ElasticitySystem Class Reference

#include <elasticity_system.h>

Inheritance diagram for ElasticitySystem:

Public Types
typedef FEMSystem	sys_type
	The type of system. More...
typedef DifferentiableSystem	Parent
	The type of the parent. More...
typedef bool(TimeSolver::*	TimeSolverResPtr) (bool, DiffContext &)
	Syntax sugar to make numerical_jacobian() declaration easier. More...
typedef std::map< std::string, SparseMatrix< Number > * >::iterator	matrices_iterator
	Matrix iterator typedefs. More...
typedef std::map< std::string, SparseMatrix< Number > * >::const_iterator	const_matrices_iterator
typedef Number(*	ValueFunctionPointer) (const Point &p, const Parameters &Parameters, const std::string &sys_name, const std::string &unknown_name)
	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, NumericVector< Number > * >::iterator	vectors_iterator
	Vector iterator typedefs. More...
typedef std::map< std::string, NumericVector< Number > * >::const_iterator	const_vectors_iterator

Public Member Functions
	ElasticitySystem (EquationSystems &es, const std::string &name_in, const unsigned int number_in)
virtual void	init_data ()
	Initializes the member data fields associated with the system, so that, e.g., assemble() may be used. More...
virtual void	init_context (DiffContext &context)
virtual bool	element_time_derivative (bool request_jacobian, DiffContext &context)
	Adds the time derivative contribution on elem to elem_residual. More...
virtual bool	side_time_derivative (bool request_jacobian, DiffContext &context)
	Adds the time derivative contribution on side of elem to elem_residual. More...
virtual bool	mass_residual (bool request_jacobian, DiffContext &context)
	Subtracts a mass vector contribution on elem from elem_residual. More...
virtual void	assembly (bool get_residual, bool get_jacobian, bool apply_heterogeneous_constraints=false, bool apply_no_constraints=false) override
	Prepares matrix or rhs for matrix assembly. More...
virtual void	solve () override
	Invokes the solver associated with the system. More...
void	mesh_position_get ()
	Tells the FEMSystem to set the degree of freedom coefficients which should correspond to mesh nodal coordinates. More...
void	mesh_position_set ()
	Tells the FEMSystem to set the mesh nodal coordinates which should correspond to degree of freedom coefficients. More...
virtual std::unique_ptr< DiffContext >	build_context () override
	Builds a FEMContext object with enough information to do evaluations on each element. More...
virtual void	postprocess () override
	Runs a postprocessing loop over all elements, and if postprocess_sides is true over all sides. More...
virtual void	assemble_qoi (const QoISet &indices=QoISet()) override
	Runs a qoi assembly loop over all elements, and if assemble_qoi_sides is true over all sides. More...
virtual void	assemble_qoi_derivative (const QoISet &qoi_indices=QoISet(), bool include_liftfunc=true, bool apply_constraints=true) override
	Runs a qoi derivative assembly loop over all elements, and if assemble_qoi_sides is true over all sides. More...
Real	numerical_jacobian_h_for_var (unsigned int var_num) const
	If numerical_jacobian_h_for_var(var_num) is changed from its default value (numerical_jacobian_h), the FEMSystem will perturb solution vector entries for variable var_num by that amount when calculating finite differences with respect to that variable. More...
void	set_numerical_jacobian_h_for_var (unsigned int var_num, Real new_h)
void	numerical_jacobian (TimeSolverResPtr res, FEMContext &context) const
	Uses the results of multiple res calls to numerically differentiate the corresponding jacobian. More...
void	numerical_elem_jacobian (FEMContext &context) const
	Uses the results of multiple element_residual() calls to numerically differentiate the corresponding jacobian on an element. More...
void	numerical_side_jacobian (FEMContext &context) const
	Uses the results of multiple side_residual() calls to numerically differentiate the corresponding jacobian on an element's side. More...
void	numerical_nonlocal_jacobian (FEMContext &context) const
	Uses the results of multiple side_residual() calls to numerically differentiate the corresponding jacobian on nonlocal DoFs. More...
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	assemble () override
	Prepares matrix and rhs for matrix assembly. More...
virtual LinearSolver< Number > *	get_linear_solver () const override
virtual std::pair< unsigned int, Real >	get_linear_solve_parameters () const override
virtual void	release_linear_solver (LinearSolver< Number > *) const override
	Releases a pointer to a linear solver acquired by this->get_linear_solver() More...
virtual std::pair< unsigned int, Real >	adjoint_solve (const QoISet &qoi_indices=QoISet()) override
	This function sets the _is_adjoint boolean member of TimeSolver to true and then calls the adjoint_solve in implicit system. More...
virtual std::unique_ptr< DifferentiablePhysics >	clone_physics () override
	We don't allow systems to be attached to each other. More...
virtual std::unique_ptr< DifferentiableQoI >	clone () override
	We don't allow systems to be attached to each other. More...
const DifferentiablePhysics *	get_physics () const
DifferentiablePhysics *	get_physics ()
void	attach_physics (DifferentiablePhysics *physics_in)
	Attach external Physics object. More...
void	swap_physics (DifferentiablePhysics *&swap_physics)
	Swap current physics object with external object. More...
const DifferentiableQoI *	get_qoi () const
DifferentiableQoI *	get_qoi ()
void	attach_qoi (DifferentiableQoI *qoi_in)
	Attach external QoI object. More...
void	set_time_solver (std::unique_ptr< TimeSolver > _time_solver)
	Sets the time_solver FIXME: This code is a little dangerous as it transfers ownership from the TimeSolver creator to this class. More...
TimeSolver &	get_time_solver ()
const TimeSolver &	get_time_solver () const
	Non-const version of the above. More...
virtual void	element_postprocess (DiffContext &)
	Does any work that needs to be done on elem in a postprocessing loop. More...
virtual void	side_postprocess (DiffContext &)
	Does any work that needs to be done on side of elem in a postprocessing loop. More...
unsigned int	get_second_order_dot_var (unsigned int var) const
	For a given second order (in time) variable var, this method will return the index to the corresponding "dot" variable. More...
bool	have_first_order_scalar_vars () const
	Check for any first order vars that are also belong to FEFamily::SCALAR. More...
bool	have_second_order_scalar_vars () const
	Check for any second order vars that are also belong to FEFamily::SCALAR. More...
sys_type &	system ()
virtual void	disable_cache () override
	Avoids use of any cached data that might affect any solve result. More...
virtual std::string	system_type () const override
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 >	weighted_sensitivity_adjoint_solve (const ParameterVector &parameters, const ParameterVector &weights, const QoISet &qoi_indices=QoISet()) override
	Assembles & solves the linear system(s) (dR/du)^T*z_w = sum(w_p*(d^2q/dudp - d^2R/dudp*z)), for those parameters p contained within parameters, weighted by the values w_p found within weights. More...
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...
SparseMatrix< Number > &	add_matrix (const std::string &mat_name)
	Adds the additional matrix mat_name to this system. More...
void	remove_matrix (const std::string &mat_name)
	Removes the additional matrix mat_name from this system. More...
bool	have_matrix (const std::string &mat_name) const
const SparseMatrix< Number > *	request_matrix (const std::string &mat_name) const
SparseMatrix< Number > *	request_matrix (const std::string &mat_name)
const SparseMatrix< Number > &	get_matrix (const std::string &mat_name) const
SparseMatrix< Number > &	get_matrix (const std::string &mat_name)
virtual unsigned int	n_matrices () const override
void	init ()
	Initializes degrees of freedom on the current mesh. More...
virtual void	reinit_constraints ()
	Reinitializes the constraints for this system. More...
bool	is_initialized ()
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
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...
NumericVector< Number > &	add_vector (const std::string &vec_name, const bool projections=true, const ParallelType type=PARALLEL)
	Adds the additional vector vec_name to this system. More...
void	remove_vector (const std::string &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 (const std::string &vec_name) const
const NumericVector< Number > *	request_vector (const std::string &vec_name) const
NumericVector< Number > *	request_vector (const std::string &vec_name)
const NumericVector< Number > *	request_vector (const unsigned int vec_num) const
NumericVector< Number > *	request_vector (const unsigned int vec_num)
const NumericVector< Number > &	get_vector (const std::string &vec_name) const
NumericVector< Number > &	get_vector (const std::string &vec_name)
const NumericVector< Number > &	get_vector (const unsigned int vec_num) const
NumericVector< Number > &	get_vector (const unsigned int vec_num)
const std::string &	vector_name (const unsigned int vec_num) const
const std::string &	vector_name (const NumericVector< Number > &vec_reference) const
void	set_vector_as_adjoint (const std::string &vec_name, int qoi_num)
	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 (const std::string &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 (const std::string &vec_name) const
NumericVector< Number > &	add_adjoint_solution (unsigned int i=0)
NumericVector< Number > &	get_adjoint_solution (unsigned int i=0)
const NumericVector< Number > &	get_adjoint_solution (unsigned int i=0) const
NumericVector< Number > &	add_sensitivity_solution (unsigned int i=0)
NumericVector< Number > &	get_sensitivity_solution (unsigned int i=0)
