Manages consistently variables, degrees of freedom, coefficient vectors, matrices and non-linear solvers for implicit systems. More...

#include <nonlinear_implicit_system.h>

Inheritance diagram for libMesh::NonlinearImplicitSystem:

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Classes
class	ComputeBounds
	Abstract base class to be used to calculate the bounds on the degrees of freedom of a nonlinear system. More...

class	ComputeJacobian
	Abstract base class to be used to calculate the Jacobian of a nonlinear system. More...

class	ComputePostCheck
	Abstract base class to be used for applying user modifications to the solution vector and/or Newton update step after each nonlinear step. More...

class	ComputePreCheck
	Abstract base class to be used for applying user modifications to the Newton search direction before the solver's line search is called. More...

class	ComputeResidual
	Abstract base class to be used to calculate the residual of a nonlinear system. More...

class	ComputeResidualandJacobian
	Abstract base class to be used to calculate the residual and Jacobian simultaneously of a nonlinear system. More...

class	ComputeVectorSubspace
	Callable abstract base class to be used as a callback to provide the solver with a basis for the system's Jacobian's nullspace (the kernel or the "zero energy modes") or near-nullspace (the "low energy modes"). More...

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

typedef ImplicitSystem	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
	NonlinearImplicitSystem (EquationSystems &es, const std::string &name, const unsigned int number)
	Constructor. More...

	NonlinearImplicitSystem (const NonlinearImplicitSystem &)=delete
	Special functions. More...

NonlinearImplicitSystem &	operator= (const NonlinearImplicitSystem &)=delete

	NonlinearImplicitSystem (NonlinearImplicitSystem &&)=default

NonlinearImplicitSystem &	operator= (NonlinearImplicitSystem &&)=delete

virtual	~NonlinearImplicitSystem ()

sys_type &	system ()

virtual void	clear () override
	Clear all the data structures associated with the system. More...

virtual void	reinit () override
	Reinitializes the member data fields associated with the system, so that, e.g., `assemble()` may be used. More...

virtual void	solve () override
	Assembles & solves the nonlinear system R(x) = 0. More...

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

virtual void	assembly (bool get_residual, bool get_jacobian, bool apply_heterogeneous_constraints=false, bool apply_no_constraints=false) override
	Assembles a residual in `rhs` and/or a jacobian in `matrix`, as requested. More...

virtual std::string	system_type () const override

unsigned int	n_nonlinear_iterations () const

Real	final_nonlinear_residual () const

unsigned	get_current_nonlinear_iteration_number () const
	If called during the solve(), for example by the user-specified residual or Jacobian function, return the current nonlinear iteration number. More...

virtual void	create_static_condensation () override
	Request that static condensation be performed for this system. More...

virtual void	assemble () override
	Prepares `matrix` and `rhs` for system assembly, then calls user assembly function. More...

virtual void	disable_cache () override
	Avoids use of any cached data that might affect any solve result. More...

virtual LinearSolver< Number > *	get_linear_solver () const

virtual void	release_linear_solver (LinearSolver< Number > *) const
	Currently a no-op. More...

virtual void	assemble_residual_derivatives (const ParameterVector &parameters) override
	Residual parameter derivative function. More...

virtual std::pair< unsigned int, Real >	sensitivity_solve (const ParameterVector &parameters) override
	Assembles & solves the linear system(s) (dR/du)*u_p = -dR/dp, for those parameters contained within `parameters`. More...

virtual std::pair< unsigned int, Real >	weighted_sensitivity_solve (const ParameterVector &parameters, const ParameterVector &weights) override
	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()) override
	Assembles & solves the linear system (dR/du)^T*z = dq/du, for those quantities of interest q specified by `qoi_indices`. More...

virtual std::pair< unsigned int, Real >	weighted_sensitivity_adjoint_solve (const ParameterVector &parameters, const ParameterVector &weights, const QoISet &qoi_indices=QoISet()) override
	Assembles & solves the linear system(s) (dR/du)^Tz_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...

virtual void	adjoint_qoi_parameter_sensitivity (const QoISet &qoi_indices, const ParameterVector &parameters, SensitivityData &sensitivities) override
	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	forward_qoi_parameter_sensitivity (const QoISet &qoi_indices, const ParameterVector &parameters, SensitivityData &sensitivities) override
	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	qoi_parameter_hessian (const QoISet &qoi_indices, const ParameterVector &parameters, SensitivityData &hessian) override
	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) override
	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...

const SparseMatrix< Number > &	get_system_matrix () const

SparseMatrix< Number > &	get_system_matrix ()

StaticCondensation &	get_static_condensation ()

virtual void	assemble_qoi (const QoISet &qoi_indices=QoISet()) override
	Prepares `qoi` for quantity of interest assembly, then calls user qoi function. More...

virtual void	assemble_qoi_derivative (const QoISet &qoi_indices=QoISet(), bool include_liftfunc=true, bool apply_constraints=true) override
	Prepares `adjoint_rhs` for quantity of interest derivative assembly, then calls user qoi derivative function. More...

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	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...

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 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 variables `vars` 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...

unsigned int	add_variable_array (const std::vector< std::string > &vars, const FEType &type, const std::set< subdomain_id_type > *const active_subdomains=nullptr)
	Adds variables `vars` 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...

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

bool	has_static_condensation () const

const Parallel::Communicator &	comm () const

processor_id_type	n_processors () const

processor_id_type	processor_id () const

Static Public Member Functions
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 unsigned int	n_objects ()
	Prints the number of outstanding (created, but not yet destroyed) objects. More...

static void	enable_print_counter_info ()
	Methods to enable/disable the reference counter output from print_info() More...

static void	disable_print_counter_info ()

Public Attributes
std::unique_ptr< NonlinearSolver< Number > >	nonlinear_solver
	The `NonlinearSolver` defines the default interface used to solve the nonlinear_implicit system. More...

std::unique_ptr< DiffSolver >	diff_solver
	The `DiffSolver` defines an optional interface used to solve the nonlinear_implicit system. More...

SparseMatrix< Number > *	matrix
	The system matrix. More...

bool	zero_out_matrix_and_rhs
	By default, the system will zero out the matrix and the right hand side. More...

std::unique_ptr< LinearSolver< Number > >	linear_solver
	This class handles all the details of interfacing with various linear algebra packages like PETSc or LASPACK. More...

NumericVector< Number > *	rhs
	The system matrix. 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...

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

Protected Member Functions
void	set_solver_parameters ()
	Copies system parameters into nonlinear solver parameters. More...

virtual void	add_matrices () override
	Adds the system matrix. More...

template<typename T >
void	setup_static_condensation_preconditioner (T &solver)
	Sets up the static condensation preconditioner for the supplied `solver`. More...

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...

virtual void	init_data ()
	Initializes the data for the system. More...

virtual void	init_matrices ()
	Initializes the matrices associated with this system. More...

bool	can_add_matrices () const

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

virtual bool	condense_constrained_dofs () const
	Whether this object should condense out constrained degrees of freedom. 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...

Protected Attributes
unsigned int	_n_nonlinear_iterations
	The number of nonlinear iterations required to solve the nonlinear system R(x)=0. More...

Real	_final_nonlinear_residual
	The final residual for the nonlinear system R(x) More...

const Parallel::Communicator &	_communicator

Static Protected Attributes
static Counts	_counts
	Actually holds the data. More...

static Threads::atomic< unsigned int >	_n_objects
	The number of objects. More...

static Threads::spin_mutex	_mutex
	Mutual exclusion object to enable thread-safe reference counting. More...

static bool	_enable_print_counter = true
	Flag to control whether reference count information is printed when print_info is called. More...

Detailed Description

Manages consistently variables, degrees of freedom, coefficient vectors, matrices and non-linear solvers for implicit systems.

An implicit system is a system that requires the solution of a system of equations. This class has the ability to create and use a non-linear solver to solve the system of equations.

The matrix NonlinearImplicitSystem::matrix and the vector NonlinearImplicitSystem::rhs should be filled during assembly.

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

Author: Benjamin S. Kirk

Date: 2005

Definition at line 54 of file nonlinear_implicit_system.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 785 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 759 of file system.h.

◆ Counts

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

protectedinherited

Data structure to log the information.

The log is identified by the class name.

Definition at line 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 542 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 784 of file system.h.

◆ Parent

typedef ImplicitSystem libMesh::NonlinearImplicitSystem::Parent

The type of the parent.

Definition at line 84 of file nonlinear_implicit_system.h.

◆ sys_type

typedef NonlinearImplicitSystem libMesh::NonlinearImplicitSystem::sys_type

The type of system.

Definition at line 79 of file nonlinear_implicit_system.h.

◆ ValueFunctionPointer

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

inherited

Projects arbitrary functions onto the current solution.

The function value fptr and its gradient gptr are represented by function pointers. A gradient gptr is only required/used for projecting onto finite element spaces with continuous derivatives.

Definition at line 538 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 758 of file system.h.

Constructor & Destructor Documentation

◆ NonlinearImplicitSystem() [1/3]

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

Constructor.

Definition at line 33 of file nonlinear_implicit_system.C.

References libMesh::System::has_static_condensation(), nonlinear_solver, libMesh::EquationSystems::parameters, libMesh::Real, libMesh::Parameters::set(), and libMesh::ImplicitSystem::setup_static_condensation_preconditioner().

