libMesh::System Class Reference

Manages consistently variables, degrees of freedom, and coefficient vectors. More...

#include <system.h>

Inheritance diagram for libMesh::System:

Classes
class	Assembly
	Abstract base class to be used for system assembly. More...
class	Constraint
	Abstract base class to be used for system constraints. More...
class	Initialization
	Abstract base class to be used for system initialization. More...
class	QOI
	Abstract base class to be used for quantities of interest. More...
class	QOIDerivative
	Abstract base class to be used for derivatives of quantities of interest. More...

Public Types
typedef System	sys_type
	The type of system. More...
typedef Number(*	ValueFunctionPointer) (const Point &p, const Parameters &Parameters, const std::string &sys_name, const std::string &unknown_name)
	Projects arbitrary functions onto the current solution. More...
typedef Gradient(*	GradientFunctionPointer) (const Point &p, const Parameters &parameters, const std::string &sys_name, const std::string &unknown_name)
typedef std::map< std::string, NumericVector< Number > * >::iterator	vectors_iterator
	Vector iterator typedefs. More...
typedef std::map< std::string, NumericVector< Number > * >::const_iterator	const_vectors_iterator

Public Member Functions
	System (EquationSystems &es, const std::string &name, const unsigned int number)
	Constructor. More...
virtual	~System ()
	Destructor. More...
sys_type &	system ()
virtual void	clear ()
	Clear all the data structures associated with the system. More...
void	init ()
	Initializes degrees of freedom on the current mesh. More...
virtual void	reinit ()
	Reinitializes degrees of freedom and other required data 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	assemble ()
	Prepares matrix and _dof_map for matrix assembly. More...
virtual void	assemble_qoi (const QoISet &qoi_indices=QoISet())
	Calls user qoi function. More...
virtual void	assemble_qoi_derivative (const QoISet &qoi_indices=QoISet(), bool include_liftfunc=true, bool apply_constraints=true)
	Calls user qoi derivative function. More...
virtual void	assemble_residual_derivatives (const ParameterVector &parameters)
	Calls residual parameter derivative function. More...
virtual void	restrict_solve_to (const SystemSubset *subset, const SubsetSolveMode subset_solve_mode=SUBSET_ZERO)
	After calling this method, any solve will be restricted to the given subdomain. More...
virtual void	solve ()
	Solves the system. More...
virtual std::pair< unsigned int, Real >	sensitivity_solve (const ParameterVector &parameters)
	Solves the sensitivity system, for the provided parameters. More...
virtual std::pair< unsigned int, Real >	weighted_sensitivity_solve (const ParameterVector &parameters, const ParameterVector &weights)
	Assembles & solves the linear system(s) (dR/du)*u_w = sum(w_p*-dR/dp), for those parameters p contained within parameters weighted by the values w_p found within weights. More...
virtual std::pair< unsigned int, Real >	adjoint_solve (const QoISet &qoi_indices=QoISet())
	Solves the adjoint system, for the specified qoi indices, or for every qoi if qoi_indices is nullptr. More...
virtual std::pair< unsigned int, Real >	weighted_sensitivity_adjoint_solve (const ParameterVector &parameters, const ParameterVector &weights, const QoISet &qoi_indices=QoISet())
	Assembles & solves the linear system(s) (dR/du)^T*z_w = sum(w_p*(d^2q/dudp - d^2R/dudp*z)), for those parameters p contained within parameters, weighted by the values w_p found within weights. More...
bool	is_adjoint_already_solved () const
	Accessor for the adjoint_already_solved boolean. More...
void	set_adjoint_already_solved (bool setting)
	Setter for the adjoint_already_solved boolean. More...
virtual void	qoi_parameter_sensitivity (const QoISet &qoi_indices, const ParameterVector &parameters, SensitivityData &sensitivities)
	Solves for the derivative of each of the system's quantities of interest q in qoi[qoi_indices] with respect to each parameter in parameters, placing the result for qoi i and parameter j into sensitivities[i][j]. More...
virtual void	adjoint_qoi_parameter_sensitivity (const QoISet &qoi_indices, const ParameterVector &parameters, SensitivityData &sensitivities)
	Solves for parameter sensitivities using the adjoint method. More...
virtual void	forward_qoi_parameter_sensitivity (const QoISet &qoi_indices, const ParameterVector &parameters, SensitivityData &sensitivities)
	Solves for parameter sensitivities using the forward method. More...
virtual void	qoi_parameter_hessian (const QoISet &qoi_indices, const ParameterVector &parameters, SensitivityData &hessian)
	For each of the system's quantities of interest q in qoi[qoi_indices], and for a vector of parameters p, the parameter sensitivity Hessian H_ij is defined as H_ij = (d^2 q)/(d p_i d p_j) This Hessian is the output of this method, where for each q_i, H_jk is stored in hessian.second_derivative(i,j,k). More...
virtual void	qoi_parameter_hessian_vector_product (const QoISet &qoi_indices, const ParameterVector &parameters, const ParameterVector &vector, SensitivityData &product)
	For each of the system's quantities of interest q in qoi[qoi_indices], and for a vector of parameters p, the parameter sensitivity Hessian H_ij is defined as H_ij = (d^2 q)/(d p_i d p_j) The Hessian-vector product, for a vector v_k in parameter space, is S_j = H_jk v_k This product is the output of this method, where for each q_i, S_j is stored in sensitivities[i][j]. More...
virtual bool	compare (const System &other_system, const Real threshold, const bool verbose) const
const std::string &	name () const
virtual std::string	system_type () 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
virtual unsigned int	n_matrices () const
unsigned int	n_vars () const
unsigned int	n_variable_groups () const
unsigned int	n_components () const
dof_id_type	n_dofs () const
dof_id_type	n_active_dofs () const
dof_id_type	n_constrained_dofs () const
dof_id_type	n_local_constrained_dofs () const
dof_id_type	n_local_dofs () const
unsigned int	add_variable (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...
virtual void	disable_cache ()
	Avoids use of any cached data that might affect any solve result. More...
Number	current_solution (const dof_id_type global_dof_number) const
unsigned int	n_qois () const
	Number of currently active quantities of interest. More...
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

