_n_A_terms() << std::endl;
    }
  else
    {
      libMesh::out << "RBThetaExpansion member is not set yet" << std::endl;
    }
  libMesh::out << "Number of parameters: " << get_n_params() << std::endl;
  for (const auto & pr : get_parameters())
    {
      const std::string & param_name = pr.first;
      libMesh::out <<   "Parameter " << param_name
                   << ": Min = " << get_parameter_min(param_name)
                   << ", Max = " << get_parameter_max(param_name) << std::endl;
    }
  print_discrete_parameter_values();
  libMesh::out << "n_training_samples: " << get_n_training_samples() << std::endl;
  libMesh::out << std::endl;
}

print_parameters()

void libMesh::RBParametrized::print_parameters ( ) const

inherited

Print the current parameters.

Definition at line 192 of file rb_parametrized.C.

References libMesh::RBParametrized::get_parameters(), libMesh::RBParametrized::parameters_initialized, and libMesh::RBParameters::print().

Referenced by libMesh::RBEIMConstruction::train_eim_approximation_with_greedy(), and libMesh::RBConstruction::train_reduced_basis_with_greedy().

{
  libmesh_error_msg_if(!parameters_initialized, "Error: parameters not initialized in RBParametrized::print_current_parameters");

  get_parameters().print();
}

process_parameters_file()

void libMesh::RBSCMConstruction::process_parameters_file ( const std::string &  parameters_filename )

virtual

Read in the parameters from file specified by parameters_filename and set the this system's member variables accordingly.

Definition at line 89 of file rb_scm_construction.C.

References libMesh::RBParametrized::get_parameters(), libMesh::RBParametrized::get_parameters_max(), libMesh::RBParametrized::get_parameters_min(), libMesh::RBParametrized::initialize_parameters(), libMesh::RBConstructionBase< CondensedEigenSystem >::initialize_training_parameters(), libMesh::Real, SCM_training_tolerance, set_SCM_training_tolerance(), libMesh::RBConstructionBase< CondensedEigenSystem >::set_training_random_seed(), and libMesh::RBParameters::set_value().

{
  // First read in data from parameters_filename
  GetPot infile(parameters_filename);
  const unsigned int n_training_samples = infile("n_training_samples",1);
  const bool deterministic_training     = infile("deterministic_training",false);

  // Read in training_parameters_random_seed value.  This is used to
  // seed the RNG when picking the training parameters.  By default the
  // value is -1, which means use std::time to seed the RNG.
  unsigned int training_parameters_random_seed_in = static_cast<unsigned int>(-1);
  training_parameters_random_seed_in = infile("training_parameters_random_seed",
                                              training_parameters_random_seed_in);
  set_training_random_seed(static_cast<int>(training_parameters_random_seed_in));

  // SCM Greedy termination tolerance
  const Real SCM_training_tolerance_in = infile("SCM_training_tolerance", SCM_training_tolerance);
  set_SCM_training_tolerance(SCM_training_tolerance_in);

  // Initialize the parameter ranges and the parameters themselves
  unsigned int n_continuous_parameters = infile.vector_variable_size("parameter_names");
  RBParameters mu_min_in;
  RBParameters mu_max_in;
  for (unsigned int i=0; i<n_continuous_parameters; i++)
    {
      // Read in the parameter names
      std::string param_name = infile("parameter_names", "NONE", i);

      {
        Real min_val = infile(param_name, 0., 0);
        mu_min_in.set_value(param_name, min_val);
      }

      {
        Real max_val = infile(param_name, 0., 1);
        mu_max_in.set_value(param_name, max_val);
      }
    }

  std::map<std::string, std::vector<Real>> discrete_parameter_values_in;

  unsigned int n_discrete_parameters = infile.vector_variable_size("discrete_parameter_names");
  for (unsigned int i=0; i<n_discrete_parameters; i++)
    {
      std::string param_name = infile("discrete_parameter_names", "NONE", i);

      unsigned int n_vals_for_param = infile.vector_variable_size(param_name);
      std::vector<Real> vals_for_param(n_vals_for_param);
      for (unsigned int j=0; j != n_vals_for_param; j++)
        vals_for_param[j] = infile(param_name, 0., j);

      discrete_parameter_values_in[param_name] = vals_for_param;
    }

  initialize_parameters(mu_min_in, mu_max_in, discrete_parameter_values_in);

  std::map<std::string,bool> log_scaling;
  const RBParameters & mu = get_parameters();
  unsigned int i=0;
  for (const auto & pr : mu)
    {
      const std::string & param_name = pr.first;
      log_scaling[param_name] = static_cast<bool>(infile("log_scaling", 0, i++));
    }

  initialize_training_parameters(this->get_parameters_min(),
                                 this->get_parameters_max(),
                                 n_training_samples,
                                 log_scaling,
                                 deterministic_training);   // use deterministic parameters
}

processor_id()

processor_id_type libMesh::ParallelObject::processor_id ( ) const

inlineinherited

Returns

The rank of this processor in the group.

Definition at line 114 of file parallel_object.h.

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

Referenced by libMesh::BoundaryInfo::_find_id_maps(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::DistributedMesh::add_elem(), libMesh::BoundaryInfo::add_elements(), libMesh::DofMap::add_neighbors_to_send_list(), libMesh::DistributedMesh::add_node(), libMesh::MeshTools::Modification::all_tri(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::FEMSystem::assembly(), libMesh::Nemesis_IO::assert_symmetric_cmaps(), libMesh::Partitioner::assign_partitioning(), libMesh::Nemesis_IO_Helper::build_element_and_node_maps(), libMesh::Partitioner::build_graph(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::MeshFunction::check_found_elem(), libMesh::DistributedMesh::clear(), libMesh::DistributedMesh::clear_elems(), libMesh::ExodusII_IO_Helper::close(), libMesh::Nemesis_IO_Helper::compute_border_node_ids(), libMesh::Nemesis_IO_Helper::compute_communication_map_parameters(), libMesh::Nemesis_IO_Helper::compute_internal_and_border_elems_and_internal_nodes(), libMesh::RBConstruction::compute_max_error_bound(), libMesh::Nemesis_IO_Helper::compute_node_communication_maps(), libMesh::Nemesis_IO_Helper::compute_num_global_elem_blocks(), libMesh::Nemesis_IO_Helper::compute_num_global_nodesets(), libMesh::Nemesis_IO_Helper::compute_num_global_sidesets(), libMesh::Nemesis_IO_Helper::construct_nemesis_filename(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::Nemesis_IO::copy_scalar_solution(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::ExodusII_IO_Helper::create(), libMesh::DistributedMesh::delete_elem(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_scalar_dofs(), libMesh::DistributedMesh::DistributedMesh(), libMesh::DofMapBase::end_dof(), libMesh::DofMapBase::end_old_dof(), libMesh::EnsightIO::EnsightIO(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::SubFunctor::find_dofs_to_send(), libMesh::UnstructuredMesh::find_neighbors(), libMesh::DofMapBase::first_dof(), libMesh::DofMapBase::first_old_dof(), libMesh::RBEIMEvaluation::gather_bfs(), libMesh::Nemesis_IO_Helper::get_cmap_params(), libMesh::Nemesis_IO_Helper::get_eb_info_global(), libMesh::Nemesis_IO_Helper::get_elem_cmap(), libMesh::Nemesis_IO_Helper::get_elem_map(), libMesh::MeshBase::get_info(), libMesh::DofMap::get_info(), libMesh::Nemesis_IO_Helper::get_init_global(), libMesh::Nemesis_IO_Helper::get_init_info(), libMesh::RBEIMEvaluation::get_interior_basis_functions_as_vecs(), libMesh::Nemesis_IO_Helper::get_loadbal_param(), libMesh::DofMap::get_local_constraints(), libMesh::MeshBase::get_local_constraints(), libMesh::Nemesis_IO_Helper::get_node_cmap(), libMesh::Nemesis_IO_Helper::get_node_map(), libMesh::Nemesis_IO_Helper::get_ns_param_global(), libMesh::Nemesis_IO_Helper::get_ss_param_global(), libMesh::SparsityPattern::Build::handle_vi_vj(), libMesh::LaplaceMeshSmoother::init(), libMesh::SystemSubsetBySubdomain::init(), HeatSystem::init_data(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::initialize_element_variables(), libMesh::ExodusII_IO_Helper::initialize_global_variables(), libMesh::ExodusII_IO_Helper::initialize_nodal_variables(), libMesh::DistributedMesh::insert_elem(), libMesh::DofMap::is_evaluable(), libMesh::SparsityPattern::Build::join(), libMesh::TransientRBEvaluation::legacy_write_offline_data_to_files(), libMesh::RBSCMEvaluation::legacy_write_offline_data_to_files(), libMesh::RBEvaluation::legacy_write_offline_data_to_files(), libMesh::MeshTools::libmesh_assert_consistent_distributed(), libMesh::MeshTools::libmesh_assert_consistent_distributed_nodes(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_object_ids(), libMesh::DofMap::local_variable_indices(), main(), libMesh::MeshRefinement::make_coarsening_compatible(), AugmentSparsityOnInterface::mesh_reinit(), libMesh::TriangulatorInterface::MeshedHole::MeshedHole(), libMesh::MeshBase::n_active_local_elem(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::MeshTools::n_connected_components(), libMesh::MeshBase::n_constraint_rows(), libMesh::BoundaryInfo::n_edge_conds(), libMesh::DofMapBase::n_local_dofs(), libMesh::MeshBase::n_local_elem(), libMesh::MeshBase::n_local_nodes(), libMesh::BoundaryInfo::n_nodeset_conds(), libMesh::BoundaryInfo::n_shellface_conds(), libMesh::RBEIMEvaluation::node_gather_bfs(), libMesh::DistributedMesh::own_node(), libMesh::BoundaryInfo::parallel_sync_node_ids(), libMesh::BoundaryInfo::parallel_sync_side_ids(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::MeshBase::print_constraint_rows(), libMesh::DofMap::print_dof_constraints(), libMesh::DofMap::process_mesh_constraint_rows(), libMesh::Nemesis_IO_Helper::put_cmap_params(), libMesh::Nemesis_IO_Helper::put_elem_cmap(), libMesh::Nemesis_IO_Helper::put_elem_map(), libMesh::Nemesis_IO_Helper::put_loadbal_param(), libMesh::Nemesis_IO_Helper::put_node_cmap(), libMesh::Nemesis_IO_Helper::put_node_map(), libMesh::NameBasedIO::read(), libMesh::Nemesis_IO::read(), libMesh::XdrIO::read(), libMesh::CheckpointIO::read(), libMesh::EquationSystems::read(), libMesh::ExodusII_IO_Helper::read_elem_num_map(), libMesh::ExodusII_IO_Helper::read_global_values(), libMesh::ExodusII_IO::read_header(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::System::read_header(), libMesh::System::read_legacy_data(), libMesh::DynaIO::read_mesh(), libMesh::ExodusII_IO_Helper::read_node_num_map(), libMesh::System::read_parallel_data(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), libMesh::System::read_SCALAR_dofs(), libMesh::XdrIO::read_serialized_bc_names(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::System::read_serialized_data(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::System::read_serialized_vector(), libMesh::System::read_serialized_vectors(), libMesh::Nemesis_IO_Helper::read_var_names_impl(), libMesh::SimplexRefiner::refine_via_edges(), libMesh::StaticCondensationDofMap::reinit(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::DistributedMesh::renumber_nodes_and_elements(), libMesh::DofMap::scatter_constraints(), libMesh::CheckpointIO::select_split_config(), libMesh::DistributedMesh::set_next_unique_id(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::RBEIMEvaluation::side_gather_bfs(), ExodusTest< elem_type >::test_read_gold(), ExodusTest< elem_type >::test_write(), MeshInputTest::testAbaqusRead(), MeshInputTest::testBadGmsh(), MeshInputTest::testCopyElementSolutionImpl(), MeshInputTest::testCopyElementVectorImpl(), MeshInputTest::testCopyNodalSolutionImpl(), DefaultCouplingTest::testCoupling(), PointNeighborCouplingTest::testCoupling(), MeshInputTest::testDynaFileMappings(), MeshInputTest::testDynaNoSplines(), MeshInputTest::testDynaReadElem(), MeshInputTest::testDynaReadPatch(), MeshInputTest::testExodusFileMappings(), MeshInputTest::testExodusIGASidesets(), MeshInputTest::testExodusWriteElementDataFromDiscontinuousNodalData(), MeshInputTest::testGmshBCIDOverlap(), MeshInputTest::testGoodGmsh(), MeshInputTest::testGoodSTL(), MeshInputTest::testGoodSTLBinary(), MeshInputTest::testLowOrderEdgeBlocks(), SystemsTest::testProjectMatrix3D(), BoundaryInfoTest::testShellFaceConstraints(), MeshInputTest::testSingleElementImpl(), WriteVecAndScalar::testSolution(), CheckpointIOTest::testSplitter(), MeshInputTest::testTetgenIO(), libMesh::MeshTools::total_weight(), libMesh::NetGenMeshInterface::triangulate(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::DistributedMesh::update_parallel_id_counts(), libMesh::DTKAdapter::update_variable_values(), libMesh::MeshTools::volume(), libMesh::STLIO::write(), libMesh::NameBasedIO::write(), libMesh::XdrIO::write(), libMesh::CheckpointIO::write(), libMesh::EquationSystems::write(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::ExodusII_IO::write_element_data(), libMesh::ExodusII_IO_Helper::write_element_values(), libMesh::ExodusII_IO_Helper::write_element_values_element_major(), libMesh::ExodusII_IO_Helper::write_elements(), libMesh::ExodusII_IO_Helper::write_elemset_data(), libMesh::ExodusII_IO_Helper::write_elemsets(), libMesh::ExodusII_IO::write_global_data(), libMesh::ExodusII_IO_Helper::write_global_values(), libMesh::System::write_header(), libMesh::ExodusII_IO::write_information_records(), libMesh::ExodusII_IO_Helper::write_information_records(), libMesh::ExodusII_IO_Helper::write_nodal_coordinates(), libMesh::UCDIO::write_nodal_data(), libMesh::VTKIO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data_common(), libMesh::ExodusII_IO::write_nodal_data_discontinuous(), libMesh::ExodusII_IO_Helper::write_nodal_values(), libMesh::ExodusII_IO_Helper::write_nodeset_data(), libMesh::Nemesis_IO_Helper::write_nodesets(), libMesh::ExodusII_IO_Helper::write_nodesets(), libMesh::RBEIMEvaluation::write_out_interior_basis_functions(), libMesh::RBEIMEvaluation::write_out_node_basis_functions(), libMesh::RBEIMEvaluation::write_out_side_basis_functions(), write_output_solvedata(), libMesh::System::write_parallel_data(), libMesh::RBConstruction::write_riesz_representors_to_files(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bc_names(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::System::write_serialized_data(), libMesh::XdrIO::write_serialized_nodes(), libMesh::XdrIO::write_serialized_nodesets(), libMesh::XdrIO::write_serialized_subdomain_names(), libMesh::System::write_serialized_vector(), libMesh::System::write_serialized_vectors(), libMesh::ExodusII_IO_Helper::write_sideset_data(), libMesh::Nemesis_IO_Helper::write_sidesets(), libMesh::ExodusII_IO_Helper::write_sidesets(), libMesh::ExodusII_IO::write_timestep(), libMesh::ExodusII_IO_Helper::write_timestep(), and libMesh::ExodusII_IO::write_timestep_discontinuous().