                                                                                 :
 
   Parent                    (es, name_in, number_in),
   nonlinear_solver          (NonlinearSolver<Number>::build(*this)),
   diff_solver               (),
   _n_nonlinear_iterations   (0),
   _final_nonlinear_residual (1.e20)
 {
   // Set default parameters
   // These were chosen to match the Petsc defaults
   es.parameters.set<Real>        ("linear solver tolerance") = 1e-5;
   es.parameters.set<Real>        ("linear solver minimum tolerance") = 1e-5;
   es.parameters.set<unsigned int>("linear solver maximum iterations") = 10000;
 
   es.parameters.set<unsigned int>("nonlinear solver maximum iterations") = 50;
   es.parameters.set<unsigned int>("nonlinear solver maximum function evaluations") = 10000;
 
   es.parameters.set<Real>("nonlinear solver absolute residual tolerance") = 1e-35;
   es.parameters.set<Real>("nonlinear solver relative residual tolerance") = 1e-8;
   es.parameters.set<Real>("nonlinear solver divergence tolerance") = 1e+4;
   es.parameters.set<Real>("nonlinear solver absolute step tolerance") = 1e-8;
   es.parameters.set<Real>("nonlinear solver relative step tolerance") = 1e-8;
 
   es.parameters.set<bool>("reuse preconditioner") = false;
   es.parameters.set<unsigned int>("reuse preconditioner maximum linear iterations") = 1;
 
   if (this->has_static_condensation())
     this->setup_static_condensation_preconditioner(*nonlinear_solver);
 }

◆ NonlinearImplicitSystem() [2/3]

libMesh::NonlinearImplicitSystem::NonlinearImplicitSystem ( const NonlinearImplicitSystem & )

delete

Special functions.

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

◆ NonlinearImplicitSystem() [3/3]

libMesh::NonlinearImplicitSystem::NonlinearImplicitSystem ( NonlinearImplicitSystem && )

default

◆ ~NonlinearImplicitSystem()

libMesh::NonlinearImplicitSystem::~NonlinearImplicitSystem ( )

virtualdefault

Member Function Documentation

◆ activate()

void libMesh::System::activate ( )

inlineinherited

Activates the system.

Only active systems are solved.

Definition at line 2399 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 2391 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 1282 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 1218 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::ImplicitSystem::add_matrices ( )

overrideprotectedvirtualinherited

Adds the system matrix.

Reimplemented from libMesh::System.

Definition at line 109 of file implicit_system.C.

References libMesh::System::add_matrices(), libMesh::System::add_matrix(), libMesh::libmesh_assert(), libMesh::ImplicitSystem::matrix, and libMesh::System::n_matrices().

 {
   Parent::add_matrices();
 
   // Possible that we cleared the _matrices but
   // forgot to update the matrix pointer?
   if (this->n_matrices() == 0)
     matrix = nullptr;
 
   // Only need to add the matrix if it isn't there
   // already!
   if (matrix == nullptr)
     matrix = &(this->add_matrix ("System Matrix"));
 
   libmesh_assert(matrix);
 }

◆ 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 995 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 2606 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 1038 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_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 1312 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 1167 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 1342 of file system.C.

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

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::AdvectionSystem::init_data(), HeatSystem::init_data(), SimpleRBConstruction::init_data(), libMesh::VariationalSmootherSystem::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().

 {
   return this->get_dof_map().add_variable(*this, 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 1351 of file system.C.

References libMesh::System::add_variable().

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

◆ add_variable_array()

unsigned int libMesh::System::add_variable_array	(	const std::vector< std::string > &	vars,
		const FEType &	type,
		const std::set< subdomain_id_type > *const	active_subdomains = `nullptr`
	)

inherited

Adds variables vars 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 the vars have no subdomain restrictions. This API will end up calling this->add_variables(). However, we will additionally store data that can be leveraged by the DofMap to build degrees of freedom containers corresponding to all the variables in this variable array

An 'array variable' is simply a sequence of contiguous variable numbers defined by pair where the first member of the pair is the first number in the variable sequence and the second member of the pair is the number of the last variable in the sequence plus one. Array variables may be used in tandem with variable grouping by downstream code to build optimized physics kernels since each variable in the array will have the same shape functions.

Returns: The index number for the last of the new variables.

Definition at line 1382 of file system.C.

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

Referenced by DofMapTest::testArrayDofIndicesWithType().

 {
   return this->get_dof_map().add_variable_array(*this, vars, type, 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 variables vars 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 the vars have no subdomain restrictions

Returns: The index number for the last of the new variables.

Definition at line 1363 of file system.C.

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

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

 {
   return this->get_dof_map().add_variables(*this, vars, type, active_subdomains);
 }

◆ 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 1372 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 753 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 1250 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 1197 of file system.C.

References libMesh::System::add_vector().

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

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

◆ adjoint_qoi_parameter_sensitivity()

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

overridevirtualinherited

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

Uses adjoint_solve() and the adjoint sensitivity method.

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

Reimplemented from libMesh::System.

Definition at line 513 of file implicit_system.C.

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

Referenced by libMesh::UnsteadySolver::integrate_adjoint_sensitivity(), and main().

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

◆ adjoint_solve()

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

overridevirtualinherited

Assembles & solves the linear system (dR/du)^T*z = dq/du, for those quantities of interest q specified by qoi_indices.

Leave qoi_indices empty to solve all adjoint problems.

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

Reimplemented from libMesh::System.

Reimplemented in libMesh::DifferentiableSystem.

Definition at line 192 of file implicit_system.C.

References libMesh::System::add_adjoint_solution(), libMesh::LinearSolver< T >::adjoint_solve(), libMesh::System::assemble_before_solve, libMesh::ExplicitSystem::assemble_qoi_derivative(), libMesh::ImplicitSystem::assembly(), libMesh::DofMap::enforce_adjoint_constraints_exactly(), libMesh::System::get_adjoint_rhs(), libMesh::System::get_adjoint_solution(), libMesh::System::get_dof_map(), libMesh::ImplicitSystem::get_linear_solve_parameters(), libMesh::ImplicitSystem::get_linear_solver(), libMesh::QoISet::has_index(), libMesh::make_range(), libMesh::ImplicitSystem::matrix, and libMesh::System::n_qois().

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

 {
   // Log how long the linear solve takes.
   LOG_SCOPE("adjoint_solve()", "ImplicitSystem");
 
   if (this->assemble_before_solve)
     // Assemble the linear system
     this->assembly (/* get_residual = */ false,
                     /* get_jacobian = */ true);
 
   // The adjoint problem is linear
   LinearSolver<Number> * solver = this->get_linear_solver();
 
   // Reset and build the RHS from the QOI derivative
   this->assemble_qoi_derivative(qoi_indices,
                                 /* include_liftfunc = */ false,
                                 /* apply_constraints = */ true);
 
   // Our iteration counts and residuals will be sums of the individual
   // results
   std::pair<unsigned int, Real> solver_params =
     this->get_linear_solve_parameters();
   std::pair<unsigned int, Real> totalrval = std::make_pair(0,0.0);
 
   for (auto i : make_range(this->n_qois()))
     if (qoi_indices.has_index(i))
       {
         const std::pair<unsigned int, Real> rval =
           solver->adjoint_solve (*matrix, this->add_adjoint_solution(i),
                                  this->get_adjoint_rhs(i),
                                  double(solver_params.second),
                                  solver_params.first);
 
         totalrval.first  += rval.first;
         totalrval.second += rval.second;
       }
 
   // The linear solver may not have fit our constraints exactly
 #ifdef LIBMESH_ENABLE_CONSTRAINTS
   for (auto i : make_range(this->n_qois()))
     if (qoi_indices.has_index(i))
       this->get_dof_map().enforce_adjoint_constraints_exactly
         (this->get_adjoint_solution(i), i);
 #endif
 
   return totalrval;
 }

◆ assemble()

void libMesh::ImplicitSystem::assemble ( )

overridevirtualinherited

Prepares matrix and rhs for system assembly, then calls user assembly function.

Can be overridden in derived classes.

Reimplemented from libMesh::System.

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

Definition at line 90 of file implicit_system.C.

References libMesh::System::assemble(), libMesh::SparseMatrix< T >::initialized(), libMesh::NumericVector< T >::initialized(), libMesh::libmesh_assert(), libMesh::ImplicitSystem::matrix, libMesh::ExplicitSystem::rhs, libMesh::NumericVector< T >::zero(), libMesh::SparseMatrix< T >::zero(), and libMesh::ImplicitSystem::zero_out_matrix_and_rhs.

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

 {
   libmesh_assert(matrix);
   libmesh_assert (matrix->initialized());
   libmesh_assert(rhs);
   libmesh_assert (rhs->initialized());
 
   if (zero_out_matrix_and_rhs)
     {
       matrix->zero ();
       rhs->zero ();
     }
 
   // Call the base class assemble function
   Parent::assemble ();
 }

◆ assemble_qoi()

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

overridevirtualinherited

Prepares qoi for quantity of interest assembly, then calls user qoi function.

Can be overridden in derived classes.

Reimplemented from libMesh::System.

Reimplemented in libMesh::FEMSystem.

Definition at line 54 of file explicit_system.C.