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	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...

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

Protected Member Functions
virtual void	init_data ()
	Initializes the data for the 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
const Parallel::Communicator &	_communicator

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

Private Member Functions
	System (const System &)
	This isn't a copyable object, so let's make sure nobody tries. More...
System &	operator= (const System &)
	This isn't a copyable object, so let's make sure nobody tries. 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
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

Manages consistently variables, degrees of freedom, and coefficient vectors.

This is the base class for classes which contain information related to any physical process that might be simulated. Such information may range from the actual solution values to algorithmic flags that may be used to control the numerical methods employed. In general, use an EquationSystems object to handle one or more of the children of this class.

Especially, this class manages the variables of the differential equation, the coefficient vectors and the DofMap, and ensures that these are consistent. It provides storage for the solution. Furthermore, (de-) serialization functionality is provided.

Author

Benjamin S. Kirk

Date

2003-2004

Definition at line 100 of file system.h.

Member Typedef Documentation

const_vectors_iterator

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

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)

Definition at line 532 of file system.h.

sys_type

typedef System libMesh::System::sys_type

The type of system.

Definition at line 243 of file system.h.

ValueFunctionPointer

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

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

Vector iterator typedefs.

Definition at line 756 of file system.h.

Constructor & Destructor Documentation

System() [1/2]

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

Constructor.

Optionally initializes required data structures.

Definition at line 61 of file system.C.

                                              :
 
  ParallelObject                    (es),
  assemble_before_solve             (true),
  use_fixed_solution                (false),
  extra_quadrature_order            (0),
  solution                          (NumericVector<Number>::build(this->comm())),
  current_local_solution            (NumericVector<Number>::build(this->comm())),
  time                              (0.),
  qoi                               (0),
  _init_system_function             (nullptr),
  _init_system_object               (nullptr),
  _assemble_system_function         (nullptr),
  _assemble_system_object           (nullptr),
  _constrain_system_function        (nullptr),
  _constrain_system_object          (nullptr),
  _qoi_evaluate_function            (nullptr),
  _qoi_evaluate_object              (nullptr),
  _qoi_evaluate_derivative_function (nullptr),
  _qoi_evaluate_derivative_object   (nullptr),
  _dof_map                          (libmesh_make_unique<DofMap>(number_in, es.get_mesh())),
  _equation_systems                 (es),
  _mesh                             (es.get_mesh()),
  _sys_name                         (name_in),
  _sys_number                       (number_in),
  _active                           (true),
  _solution_projection              (true),
  _basic_system_only                (false),
  _is_initialized                   (false),
  _identify_variable_groups         (true),
  _additional_data_written          (false),
  adjoint_already_solved            (false),
  _hide_output                      (false)
{
}

Referenced by HeatSystem::init_context().

~System()

libMesh::System::~System ( )

virtual

Destructor.

Definition at line 120 of file system.C.

{
  // Null-out the function pointers.  Since this
  // class is getting destructed it is pointless,
  // but a good habit.
  _init_system_function =
    _assemble_system_function =
    _constrain_system_function = nullptr;
 
  _qoi_evaluate_function = nullptr;
  _qoi_evaluate_derivative_function =  nullptr;
 
  // nullptr-out user-provided objects.
  _init_system_object             = nullptr;
  _assemble_system_object         = nullptr;
  _constrain_system_object        = nullptr;
  _qoi_evaluate_object            = nullptr;
  _qoi_evaluate_derivative_object = nullptr;
 
  // Clear data
  // Note: although clear() is virtual, C++ only calls
  // the clear() of the base class in the destructor.
  // Thus we add System namespace to make it clear.
  System::clear ();
 
  libmesh_exceptionless_assert (!libMesh::closed());
}

References _assemble_system_function, _assemble_system_object, _constrain_system_function, _constrain_system_object, _init_system_function, _init_system_object, _qoi_evaluate_derivative_function, _qoi_evaluate_derivative_object, _qoi_evaluate_function, _qoi_evaluate_object, clear(), and libMesh::closed().

System() [2/2]

libMesh::System::System ( const System &  other )

private

This isn't a copyable object, so let's make sure nobody tries.

We won't even bother implementing this; we'll just make sure that the compiler doesn't implement a default.

Definition at line 102 of file system.C.