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

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.

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

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.

Definition at line 1041 of file system_projection.C.

Referenced by init_sys(), initialize(), main(), set_initial_condition(), SlitMeshRefinedSystemTest::setUp(), FETestBase< order, family, elem_type, 1 >::setUp(), MeshfunctionDFEM::test_mesh_function_dfem(), MeshfunctionDFEM::test_mesh_function_dfem_grad(), MeshFunctionTest::test_p_level(), MeshFunctionTest::test_subdomain_id_sets(), MeshInputTest::testCopyElementSolutionImpl(), MeshInputTest::testCopyNodalSolutionImpl(), DefaultCouplingTest::testCoupling(), PointNeighborCouplingTest::testCoupling(), SystemsTest::testProjectCubeWithMeshFunction(), MeshInputTest::testProjectionRegression(), EquationSystemsTest::testRepartitionThenReinit(), and libMesh::MeshfreeSolutionTransfer::transfer().

{
  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.

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

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.

Definition at line 1054 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 1027 of file system_projection.C.

References fptr(), and gptr().

{
  WrappedFunction<Number> f(*this, fptr, &function_parameters);
  WrappedFunction<Gradient> g(*this, gptr, &function_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 838 of file system.h.

References libMesh::System::_solution_projection.

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), and libMesh::MemoryHistoryData::store_vectors().

  { return _solution_projection; }

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.

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

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.

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

Definition at line 1082 of file system_projection.C.

References libMesh::libmesh_assert().

Referenced by main(), libMesh::NewmarkSolver::project_initial_accel(), libMesh::SecondOrderUnsteadySolver::project_initial_rate(), libMesh::InterMeshProjection::project_system_vectors(), 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.

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

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.

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

Definition at line 1108 of file system_projection.C.

References libMesh::NumericVector< T >::close(), libMesh::FEMFunctionBase< Output >::component(), libMesh::FEType::family, libMesh::Utility::iota(), libMesh::libmesh_assert(), libMesh::libmesh_ignore(), libMesh::make_range(), n_vars, libMesh::NODEELEM, libMesh::FEMContext::pre_fe_reinit(), libMesh::RATIONAL_BERNSTEIN, libMesh::SCALAR, libMesh::DofMap::SCALAR_dof_indices(), libMesh::NumericVector< T >::set(), and libMesh::Variable::type().

{
  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);

      FEMProjector projector(*this, fw, &gw, setter, vars);
      projector.project(active_local_range);
    }
  else
    {
      FEMProjector projector(*this, fw, nullptr, setter, vars);
      projector.project(active_local_range);
    }

  // 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 (auto var : make_range(this->n_vars()))
        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]
            context.pre_fe_reinit(*this, *(this->get_mesh().active_local_elements_begin()));

            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();

  // Look for spline bases, in which case we need to backtrack
  // to calculate the spline DoF values.
  std::vector<const Variable *> rational_vars;
  for (auto varnum : vars)
    {
      const Variable & var = this->get_dof_map().variable(varnum);
      if (var.type().family == RATIONAL_BERNSTEIN)
        rational_vars.push_back(&var);
    }

  // Okay, but are we really using any *spline* bases, or just
  // unconstrained rational bases?
  bool using_spline_bases = false;
  if (!rational_vars.empty())
    {
      // Look for a spline node: a NodeElem with a rational variable
      // on it.
      for (auto & elem : active_local_range)
        if (elem->type() == NODEELEM)
          for (auto rational_var : rational_vars)
            if (rational_var->active_on_subdomain(elem->subdomain_id()))
              {
                using_spline_bases = true;
                goto checked_on_splines;
              }
    }

checked_on_splines:

  // Not every processor may have a NodeElem, especially while
  // we're not partitioning them efficiently yet.
  this->comm().max(using_spline_bases);

  if (using_spline_bases)
    this->solve_for_unconstrained_dofs(new_vector, is_adjoint);

#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);
#else
  libmesh_ignore(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.

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

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.

Definition at line 1067 of file system_projection.C.

References fptr(), and gptr().

{
  WrappedFunction<Number> f(*this, fptr, &function_parameters);
  WrappedFunction<Gradient> g(*this, gptr, &function_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 247 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 > &  old_v, NumericVector< Number > &  new_v, int  is_adjoint = -1  ) const

protectedinherited

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

This method projects the vector via L2 projections or nodal interpolations on each element.

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.

This method projects a solution from an old mesh to a current, refined mesh. The input vector old_v gives the solution on the old mesh, while the new_v gives the solution (to be computed) on the new mesh.

Definition at line 265 of file system_projection.C.

References libMesh::NumericVector< T >::clear(), libMesh::NumericVector< T >::close(), libMesh::NumericVector< T >::get(), libMesh::GHOSTED, libMesh::index_range(), libMesh::NumericVector< T >::init(), libMesh::Utility::iota(), libMesh::libmesh_assert(), libMesh::libmesh_ignore(), libMesh::NumericVector< T >::local_size(), libMesh::NumericVector< T >::localize(), libMesh::make_range(), n_vars, libMesh::PARALLEL, libMesh::Threads::parallel_reduce(), libMesh::SCALAR, libMesh::DofMap::SCALAR_dof_indices(), libMesh::BuildProjectionList::send_list, libMesh::SERIAL, libMesh::NumericVector< T >::set(), libMesh::NumericVector< T >::size(), libMesh::NumericVector< T >::type(), libMesh::TYPE_SCALAR, and libMesh::BuildProjectionList::unique().

{
  LOG_SCOPE ("project_vector(old,new)", "System");

  new_v.clear();

#ifdef LIBMESH_ENABLE_AMR

  // Resize the new vector and get a serial version.
  NumericVector<Number> * new_vector_ptr = nullptr;
  std::unique_ptr<NumericVector<Number>> new_vector_built;
  NumericVector<Number> * local_old_vector;
  std::unique_ptr<NumericVector<Number>> local_old_vector_built;
  const NumericVector<Number> * old_vector_ptr = nullptr;

  ConstElemRange active_local_elem_range
    (this->get_mesh().active_local_elements_begin(),
     this->get_mesh().active_local_elements_end());

  // If the old vector was uniprocessor, make the new
  // vector uniprocessor
  if (old_v.type() == SERIAL)
    {
      new_v.init (this->n_dofs(), false, SERIAL);
      new_vector_ptr = &new_v;
      old_vector_ptr = &old_v;
    }

  // Otherwise it is a parallel, distributed vector, which
  // we need to localize.
  else if (old_v.type() == PARALLEL)
    {
      // Build a send list for efficient localization
      BuildProjectionList projection_list(*this);
      Threads::parallel_reduce (active_local_elem_range,
                                projection_list);

      // Create a sorted, unique send_list
      projection_list.unique();

      new_v.init (this->n_dofs(), this->n_local_dofs(), false, PARALLEL);
      new_vector_built = NumericVector<Number>::build(this->comm());
      local_old_vector_built = NumericVector<Number>::build(this->comm());
      new_vector_ptr = new_vector_built.get();
      local_old_vector = local_old_vector_built.get();
      new_vector_ptr->init(this->n_dofs(), this->n_local_dofs(),
                           this->get_dof_map().get_send_list(), false,
                           GHOSTED);
      local_old_vector->init(old_v.size(), old_v.local_size(),
                             projection_list.send_list, false, GHOSTED);
      old_v.localize(*local_old_vector, projection_list.send_list);
      local_old_vector->close();
      old_vector_ptr = local_old_vector;
    }
  else if (old_v.type() == GHOSTED)
    {
      // Build a send list for efficient localization
      BuildProjectionList projection_list(*this);
      Threads::parallel_reduce (active_local_elem_range,
                                projection_list);

      // Create a sorted, unique send_list
      projection_list.unique();

      new_v.init (this->n_dofs(), this->n_local_dofs(),
                  this->get_dof_map().get_send_list(), false, GHOSTED);

      local_old_vector_built = NumericVector<Number>::build(this->comm());
      new_vector_ptr = &new_v;
      local_old_vector = local_old_vector_built.get();
      local_old_vector->init(old_v.size(), old_v.local_size(),
                             projection_list.send_list, false, GHOSTED);
      old_v.localize(*local_old_vector, projection_list.send_list);
      local_old_vector->close();
      old_vector_ptr = local_old_vector;
    }
  else // unknown old_v.type()
    libmesh_error_msg("ERROR: Unknown old_v.type() == " << old_v.type());

  // Note that the above will have zeroed the new_vector.
  // Just to be sure, assert that new_vector_ptr and old_vector_ptr
  // were successfully set before trying to deref them.
  libmesh_assert(new_vector_ptr);
  libmesh_assert(old_vector_ptr);

  NumericVector<Number> & new_vector = *new_vector_ptr;
  const NumericVector<Number> & old_vector = *old_vector_ptr;

  const unsigned int n_variables = this->n_vars();

  if (n_variables)
    {
      std::vector<unsigned int> vars(n_variables);
      std::iota(vars.begin(), vars.end(), 0);
      std::vector<unsigned int> regular_vars, vector_vars;
      for (auto var : vars)
      {
        if (FEInterface::field_type(this->variable_type(var)) == TYPE_SCALAR)
          regular_vars.push_back(var);
        else
          vector_vars.push_back(var);
      }

      VectorSetAction<Number> setter(new_vector);

      if (!regular_vars.empty())
        {
          // Use a typedef to make the calling sequence for parallel_for() a bit more readable
          typedef
            GenericProjector<OldSolutionValue<Number,   &FEMContext::point_value>,
                             OldSolutionValue<Gradient, &FEMContext::point_gradient>,
                             Number, VectorSetAction<Number>> FEMProjector;

          OldSolutionValue<Number,   &FEMContext::point_value>
            f(*this, old_vector, &regular_vars);
          OldSolutionValue<Gradient, &FEMContext::point_gradient>
            g(*this, old_vector, &regular_vars);

          FEMProjector projector(*this, f, &g, setter, regular_vars);
          projector.project(active_local_elem_range);
        }

      if (!vector_vars.empty())
        {
          typedef
            GenericProjector<OldSolutionValue<Gradient,   &FEMContext::point_value>,
                             OldSolutionValue<Tensor, &FEMContext::point_gradient>,
                             Gradient, VectorSetAction<Number>> FEMVectorProjector;

          OldSolutionValue<Gradient, &FEMContext::point_value> f_vector(*this, old_vector, &vector_vars);
          OldSolutionValue<Tensor, &FEMContext::point_gradient> g_vector(*this, old_vector, &vector_vars);

          FEMVectorProjector vector_projector(*this, f_vector, &g_vector, setter, vector_vars);
          vector_projector.project(active_local_elem_range);
        }

      // Copy the SCALAR dofs from old_vector to new_vector
      // 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 (auto var : make_range(this->n_vars()))
            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);
                for (auto i : index_range(new_SCALAR_indices))
                  new_vector.set(new_SCALAR_indices[i], old_vector(old_SCALAR_indices[i]));
              }
        }
    }

  new_vector.close();

  // If the old vector was serial, we probably need to send our values
  // to other processors
  //
  // FIXME: I'm not sure how to make a NumericVector do that without
  // creating a temporary parallel vector to use localize! - RHS
  if (old_v.type() == SERIAL)
    {
      std::unique_ptr<NumericVector<Number>> dist_v = NumericVector<Number>::build(this->comm());
      dist_v->init(this->n_dofs(), this->n_local_dofs(), false, PARALLEL);
      dist_v->close();

      for (auto i : make_range(dist_v->size()))
        if (new_vector(i) != 0.0)
          dist_v->set(i, new_vector(i));

      dist_v->close();

      dist_v->localize (new_v, this->get_dof_map().get_send_list());
      new_v.close();
    }
  // If the old vector was parallel, we need to update it
  // and free the localized copies
  else if (old_v.type() == PARALLEL)
    {
      // We may have to set dof values that this processor doesn't
      // own in certain special cases, like LAGRANGE FIRST or
      // HERMITE THIRD elements on second-order meshes?
      new_v = new_vector;
      new_v.close();
    }


  // Apply constraints only if we we are asked to
  if(this->project_with_constraints)
  {
    if (is_adjoint == -1)
    {
      this->get_dof_map().enforce_constraints_exactly(*this, &new_v);
    }
    else if (is_adjoint >= 0)
    {
      this->get_dof_map().enforce_adjoint_constraints_exactly(new_v,
                                                            is_adjoint);
    }
  }
#else

  // AMR is disabled: simply copy the vector
  new_v = old_v;

  libmesh_ignore(is_adjoint);

#endif // #ifdef LIBMESH_ENABLE_AMR
}

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.