References libMesh::System::assemble_qoi(), libMesh::QoISet::has_index(), libMesh::make_range(), libMesh::System::n_qois(), and libMesh::System::set_qoi().

Referenced by libMesh::ImplicitSystem::adjoint_qoi_parameter_sensitivity(), libMesh::ImplicitSystem::forward_qoi_parameter_sensitivity(), libMesh::Euler2Solver::integrate_qoi_timestep(), libMesh::EulerSolver::integrate_qoi_timestep(), libMesh::SteadySolver::integrate_qoi_timestep(), libMesh::ImplicitSystem::qoi_parameter_hessian(), and libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product().

 {
   // The user quantity of interest assembly gets to expect to
   // accumulate on initially zero values
   for (auto i : make_range(this->n_qois()))
     if (qoi_indices.has_index(i))
       this->set_qoi(i, 0);
 
   Parent::assemble_qoi (qoi_indices);
 }

◆ assemble_qoi_derivative()

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

overridevirtualinherited

Prepares adjoint_rhs for quantity of interest derivative assembly, then calls user qoi derivative function.

Can be overridden in derived classes.

Reimplemented from libMesh::System.

Reimplemented in libMesh::FEMSystem.

Definition at line 67 of file explicit_system.C.

References libMesh::System::add_adjoint_rhs(), libMesh::System::assemble_qoi_derivative(), libMesh::QoISet::has_index(), libMesh::make_range(), libMesh::System::n_qois(), and libMesh::NumericVector< T >::zero().

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

 {
   // The user quantity of interest derivative assembly gets to expect
   // to accumulate on initially zero vectors
   for (auto i : make_range(this->n_qois()))
     if (qoi_indices.has_index(i))
       this->add_adjoint_rhs(i).zero();
 
   Parent::assemble_qoi_derivative (qoi_indices, include_liftfunc,
                                    apply_constraints);
 }

◆ assemble_residual_derivatives()

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

overridevirtualinherited

Residual parameter derivative function.

Uses finite differences by default.

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

Can be overridden in derived classes.

Reimplemented from libMesh::System.

Definition at line 470 of file implicit_system.C.

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

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

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

◆ assembly()

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

overridevirtual

Assembles a residual in rhs and/or a jacobian in matrix, as requested.

Reimplemented from libMesh::ImplicitSystem.

Definition at line 245 of file nonlinear_implicit_system.C.

References libMesh::System::current_local_solution, libMesh::libmesh_assert(), libMesh::ImplicitSystem::matrix, nonlinear_solver, libMesh::ExplicitSystem::rhs, and libMesh::System::update().

 {
   // Get current_local_solution in sync
   this->update();
 
   //-----------------------------------------------------------------------------
   // if the user has provided both function pointers and objects only the pointer
   // will be used, so catch that as an error
   libmesh_error_msg_if(nonlinear_solver->jacobian && nonlinear_solver->jacobian_object,
                        "ERROR: cannot specify both a function and object to compute the Jacobian!");
 
   libmesh_error_msg_if(nonlinear_solver->residual && nonlinear_solver->residual_object,
                        "ERROR: cannot specify both a function and object to compute the Residual!");
 
   libmesh_error_msg_if(nonlinear_solver->matvec && nonlinear_solver->residual_and_jacobian_object,
                        "ERROR: cannot specify both a function and object to compute the combined Residual & Jacobian!");
 
 
   if (get_jacobian)
     {
       if (nonlinear_solver->jacobian != nullptr)
         nonlinear_solver->jacobian (*current_local_solution.get(), *matrix, *this);
 
       else if (nonlinear_solver->jacobian_object != nullptr)
         nonlinear_solver->jacobian_object->jacobian (*current_local_solution.get(), *matrix, *this);
 
       else if (nonlinear_solver->matvec != nullptr)
         nonlinear_solver->matvec (*current_local_solution.get(), get_residual ? rhs : nullptr, matrix, *this);
 
       else if (nonlinear_solver->residual_and_jacobian_object != nullptr)
         nonlinear_solver->residual_and_jacobian_object->residual_and_jacobian (*current_local_solution.get(), get_residual ? rhs : nullptr, matrix, *this);
 
       else
         libmesh_error_msg("Error! Unable to compute residual and/or Jacobian!");
     }
 
   if (get_residual)
     {
       if (nonlinear_solver->residual != nullptr)
         nonlinear_solver->residual (*current_local_solution.get(), *rhs, *this);
 
       else if (nonlinear_solver->residual_object != nullptr)
         nonlinear_solver->residual_object->residual (*current_local_solution.get(), *rhs, *this);
 
       else if (nonlinear_solver->matvec != nullptr)
         {
           // we might have already grabbed the residual and jacobian together
           if (!get_jacobian)
             nonlinear_solver->matvec (*current_local_solution.get(), rhs, nullptr, *this);
         }
 
       else if (nonlinear_solver->residual_and_jacobian_object != nullptr)
         {
           // we might have already grabbed the residual and jacobian together
           if (!get_jacobian)
             nonlinear_solver->residual_and_jacobian_object->residual_and_jacobian (*current_local_solution.get(), rhs, nullptr, *this);
         }
 
       else
         libmesh_error_msg("Error! Unable to compute residual and/or Jacobian!");
     }
   else
     libmesh_assert(get_jacobian);  // I can't believe you really wanted to assemble *nothing*
 }

◆ 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 1939 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 1956 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 1970 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 1987 of file system.C.

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

Referenced by libMesh::VariationalMeshSmoother::setup(), 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_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 1908 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 1925 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 2044 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 2061 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 2012 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 2030 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;
 }

◆ 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);
 }

◆ 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 1502 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 1524 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 1998 of file system.h.

References libMesh::System::_matrices_initialized.

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

1998 { return !_matrices_initialized; }

libMesh::System::_matrices_initialized

bool _matrices_initialized

false when additional matrices being added require initialization, true otherwise.

Definition: system.h:2264

◆ clear()

void libMesh::NonlinearImplicitSystem::clear ( )

overridevirtual

Clear all the data structures associated with the system.

Reimplemented from libMesh::ImplicitSystem.

Definition at line 79 of file nonlinear_implicit_system.C.

References libMesh::ImplicitSystem::clear(), and nonlinear_solver.

 {
   // clear the nonlinear solver
   nonlinear_solver->clear();
 
   // FIXME - this is necessary for petsc_auto_fieldsplit
   // nonlinear_solver->init_names(*this);
 
   // clear the parent data
   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.

98 { return _communicator; }

libMesh::ParallelObject::_communicator

const Parallel::Communicator & _communicator

Definition: parallel_object.h:120

◆ 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 603 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;
 }

◆ condense_constrained_dofs()

virtual bool libMesh::System::condense_constrained_dofs ( ) const

inlineprotectedvirtualinherited

Whether this object should condense out constrained degrees of freedom.

Reimplemented in libMesh::CondensedEigenSystem.

Definition at line 2036 of file system.h.

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

2036 { return false; }

◆ create_static_condensation()

void libMesh::NonlinearImplicitSystem::create_static_condensation ( )

overridevirtual

Request that static condensation be performed for this system.

Reimplemented from libMesh::ImplicitSystem.

Definition at line 71 of file nonlinear_implicit_system.C.

References libMesh::ImplicitSystem::create_static_condensation(), nonlinear_solver, and libMesh::ImplicitSystem::setup_static_condensation_preconditioner().

 {
   Parent::create_static_condensation();
   this->setup_static_condensation_preconditioner(*nonlinear_solver);
 }

◆ 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 163 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::SmoothnessEstimator::EstimateSmoothness::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 2407 of file system.h.

References libMesh::System::_active.

 {
   _active = false;
 }

◆ disable_cache()

void libMesh::ImplicitSystem::disable_cache ( )

overridevirtualinherited

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

Should be overridden in derived systems.

Reimplemented from libMesh::System.

Definition at line 128 of file implicit_system.C.

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

Referenced by libMesh::DifferentiableSystem::pop_physics(), libMesh::DifferentiableSystem::push_physics(), and libMesh::DifferentiableSystem::swap_physics().

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

◆ disable_print_counter_info()

void libMesh::ReferenceCounter::disable_print_counter_info ( )

staticinherited

Definition at line 100 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

 {
   _enable_print_counter = false;
   return;
 }

◆ enable_print_counter_info()

void libMesh::ReferenceCounter::enable_print_counter_info ( )

staticinherited

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

Definition at line 94 of file reference_counter.C.

References libMesh::ReferenceCounter::_enable_print_counter.

 {
   _enable_print_counter = true;
   return;
 }

◆ final_nonlinear_residual()

Real libMesh::NonlinearImplicitSystem::final_nonlinear_residual ( ) const

inline

Returns: The final residual for the nonlinear system solve.

Definition at line 310 of file nonlinear_implicit_system.h.

References _final_nonlinear_residual.

Referenced by main().

310 { return _final_nonlinear_residual; }

libMesh::NonlinearImplicitSystem::_final_nonlinear_residual

Real _final_nonlinear_residual

The final residual for the nonlinear system R(x)

Definition: nonlinear_implicit_system.h:337

◆ forward_qoi_parameter_sensitivity()

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

overridevirtualinherited

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

Uses the forward sensitivity method.

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

Reimplemented from libMesh::System.

Definition at line 623 of file implicit_system.C.

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

Referenced by main().