                                    :
  ReferenceCountedObject<System>(),
  ParallelObject(other),
  _equation_systems(other._equation_systems),
  _mesh(other._mesh),
  _sys_number(other._sys_number)
{
  libmesh_not_implemented();
}

Member Function Documentation

activate()

void libMesh::System::activate ( )

inline

Activates the system.

Only active systems are solved.

Definition at line 2123 of file system.h.

{
  _active = true;
}

References _active.

active()

bool libMesh::System::active ( ) const

inline

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 _active.

add_adjoint_rhs()

NumericVector< Number > & libMesh::System::add_adjoint_rhs

(

unsigned int

i = 0

)

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 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

)

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 add_vector(), and set_vector_as_adjoint().

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

add_sensitivity_rhs()

NumericVector< Number > & libMesh::System::add_sensitivity_rhs

(

unsigned int

i = 0

)

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 add_vector().

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

add_sensitivity_solution()

NumericVector< Number > & libMesh::System::add_sensitivity_solution

(

unsigned int

i = 0

)

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 add_vector().

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

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
	)

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

Referenced by libMesh::DifferentiableSystem::add_second_order_dot_vars(), add_variable(), assemble_and_solve(), OverlappingTestBase::init(), SolidSystem::init_data(), CurlCurlSystem::init_data(), HeatSystem::init_data(), SimpleRBConstruction::init_data(), main(), libMesh::ErrorVector::plot_error(), 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
	)

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 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
	)

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

Referenced by add_variable(), and 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
	)

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 add_variables().

add_vector()

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

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

Referenced by add_adjoint_rhs(), add_adjoint_solution(), add_sensitivity_rhs(), add_sensitivity_solution(), libMesh::ExplicitSystem::add_system_rhs(), add_weighted_sensitivity_adjoint_solution(), 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(), 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

)

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 add_vector(), and set_vector_as_adjoint().

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

add_weighted_sensitivity_solution()

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

(

)

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 add_vector().

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

adjoint_qoi_parameter_sensitivity()

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

inlinevirtual

Solves for parameter sensitivities using the adjoint method.

This method is only implemented in some derived classes.

Reimplemented in libMesh::ImplicitSystem.

Definition at line 2366 of file system.h.

{
  libmesh_not_implemented();
}

Referenced by qoi_parameter_sensitivity().

adjoint_solve()

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

inlinevirtual

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

Must be overridden in derived systems.

Returns

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

This method is only implemented in some derived classes.

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

Definition at line 2350 of file system.h.

{
  libmesh_not_implemented();
}

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

assemble()

void libMesh::System::assemble ( )

virtual

Prepares matrix and _dof_map for matrix assembly.

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

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

Definition at line 462 of file system.C.

{
  // Log how long the user's assembly code takes
  LOG_SCOPE("assemble()", "System");
 
  // Call the user-specified assembly function
  this->user_assembly();
}

References user_assembly().

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

assemble_qoi()

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

virtual

Calls user qoi function.

Can be overridden in derived classes.

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

Definition at line 473 of file system.C.

{
  // Log how long the user's assembly code takes
  LOG_SCOPE("assemble_qoi()", "System");
 
  // Call the user-specified quantity of interest function
  this->user_QOI(qoi_indices);
}

References user_QOI().

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

assemble_qoi_derivative()

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

virtual

Calls user qoi derivative function.

Can be overridden in derived classes.

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

Definition at line 484 of file system.C.

{
  // Log how long the user's assembly code takes
  LOG_SCOPE("assemble_qoi_derivative()", "System");
 
  // Call the user-specified quantity of interest function
  this->user_QOI_derivative(qoi_indices, include_liftfunc,
                            apply_constraints);
}

References user_QOI_derivative().

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

assemble_residual_derivatives()

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

inlinevirtual

Calls residual parameter derivative function.

Library subclasses use finite differences by default.

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

This method is only implemented in some derived classes.

Reimplemented in libMesh::ImplicitSystem.

Definition at line 2319 of file system.h.

{
  libmesh_not_implemented();
}

attach_assemble_function()

void libMesh::System::attach_assemble_function

(

void

fptrEquationSystems &es, const std::string &name

)

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 _assemble_system_function, _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

)

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 _assemble_system_function, _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

)

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

attach_constraint_object()

void libMesh::System::attach_constraint_object

(

System::Constraint &

constrain

)

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 _constrain_system_function, _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

)

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 _init_system_function, _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

)

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 _init_system_function, _init_system_object, and libMesh::out.

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

)

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 _qoi_evaluate_derivative_function, _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

)

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 _qoi_evaluate_derivative_function, _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

)

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

attach_QOI_object()

void libMesh::System::attach_QOI_object

(

QOI &

qoi

)

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 _qoi_evaluate_function, _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
	)

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
	)

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

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

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().

calculate_norm() [1/2]

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

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 _dof_map, _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, discrete_var_norm(), libMesh::DofMap::dof_indices(), libMesh::MeshBase::elem_dimensions(), libMesh::ReferenceElem::get(), libMesh::FEGenericBase< OutputType >::get_d2phi(), get_dof_map(), libMesh::FEGenericBase< OutputType >::get_dphi(), libMesh::FEAbstract::get_JxW(), 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(), 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

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, discrete_var_norm(), libMesh::L2, n_vars(), and libMesh::Real.