const NumericVector< Number > &	get_sensitivity_solution (unsigned int i=0) const
NumericVector< Number > &	add_weighted_sensitivity_adjoint_solution (unsigned int i=0)
NumericVector< Number > &	get_weighted_sensitivity_adjoint_solution (unsigned int i=0)
const NumericVector< Number > &	get_weighted_sensitivity_adjoint_solution (unsigned int i=0) const
NumericVector< Number > &	add_weighted_sensitivity_solution ()
NumericVector< Number > &	get_weighted_sensitivity_solution ()
const NumericVector< Number > &	get_weighted_sensitivity_solution () const
NumericVector< Number > &	add_adjoint_rhs (unsigned int i=0)
NumericVector< Number > &	get_adjoint_rhs (unsigned int i=0)
const NumericVector< Number > &	get_adjoint_rhs (unsigned int i=0) const
NumericVector< Number > &	add_sensitivity_rhs (unsigned int i=0)
NumericVector< Number > &	get_sensitivity_rhs (unsigned int i=0)
const NumericVector< Number > &	get_sensitivity_rhs (unsigned int i=0) const
unsigned int	n_vectors () const
unsigned int	n_vars () const
unsigned int	n_variable_groups () const
unsigned int	n_components () const
dof_id_type	n_dofs () const
dof_id_type	n_active_dofs () const
dof_id_type	n_constrained_dofs () const
dof_id_type	n_local_constrained_dofs () const
dof_id_type	n_local_dofs () const
unsigned int	add_variable (const std::string &var, const FEType &type, const std::set< subdomain_id_type > *const active_subdomains=nullptr)
	Adds the variable var to the list of variables for this system. More...
unsigned int	add_variable (const std::string &var, const Order order=FIRST, const FEFamily=LAGRANGE, const std::set< subdomain_id_type > *const active_subdomains=nullptr)
	Adds the variable var to the list of variables for this system. More...
unsigned int	add_variables (const std::vector< std::string > &vars, const FEType &type, const std::set< subdomain_id_type > *const active_subdomains=nullptr)
	Adds the variable var to the list of variables for this system. More...
unsigned int	add_variables (const std::vector< std::string > &vars, const Order order=FIRST, const FEFamily=LAGRANGE, const std::set< subdomain_id_type > *const active_subdomains=nullptr)
	Adds the variable var to the list of variables for this system. More...
const Variable &	variable (unsigned int var) const
	Return a constant reference to Variable var. More...
const VariableGroup &	variable_group (unsigned int vg) const
	Return a constant reference to VariableGroup vg. More...
bool	has_variable (const std::string &var) const
const std::string &	variable_name (const unsigned int i) const
unsigned short int	variable_number (const std::string &var) const
void	get_all_variable_numbers (std::vector< unsigned int > &all_variable_numbers) const
	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 (const std::string &var, unsigned int component) const
unsigned int	variable_scalar_number (unsigned int var_num, unsigned int component) const
const FEType &	variable_type (const unsigned int i) const
const FEType &	variable_type (const std::string &var) const
bool	identify_variable_groups () const
void	identify_variable_groups (const bool)
	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, const std::string &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, const std::string &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...
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...
Number	point_value (unsigned int var, const Point &p, const bool insist_on_success=true) const
Number	point_value (unsigned int var, const Point &p, const Elem &e) const
Number	point_value (unsigned int var, const Point &p, const Elem *e) const
	Calls the version of point_value() which takes a reference. More...
Gradient	point_gradient (unsigned int var, const Point &p, const bool insist_on_success=true) const
Gradient	point_gradient (unsigned int var, const Point &p, const Elem &e) const
Gradient	point_gradient (unsigned int var, const Point &p, const Elem *e) const
	Calls the version of point_gradient() which takes a reference. More...
Tensor	point_hessian (unsigned int var, const Point &p, const bool insist_on_success=true) const
Tensor	point_hessian (unsigned int var, const Point &p, const Elem &e) const
Tensor	point_hessian (unsigned int var, const Point &p, const Elem *e) const
	Calls the version of point_hessian() which takes a reference. 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 &	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...
const Parallel::Communicator &	comm () const
processor_id_type	n_processors () const
processor_id_type	processor_id () const
virtual void	clear_physics ()
	Clear any data structures associated with the physics. More...
virtual void	init_physics (const System &sys)
	Initialize any data structures associated with the physics. More...
virtual bool	element_constraint (bool request_jacobian, DiffContext &)
	Adds the constraint contribution on elem to elem_residual. More...
virtual bool	side_constraint (bool request_jacobian, DiffContext &)
	Adds the constraint contribution on side of elem to elem_residual. More...
virtual bool	nonlocal_time_derivative (bool request_jacobian, DiffContext &)
	Adds any nonlocal time derivative contributions (e.g. More...
virtual bool	nonlocal_constraint (bool request_jacobian, DiffContext &)
	Adds any nonlocal constraint contributions (e.g. More...
virtual void	time_evolving (unsigned int var)
	Tells the DiffSystem that variable var is evolving with respect to time. More...
virtual void	time_evolving (unsigned int var, unsigned int order)
	Tells the DiffSystem that variable var is evolving with respect to time. More...
bool	is_time_evolving (unsigned int var) const
virtual bool	eulerian_residual (bool request_jacobian, DiffContext &)
	Adds a pseudo-convection contribution on elem to elem_residual, if the nodes of elem are being translated by a moving mesh. More...
virtual bool	eulerian_residual (bool request_jacobian, DiffContext &context) override
	Adds a pseudo-convection contribution on elem to elem_residual, if the nodes of elem are being translated by a moving mesh. More...
virtual bool	side_mass_residual (bool request_jacobian, DiffContext &)
	Subtracts a mass vector contribution on side of elem from elem_residual. More...
virtual bool	nonlocal_mass_residual (bool request_jacobian, DiffContext &c)
	Subtracts any nonlocal mass vector contributions (e.g. More...
virtual bool	damping_residual (bool request_jacobian, DiffContext &)
	Subtracts a damping vector contribution on elem from elem_residual. More...
virtual bool	side_damping_residual (bool request_jacobian, DiffContext &)
	Subtracts a damping vector contribution on side of elem from elem_residual. More...
virtual bool	nonlocal_damping_residual (bool request_jacobian, DiffContext &)
	Subtracts any nonlocal damping vector contributions (e.g. More...
virtual void	set_mesh_system (System *sys)
	Tells the DifferentiablePhysics that system sys contains the isoparametric Lagrangian variables which correspond to the coordinates of mesh nodes, in problems where the mesh itself is expected to move in time. More...
const System *	get_mesh_system () const
System *	get_mesh_system ()
virtual void	set_mesh_x_var (unsigned int var)
	Tells the DifferentiablePhysics that variable var from the mesh system should be used to update the x coordinate of mesh nodes, in problems where the mesh itself is expected to move in time. More...
unsigned int	get_mesh_x_var () const
virtual void	set_mesh_y_var (unsigned int var)
	Tells the DifferentiablePhysics that variable var from the mesh system should be used to update the y coordinate of mesh nodes. More...
unsigned int	get_mesh_y_var () const
virtual void	set_mesh_z_var (unsigned int var)
	Tells the DifferentiablePhysics that variable var from the mesh system should be used to update the z coordinate of mesh nodes. More...
unsigned int	get_mesh_z_var () const
bool	_eulerian_time_deriv (bool request_jacobian, DiffContext &)
	This method simply combines element_time_derivative() and eulerian_residual(), which makes its address useful as a pointer-to-member-function when refactoring. More...
bool	have_first_order_vars () const
const std::set< unsigned int > &	get_first_order_vars () const
bool	is_first_order_var (unsigned int var) const
bool	have_second_order_vars () const
const std::set< unsigned int > &	get_second_order_vars () const
bool	is_second_order_var (unsigned int var) const
virtual void	init_qoi (std::vector< Number > &)
	Initialize system qoi. More...
virtual void	clear_qoi ()
	Clear all the data structures associated with the QoI. More...
virtual void	element_qoi (DiffContext &, const QoISet &)
	Does any work that needs to be done on elem in a quantity of interest assembly loop, outputting to elem_qoi. More...
virtual void	element_qoi_derivative (DiffContext &, const QoISet &)
	Does any work that needs to be done on elem in a quantity of interest derivative assembly loop, outputting to elem_qoi_derivative. More...
virtual void	side_qoi (DiffContext &, const QoISet &)
	Does any work that needs to be done on side of elem in a quantity of interest assembly loop, outputting to elem_qoi. More...
virtual void	side_qoi_derivative (DiffContext &, const QoISet &)
	Does any work that needs to be done on side of elem in a quantity of interest derivative assembly loop, outputting to elem_qoi_derivative. More...
virtual void	thread_join (std::vector< Number > &qoi, const std::vector< Number > &other_qoi, const QoISet &qoi_indices)
	Method to combine thread-local qois. More...
virtual void	parallel_op (const Parallel::Communicator &communicator, std::vector< Number > &sys_qoi, std::vector< Number > &local_qoi, const QoISet &qoi_indices)
	Method to populate system qoi data structure with process-local qoi. More...
virtual void	finalize_derivative (NumericVector< Number > &derivatives, std::size_t qoi_index)
	Method to finalize qoi derivatives which require more than just a simple sum of element contributions. More...