Definition at line 961 of file system_projection.C.

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

Referenced by libMesh::PetscDMWrapper::init_petscdm(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), and SystemsTest::testProjectMatrix3D().

{
  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, &vars);
      OldSolutionGradientCoefs g(*this, &vars);
      MatrixFillAction<Real, Number> setter(proj_mat);

      ProjMatFiller mat_filler(*this, f, &g, setter, vars);
      mat_filler.project(active_local_elem_range);

      // 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 (auto var : make_range(this->n_vars()))
            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 444 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::System::qoi_parameter_hessian ( const QoISet &  qoi_indices, const ParameterVector &  parameters, SensitivityData &  hessian  )

inlinevirtualinherited

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).

This method is only implemented in some derived classes.

Reimplemented in libMesh::ImplicitSystem.

Definition at line 2681 of file system.h.

{
  libmesh_not_implemented();
}

qoi_parameter_hessian_vector_product()

void libMesh::System::qoi_parameter_hessian_vector_product ( const QoISet &  qoi_indices, const ParameterVector &  parameters, const ParameterVector &  vector, SensitivityData &  product  )

inlinevirtualinherited

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].

This method is only implemented in some derived classes.

Reimplemented in libMesh::ImplicitSystem.

Definition at line 2690 of file system.h.

{
  libmesh_not_implemented();
}

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 602 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_vec.size())
    forward_qoi_parameter_sensitivity(qoi_indices, parameters_vec, 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_vec, 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 533 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, std::string_view  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 97 of file system_io.C.

References libMesh::System::_additional_data_written, libMesh::System::_written_var_indices, libMesh::System::add_variable(), libMesh::System::add_vector(), TIMPI::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::libmesh_assert(), 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(), and libMesh::RBEvaluation::read_in_vectors_from_multiple_files().

{
  // 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 occurrence, 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 [email protected] 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 (io.version() >= LIBMESH_VERSION_ID(1,7,0))
        {
          int vec_projection = 0;
          if (this->processor_id() == 0)
            io.data (vec_projection);
          this->comm().broadcast(vec_projection);
          int vec_type;
          if (this->processor_id() == 0)
            io.data (vec_type);
          this->comm().broadcast(vec_type);

          if (read_additional_data)
            this->add_vector(vec_name, bool(vec_projection), ParallelType(vec_type));
        }
      else 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 302 of file system_io.C.

References libMesh::System::_additional_data_written, libMesh::System::_vectors, libMesh::System::_written_var_indices, TIMPI::Communicator::broadcast(), libMesh::ParallelObject::comm(), libMesh::Xdr::data(), libMesh::System::get_mesh(), libMesh::DofObject::invalid_id, libMesh::libmesh_assert(), libMesh::make_range(), 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());

  // directly-read and reordered buffers, declared here for reuse
  // without heap juggling.
  std::vector<Number> global_vector;
  std::vector<Number> reordered_vector;

  auto reorder_vector_into =
    [this, &global_vector, &reordered_vector]
    (NumericVector<Number> & vec)
  {
    this->comm().broadcast(global_vector);

    // If we have been reading multiple vectors, they should all be
    // the same size.
    libmesh_assert (reordered_vector.empty() ||
                    reordered_vector.size() == global_vector.size());

    // 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 (auto index : make_range(node->n_comp(sys,var)))
            {
              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 (auto index : make_range(elem->n_comp(sys,var)))
            {
              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
    vec = reordered_vector;
  };

  // 10.)
  // Read and set the solution vector
  if (this->processor_id() == 0)
    io.data (global_vector);
  reorder_vector_into(*(this->solution));

  // 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");

      auto 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)
            {
              std::fill (reordered_vector.begin(),
                         reordered_vector.end(),
                         libMesh::zero);

              reorder_vector_into(*(pos->second));
            }

          // 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 449 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::libmesh_assert(), libMesh::make_range(), 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 (auto comp : make_range(node->n_comp(sys_num,var)))
              {
                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 (auto comp : make_range(elem->n_comp(sys_num,var)))
              {
                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 (auto dof : SCALAR_dofs)
                this->solution->set(dof, 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");

      auto 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 (auto comp : make_range(node->n_comp(sys_num,var)))
                          {
                            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 (auto comp : make_range(elem->n_comp(sys_num,var)))
                          {
                            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 (auto dof : SCALAR_dofs)
                            pos->second->set(dof, 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 LIBMESH_EXPORT 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 1350 of file system.h.

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

read_parameter_data_from_files()

void libMesh::RBParametrized::read_parameter_data_from_files ( const std::string &  continuous_param_file_name, const std::string &  discrete_param_file_name, const bool  read_binary_data  )

inherited

Read in the parameter ranges from files.

Definition at line 276 of file rb_parametrized.C.

References libMesh::RBParametrized::initialize_parameters(), libMesh::RBParametrized::read_discrete_parameter_values_from_file(), and libMesh::RBParametrized::read_parameter_ranges_from_file().

Referenced by libMesh::RBSCMEvaluation::legacy_read_offline_data_from_files(), and libMesh::RBEvaluation::legacy_read_offline_data_from_files().

{
  RBParameters param_min;
  RBParameters param_max;
  read_parameter_ranges_from_file(continuous_param_file_name,
                                  read_binary_data,
                                  param_min,
                                  param_max);

  std::map<std::string, std::vector<Real>> discrete_parameter_values_in;
  read_discrete_parameter_values_from_file(discrete_param_file_name,
                                           read_binary_data,
                                           discrete_parameter_values_in);

  initialize_parameters(param_min, param_max, discrete_parameter_values_in);
}

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 680 of file system_io.C.

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

Referenced by libMesh::TransientRBConstruction::initialize_truth(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), and libMesh::RBConstruction::read_riesz_representors_from_files().

{
  // 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");

      auto 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.get() : 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 LIBMESH_EXPORT 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 1308 of file system.h.

  { 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 2165 of file system_io.C.

References libMesh::Xdr::data(), libMesh::System::get_mesh(), libMesh::libmesh_assert(), libMesh::make_range(), libMesh::MeshTools::n_elem(), libMesh::MeshBase::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, and libMesh::System::variable().

Referenced by libMesh::RBEvaluation::read_in_vectors_from_multiple_files().

{
  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_error_msg_if
        (num_vecs != vectors.size(),
         "Xdr file header declares " << num_vecs << " vectors, but we were asked to read " << vectors.size());

      if (num_vecs != 0)
        {
          libmesh_error_msg_if (vectors[0] == nullptr, "vectors[0] should not be null");
          libmesh_error_msg_if (vectors[0]->size() != vector_length, "Inconsistent vector sizes");
        }
    }

  // 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 (NumericVector<Number> * vec : vectors)
    for (auto var : make_range(this->n_vars()))
      if (this->variable(var).type().family == SCALAR)
        {
          libmesh_assert_not_equal_to (vec, 0);

          read_length +=
            this->read_SCALAR_dofs (var, io, vec);
        }

  //---------------------------------------
  // last step - must close all the vectors
  for (NumericVector<Number> * vec : vectors)
    {
      libmesh_assert_not_equal_to (vec, 0);
      vec->close();
    }

  return read_length;
}

read_serialized_vectors() [2/2]

template LIBMESH_EXPORT 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 1328 of file system.h.

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

reinit()

void libMesh::CondensedEigenSystem::reinit ( )

overridevirtualinherited

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

Reimplemented from libMesh::EigenSystem.

Definition at line 83 of file condensed_eigen_system.C.

References libMesh::CondensedEigenSystem::_condensed_dofs_initialized, and libMesh::EigenSystem::reinit().

Referenced by form_functionA(), form_functionB(), and form_matrixA().

{
  Parent::reinit();
  _condensed_dofs_initialized = false;
}

reinit_constraints()

void libMesh::System::reinit_constraints ( )

virtualinherited

Reinitializes the constraints for this system.

Also prepares the send_list, whether or not constraints have changed.

Definition at line 495 of file system.C.

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

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

{
  parallel_object_only();

#ifdef LIBMESH_ENABLE_CONSTRAINTS
  get_dof_map().create_dof_constraints(_mesh, this->time);
  user_constrain();
  get_dof_map().process_constraints(_mesh);
  if (libMesh::on_command_line ("--print-constraints"))
    get_dof_map().print_dof_constraints(libMesh::out);
#endif
  get_dof_map().prepare_send_list();
}

reinit_mesh()

void libMesh::System::reinit_mesh ( )

virtualinherited

Reinitializes the system with a new mesh.

Definition at line 301 of file system.C.

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

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

{
  parallel_object_only();

  // 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();

}

remove_matrix()

void libMesh::System::remove_matrix ( std::string_view  mat_name )

inherited

Removes the additional matrix mat_name from this system.

Definition at line 1089 of file system.C.

References libMesh::System::_matrices.

{
  parallel_object_only();  // Not strictly needed, but the only safe way to keep in sync

  if (const auto pos = _matrices.find(mat_name);
      pos != _matrices.end())
    _matrices.erase(pos); // erase()'d entries are destroyed
}

remove_vector()

void libMesh::System::remove_vector ( std::string_view  vec_name )

inherited

Removes the additional vector vec_name from this system.

Definition at line 873 of file system.C.

References libMesh::System::_vector_is_adjoint, libMesh::System::_vector_projections, libMesh::System::_vectors, and libMesh::libmesh_assert().

Referenced by libMesh::AdjointRefinementEstimator::estimate_error(), and libMesh::UnsteadySolver::integrate_adjoint_sensitivity().

{
  parallel_object_only();  // Not strictly needed, but the only safe way to keep in sync

  if (const auto pos = _vectors.find(vec_name);
      pos != _vectors.end())
    {
      _vectors.erase(pos);
      auto proj_it = _vector_projections.find(vec_name);
      libmesh_assert(proj_it != _vector_projections.end());
      _vector_projections.erase(proj_it);

      auto adj_it = _vector_is_adjoint.find(vec_name);
      libmesh_assert(adj_it != _vector_is_adjoint.end());
      _vector_is_adjoint.erase(adj_it);
    }
}

request_matrix() [1/2]

const SparseMatrix< Number > * libMesh::System::request_matrix ( std::string_view  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 1100 of file system.C.

References libMesh::System::_matrices.

Referenced by libMesh::EigenSystem::has_matrix_A(), libMesh::EigenSystem::has_matrix_B(), libMesh::EigenSystem::has_precond_matrix(), libMesh::ImplicitSystem::sensitivity_solve(), libMesh::NewtonSolver::solve(), and libMesh::LinearImplicitSystem::solve().

{
  if (const auto pos = _matrices.find(mat_name);
      pos != _matrices.end())
    return pos->second.get();

  // Otherwise, mat_name does not exist
  return nullptr;
}

request_matrix() [2/2]

SparseMatrix< Number > * libMesh::System::request_matrix ( std::string_view  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 1112 of file system.C.

References libMesh::System::_matrices.

{
  if (auto pos = _matrices.find(mat_name);
      pos != _matrices.end())
    return pos->second.get();

  // Otherwise, mat_name does not exist
  return nullptr;
}

request_vector() [1/4]

const NumericVector< Number > * libMesh::System::request_vector ( std::string_view  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 891 of file system.C.

References libMesh::System::_vectors, and libMesh::NumericVector< T >::get().

