ConstantFirstOrderODE Class Reference

Implements ODE: 2.1. More...

Inheritance diagram for ConstantFirstOrderODE:

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
	ConstantFirstOrderODE (EquationSystems &es, const std::string &name_in, const unsigned int number_in)
virtual Number	F (FEMContext &, unsigned int)
virtual Number	M (FEMContext &, unsigned int)
virtual Number	u (Real t)
	Exact solution as a function of time t. More...
virtual Number	F (FEMContext &context, unsigned int qp)=0
	Value of F(u) More...
virtual Number	M (FEMContext &context, unsigned int qp)=0
	Value of M(u). More...
virtual void	init_data () override
	Initializes the member data fields associated with the system, so that, e.g., assemble() may be used. More...
virtual bool	element_time_derivative (bool request_jacobian, DiffContext &context) override
	Note the nonlinear residual is F(u)-M(u) More...
virtual bool	mass_residual (bool request_jacobian, DiffContext &context) override
	Note the nonlinear residual is F(u)-M(u) 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	init_context (DiffContext &) override
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...
template<template< typename > class>
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
	This method projects an arbitrary function onto the solution via L2 projections and nodal interpolations on each element. More...
void	project_vector (NumericVector< Number > &new_vector, FunctionBase< Number > *f, FunctionBase< Gradient > *g=nullptr, int is_adjoint=-1) const
	Projects arbitrary functions onto a vector of degree of freedom values for the current system. More...
void	project_vector (NumericVector< Number > &new_vector, FEMFunctionBase< Number > *f, FEMFunctionBase< Gradient > *g=nullptr, int is_adjoint=-1) const
	Projects arbitrary functions onto a vector of degree of freedom values for the current system. More...
void	project_vector (ValueFunctionPointer fptr, GradientFunctionPointer gptr, const Parameters &parameters, NumericVector< Number > &new_vector, int is_adjoint=-1) const
	Projects arbitrary functions onto a vector of degree of freedom values for the current system. More...
void	boundary_project_solution (const std::set< boundary_id_type > &b, const std::vector< unsigned int > &variables, FunctionBase< Number > *f, FunctionBase< Gradient > *g=nullptr)
	Projects arbitrary boundary functions onto a vector of degree of freedom values for the current system. More...
void	boundary_project_solution (const std::set< boundary_id_type > &b, const std::vector< unsigned int > &variables, ValueFunctionPointer fptr, GradientFunctionPointer gptr, const Parameters &parameters)
	Projects arbitrary boundary functions onto a vector of degree of freedom values for the current system. More...
void	boundary_project_vector (const std::set< boundary_id_type > &b, const std::vector< unsigned int > &variables, NumericVector< Number > &new_vector, FunctionBase< Number > *f, FunctionBase< Gradient > *g=nullptr, int is_adjoint=-1) const
	Projects arbitrary boundary functions onto a vector of degree of freedom values for the current system. More...
void	boundary_project_vector (const std::set< boundary_id_type > &b, const std::vector< unsigned int > &variables, ValueFunctionPointer fptr, GradientFunctionPointer gptr, const Parameters &parameters, NumericVector< Number > &new_vector, int is_adjoint=-1) const
	Projects arbitrary boundary functions onto a vector of degree of freedom values for the current system. More...
unsigned int	number () const
void	update_global_solution (std::vector< Number > &global_soln) const
	Fill the input vector global_soln so that it contains the global solution on all processors. More...
void	update_global_solution (std::vector< Number > &global_soln, const processor_id_type dest_proc) const
	Fill the input vector global_soln so that it contains the global solution on processor dest_proc. More...
const MeshBase &	get_mesh () const
MeshBase &	get_mesh ()
const DofMap &	get_dof_map () const
DofMap &	get_dof_map ()
const EquationSystems &	get_equation_systems () const
EquationSystems &	get_equation_systems ()
bool	active () const
void	activate ()
	Activates the system. More...
void	deactivate ()
	Deactivates the system. More...
void	set_basic_system_only ()
	Sets the system to be "basic only": i.e. More...
vectors_iterator	vectors_begin ()
	Beginning of vectors container. More...
const_vectors_iterator	vectors_begin () const
	Beginning of vectors container. More...
vectors_iterator	vectors_end ()
	End of vectors container. More...
const_vectors_iterator	vectors_end () const
	End of vectors container. More...
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 NumericVector< Number > *sol=nullptr) const
Number	point_value (unsigned int var, const Point &p, const Elem &e, const NumericVector< Number > *sol=nullptr) const
Number	point_value (unsigned int var, const Point &p, const Elem *e) const
	Calls the version of point_value() which takes a reference. More...
Number	point_value (unsigned int var, const Point &p, const NumericVector< Number > *sol) const
	Calls the parallel version of point_value(). More...
Gradient	point_gradient (unsigned int var, const Point &p, const bool insist_on_success=true, const NumericVector< Number > *sol=nullptr) const
Gradient	point_gradient (unsigned int var, const Point &p, const Elem &e, const NumericVector< Number > *sol=nullptr) const
Gradient	point_gradient (unsigned int var, const Point &p, const Elem *e) const
	Calls the version of point_gradient() which takes a reference. More...
Gradient	point_gradient (unsigned int var, const Point &p, const NumericVector< Number > *sol) const
	Calls the parallel version of point_gradient(). More...
Tensor	point_hessian (unsigned int var, const Point &p, const bool insist_on_success=true, const NumericVector< Number > *sol=nullptr) const
Tensor	point_hessian (unsigned int var, const Point &p, const Elem &e, const NumericVector< Number > *sol=nullptr) const
Tensor	point_hessian (unsigned int var, const Point &p, const Elem *e) const
	Calls the version of point_hessian() which takes a reference. More...
Tensor	point_hessian (unsigned int var, const Point &p, const NumericVector< Number > *sol) const
	Calls the parallel version of point_hessian(). More...
void	local_dof_indices (const unsigned int var, std::set< dof_id_type > &var_indices) const
	Fills the std::set with the degrees of freedom on the local processor corresponding the the variable number passed in. More...
void	zero_variable (NumericVector< Number > &v, unsigned int var_num) const
	Zeroes all dofs in v that correspond to variable number var_num. More...
bool &	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_time_derivative (bool request_jacobian, DiffContext &)
	Adds the time derivative contribution on side of 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
unsigned int	_u_var
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 = true
	Flag to control whether reference count information is printed when print_info is called. More...

Private Member Functions
void	add_system_matrix ()
	Add the system matrix to the _matrices data structure. More...
void	add_system_rhs ()
	Add the system right-hand-side vector to the _vectors data structure. More...
Real	discrete_var_norm (const NumericVector< Number > &v, unsigned int var, FEMNormType norm_type) const
	Finds the discrete norm for the entries in the vector corresponding to Dofs associated with var. More...
template<typename iterator_type , typename InValType >
std::size_t	read_serialized_blocked_dof_objects (const dof_id_type n_objects, const iterator_type begin, const iterator_type end, const InValType dummy, Xdr &io, const std::vector< NumericVector< Number > * > &vecs, const unsigned int var_to_read=libMesh::invalid_uint) const
	Reads an input vector from the stream io and assigns the values to a set of DofObjects. More...
unsigned int	read_SCALAR_dofs (const unsigned int var, Xdr &io, NumericVector< Number > *vec) const
	Reads the SCALAR dofs from the stream io and assigns the values to the appropriate entries of vec. More...
template<typename InValType >
numeric_index_type	read_serialized_vector (Xdr &io, NumericVector< Number > *vec)
	Reads a vector for this System. More...
numeric_index_type	read_serialized_vector (Xdr &io, NumericVector< Number > &vec)
	Non-templated version for backward compatibility. More...
template<typename iterator_type >
std::size_t	write_serialized_blocked_dof_objects (const std::vector< const NumericVector< Number > * > &vecs, const dof_id_type n_objects, const iterator_type begin, const iterator_type end, Xdr &io, const unsigned int var_to_write=libMesh::invalid_uint) const
	Writes an output vector to the stream io for a set of DofObjects. More...
unsigned int	write_SCALAR_dofs (const NumericVector< Number > &vec, const unsigned int var, Xdr &io) const
	Writes the SCALAR dofs associated with var to the stream io. More...
dof_id_type	write_serialized_vector (Xdr &io, const NumericVector< Number > &vec) const
	Writes a vector for this System. More...

Private Attributes
std::vector< Real >	_numerical_jacobian_h_for_var
std::map< std::string, SparseMatrix< Number > * >	_matrices
	Some systems need an arbitrary number of matrices. More...
bool	_can_add_matrices
	true when additional matrices may still be added, false otherwise. More...
void(*	_init_system_function )(EquationSystems &es, const std::string &name)
	Function that initializes the system. More...
Initialization *	_init_system_object
	Object that initializes the system. More...
void(*	_assemble_system_function )(EquationSystems &es, const std::string &name)
	Function that assembles the system. More...
Assembly *	_assemble_system_object
	Object that assembles the system. More...
void(*	_constrain_system_function )(EquationSystems &es, const std::string &name)
	Function to impose constraints. More...
Constraint *	_constrain_system_object
	Object that constrains the system. More...
void(*	_qoi_evaluate_function )(EquationSystems &es, const std::string &name, const QoISet &qoi_indices)
	Function to evaluate quantity of interest. More...
QOI *	_qoi_evaluate_object
	Object to compute quantities of interest. More...
void(*	_qoi_evaluate_derivative_function )(EquationSystems &es, const std::string &name, const QoISet &qoi_indices, bool include_liftfunc, bool apply_constraints)
	Function to evaluate quantity of interest derivative. More...
QOIDerivative *	_qoi_evaluate_derivative_object
	Object to compute derivatives of quantities of interest. More...
std::unique_ptr< DofMap >	_dof_map
	Data structure describing the relationship between nodes, variables, etc... More...
EquationSystems &	_equation_systems
	Constant reference to the EquationSystems object used for the simulation. More...
MeshBase &	_mesh
	Constant reference to the mesh data structure used for the simulation. More...
const std::string	_sys_name
	A name associated with this system. More...
const unsigned int	_sys_number
	The number associated with this system. More...
std::vector< Variable >	_variables
	The Variable in this System. More...
std::vector< VariableGroup >	_variable_groups
	The VariableGroup in this System. More...
std::map< std::string, unsigned short int >	_variable_numbers
	The variable numbers corresponding to user-specified names, useful for name-based lookups. More...
bool	_active
	Flag stating if the system is active or not. More...
std::map< std::string, NumericVector< Number > * >	_vectors
	Some systems need an arbitrary number of vectors. More...
std::map< std::string, bool >	_vector_projections
	Holds true if a vector by that name should be projected onto a changed grid, false if it should be zeroed. More...
std::map< std::string, int >	_vector_is_adjoint
	Holds non-negative if a vector by that name should be projected using adjoint constraints/BCs, -1 if primal. More...
std::map< std::string, ParallelType >	_vector_types
	Holds the type of a vector. More...
bool	_solution_projection
	Holds true if the solution vector should be projected onto a changed grid, false if it should be zeroed. More...
bool	_basic_system_only
	Holds true if the components of more advanced system types (e.g. More...
bool	_is_initialized
	true when additional vectors and variables do not require immediate initialization, false otherwise. More...
bool	_identify_variable_groups
	true when VariableGroup structures should be automatically identified, false otherwise. More...
unsigned int	_additional_data_written
	This flag is used only when reading in a system from file. More...
std::vector< unsigned int >	_written_var_indices
	This vector is used only when reading in a system from file. More...
bool	adjoint_already_solved
	Has the adjoint problem already been solved? If the user sets adjoint_already_solved to true, we won't waste time solving it again. More...
bool	_hide_output
	Are we allowed to write this system to file? If _hide_output is true, then EquationSystems::write will ignore this system. More...

Detailed Description

Implements ODE: 2.1.

{u} = 5, u(0) = 0;

Definition at line 13 of file first_order_unsteady_solver_test.C.

Member Typedef Documentation

const_matrices_iterator

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

inherited

Definition at line 307 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 757 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 532 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 306 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 528 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 756 of file system.h.

Constructor & Destructor Documentation

ConstantFirstOrderODE()

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

inline

Definition at line 16 of file first_order_unsteady_solver_test.C.

    : FirstOrderScalarSystemBase(es, name_in, number_in)
  {}

Member Function Documentation

_eulerian_time_deriv()

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

inherited

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

Definition at line 102 of file diff_physics.C.

{
  // For any problem we need time derivative terms
  request_jacobian =
    this->element_time_derivative(request_jacobian, context);
 
  // For a moving mesh problem we may need the pseudoconvection term too
  return this->eulerian_residual(request_jacobian, context) &&
    request_jacobian;
}

References libMesh::DifferentiablePhysics::element_time_derivative(), and libMesh::DifferentiablePhysics::eulerian_residual().

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

activate()

void libMesh::System::activate ( )

inlineinherited

Activates the system.

Only active systems are solved.

Definition at line 2123 of file system.h.

{
  _active = true;
}

References libMesh::System::_active.

active()

bool libMesh::System::active ( ) const

inlineinherited

Returns

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

Definition at line 2115 of file system.h.

{
  return _active;
}

References libMesh::System::_active.

add_adjoint_rhs()

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

inherited

Returns

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

Definition at line 1009 of file system.C.

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

References libMesh::System::add_vector().

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

add_adjoint_solution()

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

inherited

Returns

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

Definition at line 945 of file system.C.

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

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

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

add_dot_var_dirichlet_bcs()

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

protectedinherited

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

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

Definition at line 230 of file diff_system.C.

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

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

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

add_matrix() [1/2]

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.

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

Definition at line 202 of file implicit_system.C.

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

References libMesh::ImplicitSystem::_can_add_matrices, libMesh::ImplicitSystem::_matrices, libMesh::SparseMatrix< T >::build(), libMesh::ParallelObject::comm(), and libMesh::ImplicitSystem::have_matrix().

Referenced by libMesh::ImplicitSystem::add_system_matrix(), libMesh::EigenTimeSolver::init(), main(), and libMesh::NewmarkSystem::NewmarkSystem().

add_matrix() [2/2]

template<template< typename > class MatrixType>

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

inlineinherited

Adds the additional matrix mat_name to this system.

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

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

Definition at line 454 of file implicit_system.h.

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

References libMesh::ImplicitSystem::_can_add_matrices, libMesh::ImplicitSystem::_matrices, libMesh::ParallelObject::comm(), and libMesh::ImplicitSystem::have_matrix().

add_second_order_dot_vars()

void libMesh::DifferentiableSystem::add_second_order_dot_vars ( )

protectedinherited

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

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

Definition at line 198 of file diff_system.C.

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

References libMesh::DifferentiablePhysics::_second_order_dot_vars, libMesh::Variable::active_subdomains(), libMesh::DifferentiableSystem::add_dot_var_dirichlet_bcs(), libMesh::System::add_variable(), libMesh::DifferentiablePhysics::get_second_order_vars(), libMesh::Variable::name(), libMesh::DifferentiablePhysics::time_evolving(), libMesh::Variable::type(), and libMesh::System::variable().

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

add_sensitivity_rhs()

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

inherited

Returns

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

Definition at line 1039 of file system.C.

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

References libMesh::System::add_vector().

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

add_sensitivity_solution()

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

inherited

Returns

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

Definition at line 894 of file system.C.

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

References libMesh::System::add_vector().

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

add_system_matrix()

void libMesh::ImplicitSystem::add_system_matrix ( )

privateinherited

Add the system matrix to the _matrices data structure.

Useful in initialization.

Definition at line 276 of file implicit_system.C.

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

References libMesh::ImplicitSystem::_matrices, libMesh::ImplicitSystem::add_matrix(), libMesh::libmesh_assert(), and libMesh::ImplicitSystem::matrix.

Referenced by libMesh::ImplicitSystem::clear(), and libMesh::ImplicitSystem::ImplicitSystem().

add_system_rhs()

void libMesh::ExplicitSystem::add_system_rhs ( )

privateinherited

Add the system right-hand-side vector to the _vectors data structure.

Useful in initialization.

Definition at line 96 of file explicit_system.C.

{
  // Possible that we cleared the _vectors but
  // forgot to update the rhs pointer?
  if (this->n_vectors() == 0)
    rhs = nullptr;
 
 
  // Only need to add the rhs if it isn't there
  // already!
  if (rhs == nullptr)
    rhs = &(this->add_vector ("RHS Vector", false));
 
  libmesh_assert(rhs);
}

References libMesh::System::add_vector(), libMesh::libmesh_assert(), libMesh::System::n_vectors(), and libMesh::ExplicitSystem::rhs.

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

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.

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

Returns

The index number for the new variable.

Definition at line 1069 of file system.C.

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

References libMesh::System::_variable_groups, libMesh::System::_variable_numbers, libMesh::System::_variables, libMesh::System::add_variables(), libMesh::System::identify_variable_groups(), libMesh::System::is_initialized(), libMesh::libmesh_assert(), libMesh::System::n_variable_groups(), libMesh::System::n_vars(), libMesh::System::variable_name(), and libMesh::System::variable_type().

Referenced by libMesh::DifferentiableSystem::add_second_order_dot_vars(), libMesh::System::add_variable(), assemble_and_solve(), OverlappingTestBase::init(), SolidSystem::init_data(), CurlCurlSystem::init_data(), HeatSystem::init_data(), SimpleRBConstruction::init_data(), main(), libMesh::ErrorVector::plot_error(), libMesh::System::read_header(), RationalMapTest< elem_type >::setUp(), FETest< order, family, elem_type >::setUp(), SlitMeshRefinedSystemTest::setUp(), MeshfunctionDFEM::test_mesh_function_dfem(), MeshfunctionDFEM::test_mesh_function_dfem_grad(), MeshFunctionTest::test_p_level(), SystemsTest::testAssemblyWithDgFemContext(), SystemsTest::testBlockRestrictedVarNDofs(), SystemsTest::testBoundaryProjectCube(), DofMapTest::testConstraintLoopDetection(), DefaultCouplingTest::testCoupling(), PointNeighborCouplingTest::testCoupling(), SystemsTest::testDofCouplingWithVarGroups(), DofMapTest::testDofOwner(), MeshInputTest::testDynaReadPatch(), MeshInputTest::testExodusCopyElementSolution(), MeshInputTest::testExodusWriteElementDataFromDiscontinuousNodalData(), EquationSystemsTest::testPostInitAddElem(), EquationSystemsTest::testPostInitAddRealSystem(), SystemsTest::testProjectCubeWithMeshFunction(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), SystemsTest::testProjectMatrix3D(), EquationSystemsTest::testRefineThenReinitPreserveFlags(), EquationSystemsTest::testReinitWithNodeElem(), EquationSystemsTest::testRepartitionThenReinit(), BoundaryInfoTest::testShellFaceConstraints(), and WriteVecAndScalar::testWrite().

add_variable() [2/2]

unsigned int libMesh::System::add_variable ( const std::string &  var, const Order  order = FIRST, const FEFamily  family = LAGRANGE, const std::set< subdomain_id_type > *const  active_subdomains = nullptr  )

inherited

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

Same as before, but assumes LAGRANGE as default value for FEType.family. If active_subdomains is either nullptr (the default) or points to an empty set, then it will be assumed that var has no subdomain restrictions

Definition at line 1148 of file system.C.

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

References libMesh::System::add_variable().

add_variables() [1/2]

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

inherited

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

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

Returns

The index number for the new variable.

Definition at line 1160 of file system.C.

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

References libMesh::System::_variable_groups, libMesh::System::_variable_numbers, libMesh::System::_variables, libMesh::System::is_initialized(), libMesh::libmesh_assert(), libMesh::System::n_components(), libMesh::System::n_vars(), libMesh::System::variable_name(), and libMesh::System::variable_type().

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

add_variables() [2/2]

unsigned int libMesh::System::add_variables ( const std::vector< std::string > &  vars, const Order  order = FIRST, const FEFamily  family = LAGRANGE, const std::set< subdomain_id_type > *const  active_subdomains = nullptr  )

inherited

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

Same as before, but assumes LAGRANGE as default value for FEType.family. If active_subdomains is either nullptr (the default) or points to an empty set, then it will be assumed that var has no subdomain restrictions

Definition at line 1213 of file system.C.

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

References libMesh::System::add_variables().

add_vector()

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

inherited

Adds the additional vector vec_name to this system.

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

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

Definition at line 661 of file system.C.

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

References libMesh::System::_dof_map, libMesh::System::_is_initialized, libMesh::System::_vector_is_adjoint, libMesh::System::_vector_projections, libMesh::System::_vector_types, libMesh::System::_vectors, libMesh::NumericVector< T >::build(), libMesh::ParallelObject::comm(), libMesh::GHOSTED, libMesh::System::have_vector(), libMesh::NumericVector< T >::init(), libMesh::System::n_dofs(), and libMesh::System::n_local_dofs().

Referenced by libMesh::System::add_adjoint_rhs(), libMesh::System::add_adjoint_solution(), libMesh::System::add_sensitivity_rhs(), libMesh::System::add_sensitivity_solution(), libMesh::ExplicitSystem::add_system_rhs(), libMesh::System::add_weighted_sensitivity_adjoint_solution(), libMesh::System::add_weighted_sensitivity_solution(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::SecondOrderUnsteadySolver::init(), libMesh::UnsteadySolver::init(), libMesh::OptimizationSystem::init_data(), libMesh::ContinuationSystem::init_data(), main(), libMesh::NewmarkSystem::NewmarkSystem(), libMesh::System::read_header(), libMesh::FrequencySystem::set_frequencies(), libMesh::FrequencySystem::set_frequencies_by_range(), and libMesh::FrequencySystem::set_frequencies_by_steps().

add_weighted_sensitivity_adjoint_solution()

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

inherited

Returns

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

Definition at line 977 of file system.C.

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

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

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

add_weighted_sensitivity_solution()

NumericVector< Number > & libMesh::System::add_weighted_sensitivity_solution ( )

inherited

Returns

A reference to the solution of the last weighted sensitivity solve Creates the vector if it doesn't already exist.

Definition at line 924 of file system.C.

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

References libMesh::System::add_vector().

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

adjoint_qoi_parameter_sensitivity()

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

overridevirtualinherited

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

Uses adjoint_solve() and the adjoint sensitivity method.

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

Reimplemented from libMesh::System.

Definition at line 686 of file implicit_system.C.

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

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

Referenced by main().

adjoint_solve()

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

overridevirtualinherited

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

Reimplemented from libMesh::ImplicitSystem.

Definition at line 164 of file diff_system.C.

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

References libMesh::ImplicitSystem::adjoint_solve(), libMesh::DifferentiableSystem::get_time_solver(), and libMesh::TimeSolver::set_is_adjoint().

Referenced by main().

assemble()

void libMesh::DifferentiableSystem::assemble ( )

overridevirtualinherited

Prepares matrix and rhs for matrix assembly.

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

Reimplemented from libMesh::ImplicitSystem.

Definition at line 145 of file diff_system.C.

{
  this->assembly(true, true);
}

References libMesh::DifferentiableSystem::assembly().

assemble_qoi()

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

overridevirtualinherited

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

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

Reimplemented from libMesh::ExplicitSystem.

Definition at line 1117 of file fem_system.C.

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

References libMesh::MeshBase::active_local_elements_begin(), libMesh::MeshBase::active_local_elements_end(), libMesh::ParallelObject::comm(), libMesh::DifferentiableSystem::diff_qoi, libMesh::System::get_mesh(), libMesh::QoISet::has_index(), mesh, libMesh::System::n_qois(), libMesh::DifferentiableQoI::parallel_op(), libMesh::Threads::parallel_reduce(), libMesh::System::qoi, libMesh::StoredRange< iterator_type, object_type >::reset(), and libMesh::System::update().

assemble_qoi_derivative()

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

overridevirtualinherited

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

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

Reimplemented from libMesh::ExplicitSystem.

Definition at line 1147 of file fem_system.C.

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

References libMesh::MeshBase::active_local_elements_begin(), libMesh::MeshBase::active_local_elements_end(), libMesh::System::add_adjoint_rhs(), libMesh::DifferentiableSystem::diff_qoi, libMesh::DifferentiableQoI::finalize_derivative(), libMesh::System::get_mesh(), libMesh::QoISet::has_index(), mesh, libMesh::System::n_qois(), libMesh::Threads::parallel_for(), libMesh::StoredRange< iterator_type, object_type >::reset(), libMesh::System::update(), and libMesh::NumericVector< T >::zero().

assemble_residual_derivatives()

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

overridevirtualinherited

Residual parameter derivative function.

Uses finite differences by default.

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

Can be overridden in derived classes.

Reimplemented from libMesh::System.

Definition at line 643 of file implicit_system.C.

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

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

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

assembly()

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

overridevirtualinherited

Prepares matrix or rhs for matrix assembly.

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

Implements libMesh::DifferentiableSystem.

Definition at line 850 of file fem_system.C.

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

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

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

attach_assemble_function()

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

inherited

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

Definition at line 1755 of file system.C.

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

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

Referenced by assemble_and_solve(), main(), SystemsTest::testAssemblyWithDgFemContext(), and SystemsTest::testDofCouplingWithVarGroups().

attach_assemble_object()

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

inherited

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

Definition at line 1774 of file system.C.

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

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

Referenced by main().

attach_constraint_function()

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

inherited

Register a user function for imposing constraints.

Definition at line 1790 of file system.C.

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

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

attach_constraint_object()

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

inherited

Register a user object for imposing constraints.

Definition at line 1809 of file system.C.

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

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

Referenced by DofMapTest::testConstraintLoopDetection().

attach_init_function()

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

inherited

Register a user function to use in initializing the system.

Definition at line 1720 of file system.C.

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

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

Referenced by main().

attach_init_object()

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

inherited

Register a user class to use to initialize the system.

Note

This is exclusive with the attach_init_function.

Definition at line 1739 of file system.C.

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

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

attach_physics()

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

inlineinherited

Attach external Physics object.

Definition at line 196 of file diff_system.h.

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

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

attach_qoi()

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

inlineinherited

Attach external QoI object.

Definition at line 224 of file diff_system.h.

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

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

Referenced by main().

attach_QOI_derivative()

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

inherited

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

Definition at line 1861 of file system.C.

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

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

attach_QOI_derivative_object()

void libMesh::System::attach_QOI_derivative_object ( QOIDerivative &  qoi_derivative )

inherited

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

Definition at line 1880 of file system.C.

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

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

attach_QOI_function()

void libMesh::System::attach_QOI_function ( void   fptrEquationSystems &es, const std::string &name, const QoISet &qoi_indices )

inherited

Register a user function for evaluating the quantities of interest, whose values should be placed in System::qoi.

Definition at line 1825 of file system.C.

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

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

attach_QOI_object()

void libMesh::System::attach_QOI_object ( QOI &  qoi )

inherited

Register a user object for evaluating the quantities of interest, whose values should be placed in System::qoi.

Definition at line 1845 of file system.C.

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

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

boundary_project_solution() [1/2]

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

inherited

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

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

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

Definition at line 1126 of file system_projection.C.

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

Referenced by SystemsTest::testBoundaryProjectCube().

boundary_project_solution() [2/2]

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

inherited

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

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

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

Definition at line 1109 of file system_projection.C.

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

References fptr(), and gptr().

boundary_project_vector() [1/2]

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

inherited

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

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

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

Definition at line 1162 of file system_projection.C.

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

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

boundary_project_vector() [2/2]

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

inherited

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

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

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

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

Definition at line 1144 of file system_projection.C.

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

References fptr(), and gptr().

build_context()

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

overridevirtualinherited

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

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

Reimplemented from libMesh::DifferentiableSystem.

Definition at line 1314 of file fem_system.C.

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

References libMesh::DifferentiableSystem::deltat, libMesh::DifferentiablePhysics::get_mesh_system(), libMesh::DifferentiablePhysics::get_mesh_x_var(), libMesh::DifferentiablePhysics::get_mesh_y_var(), libMesh::DifferentiablePhysics::get_mesh_z_var(), libMesh::DifferentiableSystem::get_physics(), libMesh::DifferentiableSystem::get_time_solver(), libMesh::TimeSolver::is_adjoint(), libMesh::DiffContext::is_adjoint(), libMesh::libmesh_assert(), libMesh::DiffContext::set_deltat_pointer(), libMesh::FEMContext::set_mesh_system(), libMesh::FEMContext::set_mesh_x_var(), libMesh::FEMContext::set_mesh_y_var(), and libMesh::FEMContext::set_mesh_z_var().

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

calculate_norm() [1/2]

Real libMesh::System::calculate_norm ( const NumericVector< Number > &  v, const SystemNorm &  norm, std::set< unsigned int > *  skip_dimensions = nullptr  ) const

inherited

Returns

A norm of the vector v, using component_norm and component_scale to choose and weight the norms of each variable.

Definition at line 1378 of file system.C.