Static Public Member Functions
static std::string	get_info ()
	Gets a string containing the reference information. More...
static void	print_info (std::ostream &out=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
bool	fe_reinit_during_postprocess
	If fe_reinit_during_postprocess is true (it is true by default), FE objects will be reinit()ed with their default quadrature rules. More...
Real	numerical_jacobian_h
	If calculating numeric jacobians is required, the FEMSystem will perturb each solution vector entry by numerical_jacobian_h when calculating finite differences. More...
Real	verify_analytic_jacobians
	If verify_analytic_jacobian is equal to zero (as it is by default), no numeric jacobians will be calculated unless an overridden element_time_derivative(), element_constraint(), side_time_derivative(), or side_constraint() function cannot provide an analytic jacobian upon request. More...
std::unique_ptr< TimeSolver >	time_solver
	A pointer to the solver object we're going to use. More...
Real	deltat
	For time-dependent problems, this is the amount delta t to advance the solution in time. More...
bool	postprocess_sides
	If postprocess_sides is true (it is false by default), the postprocessing loop will loop over all sides as well as all elements. More...
bool	print_solution_norms
	Set print_residual_norms to true to print |U| whenever it is used in an assembly() call. More...
bool	print_solutions
	Set print_solutions to true to print U whenever it is used in an assembly() call. More...
bool	print_residual_norms
	Set print_residual_norms to true to print |F| whenever it is assembled. More...
bool	print_residuals
	Set print_residuals to true to print F whenever it is assembled. More...
bool	print_jacobian_norms
	Set print_jacobian_norms to true to print |J| whenever it is assembled. More...
bool	print_jacobians
	Set print_jacobians to true to print J whenever it is assembled. More...
bool	print_element_solutions
	Set print_element_solutions to true to print each U_elem input. More...
bool	print_element_residuals
	Set print_element_residuals to true to print each R_elem contribution. More...
bool	print_element_jacobians
	Set print_element_jacobians to true to print each J_elem contribution. 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...
NumericVector< Number > *	rhs
	The system matrix. 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...
std::vector< Number >	qoi
	Values of the quantities of interest. More...
bool	compute_internal_sides
	compute_internal_sides is false by default, indicating that side_* computations will only be done on boundary sides. More...
bool	assemble_qoi_sides
	If assemble_qoi_sides is true (it is false by default), the assembly loop for a quantity of interest or its derivatives will loop over domain boundary sides. More...
bool	assemble_qoi_internal_sides
	If assemble_qoi_internal_sides is true (it is false by default), the assembly loop for a quantity of interest or its derivatives will loop over element sides which do not fall on domain boundaries. More...
bool	assemble_qoi_elements
	If assemble_qoi_elements is false (it is true by default), the assembly loop for a quantity of interest or its derivatives will skip computing on mesh elements, and will only compute on mesh sides. 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	add_second_order_dot_vars ()
	Helper function to add "velocity" variables that are cousins to second order-in-time variables in the DifferentiableSystem. More...
void	add_dot_var_dirichlet_bcs (unsigned int var_idx, unsigned int dot_var_idx)
	Helper function to and Dirichlet boundary conditions to "dot" variable cousins of second order variables in the system. More...
virtual void	init_matrices ()
	Initializes the matrices associated with this system. 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...
void	increment_constructor_count (const std::string &name)
	Increments the construction counter. More...
void	increment_destructor_count (const std::string &name)
	Increments the destruction counter. More...

Protected Attributes
DifferentiablePhysics *	_diff_physics
	Pointer to object to use for physics assembly evaluations. More...
DifferentiableQoI *	diff_qoi
	Pointer to object to use for quantity of interest assembly evaluations. More...
const Parallel::Communicator &	_communicator
System *	_mesh_sys
	System from which to acquire moving mesh information. More...
unsigned int	_mesh_x_var
	Variables from which to acquire moving mesh information. More...
unsigned int	_mesh_y_var
unsigned int	_mesh_z_var
std::vector< unsigned int >	_time_evolving
	Stores unsigned int to tell us which variables are evolving as first order in time (1), second order in time (2), or are not time evolving (0). More...
std::set< unsigned int >	_first_order_vars
	Variable indices for those variables that are first order in time. More...
std::set< unsigned int >	_second_order_vars
	Variable indices for those variables that are second order in time. More...
std::map< unsigned int, unsigned int >	_second_order_dot_vars
	If the user adds any second order variables, then we need to also cache the map to their corresponding dot variable that will be added by this TimeSolver class. More...

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

Private Member Functions
Real	kronecker_delta (unsigned int i, unsigned int j)
Real	elasticity_tensor (unsigned int i, unsigned int j, unsigned int k, unsigned int l)

Private Attributes
unsigned int	_u_var
unsigned int	_v_var
unsigned int	_w_var
Real	_rho

Detailed Description

Definition at line 36 of file elasticity_system.h.

Member Typedef Documentation

const_matrices_iterator

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

inherited

Definition at line 306 of file implicit_system.h.

const_vectors_iterator

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

inherited

Definition at line 749 of file system.h.

Counts

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

protectedinherited

Data structure to log the information.

The log is identified by the class name.

Definition at line 117 of file reference_counter.h.

GradientFunctionPointer

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

inherited

Definition at line 524 of file system.h.

matrices_iterator

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

inherited

Matrix iterator typedefs.

Definition at line 305 of file implicit_system.h.

Parent

typedef DifferentiableSystem libMesh::FEMSystem::Parent

inherited

The type of the parent.

Definition at line 79 of file fem_system.h.

sys_type

typedef FEMSystem libMesh::FEMSystem::sys_type

inherited

The type of system.

Definition at line 74 of file fem_system.h.

TimeSolverResPtr

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

inherited

Syntax sugar to make numerical_jacobian() declaration easier.

Definition at line 214 of file fem_system.h.

ValueFunctionPointer

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

inherited

Projects arbitrary functions onto the current solution.

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

Definition at line 520 of file system.h.

vectors_iterator

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

inherited

Vector iterator typedefs.

Definition at line 748 of file system.h.

Constructor & Destructor Documentation

ElasticitySystem()

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

Definition at line 40 of file elasticity_system.h.

    : FEMSystem(es, name_in, number_in),
      _rho(1.0)
  {}

Member Function Documentation

_eulerian_time_deriv()

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

inherited

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

activate()

void libMesh::System::activate ( )

inherited

Activates the system.

Only active systems are solved.

Definition at line 2073 of file system.h.

References libMesh::System::_active.

{
  _active = true;
}

active()

bool libMesh::System::active ( ) const

inherited

Returns

true if the system is active, false otherwise. An active system will be solved.

Definition at line 2065 of file system.h.

References libMesh::System::_active.

{
  return _active;
}

add_adjoint_rhs()

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

inherited

Returns

A reference to one of the system's adjoint rhs vectors, by default the one corresponding to the first qoi. Creates the vector if it doesn't already exist.

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.

add_dot_var_dirichlet_bcs()

void libMesh::DifferentiableSystem::add_dot_var_dirichlet_bcs ( unsigned int  var_idx, unsigned int  dot_var_idx  )

protectedinherited

Helper function to and Dirichlet boundary conditions to "dot" variable cousins of second order variables in the system.

The function takes the second order variable index, it's corresponding "dot" variable index and then searches for DirichletBoundary objects for var_idx and then adds a DirichletBoundary object for dot_var_idx using the same boundary ids and functors for the var_idx DirichletBoundary.

add_matrix()

SparseMatrix<Number>& libMesh::ImplicitSystem::add_matrix ( const std::string &  mat_name )

inherited

Adds the additional matrix mat_name to this system.

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

add_second_order_dot_vars()

void libMesh::DifferentiableSystem::add_second_order_dot_vars ( )

protectedinherited

Helper function to add "velocity" variables that are cousins to second order-in-time variables in the DifferentiableSystem.

This function is only called if the TimeSolver is a FirstOrderUnsteadySolver.

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.

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.

add_variable() [1/2]

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

inherited

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

Returns

The index number for the new variable.

Referenced by SimpleRBConstruction::init_data(), and FETest< order, family, elem_type >::setUp().

add_variable() [2/2]

unsigned int libMesh::System::add_variable ( const std::string &  var, const Order  order = FIRST, const FEFamily  = 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.

add_variables() [1/2]

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

inherited

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

Returns

The index number for the new variable.

add_variables() [2/2]

unsigned int libMesh::System::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  )

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.

add_vector()

NumericVector<Number>& libMesh::System::add_vector ( const std::string &  vec_name, const bool  projections = true, const ParallelType  type = PARALLEL  )

inherited

Adds the additional vector vec_name to this system.

All the additional vectors are similarly distributed, like the solution, and initialized to zero.

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

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.

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.

adjoint_qoi_parameter_sensitivity()

virtual 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.

adjoint_solve()

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

overridevirtualinherited

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

Reimplemented from libMesh::ImplicitSystem.

assemble()

virtual void libMesh::DifferentiableSystem::assemble ( )

overridevirtualinherited

Prepares matrix and rhs for matrix assembly.

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

Reimplemented from libMesh::ImplicitSystem.

assemble_qoi()

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

overridevirtualinherited

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

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

Reimplemented from libMesh::ExplicitSystem.

assemble_qoi_derivative()

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

overridevirtualinherited

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

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

Reimplemented from libMesh::ExplicitSystem.

assemble_residual_derivatives()

virtual 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.

assembly()

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

overridevirtualinherited

Prepares matrix or rhs for matrix assembly.

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

Implements libMesh::DifferentiableSystem.

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.

attach_assemble_object()

void libMesh::System::attach_assemble_object ( Assembly &  assemble )

inherited

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

attach_constraint_function()

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

inherited

Register a user function for imposing constraints.

attach_constraint_object()

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

inherited

Register a user object for imposing constraints.