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

{
  if (const auto pos = _vectors.find(vec_name);
      pos != _vectors.end())
    return pos->second.get();

  // Otherwise, vec_name was not found
  return nullptr;
}

request_vector() [2/4]

NumericVector< Number > * libMesh::System::request_vector ( std::string_view  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 903 of file system.C.

References libMesh::System::_vectors, and libMesh::NumericVector< T >::get().

{
  if (auto pos = _vectors.find(vec_name);
      pos != _vectors.end())
    return pos->second.get();

  // Otherwise, vec_name was not found
  return nullptr;
}

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 915 of file system.C.

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

{
  // If we don't have that many vectors, return nullptr
  if (vec_num >= _vectors.size())
    return nullptr;

  // Otherwise return a pointer to the vec_num'th vector
  auto it = vectors_begin();
  std::advance(it, vec_num);
  return it->second.get();
}

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 929 of file system.C.

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

{
  // If we don't have that many vectors, return nullptr
  if (vec_num >= _vectors.size())
    return nullptr;

  // Otherwise return a pointer to the vec_num'th vector
  auto it = vectors_begin();
  std::advance(it, vec_num);
  return it->second.get();
}

resize_SCM_vectors()

void libMesh::RBSCMConstruction::resize_SCM_vectors ( )

virtual

Clear and resize the SCM data vectors.

Override in subclass as necessary.

Definition at line 188 of file rb_scm_construction.C.

References libMesh::RBSCMEvaluation::B_max, libMesh::RBSCMEvaluation::B_min, libMesh::RBSCMEvaluation::C_J, libMesh::RBSCMEvaluation::C_J_stability_vector, get_rb_theta_expansion(), rb_scm_eval, and libMesh::RBSCMEvaluation::SCM_UB_vectors.

{
  // Clear SCM data vectors
  rb_scm_eval->B_min.clear();
  rb_scm_eval->B_max.clear();
  rb_scm_eval->C_J.clear();
  rb_scm_eval->C_J_stability_vector.clear();
  for (auto & vec : rb_scm_eval->SCM_UB_vectors)
    vec.clear();
  rb_scm_eval->SCM_UB_vectors.clear();

  // Resize the bounding box vectors
  rb_scm_eval->B_min.resize(get_rb_theta_expansion().get_n_A_terms());
  rb_scm_eval->B_max.resize(get_rb_theta_expansion().get_n_A_terms());
}

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 557 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 386 of file system.C.

References libMesh::System::_dof_map, libMesh::System::_solution_projection, libMesh::System::_vector_projections, libMesh::System::_vectors, libMesh::System::current_local_solution, libMesh::NumericVector< T >::get(), 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().

{
  parallel_object_only();

#ifdef LIBMESH_ENABLE_AMR
  // Restrict the _vectors on the coarsened cells
  for (auto & [vec_name, vec] : _vectors)
    {
      NumericVector<Number> * v = vec.get();

      if (_vector_projections[vec_name])
        {
          this->project_vector (*v, this->vector_is_adjoint(vec_name));
        }
      else
        {
          const ParallelType type = vec->type();

          if (type == GHOSTED)
            {
#ifdef LIBMESH_ENABLE_GHOSTED
              vec->init (this->n_dofs(), this->n_local_dofs(),
                               _dof_map->get_send_list(), /*fast=*/false,
                               GHOSTED);
#else
              libmesh_error_msg("Cannot initialize ghosted vectors when they are not enabled.");
#endif
            }
          else
            vec->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
}

SCM_greedy_error_indicator()

virtual Real libMesh::RBSCMConstruction::SCM_greedy_error_indicator ( Real  LB, Real  UB  )

inlineprotectedvirtual

Helper function which provides an error indicator to be used in the SCM greedy.

Override in subclasses to specialize behavior.

Definition at line 224 of file rb_scm_construction.h.

Referenced by compute_SCM_bounds_on_training_set().

{ return fabs(UB-LB)/fabs(UB); }

sensitivity_solve()

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

inlinevirtualinherited

Solves the sensitivity system, for the provided parameters.

Must be overridden in derived systems.

Returns

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

This method is only implemented in some derived classes.

Reimplemented in libMesh::ImplicitSystem.

Definition at line 2632 of file system.h.

{
  libmesh_not_implemented();
}

set_adjoint_already_solved()

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

inlineinherited

Setter for the adjoint_already_solved boolean.

Definition at line 415 of file system.h.

References libMesh::System::adjoint_already_solved.

Referenced by main().

  { adjoint_already_solved = setting;}

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 2422 of file system.h.

References libMesh::System::_basic_system_only.

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

{
  _basic_system_only = true;
}

set_deterministic_training_parameter_name()

void libMesh::RBConstructionBase< CondensedEigenSystem >::set_deterministic_training_parameter_name ( const std::string &  name )

inherited

In some cases we only want to allow discrete parameter values, instead of parameters that may take any value in a specified interval.

Here we provide a method to set the d Set the discrete values for parameter mu that are allowed in the training set. This must be called before the training set is generated. Set the name of the parameter that we will generate deterministic training parameters for. Defaults to "NONE".

set_eigenproblem_type()

void libMesh::EigenSystem::set_eigenproblem_type ( EigenProblemType  ept )

inherited

Sets the type of the current eigen problem.

Definition at line 85 of file eigen_system.C.

References libMesh::EigenSystem::_eigen_problem_type, libMesh::System::can_add_matrices(), libMesh::EigenSystem::eigen_solver, libMesh::GHEP, libMesh::GHIEP, libMesh::GNHEP, libMesh::HEP, and libMesh::NHEP.

Referenced by main(), and RBSCMConstruction().

{
  if (!can_add_matrices())
    libmesh_error_msg("ERROR: Cannot change eigen problem type after system initialization");

  _eigen_problem_type = ept;

  eigen_solver->set_eigenproblem_type(ept);

  // libMesh::out << "The Problem type is set to be: " << std::endl;

  switch (_eigen_problem_type)
    {
    case HEP:
      // libMesh::out << "Hermitian" << std::endl;
      break;

    case NHEP:
      // libMesh::out << "Non-Hermitian" << std::endl;
      break;

    case GHEP:
      // libMesh::out << "Generalized Hermitian" << std::endl;
      break;

    case GNHEP:
      // libMesh::out << "Generalized Non-Hermitian" << std::endl;
      break;

    case GHIEP:
      // libMesh::out << "Generalized indefinite Hermitian" << std::endl;
      break;

    default:
      // libMesh::out << "not properly specified" << std::endl;
      libmesh_error_msg("Unrecognized _eigen_problem_type = " << _eigen_problem_type);
    }
}

set_eigensolver_properties()

virtual void libMesh::RBSCMConstruction::set_eigensolver_properties ( int  )

inlinevirtual

This function is called before truth eigensolves in compute_SCM_bounding_box and evaluate_stability_constant.

Override it to set specific properties to optimize eigensolver performance. The argument refers to the operator index in compute_SCM_bounding_box; a negative value of the argument indicates we are not performing a bounding box solve.

Definition at line 133 of file rb_scm_construction.h.

Referenced by compute_SCM_bounding_box(), and evaluate_stability_constant().

{}

set_initial_space()

void libMesh::EigenSystem::set_initial_space ( NumericVector< Number > &  initial_space_in )

inherited

Sets an initial eigen vector.

Definition at line 319 of file eigen_system.C.

References libMesh::EigenSystem::eigen_solver.

{
  eigen_solver->set_initial_space (initial_space_in);
}

set_n_converged()

void libMesh::EigenSystem::set_n_converged ( unsigned int  nconv )

inlineprotectedinherited

Set the _n_converged_eigenpairs member, useful for subclasses of EigenSystem.

Definition at line 381 of file eigen_system.h.

References libMesh::EigenSystem::_n_converged_eigenpairs.

  { _n_converged_eigenpairs = nconv; }

set_n_iterations()

void libMesh::EigenSystem::set_n_iterations ( unsigned int  its )

inlineprotectedinherited

Set the _n_iterations member, useful for subclasses of EigenSystem.

Definition at line 388 of file eigen_system.h.

References libMesh::EigenSystem::_n_iterations.

  { _n_iterations = its;}

set_normalize_solution_snapshots()

void libMesh::RBConstructionBase< CondensedEigenSystem >::set_normalize_solution_snapshots ( bool  value )

inherited

Set the boolean option that indicates if we normalization solution snapshots or not.

Definition at line 147 of file rb_construction_base.C.

References value.

{
  _normalize_solution_snapshots = value;
}

set_parameters()

bool libMesh::RBParametrized::set_parameters ( const RBParameters &  params )

inherited

Set the current parameters to params The parameters are checked for validity; an error is thrown if the number of parameters or samples is different than expected.

We

Returns

a boolean true if the new parameters are within the min/max range, and false otherwise (but the parameters are set regardless). Enabling the "verbose_mode" flag will also print more details.

Definition at line 143 of file rb_parametrized.C.

References libMesh::RBParametrized::check_if_valid_params(), libMesh::RBParametrized::parameters, and libMesh::RBParametrized::parameters_initialized.

Referenced by compute_SCM_bounds_on_training_set(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_interiors(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_nodes(), libMesh::RBEIMConstruction::enrich_eim_approximation_on_sides(), libMesh::RBConstruction::get_RB_error_bound(), SimpleRBEvaluation::get_stability_lower_bound(), libMesh::RBParametrized::initialize_parameters(), libMesh::RBSCMEvaluation::reload_current_parameters(), libMesh::RBSCMEvaluation::set_current_parameters_from_C_J(), and RBParametersTest::testRBParametrized().

{
  libmesh_error_msg_if(!parameters_initialized, "Error: parameters not initialized in RBParametrized::set_parameters");

  // Terminate if params has the wrong number of parameters or samples.
  // If the parameters are outside the min/max range, return false.
  const bool valid_params = check_if_valid_params(params);

  // Make a copy of params (default assignment operator just does memberwise copy, which is sufficient here)
  this->parameters = params;

  return valid_params;
}

set_params_from_training_set()

void libMesh::RBConstructionBase< CondensedEigenSystem >::set_params_from_training_set ( unsigned int  global_index )

protectedinherited

Set parameters to the RBParameters stored in index global_index of the global training set.

Definition at line 225 of file rb_construction_base.C.

Referenced by compute_SCM_bounds_on_training_set().

{
  set_parameters(get_params_from_training_set(global_index));
}

set_params_from_training_set_and_broadcast()

void libMesh::RBConstructionBase< CondensedEigenSystem >::set_params_from_training_set_and_broadcast ( unsigned int  global_index )

protectedvirtualinherited

Load the specified training parameter and then broadcast to all processors.

Definition at line 270 of file rb_construction_base.C.

Referenced by enrich_C_J().

{
  libmesh_error_msg_if(!_training_parameters_initialized,
                       "Error: training parameters must first be initialized.");

  processor_id_type root_id = 0;
  if ((this->get_first_local_training_index() <= global_index) &&
      (global_index < this->get_last_local_training_index()))
    {
      // Set parameters on only one processor
      set_params_from_training_set(global_index);

      // set root_id, only non-zero on one processor
      root_id = this->processor_id();
    }

  // broadcast
  this->comm().max(root_id);
  broadcast_parameters(root_id);
}

set_project_with_constraints()

void libMesh::System::set_project_with_constraints ( bool  _project_with_constraints )

inlineinherited

Definition at line 1800 of file system.h.

References libMesh::System::project_with_constraints.

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

  {
    project_with_constraints = _project_with_constraints;
  }

set_qoi() [1/2]

void libMesh::System::set_qoi ( unsigned int  qoi_index, Number  qoi_value  )

inherited

Definition at line 2378 of file system.C.

References libMesh::libmesh_assert(), and libMesh::System::qoi.

Referenced by libMesh::ExplicitSystem::assemble_qoi(), libMesh::FEMSystem::assemble_qoi(), libMesh::Euler2Solver::integrate_qoi_timestep(), libMesh::TwostepTimeSolver::integrate_qoi_timestep(), and libMesh::EulerSolver::integrate_qoi_timestep().

{
  libmesh_assert(qoi_index < qoi.size());

  qoi[qoi_index] = qoi_value;
}

set_qoi() [2/2]

void libMesh::System::set_qoi ( std::vector< Number >  new_qoi )

inherited

Definition at line 2399 of file system.C.

References libMesh::System::qoi.

{
  libmesh_assert_equal_to(this->qoi.size(), new_qoi.size());
  this->qoi = std::move(new_qoi);
}

set_qoi_error_estimate()

void libMesh::System::set_qoi_error_estimate ( unsigned int  qoi_index, Number  qoi_error_estimate  )

inherited

Definition at line 2406 of file system.C.

References libMesh::libmesh_assert(), and libMesh::System::qoi_error_estimates.

Referenced by libMesh::Euler2Solver::integrate_adjoint_refinement_error_estimate(), libMesh::TwostepTimeSolver::integrate_adjoint_refinement_error_estimate(), and libMesh::EulerSolver::integrate_adjoint_refinement_error_estimate().

{
  libmesh_assert(qoi_index < qoi_error_estimates.size());

  qoi_error_estimates[qoi_index] = qoi_error_estimate;
}

set_quiet_mode()

void libMesh::RBConstructionBase< CondensedEigenSystem >::set_quiet_mode ( bool  quiet_mode_in )

inlineinherited

Set the quiet_mode flag.