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

References libMesh::System::_dof_map, libMesh::System::_mesh, std::abs(), libMesh::TypeVector< T >::add_scaled(), libMesh::TypeTensor< T >::add_scaled(), libMesh::FEGenericBase< OutputType >::build(), libMesh::NumericVector< T >::build(), libMesh::ParallelObject::comm(), libMesh::FEType::default_quadrature_rule(), dim, libMesh::DISCRETE_L1, libMesh::DISCRETE_L2, libMesh::DISCRETE_L_INF, libMesh::System::discrete_var_norm(), libMesh::DofMap::dof_indices(), libMesh::MeshBase::elem_dimensions(), libMesh::ReferenceElem::get(), libMesh::FEGenericBase< OutputType >::get_d2phi(), libMesh::System::get_dof_map(), libMesh::FEGenericBase< OutputType >::get_dphi(), libMesh::FEAbstract::get_JxW(), libMesh::System::get_mesh(), libMesh::FEGenericBase< OutputType >::get_phi(), libMesh::H1, libMesh::H1_SEMINORM, libMesh::H2, libMesh::H2_SEMINORM, libMesh::L1, libMesh::NumericVector< T >::l1_norm(), libMesh::L2, libMesh::NumericVector< T >::l2_norm(), libMesh::L_INF, libMesh::libmesh_assert(), libMesh::NumericVector< T >::linfty_norm(), libMesh::NumericVector< T >::localize(), libMesh::QBase::n_points(), libMesh::System::n_vars(), std::norm(), libMesh::TypeVector< T >::norm(), libMesh::TypeTensor< T >::norm(), libMesh::TensorTools::norm_sq(), libMesh::TypeVector< T >::norm_sq(), libMesh::TypeTensor< T >::norm_sq(), libMesh::Real, libMesh::FEAbstract::reinit(), libMesh::SERIAL, libMesh::NumericVector< T >::size(), std::sqrt(), libMesh::DofMap::variable_type(), libMesh::W1_INF_SEMINORM, libMesh::W2_INF_SEMINORM, and libMesh::SystemNorm::weight().

calculate_norm() [2/2]

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

inherited

Returns

A norm of variable var in the vector v, in the specified norm (e.g. L2, L_INF, H1)

Definition at line 1356 of file system.C.

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

References libMesh::DISCRETE_L1, libMesh::DISCRETE_L2, libMesh::DISCRETE_L_INF, libMesh::System::discrete_var_norm(), libMesh::L2, libMesh::System::n_vars(), and libMesh::Real.

Referenced by libMesh::AdaptiveTimeSolver::calculate_norm(), libMesh::UnsteadySolver::du(), main(), and output_norms().

clear()

void libMesh::DifferentiableSystem::clear ( )

overridevirtualinherited

Clear all the data structures associated with the system.

Reimplemented from libMesh::ImplicitSystem.

Reimplemented in libMesh::ContinuationSystem.

Definition at line 69 of file diff_system.C.

{
  // If we had an attached Physics object, delete it.
  if (this->_diff_physics != this)
    {
      delete this->_diff_physics;
      this->_diff_physics = this;
    }
  // If we had no attached Physics object, clear our own Physics data
  else
    this->clear_physics();
 
  // If we had an attached QoI object, delete it.
  if (this->diff_qoi != this)
    {
      delete this->diff_qoi;
      this->diff_qoi = this;
    }
  // If we had no attached QoI object, clear our own QoI data
  else
    this->clear_qoi();
 
  use_fixed_solution = false;
}

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

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

clear_physics()

void libMesh::DifferentiablePhysics::clear_physics ( )

virtualinherited

Clear any data structures associated with the physics.

Definition at line 33 of file diff_physics.C.

{
  _time_evolving.resize(0);
}

References libMesh::DifferentiablePhysics::_time_evolving.

Referenced by libMesh::DifferentiableSystem::clear(), and libMesh::DifferentiablePhysics::~DifferentiablePhysics().

clear_qoi()

virtual void libMesh::DifferentiableQoI::clear_qoi ( )

inlinevirtualinherited

Clear all the data structures associated with the QoI.

Definition at line 77 of file diff_qoi.h.

{}

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

clone()

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

inlineoverridevirtualinherited

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

Implements libMesh::DifferentiableQoI.

Definition at line 168 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 ( )

inlineoverridevirtualinherited

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

Implements libMesh::DifferentiablePhysics.

Definition at line 158 of file diff_system.h.

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

comm()

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

inlineinherited

Returns

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

Definition at line 94 of file parallel_object.h.

  { return _communicator; }

References libMesh::ParallelObject::_communicator.

Referenced by libMesh::__libmesh_petsc_diff_solver_jacobian(), libMesh::__libmesh_petsc_diff_solver_monitor(), libMesh::__libmesh_petsc_diff_solver_residual(), libMesh::__libmesh_tao_equality_constraints(), libMesh::__libmesh_tao_equality_constraints_jacobian(), libMesh::__libmesh_tao_gradient(), libMesh::__libmesh_tao_hessian(), libMesh::__libmesh_tao_inequality_constraints(), libMesh::__libmesh_tao_inequality_constraints_jacobian(), libMesh::__libmesh_tao_objective(), libMesh::MeshRefinement::_coarsen_elements(), libMesh::ExactSolution::_compute_error(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::BoundaryInfo::_find_id_maps(), libMesh::PetscLinearSolver< Number >::_petsc_shell_matrix_get_diagonal(), libMesh::SlepcEigenSolver< libMesh::Number >::_petsc_shell_matrix_get_diagonal(), libMesh::PetscLinearSolver< Number >::_petsc_shell_matrix_mult(), libMesh::SlepcEigenSolver< libMesh::Number >::_petsc_shell_matrix_mult(), libMesh::PetscLinearSolver< Number >::_petsc_shell_matrix_mult_add(), libMesh::EquationSystems::_read_impl(), libMesh::MeshRefinement::_refine_elements(), libMesh::MeshRefinement::_smooth_flags(), libMesh::DofMap::add_constraints_to_send_list(), add_cube_convex_hull_to_mesh(), libMesh::PetscDMWrapper::add_dofs_helper(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::TransientRBConstruction::add_IC_to_RB_space(), libMesh::ImplicitSystem::add_matrix(), libMesh::RBConstruction::add_scaled_matrix_and_vector(), libMesh::DynaIO::add_spline_constraints(), libMesh::System::add_vector(), libMesh::UnstructuredMesh::all_second_order(), libMesh::MeshTools::Modification::all_tri(), libMesh::LaplaceMeshSmoother::allgather_graph(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::TransientRBConstruction::allocate_data_structures(), libMesh::RBConstruction::allocate_data_structures(), libMesh::TransientRBConstruction::assemble_affine_expansion(), libMesh::FEMSystem::assemble_qoi(), libMesh::MeshCommunication::assign_global_indices(), libMesh::DofMap::attach_matrix(), libMesh::MeshTools::Generation::build_extrusion(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::PetscDMWrapper::build_section(), libMesh::PetscDMWrapper::build_sf(), libMesh::System::calculate_norm(), libMesh::DofMap::check_dirichlet_bcid_consistency(), libMesh::RBConstruction::compute_Fq_representor_innerprods(), libMesh::RBConstruction::compute_max_error_bound(), libMesh::Nemesis_IO_Helper::compute_num_global_elem_blocks(), libMesh::Nemesis_IO_Helper::compute_num_global_nodesets(), libMesh::Nemesis_IO_Helper::compute_num_global_sidesets(), libMesh::RBConstruction::compute_output_dual_innerprods(), libMesh::RBConstruction::compute_residual_dual_norm_slow(), libMesh::RBSCMConstruction::compute_SCM_bounds_on_training_set(), libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::MeshTools::create_bounding_box(), libMesh::DofMap::create_dof_constraints(), libMesh::MeshTools::create_nodal_bounding_box(), libMesh::MeshRefinement::create_parent_error_vector(), libMesh::MeshTools::create_processor_bounding_box(), libMesh::MeshTools::create_subdomain_bounding_box(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::DofMap::distribute_dofs(), DMlibMeshFunction(), DMlibMeshJacobian(), DMlibMeshSetSystem_libMesh(), DMVariableBounds_libMesh(), libMesh::DTKSolutionTransfer::DTKSolutionTransfer(), libMesh::MeshRefinement::eliminate_unrefined_patches(), libMesh::RBEIMConstruction::enrich_RB_space(), libMesh::TransientRBConstruction::enrich_RB_space(), libMesh::RBConstruction::enrich_RB_space(), libMesh::EpetraVector< T >::EpetraVector(), AssembleOptimization::equality_constraints(), libMesh::WeightedPatchRecoveryErrorEstimator::estimate_error(), libMesh::PatchRecoveryErrorEstimator::estimate_error(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::RBEIMConstruction::evaluate_mesh_function(), libMesh::MeshRefinement::flag_elements_by_elem_fraction(), libMesh::MeshRefinement::flag_elements_by_error_fraction(), libMesh::MeshRefinement::flag_elements_by_error_tolerance(), libMesh::MeshRefinement::flag_elements_by_mean_stddev(), libMesh::MeshRefinement::flag_elements_by_nelem_target(), libMesh::DofMap::gather_constraints(), libMesh::MeshfreeInterpolation::gather_remote_data(), libMesh::CondensedEigenSystem::get_eigenpair(), libMesh::DofMap::get_info(), libMesh::ImplicitSystem::get_linear_solver(), AssembleOptimization::inequality_constraints(), AssembleOptimization::inequality_constraints_jacobian(), libMesh::LocationMap< T >::init(), libMesh::TimeSolver::init(), libMesh::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_and_attach_petscdm(), libMesh::EigenSystem::init_matrices(), libMesh::OptimizationSystem::initialize_equality_constraints_storage(), libMesh::OptimizationSystem::initialize_inequality_constraints_storage(), libMesh::RBEIMConstruction::initialize_rb_construction(), integrate_function(), libMesh::MeshTools::libmesh_assert_consistent_distributed(), libMesh::MeshTools::libmesh_assert_consistent_distributed_nodes(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_new_node_procids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_topology_consistent_procids< Node >(), libMesh::MeshTools::libmesh_assert_valid_boundary_ids(), libMesh::MeshTools::libmesh_assert_valid_dof_ids(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_flags(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_object_ids(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_p_levels(), libMesh::MeshTools::libmesh_assert_valid_refinement_flags(), libMesh::MeshTools::libmesh_assert_valid_unique_ids(), libMesh::libmesh_petsc_preconditioner_apply(), libMesh::libmesh_petsc_snes_fd_residual(), libMesh::libmesh_petsc_snes_jacobian(), libMesh::libmesh_petsc_snes_mffd_residual(), libMesh::libmesh_petsc_snes_postcheck(), libMesh::libmesh_petsc_snes_residual(), libMesh::libmesh_petsc_snes_residual_helper(), libMesh::MeshRefinement::limit_level_mismatch_at_edge(), libMesh::MeshRefinement::limit_level_mismatch_at_node(), libMesh::MeshRefinement::limit_overrefined_boundary(), libMesh::MeshRefinement::limit_underrefined_boundary(), main(), libMesh::MeshRefinement::make_coarsening_compatible(), libMesh::MeshCommunication::make_elems_parallel_consistent(), libMesh::MeshRefinement::make_flags_parallel_consistent(), libMesh::MeshCommunication::make_new_node_proc_ids_parallel_consistent(), libMesh::MeshCommunication::make_new_nodes_parallel_consistent(), libMesh::MeshCommunication::make_node_ids_parallel_consistent(), libMesh::MeshCommunication::make_node_proc_ids_parallel_consistent(), libMesh::MeshCommunication::make_node_unique_ids_parallel_consistent(), libMesh::MeshCommunication::make_nodes_parallel_consistent(), libMesh::MeshCommunication::make_p_levels_parallel_consistent(), libMesh::MeshRefinement::make_refinement_compatible(), libMesh::TransientRBConstruction::mass_matrix_scaled_matvec(), libMesh::FEMSystem::mesh_position_set(), LinearElasticityWithContact::move_mesh(), libMesh::DistributedMesh::n_active_elem(), libMesh::MeshTools::n_active_levels(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::DofMap::n_constrained_dofs(), libMesh::BoundaryInfo::n_edge_conds(), libMesh::CondensedEigenSystem::n_global_non_condensed_dofs(), libMesh::MeshTools::n_levels(), libMesh::BoundaryInfo::n_nodeset_conds(), libMesh::MeshTools::n_p_levels(), libMesh::BoundaryInfo::n_shellface_conds(), libMesh::DistributedMesh::parallel_max_elem_id(), libMesh::DistributedMesh::parallel_max_node_id(), libMesh::ReplicatedMesh::parallel_max_unique_id(), libMesh::DistributedMesh::parallel_max_unique_id(), libMesh::DistributedMesh::parallel_n_elem(), libMesh::DistributedMesh::parallel_n_nodes(), libMesh::SparsityPattern::Build::parallel_sync(), libMesh::MeshTools::paranoid_n_levels(), libMesh::petsc_auto_fieldsplit(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::DofMap::print_dof_constraints(), FEMParameters::read(), libMesh::Nemesis_IO::read(), libMesh::XdrIO::read(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::System::read_header(), libMesh::RBEvaluation::read_in_vectors_from_multiple_files(), libMesh::System::read_legacy_data(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), libMesh::System::read_SCALAR_dofs(), libMesh::XdrIO::read_serialized_bc_names(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::System::read_serialized_vector(), libMesh::MeshRefinement::refine_and_coarsen_elements(), libMesh::DistributedMesh::renumber_dof_objects(), LinearElasticityWithContact::residual_and_jacobian(), OverlappingAlgebraicGhostingTest::run_ghosting_test(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), libMesh::DofMap::scatter_constraints(), libMesh::CheckpointIO::select_split_config(), libMesh::TransientRBConstruction::set_error_temporal_data(), libMesh::RBEIMConstruction::set_explicit_sys_subvector(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::PetscDiffSolver::setup_petsc_data(), libMesh::LaplaceMeshSmoother::smooth(), libMesh::split_mesh(), libMesh::BoundaryInfo::sync(), libMesh::MeshRefinement::test_level_one(), MeshfunctionDFEM::test_mesh_function_dfem(), MeshfunctionDFEM::test_mesh_function_dfem_grad(), MeshFunctionTest::test_p_level(), libMesh::MeshRefinement::test_unflagged(), SystemsTest::testBlockRestrictedVarNDofs(), PointLocatorTest::testLocator(), BoundaryInfoTest::testMesh(), SystemsTest::testProjectCubeWithMeshFunction(), CheckpointIOTest::testSplitter(), libMesh::MeshTools::total_weight(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::MeshfreeSolutionTransfer::transfer(), libMesh::TransientRBConstruction::truth_assembly(), libMesh::RBConstruction::truth_assembly(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::TransientRBConstruction::update_RB_initial_condition_all_N(), libMesh::RBEIMConstruction::update_RB_system_matrices(), libMesh::TransientRBConstruction::update_RB_system_matrices(), libMesh::RBConstruction::update_RB_system_matrices(), libMesh::TransientRBConstruction::update_residual_terms(), libMesh::RBConstruction::update_residual_terms(), libMesh::NameBasedIO::write(), libMesh::XdrIO::write(), libMesh::VTKIO::write_nodal_data(), libMesh::RBEvaluation::write_out_vectors(), libMesh::TransientRBConstruction::write_riesz_representors_to_files(), libMesh::RBConstruction::write_riesz_representors_to_files(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), libMesh::XdrIO::write_serialized_nodesets(), libMesh::RBDataSerialization::RBEvaluationSerialization::write_to_file(), libMesh::RBDataSerialization::TransientRBEvaluationSerialization::write_to_file(), libMesh::RBDataSerialization::RBEIMEvaluationSerialization::write_to_file(), and libMesh::RBDataSerialization::RBSCMEvaluationSerialization::write_to_file().

compare()

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

virtualinherited

Returns

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

Definition at line 514 of file system.C.

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

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

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

current_solution()

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

inherited

Returns

The current solution for the specified global DOF.

Definition at line 194 of file system.C.

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

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

Referenced by libMesh::ExactSolution::_compute_error(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::HPCoarsenTest::add_projection(), LinearElasticityWithContact::compute_stresses(), LinearElasticity::compute_stresses(), compute_stresses(), LargeDeformationElasticity::compute_stresses(), libMesh::ExactErrorEstimator::estimate_error(), main(), libMesh::WeightedPatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::PatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::HPCoarsenTest::select_refinement(), SolidSystem::side_time_derivative(), libMesh::EnsightIO::write_scalar_ascii(), and libMesh::EnsightIO::write_vector_ascii().

damping_residual()

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

inlinevirtualinherited

Subtracts a damping vector contribution on elem from elem_residual.

This method is not used in first-order-in-time problems. For second-order-in-time problems, this is the \( C(u,\ddot{u})\ddot{u} \) term. This method is only called for UnsteadySolver-based TimeSolvers.

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

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

Reimplemented in SecondOrderScalarSystemFirstOrderTimeSolverBase, and SecondOrderScalarSystemSecondOrderTimeSolverBase.

Definition at line 375 of file diff_physics.h.

                                                {
    return request_jacobian;
  }

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

deactivate()

void libMesh::System::deactivate ( )

inlineinherited

Deactivates the system.

Only active systems are solved.

Definition at line 2131 of file system.h.

{
  _active = false;
}

References libMesh::System::_active.

disable_cache()

void libMesh::ImplicitSystem::disable_cache ( )

overridevirtualinherited

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

Should be overridden in derived systems.

Reimplemented from libMesh::System.

Definition at line 293 of file implicit_system.C.

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

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

disable_print_counter_info()

void libMesh::ReferenceCounter::disable_print_counter_info ( )

staticinherited

Definition at line 106 of file reference_counter.C.

{
  _enable_print_counter = false;
  return;
}

References libMesh::ReferenceCounter::_enable_print_counter.

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

discrete_var_norm()

Real libMesh::System::discrete_var_norm ( const NumericVector< Number > &  v, unsigned int  var, FEMNormType  norm_type  ) const

privateinherited

Finds the discrete norm for the entries in the vector corresponding to Dofs associated with var.

Definition at line 1337 of file system.C.

{
  std::set<dof_id_type> var_indices;
  local_dof_indices(var, var_indices);
 
  if (norm_type == DISCRETE_L1)
    return v.subset_l1_norm(var_indices);
  if (norm_type == DISCRETE_L2)
    return v.subset_l2_norm(var_indices);
  if (norm_type == DISCRETE_L_INF)
    return v.subset_linfty_norm(var_indices);
  else
    libmesh_error_msg("Invalid norm_type = " << norm_type);
}

References libMesh::DISCRETE_L1, libMesh::DISCRETE_L2, libMesh::DISCRETE_L_INF, libMesh::System::local_dof_indices(), libMesh::NumericVector< T >::subset_l1_norm(), libMesh::NumericVector< T >::subset_l2_norm(), and libMesh::NumericVector< T >::subset_linfty_norm().

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

element_constraint()

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

inlinevirtualinherited

Adds the constraint contribution on elem to elem_residual.

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

Users may need to reimplement this for their particular PDE.

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

Reimplemented in CoupledSystem, and NavierSystem.

Definition at line 143 of file diff_physics.h.

                                                  {
    return request_jacobian;
  }

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

element_postprocess()

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

inlinevirtualinherited

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

Reimplemented in LaplaceSystem, LaplaceSystem, and PoissonSystem.

Definition at line 281 of file diff_system.h.

{}

element_qoi()

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

inlinevirtualinherited

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

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

Reimplemented in LaplaceQoI.

Definition at line 110 of file diff_qoi.h.

  {}

element_qoi_derivative()

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

inlinevirtualinherited

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

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

Reimplemented in LaplaceSystem, LaplaceSystem, LaplaceQoI, and HeatSystem.

Definition at line 122 of file diff_qoi.h.

  {}

element_time_derivative()

virtual bool FirstOrderScalarSystemBase::element_time_derivative ( bool  request_jacobian, DiffContext &  context  )

inlineoverridevirtualinherited

Note the nonlinear residual is F(u)-M(u)

{u}

Reimplemented from libMesh::DifferentiablePhysics.

Reimplemented in SecondOrderScalarSystemFirstOrderTimeSolverBase.

Definition at line 118 of file time_solver_test_common.h.

  {
    FEMContext & c = cast_ref<FEMContext &>(context);
    DenseSubVector<Number> & Fu = c.get_elem_residual(_u_var);
 
    const unsigned int n_u_dofs =
      cast_int<unsigned int>(c.get_dof_indices(_u_var).size());
    unsigned int n_qpoints = c.get_element_qrule().n_points();
 
    for (unsigned int qp=0; qp != n_qpoints; qp++)
      {
        Number Fval = this->F(c,qp);
 
        for (unsigned int i=0; i != n_u_dofs; i++)
          Fu(i) += Fval;
      }
 
    return request_jacobian;
  }

References libMesh::DiffContext::get_dof_indices(), libMesh::DiffContext::get_elem_residual(), libMesh::FEMContext::get_element_qrule(), and libMesh::QBase::n_points().

enable_print_counter_info()

void libMesh::ReferenceCounter::enable_print_counter_info ( )

staticinherited

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

Definition at line 100 of file reference_counter.C.

{
  _enable_print_counter = true;
  return;
}

References libMesh::ReferenceCounter::_enable_print_counter.

eulerian_residual() [1/2]

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

inlinevirtualinherited

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

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

Reimplemented in SolidSystem, and libMesh::FEMPhysics.

Definition at line 295 of file diff_physics.h.

                                                 {
    return request_jacobian;
  }

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

eulerian_residual() [2/2]

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.

Definition at line 38 of file fem_physics.C.

{
  // Only calculate a mesh movement residual if it's necessary
  if (!_mesh_sys)
    return request_jacobian;
 
  libmesh_not_implemented();
 
#if 0
  FEMContext & context = cast_ref<FEMContext &>(c);
 
  // This function only supports fully coupled mesh motion for now
  libmesh_assert_equal_to (_mesh_sys, this);
 
  unsigned int n_qpoints = (context.get_element_qrule())->n_points();
 
  const unsigned int n_x_dofs = (_mesh_x_var == libMesh::invalid_uint) ?
    0 : context.dof_indices_var[_mesh_x_var].size();
  const unsigned int n_y_dofs = (_mesh_y_var == libMesh::invalid_uint) ?
    0 : context.dof_indices_var[_mesh_y_var].size();
  const unsigned int n_z_dofs = (_mesh_z_var == libMesh::invalid_uint) ?
    0 : context.dof_indices_var[_mesh_z_var].size();
 
  const unsigned int mesh_xyz_var = n_x_dofs ? _mesh_x_var :
    (n_y_dofs ? _mesh_y_var :
     (n_z_dofs ? _mesh_z_var :
      libMesh::invalid_uint));
 
  // If we're our own _mesh_sys, we'd better be in charge of
  // at least one coordinate, and we'd better have the same
  // FE type for all coordinates we are in charge of
  libmesh_assert_not_equal_to (mesh_xyz_var, libMesh::invalid_uint);
  libmesh_assert(!n_x_dofs || context.element_fe_var[_mesh_x_var] ==
                 context.element_fe_var[mesh_xyz_var]);
  libmesh_assert(!n_y_dofs || context.element_fe_var[_mesh_y_var] ==
                 context.element_fe_var[mesh_xyz_var]);
  libmesh_assert(!n_z_dofs || context.element_fe_var[_mesh_z_var] ==
                 context.element_fe_var[mesh_xyz_var]);
 
  const std::vector<std::vector<Real>>     & psi =
    context.element_fe_var[mesh_xyz_var]->get_phi();
 
  for (auto var : IntRange<unsigned int>(0, context.n_vars()))
    {
      // Mesh motion only affects time-evolving variables
      if (this->is_time_evolving(var))
        continue;
 
      // The mesh coordinate variables themselves are Lagrangian,
      // not Eulerian, and no convective term is desired.
      if (/*_mesh_sys == this && */
          (var == _mesh_x_var ||
           var == _mesh_y_var ||
           var == _mesh_z_var))
        continue;
 
      // Some of this code currently relies on the assumption that
      // we can pull mesh coordinate data from our own system
      if (_mesh_sys != this)
        libmesh_not_implemented();
 
      // This residual should only be called by unsteady solvers:
      // if the mesh is steady, there's no mesh convection term!
      UnsteadySolver * unsteady;
      if (this->time_solver->is_steady())
        return request_jacobian;
      else
        unsteady = cast_ptr<UnsteadySolver*>(this->time_solver.get());
 
      const std::vector<Real> & JxW =
        context.element_fe_var[var]->get_JxW();
 
      const std::vector<std::vector<Real>> & phi =
        context.element_fe_var[var]->get_phi();
 
      const std::vector<std::vector<RealGradient>> & dphi =
        context.element_fe_var[var]->get_dphi();
 
      const unsigned int n_u_dofs = context.dof_indices_var[var].size();
 
      DenseSubVector<Number> & Fu = *context.elem_subresiduals[var];
      DenseSubMatrix<Number> & Kuu = *context.elem_subjacobians[var][var];
 
      DenseSubMatrix<Number> * Kux = n_x_dofs ?
        context.elem_subjacobians[var][_mesh_x_var] : nullptr;
      DenseSubMatrix<Number> * Kuy = n_y_dofs ?
        context.elem_subjacobians[var][_mesh_y_var] : nullptr;
      DenseSubMatrix<Number> * Kuz = n_z_dofs ?
        context.elem_subjacobians[var][_mesh_z_var] : nullptr;
 
      std::vector<Real> delta_x(n_x_dofs, 0.);
      std::vector<Real> delta_y(n_y_dofs, 0.);
      std::vector<Real> delta_z(n_z_dofs, 0.);
 
      for (unsigned int i = 0; i != n_x_dofs; ++i)
        {
          unsigned int j = context.dof_indices_var[_mesh_x_var][i];
          delta_x[i] = libmesh_real(this->current_solution(j)) -
            libmesh_real(unsteady->old_nonlinear_solution(j));
        }
 
      for (unsigned int i = 0; i != n_y_dofs; ++i)
        {
          unsigned int j = context.dof_indices_var[_mesh_y_var][i];
          delta_y[i] = libmesh_real(this->current_solution(j)) -
            libmesh_real(unsteady->old_nonlinear_solution(j));
        }
 
      for (unsigned int i = 0; i != n_z_dofs; ++i)
        {
          unsigned int j = context.dof_indices_var[_mesh_z_var][i];
          delta_z[i] = libmesh_real(this->current_solution(j)) -
            libmesh_real(unsteady->old_nonlinear_solution(j));
        }
 
      for (unsigned int qp = 0; qp != n_qpoints; ++qp)
        {
          Gradient grad_u = context.interior_gradient(var, qp);
          RealGradient convection(0.);
 
          for (unsigned int i = 0; i != n_x_dofs; ++i)
            convection(0) += delta_x[i] * psi[i][qp];
          for (unsigned int i = 0; i != n_y_dofs; ++i)
            convection(1) += delta_y[i] * psi[i][qp];
          for (unsigned int i = 0; i != n_z_dofs; ++i)
            convection(2) += delta_z[i] * psi[i][qp];
 
          for (unsigned int i = 0; i != n_u_dofs; ++i)
            {
              Number JxWxPhiI = JxW[qp] * phi[i][qp];
              Fu(i) += (convection * grad_u) * JxWxPhiI;
              if (request_jacobian)
                {
                  Number JxWxPhiI = JxW[qp] * phi[i][qp];
                  for (unsigned int j = 0; j != n_u_dofs; ++j)
                    Kuu(i,j) += JxWxPhiI * (convection * dphi[j][qp]);
 
                  Number JxWxPhiIoverDT = JxWxPhiI/this->deltat;
 
                  Number JxWxPhiIxDUDXoverDT = JxWxPhiIoverDT * grad_u(0);
                  for (unsigned int j = 0; j != n_x_dofs; ++j)
                    (*Kux)(i,j) += JxWxPhiIxDUDXoverDT * psi[j][qp];
 
                  Number JxWxPhiIxDUDYoverDT = JxWxPhiIoverDT * grad_u(1);
                  for (unsigned int j = 0; j != n_y_dofs; ++j)
                    (*Kuy)(i,j) += JxWxPhiIxDUDYoverDT * psi[j][qp];
 
                  Number JxWxPhiIxDUDZoverDT = JxWxPhiIoverDT * grad_u(2);
                  for (unsigned int j = 0; j != n_z_dofs; ++j)
                    (*Kuz)(i,j) += JxWxPhiIxDUDZoverDT * psi[j][qp];
                }
            }
        }
    }
#endif // 0
 
  return request_jacobian;
}

References libMesh::DifferentiablePhysics::_mesh_sys, libMesh::DifferentiablePhysics::_mesh_x_var, libMesh::DifferentiablePhysics::_mesh_y_var, libMesh::DifferentiablePhysics::_mesh_z_var, libMesh::FEMContext::get_element_qrule(), libMesh::FEMContext::interior_gradient(), libMesh::invalid_uint, libMesh::DifferentiablePhysics::is_time_evolving(), libMesh::libmesh_assert(), libMesh::libmesh_real(), libMesh::DiffContext::n_vars(), and libMesh::UnsteadySolver::old_nonlinear_solution().

F() [1/2]

virtual Number ConstantFirstOrderODE::F ( FEMContext &  , unsigned int    )

inlinevirtual

Definition at line 22 of file first_order_unsteady_solver_test.C.

  { return 5.0; }

F() [2/2]

virtual Number FirstOrderScalarSystemBase::F ( FEMContext &  context, unsigned int  qp  )

pure virtualinherited

Value of F(u)

finalize_derivative()

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.

Definition at line 53 of file diff_qoi.C.

{
  // by default, do nothing
}

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

forward_qoi_parameter_sensitivity()

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

overridevirtualinherited

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

Uses the forward sensitivity method.

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

Reimplemented from libMesh::System.

Definition at line 796 of file implicit_system.C.

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

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

get_adjoint_rhs() [1/2]

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

inherited

Returns

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

Definition at line 1019 of file system.C.

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

References libMesh::System::get_vector().

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

get_adjoint_rhs() [2/2]

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

inherited

Returns

A reference to one of the system's adjoint rhs vectors, by default the one corresponding to the first qoi.