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.

attach_init_object()

void libMesh::System::attach_init_object ( Initialization &  init )

inherited

Register a user class to use to initialize the system.

Note

This is exclusive with the attach_init_function.

attach_physics()

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

inherited

Attach external Physics object.

Definition at line 197 of file diff_system.h.

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

  { this->_diff_physics = (physics_in->clone_physics()).release();
    this->_diff_physics->init_physics(*this);}

attach_qoi()

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

inherited

Attach external QoI object.

Definition at line 225 of file diff_system.h.

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

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

attach_QOI_derivative()

void libMesh::System::attach_QOI_derivative ( void   fptrEquationSystems &es, const std::string &name, const QoISet &qoi_indices, bool include_liftfunc, bool apply_constraints )

inherited

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

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.

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.

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.

boundary_project_solution() [1/2]

void libMesh::System::boundary_project_solution ( const std::set< boundary_id_type > &  b, const std::vector< unsigned int > &  variables, FunctionBase< Number > *  f, FunctionBase< Gradient > *  g = nullptr  )

inherited

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

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

boundary_project_solution() [2/2]

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

inherited

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

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

boundary_project_vector() [1/2]

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

inherited

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

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

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

boundary_project_vector() [2/2]

void libMesh::System::boundary_project_vector ( const std::set< boundary_id_type > &  b, const std::vector< unsigned int > &  variables, ValueFunctionPointer  fptr, GradientFunctionPointer  gptr, const Parameters &  parameters, NumericVector< Number > &  new_vector, int  is_adjoint = -1  ) const

inherited

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

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

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

build_context()

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

overridevirtualinherited

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

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

Reimplemented from libMesh::DifferentiableSystem.

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)

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.

clear()

virtual void libMesh::DifferentiableSystem::clear ( )

overridevirtualinherited

Clear all the data structures associated with the system.

Reimplemented from libMesh::ImplicitSystem.

Reimplemented in libMesh::ContinuationSystem.

clear_physics()

virtual void libMesh::DifferentiablePhysics::clear_physics ( )

virtualinherited

Clear any data structures associated with the physics.

clear_qoi()

virtual void libMesh::DifferentiableQoI::clear_qoi ( )

virtualinherited

Clear all the data structures associated with the QoI.

Definition at line 75 of file diff_qoi.h.

{}

clone()

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

overridevirtualinherited

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

Implements libMesh::DifferentiableQoI.

Definition at line 169 of file diff_system.h.

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

clone_physics()

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

overridevirtualinherited

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

Implements libMesh::DifferentiablePhysics.

Definition at line 159 of file diff_system.h.

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

comm()

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

inherited

Returns

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

Definition at line 89 of file parallel_object.h.

References libMesh::ParallelObject::_communicator.

Referenced by libMesh::EpetraVector< T >::EpetraVector(), libMesh::Parallel::sync_element_data_by_parent_id(), libMesh::Parallel::sync_node_data_by_element_id(), and libMesh::Parallel::sync_node_data_by_element_id_once().

  { return _communicator; }

compare()

virtual 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.

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.

damping_residual()

virtual bool libMesh::DifferentiablePhysics::damping_residual ( bool  request_jacobian, DiffContext &    )

virtualinherited

Subtracts a damping vector contribution on elem from elem_residual.

This method is not used in first-order-in-time problems. For second-order-in-time problems, this is the term. This method is only called for UnsteadySolver-based TimeSolvers.

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

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

Reimplemented in SecondOrderScalarSystemFirstOrderTimeSolverBase, and SecondOrderScalarSystemSecondOrderTimeSolverBase.

Definition at line 374 of file diff_physics.h.

                                                {
    return request_jacobian;
  }

deactivate()

void libMesh::System::deactivate ( )

inherited

Deactivates the system.

Only active systems are solved.

Definition at line 2081 of file system.h.

References libMesh::System::_active.

{
  _active = false;
}

disable_cache()

virtual 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.

disable_print_counter_info()

static void libMesh::ReferenceCounter::disable_print_counter_info ( )

staticinherited

elasticity_tensor()

Real ElasticitySystem::elasticity_tensor ( unsigned int  i, unsigned int  j, unsigned int  k, unsigned int  l  )

private

element_constraint()

virtual bool libMesh::DifferentiablePhysics::element_constraint ( bool  request_jacobian, DiffContext &    )

virtualinherited

Adds the constraint contribution on elem to elem_residual.

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

Users may need to reimplement this for their particular PDE.

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

Reimplemented in CoupledSystem, and NavierSystem.

Definition at line 142 of file diff_physics.h.

                                                  {
    return request_jacobian;
  }

element_postprocess()

virtual void libMesh::DifferentiableSystem::element_postprocess ( DiffContext &  )

virtualinherited

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

Reimplemented in LaplaceSystem, LaplaceSystem, and PoissonSystem.

Definition at line 282 of file diff_system.h.

{}

element_qoi()

virtual void libMesh::DifferentiableQoI::element_qoi ( DiffContext &  , const QoISet &    )

virtualinherited

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

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

Reimplemented in LaplaceQoI.

Definition at line 108 of file diff_qoi.h.

  {}

element_qoi_derivative()

virtual void libMesh::DifferentiableQoI::element_qoi_derivative ( DiffContext &  , const QoISet &    )

virtualinherited

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

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

Reimplemented in HeatSystem, LaplaceSystem, LaplaceSystem, and LaplaceQoI.

Definition at line 120 of file diff_qoi.h.

  {}

element_time_derivative()

virtual bool ElasticitySystem::element_time_derivative ( bool  request_jacobian, DiffContext &    )

virtual

Adds the time derivative contribution on elem to elem_residual.

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

Users need to reimplement this for their particular PDE.

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

Reimplemented from libMesh::DifferentiablePhysics.

enable_print_counter_info()

static void libMesh::ReferenceCounter::enable_print_counter_info ( )

staticinherited

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

eulerian_residual() [1/2]

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

overridevirtualinherited

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

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

Reimplemented from libMesh::DifferentiablePhysics.

Reimplemented in SolidSystem.

eulerian_residual() [2/2]

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

virtualinherited

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

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

Reimplemented in libMesh::FEMPhysics, and SolidSystem.

Definition at line 294 of file diff_physics.h.

                                                 {
    return request_jacobian;
  }

finalize_derivative()

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

virtualinherited

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

forward_qoi_parameter_sensitivity()

virtual 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.

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

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.

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.

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.

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.

get_dof_map() [1/2]

const DofMap & libMesh::System::get_dof_map ( ) const

inherited

Returns

A constant reference to this system's _dof_map.

Definition at line 2049 of file system.h.

References libMesh::System::_dof_map.

Referenced by SimpleRBConstruction::init_data(), and FETest< order, family, elem_type >::setUp().

{
  return *_dof_map;
}

get_dof_map() [2/2]

DofMap & libMesh::System::get_dof_map ( )

inherited

Returns

A writable reference to this system's _dof_map.

Definition at line 2057 of file system.h.

References libMesh::System::_dof_map.

{
  return *_dof_map;
}

get_equation_systems() [1/2]

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

inherited

Returns

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

Definition at line 712 of file system.h.

References libMesh::System::_equation_systems.

Referenced by libMesh::WrappedFunction< Output >::WrappedFunction().

{ return _equation_systems; }

get_equation_systems() [2/2]

EquationSystems& libMesh::System::get_equation_systems ( )

inherited

Returns

A reference to this system's parent EquationSystems object.

Definition at line 717 of file system.h.

References libMesh::System::_equation_systems.

{ return _equation_systems; }

get_first_order_vars()

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

inherited

Returns

The set of first order in time variable indices. May be empty.

Definition at line 517 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_first_order_vars.

  { return _first_order_vars; }

get_info() [1/2]

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

staticinherited

Gets a string containing the reference information.

get_info() [2/2]

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

inherited

Returns

A string containing information about the system.

get_linear_solve_parameters()

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

overridevirtualinherited

Returns

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

Reimplemented from libMesh::ImplicitSystem.

get_linear_solver()

virtual LinearSolver<Number>* libMesh::DifferentiableSystem::get_linear_solver ( ) const

overridevirtualinherited

Returns

A pointer to a linear solver appropriate for use in adjoint and/or sensitivity solves

Reimplemented from libMesh::ImplicitSystem.

get_matrix() [1/2]

const SparseMatrix<Number>& libMesh::ImplicitSystem::get_matrix ( const std::string &  mat_name ) const

inherited

Returns

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

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

get_matrix() [2/2]

SparseMatrix<Number>& libMesh::ImplicitSystem::get_matrix ( const std::string &  mat_name )

inherited

Returns

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

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

get_mesh() [1/2]

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

inherited

Returns

A constant reference to this systems's _mesh.

Definition at line 2033 of file system.h.

References libMesh::System::_mesh.

Referenced by AssemblyA0::boundary_assembly(), AssemblyA1::boundary_assembly(), and AssemblyA2::boundary_assembly().

{
  return _mesh;
}

get_mesh() [2/2]

MeshBase & libMesh::System::get_mesh ( )

inherited

Returns

A reference to this systems's _mesh.

Definition at line 2041 of file system.h.

References libMesh::System::_mesh.

{
  return _mesh;
}

get_mesh_system() [1/2]

const System * libMesh::DifferentiablePhysics::get_mesh_system ( ) const

inherited

Returns

A const reference to the system with variables corresponding to mesh nodal coordinates, or nullptr if the mesh is fixed. Useful for ALE calculations.