If quiet == false then we print out a lot of extra information during the Offline stage.

Definition at line 100 of file rb_construction_base.h.

References libMesh::RBConstructionBase< Base >::quiet_mode.

  { this->quiet_mode = quiet_mode_in; }

set_rb_scm_evaluation()

void libMesh::RBSCMConstruction::set_rb_scm_evaluation

(

RBSCMEvaluation &

rb_scm_eval_in

)

Set the RBSCMEvaluation object.

Definition at line 72 of file rb_scm_construction.C.

References rb_scm_eval.

{
  rb_scm_eval = &rb_scm_eval_in;
}

set_RB_system_name()

void libMesh::RBSCMConstruction::set_RB_system_name ( const std::string &  new_name )

inline

Set the name of the associated RB system — we need this to load the (symmetrized) affine operators.

Definition at line 139 of file rb_scm_construction.h.

References RB_system_name.

Referenced by main().

  { RB_system_name = new_name; }

set_SCM_training_tolerance()

void libMesh::RBSCMConstruction::set_SCM_training_tolerance ( Real  SCM_training_tolerance_in )

inline

Definition at line 146 of file rb_scm_construction.h.

References SCM_training_tolerance.

Referenced by process_parameters_file().

{ this->SCM_training_tolerance = SCM_training_tolerance_in; }

set_training_parameter_values()

void libMesh::RBConstructionBase< CondensedEigenSystem >::set_training_parameter_values ( const std::string &  param_name, const std::vector< RBParameter > &  values  )

inherited

Overwrite the local training samples for param_name using values.

This assumes that values.size() matches get_local_n_training_samples().

Definition at line 456 of file rb_construction_base.C.

{
  libmesh_error_msg_if(!_training_parameters_initialized,
    "Training parameters must be initialized before calling set_training_parameter_values");
  libmesh_error_msg_if(values.size() != get_local_n_training_samples(),
    "Inconsistent sizes");

  // Copy the new data, overwriting the old data.
  auto & training_vector = libmesh_map_find(_training_parameters, param_name);
  training_vector = values;
}

set_training_random_seed()

void libMesh::RBConstructionBase< CondensedEigenSystem >::set_training_random_seed ( int  seed )

inherited

Set the seed that is used to randomly generate training parameters.

Definition at line 780 of file rb_construction_base.C.

Referenced by process_parameters_file().

{
  this->_training_parameters_random_seed = seed;
}

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 1160 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().

{
  parallel_object_only();  // Not strictly needed, but the only safe way to keep in sync

  // 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 1138 of file system.C.

References libMesh::System::_vector_projections.

Referenced by libMesh::AdjointRefinementEstimator::estimate_error(), and main().

{
  parallel_object_only();  // Not strictly needed, but the only safe way to keep in sync

  _vector_projections[vec_name] = preserve;
}

solve()

void libMesh::CondensedEigenSystem::solve ( )

overridevirtualinherited

Override to solve the condensed eigenproblem with the dofs in local_non_condensed_dofs_vector stripped out of the system matrices on each processor.

Reimplemented from libMesh::EigenSystem.

Definition at line 180 of file condensed_eigen_system.C.

References libMesh::CondensedEigenSystem::_condensed_matrix_A, libMesh::CondensedEigenSystem::_condensed_matrix_B, libMesh::CondensedEigenSystem::_condensed_precond_matrix, libMesh::CondensedEigenSystem::_create_submatrices_in_solve, libMesh::CondensedEigenSystem::_have_condensed_dofs, libMesh::System::assemble(), libMesh::System::assemble_before_solve, libMesh::SparseMatrix< T >::close(), libMesh::SparseMatrix< T >::create_submatrix(), libMesh::EigenSystem::generalized(), libMesh::System::get_equation_systems(), libMesh::Parameters::have_parameter(), libMesh::libmesh_assert(), libMesh::CondensedEigenSystem::local_non_condensed_dofs_vector, libMesh::EigenSystem::matrix_A, libMesh::EigenSystem::matrix_B, libMesh::System::parameters, libMesh::EigenSystem::precond_matrix, libMesh::EigenSystem::solve(), and libMesh::EigenSystem::solve_helper().

Referenced by compute_SCM_bounding_box(), evaluate_stability_constant(), and main().

{
  LOG_SCOPE("solve()", "CondensedEigenSystem");

  // If we haven't initialized any condensed dofs,
  // just use the default eigen_system
  if (!_have_condensed_dofs)
    {
      Parent::solve();
      return;
    }

  // check that necessary parameters have been set
  libmesh_assert(
      this->get_equation_systems().parameters.have_parameter<unsigned int>("eigenpairs"));
  libmesh_assert(
      this->get_equation_systems().parameters.have_parameter<unsigned int>("basis vectors"));

  if (this->assemble_before_solve)
    {
      // Assemble the linear system
      this->assemble();

      // And close the assembled matrices; using a non-closed matrix
      // with create_submatrix() is deprecated.
      if (matrix_A)
        matrix_A->close();
      if (generalized() && matrix_B)
        matrix_B->close();
      if (precond_matrix)
        precond_matrix->close();
    }

  // If we reach here, then there should be some non-condensed dofs
  libmesh_assert(!local_non_condensed_dofs_vector.empty());

  if (_create_submatrices_in_solve)
    {
      if (matrix_A)
        matrix_A->create_submatrix(
            *_condensed_matrix_A, local_non_condensed_dofs_vector, local_non_condensed_dofs_vector);
      if (generalized() && matrix_B)
        matrix_B->create_submatrix(
            *_condensed_matrix_B, local_non_condensed_dofs_vector, local_non_condensed_dofs_vector);
      if (precond_matrix)
        precond_matrix->create_submatrix(*_condensed_precond_matrix,
                                         local_non_condensed_dofs_vector,
                                         local_non_condensed_dofs_vector);
    }

  solve_helper(
      _condensed_matrix_A.get(), _condensed_matrix_B.get(), _condensed_precond_matrix.get());
}

solve_for_unconstrained_dofs()

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

protectedinherited

Definition at line 2041 of file system_projection.C.

References libMesh::DofMap::build_sparsity(), libMesh::DofMap::computed_sparsity_already(), libMesh::DofMapBase::end_dof(), libMesh::DofMapBase::first_dof(), libMesh::NumericVector< T >::get(), libMesh::DofMap::heterogenously_constrain_element_matrix_and_vector(), libMesh::DofMap::is_constrained_dof(), libMesh::NumericVector< T >::local_size(), libMesh::DofMap::n_dofs(), libMesh::DofMap::n_local_dofs(), libMesh::PARALLEL, libMesh::Real, libMesh::NumericVector< T >::size(), and libMesh::DofMap::update_sparsity_pattern().

{
  const DofMap & dof_map = this->get_dof_map();

  std::unique_ptr<SparseMatrix<Number>> mat =
    SparseMatrix<Number>::build(this->comm());

  std::unique_ptr<SparsityPattern::Build> sp;

  if (dof_map.computed_sparsity_already())
    dof_map.update_sparsity_pattern(*mat);
  else
    {
      mat->attach_dof_map(dof_map);
      sp = dof_map.build_sparsity(this->get_mesh());
      mat->attach_sparsity_pattern(*sp);
    }

  mat->init();

  libmesh_assert_equal_to(vec.size(), dof_map.n_dofs());
  libmesh_assert_equal_to(vec.local_size(), dof_map.n_local_dofs());

  std::unique_ptr<NumericVector<Number>> rhs =
    NumericVector<Number>::build(this->comm());

  rhs->init(dof_map.n_dofs(), dof_map.n_local_dofs(), false,
            PARALLEL);

  // Here we start with the unconstrained (and indeterminate) linear
  // system, K*u = f, where K is the identity matrix for constrained
  // DoFs and 0 elsewhere, and f is the current solution values for
  // constrained DoFs and 0 elsewhere.
  // We then apply the usual heterogeneous constraint matrix C and
  // offset h, where u = C*x + h,
  // to get C^T*K*C*x = C^T*f - C^T*K*h
  // - a constrained and no-longer-singular system that finds the
  // closest approximation for the unconstrained degrees of freedom.
  //
  // Here, though "closest" is in an algebraic sense; we're
  // effectively using a pseudoinverse that optimizes in a
  // discretization-dependent norm.  That only seems to give ~0.1%
  // excess error even in coarse unit test cases, but at some point it
  // might be reasonable to weight K and f properly.

  for (dof_id_type d : IntRange<dof_id_type>(dof_map.first_dof(),
                                             dof_map.end_dof()))
    {
      if (dof_map.is_constrained_dof(d))
        {
          DenseMatrix<Number> K(1,1);
          DenseVector<Number> F(1);
          std::vector<dof_id_type> dof_indices(1, d);
          K(0,0) = 1;
          F(0) = (*this->solution)(d);
          dof_map.heterogenously_constrain_element_matrix_and_vector
            (K, F, dof_indices, false, is_adjoint);
          mat->add_matrix(K, dof_indices);
          rhs->add_vector(F, dof_indices);
        }
    }

  std::unique_ptr<LinearSolver<Number>> linear_solver =
    LinearSolver<Number>::build(this->comm());

  linear_solver->solve(*mat, vec, *rhs,
                       double(this->get_equation_systems().parameters.get<Real>("linear solver tolerance")),
                       this->get_equation_systems().parameters.get<unsigned int>("linear solver maximum iterations"));
}

solve_helper()

void libMesh::EigenSystem::solve_helper ( SparseMatrix< Number > *const  A, SparseMatrix< Number > *const  B, SparseMatrix< Number > *const  P  )

protectedinherited

Definition at line 215 of file eigen_system.C.

References libMesh::EigenSystem::_n_converged_eigenpairs, libMesh::EigenSystem::_n_iterations, libMesh::EigenSystem::_use_shell_matrices, libMesh::EigenSystem::_use_shell_precond_matrix, libMesh::EigenSystem::eigen_solver, libMesh::EigenSystem::generalized(), libMesh::Parameters::get(), libMesh::System::get_equation_systems(), libMesh::Parameters::have_parameter(), libMesh::libmesh_assert(), libMesh::EigenSystem::matrix_B, libMesh::EquationSystems::parameters, libMesh::System::parameters, libMesh::Real, libMesh::EigenSystem::shell_matrix_A, libMesh::EigenSystem::shell_matrix_B, and libMesh::EigenSystem::shell_precond_matrix.

Referenced by libMesh::EigenSystem::solve(), and libMesh::CondensedEigenSystem::solve().

{
  // A reference to the EquationSystems
  EquationSystems & es = this->get_equation_systems();

  // Get the tolerance for the solver and the maximum
  // number of iterations. Here, we simply adopt the linear solver
  // specific parameters.
  const double tol          =  parameters.have_parameter<Real>("linear solver tolerance") ?
    double(parameters.get<Real>("linear solver tolerance")) :
    double(es.parameters.get<Real>("linear solver tolerance"));

  const unsigned int maxits = parameters.have_parameter<unsigned int>("linear solver maximum iterations") ?
    parameters.get<unsigned int>("linear solver maximum iterations") :
    es.parameters.get<unsigned int>("linear solver maximum iterations");

  const unsigned int nev    = parameters.have_parameter<unsigned int>("eigenpairs") ?
    parameters.get<unsigned int>("eigenpairs") :
    es.parameters.get<unsigned int>("eigenpairs");

  const unsigned int ncv    = parameters.have_parameter<unsigned int>("basis vectors") ?
    parameters.get<unsigned int>("basis vectors") :
    es.parameters.get<unsigned int>("basis vectors");

  std::pair<unsigned int, unsigned int> solve_data;

  // call the solver depending on the type of eigenproblem

  if (_use_shell_matrices)
  {
    // Generalized eigenproblem
    if (generalized())
      // Shell preconditioning matrix
      if (_use_shell_precond_matrix)
        solve_data = eigen_solver->solve_generalized(
            *shell_matrix_A, *shell_matrix_B, *shell_precond_matrix, nev, ncv, tol, maxits);
      else
        solve_data = eigen_solver->solve_generalized(
            *shell_matrix_A, *shell_matrix_B, *P, nev, ncv, tol, maxits);

    // Standard eigenproblem
    else
    {
      libmesh_assert(!shell_matrix_B);
      // Shell preconditioning matrix
      if (_use_shell_precond_matrix)
        solve_data = eigen_solver->solve_standard(
            *shell_matrix_A, *shell_precond_matrix, nev, ncv, tol, maxits);
      else
        solve_data = eigen_solver->solve_standard(*shell_matrix_A, *P, nev, ncv, tol, maxits);
    }
  }
  else
  {
    // Generalized eigenproblem
    if (generalized())
      solve_data = eigen_solver->solve_generalized(*A, *B, nev, ncv, tol, maxits);

    // Standard eigenproblem
    else
    {
      libmesh_assert(!matrix_B);
      solve_data = eigen_solver->solve_standard(*A, nev, ncv, tol, maxits);
    }
  }

  this->_n_converged_eigenpairs = solve_data.first;
  this->_n_iterations           = solve_data.second;
}

system()

sys_type& libMesh::RBConstructionBase< CondensedEigenSystem >::system ( )

inlineinherited

Returns

A reference to *this.