Definition at line 1029 of file system.C.

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

References libMesh::System::get_vector().

get_adjoint_solution() [1/2]

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

inherited

Returns

A reference to one of the system's adjoint solution vectors, by default the one corresponding to the first qoi.

Definition at line 957 of file system.C.

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

References libMesh::System::get_vector().

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::ImplicitSystem::adjoint_solve(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::AdjointResidualErrorEstimator::estimate_error(), main(), HeatSystem::perturb_accumulate_residuals(), libMesh::ImplicitSystem::qoi_parameter_hessian(), libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product(), and libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve().

get_adjoint_solution() [2/2]

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

inherited

Returns

A reference to one of the system's adjoint solution vectors, by default the one corresponding to the first qoi.

Definition at line 967 of file system.C.

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

References libMesh::System::get_vector().

get_all_variable_numbers()

void libMesh::System::get_all_variable_numbers ( std::vector< unsigned int > &  all_variable_numbers ) const

inherited

Fills all_variable_numbers with all the variable numbers for the variables that have been added to this system.

Definition at line 1240 of file system.C.

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

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

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

get_dof_map() [1/2]

DofMap & libMesh::System::get_dof_map ( )

inlineinherited

Returns

A writable reference to this system's _dof_map.

Definition at line 2107 of file system.h.

{
  return *_dof_map;
}

References libMesh::System::_dof_map.

get_dof_map() [2/2]

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

inlineinherited

Returns

A constant reference to this system's _dof_map.

Definition at line 2099 of file system.h.

{
  return *_dof_map;
}

References libMesh::System::_dof_map.

Referenced by libMesh::__libmesh_petsc_diff_solver_jacobian(), libMesh::__libmesh_petsc_diff_solver_residual(), libMesh::ExactSolution::_compute_error(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::DifferentiableSystem::add_dot_var_dirichlet_bcs(), libMesh::HPCoarsenTest::add_projection(), libMesh::RBConstruction::add_scaled_matrix_and_vector(), libMesh::UnsteadySolver::adjoint_advance_timestep(), libMesh::ImplicitSystem::adjoint_solve(), libMesh::NewmarkSolver::advance_timestep(), libMesh::UnsteadySolver::advance_timestep(), libMesh::EquationSystems::allgather(), libMesh::TransientRBConstruction::allocate_data_structures(), libMesh::RBConstruction::allocate_data_structures(), assemble(), LinearElasticity::assemble(), assemble_1D(), AssembleOptimization::assemble_A_and_F(), assemble_and_solve(), assemble_biharmonic(), assemble_elasticity(), assemble_ellipticdg(), assemble_helmholtz(), assemble_laplace(), assemble_mass(), assemble_matrices(), assemble_matrix_and_rhs(), assemble_poisson(), assemble_SchroedingerEquation(), assemble_shell(), assemble_stokes(), assemble_wave(), libMesh::EquationSystems::build_discontinuous_solution_vector(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::PetscDMWrapper::build_sf(), libMesh::System::calculate_norm(), compute_jacobian(), compute_residual(), LinearElasticityWithContact::compute_stresses(), LinearElasticity::compute_stresses(), compute_stresses(), LargeDeformationElasticity::compute_stresses(), libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), MyConstraint::constrain(), libMesh::ExodusII_IO::copy_scalar_solution(), DMCreateDomainDecomposition_libMesh(), DMCreateFieldDecomposition_libMesh(), DMlibMeshFunction(), DMlibMeshJacobian(), DMlibMeshSetSystem_libMesh(), libMesh::RBEIMConstruction::enrich_RB_space(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::RBEIMAssembly::evaluate_basis_function(), libMesh::System::get_info(), libMesh::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_and_attach_petscdm(), libMesh::SecondOrderUnsteadySolver::init_data(), libMesh::UnsteadySolver::init_data(), HeatSystem::init_data(), SimpleRBConstruction::init_data(), LaplaceSystem::init_dirichlet_bcs(), libMesh::RBEIMConstruction::init_dof_map_between_systems(), libMesh::EigenSystem::init_matrices(), libMesh::ImplicitSystem::init_matrices(), libMesh::CondensedEigenSystem::initialize_condensed_dofs(), libMesh::OptimizationSystem::initialize_equality_constraints_storage(), libMesh::RBEIMAssembly::initialize_fe(), libMesh::OptimizationSystem::initialize_inequality_constraints_storage(), libMesh::RBEIMConstruction::initialize_rb_construction(), LaplaceYoung::jacobian(), LargeDeformationElasticity::jacobian(), libMesh::libmesh_petsc_snes_fd_residual(), libMesh::libmesh_petsc_snes_jacobian(), libMesh::libmesh_petsc_snes_mffd_residual(), libMesh::libmesh_petsc_snes_residual(), libMesh::libmesh_petsc_snes_residual_helper(), libMesh::System::local_dof_indices(), AssembleOptimization::lower_and_upper_bounds(), main(), libMesh::DofMap::max_constraint_error(), LinearElasticityWithContact::move_mesh(), libMesh::DGFEMContext::neighbor_side_fe_reinit(), libMesh::UnsteadySolver::old_nonlinear_solution(), libMesh::SecondOrderUnsteadySolver::old_solution_accel(), libMesh::SecondOrderUnsteadySolver::old_solution_rate(), libMesh::WeightedPatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::PatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::RBSCMConstruction::perform_SCM_greedy(), libMesh::petsc_auto_fieldsplit(), libMesh::ErrorVector::plot_error(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::FEMContext::pre_fe_reinit(), libMesh::RBEIMAssembly::RBEIMAssembly(), libMesh::RBEIMConstruction::RBEIMConstruction(), libMesh::System::re_update(), libMesh::System::read_parallel_data(), libMesh::System::read_SCALAR_dofs(), libMesh::SecondOrderUnsteadySolver::reinit(), libMesh::UnsteadySolver::reinit(), libMesh::EigenSystem::reinit(), libMesh::ImplicitSystem::reinit(), libMesh::System::reinit_constraints(), libMesh::EquationSystems::reinit_solutions(), LaplaceYoung::residual(), LargeDeformationElasticity::residual(), LinearElasticityWithContact::residual_and_jacobian(), libMesh::UnsteadySolver::retrieve_timestep(), OverlappingAlgebraicGhostingTest::run_ghosting_test(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), libMesh::HPCoarsenTest::select_refinement(), libMesh::ImplicitSystem::sensitivity_solve(), libMesh::RBConstruction::set_context_solution_vec(), libMesh::PetscDMWrapper::set_point_range_in_section(), set_system_parameters(), FETest< order, family, elem_type >::setUp(), SolidSystem::side_time_derivative(), libMesh::NewtonSolver::solve(), libMesh::PetscDiffSolver::solve(), libMesh::RBConstruction::solve_for_matrix_and_rhs(), MeshfunctionDFEM::test_mesh_function_dfem(), MeshfunctionDFEM::test_mesh_function_dfem_grad(), MeshFunctionTest::test_p_level(), SystemsTest::testBlockRestrictedVarNDofs(), DofMapTest::testConstraintLoopDetection(), DefaultCouplingTest::testCoupling(), PointNeighborCouplingTest::testCoupling(), EquationSystemsTest::testDisableDefaultGhosting(), SystemsTest::testDofCouplingWithVarGroups(), DofMapTest::testDofOwner(), MeshInputTest::testDynaReadPatch(), MeshInputTest::testExodusWriteElementDataFromDiscontinuousNodalData(), SystemsTest::testProjectCubeWithMeshFunction(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), SystemsTest::testProjectMatrix3D(), BoundaryInfoTest::testShellFaceConstraints(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::BoundaryVolumeSolutionTransfer::transfer_boundary_volume(), libMesh::RBEIMConstruction::truth_solve(), libMesh::RBEIMConstruction::update_RB_system_matrices(), libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve(), libMesh::ImplicitSystem::weighted_sensitivity_solve(), libMesh::Nemesis_IO_Helper::write_nodal_solution(), libMesh::System::write_parallel_data(), libMesh::EnsightIO::write_scalar_ascii(), libMesh::System::write_SCALAR_dofs(), libMesh::EnsightIO::write_vector_ascii(), and libMesh::RBConstruction::zero_constrained_dofs_on_vector().

get_equation_systems() [1/2]

EquationSystems& libMesh::System::get_equation_systems ( )

inlineinherited

Returns

A reference to this system's parent EquationSystems object.

Definition at line 725 of file system.h.

{ return _equation_systems; }

References libMesh::System::_equation_systems.

get_equation_systems() [2/2]

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

inlineinherited

Returns

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

Definition at line 720 of file system.h.

{ return _equation_systems; }

References libMesh::System::_equation_systems.

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::RBSCMConstruction::add_scaled_symm_Aq(), libMesh::NewmarkSystem::clear(), libMesh::FrequencySystem::clear_all(), compute_jacobian(), compute_residual(), LinearElasticityWithContact::compute_stresses(), SolidSystem::element_time_derivative(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::AdjointResidualErrorEstimator::estimate_error(), libMesh::ExactErrorEstimator::find_squared_element_error(), libMesh::RBEIMConstruction::get_explicit_system(), libMesh::ImplicitSystem::get_linear_solve_parameters(), SolidSystem::init_data(), HeatSystem::init_data(), libMesh::FrequencySystem::init_data(), libMesh::RBEIMConstruction::init_data(), libMesh::RBEIMConstruction::initialize_rb_construction(), LaplaceYoung::jacobian(), libMesh::RBSCMConstruction::load_matrix_B(), LinearElasticityWithContact::move_mesh(), libMesh::FrequencySystem::n_frequencies(), libMesh::RBSCMConstruction::perform_SCM_greedy(), libMesh::RBEIMConstruction::plot_parametrized_functions_in_training_set(), libMesh::System::point_gradient(), libMesh::System::point_value(), LaplaceYoung::residual(), LinearElasticityWithContact::residual_and_jacobian(), SolidSystem::save_initial_mesh(), libMesh::FrequencySystem::set_current_frequency(), libMesh::FrequencySystem::set_frequencies(), libMesh::FrequencySystem::set_frequencies_by_range(), libMesh::FrequencySystem::set_frequencies_by_steps(), libMesh::NewmarkSystem::set_newmark_parameters(), libMesh::NonlinearImplicitSystem::set_solver_parameters(), SolidSystem::side_time_derivative(), libMesh::CondensedEigenSystem::solve(), libMesh::EigenSystem::solve(), libMesh::FrequencySystem::solve(), libMesh::LinearImplicitSystem::solve(), libMesh::RBConstruction::solve_for_matrix_and_rhs(), MeshFunctionTest::test_p_level(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::MeshfreeSolutionTransfer::transfer(), libMesh::DirectSolutionTransfer::transfer(), libMesh::DTKSolutionTransfer::transfer(), libMesh::TransientRBConstruction::truth_solve(), libMesh::RBEIMConstruction::truth_solve(), libMesh::RBConstruction::truth_solve(), and libMesh::WrappedFunction< Output >::WrappedFunction().

get_first_order_vars()

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

inlineinherited

Returns

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

Definition at line 518 of file diff_physics.h.

  { return _first_order_vars; }

References libMesh::DifferentiablePhysics::_first_order_vars.

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

get_info() [1/2]

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

staticinherited

Gets a string containing the reference information.

Definition at line 47 of file reference_counter.C.

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

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

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

get_info() [2/2]

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

inherited

Returns

A string containing information about the system.

Definition at line 1636 of file system.C.

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

References libMesh::FEType::family, libMesh::System::get_dof_map(), libMesh::DofMap::get_info(), libMesh::System::n_constrained_dofs(), libMesh::System::n_dofs(), libMesh::System::n_local_constrained_dofs(), libMesh::System::n_local_dofs(), libMesh::System::n_matrices(), libMesh::System::n_variable_groups(), libMesh::VariableGroup::n_variables(), libMesh::System::n_vectors(), libMesh::VariableGroup::name(), libMesh::System::name(), libMesh::System::number(), libMesh::System::system_type(), libMesh::Variable::type(), libMesh::DofMap::variable_group(), and libMesh::System::variable_group().

get_linear_solve_parameters()

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

overridevirtualinherited

Returns

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

Reimplemented from libMesh::ImplicitSystem.

Definition at line 184 of file diff_system.C.

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

References libMesh::libmesh_assert(), and libMesh::DifferentiableSystem::time_solver.

get_linear_solver()

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

overridevirtualinherited

Returns

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

Reimplemented from libMesh::ImplicitSystem.

Definition at line 175 of file diff_system.C.

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

References libMesh::libmesh_assert(), and libMesh::DifferentiableSystem::time_solver.

Referenced by main().

get_matrix() [1/2]

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

inherited

Returns

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

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

Definition at line 269 of file implicit_system.C.

{
  return *(libmesh_map_find(_matrices, mat_name));
}

References libMesh::ImplicitSystem::_matrices.

get_matrix() [2/2]

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

inherited

Returns

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

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

Definition at line 262 of file implicit_system.C.

{
  return *(libmesh_map_find(_matrices, mat_name));
}

References libMesh::ImplicitSystem::_matrices.

Referenced by add_M_C_K_helmholtz(), assemble(), assemble_helmholtz(), libMesh::NewmarkSystem::compute_matrix(), main(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), libMesh::EigenTimeSolver::solve(), and libMesh::NewmarkSystem::update_rhs().

get_mesh() [1/2]

MeshBase & libMesh::System::get_mesh ( )

inlineinherited

Returns

A reference to this systems's _mesh.

Definition at line 2091 of file system.h.

{
  return _mesh;
}

References libMesh::System::_mesh.

get_mesh() [2/2]

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

inlineinherited

Returns

A constant reference to this systems's _mesh.

Definition at line 2083 of file system.h.

{
  return _mesh;
}

References libMesh::System::_mesh.

Referenced by libMesh::ExactSolution::_compute_error(), LinearElasticityWithContact::add_contact_edge_elements(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::HPCoarsenTest::add_projection(), libMesh::RBConstruction::add_scaled_matrix_and_vector(), AssembleOptimization::assemble_A_and_F(), libMesh::FEMSystem::assemble_qoi(), libMesh::FEMSystem::assemble_qoi_derivative(), libMesh::FEMSystem::assembly(), AssemblyA0::boundary_assembly(), AssemblyF0::boundary_assembly(), AssemblyA1::boundary_assembly(), AssemblyF1::boundary_assembly(), AssemblyF2::boundary_assembly(), AssemblyA2::boundary_assembly(), libMesh::System::calculate_norm(), compute_jacobian(), compute_residual(), LinearElasticityWithContact::compute_stresses(), DMCreateDomainDecomposition_libMesh(), DMCreateFieldDecomposition_libMesh(), DMlibMeshSetSystem_libMesh(), SolidSystem::element_time_derivative(), libMesh::RBEIMConstruction::enrich_RB_space(), libMesh::WeightedPatchRecoveryErrorEstimator::estimate_error(), libMesh::PatchRecoveryErrorEstimator::estimate_error(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::AdjointResidualErrorEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::GenericProjector(), LinearElasticityWithContact::get_least_and_max_gap_function(), libMesh::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_and_attach_petscdm(), SolidSystem::init_data(), libMesh::System::init_data(), libMesh::RBEIMConstruction::init_dof_map_between_systems(), libMesh::EigenSystem::init_matrices(), libMesh::ImplicitSystem::init_matrices(), LinearElasticityWithContact::initialize_contact_load_paths(), libMesh::RBEIMAssembly::initialize_fe(), libMesh::System::local_dof_indices(), libMesh::DofMap::max_constraint_error(), libMesh::FEMSystem::mesh_position_get(), libMesh::FEMSystem::mesh_position_set(), LinearElasticityWithContact::move_mesh(), libMesh::WeightedPatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::PatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::petsc_auto_fieldsplit(), libMesh::RBEIMConstruction::plot_parametrized_functions_in_training_set(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::FEMSystem::postprocess(), libMesh::System::read_header(), libMesh::RBEvaluation::read_in_vectors_from_multiple_files(), libMesh::System::read_legacy_data(), libMesh::System::read_parallel_data(), libMesh::System::read_serialized_vector(), libMesh::System::read_serialized_vectors(), libMesh::EigenSystem::reinit(), libMesh::ImplicitSystem::reinit(), LinearElasticityWithContact::residual_and_jacobian(), OverlappingAlgebraicGhostingTest::run_ghosting_test(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), SolidSystem::save_initial_mesh(), libMesh::HPSingularity::select_refinement(), libMesh::HPCoarsenTest::select_refinement(), libMesh::PetscDMWrapper::set_point_range_in_section(), SolidSystem::side_time_derivative(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::BoundaryVolumeSolutionTransfer::transfer(), libMesh::BoundaryVolumeSolutionTransfer::transfer_boundary_volume(), libMesh::BoundaryVolumeSolutionTransfer::transfer_volume_boundary(), libMesh::TransientRBConstruction::truth_solve(), libMesh::RBEIMConstruction::truth_solve(), libMesh::RBConstruction::truth_solve(), libMesh::System::write_header(), libMesh::RBEvaluation::write_out_vectors(), libMesh::System::write_parallel_data(), libMesh::System::write_serialized_vector(), libMesh::System::write_serialized_vectors(), and libMesh::System::zero_variable().

get_mesh_system() [1/2]

System * libMesh::DifferentiablePhysics::get_mesh_system ( )

inlineinherited

Returns

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

Definition at line 631 of file diff_physics.h.

{
  return _mesh_sys;
}

References libMesh::DifferentiablePhysics::_mesh_sys.

get_mesh_system() [2/2]

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

inlineinherited

Returns

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

Definition at line 625 of file diff_physics.h.

{
  return _mesh_sys;
}

References libMesh::DifferentiablePhysics::_mesh_sys.

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

get_mesh_x_var()

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

inlineinherited

Returns

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

Definition at line 637 of file diff_physics.h.

{
  return _mesh_x_var;
}

References libMesh::DifferentiablePhysics::_mesh_x_var.

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

get_mesh_y_var()

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

inlineinherited

Returns

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

Definition at line 643 of file diff_physics.h.

{
  return _mesh_y_var;
}

References libMesh::DifferentiablePhysics::_mesh_y_var.

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

get_mesh_z_var()

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

inlineinherited

Returns

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

Definition at line 649 of file diff_physics.h.

{
  return _mesh_z_var;
}

References libMesh::DifferentiablePhysics::_mesh_z_var.

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

get_physics() [1/2]

DifferentiablePhysics* libMesh::DifferentiableSystem::get_physics ( )

inlineinherited

Returns

A reference to a DifferentiablePhysics object.

Note

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

Definition at line 190 of file diff_system.h.

  { return this->_diff_physics; }

References libMesh::DifferentiableSystem::_diff_physics.

get_physics() [2/2]

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

inlineinherited

Returns

A const reference to a DifferentiablePhysics object.

Note

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

Definition at line 181 of file diff_system.h.

  { return this->_diff_physics; }

References libMesh::DifferentiableSystem::_diff_physics.

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

get_qoi() [1/2]

DifferentiableQoI* libMesh::DifferentiableSystem::get_qoi ( )

inlineinherited

Returns

A reference to a DifferentiableQoI object.

Note

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

Definition at line 218 of file diff_system.h.

  { return this->diff_qoi; }

References libMesh::DifferentiableSystem::diff_qoi.

get_qoi() [2/2]

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

inlineinherited

Returns

A const reference to a DifferentiableQoI object.

Note

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

Definition at line 210 of file diff_system.h.

  { return this->diff_qoi; }

References libMesh::DifferentiableSystem::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.

Definition at line 310 of file diff_system.C.

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

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

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

get_second_order_vars()

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

inlineinherited

Returns

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

Definition at line 531 of file diff_physics.h.

  { return _second_order_vars; }

References libMesh::DifferentiablePhysics::_second_order_vars.

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

get_sensitivity_rhs() [1/2]

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

inherited

Returns

A reference to one of the system's sensitivity rhs vectors, by default the one corresponding to the first parameter. By default these vectors are built by the library, using finite differences, when assemble_residual_derivatives() is called.

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

Definition at line 1049 of file system.C.

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

References libMesh::System::get_vector().

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

get_sensitivity_rhs() [2/2]

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

inherited

Returns

A reference to one of the system's sensitivity rhs vectors, by default the one corresponding to the first parameter.

Definition at line 1059 of file system.C.

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

References libMesh::System::get_vector().

get_sensitivity_solution() [1/2]

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

inherited

Returns

A reference to one of the system's solution sensitivity vectors, by default the one corresponding to the first parameter.

Definition at line 904 of file system.C.

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

References libMesh::System::get_vector().

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

get_sensitivity_solution() [2/2]

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

inherited

Returns

A reference to one of the system's solution sensitivity vectors, by default the one corresponding to the first parameter.

Definition at line 914 of file system.C.

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

References libMesh::System::get_vector().

get_time_solver() [1/2]

TimeSolver & libMesh::DifferentiableSystem::get_time_solver ( )

inlineinherited

Returns

A pointer to the time solver attached to the calling system

Definition at line 416 of file diff_system.h.

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

References libMesh::libmesh_assert(), and libMesh::DifferentiableSystem::time_solver.

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

get_time_solver() [2/2]

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

inlineinherited

Non-const version of the above.

Definition at line 424 of file diff_system.h.

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

References libMesh::libmesh_assert(), and libMesh::DifferentiableSystem::time_solver.

get_vector() [1/4]

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

inherited

Returns

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

Definition at line 781 of file system.C.

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

References libMesh::System::_vectors.

get_vector() [2/4]

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

inherited

Returns

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

Definition at line 774 of file system.C.

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

References libMesh::System::_vectors.

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

get_vector() [3/4]

NumericVector< Number > & libMesh::System::get_vector ( const unsigned int  vec_num )

inherited

Returns

A writable reference to this system's additional vector number vec_num (where the vectors are counted starting with 0).

Definition at line 804 of file system.C.

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

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

get_vector() [4/4]

const NumericVector< Number > & libMesh::System::get_vector ( const unsigned int  vec_num ) const

inherited

Returns

A const reference to this system's additional vector number vec_num (where the vectors are counted starting with 0).

Definition at line 788 of file system.C.

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

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

get_weighted_sensitivity_adjoint_solution() [1/2]

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

inherited

Returns

A reference to one of the system's weighted sensitivity adjoint solution vectors, by default the one corresponding to the first qoi.

Definition at line 989 of file system.C.

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

References libMesh::System::get_vector().

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

get_weighted_sensitivity_adjoint_solution() [2/2]

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

inherited

Returns

A reference to one of the system's weighted sensitivity adjoint solution vectors, by default the one corresponding to the first qoi.

Definition at line 999 of file system.C.

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

References libMesh::System::get_vector().

get_weighted_sensitivity_solution() [1/2]

NumericVector< Number > & libMesh::System::get_weighted_sensitivity_solution ( )

inherited

Returns

A reference to the solution of the last weighted sensitivity solve

Definition at line 931 of file system.C.

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

References libMesh::System::get_vector().

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

Definition at line 938 of file system.C.

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

References libMesh::System::get_vector().

has_variable()

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

inherited

Returns

true if a variable named var exists in this System

Definition at line 1225 of file system.C.

{
  return _variable_numbers.count(var);
}

References libMesh::System::_variable_numbers.

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

have_first_order_scalar_vars()

bool libMesh::DifferentiableSystem::have_first_order_scalar_vars ( ) const

inherited

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

Definition at line 327 of file diff_system.C.

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

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

have_first_order_vars()

bool libMesh::DifferentiablePhysics::have_first_order_vars ( ) const

inlineinherited

Definition at line 512 of file diff_physics.h.

  { return !_first_order_vars.empty(); }

References libMesh::DifferentiablePhysics::_first_order_vars.

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

have_matrix()

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

inlineinherited

Returns

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

Definition at line 439 of file implicit_system.h.

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

References libMesh::ImplicitSystem::_matrices.

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

have_second_order_scalar_vars()

bool libMesh::DifferentiableSystem::have_second_order_scalar_vars ( ) const

inherited

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

Definition at line 339 of file diff_system.C.

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

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

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

have_second_order_vars()

bool libMesh::DifferentiablePhysics::have_second_order_vars ( ) const

inlineinherited

Definition at line 525 of file diff_physics.h.

  { return !_second_order_vars.empty(); }

References libMesh::DifferentiablePhysics::_second_order_vars.

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

have_vector()

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

inlineinherited

Returns

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

Definition at line 2275 of file system.h.

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

References libMesh::System::_vectors.

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

hide_output()

bool& libMesh::System::hide_output ( )

inlineinherited

Returns

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

Definition at line 1712 of file system.h.

{ return _hide_output; }

References libMesh::System::_hide_output.

identify_variable_groups() [1/2]

bool libMesh::System::identify_variable_groups ( ) const

inlineinherited

Returns

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

Definition at line 2251 of file system.h.

{
  return _identify_variable_groups;
}

References libMesh::System::_identify_variable_groups.

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

identify_variable_groups() [2/2]

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

inlineinherited

Toggle automatic VariableGroup identification.

Definition at line 2259 of file system.h.

{
  _identify_variable_groups = ivg;
}

References libMesh::System::_identify_variable_groups.

increment_constructor_count()

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

inlineprotectedinherited

Increments the construction counter.

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

Definition at line 181 of file reference_counter.h.

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

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

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

increment_destructor_count()

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

inlineprotectedinherited

Increments the destruction counter.

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

Definition at line 194 of file reference_counter.h.

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

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

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

init()

void libMesh::System::init ( )

inherited

Initializes degrees of freedom on the current mesh.

Sets the

Definition at line 237 of file system.C.

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

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

init_context()

void FEMSystem::init_context ( DiffContext &  c )

overridevirtualinherited

Reimplemented from libMesh::DifferentiablePhysics.

Reimplemented in L2System, HeatSystem, HeatSystem, CoupledSystem, ElasticitySystem, LaplaceSystem, CurlCurlSystem, LaplaceSystem, PoissonSystem, LaplaceSystem, LaplaceSystem, CurlCurlSystem, SolidSystem, and NavierSystem.

Definition at line 1338 of file fem_system.C.

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

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

Referenced by libMesh::FEMSystem::assembly(), L2System::init_context(), libMesh::FEMSystem::mesh_position_get(), and libMesh::FEMSystem::mesh_position_set().

init_data()

virtual void FirstOrderScalarSystemBase::init_data ( )

inlineoverridevirtualinherited

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

Reimplemented from libMesh::FEMSystem.

Reimplemented in SecondOrderScalarSystemSecondOrderTimeSolverBase.

Definition at line 110 of file time_solver_test_common.h.

  {
    _u_var = this->add_variable ("u", FIRST, LAGRANGE);
    this->time_evolving(_u_var,1);
    FEMSystem::init_data();
  }

References libMesh::FIRST, libMesh::FEMSystem::init_data(), and libMesh::LAGRANGE.

init_matrices()

void libMesh::ImplicitSystem::init_matrices ( )

protectedvirtualinherited

Initializes the matrices associated with this system.

Definition at line 105 of file implicit_system.C.

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

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

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

init_physics()

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

virtualinherited

Initialize any data structures associated with the physics.

Definition at line 40 of file diff_physics.C.

{
  // give us flags for every variable that might be time evolving
  _time_evolving.resize(sys.n_vars(), false);
}

References libMesh::DifferentiablePhysics::_time_evolving, and libMesh::System::n_vars().

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

init_qoi()

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

inlinevirtualinherited

Initialize system qoi.

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

Definition at line 71 of file diff_qoi.h.

{}

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

is_adjoint_already_solved()

bool libMesh::System::is_adjoint_already_solved ( ) const

inlineinherited

Accessor for the adjoint_already_solved boolean.

Definition at line 396 of file system.h.

  { return adjoint_already_solved;}

References libMesh::System::adjoint_already_solved.

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

is_first_order_var()

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

inlineinherited

Definition at line 521 of file diff_physics.h.

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

References libMesh::DifferentiablePhysics::_first_order_vars.

is_initialized()

bool libMesh::System::is_initialized ( )

inlineinherited

Returns

true iff this system has been initialized.

Definition at line 2139 of file system.h.

{
  return _is_initialized;
}

References libMesh::System::_is_initialized.

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

is_second_order_var()

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

inlineinherited

Definition at line 534 of file diff_physics.h.

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

References libMesh::DifferentiablePhysics::_second_order_vars.

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

is_time_evolving()

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

inlineinherited

Returns

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

Definition at line 278 of file diff_physics.h.

  {
    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];
  }

References libMesh::DifferentiablePhysics::_time_evolving, and libMesh::libmesh_assert().

Referenced by libMesh::FEMPhysics::eulerian_residual(), libMesh::FEMSystem::init_context(), libMesh::FEMPhysics::mass_residual(), and libMesh::DifferentiablePhysics::nonlocal_mass_residual().

local_dof_indices()

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

inherited

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

Definition at line 1259 of file system.C.

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

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

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

M() [1/2]

virtual Number ConstantFirstOrderODE::M ( FEMContext &  , unsigned int    )

inlinevirtual

Definition at line 25 of file first_order_unsteady_solver_test.C.

  { return Real(21)/10; }

References libMesh::Real.

M() [2/2]

virtual Number FirstOrderScalarSystemBase::M ( FEMContext &  context, unsigned int  qp  )

pure virtualinherited

Value of M(u).

mass_residual()

virtual bool FirstOrderScalarSystemBase::mass_residual ( bool  request_jacobian, DiffContext &  context  )

inlineoverridevirtualinherited

Note the nonlinear residual is F(u)-M(u)

{u}

Reimplemented from libMesh::FEMPhysics.