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

◆ get_adjoint_rhs() [1/2]

NumericVector< Number > & libMesh::System::get_adjoint_rhs ( unsigned int i = 0 )

inherited

Returns: A reference to one of the system's adjoint rhs vectors, by default the one corresponding to the first qoi. This what the user's QoI derivative code should assemble when setting up an adjoint problem

Definition at line 1292 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 1302 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 1230 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 1240 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 1399 of file system.C.

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

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

 {
   this->get_dof_map().get_all_variable_numbers(all_variable_numbers);
 }

◆ get_constraint_object()

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

inherited

Return the user object for imposing constraints.

Definition at line 2004 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_current_nonlinear_iteration_number()

unsigned libMesh::NonlinearImplicitSystem::get_current_nonlinear_iteration_number ( ) const

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

Definition at line 316 of file nonlinear_implicit_system.C.

References nonlinear_solver.

 {
   return nonlinear_solver->get_current_nonlinear_iteration_number();
 }

◆ 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 2375 of file system.h.

References libMesh::System::_dof_map.

 {
   return *_dof_map;
 }

◆ get_dof_map() [2/2]

DofMap & libMesh::System::get_dof_map ( )

inlineinherited

Returns: A writable reference to this system's _dof_map.

Definition at line 2383 of file system.h.

References libMesh::System::_dof_map.

 {
   return *_dof_map;
 }

◆ get_equation_systems() [1/2]

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

inlineinherited

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

Definition at line 722 of file system.h.

References libMesh::System::_equation_systems.

722 { return _equation_systems; }

libMesh::System::_equation_systems

EquationSystems & _equation_systems

Constant reference to the EquationSystems object used for the simulation.

Definition: system.h:2208

◆ 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 727 of file system.h.

References libMesh::System::_equation_systems.

727 { return _equation_systems; }

libMesh::System::_equation_systems

EquationSystems & _equation_systems

Constant reference to the EquationSystems object used for the simulation.

Definition: system.h:2208

◆ get_info() [1/2]

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

staticinherited

Gets a string containing the reference information.

Definition at line 47 of file reference_counter.C.

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

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

 {
 #if defined(LIBMESH_ENABLE_REFERENCE_COUNTING) && defined(DEBUG)
 
   std::ostringstream oss;
 
   oss << '\n'
       << " ---------------------------------------------------------------------------- \n"
       << "| Reference count information                                                |\n"
       << " ---------------------------------------------------------------------------- \n";
 
   for (const auto & [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() [2/2]

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

inherited

Returns: A string containing information about the system.

Definition at line 1818 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_linear_solve_parameters()

std::pair< unsigned int, Real > libMesh::NonlinearImplicitSystem::get_linear_solve_parameters ( ) const

overridevirtual

Returns: An integer corresponding to the upper iteration count limit and a Real corresponding to the convergence tolerance to be used in linear adjoint and/or sensitivity solves

Reimplemented from libMesh::ImplicitSystem.

Definition at line 234 of file nonlinear_implicit_system.C.

References diff_solver, and nonlinear_solver.

 {
   if (diff_solver.get())
     return std::make_pair(this->diff_solver->max_linear_iterations,
                           this->diff_solver->relative_residual_tolerance);
   return std::make_pair(this->nonlinear_solver->max_linear_iterations,
                         this->nonlinear_solver->relative_residual_tolerance);
 }

◆ get_linear_solver()

LinearSolver< Number > * libMesh::ImplicitSystem::get_linear_solver ( ) const

virtualinherited

Returns: A dumb pointer to a local std::unique_ptr<LinearSolver> member which can be used in adjoint and/or sensitivity solves.

To mimic the previous behavior of this function, if the linear_solver member is already initialized when this function is called, this function first clears it. That is, no attempt is made to reuse an existing LinearSolver object. The user MUST NOT attempt to clean up this pointer, otherwise the std::unique_ptr held by this class will likely become corrupted.

This function is virtual so it can be overridden in derived classes if necessary, however most will probably just want to use the base class behavior.

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

Definition at line 1211 of file implicit_system.C.

References libMesh::LinearSolver< T >::build(), libMesh::ParallelObject::comm(), libMesh::ImplicitSystem::linear_solver, libMesh::System::prefix(), and libMesh::System::prefix_with_name().

Referenced by libMesh::ImplicitSystem::adjoint_solve(), libMesh::ImplicitSystem::disable_cache(), libMesh::ImplicitSystem::sensitivity_solve(), libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve(), and libMesh::ImplicitSystem::weighted_sensitivity_solve().

 {
   // Note: we always start "from scratch" to mimic the original
   // behavior of this function. The goal is not to reuse the
   // LinearSolver object, but to manage its lifetime in a more
   // consistent manner.
   linear_solver.reset();
 
   linear_solver = LinearSolver<Number>::build(this->comm());
 
   if (this->prefix_with_name())
     linear_solver->init(this->prefix().c_str());
   else
     linear_solver->init();
 
   linear_solver->init_names(*this);
 
   return linear_solver.get();
 }

◆ 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 1109 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 1116 of file system.C.

References libMesh::System::_matrices.

 {
   return *libmesh_map_find(_matrices, mat_name);
 }

◆ get_mesh() [1/2]

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

inlineinherited

Returns: A constant reference to this systems's _mesh.

Definition at line 2359 of file system.h.

References libMesh::System::_mesh.

 {
   return _mesh;
 }

◆ get_mesh() [2/2]

MeshBase & libMesh::System::get_mesh ( )

inlineinherited

Returns: A reference to this systems's _mesh.

Definition at line 2367 of file system.h.

References libMesh::System::_mesh.

 {
   return _mesh;
 }

◆ get_project_with_constraints()

bool libMesh::System::get_project_with_constraints ( )

inlineinherited

Setter and getter functions for project_with_constraints boolean.

Definition at line 1818 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 2191 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 2164 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 2171 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_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 1322 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 1332 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 1177 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 1187 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_static_condensation()

StaticCondensation & libMesh::ImplicitSystem::get_static_condensation ( )

inlineinherited

Returns: The static condensation system matrix

Definition at line 373 of file implicit_system.h.

References libMesh::ImplicitSystem::_sc_system_matrix, and libMesh::libmesh_assert().

Referenced by assemble_poisson().

 {
   libmesh_assert(_sc_system_matrix);
   return *_sc_system_matrix;
 }

◆ get_system_matrix() [1/2]

const SparseMatrix< Number > & libMesh::ImplicitSystem::get_system_matrix ( ) const

inherited

Returns: A const reference to the system's primary matrix.

Definition at line 1261 of file implicit_system.C.

References libMesh::System::get_matrix(), libMesh::libmesh_assert(), and libMesh::ImplicitSystem::matrix.

Referenced by libMesh::HDGProblem::add_matrix(), assemble(), LinearElasticity::assemble(), assemble_1D(), assemble_biharmonic(), assemble_divgrad(), assemble_elasticity(), assemble_ellipticdg(), assemble_graddiv(), assemble_helmholtz(), assemble_laplace(), assemble_matrix_and_rhs(), assemble_poisson(), assemble_shell(), assemble_stokes(), assemble_wave(), assembly_with_dg_fem_context(), libMesh::HDGProblem::jacobian(), libMesh::libmesh_petsc_snes_residual(), main(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), and libMesh::EigenTimeSolver::solve().

 {
   libmesh_assert(matrix);
   libmesh_assert_equal_to(&get_matrix("System Matrix"), matrix);
   return *matrix;
 }

◆ get_system_matrix() [2/2]

SparseMatrix< Number > & libMesh::ImplicitSystem::get_system_matrix ( )

inherited

Returns: A reference to the system's primary matrix.

Definition at line 1270 of file implicit_system.C.

References libMesh::System::get_matrix(), libMesh::libmesh_assert(), and libMesh::ImplicitSystem::matrix.

 {
   libmesh_assert(matrix);
   libmesh_assert_equal_to(&get_matrix("System Matrix"), matrix);
   return *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 928 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 935 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 942 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 955 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 1262 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 1272 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 1204 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 1211 of file system.C.

References libMesh::System::get_vector().

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

◆ 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 1999 of file system.C.

References libMesh::System::_constrain_system_object.

 {
   return _constrain_system_object != nullptr;
 }

◆ has_static_condensation()

bool libMesh::System::has_static_condensation ( ) const

inherited

Returns: Whether this system will be statically condensed

Definition at line 2649 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 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 1389 of file system.C.

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

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

 {
   return this->get_dof_map().has_variable(var);
 }

◆ 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 1914 of file system.h.

References libMesh::System::_matrices.

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

1914 { return _matrices.count(mat_name); }

libMesh::System::_matrices

std::map< std::string, std::unique_ptr< SparseMatrix< Number > >, std::less<> > _matrices

Some systems need an arbitrary number of matrices.

Definition: system.h:2254

◆ 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 2449 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 1833 of file system.h.

References libMesh::System::_hide_output.

1833 { return _hide_output; }

libMesh::System::_hide_output

bool _hide_output

Are we allowed to write this system to file? If _hide_output is true, then EquationSystems::write wil...

Definition: system.h:2315

◆ identify_variable_groups() [1/2]

bool libMesh::System::identify_variable_groups ( ) const

inherited

Returns: true when VariableGroup structures should be automatically identified, false otherwise.