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

clear()

void libMesh::System::clear ( )

virtual

Clear all the data structures associated with the system.

Reimplemented in libMesh::OptimizationSystem, libMesh::NonlinearImplicitSystem, libMesh::RBConstruction, libMesh::ImplicitSystem, libMesh::EigenSystem, libMesh::LinearImplicitSystem, libMesh::TransientSystem< RBConstruction >, libMesh::DifferentiableSystem, libMesh::ContinuationSystem, libMesh::FrequencySystem, libMesh::RBSCMConstruction, libMesh::RBEIMConstruction, libMesh::TransientRBConstruction, libMesh::ExplicitSystem, libMesh::NewmarkSystem, libMesh::RBConstructionBase< LinearImplicitSystem >, and libMesh::RBConstructionBase< CondensedEigenSystem >.

Definition at line 205 of file system.C.

{
  _variables.clear();
 
  _variable_numbers.clear();
 
  _dof_map->clear ();
 
  solution->clear ();
 
  current_local_solution->clear ();
 
  // clear any user-added vectors
  {
    for (auto & pr : _vectors)
      {
        pr.second->clear ();
        delete pr.second;
        pr.second = nullptr;
      }
 
    _vectors.clear();
    _vector_projections.clear();
    _vector_is_adjoint.clear();
    _vector_types.clear();
    _is_initialized = false;
  }
 
}

References _dof_map, _is_initialized, _variable_numbers, _variables, _vector_is_adjoint, _vector_projections, _vector_types, _vectors, current_local_solution, and solution.

Referenced by libMesh::ExplicitSystem::clear(), libMesh::EigenSystem::clear(), read_header(), and ~System().

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(), 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(), 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(), point_gradient(), point_hessian(), point_value(), libMesh::DofMap::print_dof_constraints(), FEMParameters::read(), libMesh::Nemesis_IO::read(), libMesh::XdrIO::read(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), read_header(), libMesh::RBEvaluation::read_in_vectors_from_multiple_files(), read_legacy_data(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), read_SCALAR_dofs(), libMesh::XdrIO::read_serialized_bc_names(), libMesh::XdrIO::read_serialized_bcs_helper(), 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(), 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(), write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bcs_helper(), 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

virtual

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

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

current_solution()

Number libMesh::System::current_solution

(

const dof_id_type

global_dof_number

)

const

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 _dof_map, and 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().

deactivate()

void libMesh::System::deactivate ( )

inline

Deactivates the system.

Only active systems are solved.

Definition at line 2131 of file system.h.

{
  _active = false;
}

References _active.

disable_cache()

void libMesh::System::disable_cache ( )

inlinevirtual

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

Should be overridden in derived systems.

Reimplemented in libMesh::ImplicitSystem.

Definition at line 2325 of file system.h.

{ assemble_before_solve = true; }

References assemble_before_solve.

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

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

private

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, local_dof_indices(), libMesh::NumericVector< T >::subset_l1_norm(), libMesh::NumericVector< T >::subset_l2_norm(), and libMesh::NumericVector< T >::subset_linfty_norm().

Referenced by calculate_norm().

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.

forward_qoi_parameter_sensitivity()

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

inlinevirtual

Solves for parameter sensitivities using the forward method.

This method is only implemented in some derived classes.

Reimplemented in libMesh::ImplicitSystem.

Definition at line 2375 of file system.h.

{
  libmesh_not_implemented();
}

Referenced by qoi_parameter_sensitivity().

get_adjoint_rhs() [1/2]

NumericVector< Number > & libMesh::System::get_adjoint_rhs

(

unsigned int

i = 0

)

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 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

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 get_vector().

get_adjoint_solution() [1/2]

NumericVector< Number > & libMesh::System::get_adjoint_solution

(

unsigned int

i = 0

)

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 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

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 get_vector().

get_all_variable_numbers()

void libMesh::System::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.

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 _variable_numbers, and 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 ( )

inline

Returns

A writable reference to this system's _dof_map.

Definition at line 2107 of file system.h.

{
  return *_dof_map;
}

References _dof_map.

get_dof_map() [2/2]

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

inline

Returns

A constant reference to this system's _dof_map.

Definition at line 2099 of file system.h.

{
  return *_dof_map;
}

References _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(), 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(), 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(), 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(), point_gradient(), point_hessian(), point_value(), libMesh::FEMContext::pre_fe_reinit(), libMesh::RBEIMAssembly::RBEIMAssembly(), libMesh::RBEIMConstruction::RBEIMConstruction(), re_update(), read_parallel_data(), read_SCALAR_dofs(), libMesh::SecondOrderUnsteadySolver::reinit(), libMesh::UnsteadySolver::reinit(), libMesh::EigenSystem::reinit(), libMesh::ImplicitSystem::reinit(), 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(), write_parallel_data(), libMesh::EnsightIO::write_scalar_ascii(), 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 ( )

inline

Returns

A reference to this system's parent EquationSystems object.

Definition at line 725 of file system.h.

{ return _equation_systems; }

References _equation_systems.

get_equation_systems() [2/2]

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

inline

Returns

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

Definition at line 720 of file system.h.