Reimplemented in SecondOrderScalarSystemFirstOrderTimeSolverBase, and SecondOrderScalarSystemSecondOrderTimeSolverBase.

Definition at line 140 of file time_solver_test_common.h.

  {
    FEMContext & c = cast_ref<FEMContext &>(context);
    DenseSubVector<Number> & Fu = c.get_elem_residual(_u_var);
    DenseSubMatrix<Number> & Kuu = c.get_elem_jacobian(_u_var, _u_var);
 
    const unsigned int n_u_dofs =
      cast_int<unsigned int>(c.get_dof_indices(_u_var).size());
    unsigned int n_qpoints = c.get_element_qrule().n_points();
 
    for (unsigned int qp=0; qp != n_qpoints; qp++)
      {
        libMesh::Number udot;
        c.interior_rate(_u_var,qp,udot);
 
        Number Mval = this->M(c,qp);
 
        for (unsigned int i=0; i != n_u_dofs; i++)
          {
            Fu(i) -= Mval*udot;
 
            if (request_jacobian)
              for (unsigned int j=0; j != n_u_dofs; j++)
                Kuu(i,j) -= Mval*context.get_elem_solution_rate_derivative();
          }
      }
 
    return request_jacobian;
  }

References libMesh::DiffContext::get_dof_indices(), libMesh::DiffContext::get_elem_jacobian(), libMesh::DiffContext::get_elem_residual(), libMesh::DiffContext::get_elem_solution_rate_derivative(), libMesh::FEMContext::get_element_qrule(), libMesh::FEMContext::interior_rate(), and libMesh::QBase::n_points().

mesh_position_get()

void FEMSystem::mesh_position_get ( )

inherited

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

Definition at line 1385 of file fem_system.C.

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

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

Referenced by SolidSystem::init_data().

mesh_position_set()

void FEMSystem::mesh_position_set ( )

inherited

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

Definition at line 1057 of file fem_system.C.

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

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

Referenced by libMesh::FEMSystem::solve(), and SolidSystem::update().

n_active_dofs()

dof_id_type libMesh::System::n_active_dofs ( ) const

inlineinherited

Returns

The number of active degrees of freedom for this System.

Definition at line 2267 of file system.h.

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

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

n_components()

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

inlineinherited

Returns

The total number of scalar components in the system's variables. This will equal n_vars() in the case of all scalar-valued variables.

Definition at line 2171 of file system.h.

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

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

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

n_constrained_dofs()

dof_id_type libMesh::System::n_constrained_dofs ( ) const

inherited

Returns

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

Definition at line 157 of file system.C.

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

References libMesh::System::_dof_map.

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

n_dofs()

dof_id_type libMesh::System::n_dofs ( ) const

inherited

Returns

The number of degrees of freedom in the system

Definition at line 150 of file system.C.

{
  return _dof_map->n_dofs();
}

References libMesh::System::_dof_map.

Referenced by libMesh::TransientRBConstruction::add_IC_to_RB_space(), libMesh::System::add_vector(), libMesh::TransientRBConstruction::allocate_data_structures(), libMesh::RBConstruction::allocate_data_structures(), libMesh::TransientRBConstruction::assemble_affine_expansion(), libMesh::RBConstruction::compute_Fq_representor_innerprods(), libMesh::RBConstruction::compute_output_dual_innerprods(), libMesh::RBConstruction::compute_residual_dual_norm_slow(), libMesh::RBEIMConstruction::enrich_RB_space(), libMesh::TransientRBConstruction::enrich_RB_space(), libMesh::RBConstruction::enrich_RB_space(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::System::get_info(), libMesh::SecondOrderUnsteadySolver::init_data(), libMesh::UnsteadySolver::init_data(), libMesh::System::init_data(), libMesh::RBEIMConstruction::init_dof_map_between_systems(), libMesh::OptimizationSystem::initialize_equality_constraints_storage(), libMesh::OptimizationSystem::initialize_inequality_constraints_storage(), libMesh::RBEIMConstruction::initialize_rb_construction(), main(), libMesh::TransientRBConstruction::mass_matrix_scaled_matvec(), libMesh::System::n_active_dofs(), libMesh::CondensedEigenSystem::n_global_non_condensed_dofs(), libMesh::FEMSystem::numerical_jacobian(), libMesh::RBSCMConstruction::perform_SCM_greedy(), libMesh::RBEIMAssembly::RBEIMAssembly(), libMesh::RBEvaluation::read_in_vectors_from_multiple_files(), libMesh::System::read_legacy_data(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), libMesh::SecondOrderUnsteadySolver::reinit(), libMesh::UnsteadySolver::reinit(), libMesh::System::restrict_vectors(), OverlappingAlgebraicGhostingTest::run_ghosting_test(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), libMesh::TransientRBConstruction::set_error_temporal_data(), libMesh::RBEIMConstruction::set_explicit_sys_subvector(), MeshfunctionDFEM::test_mesh_function_dfem(), MeshfunctionDFEM::test_mesh_function_dfem_grad(), MeshFunctionTest::test_p_level(), SystemsTest::testProjectCubeWithMeshFunction(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), SystemsTest::testProjectMatrix3D(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::TransientRBConstruction::truth_assembly(), libMesh::RBConstruction::truth_assembly(), libMesh::TransientRBConstruction::update_RB_initial_condition_all_N(), libMesh::RBEIMConstruction::update_RB_system_matrices(), libMesh::TransientRBConstruction::update_RB_system_matrices(), libMesh::RBConstruction::update_RB_system_matrices(), libMesh::TransientRBConstruction::update_residual_terms(), and libMesh::RBConstruction::update_residual_terms().

n_local_constrained_dofs()

dof_id_type libMesh::System::n_local_constrained_dofs ( ) const

inherited

Returns

The number of constrained degrees of freedom on this processor.

Definition at line 172 of file system.C.

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

References libMesh::System::_dof_map.

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

n_local_dofs()

dof_id_type libMesh::System::n_local_dofs ( ) const

inherited

Returns

The number of degrees of freedom local to this processor

Definition at line 187 of file system.C.

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

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

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

n_matrices()

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

inlineoverridevirtualinherited

Returns

The number of matrices handled by this system

Reimplemented from libMesh::System.

Definition at line 446 of file implicit_system.h.

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

References libMesh::ImplicitSystem::_matrices.

n_objects()

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

inlinestaticinherited

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

Definition at line 83 of file reference_counter.h.

  { return _n_objects; }

References libMesh::ReferenceCounter::_n_objects.

n_processors()

processor_id_type libMesh::ParallelObject::n_processors ( ) const

inlineinherited

Returns

The number of processors in the group.

Definition at line 100 of file parallel_object.h.

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

References libMesh::ParallelObject::_communicator.

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

n_qois()

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

inlineinherited

Number of currently active quantities of interest.

Definition at line 2328 of file system.h.

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

References libMesh::System::qoi.

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

n_variable_groups()

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

inlineinherited

Returns

The number of VariableGroup variable groups in the system

Definition at line 2163 of file system.h.

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

References libMesh::System::_variable_groups.

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

n_vars()

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

inlineinherited

Returns

The number of variables in the system

Definition at line 2155 of file system.h.

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

References libMesh::System::_variables.

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

n_vectors()

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

inlineinherited

Returns

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

Definition at line 2283 of file system.h.

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

References libMesh::System::_vectors.

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

name()

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

inlineinherited

Returns

The system name.

Definition at line 2067 of file system.h.

{
  return _sys_name;
}

References libMesh::System::_sys_name.

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

nonlocal_constraint()

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

inlinevirtualinherited

Adds any nonlocal constraint contributions (e.g.

some components of constraints in scalar variable equations) to elem_residual

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

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

Definition at line 228 of file diff_physics.h.

                                                   {
    return request_jacobian;
  }

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

nonlocal_damping_residual()

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

inlinevirtualinherited

Subtracts any nonlocal damping vector contributions (e.g.

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

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

Definition at line 407 of file diff_physics.h.

                                                         {
    return request_jacobian;
  }

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

nonlocal_mass_residual()

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.

Definition at line 63 of file diff_physics.C.

{
  FEMContext & context = cast_ref<FEMContext &>(c);
 
  for (auto var : IntRange<unsigned int>(0, context.n_vars()))
    {
      if (!this->is_time_evolving(var))
        continue;
 
      if (c.get_system().variable(var).type().family != SCALAR)
        continue;
 
      const std::vector<dof_id_type> & dof_indices =
        context.get_dof_indices(var);
 
      const unsigned int n_dofs = cast_int<unsigned int>
        (dof_indices.size());
 
      DenseSubVector<Number> & Fs = context.get_elem_residual(var);
      DenseSubMatrix<Number> & Kss = context.get_elem_jacobian( var, var );
 
      const libMesh::DenseSubVector<libMesh::Number> & Us =
        context.get_elem_solution(var);
 
      for (unsigned int i=0; i != n_dofs; ++i)
        {
          Fs(i) -= Us(i);
 
          if (request_jacobian)
            Kss(i,i) -= context.elem_solution_rate_derivative;
        }
    }
 
  return request_jacobian;
}

References libMesh::DiffContext::elem_solution_rate_derivative, libMesh::FEType::family, libMesh::DiffContext::get_dof_indices(), libMesh::DiffContext::get_elem_jacobian(), libMesh::DiffContext::get_elem_residual(), libMesh::DiffContext::get_elem_solution(), libMesh::DiffContext::get_system(), libMesh::DifferentiablePhysics::is_time_evolving(), libMesh::DiffContext::n_vars(), libMesh::SCALAR, libMesh::Variable::type(), and libMesh::System::variable().

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

nonlocal_time_derivative()

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

inlinevirtualinherited

Adds any nonlocal time derivative contributions (e.g.

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

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

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

Definition at line 210 of file diff_physics.h.

                                                        {
    return request_jacobian;
  }

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

number()

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

inlineinherited

Returns

The system number.

Definition at line 2075 of file system.h.

{
  return _sys_number;
}

References libMesh::System::_sys_number.

Referenced by libMesh::ExactSolution::_compute_error(), libMesh::PetscDMWrapper::add_dofs_helper(), assemble_matrix_and_rhs(), assemble_shell(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ExactErrorEstimator::find_squared_element_error(), libMesh::EquationSystems::find_variable_numbers(), libMesh::System::get_info(), main(), libMesh::System::read_legacy_data(), libMesh::System::read_parallel_data(), libMesh::System::read_serialized_blocked_dof_objects(), LinearElasticityWithContact::residual_and_jacobian(), SolidSystem::save_initial_mesh(), libMesh::HPCoarsenTest::select_refinement(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::MeshfreeSolutionTransfer::transfer(), libMesh::BoundaryVolumeSolutionTransfer::transfer_boundary_volume(), libMesh::BoundaryVolumeSolutionTransfer::transfer_volume_boundary(), libMesh::DTKAdapter::update_variable_values(), libMesh::System::write_parallel_data(), libMesh::System::write_serialized_blocked_dof_objects(), and libMesh::System::zero_variable().

numerical_elem_jacobian()

void FEMSystem::numerical_elem_jacobian ( FEMContext &  context ) const

inherited

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

Definition at line 1290 of file fem_system.C.

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

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

numerical_jacobian()

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

inherited

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

Definition at line 1178 of file fem_system.C.

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

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

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

numerical_jacobian_h_for_var()

Real FEMSystem::numerical_jacobian_h_for_var ( unsigned int  var_num ) const

inlineinherited

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

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

Definition at line 259 of file fem_system.h.

{
  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];
}

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

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

numerical_nonlocal_jacobian()

void FEMSystem::numerical_nonlocal_jacobian ( FEMContext &  context ) const

inherited

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

Definition at line 1306 of file fem_system.C.

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

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

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

numerical_side_jacobian()

void FEMSystem::numerical_side_jacobian ( FEMContext &  context ) const

inherited

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

Definition at line 1298 of file fem_system.C.

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

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

parallel_op()

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.

Definition at line 41 of file diff_qoi.C.

{
  // Sum everything into local_qoi
  communicator.sum(local_qoi);
 
  // Now put into system qoi
  sys_qoi = local_qoi;
}

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

point_gradient() [1/4]

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

inherited

Returns

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

Definition at line 2100 of file system.C.

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

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

Referenced by line_print(), and libMesh::System::point_gradient().

point_gradient() [2/4]

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

inherited

Returns

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

Definition at line 2162 of file system.C.

{
  // Ensuring that the given point is really in the element is an
  // expensive assert, but as long as debugging is turned on we might
  // as well try to catch a particularly nasty potential error
  libmesh_assert (e.contains_point(p));
 
  if (!sol)
    sol = this->current_local_solution.get();
 
  // Get the dof map to get the proper indices for our computation
  const DofMap & dof_map = this->get_dof_map();
 
  // write the element dimension into a separate variable.
  const unsigned int dim = e.dim();
 
  // Make sure we can evaluate on this element.
  libmesh_assert (dof_map.is_evaluable(e, var));
 
  // Need dof_indices for phi[i][j]
  std::vector<dof_id_type> dof_indices;
 
  // Fill in the dof_indices for our element
  dof_map.dof_indices (&e, dof_indices, var);
 
  // Get the no of dofs associated with this point
  const unsigned int num_dofs = cast_int<unsigned int>
    (dof_indices.size());
 
  FEType fe_type = dof_map.variable_type(var);
 
  // Map the physical co-ordinates to the master co-ordinates using the inverse_map from fe_interface.h.
  Point coor = FEMap::inverse_map(dim, &e, p);
 
  // get the shape function value via the FEInterface to also handle the case
  // of infinite elements correcly, the shape function is not fe->phi().
  FEComputeData fe_data(this->get_equation_systems(), coor);
  fe_data.enable_derivative();
  FEInterface::compute_data(dim, fe_type, &e, fe_data);
 
  // Get ready to accumulate a gradient
  Gradient grad_u;
 
  for (unsigned int l=0; l<num_dofs; l++)
    {
      // Chartesian coordinates have allways LIBMESH_DIM entries,
      // local coordinates have as many coordinates as the element has.
      for (std::size_t v=0; v<dim; v++)
        for (std::size_t xyz=0; xyz<LIBMESH_DIM; xyz++)
          {
            // FIXME: this needs better syntax: It is matrix-vector multiplication.
            grad_u(xyz) += fe_data.local_transform[v][xyz]
              * fe_data.dshape[l](v)
              * (*sol)(dof_indices[l]);
          }
    }
 
  return grad_u;
}

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

point_gradient() [3/4]

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

inherited

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

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

Definition at line 2227 of file system.C.

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

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

point_gradient() [4/4]

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

inherited

Calls the parallel version of point_gradient().

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

Definition at line 2235 of file system.C.

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

References libMesh::System::point_gradient().

point_hessian() [1/4]

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

inherited

Returns

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

Definition at line 2244 of file system.C.

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

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

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

point_hessian() [2/4]

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

inherited

Returns

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

Definition at line 2305 of file system.C.

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

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

point_hessian() [3/4]

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

inherited

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

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

Definition at line 2367 of file system.C.

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

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

point_hessian() [4/4]

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

inherited

Calls the parallel version of point_hessian().

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

Definition at line 2375 of file system.C.

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

References libMesh::System::point_hessian().

point_value() [1/4]

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

inherited

Returns

The value of the solution variable var at the physical point p in the mesh, without knowing a priori which element contains p, using the degree of freedom coefficients in sol (or in current_local_solution if sol is left null).

Note

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

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

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

Definition at line 1971 of file system.C.

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

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

Referenced by line_print(), main(), libMesh::System::point_value(), DefaultCouplingTest::testCoupling(), PointNeighborCouplingTest::testCoupling(), MeshInputTest::testExodusCopyElementSolution(), MeshInputTest::testExodusWriteElementDataFromDiscontinuousNodalData(), SystemsTest::testProjectCubeWithMeshFunction(), and EquationSystemsTest::testRepartitionThenReinit().

point_value() [2/4]

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

inherited

Returns

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

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

Definition at line 2032 of file system.C.

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

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

point_value() [3/4]

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

inherited

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

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

Definition at line 2084 of file system.C.

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

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

point_value() [4/4]

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

inherited

Calls the parallel version of point_value().

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

Definition at line 2092 of file system.C.

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

References libMesh::System::point_value().

postprocess()

void FEMSystem::postprocess ( void  )

overridevirtualinherited

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

Reimplemented from libMesh::DifferentiableSystem.

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

Definition at line 1097 of file fem_system.C.

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

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

Referenced by main(), PoissonSystem::postprocess(), and LaplaceSystem::postprocess().

print_info()

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

staticinherited

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

Definition at line 87 of file reference_counter.C.

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

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

processor_id()

processor_id_type libMesh::ParallelObject::processor_id ( ) const

inlineinherited

Returns

The rank of this processor in the group.

Definition at line 106 of file parallel_object.h.

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

References libMesh::ParallelObject::_communicator.

Referenced by libMesh::BoundaryInfo::_find_id_maps(), libMesh::EquationSystems::_read_impl(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::DistributedMesh::add_elem(), libMesh::BoundaryInfo::add_elements(), libMesh::DofMap::add_neighbors_to_send_list(), libMesh::DistributedMesh::add_node(), libMesh::UnstructuredMesh::all_second_order(), libMesh::MeshTools::Modification::all_tri(), libMesh::DofMap::allgather_recursive_constraints(), libMesh::FEMSystem::assembly(), libMesh::Nemesis_IO_Helper::build_element_and_node_maps(), libMesh::InfElemBuilder::build_inf_elem(), libMesh::BoundaryInfo::build_node_list_from_side_list(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::DistributedMesh::clear(), libMesh::ExodusII_IO_Helper::close(), libMesh::Nemesis_IO_Helper::compute_border_node_ids(), libMesh::Nemesis_IO_Helper::compute_communication_map_parameters(), libMesh::Nemesis_IO_Helper::compute_internal_and_border_elems_and_internal_nodes(), libMesh::RBConstruction::compute_max_error_bound(), libMesh::Nemesis_IO_Helper::compute_node_communication_maps(), libMesh::Nemesis_IO_Helper::compute_num_global_elem_blocks(), libMesh::Nemesis_IO_Helper::compute_num_global_nodesets(), libMesh::Nemesis_IO_Helper::compute_num_global_sidesets(), libMesh::Nemesis_IO_Helper::construct_nemesis_filename(), libMesh::ExodusII_IO::copy_scalar_solution(), libMesh::MeshTools::correct_node_proc_ids(), libMesh::ExodusII_IO_Helper::create(), libMesh::DistributedMesh::delete_elem(), libMesh::DistributedMesh::delete_node(), libMesh::MeshCommunication::delete_remote_elements(), libMesh::DofMap::distribute_dofs(), libMesh::DofMap::distribute_local_dofs_node_major(), libMesh::DofMap::distribute_local_dofs_var_major(), libMesh::DistributedMesh::DistributedMesh(), libMesh::DofMap::end_dof(), libMesh::DofMap::end_old_dof(), libMesh::EnsightIO::EnsightIO(), libMesh::RBEIMConstruction::evaluate_mesh_function(), libMesh::MeshFunction::find_element(), libMesh::MeshFunction::find_elements(), libMesh::UnstructuredMesh::find_neighbors(), libMesh::DofMap::first_dof(), libMesh::DofMap::first_old_dof(), libMesh::Nemesis_IO_Helper::get_cmap_params(), libMesh::Nemesis_IO_Helper::get_eb_info_global(), libMesh::Nemesis_IO_Helper::get_elem_cmap(), libMesh::Nemesis_IO_Helper::get_elem_map(), libMesh::DofMap::get_info(), libMesh::Nemesis_IO_Helper::get_init_global(), libMesh::Nemesis_IO_Helper::get_init_info(), libMesh::Nemesis_IO_Helper::get_loadbal_param(), libMesh::DofMap::get_local_constraints(), libMesh::Nemesis_IO_Helper::get_node_cmap(), libMesh::Nemesis_IO_Helper::get_node_map(), libMesh::Nemesis_IO_Helper::get_ns_param_global(), libMesh::Nemesis_IO_Helper::get_ss_param_global(), libMesh::SparsityPattern::Build::handle_vi_vj(), libMesh::SystemSubsetBySubdomain::init(), libMesh::PetscDMWrapper::init_and_attach_petscdm(), HeatSystem::init_data(), libMesh::ExodusII_IO_Helper::initialize(), libMesh::ExodusII_IO_Helper::initialize_element_variables(), libMesh::ExodusII_IO_Helper::initialize_global_variables(), libMesh::ExodusII_IO_Helper::initialize_nodal_variables(), libMesh::DistributedMesh::insert_elem(), libMesh::DofMap::is_evaluable(), libMesh::SparsityPattern::Build::join(), libMesh::DofMap::last_dof(), libMesh::TransientRBEvaluation::legacy_write_offline_data_to_files(), libMesh::RBEIMEvaluation::legacy_write_offline_data_to_files(), libMesh::RBEvaluation::legacy_write_offline_data_to_files(), libMesh::RBSCMEvaluation::legacy_write_offline_data_to_files(), libMesh::RBEIMEvaluation::legacy_write_out_interpolation_points_elem(), libMesh::MeshTools::libmesh_assert_consistent_distributed(), libMesh::MeshTools::libmesh_assert_consistent_distributed_nodes(), libMesh::MeshTools::libmesh_assert_contiguous_dof_ids(), libMesh::MeshTools::libmesh_assert_parallel_consistent_procids< Elem >(), libMesh::MeshTools::libmesh_assert_valid_neighbors(), libMesh::DistributedMesh::libmesh_assert_valid_parallel_object_ids(), libMesh::DofMap::local_variable_indices(), main(), libMesh::MeshRefinement::make_coarsening_compatible(), AugmentSparsityOnInterface::mesh_reinit(), libMesh::MeshBase::n_active_local_elem(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::BoundaryInfo::n_edge_conds(), libMesh::DofMap::n_local_dofs(), libMesh::System::n_local_dofs(), libMesh::MeshBase::n_local_elem(), libMesh::MeshBase::n_local_nodes(), libMesh::BoundaryInfo::n_nodeset_conds(), libMesh::BoundaryInfo::n_shellface_conds(), libMesh::SparsityPattern::Build::operator()(), libMesh::DistributedMesh::own_node(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::DofMap::print_dof_constraints(), libMesh::Nemesis_IO_Helper::put_cmap_params(), libMesh::Nemesis_IO_Helper::put_elem_cmap(), libMesh::Nemesis_IO_Helper::put_elem_map(), libMesh::Nemesis_IO_Helper::put_loadbal_param(), libMesh::Nemesis_IO_Helper::put_node_cmap(), libMesh::Nemesis_IO_Helper::put_node_map(), libMesh::NameBasedIO::read(), libMesh::Nemesis_IO::read(), libMesh::XdrIO::read(), libMesh::CheckpointIO::read(), libMesh::ExodusII_IO_Helper::read_elem_num_map(), libMesh::ExodusII_IO_Helper::read_global_values(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::System::read_header(), libMesh::RBEvaluation::read_in_vectors_from_multiple_files(), libMesh::System::read_legacy_data(), libMesh::ExodusII_IO_Helper::read_node_num_map(), libMesh::System::read_parallel_data(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), libMesh::System::read_SCALAR_dofs(), libMesh::XdrIO::read_serialized_bc_names(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::System::read_serialized_data(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::System::read_serialized_vector(), libMesh::System::read_serialized_vectors(), libMesh::DistributedMesh::renumber_dof_objects(), libMesh::DofMap::scatter_constraints(), libMesh::CheckpointIO::select_split_config(), libMesh::DofMap::set_nonlocal_dof_objects(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::LaplaceMeshSmoother::smooth(), DefaultCouplingTest::testCoupling(), PointNeighborCouplingTest::testCoupling(), MeshInputTest::testDynaReadElem(), MeshInputTest::testDynaReadPatch(), MeshInputTest::testExodusCopyElementSolution(), MeshInputTest::testExodusWriteElementDataFromDiscontinuousNodalData(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), SystemsTest::testProjectMatrix3D(), BoundaryInfoTest::testShellFaceConstraints(), CheckpointIOTest::testSplitter(), WriteVecAndScalar::testWrite(), libMesh::MeshTools::total_weight(), libMesh::MeshRefinement::uniformly_coarsen(), libMesh::Parallel::Packing< Node * >::unpack(), libMesh::Parallel::Packing< Elem * >::unpack(), libMesh::DistributedMesh::update_parallel_id_counts(), libMesh::DTKAdapter::update_variable_values(), libMesh::NameBasedIO::write(), libMesh::XdrIO::write(), libMesh::CheckpointIO::write(), libMesh::EquationSystems::write(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::ExodusII_IO::write_element_data(), libMesh::ExodusII_IO_Helper::write_element_values(), libMesh::ExodusII_IO_Helper::write_element_values_element_major(), libMesh::ExodusII_IO_Helper::write_elements(), libMesh::ExodusII_IO::write_global_data(), libMesh::ExodusII_IO_Helper::write_global_values(), libMesh::System::write_header(), libMesh::ExodusII_IO::write_information_records(), libMesh::ExodusII_IO_Helper::write_information_records(), libMesh::ExodusII_IO_Helper::write_nodal_coordinates(), libMesh::VTKIO::write_nodal_data(), libMesh::UCDIO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data_discontinuous(), libMesh::ExodusII_IO_Helper::write_nodal_values(), libMesh::Nemesis_IO_Helper::write_nodesets(), libMesh::ExodusII_IO_Helper::write_nodesets(), libMesh::RBEvaluation::write_out_vectors(), write_output_solvedata(), libMesh::System::write_parallel_data(), libMesh::RBConstruction::write_riesz_representors_to_files(), libMesh::System::write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bc_names(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::System::write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::System::write_serialized_data(), libMesh::XdrIO::write_serialized_nodes(), libMesh::XdrIO::write_serialized_nodesets(), libMesh::XdrIO::write_serialized_subdomain_names(), libMesh::System::write_serialized_vector(), libMesh::System::write_serialized_vectors(), libMesh::ExodusII_IO_Helper::write_sideset_data(), libMesh::Nemesis_IO_Helper::write_sidesets(), libMesh::ExodusII_IO_Helper::write_sidesets(), libMesh::ExodusII_IO::write_timestep(), libMesh::ExodusII_IO_Helper::write_timestep(), and libMesh::ExodusII_IO::write_timestep_discontinuous().

project_solution() [1/3]

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

inherited

Projects arbitrary functions onto the current solution.

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

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

Definition at line 963 of file system_projection.C.

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

project_solution() [2/3]

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

inherited

Projects arbitrary functions onto the current solution.

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

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

Definition at line 950 of file system_projection.C.

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

Referenced by init_sys(), initialize(), main(), FETest< order, family, elem_type >::setUp(), SlitMeshRefinedSystemTest::setUp(), MeshfunctionDFEM::test_mesh_function_dfem(), MeshfunctionDFEM::test_mesh_function_dfem_grad(), MeshFunctionTest::test_p_level(), DefaultCouplingTest::testCoupling(), PointNeighborCouplingTest::testCoupling(), MeshInputTest::testExodusCopyElementSolution(), SystemsTest::testProjectCubeWithMeshFunction(), EquationSystemsTest::testRepartitionThenReinit(), and libMesh::MeshfreeSolutionTransfer::transfer().

project_solution() [3/3]

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

inherited

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

Definition at line 936 of file system_projection.C.

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

References fptr(), and gptr().

project_solution_on_reinit()

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

inlineinherited

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

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

Definition at line 802 of file system.h.

  { return _solution_projection; }

References libMesh::System::_solution_projection.

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

project_vector() [1/5]

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

protectedinherited

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

This method projects the vector via L2 projections or nodal interpolations on each element.

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

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

This method projects a solution from an old mesh to a current, refined mesh. The input vector old_v gives the solution on the old mesh, while the new_v gives the solution (to be computed) on the new mesh.

Definition at line 270 of file system_projection.C.