Definition at line 87 of file rb_construction_base.h.

{ return *this; }

system_type()

virtual std::string libMesh::EigenSystem::system_type ( ) const

inlineoverridevirtualinherited

Returns

"Eigen". Helps in identifying the system type in an equation system file.

Reimplemented from libMesh::System.

Definition at line 125 of file eigen_system.h.

{ return "Eigen"; }

update()

void libMesh::System::update ( )

virtualinherited

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

Reimplemented in SolidSystem.

Definition at line 510 of file system.C.

References libMesh::System::_dof_map, libMesh::System::current_local_solution, libMesh::libmesh_assert(), 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(), compute_stresses(), LinearElasticityWithContact::compute_stresses(), LinearElasticity::compute_stresses(), LargeDeformationElasticity::compute_stresses(), libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::Nemesis_IO::copy_elemental_solution(), libMesh::GMVIO::copy_nodal_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::Nemesis_IO::copy_nodal_solution(), libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::Nemesis_IO::copy_scalar_solution(), DMlibMeshFunction(), DMlibMeshJacobian(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::CondensedEigenSystem::get_eigenpair(), libMesh::TransientRBConstruction::initialize_truth(), libMesh::Euler2Solver::integrate_adjoint_refinement_error_estimate(), libMesh::EulerSolver::integrate_adjoint_refinement_error_estimate(), 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::NewtonSolver::line_search(), libMesh::RBConstruction::load_basis_function(), libMesh::TransientRBConstruction::load_rb_solution(), libMesh::RBConstruction::load_rb_solution(), main(), libMesh::FEMSystem::mesh_position_get(), HeatSystem::perturb_accumulate_residuals(), libMesh::FEMSystem::postprocess(), libMesh::ImplicitSystem::qoi_parameter_hessian(), libMesh::MemorySolutionHistory::retrieve(), libMesh::FileSolutionHistory::retrieve(), libMesh::NewtonSolver::solve(), libMesh::ExplicitSystem::solve(), libMesh::LinearImplicitSystem::solve(), libMesh::OptimizationSystem::solve(), libMesh::NonlinearImplicitSystem::solve(), libMesh::ClawSystem::solve_conservation_law(), libMesh::RBConstruction::solve_for_matrix_and_rhs(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::DirectSolutionTransfer::transfer(), and update_current_local_solution().

{
  parallel_object_only();

  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 745 of file system.C.

References libMesh::System::solution.

Referenced by libMesh::ExactSolution::_compute_error(), libMesh::ExactErrorEstimator::estimate_error(), main(), and libMesh::InterMeshProjection::project_system_vectors().

{
  parallel_object_only();

  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 756 of file system.C.

References libMesh::System::solution.

{
  parallel_object_only();

  global_soln.resize        (solution->size());

  solution->localize_to_one (global_soln, dest_proc);
}

use_shell_matrices() [1/2]

bool libMesh::EigenSystem::use_shell_matrices ( ) const

inlineinherited

Returns

true if the shell matrices are used

Definition at line 161 of file eigen_system.h.

References libMesh::EigenSystem::_use_shell_matrices.

Referenced by libMesh::CondensedEigenSystem::add_matrices().

{ return _use_shell_matrices; }

use_shell_matrices() [2/2]

void libMesh::EigenSystem::use_shell_matrices ( bool  use_shell_matrices )

inlineinherited

Set a flag to use shell matrices.

Definition at line 166 of file eigen_system.h.

References libMesh::EigenSystem::_use_shell_matrices, and libMesh::EigenSystem::use_shell_matrices().

Referenced by libMesh::EigenSystem::use_shell_matrices().

{ _use_shell_matrices = use_shell_matrices; }

use_shell_precond_matrix() [1/2]

bool libMesh::EigenSystem::use_shell_precond_matrix ( ) const

inlineinherited

Returns

true if a shell preconditioning matrix is used

Definition at line 171 of file eigen_system.h.

References libMesh::EigenSystem::_use_shell_precond_matrix.

Referenced by libMesh::CondensedEigenSystem::add_matrices().

{ return _use_shell_precond_matrix; }

use_shell_precond_matrix() [2/2]

void libMesh::EigenSystem::use_shell_precond_matrix ( bool  use_shell_precond_matrix )

inlineinherited

Set a flag to use a shell preconditioning matrix.

Definition at line 176 of file eigen_system.h.

References libMesh::EigenSystem::_use_shell_precond_matrix, and libMesh::EigenSystem::use_shell_precond_matrix().

Referenced by libMesh::EigenSystem::use_shell_precond_matrix().

{ _use_shell_precond_matrix = use_shell_precond_matrix; }

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 2311 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 2325 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 2297 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::NewmarkSystem::initial_conditions(), and libMesh::System::reinit_mesh().

{
  // 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 2339 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 2353 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 2458 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::System::add_variable(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::FirstOrderUnsteadySolver::compute_second_order_eqns(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::SubFunctor::find_dofs_to_send(), libMesh::DifferentiableSystem::have_first_order_scalar_vars(), libMesh::DifferentiableSystem::have_second_order_scalar_vars(), main(), libMesh::DifferentiablePhysics::nonlocal_mass_residual(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::SortAndCopy::operator()(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::ProjectVertices::operator()(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::ProjectEdges::operator()(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::ProjectSides::operator()(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::ProjectInteriors::operator()(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), 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::Nemesis_IO_Helper::write_nodal_solution(), 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 2468 of file system.h.

References libMesh::System::_variable_groups.

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

{
  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 2478 of file system.h.

References libMesh::System::_variables.

Referenced by libMesh::System::add_variable(), libMesh::System::add_variables(), libMesh::PetscDMWrapper::build_section(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::ExactSolution::ExactSolution(), libMesh::EquationSystems::find_variable_numbers(), main(), output_norms(), libMesh::petsc_auto_fieldsplit(), libMesh::InterMeshProjection::project_system_vectors(), MeshInputTest::testExodusWriteElementDataFromDiscontinuousNodalData(), libMesh::System::write_header(), and libMesh::Nemesis_IO_Helper::write_nodal_solution().

{
  libmesh_assert_less (i, _variables.size());

  return _variables[i].name();
}

variable_number()

unsigned int libMesh::System::variable_number ( std::string_view  var ) const

inherited

Returns

The variable number associated with the user-specified variable named var.

Definition at line 1609 of file system.C.

References libMesh::System::_variable_numbers, libMesh::System::_variables, and libMesh::System::name().

Referenced by libMesh::ExactSolution::_compute_error(), alternative_fe_assembly(), LinearElasticity::assemble(), AssembleOptimization::assemble_A_and_F(), assemble_divgrad(), assemble_elasticity(), assemble_graddiv(), assemble_matrix_and_rhs(), assemble_shell(), assemble_stokes(), compute_enriched_soln(), compute_stresses(), LinearElasticityWithContact::compute_stresses(), LinearElasticity::compute_stresses(), LargeDeformationElasticity::compute_stresses(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::Nemesis_IO::copy_elemental_solution(), libMesh::GMVIO::copy_nodal_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::Nemesis_IO::copy_nodal_solution(), libMesh::ExactErrorEstimator::estimate_error(), fe_assembly(), libMesh::ExactErrorEstimator::find_squared_element_error(), CoupledSystemQoI::init_context(), libMesh::HDGProblem::jacobian(), LargeDeformationElasticity::jacobian(), line_print(), main(), LinearElasticityWithContact::move_mesh(), libMesh::System::read_header(), libMesh::HDGProblem::residual(), LargeDeformationElasticity::residual(), LinearElasticityWithContact::residual_and_jacobian(), OverlappingAlgebraicGhostingTest::run_ghosting_test(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), OverlappingTestBase::setup_coupling_matrix(), libMesh::DTKAdapter::update_variable_values(), libMesh::System::variable_scalar_number(), libMesh::System::variable_type(), libMesh::EnsightIO::write_scalar_ascii(), and libMesh::EnsightIO::write_vector_ascii().

{
  auto var_num = libmesh_map_find(_variable_numbers, var);
  libmesh_assert_equal_to (_variables[var_num].name(), var);
  return var_num;
}

variable_scalar_number() [1/2]

unsigned int libMesh::System::variable_scalar_number ( std::string_view  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 2489 of file system.h.

References libMesh::System::variable_number().

Referenced by libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::Nemesis_IO::copy_scalar_solution(), libMesh::ExactErrorEstimator::find_squared_element_error(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::ProjectVertices::operator()(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::ProjectEdges::operator()(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::ProjectSides::operator()(), and libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::ProjectInteriors::operator()().

{
  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 2499 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 2508 of file system.h.

References libMesh::System::_variables.

Referenced by libMesh::ExactSolution::_compute_error(), libMesh::System::add_variable(), libMesh::System::add_variables(), alternative_fe_assembly(), assemble(), libMesh::ClawSystem::assemble_advection_matrices(), libMesh::ClawSystem::assemble_avg_coupling_matrices(), libMesh::ClawSystem::assemble_boundary_condition_matrices(), assemble_ellipticdg(), libMesh::ClawSystem::assemble_jump_coupling_matrix(), libMesh::ClawSystem::assemble_mass_matrix(), assemble_shell(), assemble_stokes(), libMesh::FEMContext::attach_quadrature_rules(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::Nemesis_IO::copy_elemental_solution(), libMesh::GMVIO::copy_nodal_solution(), libMesh::DGFEMContext::DGFEMContext(), fe_assembly(), libMesh::FEMContext::find_hardest_fe_type(), libMesh::EquationSystems::find_variable_numbers(), form_functionA(), form_functionB(), form_matrixA(), libMesh::FEMSystem::init_context(), libMesh::FEMContext::init_internal_data(), RationalMapTest< elem_type >::setUp(), FETestBase< order, family, elem_type, 1 >::setUp(), EquationSystemsTest::testBadVarNames(), libMesh::Nemesis_IO_Helper::write_element_values(), libMesh::System::write_header(), libMesh::Nemesis_IO_Helper::write_nodal_solution(), 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 ( std::string_view  var ) const

inlineinherited

Returns

The finite element type for variable var.

Definition at line 2518 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 ( std::string_view  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 1173 of file system.C.

References libMesh::System::_vector_is_adjoint, and libMesh::libmesh_assert().

Referenced by libMesh::InterMeshProjection::project_system_vectors(), and libMesh::System::restrict_vectors().

{
  const auto it = _vector_is_adjoint.find(vec_name);
  libmesh_assert(it != _vector_is_adjoint.end());
  return it->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 983 of file system.C.

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

Referenced by libMesh::AdjointRefinementEstimator::estimate_error(), and main().

{
  // If we don't have that many vectors, throw an error
  libmesh_assert_less(vec_num, _vectors.size());

  // Otherwise return a reference to the vec_num'th vector name
  auto it = vectors_begin();
  std::advance(it, vec_num);
  return it->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 994 of file system.C.

References libMesh::System::_vectors, libMesh::NumericVector< T >::get(), libMesh::libmesh_assert(), libMesh::System::vectors_begin(), and libMesh::System::vectors_end().

{
  // Linear search for a vector whose pointer matches vec_reference
  auto it = std::find_if(vectors_begin(), vectors_end(),
                         [&vec_reference](const decltype(_vectors)::value_type & pr)
                         { return &vec_reference == pr.second.get(); });

  // Before returning, make sure we didn't loop till the end and not find any match
  libmesh_assert (it != vectors_end());

  // Return the string associated with the current vector
  return it->first;
}

vector_preservation()

bool libMesh::System::vector_preservation ( std::string_view  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 1148 of file system.C.

References libMesh::System::_vector_projections.

Referenced by libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::MemoryHistoryData::store_vectors(), SystemsTest::testAddVectorProjChange(), SystemsTest::testAddVectorTypeChange(), and SystemsTest::testPostInitAddVectorTypeChange().

{
  if (auto it = _vector_projections.find(vec_name);
      it != _vector_projections.end())
    return it->second;

  // vec_name was not in the map, return false
  return false;
}

vectors_begin() [1/2]

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

inlineinherited

Beginning of vectors container.

Definition at line 2564 of file system.h.

References libMesh::System::_vectors.

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::System::get_vector(), libMesh::InterMeshProjection::project_system_vectors(), libMesh::System::request_vector(), libMesh::MemoryHistoryData::store_vectors(), 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 2570 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 2576 of file system.h.

References libMesh::System::_vectors.

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::InterMeshProjection::project_system_vectors(), libMesh::MemoryHistoryData::store_vectors(), 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 2582 of file system.h.

References libMesh::System::_vectors.

{
  return _vectors.end();
}

weighted_sensitivity_adjoint_solve()

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

inlinevirtualinherited

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

This method is only implemented in some derived classes.

Reimplemented in libMesh::ImplicitSystem.

Definition at line 2654 of file system.h.

{
  libmesh_not_implemented();
}

weighted_sensitivity_solve()

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

inlinevirtualinherited

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

This method is only implemented in some derived classes.

Reimplemented in libMesh::ImplicitSystem.