{ return _equation_systems; }

References _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(), point_gradient(), 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_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

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

get_mesh() [1/2]

MeshBase & libMesh::System::get_mesh ( )

inline

Returns

A reference to this systems's _mesh.

Definition at line 2091 of file system.h.

{
  return _mesh;
}

References _mesh.

get_mesh() [2/2]

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

inline

Returns

A constant reference to this systems's _mesh.

Definition at line 2083 of file system.h.

{
  return _mesh;
}

References _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(), 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(), 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(), 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(), point_gradient(), point_hessian(), point_value(), libMesh::FEMSystem::postprocess(), read_header(), libMesh::RBEvaluation::read_in_vectors_from_multiple_files(), read_legacy_data(), read_parallel_data(), read_serialized_vector(), 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(), write_header(), libMesh::RBEvaluation::write_out_vectors(), write_parallel_data(), write_serialized_vector(), write_serialized_vectors(), and zero_variable().

get_sensitivity_rhs() [1/2]

NumericVector< Number > & libMesh::System::get_sensitivity_rhs

(

unsigned int

i = 0

)

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 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

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 get_vector().

get_sensitivity_solution() [1/2]

NumericVector< Number > & libMesh::System::get_sensitivity_solution

(

unsigned int

i = 0

)

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 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

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 get_vector().

get_vector() [1/4]

NumericVector< Number > & libMesh::System::get_vector

(

const std::string &

vec_name

)

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 _vectors.

get_vector() [2/4]

const NumericVector< Number > & libMesh::System::get_vector

(

const std::string &

vec_name

)

const

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 _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(), compare(), libMesh::NewmarkSolver::compute_initial_accel(), libMesh::UnsteadySolver::du(), libMesh::AdjointRefinementEstimator::estimate_error(), get_adjoint_rhs(), get_adjoint_solution(), get_sensitivity_rhs(), get_sensitivity_solution(), get_weighted_sensitivity_adjoint_solution(), 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

)

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(), vectors_begin(), and vectors_end().

get_vector() [4/4]

const NumericVector< Number > & libMesh::System::get_vector

(

const unsigned int

vec_num

)

const

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(), vectors_begin(), and vectors_end().

get_weighted_sensitivity_adjoint_solution() [1/2]

NumericVector< Number > & libMesh::System::get_weighted_sensitivity_adjoint_solution

(

unsigned int

i = 0

)

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 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

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 get_vector().

get_weighted_sensitivity_solution() [1/2]

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

(

)

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 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

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 get_vector().

has_variable()

bool libMesh::System::has_variable

(

const std::string &

var

)

const

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 _variable_numbers.

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

have_vector()

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

inline

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 _vectors.

Referenced by add_vector().

hide_output()

bool& libMesh::System::hide_output ( )

inline

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 _hide_output.

identify_variable_groups() [1/2]

bool libMesh::System::identify_variable_groups ( ) const

inline

Returns

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

Definition at line 2251 of file system.h.

{
  return _identify_variable_groups;
}

References _identify_variable_groups.

Referenced by add_variable().

identify_variable_groups() [2/2]

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

inline

Toggle automatic VariableGroup identification.

Definition at line 2259 of file system.h.

{
  _identify_variable_groups = ivg;
}

References _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

(

)

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

init_data()

void libMesh::System::init_data ( )

protectedvirtual

Initializes the data for the system.

Note

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

Reimplemented in libMesh::ImplicitSystem, libMesh::DifferentiableSystem, libMesh::ContinuationSystem, libMesh::RBEIMConstruction, libMesh::FEMSystem, libMesh::OptimizationSystem, libMesh::FrequencySystem, libMesh::EigenSystem, SecondOrderScalarSystemSecondOrderTimeSolverBase, FirstOrderScalarSystemBase, libMesh::LinearImplicitSystem, libMesh::RBConstructionBase< LinearImplicitSystem >, libMesh::RBConstructionBase< CondensedEigenSystem >, SimpleRBConstruction, SimpleRBConstruction, SimpleRBConstruction, SimpleRBConstruction, SimpleRBConstruction, HeatSystem, SimpleRBConstruction, ElasticityRBConstruction, CoupledSystem, L2System, ElasticitySystem, LaplaceSystem, CurlCurlSystem, LaplaceSystem, PoissonSystem, LaplaceSystem, LaplaceSystem, CurlCurlSystem, SolidSystem, NavierSystem, and HeatSystem.

Definition at line 262 of file system.C.