{
  LOG_SCOPE ("project_vector(old,new)", "System");
 
  new_v.clear();
 
#ifdef LIBMESH_ENABLE_AMR
 
  // Resize the new vector and get a serial version.
  NumericVector<Number> * new_vector_ptr = nullptr;
  std::unique_ptr<NumericVector<Number>> new_vector_built;
  NumericVector<Number> * local_old_vector;
  std::unique_ptr<NumericVector<Number>> local_old_vector_built;
  const NumericVector<Number> * old_vector_ptr = nullptr;
 
  ConstElemRange active_local_elem_range
    (this->get_mesh().active_local_elements_begin(),
     this->get_mesh().active_local_elements_end());
 
  // If the old vector was uniprocessor, make the new
  // vector uniprocessor
  if (old_v.type() == SERIAL)
    {
      new_v.init (this->n_dofs(), false, SERIAL);
      new_vector_ptr = &new_v;
      old_vector_ptr = &old_v;
    }
 
  // Otherwise it is a parallel, distributed vector, which
  // we need to localize.
  else if (old_v.type() == PARALLEL)
    {
      // Build a send list for efficient localization
      BuildProjectionList projection_list(*this);
      Threads::parallel_reduce (active_local_elem_range,
                                projection_list);
 
      // Create a sorted, unique send_list
      projection_list.unique();
 
      new_v.init (this->n_dofs(), this->n_local_dofs(), false, PARALLEL);
      new_vector_built = NumericVector<Number>::build(this->comm());
      local_old_vector_built = NumericVector<Number>::build(this->comm());
      new_vector_ptr = new_vector_built.get();
      local_old_vector = local_old_vector_built.get();
      new_vector_ptr->init(this->n_dofs(), false, SERIAL);
      local_old_vector->init(old_v.size(), false, SERIAL);
      old_v.localize(*local_old_vector, projection_list.send_list);
      local_old_vector->close();
      old_vector_ptr = local_old_vector;
    }
  else if (old_v.type() == GHOSTED)
    {
      // Build a send list for efficient localization
      BuildProjectionList projection_list(*this);
      Threads::parallel_reduce (active_local_elem_range,
                                projection_list);
 
      // Create a sorted, unique send_list
      projection_list.unique();
 
      new_v.init (this->n_dofs(), this->n_local_dofs(),
                  this->get_dof_map().get_send_list(), false, GHOSTED);
 
      local_old_vector_built = NumericVector<Number>::build(this->comm());
      new_vector_ptr = &new_v;
      local_old_vector = local_old_vector_built.get();
      local_old_vector->init(old_v.size(), old_v.local_size(),
                             projection_list.send_list, false, GHOSTED);
      old_v.localize(*local_old_vector, projection_list.send_list);
      local_old_vector->close();
      old_vector_ptr = local_old_vector;
    }
  else // unknown old_v.type()
    libmesh_error_msg("ERROR: Unknown old_v.type() == " << old_v.type());
 
  // Note that the above will have zeroed the new_vector.
  // Just to be sure, assert that new_vector_ptr and old_vector_ptr
  // were successfully set before trying to deref them.
  libmesh_assert(new_vector_ptr);
  libmesh_assert(old_vector_ptr);
 
  NumericVector<Number> & new_vector = *new_vector_ptr;
  const NumericVector<Number> & old_vector = *old_vector_ptr;
 
  const unsigned int n_variables = this->n_vars();
 
  if (n_variables)
    {
      std::vector<unsigned int> vars(n_variables);
      std::iota(vars.begin(), vars.end(), 0);
 
      // Use a typedef to make the calling sequence for parallel_for() a bit more readable
      typedef
        GenericProjector<OldSolutionValue<Number,   &FEMContext::point_value>,
                         OldSolutionValue<Gradient, &FEMContext::point_gradient>,
                         Number, VectorSetAction<Number>> FEMProjector;
 
      OldSolutionValue<Number,   &FEMContext::point_value>    f(*this, old_vector);
      OldSolutionValue<Gradient, &FEMContext::point_gradient> g(*this, old_vector);
      VectorSetAction<Number> setter(new_vector);
 
      FEMProjector projector(*this, f, &g, setter, vars);
      projector.project(active_local_elem_range);
 
      // Copy the SCALAR dofs from old_vector to new_vector
      // Note: We assume that all SCALAR dofs are on the
      // processor with highest ID
      if (this->processor_id() == (this->n_processors()-1))
        {
          const DofMap & dof_map = this->get_dof_map();
          for (auto var : IntRange<unsigned int>(0, this->n_vars()))
            if (this->variable(var).type().family == SCALAR)
              {
                // We can just map SCALAR dofs directly across
                std::vector<dof_id_type> new_SCALAR_indices, old_SCALAR_indices;
                dof_map.SCALAR_dof_indices (new_SCALAR_indices, var, false);
                dof_map.SCALAR_dof_indices (old_SCALAR_indices, var, true);
                for (auto i : index_range(new_SCALAR_indices))
                  new_vector.set(new_SCALAR_indices[i], old_vector(old_SCALAR_indices[i]));
              }
        }
    }
 
  new_vector.close();
 
  // If the old vector was serial, we probably need to send our values
  // to other processors
  //
  // FIXME: I'm not sure how to make a NumericVector do that without
  // creating a temporary parallel vector to use localize! - RHS
  if (old_v.type() == SERIAL)
    {
      std::unique_ptr<NumericVector<Number>> dist_v = NumericVector<Number>::build(this->comm());
      dist_v->init(this->n_dofs(), this->n_local_dofs(), false, PARALLEL);
      dist_v->close();
 
      for (auto i : IntRange<dof_id_type>(0, dist_v->size()))
        if (new_vector(i) != 0.0)
          dist_v->set(i, new_vector(i));
 
      dist_v->close();
 
      dist_v->localize (new_v, this->get_dof_map().get_send_list());
      new_v.close();
    }
  // If the old vector was parallel, we need to update it
  // and free the localized copies
  else if (old_v.type() == PARALLEL)
    {
      // We may have to set dof values that this processor doesn't
      // own in certain special cases, like LAGRANGE FIRST or
      // HERMITE THIRD elements on second-order meshes
      for (auto i : IntRange<dof_id_type>(0, new_v.size()))
        if (new_vector(i) != 0.0)
          new_v.set(i, new_vector(i));
      new_v.close();
    }
 
  if (is_adjoint == -1)
    this->get_dof_map().enforce_constraints_exactly(*this, &new_v);
  else if (is_adjoint >= 0)
    this->get_dof_map().enforce_adjoint_constraints_exactly(new_v,
                                                            is_adjoint);
 
#else
 
  // AMR is disabled: simply copy the vector
  new_v = old_v;
 
  libmesh_ignore(is_adjoint);
 
#endif // #ifdef LIBMESH_ENABLE_AMR
}

References libMesh::NumericVector< T >::clear(), libMesh::NumericVector< T >::close(), libMesh::NumericVector< T >::get(), libMesh::GHOSTED, libMesh::index_range(), libMesh::NumericVector< T >::init(), libMesh::Utility::iota(), libMesh::libmesh_assert(), libMesh::libmesh_ignore(), libMesh::NumericVector< T >::local_size(), libMesh::NumericVector< T >::localize(), n_vars, libMesh::PARALLEL, libMesh::Threads::parallel_reduce(), libMesh::SCALAR, libMesh::DofMap::SCALAR_dof_indices(), libMesh::BuildProjectionList::send_list, libMesh::SERIAL, libMesh::NumericVector< T >::set(), libMesh::NumericVector< T >::size(), libMesh::NumericVector< T >::type(), and libMesh::BuildProjectionList::unique().

project_vector() [2/5]

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

protectedinherited

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

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

Definition at line 252 of file system_projection.C.

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

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

project_vector() [3/5]

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

inherited

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

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

The function value f and its gradient g are user-provided cloneable functors. A gradient g is only required/used for projecting onto finite element spaces with continuous derivatives. 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.

Definition at line 1017 of file system_projection.C.

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

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

project_vector() [4/5]

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

inherited

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

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

The function value f and its gradient g are user-provided cloneable functors. A gradient g is only required/used for projecting onto finite element spaces with continuous derivatives. 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.

Definition at line 991 of file system_projection.C.

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

References libMesh::libmesh_assert().

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

project_vector() [5/5]

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

inherited

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

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

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

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

Definition at line 976 of file system_projection.C.

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

References fptr(), and gptr().

projection_matrix()

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

inherited

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

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

Definition at line 870 of file system_projection.C.

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

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

Referenced by libMesh::PetscDMWrapper::init_and_attach_petscdm(), SystemsTest::testProjectMatrix1D(), SystemsTest::testProjectMatrix2D(), and SystemsTest::testProjectMatrix3D().

prolong_vectors()

void libMesh::System::prolong_vectors ( )

virtualinherited

Prolong vectors after the mesh has refined.

Definition at line 380 of file system.C.

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

References libMesh::System::restrict_vectors().

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

qoi_parameter_hessian()

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

overridevirtualinherited

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

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

Reimplemented from libMesh::System.

Definition at line 1091 of file implicit_system.C.

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

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

qoi_parameter_hessian_vector_product()

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

overridevirtualinherited

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

Reimplemented from libMesh::System.

Definition at line 886 of file implicit_system.C.

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

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

qoi_parameter_sensitivity()

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

virtualinherited

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

Note

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

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

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

Definition at line 498 of file system.C.

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

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

re_update()

void libMesh::System::re_update ( )

virtualinherited

Re-update the local values when the mesh has changed.

This method takes the data updated by update() and makes it up-to-date on the current mesh.

Reimplemented in libMesh::TransientSystem< RBConstruction >.

Definition at line 429 of file system.C.

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

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

read_header()

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

inherited

Reads the basic data header for this System.

Definition at line 114 of file system_io.C.

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

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

Referenced by libMesh::EquationSystems::_read_impl(), and libMesh::RBEvaluation::read_in_vectors_from_multiple_files().

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.

Definition at line 309 of file system_io.C.

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

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

read_parallel_data() [1/2]

template<typename InValType >

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

inherited

Reads additional data, namely vectors, for this System.

This method may safely be called on a distributed-memory mesh. This method will read an individual file for each processor in the simulation where the local solution components for that processor are stored.

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

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

for each additional vector in the object

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

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

Definition at line 492 of file system_io.C.

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

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

read_parallel_data() [2/2]

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

inlineinherited

Non-templated version for backward compatibility.

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

Definition at line 1315 of file system.h.

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

read_SCALAR_dofs()

unsigned int libMesh::System::read_SCALAR_dofs ( const unsigned int  var, Xdr &  io, NumericVector< Number > *  vec  ) const

privateinherited

Reads the SCALAR dofs from the stream io and assigns the values to the appropriate entries of vec.

Returns

The number of dofs read.

Reads data and discards it if vec is a null pointer.

Definition at line 1120 of file system_io.C.

{
  unsigned int n_assigned_vals = 0; // the number of values assigned, this will be returned.
 
  // Processor 0 will read the block from the buffer stream and send it to the last processor
  const unsigned int n_SCALAR_dofs = this->variable(var).type().order.get_order();
  std::vector<Number> input_buffer(n_SCALAR_dofs);
  if (this->processor_id() == 0)
    io.data_stream(input_buffer.data(), n_SCALAR_dofs);
 
#ifdef LIBMESH_HAVE_MPI
  if (this->n_processors() > 1)
    {
      const Parallel::MessageTag val_tag = this->comm().get_unique_tag();
 
      // Post the receive on the last processor
      if (this->processor_id() == (this->n_processors()-1))
        this->comm().receive(0, input_buffer, val_tag);
 
      // Send the data to processor 0
      if (this->processor_id() == 0)
        this->comm().send(this->n_processors()-1, input_buffer, val_tag);
    }
#endif
 
  // Finally, set the SCALAR values
  if (this->processor_id() == (this->n_processors()-1))
    {
      const DofMap & dof_map = this->get_dof_map();
      std::vector<dof_id_type> SCALAR_dofs;
      dof_map.SCALAR_dof_indices(SCALAR_dofs, var);
 
      for (auto i : index_range(SCALAR_dofs))
        {
          if (vec)
            vec->set (SCALAR_dofs[i], input_buffer[i]);
          ++n_assigned_vals;
        }
    }
 
  return n_assigned_vals;
}

References libMesh::ParallelObject::comm(), libMesh::Xdr::data_stream(), libMesh::System::get_dof_map(), libMesh::OrderWrapper::get_order(), libMesh::index_range(), libMesh::ParallelObject::n_processors(), libMesh::FEType::order, libMesh::ParallelObject::processor_id(), libMesh::DofMap::SCALAR_dof_indices(), libMesh::NumericVector< T >::set(), libMesh::Variable::type(), and libMesh::System::variable().

Referenced by libMesh::System::read_serialized_vector(), and libMesh::System::read_serialized_vectors().

read_serialized_blocked_dof_objects()

template<typename iterator_type , typename InValType >

std::size_t libMesh::System::read_serialized_blocked_dof_objects ( const dof_id_type  n_objects, const iterator_type  begin, const iterator_type  end, const InValType  dummy, Xdr &  io, const std::vector< NumericVector< Number > * > &  vecs, const unsigned int  var_to_read = libMesh::invalid_uint  ) const

privateinherited

Reads an input vector from the stream io and assigns the values to a set of DofObjects.

This method uses blocked input and is safe to call on a distributed memory-mesh. Unless otherwise specified, all variables are read.

If an entry in vecs is a null pointer, the corresponding data is read (incrementing the file read location) but discarded.

Definition at line 810 of file system_io.C.

{
  //-------------------------------------------------------
  // General order: (IO format 0.7.4 & greater)
  //
  // for (objects ...)
  //   for (vecs ....)
  //     for (vars ....)
  //       for (comps ...)
  //
  // where objects are nodes or elements, sorted to be
  // partition independent,
  // vecs are one or more *identically distributed* solution
  // coefficient vectors, vars are one or more variables
  // to write, and comps are all the components for said
  // vars on the object.
 
  // variables to read.  Unless specified otherwise, defaults to _written_var_indices.
  std::vector<unsigned int> vars_to_read (_written_var_indices);
 
  if (var_to_read != libMesh::invalid_uint)
    {
      vars_to_read.clear();
      vars_to_read.push_back(var_to_read);
    }
 
  const unsigned int
    sys_num    = this->number(),
    num_vecs   = cast_int<unsigned int>(vecs.size());
  const dof_id_type
    io_blksize = cast_int<dof_id_type>(std::min(max_io_blksize, static_cast<std::size_t>(n_objs))),
    num_blks   = cast_int<unsigned int>(std::ceil(static_cast<double>(n_objs)/
                                                  static_cast<double>(io_blksize)));
 
  libmesh_assert_less_equal (_written_var_indices.size(), this->n_vars());
 
  std::size_t n_read_values=0;
 
  std::vector<std::vector<dof_id_type>> xfer_ids(num_blks);  // The global IDs and # of components for the local objects in all blocks
  std::vector<std::vector<Number>>      recv_vals(num_blks); // The raw values for the local objects in all blocks
  std::vector<Parallel::Request>
    id_requests(num_blks), val_requests(num_blks);
  std::vector<Parallel::MessageTag>
    id_tags(num_blks), val_tags(num_blks);
 
  // ------------------------------------------------------
  // First pass - count the number of objects in each block
  // traverse all the objects and figure out which block they
  // will ultimately live in.
  std::vector<std::size_t>
    xfer_ids_size  (num_blks,0),
    recv_vals_size (num_blks,0);
 
 
  for (iterator_type it=begin; it!=end; ++it)
    {
      const dof_id_type
        id    = (*it)->id(),
        block = id/io_blksize;
 
      libmesh_assert_less (block, num_blks);
 
      xfer_ids_size[block] += 2; // for each object, we send its id, as well as the total number of components for all variables
 
      dof_id_type n_comp_tot=0;
      for (const auto & var : vars_to_read)
        n_comp_tot += (*it)->n_comp(sys_num, var); // for each variable, we will receive the nonzero components
 
      recv_vals_size[block] += n_comp_tot*num_vecs;
    }
 
  // knowing the recv_vals_size[block] for each processor allows
  // us to sum them and find the global size for each block.
  std::vector<std::size_t> tot_vals_size(recv_vals_size);
  this->comm().sum (tot_vals_size);
 
 
  //------------------------------------------
  // Collect the ids & number of values needed
  // for all local objects, binning them into
  // 'blocks' that will be sent to processor 0
  for (dof_id_type blk=0; blk<num_blks; blk++)
    {
      // Each processor should build up its transfer buffers for its
      // local objects in [first_object,last_object).
      const dof_id_type
        first_object = blk*io_blksize,
        last_object  = std::min(cast_int<dof_id_type>((blk+1)*io_blksize), n_objs);
 
      // convenience
      std::vector<dof_id_type> & ids (xfer_ids[blk]);
      std::vector<Number> & vals (recv_vals[blk]);
 
      // we now know the number of values we will store for each block,
      // so we can do efficient preallocation
      ids.clear();  ids.reserve (xfer_ids_size[blk]);
      vals.resize(recv_vals_size[blk]);
 
      if (recv_vals_size[blk] != 0) // only if there are nonzero values to receive
        for (iterator_type it=begin; it!=end; ++it)
          if (((*it)->id() >= first_object) && // object in [first_object,last_object)
              ((*it)->id() <   last_object))
            {
              ids.push_back((*it)->id());
 
              unsigned int n_comp_tot=0;
 
              for (const auto & var : vars_to_read)
                n_comp_tot += (*it)->n_comp(sys_num, var);
 
              ids.push_back (n_comp_tot*num_vecs);
            }
 
#ifdef LIBMESH_HAVE_MPI
      id_tags[blk]  = this->comm().get_unique_tag(100*num_blks + blk);
      val_tags[blk] = this->comm().get_unique_tag(200*num_blks + blk);
 
      // nonblocking send the data for this block
      this->comm().send (0, ids,  id_requests[blk],  id_tags[blk]);
 
      // Go ahead and post the receive too
      this->comm().receive (0, vals, val_requests[blk], val_tags[blk]);
#endif
    }
 
  //---------------------------------------------------
  // Here processor 0 will read and distribute the data.
  // We have to do this block-wise to ensure that we
  // do not exhaust memory on processor 0.
 
  // give these variables scope outside the block to avoid reallocation
  std::vector<std::vector<dof_id_type>> recv_ids       (this->n_processors());
  std::vector<std::vector<Number>>      send_vals      (this->n_processors());
  std::vector<Parallel::Request>         reply_requests (this->n_processors());
  std::vector<unsigned int>              obj_val_offsets;          // map to traverse entry-wise rather than processor-wise
  std::vector<Number>                    input_vals;               // The input buffer for the current block
  std::vector<InValType>                 input_vals_tmp;               // The input buffer for the current block
 
  for (dof_id_type blk=0; blk<num_blks; blk++)
    {
      // Each processor should build up its transfer buffers for its
      // local objects in [first_object,last_object).
      const dof_id_type
        first_object  = blk*io_blksize,
        last_object   = std::min(cast_int<dof_id_type>((blk+1)*io_blksize), n_objs),
        n_objects_blk = last_object - first_object;
 
      // Processor 0 has a special job.  It needs to gather the requested indices
      // in [first_object,last_object) from all processors, read the data from
      // disk, and reply
      if (this->processor_id() == 0)
        {
          // we know the input buffer size for this block and can begin reading it now
          input_vals.resize(tot_vals_size[blk]);
          input_vals_tmp.resize(tot_vals_size[blk]);
 
          // a ThreadedIO object to perform asynchronous file IO
          ThreadedIO<InValType> threaded_io(io, input_vals_tmp);
          Threads::Thread async_io(threaded_io);
 
          // offset array. this will define where each object's values
          // map into the actual input_vals buffer.  this must get
          // 0-initialized because 0-component objects are not actually sent
          obj_val_offsets.resize (n_objects_blk);  std::fill (obj_val_offsets.begin(), obj_val_offsets.end(), 0);
          recv_vals_size.resize(this->n_processors()); // reuse this to count how many values are going to each processor
 
#ifndef NDEBUG
          std::size_t n_vals_blk = 0;
#endif
 
          // loop over all processors and process their index request
          for (processor_id_type comm_step=0, tnp=this->n_processors(); comm_step != tnp; ++comm_step)
            {
#ifdef LIBMESH_HAVE_MPI
              // blocking receive indices for this block, imposing no particular order on processor
              Parallel::Status id_status (this->comm().probe (Parallel::any_source, id_tags[blk]));
              std::vector<dof_id_type> & ids (recv_ids[id_status.source()]);
              std::size_t & n_vals_proc (recv_vals_size[id_status.source()]);
              this->comm().receive (id_status.source(), ids, id_tags[blk]);
#else
              // straight copy without MPI
              std::vector<dof_id_type> & ids (recv_ids[0]);
              std::size_t & n_vals_proc (recv_vals_size[0]);
              ids = xfer_ids[blk];
#endif
 
              n_vals_proc = 0;
 
              // note its possible we didn't receive values for objects in
              // this block if they have no components allocated.
              for (std::size_t idx=0, sz=ids.size(); idx<sz; idx+=2)
                {
                  const dof_id_type
                    local_idx          = ids[idx+0]-first_object,
                    n_vals_tot_allvecs = ids[idx+1];
 
                  libmesh_assert_less (local_idx, n_objects_blk);
 
                  obj_val_offsets[local_idx] = n_vals_tot_allvecs;
                  n_vals_proc += n_vals_tot_allvecs;
                }
 
#ifndef NDEBUG
              n_vals_blk += n_vals_proc;
#endif
            }
 
          // We need the offsets into the input_vals vector for each object.
          // fortunately, this is simply the partial sum of the total number
          // of components for each object
          std::partial_sum(obj_val_offsets.begin(), obj_val_offsets.end(),
                           obj_val_offsets.begin());
 
          libmesh_assert_equal_to (n_vals_blk, obj_val_offsets.back());
          libmesh_assert_equal_to (n_vals_blk, tot_vals_size[blk]);
 
          // Wait for read completion
          async_io.join();
          // now copy the values back to the main vector for transfer
          for (auto i_val : index_range(input_vals))
            input_vals[i_val] = input_vals_tmp[i_val];
 
          n_read_values += input_vals.size();
 
          // pack data replies for each processor
          for (auto proc : IntRange<processor_id_type>(0, this->n_processors()))
            {
              const std::vector<dof_id_type> & ids (recv_ids[proc]);
              std::vector<Number> & vals (send_vals[proc]);
              const std::size_t & n_vals_proc (recv_vals_size[proc]);
 
              vals.clear();  vals.reserve(n_vals_proc);
 
              for (std::size_t idx=0, sz=ids.size(); idx<sz; idx+=2)
                {
                  const dof_id_type
                    local_idx          = ids[idx+0]-first_object,
                    n_vals_tot_allvecs = ids[idx+1];
 
                  std::vector<Number>::const_iterator in_vals(input_vals.begin());
                  if (local_idx != 0)
                    std::advance (in_vals, obj_val_offsets[local_idx-1]);
 
                  for (unsigned int val=0; val<n_vals_tot_allvecs; val++, ++in_vals)
                    {
                      libmesh_assert (in_vals != input_vals.end());
                      //libMesh::out << "*in_vals=" << *in_vals << '\n';
                      vals.push_back(*in_vals);
                    }
                }
 
#ifdef LIBMESH_HAVE_MPI
              // send the relevant values to this processor
              this->comm().send (proc, vals, reply_requests[proc], val_tags[blk]);
#else
              recv_vals[blk] = vals;
#endif
            }
        } // end processor 0 read/reply
 
      // all processors complete the (already posted) read for this block
      {
        Parallel::wait (val_requests[blk]);
 
        const std::vector<Number> & vals (recv_vals[blk]);
        std::vector<Number>::const_iterator val_it(vals.begin());
 
        if (!recv_vals[blk].empty()) // nonzero values to receive
          for (iterator_type it=begin; it!=end; ++it)
            if (((*it)->id() >= first_object) && // object in [first_object,last_object)
                ((*it)->id() <   last_object))
              // unpack & set the values
              for (auto & vec : vecs)
                for (const auto & var : vars_to_read)
                  {
                    const unsigned int n_comp = (*it)->n_comp(sys_num, var);
 
                    for (unsigned int comp=0; comp<n_comp; comp++, ++val_it)
                      {
                        const dof_id_type dof_index = (*it)->dof_number (sys_num, var, comp);
                        libmesh_assert (val_it != vals.end());
                        if (vec)
                          {
                            libmesh_assert_greater_equal (dof_index, vec->first_local_index());
                            libmesh_assert_less (dof_index, vec->last_local_index());
                            //libMesh::out << "dof_index, *val_it = \t" << dof_index << ", " << *val_it << '\n';
                            vec->set (dof_index, *val_it);
                          }
                      }
                  }
      }
 
      // processor 0 needs to make sure all replies have been handed off
      if (this->processor_id () == 0)
        Parallel::wait(reply_requests);
    }
 
  Parallel::wait(id_requests);
 
  return n_read_values;
}

References libMesh::System::_written_var_indices, libMesh::ParallelObject::comm(), end, libMesh::MeshTools::Generation::Private::idx(), libMesh::index_range(), libMesh::invalid_uint, libMesh::Threads::NonConcurrentThread::join(), libMesh::libmesh_assert(), libMesh::ParallelObject::n_processors(), libMesh::System::n_vars(), libMesh::System::number(), and libMesh::ParallelObject::processor_id().

Referenced by libMesh::System::read_serialized_vector(), and libMesh::System::read_serialized_vectors().

read_serialized_data() [1/2]

template<typename InValType >

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

inherited

Reads additional data, namely vectors, for this System.

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

Definition at line 724 of file system_io.C.

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

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

Referenced by libMesh::TransientRBConstruction::initialize_truth(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), and libMesh::RBConstruction::read_riesz_representors_from_files().

read_serialized_data() [2/2]

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

inlineinherited

Non-templated version for backward compatibility.

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

Definition at line 1273 of file system.h.

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

read_serialized_vector() [1/2]

numeric_index_type libMesh::System::read_serialized_vector ( Xdr &  io, NumericVector< Number > &  vec  )

inlineprivateinherited

Non-templated version for backward compatibility.

Reads a vector for this System. This method may safely be called on a distributed-memory mesh.

Returns

The length of the vector read.

Definition at line 1835 of file system.h.

  { return read_serialized_vector<Number>(io, &vec); }

read_serialized_vector() [2/2]

template<typename InValType >

numeric_index_type libMesh::System::read_serialized_vector ( Xdr &  io, NumericVector< Number > *  vec  )

privateinherited

Reads a vector for this System.

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

Returns

The length of the vector read.

Reads data and discards it if vec is a null pointer.

Definition at line 1167 of file system_io.C.

{
  parallel_object_only();
 
#ifndef NDEBUG
  // In parallel we better be reading a parallel vector -- if not
  // we will not set all of its components below!!
  if (this->n_processors() > 1 && vec)
    {
      libmesh_assert (vec->type() == PARALLEL ||
                      vec->type() == GHOSTED);
    }
#endif
 
  libmesh_assert (io.reading());
 
  // vector length
  unsigned int vector_length=0; // FIXME?  size_t would break binary compatibility...
#ifndef NDEBUG
  std::size_t n_assigned_vals=0;
#endif
 
  // Get the buffer size
  if (this->processor_id() == 0)
    io.data(vector_length, "# vector length");
  this->comm().broadcast(vector_length);
 
  const unsigned int nv = cast_int<unsigned int>
    (this->_written_var_indices.size());
  const dof_id_type
    n_nodes = this->get_mesh().n_nodes(),
    n_elem  = this->get_mesh().n_elem();
 
  libmesh_assert_less_equal (nv, this->n_vars());
 
  // for newer versions, read variables node/elem major
  if (io.version() >= LIBMESH_VERSION_ID(0,7,4))
    {
      //---------------------------------
      // Collect the values for all nodes
#ifndef NDEBUG
      n_assigned_vals +=
#endif
        this->read_serialized_blocked_dof_objects (n_nodes,
                                                   this->get_mesh().local_nodes_begin(),
                                                   this->get_mesh().local_nodes_end(),
                                                   InValType(),
                                                   io,
                                                   std::vector<NumericVector<Number> *> (1,vec));
 
 
      //------------------------------------
      // Collect the values for all elements
#ifndef NDEBUG
      n_assigned_vals +=
#endif
        this->read_serialized_blocked_dof_objects (n_elem,
                                                   this->get_mesh().local_elements_begin(),
                                                   this->get_mesh().local_elements_end(),
                                                   InValType(),
                                                   io,
                                                   std::vector<NumericVector<Number> *> (1,vec));
    }
 
  // for older versions, read variables var-major
  else
    {
      // Loop over each variable in the system, and then each node/element in the mesh.
      for (unsigned int data_var=0; data_var<nv; data_var++)
        {
          const unsigned int var = _written_var_indices[data_var];
          if (this->variable(var).type().family != SCALAR)
            {
              //---------------------------------
              // Collect the values for all nodes
#ifndef NDEBUG
              n_assigned_vals +=
#endif
                this->read_serialized_blocked_dof_objects (n_nodes,
                                                           this->get_mesh().local_nodes_begin(),
                                                           this->get_mesh().local_nodes_end(),
                                                           InValType(),
                                                           io,
                                                           std::vector<NumericVector<Number> *> (1,vec),
                                                           var);
 
 
              //------------------------------------
              // Collect the values for all elements
#ifndef NDEBUG
              n_assigned_vals +=
#endif
                this->read_serialized_blocked_dof_objects (n_elem,
                                                           this->get_mesh().local_elements_begin(),
                                                           this->get_mesh().local_elements_end(),
                                                           InValType(),
                                                           io,
                                                           std::vector<NumericVector<Number> *> (1,vec),
                                                           var);
            } // end variable loop
        }
    }
 
  //-------------------------------------------
  // Finally loop over all the SCALAR variables
  for (unsigned int data_var=0; data_var<nv; data_var++)
    {
      const unsigned int var = _written_var_indices[data_var];
      if (this->variable(var).type().family == SCALAR)
        {
#ifndef NDEBUG
          n_assigned_vals +=
#endif
            this->read_SCALAR_dofs (var, io, vec);
        }
    }
 
  if (vec)
    vec->close();
 
#ifndef NDEBUG
  this->comm().sum (n_assigned_vals);
  libmesh_assert_equal_to (n_assigned_vals, vector_length);
#endif
 
  return vector_length;
}

References libMesh::System::_written_var_indices, libMesh::NumericVector< T >::close(), libMesh::ParallelObject::comm(), libMesh::Xdr::data(), libMesh::System::get_mesh(), libMesh::GHOSTED, libMesh::libmesh_assert(), libMesh::MeshBase::n_elem(), libMesh::MeshTools::n_elem(), n_nodes, libMesh::MeshBase::n_nodes(), libMesh::ParallelObject::n_processors(), libMesh::System::n_vars(), libMesh::PARALLEL, libMesh::ParallelObject::processor_id(), libMesh::System::read_SCALAR_dofs(), libMesh::System::read_serialized_blocked_dof_objects(), libMesh::Xdr::reading(), libMesh::SCALAR, libMesh::NumericVector< T >::type(), libMesh::System::variable(), and libMesh::Xdr::version().

read_serialized_vectors() [1/2]

template<typename InValType >

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

inherited

Read a number of identically distributed vectors.