Definition at line 2639 of file system.h.

{
  libmesh_not_implemented();
}

write_header()

void libMesh::System::write_header ( Xdr &  io, std::string_view  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 1267 of file system_io.C.

References libMesh::System::_vector_projections, libMesh::System::_vectors, libMesh::Variable::active_subdomains(), libMesh::Xdr::data(), libMesh::FEType::family, libMesh::System::get_mesh(), libMesh::FEType::inf_map, libMesh::libmesh_assert(), libMesh::make_range(), 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().

Referenced by libMesh::RBEvaluation::write_out_vectors().

{
  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;

  // 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);
  }


  for (auto var : make_range(this->n_vars()))
    {
      // 6.)
      // Write the name of the var-th variable
      {
        // set up the comment
        comment  = "#   Name, Variable No. ";
        comment += std::to_string(var);
        comment += ", System \"";
        comment += this->name();
        comment += "\"";

        std::string var_name = this->variable_name(var);
        io.data (var_name, comment);
      }

      // 6.1.) Variable subdomains
      {
        // set up the comment
        comment  = "#     Subdomains, Variable \"";
        comment += this->variable_name(var);
        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);
      }

      // 7.)
      // Write the approximation order of the var-th variable
      // in this system
      {
        // set up the comment
        comment = "#     Approximation Order, Variable \"";
        comment += this->variable_name(var);
        comment += "\", System \"";
        comment += this->name();
        comment += "\"";

        int order = static_cast<int>(this->variable_type(var).order);
        io.data (order, comment);
      }


#ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS

      // do the same for radial_order
      {
        comment = "#     Radial Approximation Order, Variable \"";
        comment += this->variable_name(var);
        comment += "\", System \"";
        comment += this->name();
        comment += "\"";

        int rad_order = static_cast<int>(this->variable_type(var).radial_order);
        io.data (rad_order, comment);
      }

#endif

      // Write the Finite Element type of the var-th variable
      // in this System
      {
        // set up the comment
        comment = "#     FE Family, Variable \"";
        comment += this->variable_name(var);
        comment += "\", System \"";
        comment += this->name();
        comment += "\"";

        const FEType & type = this->variable_type(var);
        int fam = static_cast<int>(type.family);
        io.data (fam, comment);

#ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS

        comment = "#     Radial FE Family, Variable \"";
        comment += this->variable_name(var);
        comment += "\", System \"";
        comment += this->name();
        comment += "\"";

        int radial_fam = static_cast<int>(type.radial_family);
        io.data (radial_fam, comment);

        comment = "#     Infinite Mapping Type, Variable \"";
        comment += this->variable_name(var);
        comment += "\", System \"";
        comment += this->name();
        comment += "\"";

        int i_map = static_cast<int>(type.inf_map);
        io.data (i_map, comment);
#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);
    }

    if (write_additional_data)
      {
        unsigned int cnt=0;
        for (const auto & [vec_name, vec] : _vectors)
          {
            // 9.)
            // write the name of the cnt-th additional vector
            const std::string dth_vector = std::to_string(cnt++)+"th vector";
            comment =  "# Name of " + dth_vector;
            std::string nonconst_vec_name = vec_name; // Stupid XDR API

            io.data (nonconst_vec_name, comment);
            int vec_projection = _vector_projections.at(vec_name);
            comment = "# Whether to do projections for " + dth_vector;
            io.data (vec_projection, comment);
            int vec_type = vec->type();
            comment = "# Parallel type of " + dth_vector;
            io.data (vec_type, comment);
          }
      }
  }
}

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 1468 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::libmesh_assert(), libMesh::make_range(), 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 (auto comp : make_range(node->n_comp(sys_num,var)))
            {
              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 (auto comp : make_range(elem->n_comp(sys_num,var)))
            {
              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 (auto var : make_range(this->n_vars()))
    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 (auto dof : SCALAR_dofs)
              io_buffer.push_back((*this->solution)(dof));
          }
      }

  // 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);

  // total_written_size += io_buffer.size();

  // Only write additional vectors if wanted
  if (write_additional_data)
    {
      for (auto & [vec_name, vec] : _vectors)
        {
          io_buffer.clear();
          io_buffer.reserve(vec->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 (auto comp : make_range(node->n_comp(sys_num,var)))
                    {
                      libmesh_assert_not_equal_to (node->dof_number(sys_num, var, comp),
                                                   DofObject::invalid_id);

                      io_buffer.push_back((*vec)(node->dof_number(sys_num, var, comp)));
                    }

                // Then write the element DOF values
                for (const auto & elem : ordered_elements)
                  for (auto comp : make_range(elem->n_comp(sys_num,var)))
                    {
                      libmesh_assert_not_equal_to (elem->dof_number(sys_num, var, comp),
                                                   DofObject::invalid_id);

                      io_buffer.push_back((*vec)(elem->dof_number(sys_num, var, comp)));
                    }
              }

          // Finally, write the SCALAR data on the last processor
          for (auto var : make_range(this->n_vars()))
            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 (auto dof : SCALAR_dofs)
                      io_buffer.push_back((*vec)(dof));
                  }
              }

          // 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 += vec_name;
            comment += "\"";
          }

          io.data (io_buffer, comment);

          // 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_parameter_data_to_files()

void libMesh::RBParametrized::write_parameter_data_to_files ( const std::string &  continuous_param_file_name, const std::string &  discrete_param_file_name, const bool  write_binary_data  )

inherited

Write out the parameter ranges to files.

Definition at line 199 of file rb_parametrized.C.

References libMesh::RBParametrized::write_discrete_parameter_values_to_file(), and libMesh::RBParametrized::write_parameter_ranges_to_file().

Referenced by libMesh::RBSCMEvaluation::legacy_write_offline_data_to_files(), and libMesh::RBEvaluation::legacy_write_offline_data_to_files().

{
  write_parameter_ranges_to_file(continuous_param_file_name, write_binary_data);
  write_discrete_parameter_values_to_file(discrete_param_file_name, write_binary_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 1668 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().

Referenced by libMesh::TransientRBConstruction::write_riesz_representors_to_files(), and libMesh::RBConstruction::write_riesz_representors_to_files().

{
  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)
    {
      for (auto & pair : this->_vectors)
        {
          // total_written_size +=
          this->write_serialized_vector(io, *pair.second);

          // set up the comment
          if (this->processor_id() == 0)
            {
              comment = "# System \"";
              comment += this->name();
              comment += "\" Additional Vector \"";
              comment += pair.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 2261 of file system_io.C.

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

Referenced by libMesh::RBEvaluation::write_out_vectors().

{
  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 (const NumericVector<Number> * vec : vectors)
    for (auto var : make_range(this->n_vars()))
      if (this->variable(var).type().family == SCALAR)
        {
          libmesh_assert_not_equal_to (vec, 0);

          written_length +=
            this->write_SCALAR_dofs (*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 1668 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 120 of file parallel_object.h.

Referenced by libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::StaticCondensation::close(), libMesh::ParallelObject::comm(), libMesh::CondensedEigenSystem::initialize_condensed_matrices(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::operator=(), libMesh::ParallelObject::processor_id(), libMesh::BoundaryInfo::regenerate_id_sets(), and libMesh::StaticCondensationDofMap::reinit().

_counts [1/2]

ReferenceCounter::Counts libMesh::ReferenceCounter::_counts

staticprotectedinherited

Actually holds the data.

Definition at line 124 of file reference_counter.h.

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

_counts [2/2]

ReferenceCounter::Counts libMesh::ReferenceCounter::_counts

staticprotectedinherited

Actually holds the data.

Definition at line 124 of file reference_counter.h.

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

_enable_print_counter [1/2]

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 143 of file reference_counter.h.

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

_enable_print_counter [2/2]

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 143 of file reference_counter.h.

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

_mutex [1/2]

Threads::spin_mutex libMesh::ReferenceCounter::_mutex

staticprotectedinherited

Mutual exclusion object to enable thread-safe reference counting.

Definition at line 137 of file reference_counter.h.

_mutex [2/2]

Threads::spin_mutex libMesh::ReferenceCounter::_mutex

staticprotectedinherited

Mutual exclusion object to enable thread-safe reference counting.

Definition at line 137 of file reference_counter.h.

_n_objects [1/2]

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 132 of file reference_counter.h.

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

_n_objects [2/2]

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 132 of file reference_counter.h.

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

_normalize_solution_snapshots

bool libMesh::RBConstructionBase< CondensedEigenSystem >::_normalize_solution_snapshots

protectedinherited

Set this boolean to true if we want to normalize solution snapshots used in training to have norm of 1.

This is relevant if snapshots have differing magnitudes and we want to approximate them all with equal accuracy.

Definition at line 281 of file rb_construction_base.h.

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 1547 of file system.h.

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

condensed_matrix_A

SparseMatrix<Number>* libMesh::CondensedEigenSystem::condensed_matrix_A

inherited

The (condensed) system matrix for standard eigenvalue problems.

Public access to this member variable will be deprecated in the future! Use get_condensed_matrix_A() instead.

Definition at line 178 of file condensed_eigen_system.h.

Referenced by libMesh::CondensedEigenSystem::set_raw_pointers().

condensed_matrix_B

SparseMatrix<Number>* libMesh::CondensedEigenSystem::condensed_matrix_B

inherited

A second (condensed) system matrix for generalized eigenvalue problems.

Public access to this member variable will be deprecated in the future! Use get_condensed_matrix_B() instead.

Definition at line 186 of file condensed_eigen_system.h.

Referenced by libMesh::CondensedEigenSystem::set_raw_pointers().

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 1605 of file system.h.

Referenced by libMesh::__libmesh_petsc_diff_solver_jacobian(), libMesh::__libmesh_petsc_diff_solver_residual(), libMesh::UniformRefinementEstimator::_estimate_error(), alternative_fe_assembly(), libMesh::VariationalSmootherSystem::assembly(), 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(), fe_assembly(), libMesh::StaticCondensation::init(), 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::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::FEMContext::pre_fe_reinit(), libMesh::System::re_update(), libMesh::System::reinit(), libMesh::System::restrict_vectors(), OverlappingAlgebraicGhostingTest::run_ghosting_test(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), SolidSystem::save_initial_mesh(), libMesh::RBConstruction::set_context_solution_vec(), setup(), MeshFunctionTest::test_subdomain_id_sets(), MeshInputTest::testCopyElementVectorImpl(), libMesh::BoundaryVolumeSolutionTransfer::transfer_boundary_volume(), libMesh::TransientRBConstruction::truth_assembly(), libMesh::TransientRBConstruction::truth_solve(), libMesh::System::update(), libMesh::Nemesis_IO_Helper::write_element_values(), and libMesh::Nemesis_IO_Helper::write_nodal_solution().

eigen_solver

std::unique_ptr<EigenSolver<Number> > libMesh::EigenSystem::eigen_solver

inherited

The EigenSolver, defining which interface, i.e solver package to use.

Public access to this member variable will be deprecated in the future! Use get_eigen_solver instead.

Definition at line 362 of file eigen_system.h.

Referenced by libMesh::EigenSystem::clear(), compute_SCM_bounding_box(), evaluate_stability_constant(), libMesh::EigenSystem::get_eigen_solver(), libMesh::EigenSystem::get_eigenpair(), libMesh::CondensedEigenSystem::get_eigenpair(), libMesh::EigenSystem::get_eigenvalue(), libMesh::EigenSystem::set_eigenproblem_type(), libMesh::EigenSystem::set_initial_space(), and libMesh::EigenSystem::solve_helper().

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 1578 of file system.h.

Referenced by CurlCurlSystem::init_data(), and set_system_parameters().

inner_product_storage_vector

std::unique_ptr<NumericVector<Number> > libMesh::RBConstructionBase< CondensedEigenSystem >::inner_product_storage_vector

protectedinherited

We keep an extra temporary vector that is useful for performing inner products (avoids unnecessary memory allocation/deallocation).

Definition at line 288 of file rb_construction_base.h.

Referenced by Aq_inner_product(), and B_inner_product().

local_non_condensed_dofs_vector

std::vector<dof_id_type> libMesh::CondensedEigenSystem::local_non_condensed_dofs_vector

inherited

Vector storing the local dof indices that will not be condensed.

All dofs that are not in this vector will be eliminated from the system when we perform a solve.

Definition at line 194 of file condensed_eigen_system.h.

Referenced by libMesh::CondensedEigenSystem::copy_sub_to_super(), libMesh::CondensedEigenSystem::copy_super_to_sub(), libMesh::CondensedEigenSystem::get_eigenpair(), libMesh::CondensedEigenSystem::initialize_condensed_dofs(), libMesh::CondensedEigenSystem::initialize_condensed_matrices(), libMesh::CondensedEigenSystem::n_global_non_condensed_dofs(), and libMesh::CondensedEigenSystem::solve().

matrix_A

SparseMatrix<Number>* libMesh::EigenSystem::matrix_A

inherited

The system matrix for standard eigenvalue problems.

Public access to this member variable will be deprecated in the future! Use get_matrix_A() instead.

Definition at line 313 of file eigen_system.h.