Definition at line 2664 of file system.C.

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

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

◆ identify_variable_groups() [2/2]

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

inherited

Toggle automatic VariableGroup identification.

Definition at line 2669 of file system.C.

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

 {
   this->get_dof_map().identify_variable_groups(ivg);
 }

◆ increment_constructor_count()

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()

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 193 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::System::init_data ( )

protectedvirtualinherited

Initializes the data for the system.

Note: This is called before any user-supplied initialization function so that all required storage will be available.

Reimplemented in libMesh::DifferentiableSystem, libMesh::ContinuationSystem, libMesh::FEMSystem, libMesh::OptimizationSystem, libMesh::RBConstructionBase< LinearImplicitSystem >, libMesh::RBConstructionBase< System >, libMesh::RBConstructionBase< CondensedEigenSystem >, libMesh::FrequencySystem, SecondOrderScalarSystemSecondOrderTimeSolverBase, libMesh::ClawSystem, libMesh::VariationalSmootherSystem, SimpleRBConstruction, FirstOrderScalarSystemBase, SimpleRBConstruction, SimpleRBConstruction, SimpleRBConstruction, SimpleRBConstruction, libMesh::LinearImplicitSystem, HeatSystem, SimpleRBConstruction, libMesh::AdvectionSystem, HilbertSystem, ElasticityRBConstruction, CoupledSystem, SimpleEIMConstruction, SimpleEIMConstruction, ElasticitySystem, ElasticitySystem, HeatSystem, LaplaceSystem, CurlCurlSystem, LaplaceSystem, PoissonSystem, LaplaceSystem, LaplaceSystem, CurlCurlSystem, SolidSystem, NavierSystem, and HeatSystem.

Definition at line 204 of file system.C.

References libMesh::System::_basic_system_only, libMesh::System::_dof_map, libMesh::System::_is_initialized, libMesh::System::_matrices, libMesh::System::_vectors, libMesh::System::add_matrices(), libMesh::System::current_local_solution, libMesh::System::get_mesh(), libMesh::GHOSTED, libMesh::System::init_matrices(), libMesh::libmesh_ignore(), mesh, libMesh::System::n_dofs(), libMesh::System::n_local_dofs(), libMesh::PARALLEL, libMesh::System::reinit_constraints(), libMesh::SERIAL, and libMesh::System::solution.

Referenced by libMesh::LinearImplicitSystem::init_data(), libMesh::OptimizationSystem::init_data(), libMesh::DifferentiableSystem::init_data(), and libMesh::System::reinit_mesh().

 {
   parallel_object_only();
 
   MeshBase & mesh = this->get_mesh();
 
   // Distribute the degrees of freedom on the mesh
   auto total_dofs = _dof_map->distribute_dofs (mesh);
 
   // Throw an error if the total number of DOFs is not capable of
   // being indexed by our solution vector.
   auto max_allowed_id = solution->max_allowed_id();
   libmesh_error_msg_if(total_dofs > max_allowed_id,
                        "Cannot allocate a NumericVector with " << total_dofs << " degrees of freedom. "
                        "The vector can only index up to " << max_allowed_id << " entries.");
 
   // Recreate any user or internal constraints
   this->reinit_constraints();
 
   // Even if there weren't any constraint changes,
   // reinit_constraints() did prepare_send_list() for us.
 
   // Now finally after dof distribution and construction of any
   // possible constraints, we may init any static condensation
   // data
   _dof_map->reinit_static_condensation();
 
   // Resize the solution conformal to the current mesh
   solution->init (this->n_dofs(), this->n_local_dofs(), false, PARALLEL);
 
   // Resize the current_local_solution for the current mesh
 #ifdef LIBMESH_ENABLE_GHOSTED
   current_local_solution->init (this->n_dofs(), this->n_local_dofs(),
                                 _dof_map->get_send_list(), /*fast=*/false,
                                 GHOSTED);
 #else
   current_local_solution->init (this->n_dofs(), false, SERIAL);
 #endif
 
   // from now on, adding additional vectors or variables can't be done
   // without immediately initializing them
   _is_initialized = true;
 
   // initialize & zero other vectors, if necessary
   for (auto & [vec_name, vec] : _vectors)
     {
       libmesh_ignore(vec_name); // spurious warning from old gcc
       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 if (type == SERIAL)
         {
           vec->init (this->n_dofs(), false, type);
         }
       else
         {
           libmesh_assert_equal_to(type, PARALLEL);
           vec->init (this->n_dofs(), this->n_local_dofs(), false, type);
         }
     }
 
   // Add matrices
   this->add_matrices();
 
   // Clear any existing matrices
   for (auto & pr : _matrices)
     pr.second->clear();
 
   // Initialize the matrices for the system
   if (!_basic_system_only)
    this->init_matrices();
 }

◆ init_matrices()

void libMesh::System::init_matrices ( )

protectedvirtualinherited

Initializes the matrices associated with this system.

Reimplemented in libMesh::EigenSystem.

Definition at line 308 of file system.C.

References libMesh::System::_matrices, libMesh::System::_matrices_initialized, libMesh::System::_matrix_types, libMesh::System::_prefer_hash_table_matrix_assembly, libMesh::System::_require_sparsity_pattern, libMesh::DofMap::attach_matrix(), libMesh::DofMap::compute_sparsity(), libMesh::System::get_dof_map(), libMesh::System::get_mesh(), libMesh::SparseMatrix< T >::initialized(), libMesh::DofMap::is_attached(), libMesh::libmesh_assert(), and libMesh::System::name().

Referenced by libMesh::System::init_data(), and libMesh::EigenSystem::init_matrices().

 {
   parallel_object_only();
 
   // No matrices to init
   if (_matrices.empty())
     {
       // any future matrices to be added will need their own
       // initialization
       _matrices_initialized = true;
 
       return;
     }
 
   // Check for quick return in case the first matrix
   // (and by extension all the matrices) has already
   // been initialized
   if (_matrices.begin()->second->initialized())
     {
       libmesh_assert(_matrices_initialized);
       return;
     }
 
   _matrices_initialized = true;
 
   // Tell the matrices about the dof map, and vice versa
   for (auto & pr : _matrices)
     {
       SparseMatrix<Number> & m = *(pr.second);
       libmesh_assert (!m.initialized());
 
       // We want to allow repeated init() on systems, but we don't
       // want to attach the same matrix to the DofMap twice
       if (!this->get_dof_map().is_attached(m))
         this->get_dof_map().attach_matrix(m);
 
       // If the user has already explicitly requested that this matrix use a hash table, then we
       // always honor that
       const bool use_hash =
           pr.second->use_hash_table() ||
           (this->_prefer_hash_table_matrix_assembly && pr.second->supports_hash_table());
       pr.second->use_hash_table(use_hash);
       // Make this call after we've determined whether the matrix is using a hash table
       if (pr.second->require_sparsity_pattern())
         this->_require_sparsity_pattern = true;
     }
 
   // Compute the sparsity pattern for the current
   // mesh and DOF distribution.  This also updates
   // additional matrices, \p DofMap now knows them
   if (this->_require_sparsity_pattern)
     this->get_dof_map().compute_sparsity(this->get_mesh());
 
   // Initialize matrices and set to zero
   for (auto & [name, mat] : _matrices)
     {
       mat->init(_matrix_types[name]);
       mat->zero();
     }
 }

◆ init_qois()

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

inherited

Accessors for qoi and qoi_error_estimates vectors.

Definition at line 2149 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);
 }

◆ is_adjoint_already_solved()

bool libMesh::System::is_adjoint_already_solved ( ) const

inlineinherited

Accessor for the adjoint_already_solved boolean.

Definition at line 410 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().

411 { return adjoint_already_solved;}

libMesh::System::adjoint_already_solved

bool adjoint_already_solved

Has the adjoint problem already been solved? If the user sets adjoint_already_solved to true...

Definition: system.h:2309

◆ is_initialized()

bool libMesh::System::is_initialized ( ) const

inlineinherited

Returns: true iff this system has been initialized.

Definition at line 2415 of file system.h.

References libMesh::System::_is_initialized.

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

 {
   return _is_initialized;
 }

◆ 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 1405 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 2487 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 2493 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 2499 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 2505 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 2441 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

inherited

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 2674 of file system.C.

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

 {
   return this->get_dof_map().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 126 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 119 of file system.C.

References libMesh::System::_dof_map.

 {
   return _dof_map->n_dofs();
 }

◆ n_local_constrained_dofs()

dof_id_type libMesh::System::n_local_constrained_dofs ( ) const

inherited

Returns: The number of constrained degrees of freedom on this processor.

Definition at line 141 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 156 of file system.C.

References libMesh::System::_dof_map.

 {
   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 2598 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_nonlinear_iterations()

unsigned int libMesh::NonlinearImplicitSystem::n_nonlinear_iterations ( ) const

inline

Returns: The number of iterations taken for the most recent nonlinear solve.

Definition at line 305 of file nonlinear_implicit_system.h.

References _n_nonlinear_iterations.

Referenced by main().

305 { return _n_nonlinear_iterations; }

libMesh::NonlinearImplicitSystem::_n_nonlinear_iterations

unsigned int _n_nonlinear_iterations

The number of nonlinear iterations required to solve the nonlinear system R(x)=0. ...