Definition at line 624 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_mesh_sys.

{
  return _mesh_sys;
}

get_mesh_system() [2/2]

System * libMesh::DifferentiablePhysics::get_mesh_system ( )

inherited

Returns

A reference to the system with variables corresponding to mesh nodal coordinates, or nullptr if the mesh is fixed.

Definition at line 630 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_mesh_sys.

{
  return _mesh_sys;
}

get_mesh_x_var()

unsigned int libMesh::DifferentiablePhysics::get_mesh_x_var ( ) const

inherited

Returns

The variable number corresponding to the mesh x coordinate. Useful for ALE calculations.

Definition at line 636 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_mesh_x_var.

{
  return _mesh_x_var;
}

get_mesh_y_var()

unsigned int libMesh::DifferentiablePhysics::get_mesh_y_var ( ) const

inherited

Returns

The variable number corresponding to the mesh y coordinate. Useful for ALE calculations.

Definition at line 642 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_mesh_y_var.

{
  return _mesh_y_var;
}

get_mesh_z_var()

unsigned int libMesh::DifferentiablePhysics::get_mesh_z_var ( ) const

inherited

Returns

The variable number corresponding to the mesh z coordinate. Useful for ALE calculations.

Definition at line 648 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_mesh_z_var.

{
  return _mesh_z_var;
}

get_physics() [1/2]

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

inherited

Returns

A const reference to a DifferentiablePhysics object.

Note

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

Definition at line 182 of file diff_system.h.

References libMesh::DifferentiableSystem::_diff_physics.

  { return this->_diff_physics; }

get_physics() [2/2]

DifferentiablePhysics* libMesh::DifferentiableSystem::get_physics ( )

inherited

Returns

A reference to a DifferentiablePhysics object.

Note

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

Definition at line 191 of file diff_system.h.

References libMesh::DifferentiableSystem::_diff_physics.

  { return this->_diff_physics; }

get_qoi() [1/2]

const DifferentiableQoI* libMesh::DifferentiableSystem::get_qoi ( ) const

inherited

Returns

A const reference to a DifferentiableQoI object.

Note

If no external QoI object is attached, the default is this.

Definition at line 211 of file diff_system.h.

References libMesh::DifferentiableSystem::diff_qoi.

  { return this->diff_qoi; }

get_qoi() [2/2]

DifferentiableQoI* libMesh::DifferentiableSystem::get_qoi ( )

inherited

Returns

A reference to a DifferentiableQoI object.

Note

If no external QoI object is attached, the default is this.

Definition at line 219 of file diff_system.h.

References libMesh::DifferentiableSystem::diff_qoi.

  { return this->diff_qoi; }

get_second_order_dot_var()

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

inherited

For a given second order (in time) variable var, this method will return the index to the corresponding "dot" variable.

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

get_second_order_vars()

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

inherited

Returns

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

Definition at line 530 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_second_order_vars.

  { return _second_order_vars; }

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)

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.

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.

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.

get_time_solver() [1/2]

TimeSolver & libMesh::DifferentiableSystem::get_time_solver ( )

inherited

Returns

A pointer to the time solver attached to the calling system

Definition at line 415 of file diff_system.h.

References libMesh::DifferentiableSystem::time_solver.

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

get_time_solver() [2/2]

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

inherited

Non-const version of the above.

Definition at line 423 of file diff_system.h.

References libMesh::DifferentiableSystem::time_solver.

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

get_vector() [1/4]

const NumericVector<Number>& libMesh::System::get_vector ( const std::string &  vec_name ) const

inherited

Returns

A const reference to this system's additional vector named vec_name. Access is only granted when the vector is already properly initialized.

get_vector() [2/4]

NumericVector<Number>& libMesh::System::get_vector ( const std::string &  vec_name )

inherited

Returns

A writable reference to this system's additional vector named vec_name. Access is only granted when the vector is already properly initialized.

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).

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).

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.

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.

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

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

has_variable()

bool libMesh::System::has_variable ( const std::string &  var ) const

inherited

Returns

true if a variable named var exists in this System

have_first_order_scalar_vars()

bool libMesh::DifferentiableSystem::have_first_order_scalar_vars ( ) const

inherited

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

have_first_order_vars()

bool libMesh::DifferentiablePhysics::have_first_order_vars ( ) const

inherited

Definition at line 511 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_first_order_vars.

  { return !_first_order_vars.empty(); }

have_matrix()

bool libMesh::ImplicitSystem::have_matrix ( const std::string &  mat_name ) const

inherited

Returns

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

Definition at line 419 of file implicit_system.h.

References libMesh::ImplicitSystem::_matrices.

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

have_second_order_scalar_vars()

bool libMesh::DifferentiableSystem::have_second_order_scalar_vars ( ) const

inherited

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

have_second_order_vars()

bool libMesh::DifferentiablePhysics::have_second_order_vars ( ) const

inherited

Definition at line 524 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_second_order_vars.

  { return !_second_order_vars.empty(); }

have_vector()

bool libMesh::System::have_vector ( const std::string &  vec_name ) const

inherited

Returns

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

Definition at line 2225 of file system.h.

References libMesh::System::_vectors.

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

hide_output()

bool& libMesh::System::hide_output ( )

inherited

Returns

A writable reference to a boolean that determines if this system can be written to file or not. If set to true, then EquationSystems::write will ignore this system.

Definition at line 1662 of file system.h.

References libMesh::System::_hide_output.

{ return _hide_output; }

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 2201 of file system.h.

References libMesh::System::_identify_variable_groups.

{
  return _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 2209 of file system.h.

References libMesh::System::_identify_variable_groups.

{
  _identify_variable_groups = ivg;
}

increment_constructor_count()

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

protectedinherited

Increments the construction counter.

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

Definition at line 181 of file reference_counter.h.

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

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

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

  p.first++;
}

increment_destructor_count()

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

protectedinherited

Increments the destruction counter.

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

Definition at line 194 of file reference_counter.h.

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

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

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

  p.second++;
}

init()

void libMesh::System::init ( )

inherited

Initializes degrees of freedom on the current mesh.

Sets the

init_context()

virtual void ElasticitySystem::init_context ( DiffContext &  context )

virtual

Reimplemented from libMesh::FEMSystem.

init_data()

virtual void ElasticitySystem::init_data ( )

virtual

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

Reimplemented from libMesh::FEMSystem.

init_matrices()

virtual void libMesh::ImplicitSystem::init_matrices ( )

protectedvirtualinherited

Initializes the matrices associated with this system.

init_physics()

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

virtualinherited

Initialize any data structures associated with the physics.

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

init_qoi()

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

virtualinherited

Initialize system qoi.

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

Definition at line 69 of file diff_qoi.h.

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

{}

is_adjoint_already_solved()

bool libMesh::System::is_adjoint_already_solved ( ) const

inherited

Accessor for the adjoint_already_solved boolean.

Definition at line 388 of file system.h.

References libMesh::System::adjoint_already_solved.

  { return adjoint_already_solved;}

is_first_order_var()

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

inherited

Definition at line 520 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_first_order_vars.

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

is_initialized()

bool libMesh::System::is_initialized ( )

inherited

Returns

true iff this system has been initialized.

Definition at line 2089 of file system.h.

References libMesh::System::_is_initialized.

{
  return _is_initialized;
}

is_second_order_var()

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

inherited

Definition at line 533 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_second_order_vars.

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

is_time_evolving()

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

inherited

Returns

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

Definition at line 277 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_time_evolving.

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

kronecker_delta()

Real ElasticitySystem::kronecker_delta ( unsigned int  i, unsigned int  j  )

private

Definition at line 72 of file elasticity_system.h.

  {
    return i == j ? 1. : 0.;
  }

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.

mass_residual()

virtual bool ElasticitySystem::mass_residual ( bool  request_jacobian, DiffContext &    )

virtual

Subtracts a mass vector contribution on elem from elem_residual.

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

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

Reimplemented from libMesh::FEMPhysics.

mesh_position_get()

void libMesh::FEMSystem::mesh_position_get ( )

inherited

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

mesh_position_set()

void libMesh::FEMSystem::mesh_position_set ( )

inherited

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

n_active_dofs()

dof_id_type libMesh::System::n_active_dofs ( ) const

inherited

Returns

The number of active degrees of freedom for this System.

Definition at line 2217 of file system.h.

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

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

n_components()

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

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 2121 of file system.h.

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

{
  if (_variables.empty())
    return 0;

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

n_constrained_dofs()

dof_id_type libMesh::System::n_constrained_dofs ( ) const

inherited

Returns

The total number of constrained degrees of freedom in the system.

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

n_dofs()

dof_id_type libMesh::System::n_dofs ( ) const

inherited

Returns

The number of degrees of freedom in the system

Referenced by libMesh::System::n_active_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.

n_local_dofs()

dof_id_type libMesh::System::n_local_dofs ( ) const

inherited

Returns

The number of degrees of freedom local to this processor

n_matrices()

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

overridevirtualinherited

Returns

The number of matrices handled by this system

Reimplemented from libMesh::System.

Definition at line 426 of file implicit_system.h.

References libMesh::ImplicitSystem::_matrices.

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

n_objects()

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

staticinherited

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

Definition at line 83 of file reference_counter.h.

References libMesh::ReferenceCounter::_n_objects.

  { return _n_objects; }

n_processors()

processor_id_type libMesh::ParallelObject::n_processors ( ) const

inherited

Returns

The number of processors in the group.