This method allows for optimization for the multiple vector case by only communicating the metadata once.

Definition at line 2199 of file system_io.C.

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

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

Referenced by libMesh::RBEvaluation::read_in_vectors_from_multiple_files().

read_serialized_vectors() [2/2]

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

inlineinherited

Non-templated version for backward compatibility.

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

Definition at line 1293 of file system.h.

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

reinit()

void libMesh::DifferentiableSystem::reinit ( )

overridevirtualinherited

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

Reimplemented from libMesh::ImplicitSystem.

Definition at line 96 of file diff_system.C.

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

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

reinit_constraints()

void libMesh::System::reinit_constraints ( )

virtualinherited

Reinitializes the constraints for this system.

Definition at line 397 of file system.C.

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

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

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

release_linear_solver()

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

overridevirtualinherited

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

Reimplemented from libMesh::ImplicitSystem.

Definition at line 194 of file diff_system.C.

{
}

remove_matrix()

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

inherited

Removes the additional matrix mat_name from this system.

Definition at line 221 of file implicit_system.C.

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

References libMesh::ImplicitSystem::_matrices.

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

remove_vector()

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

inherited

Removes the additional vector vec_name from this system.

Definition at line 699 of file system.C.

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

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

request_matrix() [1/2]

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

inherited

Returns

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

Definition at line 249 of file implicit_system.C.

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

References libMesh::ImplicitSystem::_matrices.

request_matrix() [2/2]

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

inherited

Returns

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

Definition at line 236 of file implicit_system.C.

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

References libMesh::ImplicitSystem::_matrices.

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

request_vector() [1/4]

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

inherited

Returns

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

Definition at line 728 of file system.C.

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

References libMesh::System::_vectors.

request_vector() [2/4]

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

inherited

Returns

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

Definition at line 716 of file system.C.

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

References libMesh::System::_vectors.

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

request_vector() [3/4]

NumericVector< Number > * libMesh::System::request_vector ( const unsigned int  vec_num )

inherited

Returns

A writable pointer to this system's additional vector number vec_num (where the vectors are counted starting with 0), or nullptr if the system has no such vector.

Definition at line 757 of file system.C.

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

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

request_vector() [4/4]

const NumericVector< Number > * libMesh::System::request_vector ( const unsigned int  vec_num ) const

inherited

Returns

A const pointer to this system's additional vector number vec_num (where the vectors are counted starting with 0), or nullptr if the system has no such vector.

Definition at line 740 of file system.C.

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

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

restrict_solve_to()

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

virtualinherited

After calling this method, any solve will be restricted to the given subdomain.

To disable this mode, call this method with subset being a nullptr.

Reimplemented in libMesh::LinearImplicitSystem.

Definition at line 453 of file system.C.

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

restrict_vectors()

void libMesh::System::restrict_vectors ( )

virtualinherited

Restrict vectors after the mesh has coarsened.

Definition at line 324 of file system.C.

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

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

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

sensitivity_solve()

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

overridevirtualinherited

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

Returns

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

Reimplemented from libMesh::System.

Definition at line 301 of file implicit_system.C.

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

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

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

set_adjoint_already_solved()

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

inlineinherited

Setter for the adjoint_already_solved boolean.

Definition at line 402 of file system.h.

  { adjoint_already_solved = setting;}

References libMesh::System::adjoint_already_solved.

Referenced by main().

set_basic_system_only()

void libMesh::System::set_basic_system_only ( )

inlineinherited

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

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

Definition at line 2147 of file system.h.

{
  _basic_system_only = true;
}

References libMesh::System::_basic_system_only.

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

set_mesh_system()

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

inlinevirtualinherited

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

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

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

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

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

Definition at line 581 of file diff_physics.h.

{
  // 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;
}

References libMesh::DifferentiablePhysics::_mesh_sys.

Referenced by SolidSystem::init_data().

set_mesh_x_var()

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

inlinevirtualinherited

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

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

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

Definition at line 601 of file diff_physics.h.

{
  _mesh_x_var = var;
}

References libMesh::DifferentiablePhysics::_mesh_x_var.

Referenced by SolidSystem::init_data().

set_mesh_y_var()

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

inlinevirtualinherited

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

Definition at line 609 of file diff_physics.h.

{
  _mesh_y_var = var;
}

References libMesh::DifferentiablePhysics::_mesh_y_var.

Referenced by SolidSystem::init_data().

set_mesh_z_var()

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

inlinevirtualinherited

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

Definition at line 617 of file diff_physics.h.

{
  _mesh_z_var = var;
}

References libMesh::DifferentiablePhysics::_mesh_z_var.

Referenced by SolidSystem::init_data().

set_numerical_jacobian_h_for_var()

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

inlineinherited

Definition at line 269 of file fem_system.h.

{
  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;
}

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

set_time_solver()

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

inlineinherited

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

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

Definition at line 241 of file diff_system.h.

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

References libMesh::DifferentiableSystem::time_solver.

set_vector_as_adjoint()

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

inherited

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

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

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

Definition at line 873 of file system.C.

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

References libMesh::System::_vector_is_adjoint.

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

set_vector_preservation()

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

inherited

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

Definition at line 855 of file system.C.

{
  _vector_projections[vec_name] = preserve;
}

References libMesh::System::_vector_projections.

Referenced by main().

side_constraint()

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

inlinevirtualinherited

Adds the constraint contribution on side of elem to elem_residual.

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

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

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

Reimplemented in LaplaceSystem, LaplaceSystem, LaplaceSystem, and NavierSystem.

Definition at line 192 of file diff_physics.h.

                                               {
    return request_jacobian;
  }

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

side_damping_residual()

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

inlinevirtualinherited

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

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

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

Definition at line 392 of file diff_physics.h.

                                                     {
    return request_jacobian;
  }

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

side_mass_residual()

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

inlinevirtualinherited

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

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

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

Definition at line 336 of file diff_physics.h.

                                                  {
    return request_jacobian;
  }

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

side_postprocess()

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

inlinevirtualinherited

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

Reimplemented in LaplaceSystem, and LaplaceSystem.

Definition at line 287 of file diff_system.h.

{}

side_qoi()

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

inlinevirtualinherited

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

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

Reimplemented in CoupledSystemQoI.

Definition at line 133 of file diff_qoi.h.

  {}

side_qoi_derivative()

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

inlinevirtualinherited

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

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

Reimplemented in LaplaceSystem, LaplaceSystem, and CoupledSystemQoI.

Definition at line 145 of file diff_qoi.h.

  {}

side_time_derivative()

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

inlinevirtualinherited

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

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

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

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

Reimplemented in ElasticitySystem, CurlCurlSystem, CurlCurlSystem, and SolidSystem.

Definition at line 172 of file diff_physics.h.

                                                    {
    return request_jacobian;
  }

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

solve()

void 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.

Definition at line 1046 of file fem_system.C.

{
  // We are solving the primal problem
  Parent::solve();
 
  // On a moving mesh we want the mesh to reflect the new solution
  this->mesh_position_set();
}

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

Referenced by main().

swap_physics()

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

inherited

Swap current physics object with external object.

Definition at line 353 of file diff_system.C.

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

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

system()

sys_type& libMesh::ImplicitSystem::system ( )

inlineinherited

Returns

A reference to *this.

Definition at line 82 of file implicit_system.h.

{ return *this; }

system_type()

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

inlineoverridevirtualinherited

Returns

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

Reimplemented from libMesh::ExplicitSystem.

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

Definition at line 118 of file implicit_system.h.

{ return "Implicit"; }

thread_join()

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.

Definition at line 33 of file diff_qoi.C.

{
  for (auto i : index_range(qoi))
    qoi[i] += other_qoi[i];
}

References libMesh::index_range().

time_evolving() [1/2]

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

inlinevirtualinherited

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

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

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

Definition at line 250 of file diff_physics.h.

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

Referenced by libMesh::DifferentiableSystem::add_second_order_dot_vars(), CurlCurlSystem::init_data(), and HeatSystem::init_data().

time_evolving() [2/2]

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.

Definition at line 46 of file diff_physics.C.

{
  if (order != 1 && order != 2)
    libmesh_error_msg("Input order must be 1 or 2!");
 
  if (_time_evolving.size() <= var)
    _time_evolving.resize(var+1, 0);
 
  _time_evolving[var] = order;
 
  if (order == 1)
    _first_order_vars.insert(var);
  else
    _second_order_vars.insert(var);
}

References libMesh::DifferentiablePhysics::_first_order_vars, libMesh::DifferentiablePhysics::_second_order_vars, and libMesh::DifferentiablePhysics::_time_evolving.

u()

virtual Number ConstantFirstOrderODE::u ( Real  t )

inlinevirtual

Exact solution as a function of time t.

Implements FirstOrderScalarSystemBase.

Definition at line 28 of file first_order_unsteady_solver_test.C.

  { return Real(50)/21*t; }

References libMesh::Real.

update()

void libMesh::System::update ( )

virtualinherited

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

Reimplemented in SolidSystem.

Definition at line 408 of file system.C.

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

References libMesh::System::_dof_map, libMesh::System::current_local_solution, libMesh::libmesh_assert(), and libMesh::System::solution.

Referenced by libMesh::__libmesh_petsc_diff_solver_jacobian(), libMesh::__libmesh_petsc_diff_solver_residual(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::FEMSystem::assemble_qoi(), libMesh::FEMSystem::assemble_qoi_derivative(), libMesh::NonlinearImplicitSystem::assembly(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::NewmarkSolver::compute_initial_accel(), LinearElasticityWithContact::compute_stresses(), LinearElasticity::compute_stresses(), compute_stresses(), LargeDeformationElasticity::compute_stresses(), libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::GMVIO::copy_nodal_solution(), libMesh::ExodusII_IO::copy_scalar_solution(), DMlibMeshFunction(), DMlibMeshJacobian(), libMesh::RBEIMConstruction::enrich_RB_space(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::CondensedEigenSystem::get_eigenpair(), libMesh::TransientRBConstruction::initialize_truth(), libMesh::libmesh_petsc_snes_jacobian(), libMesh::libmesh_petsc_snes_residual_helper(), libMesh::NewtonSolver::line_search(), libMesh::RBEIMConstruction::load_basis_function(), libMesh::RBConstruction::load_basis_function(), libMesh::RBEIMConstruction::load_rb_solution(), libMesh::RBConstruction::load_rb_solution(), libMesh::TransientRBConstruction::load_rb_solution(), libMesh::FEMSystem::mesh_position_get(), HeatSystem::perturb_accumulate_residuals(), libMesh::FEMSystem::postprocess(), libMesh::ImplicitSystem::qoi_parameter_hessian(), libMesh::NewtonSolver::solve(), libMesh::ExplicitSystem::solve(), libMesh::LinearImplicitSystem::solve(), libMesh::NonlinearImplicitSystem::solve(), libMesh::OptimizationSystem::solve(), libMesh::RBConstruction::solve_for_matrix_and_rhs(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::DirectSolutionTransfer::transfer(), and libMesh::RBEIMConstruction::truth_solve().

update_global_solution() [1/2]

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

inherited

Fill the input vector global_soln so that it contains the global solution on all processors.

Requires communication with all other processors.

Definition at line 642 of file system.C.

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

References libMesh::System::solution.

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

update_global_solution() [2/2]

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

inherited

Fill the input vector global_soln so that it contains the global solution on processor dest_proc.

Requires communication with all other processors.

Definition at line 651 of file system.C.

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

References libMesh::System::solution.

user_assembly()

void libMesh::System::user_assembly ( )

virtualinherited

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

Definition at line 1910 of file system.C.

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

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

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

user_constrain()

void libMesh::System::user_constrain ( )

virtualinherited

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

Definition at line 1924 of file system.C.

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

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

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

user_initialization()

void libMesh::System::user_initialization ( )

virtualinherited

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

Definition at line 1896 of file system.C.

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

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

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

user_QOI()

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

virtualinherited

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

Definition at line 1938 of file system.C.

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

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

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

user_QOI_derivative()

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

virtualinherited

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

Definition at line 1952 of file system.C.

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

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

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

variable()

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

inlineinherited

Return a constant reference to Variable var.

Definition at line 2183 of file system.h.

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

References libMesh::System::_variables.

Referenced by libMesh::ExactSolution::_compute_error(), libMesh::PetscDMWrapper::add_dofs_to_section(), libMesh::DifferentiableSystem::add_second_order_dot_vars(), libMesh::EquationSystems::build_discontinuous_solution_vector(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::FirstOrderUnsteadySolver::compute_second_order_eqns(), libMesh::DifferentiableSystem::have_first_order_scalar_vars(), libMesh::DifferentiableSystem::have_second_order_scalar_vars(), main(), libMesh::DifferentiablePhysics::nonlocal_mass_residual(), libMesh::GenericProjector< FFunctor, GFunctor, FValue, ProjectionAction >::SortAndCopy::operator()(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::System::read_parallel_data(), libMesh::System::read_SCALAR_dofs(), libMesh::System::read_serialized_vector(), libMesh::System::read_serialized_vectors(), libMesh::PetscDMWrapper::set_point_range_in_section(), libMesh::System::write_header(), libMesh::System::write_parallel_data(), libMesh::System::write_serialized_vector(), and libMesh::System::write_serialized_vectors().

variable_group()

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

inlineinherited

Return a constant reference to VariableGroup vg.

Definition at line 2193 of file system.h.

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

References libMesh::System::_variable_groups.

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

variable_name()

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

inlineinherited

Returns

The name of variable i.

Definition at line 2203 of file system.h.

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

References libMesh::System::_variables.

Referenced by libMesh::System::add_variable(), libMesh::System::add_variables(), libMesh::EquationSystems::build_discontinuous_solution_vector(), libMesh::PetscDMWrapper::build_section(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::ExactSolution::ExactSolution(), libMesh::EquationSystems::find_variable_numbers(), main(), output_norms(), libMesh::petsc_auto_fieldsplit(), MeshInputTest::testExodusWriteElementDataFromDiscontinuousNodalData(), libMesh::System::write_header(), and libMesh::Nemesis_IO_Helper::write_nodal_solution().

variable_number()

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

inherited

Returns

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

Definition at line 1232 of file system.C.

{
  auto var_num = libmesh_map_find(_variable_numbers, var);
  libmesh_assert_equal_to (_variables[var_num].name(), var);
  return var_num;
}

References libMesh::System::_variable_numbers, libMesh::System::_variables, and libMesh::System::name().

Referenced by libMesh::ExactSolution::_compute_error(), LinearElasticity::assemble(), AssembleOptimization::assemble_A_and_F(), assemble_elasticity(), assemble_matrix_and_rhs(), assemble_shell(), assemble_stokes(), LinearElasticityWithContact::compute_stresses(), LinearElasticity::compute_stresses(), compute_stresses(), LargeDeformationElasticity::compute_stresses(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::GMVIO::copy_nodal_solution(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::ExactErrorEstimator::find_squared_element_error(), LargeDeformationElasticity::jacobian(), line_print(), main(), LinearElasticityWithContact::move_mesh(), libMesh::System::read_header(), LargeDeformationElasticity::residual(), LinearElasticityWithContact::residual_and_jacobian(), OverlappingAlgebraicGhostingTest::run_ghosting_test(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), OverlappingTestBase::setup_coupling_matrix(), libMesh::DTKAdapter::update_variable_values(), libMesh::System::variable_scalar_number(), libMesh::System::variable_type(), libMesh::EnsightIO::write_scalar_ascii(), and libMesh::EnsightIO::write_vector_ascii().

variable_scalar_number() [1/2]

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

inlineinherited

Returns

An index, starting from 0 for the first component of the first variable, and incrementing for each component of each (potentially vector-valued) variable in the system in order. For systems with only scalar-valued variables, this will be the same as variable_number(var)

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

Definition at line 2214 of file system.h.

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

References libMesh::System::variable_number().

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

variable_scalar_number() [2/2]

unsigned int libMesh::System::variable_scalar_number ( unsigned int  var_num, unsigned int  component  ) const

inlineinherited

Returns

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

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

Definition at line 2224 of file system.h.

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

References libMesh::System::_variables.

variable_type() [1/2]

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

inlineinherited

Returns

The finite element type for variable var.

Definition at line 2243 of file system.h.

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

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

variable_type() [2/2]

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

inlineinherited

Returns

The finite element type variable number i.

Definition at line 2233 of file system.h.

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

References libMesh::System::_variables.

Referenced by libMesh::System::add_variable(), libMesh::System::add_variables(), assemble(), assemble_ellipticdg(), assemble_shell(), assemble_stokes(), libMesh::FEMContext::attach_quadrature_rules(), libMesh::EquationSystems::build_discontinuous_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::GMVIO::copy_nodal_solution(), libMesh::DGFEMContext::DGFEMContext(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::FEMContext::find_hardest_fe_type(), libMesh::EquationSystems::find_variable_numbers(), libMesh::FEMSystem::init_context(), libMesh::FEMContext::init_internal_data(), RationalMapTest< elem_type >::setUp(), FETest< order, family, elem_type >::setUp(), libMesh::System::write_header(), libMesh::Nemesis_IO_Helper::write_nodal_solution(), libMesh::EnsightIO::write_scalar_ascii(), and libMesh::EnsightIO::write_vector_ascii().

vector_is_adjoint()

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

inherited

Returns

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

Definition at line 884 of file system.C.

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

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

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

vector_name() [1/2]

const std::string & libMesh::System::vector_name ( const NumericVector< Number > &  vec_reference ) const

inherited

Returns

The name of a system vector, given a reference to that vector

Definition at line 834 of file system.C.

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

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

vector_name() [2/2]

const std::string & libMesh::System::vector_name ( const unsigned int  vec_num ) const

inherited

Returns

The name of this system's additional vector number vec_num (where the vectors are counted starting with 0).

Definition at line 820 of file system.C.

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

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

Referenced by main().

vector_preservation()

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

inherited

Returns

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

Definition at line 863 of file system.C.

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

References libMesh::System::_vector_projections.

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

vectors_begin() [1/2]

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

inlineinherited

Beginning of vectors container.

Definition at line 2295 of file system.h.

{
  return _vectors.begin();
}

References libMesh::System::_vectors.

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

vectors_begin() [2/2]

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

inlineinherited

Beginning of vectors container.

Definition at line 2301 of file system.h.

{
  return _vectors.begin();
}

References libMesh::System::_vectors.

vectors_end() [1/2]

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

inlineinherited

End of vectors container.

Definition at line 2307 of file system.h.

{
  return _vectors.end();
}

References libMesh::System::_vectors.

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

vectors_end() [2/2]

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

inlineinherited

End of vectors container.

Definition at line 2313 of file system.h.

{
  return _vectors.end();
}

References libMesh::System::_vectors.

weighted_sensitivity_adjoint_solve()

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

overridevirtualinherited

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

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

Returns

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

Reimplemented from libMesh::System.

Definition at line 412 of file implicit_system.C.

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

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

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

weighted_sensitivity_solve()

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

overridevirtualinherited

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

Returns

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

Reimplemented from libMesh::System.

Definition at line 560 of file implicit_system.C.

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

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

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

write_header()

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

inherited

Writes the basic data header for this System.

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

for this system

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

for each variable in the system

6.) The name of the variable (string)

6.1.) subdomain where the variable lives

7.) Combined in an FEType:

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

end variable loop

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

for each additional vector in the system object

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

end system

Definition at line 1298 of file system_io.C.

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

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

Referenced by libMesh::RBEvaluation::write_out_vectors().

write_parallel_data()

void libMesh::System::write_parallel_data ( Xdr &  io, const bool  write_additional_data  ) const

inherited

Writes additional data, namely vectors, for this System.

This method may safely be called on a distributed-memory mesh. This method will create an individual file for each processor in the simulation where the local solution components for that processor will be stored.

This method implements the output of the vectors contained in this System object, embedded in the output of an EquationSystems<T_sys>.

9.) The global solution vector, re-ordered to be node-major (More on this later.)

for each additional vector in the object

10.) The global additional vector, re-ordered to be node-major (More on this later.)

Note that the actual IO is handled through the Xdr class (to be renamed later?) which provides a uniform interface to both the XDR (eXternal Data Representation) interface and standard ASCII output. Thus this one section of code will read XDR or ASCII files with no changes.

Definition at line 1503 of file system_io.C.

{
  // PerfLog pl("IO Performance",false);
  // pl.push("write_parallel_data");
  // std::size_t total_written_size = 0;
 
  std::string comment;
 
  libmesh_assert (io.writing());
 
  std::vector<Number> io_buffer; io_buffer.reserve(this->solution->local_size());
 
  // build the ordered nodes and element maps.
  // when writing/reading parallel files we need to iterate
  // over our nodes/elements in order of increasing global id().
  // however, this is not guaranteed to be ordering we obtain
  // by using the node_iterators/element_iterators directly.
  // so build a set, sorted by id(), that provides the ordering.
  // further, for memory economy build the set but then transfer
  // its contents to vectors, which will be sorted.
  std::vector<const DofObject *> ordered_nodes, ordered_elements;
  {
    std::set<const DofObject *, CompareDofObjectsByID>
      ordered_nodes_set (this->get_mesh().local_nodes_begin(),
                         this->get_mesh().local_nodes_end());
 
    ordered_nodes.insert(ordered_nodes.end(),
                         ordered_nodes_set.begin(),
                         ordered_nodes_set.end());
  }
  {
    std::set<const DofObject *, CompareDofObjectsByID>
      ordered_elements_set (this->get_mesh().local_elements_begin(),
                            this->get_mesh().local_elements_end());
 
    ordered_elements.insert(ordered_elements.end(),
                            ordered_elements_set.begin(),
                            ordered_elements_set.end());
  }
 
  const unsigned int sys_num = this->number();
  const unsigned int nv      = this->n_vars();
 
  // Loop over each non-SCALAR variable and each node, and write out the value.
  for (unsigned int var=0; var<nv; var++)
    if (this->variable(var).type().family != SCALAR)
      {
        // First write the node DOF values
        for (const auto & node : ordered_nodes)
          for (auto comp : IntRange<unsigned int>(0, node->n_comp(sys_num,var)))
            {
              libmesh_assert_not_equal_to (node->dof_number(sys_num, var, comp),
                                           DofObject::invalid_id);
 
              io_buffer.push_back((*this->solution)(node->dof_number(sys_num, var, comp)));
            }
 
        // Then write the element DOF values
        for (const auto & elem : ordered_elements)
          for (auto comp : IntRange<unsigned int>(0, elem->n_comp(sys_num,var)))
            {
              libmesh_assert_not_equal_to (elem->dof_number(sys_num, var, comp),
                                           DofObject::invalid_id);
 
              io_buffer.push_back((*this->solution)(elem->dof_number(sys_num, var, comp)));
            }
      }
 
  // Finally, write the SCALAR data on the last processor
  for (auto var : IntRange<unsigned int>(0, this->n_vars()))
    if (this->variable(var).type().family == SCALAR)
      {
        if (this->processor_id() == (this->n_processors()-1))
          {
            const DofMap & dof_map = this->get_dof_map();
            std::vector<dof_id_type> SCALAR_dofs;
            dof_map.SCALAR_dof_indices(SCALAR_dofs, var);
 
            for (auto dof : SCALAR_dofs)
              io_buffer.push_back((*this->solution)(dof));
          }
      }
 
  // 9.)
  //
  // Actually write the reordered solution vector
  // for the ith system to disk
 
  // set up the comment
  {
    comment = "# System \"";
    comment += this->name();
    comment += "\" Solution Vector";
  }
 
  io.data (io_buffer, comment.c_str());
 
  // total_written_size += io_buffer.size();
 
  // Only write additional vectors if wanted
  if (write_additional_data)
    {
      for (auto & pr : _vectors)
        {
          io_buffer.clear();
          io_buffer.reserve(pr.second->local_size());
 
          // Loop over each non-SCALAR variable and each node, and write out the value.
          for (unsigned int var=0; var<nv; var++)
            if (this->variable(var).type().family != SCALAR)
              {
                // First write the node DOF values
                for (const auto & node : ordered_nodes)
                  for (auto comp : IntRange<unsigned int>(0, node->n_comp(sys_num,var)))
                    {
                      libmesh_assert_not_equal_to (node->dof_number(sys_num, var, comp),
                                                   DofObject::invalid_id);
 
                      io_buffer.push_back((*pr.second)(node->dof_number(sys_num, var, comp)));
                    }
 
                // Then write the element DOF values
                for (const auto & elem : ordered_elements)
                  for (auto comp : IntRange<unsigned int>(0, elem->n_comp(sys_num,var)))
                    {
                      libmesh_assert_not_equal_to (elem->dof_number(sys_num, var, comp),
                                                   DofObject::invalid_id);
 
                      io_buffer.push_back((*pr.second)(elem->dof_number(sys_num, var, comp)));
                    }
              }
 
          // Finally, write the SCALAR data on the last processor
          for (auto var : IntRange<unsigned int>(0, this->n_vars()))
            if (this->variable(var).type().family == SCALAR)
              {
                if (this->processor_id() == (this->n_processors()-1))
                  {
                    const DofMap & dof_map = this->get_dof_map();
                    std::vector<dof_id_type> SCALAR_dofs;
                    dof_map.SCALAR_dof_indices(SCALAR_dofs, var);
 
                    for (auto dof : SCALAR_dofs)
                      io_buffer.push_back((*pr.second)(dof));
                  }
              }
 
          // 10.)
          //
          // Actually write the reordered additional vector
          // for this system to disk
 
          // set up the comment
          {
            comment = "# System \"";
            comment += this->name();
            comment += "\" Additional Vector \"";
            comment += pr.first;
            comment += "\"";
          }
 
          io.data (io_buffer, comment.c_str());
 
          // total_written_size += io_buffer.size();
        }
    }
 
  // const Real
  //   dt   = pl.get_elapsed_time(),
  //   rate = total_written_size*sizeof(Number)/dt;
 
  // libMesh::err << "Write " << total_written_size << " \"Number\" values\n"
  //     << " Elapsed time = " << dt << '\n'
  //     << " Rate = " << rate/1.e6 << "(MB/sec)\n\n";
 
  // pl.pop("write_parallel_data");
}

References libMesh::System::_vectors, libMesh::Xdr::data(), libMesh::FEType::family, libMesh::System::get_dof_map(), libMesh::System::get_mesh(), libMesh::DofObject::invalid_id, libMesh::libmesh_assert(), libMesh::ParallelObject::n_processors(), libMesh::System::n_vars(), libMesh::System::name(), libMesh::System::number(), libMesh::ParallelObject::processor_id(), libMesh::SCALAR, libMesh::DofMap::SCALAR_dof_indices(), libMesh::System::solution, libMesh::Variable::type(), libMesh::System::variable(), and libMesh::Xdr::writing().

write_SCALAR_dofs()

unsigned int libMesh::System::write_SCALAR_dofs ( const NumericVector< Number > &  vec, const unsigned int  var, Xdr &  io  ) const

privateinherited

Writes the SCALAR dofs associated with var to the stream io.

Returns

The number of values written.

Definition at line 2097 of file system_io.C.

{
  unsigned int written_length=0;
  std::vector<Number> vals; // The raw values for the local objects in the current block
  // Collect the SCALARs for the current variable
  if (this->processor_id() == (this->n_processors()-1))
    {
      const DofMap & dof_map = this->get_dof_map();
      std::vector<dof_id_type> SCALAR_dofs;
      dof_map.SCALAR_dof_indices(SCALAR_dofs, var);
      const unsigned int n_scalar_dofs = cast_int<unsigned int>
        (SCALAR_dofs.size());
 
      for (unsigned int i=0; i<n_scalar_dofs; i++)
        {
          vals.push_back( vec(SCALAR_dofs[i]) );
        }
    }
 
#ifdef LIBMESH_HAVE_MPI
  if (this->n_processors() > 1)
    {
      const Parallel::MessageTag val_tag(1);
 
      // Post the receive on processor 0
      if (this->processor_id() == 0)
        {
          this->comm().receive(this->n_processors()-1, vals, val_tag);
        }
 
      // Send the data to processor 0
      if (this->processor_id() == (this->n_processors()-1))
        {
          this->comm().send(0, vals, val_tag);
        }
    }
#endif
 
  // -------------------------------------------------------
  // Write the output on processor 0.
  if (this->processor_id() == 0)
    {
      const unsigned int vals_size =
        cast_int<unsigned int>(vals.size());
      io.data_stream (vals.data(), vals_size);
      written_length += vals_size;
    }
 
  return written_length;
}

References libMesh::ParallelObject::comm(), libMesh::Xdr::data_stream(), libMesh::System::get_dof_map(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::processor_id(), and libMesh::DofMap::SCALAR_dof_indices().

Referenced by libMesh::System::write_serialized_vector(), and libMesh::System::write_serialized_vectors().

write_serialized_blocked_dof_objects()

template<typename iterator_type >

std::size_t libMesh::System::write_serialized_blocked_dof_objects ( const std::vector< const NumericVector< Number > * > &  vecs, const dof_id_type  n_objects, const iterator_type  begin, const iterator_type  end, Xdr &  io, const unsigned int  var_to_write = libMesh::invalid_uint  ) const

privateinherited

Writes an output vector to the stream io for a set of DofObjects.

This method uses blocked output and is safe to call on a distributed memory-mesh.

Returns

The number of values written

Definition at line 1811 of file system_io.C.