Definition: nonlinear_implicit_system.h:332

◆ n_objects()

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().

86 { return _n_objects; }

libMesh::ReferenceCounter::_n_objects

static Threads::atomic< unsigned int > _n_objects

The number of objects.

Definition: reference_counter.h:132

◆ 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().

   {
     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 2520 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

inherited

Returns: The number of VariableGroup variable groups in the system

Definition at line 2679 of file system.C.

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

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

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

◆ n_vars()

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

inherited

Returns: The number of variables in the system

Definition at line 2654 of file system.C.

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

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::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::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::SmoothnessEstimator::EstimateSmoothness::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 this->get_dof_map().n_vars();
 }

◆ 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 2457 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 2343 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(), libMesh::RBSCMConstruction::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::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 2351 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::VariationalSmootherConstraint::constrain_node_to_line(), libMesh::VariationalSmootherConstraint::constrain_node_to_plane(), 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]

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

delete

◆ operator=() [2/2]

NonlinearImplicitSystem& libMesh::NonlinearImplicitSystem::operator= ( NonlinearImplicitSystem && )

delete

◆ 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 2328 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 2390 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 2455 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 2463 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 2472 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 2533 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 2593 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 2601 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 2199 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 2260 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 2312 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 2320 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 2627 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 1961 of file system.h.

References libMesh::System::name().

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

1961 { return this->name() + "_"; }

libMesh::System::name

const std::string & name() const

Definition: system.h:2343

◆ 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 1950 of file system.h.

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

1950 { _prefix_with_name = value; }

value

static const bool value

Definition: xdr_io.C:55

libMesh::System::_prefix_with_name

bool _prefix_with_name

Whether we are name prefixing solver options.

Definition: system.h:2335

◆ prefix_with_name() [2/2]

bool libMesh::System::prefix_with_name ( ) const

inlineinherited

Returns: Whether we are name prefixing

Definition at line 1955 of file system.h.

References libMesh::System::_prefix_with_name.

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

1955 { return _prefix_with_name; }

libMesh::System::_prefix_with_name

bool _prefix_with_name

Whether we are name prefixing solver options.

Definition: system.h:2335

◆ print_info()

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();
 }

◆ 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().

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

TIMPI::Communicator::rank

processor_id_type rank() const

libMesh::ParallelObject::_communicator

const Parallel::Communicator & _communicator

Definition: parallel_object.h:120

◆ 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 839 of file system.h.

References libMesh::System::_solution_projection.

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), and libMesh::MemoryHistoryData::store_vectors().

840 { return _solution_projection; }

libMesh::System::_solution_projection

bool _solution_projection

Holds true if the solution vector should be projected onto a changed grid, false if it should be zero...

Definition: system.h:2271

◆ 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.

 {
   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 429 of file system.C.

References libMesh::System::restrict_vectors().

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

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

◆ qoi_parameter_hessian()

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

overridevirtualinherited

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

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

Reimplemented from libMesh::System.

Definition at line 918 of file implicit_system.C.

References libMesh::ImplicitSystem::adjoint_solve(), libMesh::SensitivityData::allocate_hessian_data(), libMesh::ExplicitSystem::assemble_qoi(), libMesh::ExplicitSystem::assemble_qoi_derivative(), libMesh::ImplicitSystem::assembly(), libMesh::NumericVector< T >::close(), libMesh::SparseMatrix< T >::close(), libMesh::NumericVector< T >::dot(), libMesh::System::get_adjoint_rhs(), libMesh::System::get_adjoint_solution(), libMesh::System::get_qoi_value(), libMesh::System::get_qoi_values(), libMesh::System::get_sensitivity_solution(), libMesh::QoISet::has_index(), libMesh::System::is_adjoint_already_solved(), libMesh::ImplicitSystem::matrix, libMesh::System::n_qois(), libMesh::Real, libMesh::ExplicitSystem::rhs, libMesh::SensitivityData::second_derivative(), libMesh::ImplicitSystem::sensitivity_solve(), libMesh::ParameterVector::size(), libMesh::System::solution, libMesh::TOLERANCE, libMesh::System::update(), and libMesh::SparseMatrix< T >::vector_mult().

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

◆ qoi_parameter_hessian_vector_product()

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

overridevirtualinherited

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

Reimplemented from libMesh::System.

Definition at line 713 of file implicit_system.C.

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

◆ qoi_parameter_sensitivity()

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

virtualinherited

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

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

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

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

Definition at line 587 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 518 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::Utility::contains(), 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 =
     Utility::contains(version, " with infinite elements") ||
     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 1373 of file system.h.

1375 { read_parallel_data<Number>(io, read_additional_data); }

◆ read_serialized_data() [1/2]

template<typename InValType >

void libMesh::System::read_serialized_data	(	Xdr &	io,
		const bool	read_additional_data = `true`
	)

inherited

Reads additional data, namely vectors, for this System.

This method may safely be called on a distributed-memory mesh.

Definition at line 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 1331 of file system.h.

1333 { 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 1351 of file system.h.

1353 { return read_serialized_vectors<Number>(io, vectors); }

◆ reinit()

void libMesh::NonlinearImplicitSystem::reinit ( )

overridevirtual

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

Reimplemented from libMesh::System.

Definition at line 93 of file nonlinear_implicit_system.C.

References diff_solver, nonlinear_solver, and libMesh::System::reinit().

 {
   // re-initialize the nonlinear solver interface
   nonlinear_solver->clear();
 
   // force the solver to get a new preconditioner, in
   // case reuse was set
   nonlinear_solver->force_new_preconditioner();
 
   // FIXME - this is necessary for petsc_auto_fieldsplit
   // nonlinear_solver->init_names(*this);
 
   if (diff_solver.get())
     diff_solver->reinit();
 
   // initialize parent data
   Parent::reinit();
 }

◆ 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 480 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 286 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();
 
 }

◆ release_linear_solver()

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

virtualinherited

Currently a no-op.

Deprecated:: This function no longer needs to be called, since get_linear_solver() no longer returns a heap-allocated dumb pointer.

Definition at line 1248 of file implicit_system.C.

 {
   // This function was originally paired with get_linear_solver()
   // calls when that returned a dumb pointer which needed to be
   // cleaned up. Since get_linear_solver() now just returns a pointer
   // to a LinearSolver object managed by this class, this function no
   // longer needs to do any cleanup.
   libmesh_deprecated();
 }

◆ 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 1074 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 858 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 1085 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 1097 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 876 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 888 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 900 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 914 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();
 }

◆ 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 542 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 371 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
 }

◆ sensitivity_solve()

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

overridevirtualinherited

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

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

Reimplemented from libMesh::System.

Definition at line 136 of file implicit_system.C.

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

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

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

◆ set_adjoint_already_solved()

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

inlineinherited

Setter for the adjoint_already_solved boolean.

Definition at line 416 of file system.h.

References libMesh::System::adjoint_already_solved.

Referenced by main().

417 { adjoint_already_solved = setting;}

libMesh::System::adjoint_already_solved

bool adjoint_already_solved

Has the adjoint problem already been solved? If the user sets adjoint_already_solved to true...

Definition: system.h:2309

◆ 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 2423 of file system.h.

References libMesh::System::_basic_system_only.

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

 {
   _basic_system_only = true;
 }

◆ set_project_with_constraints()

void libMesh::System::set_project_with_constraints ( bool _project_with_constraints )

inlineinherited

Definition at line 1823 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 2156 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 2177 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 2184 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_solver_parameters()

void libMesh::NonlinearImplicitSystem::set_solver_parameters ( )

protected

Copies system parameters into nonlinear solver parameters.

Definition at line 114 of file nonlinear_implicit_system.C.

References diff_solver, libMesh::Parameters::get(), libMesh::System::get_equation_systems(), libMesh::ImplicitSystem::get_linear_solve_parameters(), libMesh::Parameters::have_parameter(), nonlinear_solver, libMesh::EquationSystems::parameters, libMesh::System::parameters, and libMesh::Real.

Referenced by solve().