Definition at line 95 of file parallel_object.h.

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

Referenced by libMesh::MeshBase::partition().

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

n_qois()

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

inherited

Number of currently active quantities of interest.

Definition at line 2278 of file system.h.

References libMesh::System::qoi.

Referenced by libMesh::SensitivityData::allocate_data(), and libMesh::SensitivityData::allocate_hessian_data().

{
  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 2113 of file system.h.

References libMesh::System::_variable_groups.

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

n_vars()

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

inherited

Returns

The number of variables in the system

Definition at line 2105 of file system.h.

References libMesh::System::_variables.

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

n_vectors()

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

inherited

Returns

The number of vectors (in addition to the solution) handled by this system This is the size of the _vectors map

Definition at line 2233 of file system.h.

References libMesh::System::_vectors.

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

name()

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

inherited

Returns

The system name.

Definition at line 2017 of file system.h.

References libMesh::System::_sys_name.

{
  return _sys_name;
}

nonlocal_constraint()

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

virtualinherited

Adds any nonlocal constraint contributions (e.g.

some components of constraints in scalar variable equations) to elem_residual

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

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

Definition at line 227 of file diff_physics.h.

                                                   {
    return request_jacobian;
  }

nonlocal_damping_residual()

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

virtualinherited

Subtracts any nonlocal damping vector contributions (e.g.

any first time derivative coefficients in scalar variable equations) from elem_residual

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

Definition at line 406 of file diff_physics.h.

                                                         {
    return request_jacobian;
  }

nonlocal_mass_residual()

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

virtualinherited

Subtracts any nonlocal mass vector contributions (e.g.

any time derivative coefficients in scalar variable equations) from elem_residual

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

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

nonlocal_time_derivative()

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

virtualinherited

Adds any nonlocal time derivative contributions (e.g.

some components of time derivatives in scalar variable equations) to elem_residual

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

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

Definition at line 209 of file diff_physics.h.

                                                        {
    return request_jacobian;
  }

number()

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

inherited

Returns

The system number.

Definition at line 2025 of file system.h.

References libMesh::System::_sys_number.

{
  return _sys_number;
}

numerical_elem_jacobian()

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

inherited

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

numerical_jacobian()

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

inherited

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

numerical_jacobian_h_for_var()

Real FEMSystem::numerical_jacobian_h_for_var ( unsigned int  var_num ) const

inherited

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

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

Definition at line 259 of file fem_system.h.

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

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

  return _numerical_jacobian_h_for_var[var_num];
}

numerical_nonlocal_jacobian()

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

inherited

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

numerical_side_jacobian()

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

inherited

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

parallel_op()

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

virtualinherited

Method to populate system qoi data structure with process-local qoi.

By default, simply sums process qois into system qoi.

point_gradient() [1/3]

Gradient libMesh::System::point_gradient ( unsigned int  var, const Point &  p, const bool  insist_on_success = true  ) const

inherited

Returns

The gradient of the solution variable var at the physical point p in the mesh, similarly to point_value.

point_gradient() [2/3]

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

inherited

Returns

The gradient of the solution variable var at the physical point p in local Elem e in the mesh, similarly to point_value.

point_gradient() [3/3]

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

inherited

Calls the version of point_gradient() which takes a reference.

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

point_hessian() [1/3]

Tensor libMesh::System::point_hessian ( unsigned int  var, const Point &  p, const bool  insist_on_success = true  ) const

inherited

Returns

The second derivative tensor of the solution variable var at the physical point p in the mesh, similarly to point_value.

point_hessian() [2/3]

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

inherited

Returns

The second derivative tensor of the solution variable var at the physical point p in local Elem e in the mesh, similarly to point_value.

point_hessian() [3/3]

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

inherited

Calls the version of point_hessian() which takes a reference.

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

point_value() [1/3]

Number libMesh::System::point_value ( unsigned int  var, const Point &  p, const bool  insist_on_success = true  ) const

inherited

Returns

The value of the solution variable var at the physical point p in the mesh, without knowing a priori which element contains p.

Note

This function uses MeshBase::sub_point_locator(); users may or may not want to call MeshBase::clear_point_locator() afterward. Also, point_locator() is expensive (N log N for initial construction, log N for evaluations). Avoid using this function in any context where you are already looping over elements.

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

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

point_value() [2/3]

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

inherited

Returns

The value of the solution variable var at the physical point p contained in local Elem e

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

point_value() [3/3]

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

inherited

Calls the version of point_value() which takes a reference.

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

postprocess()

virtual void libMesh::FEMSystem::postprocess ( )

overridevirtualinherited

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

Reimplemented from libMesh::DifferentiableSystem.

Reimplemented in CoupledSystem, NavierSystem, LaplaceSystem, LaplaceSystem, and PoissonSystem.

print_info()

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

staticinherited

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

processor_id()

processor_id_type libMesh::ParallelObject::processor_id ( ) const

inherited

Returns

The rank of this processor in the group.

Definition at line 101 of file parallel_object.h.

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

Referenced by libMesh::DofMap::end_dof(), libMesh::DofMap::end_old_dof(), libMesh::DofMap::first_dof(), libMesh::DofMap::first_old_dof(), libMesh::DofMap::last_dof(), libMesh::MeshBase::n_active_local_elem(), libMesh::DofMap::n_local_dofs(), libMesh::MeshBase::n_local_elem(), libMesh::MeshBase::n_local_nodes(), and libMesh::MeshTools::weight().

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

project_solution() [1/3]

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

inherited

Projects arbitrary functions onto the current solution.

The function value f and its gradient g are user-provided cloneable functors. A gradient g is only required/used for projecting onto finite element spaces with continuous derivatives. If non-default Parameters are to be used, they can be provided in the parameters argument.

Referenced by FETest< order, family, elem_type >::setUp().

project_solution() [2/3]

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

inherited

Projects arbitrary functions onto the current solution.

The function value f and its gradient g are user-provided cloneable functors. A gradient g is only required/used for projecting onto finite element spaces with continuous derivatives. If non-default Parameters are to be used, they can be provided in the parameters argument.

project_solution() [3/3]

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

inherited

project_solution_on_reinit()

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

inherited

Tells the System whether or not to project the solution vector onto new grids when the system is reinitialized.

The solution will be projected unless project_solution_on_reinit() = false is called.

Definition at line 794 of file system.h.

References libMesh::System::_solution_projection.

  { return _solution_projection; }

project_vector() [1/5]

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

inherited

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

The function value f and its gradient g are user-provided cloneable functors. A gradient g is only required/used for projecting onto finite element spaces with continuous derivatives. If non-default Parameters are to be used, they can be provided in the parameters argument.

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

project_vector() [2/5]

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

inherited

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

The function value f and its gradient g are user-provided cloneable functors. A gradient g is only required/used for projecting onto finite element spaces with continuous derivatives. If non-default Parameters are to be used, they can be provided in the parameters argument.

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

project_vector() [3/5]

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

inherited

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

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

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

project_vector() [4/5]

void libMesh::System::project_vector ( NumericVector< Number > &  , 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.

project_vector() [5/5]

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

protectedinherited

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

The original vector is unchanged and the new vector is passed through the second argument.

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

projection_matrix()

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

inherited

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

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

prolong_vectors()

virtual void libMesh::System::prolong_vectors ( )

virtualinherited

Prolong vectors after the mesh has refined.

qoi_parameter_hessian()

virtual 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.

qoi_parameter_hessian_vector_product()

virtual 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.

qoi_parameter_sensitivity()

virtual 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.

re_update()

virtual 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 >.

read_header()

void libMesh::System::read_header ( Xdr &  io, const std::string &  version, const bool  read_header = true, const bool  read_additional_data = true, const bool  read_legacy_format = false  )

inherited

Reads the basic data header for this System.

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.

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.

read_parallel_data() [2/2]

void libMesh::System::read_parallel_data ( Xdr &  io, const bool  read_additional_data  )

inherited

Non-templated version for backward compatibility.

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

Definition at line 1299 of file system.h.

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

read_serialized_data() [1/2]

template<typename ValType >

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.

read_serialized_data() [2/2]

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

inherited

Non-templated version for backward compatibility.

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

Definition at line 1257 of file system.h.

  { 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.

read_serialized_vectors() [2/2]

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

inherited

Non-templated version for backward compatibility.

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

Definition at line 1277 of file system.h.

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

reinit()

virtual void libMesh::DifferentiableSystem::reinit ( )

overridevirtualinherited

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

Reimplemented from libMesh::ImplicitSystem.

reinit_constraints()

virtual void libMesh::System::reinit_constraints ( )

virtualinherited

Reinitializes the constraints for this system.

release_linear_solver()

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

overridevirtualinherited

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

Reimplemented from libMesh::ImplicitSystem.

remove_matrix()

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

inherited

Removes the additional matrix mat_name from this system.

remove_vector()

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

inherited

Removes the additional vector vec_name from this system.

request_matrix() [1/2]

const SparseMatrix<Number>* libMesh::ImplicitSystem::request_matrix ( const std::string &  mat_name ) const

inherited

Returns

A const pointer to this system's additional matrix named mat_name, or nullptr if no matrix by that name exists.

request_matrix() [2/2]

SparseMatrix<Number>* libMesh::ImplicitSystem::request_matrix ( const std::string &  mat_name )

inherited

Returns

A writable pointer to this system's additional matrix named mat_name, or nullptr if no matrix by that name exists.

request_vector() [1/4]

const NumericVector<Number>* libMesh::System::request_vector ( const std::string &  vec_name ) const

inherited

Returns

A const pointer to the vector if this System has a vector associated with the given name, nullptr otherwise.

request_vector() [2/4]

NumericVector<Number>* libMesh::System::request_vector ( const std::string &  vec_name )

inherited

Returns

A pointer to the vector if this System has a vector associated with the given name, nullptr otherwise.