{
  MeshBase & mesh = this->get_mesh();
 
  // Add all variable groups to our underlying DofMap
  for (auto vg : IntRange<unsigned int>(0, this->n_variable_groups()))
    _dof_map->add_variable_group(this->variable_group(vg));
 
  // Distribute the degrees of freedom on the mesh
  _dof_map->distribute_dofs (mesh);
 
  // Recreate any user or internal constraints
  this->reinit_constraints();
 
  // And clean up the send_list before we first use it
  _dof_map->prepare_send_list();
 
  // Resize the solution conformal to the current mesh
  solution->init (this->n_dofs(), this->n_local_dofs(), false, PARALLEL);
 
  // Resize the current_local_solution for the current mesh
#ifdef LIBMESH_ENABLE_GHOSTED
  current_local_solution->init (this->n_dofs(), this->n_local_dofs(),
                                _dof_map->get_send_list(), false,
                                GHOSTED);
#else
  current_local_solution->init (this->n_dofs(), false, SERIAL);
#endif
 
  // from now on, adding additional vectors or variables can't be done
  // without immediately initializing them
  _is_initialized = true;
 
  // initialize & zero other vectors, if necessary
  for (auto & pr : _vectors)
    {
      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 if (type == SERIAL)
        {
          pr.second->init (this->n_dofs(), false, type);
        }
      else
        {
          libmesh_assert_equal_to(type, PARALLEL);
          pr.second->init (this->n_dofs(), this->n_local_dofs(), false, type);
        }
    }
}

References _dof_map, _is_initialized, _vector_types, _vectors, current_local_solution, get_mesh(), libMesh::GHOSTED, mesh, n_dofs(), n_local_dofs(), n_variable_groups(), libMesh::PARALLEL, reinit_constraints(), libMesh::SERIAL, solution, and variable_group().

Referenced by init(), libMesh::EigenSystem::init_data(), and libMesh::ImplicitSystem::init_data().

is_adjoint_already_solved()

bool libMesh::System::is_adjoint_already_solved ( ) const

inline

Accessor for the adjoint_already_solved boolean.

Definition at line 396 of file system.h.

  { return adjoint_already_solved;}

References 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_initialized()

bool libMesh::System::is_initialized ( )

inline

Returns

true iff this system has been initialized.

Definition at line 2139 of file system.h.

{
  return _is_initialized;
}

References _is_initialized.

Referenced by add_variable(), add_variables(), and init().

local_dof_indices()

void libMesh::System::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.

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(), get_dof_map(), get_mesh(), and libMesh::libmesh_assert().

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

n_active_dofs()

dof_id_type libMesh::System::n_active_dofs ( ) const

inline

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 n_constrained_dofs(), and n_dofs().

n_components()

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

inline

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

Referenced by add_variables().

n_constrained_dofs()

dof_id_type libMesh::System::n_constrained_dofs

(

)

const

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 _dof_map.

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

n_dofs()

dof_id_type libMesh::System::n_dofs

(

)

const

Returns

The number of degrees of freedom in the system

Definition at line 150 of file system.C.

{
  return _dof_map->n_dofs();
}

References _dof_map.

Referenced by libMesh::TransientRBConstruction::add_IC_to_RB_space(), 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(), get_info(), libMesh::SecondOrderUnsteadySolver::init_data(), libMesh::UnsteadySolver::init_data(), 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(), 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(), read_legacy_data(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), libMesh::SecondOrderUnsteadySolver::reinit(), libMesh::UnsteadySolver::reinit(), 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

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 _dof_map.

Referenced by get_info().

n_local_dofs()

dof_id_type libMesh::System::n_local_dofs

(

)

const

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

Referenced by libMesh::TransientRBConstruction::add_IC_to_RB_space(), 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(), get_info(), libMesh::SecondOrderUnsteadySolver::init_data(), libMesh::UnsteadySolver::init_data(), 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(), 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::System::n_matrices ( ) const

inlinevirtual

Returns

The number of matrices handled by this system.

This will return 0 by default but can be overridden.

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

Definition at line 2289 of file system.h.

{
  return 0;
}

Referenced by get_info().

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(), point_gradient(), point_hessian(), 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(), read_parallel_data(), read_SCALAR_dofs(), read_serialized_blocked_dof_objects(), 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(), write_parallel_data(), write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bcs_helper(), 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

inline

Number of currently active quantities of interest.

Definition at line 2328 of file system.h.

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

References 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

inline

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 _variable_groups.

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

n_vars()

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

inline

Returns

The number of variables in the system

Definition at line 2155 of file system.h.

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

References _variables.

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), libMesh::PetscDMWrapper::add_dofs_helper(), libMesh::DiffContext::add_localized_vector(), libMesh::RBConstruction::add_scaled_matrix_and_vector(), add_variable(), add_variables(), libMesh::FEMContext::attach_quadrature_rules(), libMesh::EquationSystems::build_discontinuous_solution_vector(), libMesh::EquationSystems::build_parallel_solution_vector(), libMesh::PetscDMWrapper::build_section(), 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(), get_all_variable_numbers(), 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(), re_update(), read_legacy_data(), read_parallel_data(), read_serialized_blocked_dof_objects(), read_serialized_vector(), 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(), write_header(), write_parallel_data(), write_serialized_blocked_dof_objects(), write_serialized_vector(), write_serialized_vectors(), and zero_variable().

n_vectors()

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

inline

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 _vectors.

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

name()

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

inline

Returns

The system name.

Definition at line 2067 of file system.h.

{
  return _sys_name;
}

References _sys_name.

Referenced by compare(), compute_jacobian(), compute_residual(), libMesh::ContinuationSystem::ContinuationSystem(), DMlibMeshSetUpName_Private(), libMesh::ExactErrorEstimator::estimate_error(), libMesh::ExactSolution::ExactSolution(), libMesh::ExactErrorEstimator::find_squared_element_error(), 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(), user_assembly(), user_constrain(), user_initialization(), user_QOI(), user_QOI_derivative(), variable_number(), write_header(), write_parallel_data(), and write_serialized_data().

number()

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

inline

Returns

The system number.