Referenced by libMesh::EigenSystem::add_matrices(), Aq_inner_product(), libMesh::EigenSystem::clear(), compute_SCM_bounding_box(), evaluate_stability_constant(), libMesh::EigenSystem::get_matrix_A(), libMesh::EigenSystem::has_matrix_A(), libMesh::EigenSystem::solve(), and libMesh::CondensedEigenSystem::solve().

matrix_B

SparseMatrix<Number>* libMesh::EigenSystem::matrix_B

inherited

A second system matrix for generalized eigenvalue problems.

Public access to this member variable will be deprecated in the future! Use get_matrix_B() instead.

Definition at line 321 of file eigen_system.h.

Referenced by libMesh::EigenSystem::add_matrices(), B_inner_product(), libMesh::EigenSystem::clear(), libMesh::EigenSystem::get_matrix_B(), libMesh::EigenSystem::has_matrix_B(), load_matrix_B(), libMesh::EigenSystem::solve(), libMesh::CondensedEigenSystem::solve(), and libMesh::EigenSystem::solve_helper().

parameters

Parameters libMesh::System::parameters

inherited

Parameters for the system. If a parameter is not provided, it should be retrieved from the EquationSystems.

Definition at line 1526 of file system.h.

Referenced by libMesh::ImplicitSystem::get_linear_solve_parameters(), libMesh::FrequencySystem::init_data(), libMesh::NonlinearImplicitSystem::set_solver_parameters(), libMesh::EigenSystem::solve(), libMesh::CondensedEigenSystem::solve(), and libMesh::EigenSystem::solve_helper().

precond_matrix

SparseMatrix<Number>* libMesh::EigenSystem::precond_matrix

inherited

A preconditioning matrix.

Public access to this member variable will be deprecated in the future! Use get_precond_matrix() instead.

Definition at line 345 of file eigen_system.h.

Referenced by libMesh::EigenSystem::add_matrices(), libMesh::EigenSystem::clear(), libMesh::EigenSystem::get_precond_matrix(), libMesh::EigenSystem::has_precond_matrix(), libMesh::EigenSystem::solve(), and libMesh::CondensedEigenSystem::solve().

quiet_mode

bool libMesh::RBConstructionBase< CondensedEigenSystem >::quiet_mode

protectedinherited

Flag to indicate whether we print out extra information during the Offline stage.

Definition at line 265 of file rb_construction_base.h.

rb_scm_eval

RBSCMEvaluation* libMesh::RBSCMConstruction::rb_scm_eval

private

The current RBSCMEvaluation object we are using to perform the Evaluation stage of the SCM.

Definition at line 244 of file rb_scm_construction.h.

Referenced by compute_SCM_bounding_box(), compute_SCM_bounds_on_training_set(), enrich_C_J(), evaluate_stability_constant(), get_rb_scm_evaluation(), perform_SCM_greedy(), print_info(), resize_SCM_vectors(), and set_rb_scm_evaluation().

RB_system_name

std::string libMesh::RBSCMConstruction::RB_system_name

protected

The name of the associated RB system.

Definition at line 236 of file rb_scm_construction.h.

Referenced by add_scaled_symm_Aq(), load_matrix_B(), perform_SCM_greedy(), and set_RB_system_name().

SCM_training_tolerance

Real libMesh::RBSCMConstruction::SCM_training_tolerance

protected

Tolerance which controls when to terminate the SCM Greedy.

Definition at line 231 of file rb_scm_construction.h.

Referenced by get_SCM_training_tolerance(), perform_SCM_greedy(), process_parameters_file(), and set_SCM_training_tolerance().

serial_training_set

bool libMesh::RBConstructionBase< CondensedEigenSystem >::serial_training_set

protectedinherited

This boolean flag indicates whether or not the training set should be the same on all processors.

By default it is false, but in the case of the Empirical Interpolation Method (RBEIMConstruction), for example, we need the training set to be identical on all processors.

Definition at line 273 of file rb_construction_base.h.

shell_matrix_A

std::unique_ptr<ShellMatrix<Number> > libMesh::EigenSystem::shell_matrix_A

inherited

The system shell matrix for standard eigenvalue problems.

Public access to this member variable will be deprecated in the future! Use get_shell_matrix_A() instead.

Definition at line 329 of file eigen_system.h.

Referenced by libMesh::EigenSystem::add_matrices(), libMesh::EigenSystem::clear(), libMesh::EigenSystem::get_shell_matrix_A(), libMesh::EigenSystem::has_shell_matrix_A(), libMesh::EigenSystem::init_matrices(), libMesh::EigenSystem::reinit(), and libMesh::EigenSystem::solve_helper().

shell_matrix_B

std::unique_ptr<ShellMatrix<Number> > libMesh::EigenSystem::shell_matrix_B

inherited

A second system shell matrix for generalized eigenvalue problems.

Public access to this member variable will be deprecated in the future! Use get_shell_matrix_B() instead.

Definition at line 337 of file eigen_system.h.

Referenced by libMesh::EigenSystem::add_matrices(), libMesh::EigenSystem::clear(), libMesh::EigenSystem::get_shell_matrix_B(), libMesh::EigenSystem::has_shell_matrix_B(), libMesh::EigenSystem::init_matrices(), libMesh::EigenSystem::reinit(), and libMesh::EigenSystem::solve_helper().

shell_precond_matrix

std::unique_ptr<ShellMatrix<Number> > libMesh::EigenSystem::shell_precond_matrix

inherited

A preconditioning shell matrix.

Public access to this member variable will be deprecated in the future! Use get_shell_precond_matrix() instead.

Definition at line 353 of file eigen_system.h.

Referenced by libMesh::EigenSystem::add_matrices(), libMesh::EigenSystem::clear(), libMesh::EigenSystem::get_shell_precond_matrix(), libMesh::EigenSystem::has_shell_precond_matrix(), libMesh::EigenSystem::init_matrices(), libMesh::EigenSystem::reinit(), and libMesh::EigenSystem::solve_helper().

solution

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

inherited

Data structure to hold solution values.

Definition at line 1593 of file system.h.

Referenced by libMesh::__libmesh_petsc_diff_solver_jacobian(), libMesh::__libmesh_petsc_diff_solver_residual(), libMesh::ExactSolution::_compute_error(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::TransientRBConstruction::add_IC_to_RB_space(), libMesh::NewmarkSolver::advance_timestep(), libMesh::AdaptiveTimeSolver::advance_timestep(), libMesh::UnsteadySolver::advance_timestep(), libMesh::ContinuationSystem::apply_predictor(), libMesh::TransientRBConstruction::assemble_affine_expansion(), libMesh::VariationalSmootherSystem::assembly(), libMesh::FEMSystem::assembly(), libMesh::LinearImplicitSystem::assembly(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::RBConstruction::check_if_zero_truth_solve(), libMesh::System::clear(), libMesh::System::compare(), compute_enriched_soln(), libMesh::RBConstruction::compute_Fq_representor_innerprods(), libMesh::NewmarkSolver::compute_initial_accel(), libMesh::RBConstruction::compute_output_dual_innerprods(), libMesh::RBConstruction::compute_residual_dual_norm_slow(), compute_stresses(), LinearElasticityWithContact::compute_stresses(), LinearElasticity::compute_stresses(), LargeDeformationElasticity::compute_stresses(), libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), libMesh::ContinuationSystem::continuation_solve(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::Nemesis_IO::copy_elemental_solution(), libMesh::GMVIO::copy_nodal_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::Nemesis_IO::copy_nodal_solution(), libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::Nemesis_IO::copy_scalar_solution(), create_wrapped_function(), DMCreateGlobalVector_libMesh(), DMlibMeshFunction(), DMlibMeshJacobian(), libMesh::UnsteadySolver::du(), libMesh::RBConstruction::enrich_RB_space(), libMesh::PatchRecoveryErrorEstimator::estimate_error(), libMesh::WeightedPatchRecoveryErrorEstimator::estimate_error(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::AdjointResidualErrorEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), evaluate_stability_constant(), libMesh::EigenSystem::get_eigenpair(), libMesh::CondensedEigenSystem::get_eigenpair(), LinearElasticityWithContact::get_least_and_max_gap_function(), libMesh::VariationalSmootherSystem::init_data(), libMesh::System::init_data(), libMesh::ContinuationSystem::initialize_tangent(), libMesh::TransientRBConstruction::initialize_truth(), 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::RBConstruction::load_basis_function(), libMesh::TransientRBConstruction::load_rb_solution(), libMesh::RBConstruction::load_rb_solution(), main(), libMesh::DofMap::max_constraint_error(), libMesh::FEMSystem::mesh_position_get(), libMesh::ErrorVector::plot_error(), libMesh::RBConstruction::print_basis_function_orthogonality(), libMesh::InterMeshProjection::project_system_vectors(), libMesh::ImplicitSystem::qoi_parameter_hessian(), libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product(), libMesh::System::re_update(), libMesh::System::read_legacy_data(), libMesh::System::read_parallel_data(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), libMesh::System::read_serialized_data(), libMesh::System::reinit(), libMesh::System::restrict_vectors(), libMesh::MemoryHistoryData::retrieve_vectors(), OverlappingAlgebraicGhostingTest::run_ghosting_test(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), libMesh::ContinuationSystem::save_current_solution(), libMesh::TransientRBConstruction::set_error_temporal_data(), setup(), WriteVecAndScalar::setupTests(), libMesh::TwostepTimeSolver::solve(), libMesh::NewtonSolver::solve(), libMesh::PetscDiffSolver::solve(), libMesh::FrequencySystem::solve(), libMesh::LinearImplicitSystem::solve(), libMesh::NonlinearImplicitSystem::solve(), libMesh::ClawSystem::solve_conservation_law(), libMesh::RBConstruction::solve_for_matrix_and_rhs(), libMesh::ContinuationSystem::solve_tangent(), libMesh::MemoryHistoryData::store_vectors(), ConstraintOperatorTest::test1DCoarseningOperator(), MeshfunctionDFEM::test_mesh_function_dfem(), MeshfunctionDFEM::test_mesh_function_dfem_grad(), MeshFunctionTest::test_p_level(), SystemsTest::testBoundaryProjectCube(), ConstraintOperatorTest::testCoreform(), SystemsTest::testDofCouplingWithVarGroups(), MeshInputTest::testExodusWriteElementDataFromDiscontinuousNodalData(), SystemsTest::testPostInitAddVector(), SystemsTest::testProjectCubeWithMeshFunction(), MeshInputTest::testProjectionRegression(), WriteVecAndScalar::testSolution(), libMesh::RBConstruction::train_reduced_basis_with_POD(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::DirectSolutionTransfer::transfer(), libMesh::MeshfreeSolutionTransfer::transfer(), libMesh::BoundaryVolumeSolutionTransfer::transfer_boundary_volume(), libMesh::BoundaryVolumeSolutionTransfer::transfer_volume_boundary(), libMesh::TransientRBConstruction::truth_solve(), libMesh::RBConstruction::truth_solve(), libMesh::System::update(), update_current_local_solution(), libMesh::System::update_global_solution(), libMesh::TransientRBConstruction::update_RB_initial_condition_all_N(), libMesh::TransientRBConstruction::update_residual_terms(), libMesh::RBConstruction::update_residual_terms(), libMesh::ContinuationSystem::update_solution(), libMesh::NewmarkSystem::update_u_v_a(), libMesh::DTKAdapter::update_variable_values(), libMesh::System::write_parallel_data(), libMesh::TransientRBConstruction::write_riesz_representors_to_files(), libMesh::RBConstruction::write_riesz_representors_to_files(), and libMesh::System::write_serialized_data().

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 1615 of file system.h.

Referenced by libMesh::AdaptiveTimeSolver::adjoint_advance_timestep(), libMesh::UnsteadySolver::adjoint_advance_timestep(), libMesh::TwostepTimeSolver::adjoint_solve(), libMesh::AdaptiveTimeSolver::advance_timestep(), libMesh::UnsteadySolver::advance_timestep(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::SubProjector::construct_projection(), HeatSystem::element_qoi(), fill_dirichlet_bc(), libMesh::ExactErrorEstimator::find_squared_element_error(), initialize(), libMesh::Euler2Solver::integrate_adjoint_refinement_error_estimate(), libMesh::EulerSolver::integrate_adjoint_refinement_error_estimate(), libMesh::UnsteadySolver::integrate_adjoint_sensitivity(), libMesh::Euler2Solver::integrate_qoi_timestep(), libMesh::EulerSolver::integrate_qoi_timestep(), main(), libMesh::WeightedPatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::ProjectVertices::operator()(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::ProjectEdges::operator()(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::ProjectSides::operator()(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::ProjectInteriors::operator()(), libMesh::System::reinit_constraints(), libMesh::UnsteadySolver::retrieve_timestep(), and libMesh::TwostepTimeSolver::solve().

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 1563 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().

verbose_mode

bool libMesh::RBParametrized::verbose_mode

inherited

Public boolean to toggle verbose mode.

Definition at line 193 of file rb_parametrized.h.

Referenced by libMesh::RBParametrized::check_if_valid_params().

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

• include/reduced_basis/rb_scm_construction.h
• src/reduced_basis/rb_scm_construction.C