{
  parallel_object_only();
 
  //-------------------------------------------------------
  // General order: (IO format 0.7.4 & greater)
  //
  // for (objects ...)
  //   for (vecs ....)
  //     for (vars ....)
  //       for (comps ...)
  //
  // where objects are nodes or elements, sorted to be
  // partition independent,
  // vecs are one or more *identically distributed* solution
  // coefficient vectors, vars are one or more variables
  // to write, and comps are all the components for said
  // vars on the object.
 
  // We will write all variables unless requested otherwise.
  std::vector<unsigned int> vars_to_write(1, var_to_write);
 
  if (var_to_write == libMesh::invalid_uint)
    {
      vars_to_write.clear();  vars_to_write.reserve(this->n_vars());
      for (auto var : IntRange<unsigned int>(0, this->n_vars()))
        vars_to_write.push_back(var);
    }
 
  const dof_id_type io_blksize = cast_int<dof_id_type>
    (std::min(max_io_blksize, static_cast<std::size_t>(n_objs)));
 
  const unsigned int
    sys_num  = this->number(),
    num_vecs = cast_int<unsigned int>(vecs.size()),
    num_blks = cast_int<unsigned int>(std::ceil(static_cast<double>(n_objs)/
                                                static_cast<double>(io_blksize)));
 
  // libMesh::out << "io_blksize = "    << io_blksize
  //     << ", num_objects = " << n_objs
  //     << ", num_blks = "    << num_blks
  //     << std::endl;
 
  std::size_t written_length=0;                                  // The numer of values written.  This will be returned
  std::vector<std::vector<dof_id_type>> xfer_ids(num_blks);      // The global IDs and # of components for the local objects in all blocks
  std::vector<std::vector<Number>>      send_vals(num_blks);     // The raw values for the local objects in all blocks
  std::vector<Parallel::Request>
    id_requests(num_blks), val_requests(num_blks);               // send request handle for each block
  std::vector<Parallel::MessageTag>
    id_tags(num_blks), val_tags(num_blks);                       // tag number for each block
 
  // ------------------------------------------------------
  // First pass - count the number of objects in each block
  // traverse all the objects and figure out which block they
  // will ultimately live in.
  std::vector<unsigned int>
    xfer_ids_size  (num_blks,0),
    send_vals_size (num_blks,0);
 
  for (iterator_type it=begin; it!=end; ++it)
    {
      const dof_id_type
        id    = (*it)->id(),
        block = id/io_blksize;
 
      libmesh_assert_less (block, num_blks);
 
      xfer_ids_size[block] += 2; // for each object, we store its id, as well as the total number of components for all variables
 
      unsigned int n_comp_tot=0;
 
      for (const auto & var : vars_to_write)
        n_comp_tot += (*it)->n_comp(sys_num, var); // for each variable, we will store the nonzero components
 
      send_vals_size[block] += n_comp_tot*num_vecs;
    }
 
  //-----------------------------------------
  // Collect the values for all local objects,
  // binning them into 'blocks' that will be
  // sent to processor 0
  for (unsigned int blk=0; blk<num_blks; blk++)
    {
      // libMesh::out << "Writing object block " << blk << std::endl;
 
      // Each processor should build up its transfer buffers for its
      // local objects in [first_object,last_object).
      const dof_id_type
        first_object = blk*io_blksize,
        last_object  = std::min(cast_int<dof_id_type>((blk+1)*io_blksize), n_objs);
 
      // convenience
      std::vector<dof_id_type> & ids  (xfer_ids[blk]);
      std::vector<Number>      & vals (send_vals[blk]);
 
      // we now know the number of values we will store for each block,
      // so we can do efficient preallocation
      ids.clear();   ids.reserve  (xfer_ids_size[blk]);
      vals.clear();  vals.reserve (send_vals_size[blk]);
 
      if (send_vals_size[blk] != 0) // only send if we have nonzero components to write
        for (iterator_type it=begin; it!=end; ++it)
          if (((*it)->id() >= first_object) && // object in [first_object,last_object)
              ((*it)->id() <   last_object))
            {
              ids.push_back((*it)->id());
 
              // count the total number of nonzeros transferred for this object
              {
                unsigned int n_comp_tot=0;
 
                for (const auto & var : vars_to_write)
                  n_comp_tot += (*it)->n_comp(sys_num, var);
 
                ids.push_back (n_comp_tot*num_vecs); // even if 0 - processor 0 has no way of knowing otherwise...
              }
 
              // pack the values to send
              for (const auto & vec : vecs)
                for (const auto & var : vars_to_write)
                  {
                    const unsigned int n_comp = (*it)->n_comp(sys_num, var);
 
                    for (unsigned int comp=0; comp<n_comp; comp++)
                      {
                        libmesh_assert_greater_equal ((*it)->dof_number(sys_num, var, comp), vec->first_local_index());
                        libmesh_assert_less ((*it)->dof_number(sys_num, var, comp), vec->last_local_index());
                        vals.push_back((*vec)((*it)->dof_number(sys_num, var, comp)));
                      }
                  }
            }
 
#ifdef LIBMESH_HAVE_MPI
      id_tags[blk]  = this->comm().get_unique_tag(100*num_blks + blk);
      val_tags[blk] = this->comm().get_unique_tag(200*num_blks + blk);
 
      // nonblocking send the data for this block
      this->comm().send (0, ids,  id_requests[blk],  id_tags[blk]);
      this->comm().send (0, vals, val_requests[blk], val_tags[blk]);
#endif
    }
 
 
  if (this->processor_id() == 0)
    {
      std::vector<std::vector<dof_id_type>> recv_ids  (this->n_processors());
      std::vector<std::vector<Number>>      recv_vals (this->n_processors());
      std::vector<unsigned int> obj_val_offsets;          // map to traverse entry-wise rather than processor-wise
      std::vector<Number>       output_vals;              // The output buffer for the current block
 
      // a ThreadedIO object to perform asynchronous file IO
      ThreadedIO<Number> threaded_io(io, output_vals);
      std::unique_ptr<Threads::Thread> async_io;
 
      for (unsigned int blk=0; blk<num_blks; blk++)
        {
          // Each processor should build up its transfer buffers for its
          // local objects in [first_object,last_object).
          const dof_id_type
            first_object  = cast_int<dof_id_type>(blk*io_blksize),
            last_object   = std::min(cast_int<dof_id_type>((blk+1)*io_blksize), n_objs),
            n_objects_blk = last_object - first_object;
 
          // offset array. this will define where each object's values
          // map into the actual output_vals buffer.  this must get
          // 0-initialized because 0-component objects are not actually sent
          obj_val_offsets.resize (n_objects_blk);  std::fill (obj_val_offsets.begin(), obj_val_offsets.end(), 0);
 
          std::size_t n_val_recvd_blk=0;
 
          // receive this block of data from all processors.
          for (processor_id_type comm_step=0, tnp=this->n_processors(); comm_step != tnp; ++comm_step)
            {
#ifdef LIBMESH_HAVE_MPI
              // blocking receive indices for this block, imposing no particular order on processor
              Parallel::Status id_status (this->comm().probe (Parallel::any_source, id_tags[blk]));
              std::vector<dof_id_type> & ids (recv_ids[id_status.source()]);
              this->comm().receive (id_status.source(), ids, id_tags[blk]);
#else
              std::vector<dof_id_type> & ids (recv_ids[0]);
              ids = xfer_ids[blk];
#endif
 
              // note its possible we didn't receive values for objects in
              // this block if they have no components allocated.
              for (std::size_t idx=0, sz=ids.size(); idx<sz; idx+=2)
                {
                  const dof_id_type
                    local_idx          = ids[idx+0]-first_object,
                    n_vals_tot_allvecs = ids[idx+1];
 
                  libmesh_assert_less (local_idx, n_objects_blk);
                  libmesh_assert_less (local_idx, obj_val_offsets.size());
 
                  obj_val_offsets[local_idx] = n_vals_tot_allvecs;
                }
 
#ifdef LIBMESH_HAVE_MPI
              // blocking receive values for this block, imposing no particular order on processor
              Parallel::Status val_status  (this->comm().probe (Parallel::any_source, val_tags[blk]));
              std::vector<Number> & vals    (recv_vals[val_status.source()]);
              this->comm().receive (val_status.source(), vals, val_tags[blk]);
#else
              // straight copy without MPI
              std::vector<Number> & vals (recv_vals[0]);
              vals = send_vals[blk];
#endif
 
              n_val_recvd_blk += vals.size();
            }
 
          // We need the offsets into the output_vals vector for each object.
          // fortunately, this is simply the partial sum of the total number
          // of components for each object
          std::partial_sum(obj_val_offsets.begin(), obj_val_offsets.end(),
                           obj_val_offsets.begin());
 
          // wait on any previous asynchronous IO - this *must* complete before
          // we start messing with the output_vals buffer!
          if (async_io.get()) async_io->join();
 
          // this is the actual output buffer that will be written to disk.
          // at ths point we finally know wha size it will be.
          output_vals.resize(n_val_recvd_blk);
 
          // pack data from all processors into output values
          for (auto proc : IntRange<unsigned int>(0, this->n_processors()))
            {
              const std::vector<dof_id_type> & ids (recv_ids [proc]);
              const std::vector<Number>      & vals(recv_vals[proc]);
              std::vector<Number>::const_iterator proc_vals(vals.begin());
 
              for (std::size_t idx=0, sz=ids.size(); idx<sz; idx+=2)
                {
                  const dof_id_type
                    local_idx          = ids[idx+0]-first_object,
                    n_vals_tot_allvecs = ids[idx+1];
 
                  // put this object's data into the proper location
                  // in  the output buffer
                  std::vector<Number>::iterator out_vals(output_vals.begin());
                  if (local_idx != 0)
                    std::advance (out_vals, obj_val_offsets[local_idx-1]);
 
                  for (unsigned int val=0; val<n_vals_tot_allvecs; val++, ++out_vals, ++proc_vals)
                    {
                      libmesh_assert (out_vals  != output_vals.end());
                      libmesh_assert (proc_vals != vals.end());
                      *out_vals = *proc_vals;
                    }
                }
            }
 
          // output_vals buffer is now filled for this block.
          // write it to disk
          async_io = libmesh_make_unique<Threads::Thread>(threaded_io);
          written_length += output_vals.size();
        }
 
      // wait on any previous asynchronous IO - this *must* complete before
      // our stuff goes out of scope
      async_io->join();
    }
 
  Parallel::wait(id_requests);
  Parallel::wait(val_requests);
 
  // we need some synchronization here.  Because this method
  // can be called for a range of nodes, then a range of elements,
  // we need some mechanism to prevent processors from racing past
  // to the next range and overtaking ongoing communication.  one
  // approach would be to figure out unique tags for each range,
  // but for now we just impose a barrier here.  And might as
  // well have it do some useful work.
  this->comm().broadcast(written_length);
 
  return written_length;
}

References libMesh::ParallelObject::comm(), end, libMesh::MeshTools::Generation::Private::idx(), libMesh::invalid_uint, libMesh::libmesh_assert(), libMesh::ParallelObject::n_processors(), libMesh::System::n_vars(), libMesh::System::number(), and libMesh::ParallelObject::processor_id().

Referenced by libMesh::System::write_serialized_vector(), and libMesh::System::write_serialized_vectors().

write_serialized_data()

void libMesh::System::write_serialized_data ( Xdr &  io, const bool  write_additional_data = true  ) const

inherited

Writes additional data, namely vectors, for this System.

This method may safely be called on a distributed-memory mesh.

This method implements the output of the vectors contained in this System object, embedded in the output of an EquationSystems<T_sys>.

9.) The global solution vector, re-ordered to be node-major (More on this later.)

for each additional vector in the object

10.) The global additional vector, re-ordered to be node-major (More on this later.)

Definition at line 1703 of file system_io.C.

{
  parallel_object_only();
  std::string comment;
 
  // PerfLog pl("IO Performance",false);
  // pl.push("write_serialized_data");
  // std::size_t total_written_size = 0;
 
  // total_written_size +=
  this->write_serialized_vector(io, *this->solution);
 
  // set up the comment
  if (this->processor_id() == 0)
    {
      comment = "# System \"";
      comment += this->name();
      comment += "\" Solution Vector";
 
      io.comment (comment);
    }
 
  // Only write additional vectors if wanted
  if (write_additional_data)
    {
      for (auto & pair : this->_vectors)
        {
          // total_written_size +=
          this->write_serialized_vector(io, *pair.second);
 
          // set up the comment
          if (this->processor_id() == 0)
            {
              comment = "# System \"";
              comment += this->name();
              comment += "\" Additional Vector \"";
              comment += pair.first;
              comment += "\"";
              io.comment (comment);
            }
        }
    }
 
  // const Real
  //   dt   = pl.get_elapsed_time(),
  //   rate = total_written_size*sizeof(Number)/dt;
 
  // libMesh::out << "Write " << total_written_size << " \"Number\" values\n"
  //     << " Elapsed time = " << dt << '\n'
  //     << " Rate = " << rate/1.e6 << "(MB/sec)\n\n";
 
  // pl.pop("write_serialized_data");
 
 
 
 
  // // test the new method
  // {
  //   std::vector<std::string> names;
  //   std::vector<NumericVector<Number> *> vectors_to_write;
 
  //   names.push_back("Solution Vector");
  //   vectors_to_write.push_back(this->solution.get());
 
  //   // Only write additional vectors if wanted
  //   if (write_additional_data)
  //     {
  // std::map<std::string, NumericVector<Number> *>::const_iterator
  //   pos = _vectors.begin();
 
  // for (; pos != this->_vectors.end(); ++pos)
  //   {
  //     names.push_back("Additional Vector " + pos->first);
  //     vectors_to_write.push_back(pos->second);
  //   }
  //     }
 
  //   total_written_size =
  //     this->write_serialized_vectors (io, names, vectors_to_write);
 
  //   const Real
  //     dt2   = pl.get_elapsed_time(),
  //     rate2 = total_written_size*sizeof(Number)/(dt2-dt);
 
  //   libMesh::out << "Write (new) " << total_written_size << " \"Number\" values\n"
  //       << " Elapsed time = " << (dt2-dt) << '\n'
  //       << " Rate = " << rate2/1.e6 << "(MB/sec)\n\n";
 
  // }
}

References libMesh::System::_vectors, libMesh::Xdr::comment(), libMesh::System::name(), libMesh::ParallelObject::processor_id(), libMesh::System::solution, and libMesh::System::write_serialized_vector().

Referenced by libMesh::TransientRBConstruction::write_riesz_representors_to_files(), and libMesh::RBConstruction::write_riesz_representors_to_files().

write_serialized_vector()

dof_id_type libMesh::System::write_serialized_vector ( Xdr &  io, const NumericVector< Number > &  vec  ) const

privateinherited

Writes a vector for this System.

This method may safely be called on a distributed-memory mesh.

Returns

The number of values written.

Definition at line 2152 of file system_io.C.

{
  parallel_object_only();
 
  libmesh_assert (io.writing());
 
  dof_id_type vec_length = vec.size();
  if (this->processor_id() == 0) io.data (vec_length, "# vector length");
 
  dof_id_type written_length = 0;
 
  //---------------------------------
  // Collect the values for all nodes
  written_length += cast_int<dof_id_type>
    (this->write_serialized_blocked_dof_objects (std::vector<const NumericVector<Number> *>(1,&vec),
                                                 this->get_mesh().n_nodes(),
                                                 this->get_mesh().local_nodes_begin(),
                                                 this->get_mesh().local_nodes_end(),
                                                 io));
 
  //------------------------------------
  // Collect the values for all elements
  written_length += cast_int<dof_id_type>
    (this->write_serialized_blocked_dof_objects (std::vector<const NumericVector<Number> *>(1,&vec),
                                                 this->get_mesh().n_elem(),
                                                 this->get_mesh().local_elements_begin(),
                                                 this->get_mesh().local_elements_end(),
                                                 io));
 
  //-------------------------------------------
  // Finally loop over all the SCALAR variables
  for (auto var : IntRange<unsigned int>(0, this->n_vars()))
    if (this->variable(var).type().family == SCALAR)
      {
        written_length +=
          this->write_SCALAR_dofs (vec, var, io);
      }
 
  if (this->processor_id() == 0)
    libmesh_assert_equal_to (written_length, vec_length);
 
  return written_length;
}

References libMesh::Xdr::data(), libMesh::System::get_mesh(), libMesh::libmesh_assert(), libMesh::MeshTools::n_elem(), n_nodes, libMesh::System::n_vars(), libMesh::ParallelObject::processor_id(), libMesh::SCALAR, libMesh::NumericVector< T >::size(), libMesh::System::variable(), libMesh::System::write_SCALAR_dofs(), libMesh::System::write_serialized_blocked_dof_objects(), and libMesh::Xdr::writing().

Referenced by libMesh::System::write_serialized_data().

write_serialized_vectors()

std::size_t libMesh::System::write_serialized_vectors ( Xdr &  io, const std::vector< const NumericVector< Number > * > &  vectors  ) const

inherited

Serialize & write a number of identically distributed vectors.

This method allows for optimization for the multiple vector case by only communicating the metadata once.

Definition at line 2293 of file system_io.C.

{
  parallel_object_only();
 
  libmesh_assert (io.writing());
 
  // Cache these - they are not free!
  const dof_id_type
    n_nodes       = this->get_mesh().n_nodes(),
    n_elem        = this->get_mesh().n_elem();
 
  std::size_t written_length = 0;
 
  if (this->processor_id() == 0)
    {
      unsigned int
        n_vec    = cast_int<unsigned int>(vectors.size());
      dof_id_type
        vec_size = vectors.empty() ? 0 : vectors[0]->size();
      // Set the number of vectors
      io.data(n_vec, "# number of vectors");
      // Set the buffer size
      io.data(vec_size, "# vector length");
    }
 
  //---------------------------------
  // Collect the values for all nodes
  written_length +=
    this->write_serialized_blocked_dof_objects (vectors,
                                                n_nodes,
                                                this->get_mesh().local_nodes_begin(),
                                                this->get_mesh().local_nodes_end(),
                                                io);
 
  //------------------------------------
  // Collect the values for all elements
  written_length +=
    this->write_serialized_blocked_dof_objects (vectors,
                                                n_elem,
                                                this->get_mesh().local_elements_begin(),
                                                this->get_mesh().local_elements_end(),
                                                io);
 
  //-------------------------------------------
  // Finally loop over all the SCALAR variables
  for (const NumericVector<Number> * vec : vectors)
    for (auto var : IntRange<unsigned int>(0, this->n_vars()))
      if (this->variable(var).type().family == SCALAR)
        {
          libmesh_assert_not_equal_to (vec, 0);
 
          written_length +=
            this->write_SCALAR_dofs (*vec, var, io);
        }
 
  return written_length;
}

References libMesh::Xdr::data(), libMesh::System::get_mesh(), libMesh::libmesh_assert(), libMesh::MeshBase::n_elem(), libMesh::MeshTools::n_elem(), n_nodes, libMesh::MeshBase::n_nodes(), libMesh::System::n_vars(), libMesh::ParallelObject::processor_id(), libMesh::SCALAR, libMesh::System::variable(), libMesh::System::write_SCALAR_dofs(), libMesh::System::write_serialized_blocked_dof_objects(), and libMesh::Xdr::writing().

Referenced by libMesh::RBEvaluation::write_out_vectors().

zero_variable()

void libMesh::System::zero_variable ( NumericVector< Number > &  v, unsigned int  var_num  ) const

inherited

Zeroes all dofs in v that correspond to variable number var_num.

Definition at line 1300 of file system.C.

{
  /* Make sure the call makes sense.  */
  libmesh_assert_less (var_num, this->n_vars());
 
  /* Get a reference to the mesh.  */
  const MeshBase & mesh = this->get_mesh();
 
  /* Check which system we are.  */
  const unsigned int sys_num = this->number();
 
  // Loop over nodes.
  for (const auto & node : mesh.local_node_ptr_range())
    {
      unsigned int n_comp = node->n_comp(sys_num,var_num);
      for (unsigned int i=0; i<n_comp; i++)
        {
          const dof_id_type index = node->dof_number(sys_num,var_num,i);
          v.set(index,0.0);
        }
    }
 
  // Loop over elements.
  for (const auto & elem : mesh.active_local_element_ptr_range())
    {
      unsigned int n_comp = elem->n_comp(sys_num,var_num);
      for (unsigned int i=0; i<n_comp; i++)
        {
          const dof_id_type index = elem->dof_number(sys_num,var_num,i);
          v.set(index,0.0);
        }
    }
}

References libMesh::System::get_mesh(), mesh, libMesh::System::n_vars(), libMesh::System::number(), and libMesh::NumericVector< T >::set().

Member Data Documentation

_active

bool libMesh::System::_active

privateinherited

Flag stating if the system is active or not.

Definition at line 1977 of file system.h.

Referenced by libMesh::System::activate(), libMesh::System::active(), and libMesh::System::deactivate().

_additional_data_written

unsigned int libMesh::System::_additional_data_written

privateinherited

This flag is used only when reading in a system from file.

Based on the system header, it keeps track of how many additional vectors were actually written for this file.

Definition at line 2034 of file system.h.

Referenced by libMesh::System::read_header(), libMesh::System::read_legacy_data(), libMesh::System::read_parallel_data(), and libMesh::System::read_serialized_data().

_assemble_system_function

void(* libMesh::System::_assemble_system_function) (EquationSystems &es, const std::string &name)

privateinherited

Function that assembles the system.

Definition at line 1885 of file system.h.

Referenced by libMesh::System::attach_assemble_function(), libMesh::System::attach_assemble_object(), libMesh::System::user_assembly(), and libMesh::System::~System().

_assemble_system_object

Assembly* libMesh::System::_assemble_system_object

privateinherited

Object that assembles the system.

Definition at line 1891 of file system.h.

Referenced by libMesh::System::attach_assemble_function(), libMesh::System::attach_assemble_object(), libMesh::System::user_assembly(), and libMesh::System::~System().

_basic_system_only

bool libMesh::System::_basic_system_only

privateinherited

Holds true if the components of more advanced system types (e.g.

system matrices) should not be initialized.

Definition at line 2015 of file system.h.

Referenced by libMesh::System::init(), and libMesh::System::set_basic_system_only().

_can_add_matrices

bool libMesh::ImplicitSystem::_can_add_matrices

privateinherited

true when additional matrices may still be added, false otherwise.

Definition at line 431 of file implicit_system.h.

Referenced by libMesh::ImplicitSystem::add_matrix(), libMesh::ImplicitSystem::clear(), and libMesh::ImplicitSystem::init_matrices().

_communicator

const Parallel::Communicator& libMesh::ParallelObject::_communicator

protectedinherited

Definition at line 112 of file parallel_object.h.

Referenced by libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::ParallelObject::comm(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::operator=(), and libMesh::ParallelObject::processor_id().

_constrain_system_function

void(* libMesh::System::_constrain_system_function) (EquationSystems &es, const std::string &name)

privateinherited

Function to impose constraints.

Definition at line 1896 of file system.h.

Referenced by libMesh::System::attach_constraint_function(), libMesh::System::attach_constraint_object(), libMesh::System::user_constrain(), and libMesh::System::~System().

_constrain_system_object

Constraint* libMesh::System::_constrain_system_object

privateinherited

Object that constrains the system.

Definition at line 1902 of file system.h.

Referenced by libMesh::System::attach_constraint_function(), libMesh::System::attach_constraint_object(), libMesh::System::user_constrain(), and libMesh::System::~System().

_counts

ReferenceCounter::Counts libMesh::ReferenceCounter::_counts

staticprotectedinherited

Actually holds the data.

Definition at line 122 of file reference_counter.h.

Referenced by libMesh::ReferenceCounter::get_info(), libMesh::ReferenceCounter::increment_constructor_count(), and libMesh::ReferenceCounter::increment_destructor_count().

_diff_physics

DifferentiablePhysics* libMesh::DifferentiableSystem::_diff_physics

protectedinherited

Pointer to object to use for physics assembly evaluations.

Defaults to this for backwards compatibility; in the future users should create separate physics objects.

Definition at line 370 of file diff_system.h.

Referenced by libMesh::DifferentiableSystem::attach_physics(), libMesh::DifferentiableSystem::clear(), libMesh::DifferentiableSystem::get_physics(), libMesh::DifferentiableSystem::init_data(), libMesh::DifferentiableSystem::swap_physics(), and libMesh::DifferentiableSystem::~DifferentiableSystem().

_dof_map

std::unique_ptr<DofMap> libMesh::System::_dof_map

privateinherited

Data structure describing the relationship between nodes, variables, etc...

and degrees of freedom.

Definition at line 1934 of file system.h.

Referenced by libMesh::System::add_vector(), libMesh::System::calculate_norm(), libMesh::System::clear(), libMesh::System::current_solution(), libMesh::System::get_dof_map(), libMesh::System::init_data(), libMesh::System::n_constrained_dofs(), libMesh::System::n_dofs(), libMesh::System::n_local_constrained_dofs(), libMesh::System::n_local_dofs(), libMesh::System::restrict_vectors(), and libMesh::System::update().

_enable_print_counter

bool libMesh::ReferenceCounter::_enable_print_counter = true

staticprotectedinherited

Flag to control whether reference count information is printed when print_info is called.

Definition at line 141 of file reference_counter.h.

Referenced by libMesh::ReferenceCounter::disable_print_counter_info(), libMesh::ReferenceCounter::enable_print_counter_info(), and libMesh::ReferenceCounter::print_info().

_equation_systems

EquationSystems& libMesh::System::_equation_systems

privateinherited

Constant reference to the EquationSystems object used for the simulation.

Definition at line 1940 of file system.h.

Referenced by libMesh::System::get_equation_systems(), libMesh::System::user_assembly(), libMesh::System::user_constrain(), libMesh::System::user_initialization(), libMesh::System::user_QOI(), and libMesh::System::user_QOI_derivative().

_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 560 of file diff_physics.h.

Referenced by libMesh::DifferentiablePhysics::get_first_order_vars(), libMesh::DifferentiablePhysics::have_first_order_vars(), libMesh::DifferentiablePhysics::is_first_order_var(), and libMesh::DifferentiablePhysics::time_evolving().

_hide_output

bool libMesh::System::_hide_output

privateinherited

Are we allowed to write this system to file? If _hide_output is true, then EquationSystems::write will ignore this system.

Definition at line 2059 of file system.h.

Referenced by libMesh::System::hide_output().

_identify_variable_groups

bool libMesh::System::_identify_variable_groups

privateinherited

true when VariableGroup structures should be automatically identified, false otherwise.

Defaults to true.

Definition at line 2027 of file system.h.

Referenced by libMesh::System::identify_variable_groups().

_init_system_function

void(* libMesh::System::_init_system_function) (EquationSystems &es, const std::string &name)

privateinherited

Function that initializes the system.

Definition at line 1874 of file system.h.

Referenced by libMesh::System::attach_init_function(), libMesh::System::attach_init_object(), libMesh::System::user_initialization(), and libMesh::System::~System().

_init_system_object

Initialization* libMesh::System::_init_system_object

privateinherited

Object that initializes the system.

Definition at line 1880 of file system.h.

Referenced by libMesh::System::attach_init_function(), libMesh::System::attach_init_object(), libMesh::System::user_initialization(), and libMesh::System::~System().

_is_initialized

bool libMesh::System::_is_initialized

privateinherited

true when additional vectors and variables do not require immediate initialization, false otherwise.

Definition at line 2021 of file system.h.

Referenced by libMesh::System::add_vector(), libMesh::System::clear(), libMesh::System::compare(), libMesh::System::init_data(), and libMesh::System::is_initialized().

_matrices

std::map<std::string, SparseMatrix<Number> *> libMesh::ImplicitSystem::_matrices

privateinherited

Some systems need an arbitrary number of matrices.

Definition at line 426 of file implicit_system.h.

Referenced by libMesh::ImplicitSystem::add_matrix(), libMesh::ImplicitSystem::add_system_matrix(), libMesh::ImplicitSystem::clear(), libMesh::ImplicitSystem::get_matrix(), libMesh::ImplicitSystem::have_matrix(), libMesh::ImplicitSystem::init_data(), libMesh::ImplicitSystem::init_matrices(), libMesh::ImplicitSystem::n_matrices(), libMesh::ImplicitSystem::reinit(), libMesh::ImplicitSystem::remove_matrix(), and libMesh::ImplicitSystem::request_matrix().

_mesh

MeshBase& libMesh::System::_mesh

privateinherited

Constant reference to the mesh data structure used for the simulation.

Definition at line 1946 of file system.h.

Referenced by libMesh::System::calculate_norm(), libMesh::System::get_mesh(), and libMesh::System::reinit_constraints().

_mesh_sys

System* libMesh::DifferentiablePhysics::_mesh_sys

protectedinherited

System from which to acquire moving mesh information.

Definition at line 543 of file diff_physics.h.

Referenced by libMesh::FEMPhysics::eulerian_residual(), libMesh::DifferentiablePhysics::get_mesh_system(), libMesh::FEMSystem::mesh_position_get(), libMesh::FEMSystem::mesh_position_set(), libMesh::FEMSystem::numerical_jacobian(), and libMesh::DifferentiablePhysics::set_mesh_system().

_mesh_x_var

unsigned int libMesh::DifferentiablePhysics::_mesh_x_var

protectedinherited

Variables from which to acquire moving mesh information.

Definition at line 548 of file diff_physics.h.

Referenced by libMesh::FEMPhysics::eulerian_residual(), libMesh::DifferentiablePhysics::get_mesh_x_var(), libMesh::FEMSystem::mesh_position_get(), libMesh::FEMSystem::numerical_jacobian(), and libMesh::DifferentiablePhysics::set_mesh_x_var().