Definition at line 2075 of file system.h.

{
  return _sys_number;
}

References _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(), get_info(), main(), read_legacy_data(), read_parallel_data(), 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(), write_parallel_data(), write_serialized_blocked_dof_objects(), and zero_variable().

operator=()

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

private

This isn't a copyable object, so let's make sure nobody tries.

We won't even bother implementing this; we'll just make sure that the compiler doesn't implement a default.

Definition at line 114 of file system.C.

{
  libmesh_not_implemented();
}

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

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(), get_dof_map(), get_mesh(), libMesh::libmesh_assert(), mesh, libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::processor_id(), libMesh::DofObject::processor_id(), and variable().

Referenced by line_print(), and 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

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(), current_local_solution, dim, libMesh::Elem::dim(), libMesh::DofMap::dof_indices(), libMesh::FEComputeData::dshape, libMesh::FEComputeData::enable_derivative(), get_dof_map(), 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

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 point_gradient().

point_gradient() [4/4]

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

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 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

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(), get_dof_map(), get_mesh(), libMesh::libmesh_assert(), mesh, libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::processor_id(), libMesh::DofObject::processor_id(), and variable().

Referenced by 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

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(), current_local_solution, libMesh::Elem::dim(), libMesh::DofMap::dof_indices(), 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

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 point_hessian().

point_hessian() [4/4]

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

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 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

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(), get_dof_map(), get_mesh(), libMesh::libmesh_assert(), mesh, libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::processor_id(), libMesh::DofObject::processor_id(), and variable().

Referenced by line_print(), main(), 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

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(), current_local_solution, libMesh::Elem::dim(), libMesh::DofMap::dof_indices(), get_dof_map(), 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

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 point_value().

point_value() [4/4]

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

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 point_value().

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(), 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(), point_gradient(), point_hessian(), 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(), read_header(), libMesh::RBEvaluation::read_in_vectors_from_multiple_files(), read_legacy_data(), libMesh::ExodusII_IO_Helper::read_node_num_map(), read_parallel_data(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), read_SCALAR_dofs(), libMesh::XdrIO::read_serialized_bc_names(), libMesh::XdrIO::read_serialized_bcs_helper(), read_serialized_blocked_dof_objects(), libMesh::XdrIO::read_serialized_connectivity(), read_serialized_data(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), read_serialized_vector(), 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(), 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(), write_parallel_data(), libMesh::RBConstruction::write_riesz_representors_to_files(), write_SCALAR_dofs(), libMesh::XdrIO::write_serialized_bc_names(), libMesh::XdrIO::write_serialized_bcs_helper(), write_serialized_blocked_dof_objects(), libMesh::XdrIO::write_serialized_connectivity(), write_serialized_data(), libMesh::XdrIO::write_serialized_nodes(), libMesh::XdrIO::write_serialized_nodesets(), libMesh::XdrIO::write_serialized_subdomain_names(), write_serialized_vector(), 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

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

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

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  )

inline

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 _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

protected

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

protected

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

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

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 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

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

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 ( )

virtual

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 restrict_vectors().

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

qoi_parameter_hessian()

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

inlinevirtual

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

This method is only implemented in some derived classes.

Reimplemented in libMesh::ImplicitSystem.

Definition at line 2384 of file system.h.

{
  libmesh_not_implemented();
}

qoi_parameter_hessian_vector_product()

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

inlinevirtual

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

This method is only implemented in some derived classes.

Reimplemented in libMesh::ImplicitSystem.

Definition at line 2393 of file system.h.

{
  libmesh_not_implemented();
}

qoi_parameter_sensitivity()

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

virtual

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

re_update()

void libMesh::System::re_update ( )

virtual

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 current_local_solution, get_dof_map(), libMesh::DofMap::get_send_list(), n_vars(), and 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
	)

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 _additional_data_written, _written_var_indices, add_variable(), add_vector(), clear(), libMesh::ParallelObject::comm(), libMesh::Xdr::data(), libMesh::FEType::family, 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(), 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
	)

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 _additional_data_written, _vectors, _written_var_indices, libMesh::ParallelObject::comm(), libMesh::Xdr::data(), get_mesh(), libMesh::DofObject::invalid_id, libMesh::libmesh_assert(), n_dofs(), n_vars(), number(), libMesh::ParallelObject::processor_id(), libMesh::Xdr::reading(), 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
	)

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

read_parallel_data() [2/2]

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

inline

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

private

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(), 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 variable().

Referenced by read_serialized_vector(), and 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

private

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 _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(), n_vars(), number(), and libMesh::ParallelObject::processor_id().

Referenced by read_serialized_vector(), and 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
	)

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 _additional_data_written, _vectors, libMesh::Xdr::comment(), libMesh::ParallelObject::processor_id(), and 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  )

inline

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  )

inlineprivate

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  )

private

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 _written_var_indices, libMesh::NumericVector< T >::close(), libMesh::ParallelObject::comm(), libMesh::Xdr::data(), 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(), n_vars(), libMesh::PARALLEL, libMesh::ParallelObject::processor_id(), read_SCALAR_dofs(), read_serialized_blocked_dof_objects(), libMesh::Xdr::reading(), libMesh::SCALAR, libMesh::NumericVector< T >::type(), 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

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

inline

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::System::reinit ( )

virtual

Reinitializes degrees of freedom and other required data on the current mesh.