 {
   // Get a reference to the EquationSystems
   const EquationSystems & es =
     this->get_equation_systems();
 
   // Get the user-specified nonlinear solver tolerances
   const unsigned int maxits = parameters.have_parameter<unsigned int>("nonlinear solver maximum iterations") ?
     parameters.get<unsigned int>("nonlinear solver maximum iterations") :
     es.parameters.get<unsigned int>("nonlinear solver maximum iterations");
 
   const unsigned int maxfuncs = parameters.have_parameter<unsigned int>("nonlinear solver maximum function evaluations") ?
     parameters.get<unsigned int>("nonlinear solver maximum function evaluations") :
     es.parameters.get<unsigned int>("nonlinear solver maximum function evaluations");
 
   const double abs_resid_tol = parameters.have_parameter<Real>("nonlinear solver absolute residual tolerance") ?
     double(parameters.get<Real>("nonlinear solver absolute residual tolerance")) :
     double(es.parameters.get<Real>("nonlinear solver absolute residual tolerance"));
 
   const double rel_resid_tol = parameters.have_parameter<Real>("nonlinear solver relative residual tolerance") ?
     double(parameters.get<Real>("nonlinear solver relative residual tolerance")) :
     double(es.parameters.get<Real>("nonlinear solver relative residual tolerance"));
 
   const double div_tol = parameters.have_parameter<Real>("nonlinear solver divergence tolerance") ?
     double(parameters.get<Real>("nonlinear solver divergence tolerance")) :
     double(es.parameters.get<Real>("nonlinear solver divergence tolerance"));
 
   const double abs_step_tol = parameters.have_parameter<Real>("nonlinear solver absolute step tolerance") ?
     double(parameters.get<Real>("nonlinear solver absolute step tolerance")) :
     double(es.parameters.get<Real>("nonlinear solver absolute step tolerance"));
 
   const double rel_step_tol = parameters.have_parameter<Real>("nonlinear solver relative step tolerance")?
     double(parameters.get<Real>("nonlinear solver relative step tolerance")) :
     double(es.parameters.get<Real>("nonlinear solver relative step tolerance"));
 
   // Get the user-specified linear solver tolerances
   const auto [maxlinearits, linear_tol] = this->Parent::get_linear_solve_parameters();
 
   const double linear_min_tol = parameters.have_parameter<Real>("linear solver minimum tolerance") ?
     double(parameters.get<Real>("linear solver minimum tolerance")) :
     double(es.parameters.get<Real>("linear solver minimum tolerance"));
 
   const bool reuse_preconditioner = parameters.have_parameter<unsigned int>("reuse preconditioner") ?
     parameters.get<unsigned int>("reuse preconditioner") :
       es.parameters.get<bool>("reuse preconditioner");
   const unsigned int reuse_preconditioner_max_linear_its =
     parameters.have_parameter<unsigned int>("reuse preconditioner maximum linear iterations") ?
     parameters.get<unsigned int>("reuse preconditioner maximum linear iterations") :
       es.parameters.get<unsigned int>("reuse preconditioner maximum linear iterations");
 
   // Set all the parameters on the NonlinearSolver
   nonlinear_solver->max_nonlinear_iterations = maxits;
   nonlinear_solver->max_function_evaluations = maxfuncs;
   nonlinear_solver->absolute_residual_tolerance = abs_resid_tol;
   nonlinear_solver->relative_residual_tolerance = rel_resid_tol;
   nonlinear_solver->divergence_tolerance = div_tol;
   nonlinear_solver->absolute_step_tolerance = abs_step_tol;
   nonlinear_solver->relative_step_tolerance = rel_step_tol;
   nonlinear_solver->max_linear_iterations = maxlinearits;
   nonlinear_solver->initial_linear_tolerance = linear_tol;
   nonlinear_solver->minimum_linear_tolerance = linear_min_tol;
   nonlinear_solver->set_reuse_preconditioner(reuse_preconditioner);
   nonlinear_solver->set_reuse_preconditioner_max_linear_its(reuse_preconditioner_max_linear_its);
 
   if (diff_solver.get())
     {
       diff_solver->max_nonlinear_iterations = maxits;
       diff_solver->absolute_residual_tolerance = abs_resid_tol;
       diff_solver->relative_residual_tolerance = rel_resid_tol;
       diff_solver->absolute_step_tolerance = abs_step_tol;
       diff_solver->relative_step_tolerance = rel_step_tol;
       diff_solver->max_linear_iterations = maxlinearits;
       diff_solver->initial_linear_tolerance = linear_tol;
       diff_solver->minimum_linear_tolerance = linear_min_tol;
     }
 }

◆ 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 1145 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 1123 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;
 }

◆ setup_static_condensation_preconditioner()

template<typename T >

template void libMesh::ImplicitSystem::setup_static_condensation_preconditioner ( T & solver )

protectedinherited

Sets up the static condensation preconditioner for the supplied solver.

Definition at line 71 of file implicit_system.C.

References libMesh::ImplicitSystem::_sc_system_matrix, libMesh::StaticCondensation::get_preconditioner(), and libMesh::libmesh_assert().

Referenced by libMesh::LinearImplicitSystem::create_static_condensation(), create_static_condensation(), libMesh::LinearImplicitSystem::LinearImplicitSystem(), and NonlinearImplicitSystem().

 {
   libmesh_assert(_sc_system_matrix);
   solver.attach_preconditioner(&_sc_system_matrix->get_preconditioner());
 }

◆ solve()

void libMesh::NonlinearImplicitSystem::solve ( )

overridevirtual

Assembles & solves the nonlinear system R(x) = 0.

Reimplemented from libMesh::ImplicitSystem.

Definition at line 193 of file nonlinear_implicit_system.C.

References _final_nonlinear_residual, _n_nonlinear_iterations, diff_solver, libMesh::ImplicitSystem::matrix, nonlinear_solver, libMesh::System::prefix(), libMesh::System::prefix_with_name(), libMesh::ExplicitSystem::rhs, set_solver_parameters(), libMesh::System::solution, and libMesh::System::update().

Referenced by main().

 {
   // Log how long the nonlinear solve takes.
   LOG_SCOPE("solve()", "System");
 
   this->set_solver_parameters();
 
   if (diff_solver.get())
     {
       diff_solver->solve();
 
       // Store the number of nonlinear iterations required to
       // solve and the final residual.
       _n_nonlinear_iterations   = diff_solver->total_outer_iterations();
       _final_nonlinear_residual = 0.; // FIXME - support this!
     }
   else
     {
       if (this->prefix_with_name())
         nonlinear_solver->init(this->prefix().c_str());
       else
         nonlinear_solver->init();
 
       // FIXME - this is necessary for petsc_auto_fieldsplit
       // nonlinear_solver->init_names(*this);
 
       // Solve the nonlinear system.
       // Store the number of nonlinear iterations required to
       // solve and the final residual.
       std::tie(_n_nonlinear_iterations, _final_nonlinear_residual) =
         nonlinear_solver->solve (*matrix, *solution, *rhs,
                                  nonlinear_solver->relative_residual_tolerance,
                                  nonlinear_solver->max_linear_iterations);
     }
 
   // Update the system after the solve
   this->update();
 }

◆ 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"));
 }

◆ system()

sys_type& libMesh::NonlinearImplicitSystem::system ( )

inline

Returns: A reference to *this.

Definition at line 245 of file nonlinear_implicit_system.h.

Referenced by libMesh::NoxNonlinearSolver< Number >::solve().

245 { return *this; }

◆ system_type()

virtual std::string libMesh::NonlinearImplicitSystem::system_type ( ) const

inlineoverridevirtual

Returns: "NonlinearImplicit". Helps in identifying the system type in an equation system file.

Reimplemented from libMesh::ImplicitSystem.

Definition at line 285 of file nonlinear_implicit_system.h.

285 { return "NonlinearImplicit"; }

◆ update()

void libMesh::System::update ( )

virtualinherited

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

Reimplemented in SolidSystem.

Definition at line 495 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(), 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::ErrorVector::plot_error(), 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(), 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 730 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 741 of file system.C.

References libMesh::System::solution.

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

◆ 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 2089 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 2103 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 2075 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 2117 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 2131 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

inherited

Return a constant reference to Variable var.

Definition at line 2684 of file system.C.

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

 {
   return this->get_dof_map().variable(i);
 }

◆ variable_group()

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

inherited

Return a constant reference to VariableGroup vg.

Definition at line 2689 of file system.C.

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

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

 {
   return this->get_dof_map().variable_group(vg);
 }

◆ variable_name()

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

inherited

Returns: The name of variable i.

Definition at line 2659 of file system.C.

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

Referenced by 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().

 {
   return this->get_dof_map().variable_name(i);
 }

◆ 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 1394 of file system.C.

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

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::EnsightIO::write_scalar_ascii(), and libMesh::EnsightIO::write_vector_ascii().

 {
   return this->get_dof_map().variable_number(var);
 }

◆ 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 2432 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

inherited

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 2695 of file system.C.

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

 {
   return this->get_dof_map().variable_scalar_number(var_num, component);
 }

◆ variable_type() [1/2]

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

inherited

Returns: The finite element type variable number i.

Definition at line 2701 of file system.C.

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

Referenced by libMesh::ExactSolution::_compute_error(), 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().

 {
   return this->get_dof_map().variable_type(i);
 }

◆ variable_type() [2/2]

const FEType & libMesh::System::variable_type ( std::string_view var ) const

inherited

Returns: The finite element type for variable var.

Definition at line 2706 of file system.C.

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

 {
   return this->get_dof_map().variable_type(var);
 }

◆ 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 1158 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 968 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 979 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 1133 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 2463 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 2469 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 2475 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 2481 of file system.h.

References libMesh::System::_vectors.

 {
   return _vectors.end();
 }

◆ weighted_sensitivity_adjoint_solve()

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

overridevirtualinherited

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

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

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

Reimplemented from libMesh::System.

Definition at line 243 of file implicit_system.C.

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

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

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

◆ weighted_sensitivity_solve()

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

overridevirtualinherited

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

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

Reimplemented from libMesh::System.

Definition at line 389 of file implicit_system.C.

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

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

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

◆ write_header()

void libMesh::System::write_header	(	Xdr &	io,
		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_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 1446 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(), libMesh::StaticCondensationDofMap::reinit(), and libMesh::BoundaryInfo::synchronize_global_id_set().

◆ _counts

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

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().

◆ _final_nonlinear_residual

Real libMesh::NonlinearImplicitSystem::_final_nonlinear_residual

protected

The final residual for the nonlinear system R(x)

Definition at line 337 of file nonlinear_implicit_system.h.