_mesh_y_var

unsigned int libMesh::DifferentiablePhysics::_mesh_y_var

protectedinherited

Definition at line 548 of file diff_physics.h.

Referenced by libMesh::FEMPhysics::eulerian_residual(), libMesh::DifferentiablePhysics::get_mesh_y_var(), libMesh::FEMSystem::mesh_position_get(), libMesh::FEMSystem::numerical_jacobian(), and libMesh::DifferentiablePhysics::set_mesh_y_var().

_mesh_z_var

unsigned int libMesh::DifferentiablePhysics::_mesh_z_var

protectedinherited

Definition at line 548 of file diff_physics.h.

Referenced by libMesh::FEMPhysics::eulerian_residual(), libMesh::DifferentiablePhysics::get_mesh_z_var(), libMesh::FEMSystem::mesh_position_get(), libMesh::FEMSystem::numerical_jacobian(), and libMesh::DifferentiablePhysics::set_mesh_z_var().

_mutex

Threads::spin_mutex libMesh::ReferenceCounter::_mutex

staticprotectedinherited

Mutual exclusion object to enable thread-safe reference counting.

Definition at line 135 of file reference_counter.h.

_n_objects

Threads::atomic< unsigned int > libMesh::ReferenceCounter::_n_objects

staticprotectedinherited

The number of objects.

Print the reference count information when the number returns to 0.

Definition at line 130 of file reference_counter.h.

Referenced by libMesh::ReferenceCounter::n_objects(), libMesh::ReferenceCounter::ReferenceCounter(), and libMesh::ReferenceCounter::~ReferenceCounter().

_numerical_jacobian_h_for_var

std::vector<Real> libMesh::FEMSystem::_numerical_jacobian_h_for_var

privateinherited

Definition at line 252 of file fem_system.h.

Referenced by libMesh::FEMSystem::numerical_jacobian_h_for_var(), and libMesh::FEMSystem::set_numerical_jacobian_h_for_var().

_qoi_evaluate_derivative_function

void(* libMesh::System::_qoi_evaluate_derivative_function) (EquationSystems &es, const std::string &name, const QoISet &qoi_indices, bool include_liftfunc, bool apply_constraints)

privateinherited

Function to evaluate quantity of interest derivative.

Definition at line 1919 of file system.h.

Referenced by libMesh::System::attach_QOI_derivative(), libMesh::System::attach_QOI_derivative_object(), libMesh::System::user_QOI_derivative(), and libMesh::System::~System().

_qoi_evaluate_derivative_object

QOIDerivative* libMesh::System::_qoi_evaluate_derivative_object

privateinherited

Object to compute derivatives of quantities of interest.

Definition at line 1928 of file system.h.

Referenced by libMesh::System::attach_QOI_derivative(), libMesh::System::attach_QOI_derivative_object(), libMesh::System::user_QOI_derivative(), and libMesh::System::~System().

_qoi_evaluate_function

void(* libMesh::System::_qoi_evaluate_function) (EquationSystems &es, const std::string &name, const QoISet &qoi_indices)

privateinherited

Function to evaluate quantity of interest.

Definition at line 1907 of file system.h.

Referenced by libMesh::System::attach_QOI_function(), libMesh::System::attach_QOI_object(), libMesh::System::user_QOI(), and libMesh::System::~System().

_qoi_evaluate_object

QOI* libMesh::System::_qoi_evaluate_object

privateinherited

Object to compute quantities of interest.

Definition at line 1914 of file system.h.

Referenced by libMesh::System::attach_QOI_function(), libMesh::System::attach_QOI_object(), libMesh::System::user_QOI(), and libMesh::System::~System().

_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 572 of file diff_physics.h.

Referenced by libMesh::DifferentiableSystem::add_second_order_dot_vars(), and libMesh::DifferentiableSystem::get_second_order_dot_var().

_second_order_vars

std::set<unsigned int> libMesh::DifferentiablePhysics::_second_order_vars

protectedinherited

Variable indices for those variables that are second order in time.

Definition at line 565 of file diff_physics.h.

Referenced by libMesh::DifferentiablePhysics::get_second_order_vars(), libMesh::DifferentiablePhysics::have_second_order_vars(), libMesh::DifferentiablePhysics::is_second_order_var(), and libMesh::DifferentiablePhysics::time_evolving().

_solution_projection

bool libMesh::System::_solution_projection

privateinherited

Holds true if the solution vector should be projected onto a changed grid, false if it should be zeroed.

This is true by default.

Definition at line 2009 of file system.h.

Referenced by libMesh::System::project_solution_on_reinit(), and libMesh::System::restrict_vectors().

_sys_name

const std::string libMesh::System::_sys_name

privateinherited

A name associated with this system.

Definition at line 1951 of file system.h.

Referenced by libMesh::System::compare(), and libMesh::System::name().

_sys_number

const unsigned int libMesh::System::_sys_number

privateinherited

The number associated with this system.

Definition at line 1956 of file system.h.

Referenced by libMesh::System::number().

_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 555 of file diff_physics.h.

Referenced by libMesh::DifferentiablePhysics::clear_physics(), libMesh::DifferentiablePhysics::init_physics(), libMesh::DifferentiablePhysics::is_time_evolving(), and libMesh::DifferentiablePhysics::time_evolving().

_u_var

unsigned int FirstOrderScalarSystemBase::_u_var

protectedinherited

Definition at line 172 of file time_solver_test_common.h.

_variable_groups

std::vector<VariableGroup> libMesh::System::_variable_groups

privateinherited

The VariableGroup in this System.

Definition at line 1966 of file system.h.

Referenced by libMesh::System::add_variable(), libMesh::System::add_variables(), libMesh::System::n_variable_groups(), and libMesh::System::variable_group().

_variable_numbers

std::map<std::string, unsigned short int> libMesh::System::_variable_numbers

privateinherited

The variable numbers corresponding to user-specified names, useful for name-based lookups.

Definition at line 1972 of file system.h.

Referenced by libMesh::System::add_variable(), libMesh::System::add_variables(), libMesh::System::clear(), libMesh::System::get_all_variable_numbers(), libMesh::System::has_variable(), and libMesh::System::variable_number().

_variables

std::vector<Variable> libMesh::System::_variables

privateinherited

The Variable in this System.

Definition at line 1961 of file system.h.

Referenced by libMesh::System::add_variable(), libMesh::System::add_variables(), libMesh::System::clear(), libMesh::System::n_components(), libMesh::System::n_vars(), libMesh::System::variable(), libMesh::System::variable_name(), libMesh::System::variable_number(), libMesh::System::variable_scalar_number(), and libMesh::System::variable_type().

_vector_is_adjoint

std::map<std::string, int> libMesh::System::_vector_is_adjoint

privateinherited

Holds non-negative if a vector by that name should be projected using adjoint constraints/BCs, -1 if primal.

Definition at line 1997 of file system.h.

Referenced by libMesh::System::add_vector(), libMesh::System::clear(), libMesh::System::remove_vector(), libMesh::System::set_vector_as_adjoint(), and libMesh::System::vector_is_adjoint().

_vector_projections

std::map<std::string, bool> libMesh::System::_vector_projections

privateinherited

Holds true if a vector by that name should be projected onto a changed grid, false if it should be zeroed.

Definition at line 1991 of file system.h.

Referenced by libMesh::System::add_vector(), libMesh::System::clear(), libMesh::System::remove_vector(), libMesh::System::restrict_vectors(), libMesh::System::set_vector_preservation(), and libMesh::System::vector_preservation().

_vector_types

std::map<std::string, ParallelType> libMesh::System::_vector_types

privateinherited

Holds the type of a vector.

Definition at line 2002 of file system.h.

Referenced by libMesh::System::add_vector(), libMesh::System::clear(), libMesh::System::init_data(), libMesh::System::remove_vector(), and libMesh::System::restrict_vectors().

_vectors

std::map<std::string, NumericVector<Number> * > libMesh::System::_vectors

privateinherited

Some systems need an arbitrary number of vectors.

This map allows names to be associated with arbitrary vectors. All the vectors in this map will be distributed in the same way as the solution vector.

Definition at line 1985 of file system.h.

Referenced by libMesh::System::add_vector(), libMesh::System::clear(), libMesh::System::compare(), libMesh::System::get_vector(), libMesh::System::have_vector(), libMesh::System::init_data(), libMesh::System::n_vectors(), libMesh::System::read_legacy_data(), libMesh::System::read_parallel_data(), libMesh::System::read_serialized_data(), libMesh::System::remove_vector(), libMesh::System::request_vector(), libMesh::System::restrict_vectors(), libMesh::System::vectors_begin(), libMesh::System::vectors_end(), libMesh::System::write_header(), libMesh::System::write_parallel_data(), and libMesh::System::write_serialized_data().

_written_var_indices

std::vector<unsigned int> libMesh::System::_written_var_indices

privateinherited

This vector is used only when reading in a system from file.

Based on the system header, it keeps track of any index remapping between variable names in the data file and variable names in the already-constructed system. I.e. if we have a system with variables "A1", "A2", "B1", and "B2", but we read in a data file with only "A1" and "B1" defined, then we don't want to try and read in A2 or B2, and we don't want to assign A1 and B1 values to different dof indices.

Definition at line 2046 of file system.h.

Referenced by libMesh::System::read_header(), libMesh::System::read_legacy_data(), libMesh::System::read_parallel_data(), libMesh::System::read_serialized_blocked_dof_objects(), and libMesh::System::read_serialized_vector().

adjoint_already_solved

bool libMesh::System::adjoint_already_solved

privateinherited

Has the adjoint problem already been solved? If the user sets adjoint_already_solved to true, we won't waste time solving it again.

Definition at line 2053 of file system.h.

Referenced by libMesh::System::is_adjoint_already_solved(), and libMesh::System::set_adjoint_already_solved().

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 1493 of file system.h.

Referenced by libMesh::ImplicitSystem::adjoint_solve(), libMesh::ImplicitSystem::disable_cache(), libMesh::System::disable_cache(), main(), libMesh::RBConstruction::RBConstruction(), libMesh::RBSCMConstruction::RBSCMConstruction(), libMesh::ImplicitSystem::sensitivity_solve(), libMesh::CondensedEigenSystem::solve(), libMesh::EigenSystem::solve(), and libMesh::LinearImplicitSystem::solve().

assemble_qoi_elements

bool libMesh::DifferentiableQoI::assemble_qoi_elements

inherited

If assemble_qoi_elements is false (it is true by default), the assembly loop for a quantity of interest or its derivatives will skip computing on mesh elements, and will only compute on mesh sides.

Definition at line 101 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 93 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 85 of file diff_qoi.h.

Referenced by main().

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 154 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 1551 of file system.h.

Referenced by libMesh::__libmesh_petsc_diff_solver_jacobian(), libMesh::__libmesh_petsc_diff_solver_residual(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::NonlinearImplicitSystem::assembly(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::System::clear(), libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), libMesh::System::current_solution(), DMlibMeshFunction(), DMlibMeshJacobian(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::System::init_data(), libMesh::libmesh_petsc_snes_fd_residual(), libMesh::libmesh_petsc_snes_jacobian(), libMesh::libmesh_petsc_snes_mffd_residual(), libMesh::libmesh_petsc_snes_residual(), libMesh::libmesh_petsc_snes_residual_helper(), libMesh::System::point_gradient(), libMesh::System::point_hessian(), libMesh::System::point_value(), libMesh::FEMContext::pre_fe_reinit(), libMesh::System::re_update(), libMesh::System::reinit(), libMesh::System::restrict_vectors(), OverlappingAlgebraicGhostingTest::run_ghosting_test(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), SolidSystem::save_initial_mesh(), libMesh::RBConstruction::set_context_solution_vec(), setup(), FETest< order, family, elem_type >::testGradU(), FETest< order, family, elem_type >::testGradUComp(), FETest< order, family, elem_type >::testU(), libMesh::BoundaryVolumeSolutionTransfer::transfer_boundary_volume(), libMesh::TransientRBConstruction::truth_assembly(), libMesh::TransientRBConstruction::truth_solve(), libMesh::System::update(), and libMesh::Nemesis_IO_Helper::write_nodal_solution().

deltat

Real libMesh::DifferentiableSystem::deltat

inherited

For time-dependent problems, this is the amount delta t to advance the solution in time.

Definition at line 260 of file diff_system.h.

Referenced by libMesh::EulerSolver::_general_residual(), libMesh::Euler2Solver::_general_residual(), libMesh::NewmarkSolver::_general_residual(), libMesh::UnsteadySolver::adjoint_advance_timestep(), libMesh::NewmarkSolver::advance_timestep(), libMesh::UnsteadySolver::advance_timestep(), libMesh::FEMSystem::build_context(), libMesh::DifferentiableSystem::build_context(), libMesh::FEMSystem::init_context(), SolidSystem::init_data(), main(), set_system_parameters(), libMesh::TwostepTimeSolver::solve(), and libMesh::UnsteadySolver::solve().

diff_qoi

DifferentiableQoI* libMesh::DifferentiableSystem::diff_qoi

protectedinherited

Pointer to object to use for quantity of interest assembly evaluations.

Defaults to this for backwards compatibility; in the future users should create separate physics objects.

Definition at line 377 of file diff_system.h.

Referenced by libMesh::FEMSystem::assemble_qoi(), libMesh::FEMSystem::assemble_qoi_derivative(), libMesh::DifferentiableSystem::attach_qoi(), libMesh::DifferentiableSystem::clear(), libMesh::DifferentiableSystem::get_qoi(), and libMesh::DifferentiableSystem::~DifferentiableSystem().

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 1524 of file system.h.

Referenced by libMesh::JumpErrorEstimator::estimate_error(), CurlCurlSystem::init_data(), and set_system_parameters().

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 393 of file implicit_system.h.

Referenced by libMesh::__libmesh_petsc_diff_solver_jacobian(), add_M_C_K_helmholtz(), libMesh::ImplicitSystem::add_system_matrix(), libMesh::ImplicitSystem::adjoint_solve(), assemble(), libMesh::ImplicitSystem::assemble(), LinearElasticity::assemble(), assemble_1D(), assemble_biharmonic(), assemble_elasticity(), assemble_ellipticdg(), assemble_helmholtz(), assemble_laplace(), assemble_matrix_and_rhs(), assemble_poisson(), assemble_shell(), assemble_stokes(), assemble_wave(), libMesh::FEMSystem::assembly(), libMesh::LinearImplicitSystem::assembly(), libMesh::NonlinearImplicitSystem::assembly(), assembly_with_dg_fem_context(), libMesh::NewmarkSystem::compute_matrix(), libMesh::RBConstruction::compute_residual_dual_norm_slow(), libMesh::ContinuationSystem::continuation_solve(), DMlibMeshJacobian(), libMesh::RBConstruction::enrich_basis_from_rhs_terms(), fill_dirichlet_bc(), libMesh::ImplicitSystem::forward_qoi_parameter_sensitivity(), libMesh::ImplicitSystem::init_matrices(), main(), libMesh::ImplicitSystem::qoi_parameter_hessian(), libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), libMesh::ImplicitSystem::sensitivity_solve(), libMesh::NewtonSolver::solve(), libMesh::PetscDiffSolver::solve(), libMesh::NoxNonlinearSolver< Number >::solve(), libMesh::EigenTimeSolver::solve(), libMesh::FrequencySystem::solve(), libMesh::LinearImplicitSystem::solve(), libMesh::NonlinearImplicitSystem::solve(), libMesh::ContinuationSystem::solve_tangent(), libMesh::TransientRBConstruction::truth_assembly(), libMesh::RBConstruction::truth_assembly(), libMesh::TransientRBConstruction::truth_solve(), libMesh::RBConstruction::truth_solve(), libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve(), and libMesh::ImplicitSystem::weighted_sensitivity_solve().

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(), libMesh::FEMSystem::numerical_jacobian_h_for_var(), and set_system_parameters().

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 314 of file diff_system.h.

Referenced by main().

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 361 of file diff_system.h.

Referenced by CurlCurlSystem::init_data(), and set_system_parameters().

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 356 of file diff_system.h.

Referenced by set_system_parameters().

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 351 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 341 of file diff_system.h.

Referenced by libMesh::FEMSystem::assembly(), and set_system_parameters().

print_jacobians

bool libMesh::DifferentiableSystem::print_jacobians

inherited

Set print_jacobians to true to print J whenever it is assembled.

Definition at line 346 of file diff_system.h.

Referenced by libMesh::FEMSystem::assembly(), CurlCurlSystem::init_data(), and set_system_parameters().

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 331 of file diff_system.h.

Referenced by libMesh::FEMSystem::assembly(), and set_system_parameters().

print_residuals

bool libMesh::DifferentiableSystem::print_residuals

inherited

Set print_residuals to true to print F whenever it is assembled.

Definition at line 336 of file diff_system.h.

Referenced by libMesh::FEMSystem::assembly(), and set_system_parameters().

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 320 of file diff_system.h.

Referenced by libMesh::FEMSystem::assembly(), and set_system_parameters().

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 326 of file diff_system.h.

Referenced by libMesh::FEMSystem::assembly(), and set_system_parameters().

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 1574 of file system.h.

Referenced by libMesh::ImplicitSystem::adjoint_qoi_parameter_sensitivity(), libMesh::ExplicitSystem::assemble_qoi(), libMesh::FEMSystem::assemble_qoi(), libMesh::DifferentiableSystem::attach_qoi(), libMesh::DiffContext::DiffContext(), libMesh::ImplicitSystem::forward_qoi_parameter_sensitivity(), libMesh::System::n_qois(), CoupledSystem::postprocess(), libMesh::ImplicitSystem::qoi_parameter_hessian(), and libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product().

rhs

NumericVector<Number>* libMesh::ExplicitSystem::rhs

inherited

The system matrix.

Implicit systems are characterized by the need to solve the linear system Ax=b. This is the right-hand-side vector b.

Definition at line 114 of file explicit_system.h.

Referenced by libMesh::__libmesh_petsc_diff_solver_residual(), add_M_C_K_helmholtz(), libMesh::ExplicitSystem::add_system_rhs(), assemble(), libMesh::ImplicitSystem::assemble(), LinearElasticity::assemble(), assemble_1D(), assemble_biharmonic(), assemble_elasticity(), assemble_ellipticdg(), assemble_laplace(), assemble_matrix_and_rhs(), assemble_poisson(), libMesh::ImplicitSystem::assemble_residual_derivatives(), assemble_shell(), assemble_stokes(), assemble_wave(), libMesh::FEMSystem::assembly(), libMesh::LinearImplicitSystem::assembly(), libMesh::NonlinearImplicitSystem::assembly(), assembly_with_dg_fem_context(), libMesh::RBConstruction::compute_Fq_representor_innerprods(), libMesh::RBConstruction::compute_output_dual_innerprods(), libMesh::RBConstruction::compute_residual_dual_norm_slow(), libMesh::Problem_Interface::computeF(), libMesh::ContinuationSystem::continuation_solve(), DMlibMeshFunction(), libMesh::RBConstruction::enrich_basis_from_rhs_terms(), fill_dirichlet_bc(), libMesh::ImplicitSystem::forward_qoi_parameter_sensitivity(), libMesh::NewtonSolver::line_search(), HeatSystem::perturb_accumulate_residuals(), libMesh::ImplicitSystem::qoi_parameter_hessian(), libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product(), libMesh::NewtonSolver::solve(), libMesh::PetscDiffSolver::solve(), libMesh::FrequencySystem::solve(), libMesh::LinearImplicitSystem::solve(), libMesh::NonlinearImplicitSystem::solve(), libMesh::ContinuationSystem::solve_tangent(), libMesh::TransientRBConstruction::truth_assembly(), libMesh::RBConstruction::truth_assembly(), libMesh::TransientRBConstruction::truth_solve(), libMesh::RBEIMConstruction::truth_solve(), libMesh::RBConstruction::truth_solve(), libMesh::TransientRBConstruction::update_residual_terms(), libMesh::RBConstruction::update_residual_terms(), libMesh::NewmarkSystem::update_rhs(), libMesh::ImplicitSystem::weighted_sensitivity_adjoint_solve(), and libMesh::ImplicitSystem::weighted_sensitivity_solve().

solution

std::unique_ptr<NumericVector<Number> > libMesh::System::solution

inherited

Data structure to hold solution values.

Definition at line 1539 of file system.h.

Referenced by libMesh::__libmesh_petsc_diff_solver_jacobian(), libMesh::__libmesh_petsc_diff_solver_residual(), libMesh::ExactSolution::_compute_error(), libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::TransientRBConstruction::add_IC_to_RB_space(), libMesh::NewmarkSolver::advance_timestep(), libMesh::AdaptiveTimeSolver::advance_timestep(), libMesh::UnsteadySolver::advance_timestep(), libMesh::ContinuationSystem::apply_predictor(), libMesh::TransientRBConstruction::assemble_affine_expansion(), libMesh::FEMSystem::assembly(), libMesh::LinearImplicitSystem::assembly(), libMesh::EquationSystems::build_parallel_elemental_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::System::clear(), libMesh::System::compare(), libMesh::RBEIMConstruction::compute_best_fit_error(), libMesh::RBConstruction::compute_Fq_representor_innerprods(), libMesh::NewmarkSolver::compute_initial_accel(), libMesh::RBConstruction::compute_output_dual_innerprods(), libMesh::RBConstruction::compute_residual_dual_norm_slow(), LinearElasticityWithContact::compute_stresses(), LinearElasticity::compute_stresses(), compute_stresses(), LargeDeformationElasticity::compute_stresses(), libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), libMesh::ContinuationSystem::continuation_solve(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), libMesh::GMVIO::copy_nodal_solution(), libMesh::ExodusII_IO::copy_scalar_solution(), DMCreateGlobalVector_libMesh(), DMlibMeshFunction(), DMlibMeshJacobian(), libMesh::UnsteadySolver::du(), libMesh::RBEIMConstruction::enrich_RB_space(), libMesh::RBConstruction::enrich_RB_space(), libMesh::WeightedPatchRecoveryErrorEstimator::estimate_error(), libMesh::PatchRecoveryErrorEstimator::estimate_error(), libMesh::JumpErrorEstimator::estimate_error(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::AdjointResidualErrorEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::RBSCMConstruction::evaluate_stability_constant(), libMesh::CondensedEigenSystem::get_eigenpair(), libMesh::EigenSystem::get_eigenpair(), LinearElasticityWithContact::get_least_and_max_gap_function(), libMesh::System::init_data(), libMesh::RBEIMConstruction::initialize_parametrized_functions_in_training_set(), libMesh::ContinuationSystem::initialize_tangent(), libMesh::TransientRBConstruction::initialize_truth(), libMesh::libmesh_petsc_snes_jacobian(), libMesh::libmesh_petsc_snes_residual_helper(), libMesh::RBEIMConstruction::load_basis_function(), libMesh::RBConstruction::load_basis_function(), libMesh::RBEIMConstruction::load_rb_solution(), libMesh::RBConstruction::load_rb_solution(), libMesh::TransientRBConstruction::load_rb_solution(), main(), libMesh::DofMap::max_constraint_error(), libMesh::FEMSystem::mesh_position_get(), libMesh::ErrorVector::plot_error(), libMesh::RBEIMConstruction::plot_parametrized_functions_in_training_set(), libMesh::RBConstruction::print_basis_function_orthogonality(), libMesh::ImplicitSystem::qoi_parameter_hessian(), libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product(), libMesh::System::re_update(), libMesh::System::read_legacy_data(), libMesh::System::read_parallel_data(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), libMesh::System::read_serialized_data(), libMesh::System::reinit(), libMesh::System::restrict_vectors(), libMesh::MemorySolutionHistory::retrieve(), OverlappingAlgebraicGhostingTest::run_ghosting_test(), OverlappingCouplingGhostingTest::run_sparsity_pattern_test(), libMesh::ContinuationSystem::save_current_solution(), libMesh::TransientRBConstruction::set_error_temporal_data(), setup(), libMesh::TwostepTimeSolver::solve(), libMesh::NewtonSolver::solve(), libMesh::PetscDiffSolver::solve(), libMesh::FrequencySystem::solve(), libMesh::LinearImplicitSystem::solve(), libMesh::NonlinearImplicitSystem::solve(), libMesh::RBConstruction::solve_for_matrix_and_rhs(), libMesh::ContinuationSystem::solve_tangent(), libMesh::MemorySolutionHistory::store(), MeshfunctionDFEM::test_mesh_function_dfem(), MeshfunctionDFEM::test_mesh_function_dfem_grad(), MeshFunctionTest::test_p_level(), SystemsTest::testBoundaryProjectCube(), SystemsTest::testDofCouplingWithVarGroups(), MeshInputTest::testExodusWriteElementDataFromDiscontinuousNodalData(), SystemsTest::testProjectCubeWithMeshFunction(), WriteVecAndScalar::testWrite(), libMesh::MeshFunctionSolutionTransfer::transfer(), libMesh::MeshfreeSolutionTransfer::transfer(), libMesh::DirectSolutionTransfer::transfer(), libMesh::BoundaryVolumeSolutionTransfer::transfer_boundary_volume(), libMesh::BoundaryVolumeSolutionTransfer::transfer_volume_boundary(), libMesh::TransientRBConstruction::truth_solve(), libMesh::RBEIMConstruction::truth_solve(), libMesh::RBConstruction::truth_solve(), libMesh::System::update(), libMesh::System::update_global_solution(), libMesh::TransientRBConstruction::update_RB_initial_condition_all_N(), libMesh::RBEIMConstruction::update_RB_system_matrices(), libMesh::TransientRBConstruction::update_residual_terms(), libMesh::RBConstruction::update_residual_terms(), libMesh::ContinuationSystem::update_solution(), libMesh::NewmarkSystem::update_u_v_a(), libMesh::DTKAdapter::update_variable_values(), libMesh::System::write_parallel_data(), libMesh::TransientRBConstruction::write_riesz_representors_to_files(), libMesh::RBConstruction::write_riesz_representors_to_files(), and libMesh::System::write_serialized_data().

time

Real libMesh::System::time

inherited

For time-dependent problems, this is the time t at the beginning of the current timestep.

Note

For DifferentiableSystem users: do not access this time during an assembly! Use the DiffContext::time value instead to get correct results.

Definition at line 1561 of file system.h.

Referenced by libMesh::UnsteadySolver::adjoint_advance_timestep(), libMesh::AdaptiveTimeSolver::advance_timestep(), libMesh::UnsteadySolver::advance_timestep(), fill_dirichlet_bc(), libMesh::ExactErrorEstimator::find_squared_element_error(), libMesh::MemorySolutionHistory::find_stored_entry(), initialize(), main(), libMesh::WeightedPatchRecoveryErrorEstimator::EstimateError::operator()(), libMesh::System::reinit_constraints(), libMesh::MemorySolutionHistory::retrieve(), libMesh::TwostepTimeSolver::solve(), and libMesh::MemorySolutionHistory::store().

time_solver

std::unique_ptr<TimeSolver> libMesh::DifferentiableSystem::time_solver

inherited

A pointer to the solver object we're going to use.

This must be instantiated by the user before solving!

Definition at line 233 of file diff_system.h.

Referenced by libMesh::FEMSystem::assembly(), libMesh::ContinuationSystem::continuation_solve(), libMesh::DifferentiableSystem::get_linear_solve_parameters(), libMesh::DifferentiableSystem::get_linear_solver(), libMesh::DifferentiableSystem::get_second_order_dot_var(), libMesh::DifferentiableSystem::get_time_solver(), SolidSystem::init_data(), libMesh::DifferentiableSystem::init_data(), main(), libMesh::DifferentiableSystem::reinit(), set_system_parameters(), libMesh::DifferentiableSystem::set_time_solver(), SolidSystem::SolidSystem(), libMesh::DifferentiableSystem::solve(), and libMesh::ContinuationSystem::solve_tangent().

use_fixed_solution

bool libMesh::System::use_fixed_solution

inherited

A boolean to be set to true by systems using elem_fixed_solution, for optional use by e.g.

stabilized methods. False by default.

Note

For FEMSystem users, if this variable is set to true, it must be before init_data() is called.

Definition at line 1509 of file system.h.

Referenced by libMesh::EulerSolver::_general_residual(), libMesh::Euler2Solver::_general_residual(), libMesh::SteadySolver::_general_residual(), libMesh::NewmarkSolver::_general_residual(), libMesh::DifferentiableSystem::clear(), libMesh::DiffContext::DiffContext(), and libMesh::FEMContext::pre_fe_reinit().

verify_analytic_jacobians

Real libMesh::FEMSystem::verify_analytic_jacobians

inherited

If verify_analytic_jacobian is equal to zero (as it is by default), no numeric jacobians will be calculated unless an overridden element_time_derivative(), element_constraint(), side_time_derivative(), or side_constraint() function cannot provide an analytic jacobian upon request.

If verify_analytic_jacobian is equal to the positive value tol, then any time a full analytic element jacobian can be calculated it will be tested against a numerical jacobian on the same element, and the program will abort if the relative error (in matrix l1 norms) exceeds tol.

Definition at line 209 of file fem_system.h.

Referenced by libMesh::FEMSystem::assembly(), CurlCurlSystem::init_data(), and set_system_parameters().

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 400 of file implicit_system.h.

Referenced by libMesh::ImplicitSystem::assemble().

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The documentation for this class was generated from the following file:

• tests/solvers/first_order_unsteady_solver_test.C