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.

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.

restrict_solve_to()

virtual 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.

restrict_vectors()

virtual void libMesh::System::restrict_vectors ( )

virtualinherited

Restrict vectors after the mesh has coarsened.

sensitivity_solve()

virtual 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.

set_adjoint_already_solved()

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

inherited

Setter for the adjoint_already_solved boolean.

Definition at line 394 of file system.h.

References libMesh::System::adjoint_already_solved.

  { adjoint_already_solved = setting;}

set_basic_system_only()

void libMesh::System::set_basic_system_only ( )

inherited

Sets the system to be "basic only": i.e.

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

Definition at line 2097 of file system.h.

References libMesh::System::_basic_system_only.

{
  _basic_system_only = true;
}

set_mesh_system()

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

virtualinherited

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

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

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

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

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

Definition at line 580 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_mesh_sys.

{
  // For now we assume that we're doing fully coupled mesh motion
  //  if (sys && sys != this)
  //    libmesh_not_implemented();

  // For the foreseeable future we'll assume that we keep these
  // Systems in the same EquationSystems
  // libmesh_assert_equal_to (&this->get_equation_systems(),
  //                          &sys->get_equation_systems());

  // And for the immediate future this code may not even work
  libmesh_experimental();

  _mesh_sys = sys;
}

set_mesh_x_var()

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

virtualinherited

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

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

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

Definition at line 600 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_mesh_x_var.

{
  _mesh_x_var = var;
}

set_mesh_y_var()

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

virtualinherited

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

Definition at line 608 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_mesh_y_var.

{
  _mesh_y_var = var;
}

set_mesh_z_var()

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

virtualinherited

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

Definition at line 616 of file diff_physics.h.

References libMesh::DifferentiablePhysics::_mesh_z_var.

{
  _mesh_z_var = var;
}

set_numerical_jacobian_h_for_var()

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

inherited

Definition at line 269 of file fem_system.h.

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

{
  if (_numerical_jacobian_h_for_var.size() <= var_num)
    _numerical_jacobian_h_for_var.resize(var_num+1,Real(0));

  libmesh_assert_greater(new_h, 0);

  _numerical_jacobian_h_for_var[var_num] = new_h;
}

set_time_solver()

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

inherited

Sets the time_solver FIXME: This code is a little dangerous as it transfers ownership from the TimeSolver creator to this class.

The user must no longer access his original TimeSolver object after calling this function.

Definition at line 242 of file diff_system.h.

References libMesh::DifferentiableSystem::time_solver.

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

set_vector_as_adjoint()

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

inherited

Allows one to set the QoI index controlling whether the vector identified by vec_name represents a solution from the adjoint (qoi_num >= 0) or primal (qoi_num == -1) space.

This becomes significant if those spaces have differing heterogeneous Dirichlet constraints.

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

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.

side_constraint()

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

virtualinherited

Adds the constraint contribution on side of elem to elem_residual.

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

Users may need to reimplement this for their particular PDE depending on the boundary conditions.

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

Reimplemented in LaplaceSystem, LaplaceSystem, LaplaceSystem, and NavierSystem.

Definition at line 191 of file diff_physics.h.

                                               {
    return request_jacobian;
  }

side_damping_residual()

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

virtualinherited

Subtracts a damping vector contribution on side of elem from elem_residual.

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

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

Definition at line 391 of file diff_physics.h.

                                                     {
    return request_jacobian;
  }

side_mass_residual()

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

virtualinherited

Subtracts a mass vector contribution on side of elem from elem_residual.

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

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

Definition at line 335 of file diff_physics.h.

                                                  {
    return request_jacobian;
  }

side_postprocess()

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

virtualinherited

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

Reimplemented in LaplaceSystem, and LaplaceSystem.

Definition at line 288 of file diff_system.h.

{}

side_qoi()

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

virtualinherited

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

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

Reimplemented in CoupledSystemQoI.

Definition at line 131 of file diff_qoi.h.

  {}

side_qoi_derivative()

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

virtualinherited

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

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

Reimplemented in LaplaceSystem, LaplaceSystem, and CoupledSystemQoI.

Definition at line 143 of file diff_qoi.h.

  {}

side_time_derivative()

virtual bool ElasticitySystem::side_time_derivative ( bool  request_jacobian, DiffContext &    )

virtual

Adds the time derivative contribution on side of elem to elem_residual.

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

Users may need to reimplement this for their particular PDE depending on the boundary conditions.

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

Reimplemented from libMesh::DifferentiablePhysics.

solve()

virtual void libMesh::FEMSystem::solve ( )

overridevirtualinherited

Invokes the solver associated with the system.

For steady state solvers, this will find a root x where F(x) = 0. For transient solvers, this will integrate dx/dt = F(x).

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

Reimplemented from libMesh::DifferentiableSystem.

Reimplemented in libMesh::ContinuationSystem.

swap_physics()

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

inherited

Swap current physics object with external object.

system()

sys_type& libMesh::ImplicitSystem::system ( )

inherited

Returns

A reference to *this.

Definition at line 81 of file implicit_system.h.

{ return *this; }

system_type()

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

overridevirtualinherited

Returns

"Implicit". Helps in identifying the system type in an equation system file.

Reimplemented from libMesh::ExplicitSystem.

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

Definition at line 117 of file implicit_system.h.

{ return "Implicit"; }

thread_join()

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

virtualinherited

Method to combine thread-local qois.

By default, simply sums thread qois.

time_evolving() [1/2]

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

virtualinherited

Tells the DiffSystem that variable var is evolving with respect to time.

In general, the user's init() function should call time_evolving() for any variables which behave like du/dt = F(u), and should not call time_evolving() for any variables which behave like 0 = G(u).

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

Deprecated:

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

Definition at line 249 of file diff_physics.h.

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

time_evolving() [2/2]

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

virtualinherited

Tells the DiffSystem that variable var is evolving with respect to time.

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

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

update()

virtual void libMesh::System::update ( )

virtualinherited

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

Reimplemented in SolidSystem.

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.

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.

user_assembly()

virtual void libMesh::System::user_assembly ( )

virtualinherited

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

user_constrain()

virtual void libMesh::System::user_constrain ( )

virtualinherited

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

user_initialization()

virtual void libMesh::System::user_initialization ( )

virtualinherited

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

user_QOI()

virtual 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.

user_QOI_derivative()

virtual 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.

variable()

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

inherited

Return a constant reference to Variable var.

Definition at line 2133 of file system.h.

References libMesh::System::_variables.

{
  libmesh_assert_less (i, _variables.size());

  return _variables[i];
}

variable_group()

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

inherited

Return a constant reference to VariableGroup vg.

Definition at line 2143 of file system.h.

References libMesh::System::_variable_groups.

{
  libmesh_assert_less (vg, _variable_groups.size());

  return _variable_groups[vg];
}

variable_name()

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

inherited

Returns

The name of variable i.

Definition at line 2153 of file system.h.

References libMesh::System::_variables.

{
  libmesh_assert_less (i, _variables.size());

  return _variables[i].name();
}

variable_number()

unsigned short int libMesh::System::variable_number ( const std::string &  var ) const

inherited

Returns

The variable number associated with the user-specified variable named var.

Referenced by libMesh::System::variable_scalar_number(), and libMesh::System::variable_type().

variable_scalar_number() [1/2]

unsigned int libMesh::System::variable_scalar_number ( const std::string &  var, 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 variable_number(var)

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

Definition at line 2164 of file system.h.

References libMesh::System::variable_number().

{
  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 2174 of file system.h.

References libMesh::System::_variables.

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

variable_type() [1/2]

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

inherited

Returns

The finite element type variable number i.

Definition at line 2183 of file system.h.

References libMesh::System::_variables.

Referenced by FETest< order, family, elem_type >::setUp().

{
  libmesh_assert_less (i, _variables.size());

  return _variables[i].type();
}

variable_type() [2/2]

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

inherited

Returns

The finite element type for variable var.

Definition at line 2193 of file system.h.

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

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

vector_is_adjoint()

int libMesh::System::vector_is_adjoint ( const std::string &  vec_name ) const

inherited

Returns

The integer describing whether the vector identified by vec_name represents a solution from an adjoint (non-negative) or the primal (-1) space.

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).

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

vector_preservation()

bool libMesh::System::vector_preservation ( const std::string &  vec_name ) const

inherited

Returns

The boolean describing whether the vector identified by vec_name should be "preserved": projected to new meshes, saved, etc.

vectors_begin() [1/2]

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

inherited

Beginning of vectors container.

Definition at line 2245 of file system.h.

References libMesh::System::_vectors.

{
  return _vectors.begin();
}

vectors_begin() [2/2]

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

inherited

Beginning of vectors container.

Definition at line 2251 of file system.h.

References libMesh::System::_vectors.

{
  return _vectors.begin();
}

vectors_end() [1/2]

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

inherited

End of vectors container.

Definition at line 2257 of file system.h.

References libMesh::System::_vectors.