Referenced by final_nonlinear_residual(), and solve().

◆ _mutex

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_nonlinear_iterations

unsigned int libMesh::NonlinearImplicitSystem::_n_nonlinear_iterations

protected

The number of nonlinear iterations required to solve the nonlinear system R(x)=0.

Definition at line 332 of file nonlinear_implicit_system.h.

Referenced by n_nonlinear_iterations(), and solve().

◆ _n_objects

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

staticprotectedinherited

The number of objects.

Print the reference count information when the number returns to 0.

Definition at line 132 of file reference_counter.h.

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

◆ 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 1570 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(), libMesh::RBSCMConstruction::RBSCMConstruction(), libMesh::ImplicitSystem::sensitivity_solve(), libMesh::EigenSystem::solve(), libMesh::CondensedEigenSystem::solve(), and libMesh::LinearImplicitSystem::solve().

◆ current_local_solution

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

inherited

All the values I need to compute my contribution to the simulation at hand.

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

Definition at line 1628 of file system.h.

◆ diff_solver

std::unique_ptr<DiffSolver> libMesh::NonlinearImplicitSystem::diff_solver

The DiffSolver defines an optional interface used to solve the nonlinear_implicit system.

Definition at line 299 of file nonlinear_implicit_system.h.

Referenced by get_linear_solve_parameters(), reinit(), set_solver_parameters(), and solve().

◆ 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 1601 of file system.h.

Referenced by CurlCurlSystem::init_data(), and set_system_parameters().

◆ linear_solver

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

mutableinherited

This class handles all the details of interfacing with various linear algebra packages like PETSc or LASPACK.

This is a public member for backwards compatibility reasons, but in general it's better to use get_linear_solver() to access this member, since that function will also handle initialization if it hasn't already been taken care of.

Definition at line 339 of file implicit_system.h.

Referenced by libMesh::LinearImplicitSystem::clear(), libMesh::RBConstruction::compute_output_dual_innerprods(), libMesh::ContinuationSystem::continuation_solve(), libMesh::ContinuationSystem::ContinuationSystem(), libMesh::LinearImplicitSystem::create_static_condensation(), libMesh::ImplicitSystem::get_linear_solver(), libMesh::LinearImplicitSystem::get_linear_solver(), libMesh::LinearImplicitSystem::init_data(), libMesh::LinearImplicitSystem::LinearImplicitSystem(), libMesh::LinearImplicitSystem::reinit(), libMesh::FrequencySystem::solve(), libMesh::LinearImplicitSystem::solve(), libMesh::ClawSystem::solve_conservation_law(), libMesh::ContinuationSystem::solve_tangent(), and libMesh::TransientRBConstruction::truth_solve().

◆ matrix

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

inherited

The system matrix.

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

Public access to this member variable will be deprecated in the future! Use get_system_matrix() instead.

Definition at line 322 of file implicit_system.h.

◆ nonlinear_solver

std::unique_ptr<NonlinearSolver<Number> > libMesh::NonlinearImplicitSystem::nonlinear_solver

The NonlinearSolver defines the default interface used to solve the nonlinear_implicit system.

This class handles all the details of interfacing with various nonlinear algebra packages like PETSc or LASPACK.

Definition at line 293 of file nonlinear_implicit_system.h.

Referenced by assembly(), clear(), create_static_condensation(), DMlibMeshFunction(), DMlibMeshJacobian(), DMSetUp_libMesh(), DMVariableBounds_libMesh(), get_current_nonlinear_iteration_number(), get_linear_solve_parameters(), main(), NonlinearImplicitSystem(), reinit(), set_solver_parameters(), and solve().

◆ 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 1549 of file system.h.

Referenced by libMesh::ImplicitSystem::get_linear_solve_parameters(), libMesh::FrequencySystem::init_data(), set_solver_parameters(), libMesh::EigenSystem::solve(), libMesh::CondensedEigenSystem::solve(), and libMesh::EigenSystem::solve_helper().

◆ rhs

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

inherited

The system matrix.

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

Definition at line 124 of file explicit_system.h.

Referenced by libMesh::__libmesh_petsc_diff_solver_residual(), add_M_C_K_helmholtz(), libMesh::ExplicitSystem::add_system_rhs(), assemble(), libMesh::ImplicitSystem::assemble(), LinearElasticity::assemble(), assemble_1D(), assemble_biharmonic(), libMesh::AdvectionSystem::assemble_claw_rhs(), assemble_divgrad(), assemble_elasticity(), assemble_ellipticdg(), assemble_func(), assemble_graddiv(), assemble_laplace(), assemble_matrix_and_rhs(), assemble_poisson(), libMesh::ImplicitSystem::assemble_residual_derivatives(), assemble_shell(), assemble_stokes(), assemble_wave(), libMesh::FEMSystem::assembly(), libMesh::VariationalSmootherSystem::assembly(), libMesh::LinearImplicitSystem::assembly(), assembly(), assembly_with_dg_fem_context(), libMesh::RBConstruction::compute_Fq_representor_innerprods(), libMesh::RBConstruction::compute_output_dual_innerprods(), libMesh::RBConstruction::compute_residual_dual_norm_slow(), libMesh::Problem_Interface::computeF(), libMesh::ContinuationSystem::continuation_solve(), DMlibMeshFunction(), libMesh::RBConstruction::enrich_basis_from_rhs_terms(), fill_dirichlet_bc(), libMesh::ImplicitSystem::forward_qoi_parameter_sensitivity(), libMesh::NewtonSolver::line_search(), periodic_bc_test_poisson(), HeatSystem::perturb_accumulate_residuals(), libMesh::ImplicitSystem::qoi_parameter_hessian(), libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product(), libMesh::NewtonSolver::solve(), libMesh::PetscDiffSolver::solve(), libMesh::FrequencySystem::solve(), libMesh::LinearImplicitSystem::solve(), solve(), libMesh::ContinuationSystem::solve_tangent(), libMesh::TransientRBConstruction::truth_assembly(), libMesh::RBConstruction::truth_assembly(), libMesh::TransientRBConstruction::truth_solve(), libMesh::RBConstruction::truth_solve(), libMesh::TransientRBConstruction::update_residual_terms(), libMesh::RBConstruction::update_residual_terms(), libMesh::NewmarkSystem::update_rhs(), libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve(), and libMesh::ImplicitSystem::weighted_sensitivity_solve().

◆ solution

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

inherited

Data structure to hold solution values.

Definition at line 1616 of file system.h.

◆ 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 1638 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 1586 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().

◆ zero_out_matrix_and_rhs

bool libMesh::ImplicitSystem::zero_out_matrix_and_rhs

inherited

By default, the system will zero out the matrix and the right hand side.

If this flag is false, it is the responsibility of the client code to take care of setting these to zero before assembly begins

Definition at line 329 of file implicit_system.h.

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

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

include/systems/nonlinear_implicit_system.h
src/systems/nonlinear_implicit_system.C

Classes

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Types

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Member Typedef Documentation

◆ const_matrices_iterator

◆ const_vectors_iterator

◆ Counts

◆ GradientFunctionPointer

◆ matrices_iterator

◆ Parent

◆ sys_type

◆ ValueFunctionPointer

◆ vectors_iterator

Constructor & Destructor Documentation

◆ NonlinearImplicitSystem() [1/3]

◆ NonlinearImplicitSystem() [2/3]

◆ NonlinearImplicitSystem() [3/3]

◆ ~NonlinearImplicitSystem()

Member Function Documentation

◆ activate()

◆ active()

◆ add_adjoint_rhs()

◆ add_adjoint_solution()

◆ add_matrices()

◆ add_matrix() [1/3]

◆ add_matrix() [2/3]

◆ add_matrix() [3/3]

◆ add_sensitivity_rhs()

◆ add_sensitivity_solution()

◆ add_variable() [1/2]

◆ add_variable() [2/2]

◆ add_variable_array()

◆ add_variables() [1/2]

◆ add_variables() [2/2]

◆ add_vector()

◆ add_weighted_sensitivity_adjoint_solution()

◆ add_weighted_sensitivity_solution()

◆ adjoint_qoi_parameter_sensitivity()

◆ adjoint_solve()

◆ assemble()

◆ assemble_qoi()

◆ assemble_qoi_derivative()

◆ assemble_residual_derivatives()

◆ assembly()

◆ attach_assemble_function()

◆ attach_assemble_object()

◆ attach_constraint_function()

◆ attach_constraint_object()

◆ attach_init_function()

◆ attach_init_object()

◆ attach_QOI_derivative()

◆ attach_QOI_derivative_object()

◆ attach_QOI_function()

◆ attach_QOI_object()

◆ boundary_project_solution() [1/2]

◆ boundary_project_solution() [2/2]

◆ boundary_project_vector() [1/2]

◆ boundary_project_vector() [2/2]

◆ calculate_norm() [1/2]

◆ calculate_norm() [2/2]

◆ can_add_matrices()

◆ clear()

◆ comm()

◆ compare()

◆ condense_constrained_dofs()

◆ create_static_condensation()

◆ current_solution()

◆ deactivate()

◆ disable_cache()

◆ disable_print_counter_info()

◆ enable_print_counter_info()

◆ final_nonlinear_residual()

◆ forward_qoi_parameter_sensitivity()