{
  return _vectors.end();
}

vectors_end() [2/2]

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

inherited

End of vectors container.

Definition at line 2263 of file system.h.

References libMesh::System::_vectors.

{
  return _vectors.end();
}

weighted_sensitivity_adjoint_solve()

virtual 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.

weighted_sensitivity_solve()

virtual 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.

write_header()

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

inherited

Writes the basic data header for this System.

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.

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.

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.

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.

Member Data Documentation

_communicator

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

protectedinherited

Definition at line 107 of file parallel_object.h.

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

_counts

Counts libMesh::ReferenceCounter::_counts

staticprotectedinherited

Actually holds the data.

Definition at line 122 of file reference_counter.h.

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

_diff_physics

DifferentiablePhysics* libMesh::DifferentiableSystem::_diff_physics

protectedinherited

Pointer to object to use for physics assembly evaluations.

Defaults to this for backwards compatibility; in the future users should create separate physics objects.

Definition at line 371 of file diff_system.h.

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

_enable_print_counter

bool libMesh::ReferenceCounter::_enable_print_counter

staticprotectedinherited

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

Definition at line 141 of file reference_counter.h.

_first_order_vars

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

protectedinherited

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

Definition at line 559 of file diff_physics.h.

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

_mesh_sys

System* libMesh::DifferentiablePhysics::_mesh_sys

protectedinherited

System from which to acquire moving mesh information.

Definition at line 542 of file diff_physics.h.

Referenced by libMesh::DifferentiablePhysics::get_mesh_system(), and libMesh::DifferentiablePhysics::set_mesh_system().

_mesh_x_var

unsigned int libMesh::DifferentiablePhysics::_mesh_x_var

protectedinherited

Variables from which to acquire moving mesh information.

Definition at line 547 of file diff_physics.h.

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

_mesh_y_var

unsigned int libMesh::DifferentiablePhysics::_mesh_y_var

protectedinherited

Definition at line 547 of file diff_physics.h.

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

_mesh_z_var

unsigned int libMesh::DifferentiablePhysics::_mesh_z_var

protectedinherited

Definition at line 547 of file diff_physics.h.

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

_mutex

Threads::spin_mutex libMesh::ReferenceCounter::_mutex

staticprotectedinherited

Mutual exclusion object to enable thread-safe reference counting.

Definition at line 135 of file reference_counter.h.

_n_objects

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

staticprotectedinherited

The number of objects.

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

Definition at line 130 of file reference_counter.h.

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

_rho

Real ElasticitySystem::_rho

private

Definition at line 70 of file elasticity_system.h.

_second_order_dot_vars

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

protectedinherited

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

Definition at line 571 of file diff_physics.h.

_second_order_vars

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

protectedinherited

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

Definition at line 564 of file diff_physics.h.

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

_time_evolving

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

protectedinherited

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

Definition at line 554 of file diff_physics.h.

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

_u_var

unsigned int ElasticitySystem::_u_var

private

Definition at line 68 of file elasticity_system.h.

_v_var

unsigned int ElasticitySystem::_v_var

private

Definition at line 68 of file elasticity_system.h.

_w_var

unsigned int ElasticitySystem::_w_var

private

Definition at line 68 of file elasticity_system.h.

assemble_before_solve

bool libMesh::System::assemble_before_solve

inherited

Flag which tells the system to whether or not to call the user assembly function during each call to solve().

By default, every call to solve() begins with a call to the user assemble, so this flag is true. (For explicit systems, "solving" the system occurs during the assembly step, so this flag is always true for explicit systems.)

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

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

Definition at line 1477 of file system.h.

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

assemble_qoi_elements

bool libMesh::DifferentiableQoI::assemble_qoi_elements

inherited

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

Definition at line 99 of file diff_qoi.h.

assemble_qoi_internal_sides

bool libMesh::DifferentiableQoI::assemble_qoi_internal_sides

inherited

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

Definition at line 91 of file diff_qoi.h.

assemble_qoi_sides

bool libMesh::DifferentiableQoI::assemble_qoi_sides

inherited

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

To add domain interior sides, also set assemble_qoi_internal_sides to true.

Definition at line 83 of file diff_qoi.h.

compute_internal_sides

bool libMesh::DifferentiablePhysics::compute_internal_sides

inherited

compute_internal_sides is false by default, indicating that side_* computations will only be done on boundary sides.

If compute_internal_sides is true, computations will be done on sides between elements as well.

Definition at line 153 of file diff_physics.h.

current_local_solution

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

inherited

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

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

Definition at line 1535 of file system.h.

Referenced by FETest< order, family, elem_type >::testGradU(), FETest< order, family, elem_type >::testGradUComp(), and FETest< order, family, elem_type >::testU().

deltat

Real libMesh::DifferentiableSystem::deltat

inherited

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

Definition at line 261 of file diff_system.h.

diff_qoi

DifferentiableQoI* libMesh::DifferentiableSystem::diff_qoi

protectedinherited

Pointer to object to use for quantity of interest assembly evaluations.

Defaults to this for backwards compatibility; in the future users should create separate physics objects.

Definition at line 378 of file diff_system.h.

Referenced by libMesh::DifferentiableSystem::attach_qoi(), and libMesh::DifferentiableSystem::get_qoi().

extra_quadrature_order

int libMesh::System::extra_quadrature_order

inherited

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

Note

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

Definition at line 1508 of file system.h.

fe_reinit_during_postprocess

bool libMesh::FEMSystem::fe_reinit_during_postprocess

inherited

If fe_reinit_during_postprocess is true (it is true by default), FE objects will be reinit()ed with their default quadrature rules.

If false, FE objects will need to be reinit()ed by the user or will be in an undefined state.

Definition at line 170 of file fem_system.h.

matrix

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

inherited

The system matrix.

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

Definition at line 373 of file implicit_system.h.

numerical_jacobian_h

Real libMesh::FEMSystem::numerical_jacobian_h

inherited

If calculating numeric jacobians is required, the FEMSystem will perturb each solution vector entry by numerical_jacobian_h when calculating finite differences.

This defaults to the libMesh TOLERANCE but can be set manually.

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

Definition at line 181 of file fem_system.h.

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

postprocess_sides

bool libMesh::DifferentiableSystem::postprocess_sides

inherited

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

Definition at line 315 of file diff_system.h.

print_element_jacobians

bool libMesh::DifferentiableSystem::print_element_jacobians

inherited

Set print_element_jacobians to true to print each J_elem contribution.

Definition at line 362 of file diff_system.h.

print_element_residuals

bool libMesh::DifferentiableSystem::print_element_residuals

inherited

Set print_element_residuals to true to print each R_elem contribution.

Definition at line 357 of file diff_system.h.

print_element_solutions

bool libMesh::DifferentiableSystem::print_element_solutions

inherited

Set print_element_solutions to true to print each U_elem input.

Definition at line 352 of file diff_system.h.

print_jacobian_norms

bool libMesh::DifferentiableSystem::print_jacobian_norms

inherited

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

Definition at line 342 of file diff_system.h.

print_jacobians

bool libMesh::DifferentiableSystem::print_jacobians

inherited

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

Definition at line 347 of file diff_system.h.

print_residual_norms

bool libMesh::DifferentiableSystem::print_residual_norms

inherited

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

Definition at line 332 of file diff_system.h.

print_residuals

bool libMesh::DifferentiableSystem::print_residuals

inherited

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

Definition at line 337 of file diff_system.h.

print_solution_norms

bool libMesh::DifferentiableSystem::print_solution_norms

inherited

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

Definition at line 321 of file diff_system.h.

print_solutions

bool libMesh::DifferentiableSystem::print_solutions

inherited

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

Definition at line 327 of file diff_system.h.

qoi

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

inherited

Values of the quantities of interest.

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

Definition at line 1558 of file system.h.

Referenced by libMesh::DifferentiableSystem::attach_qoi(), and libMesh::System::n_qois().

rhs

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

inherited

The system matrix.

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

Definition at line 114 of file explicit_system.h.

solution

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

inherited

Data structure to hold solution values.

Definition at line 1523 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 1545 of file system.h.

time_solver

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

inherited

A pointer to the solver object we're going to use.

This must be instantiated by the user before solving!

Definition at line 234 of file diff_system.h.

Referenced by libMesh::DifferentiableSystem::get_time_solver(), and libMesh::DifferentiableSystem::set_time_solver().

use_fixed_solution

bool libMesh::System::use_fixed_solution

inherited

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

stabilized methods. False by default.

Note

For FEMSystem users, if this variable is set to true, it must be before init_data() is called.

Definition at line 1493 of file system.h.

verify_analytic_jacobians

Real libMesh::FEMSystem::verify_analytic_jacobians

inherited

If verify_analytic_jacobian is equal to zero (as it is by default), no numeric jacobians will be calculated unless an overridden element_time_derivative(), element_constraint(), side_time_derivative(), or side_constraint() function cannot provide an analytic jacobian upon request.

If verify_analytic_jacobian is equal to the positive value tol, then any time a full analytic element jacobian can be calculated it will be tested against a numerical jacobian on the same element, and the program will abort if the relative error (in matrix l1 norms) exceeds tol.

Definition at line 209 of file fem_system.h.

zero_out_matrix_and_rhs

bool libMesh::ImplicitSystem::zero_out_matrix_and_rhs

inherited

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

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

Definition at line 380 of file implicit_system.h.

---

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

• examples/fem_system/fem_system_ex3/elasticity_system.h