Note

The matrix is not initialized at this time since it may not be required for all applications. Should be overridden in derived classes.

Reimplemented in libMesh::OptimizationSystem, libMesh::NonlinearImplicitSystem, libMesh::LinearImplicitSystem, libMesh::ImplicitSystem, libMesh::EigenSystem, libMesh::DifferentiableSystem, and libMesh::NewmarkSystem.

Definition at line 390 of file system.C.

{
  // project_vector handles vector initialization now
  libmesh_assert_equal_to (solution->size(), current_local_solution->size());
}

References current_local_solution, and solution.

Referenced by libMesh::EigenSystem::reinit(), and libMesh::ImplicitSystem::reinit().

reinit_constraints()

void libMesh::System::reinit_constraints ( )

virtual

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

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

remove_vector()

void libMesh::System::remove_vector

(

const std::string &

vec_name

)

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 _vector_is_adjoint, _vector_projections, _vector_types, and _vectors.

request_vector() [1/4]

NumericVector< Number > * libMesh::System::request_vector

(

const std::string &

vec_name

)

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 _vectors.

request_vector() [2/4]

const NumericVector< Number > * libMesh::System::request_vector

(

const std::string &

vec_name

)

const

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 _vectors.

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

request_vector() [3/4]

NumericVector< Number > * libMesh::System::request_vector

(

const unsigned int

vec_num

)

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 vectors_begin(), and vectors_end().

request_vector() [4/4]

const NumericVector< Number > * libMesh::System::request_vector

(

const unsigned int

vec_num

)

const

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 vectors_begin(), and vectors_end().

restrict_solve_to()

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

virtual

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 ( )

virtual

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

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

sensitivity_solve()

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

inlinevirtual

Solves the sensitivity system, for the provided parameters.

Must be overridden in derived systems.

Returns

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

This method is only implemented in some derived classes.

Reimplemented in libMesh::ImplicitSystem.

Definition at line 2335 of file system.h.

{
  libmesh_not_implemented();
}

set_adjoint_already_solved()

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

inline

Setter for the adjoint_already_solved boolean.

Definition at line 402 of file system.h.

  { adjoint_already_solved = setting;}

References adjoint_already_solved.

Referenced by main().

set_basic_system_only()

void libMesh::System::set_basic_system_only ( )

inline

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 _basic_system_only.

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

set_vector_as_adjoint()

void libMesh::System::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.

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 _vector_is_adjoint.

Referenced by add_adjoint_solution(), and add_weighted_sensitivity_adjoint_solution().

set_vector_preservation()

void libMesh::System::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.

Definition at line 855 of file system.C.

{
  _vector_projections[vec_name] = preserve;
}

References _vector_projections.

Referenced by main().

solve()

virtual void libMesh::System::solve ( )

inlinevirtual

Solves the system.

Should be overridden in derived systems.

Reimplemented in libMesh::OptimizationSystem, libMesh::NonlinearImplicitSystem, libMesh::ImplicitSystem, libMesh::DifferentiableSystem, libMesh::LinearImplicitSystem, libMesh::FEMSystem, libMesh::FrequencySystem, libMesh::EigenSystem, libMesh::ExplicitSystem, libMesh::CondensedEigenSystem, and libMesh::ContinuationSystem.

Definition at line 334 of file system.h.

{}

Referenced by libMesh::UniformRefinementEstimator::_estimate_error(), and SystemsTest::testAssemblyWithDgFemContext().

system()

sys_type& libMesh::System::system ( )

inline

Returns

A reference to *this.

Definition at line 248 of file system.h.

{ return *this; }

system_type()

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

inlinevirtual

Returns

The type of system, helpful in identifying which system type to use when reading equation system data from file. Should be overridden in derived classes.

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

Definition at line 495 of file system.h.

{ return "Basic"; }

Referenced by get_info().

update()

void libMesh::System::update ( )

virtual

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 _dof_map, current_local_solution, libMesh::libmesh_assert(), and 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

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 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

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 solution.

user_assembly()

void libMesh::System::user_assembly ( )

virtual

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 _assemble_system_function, _assemble_system_object, _equation_systems, libMesh::System::Assembly::assemble(), and name().

Referenced by assemble().

user_constrain()

void libMesh::System::user_constrain ( )

virtual

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 _constrain_system_function, _constrain_system_object, _equation_systems, libMesh::System::Constraint::constrain(), and name().

Referenced by reinit_constraints().

user_initialization()

void libMesh::System::user_initialization ( )

virtual

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 _equation_systems, _init_system_function, _init_system_object, libMesh::System::Initialization::initialize(), and name().

Referenced by init(), and libMesh::NewmarkSystem::initial_conditions().

user_QOI()

void libMesh::System::user_QOI ( const QoISet &  qoi_indices )

virtual

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 _equation_systems, _qoi_evaluate_function, _qoi_evaluate_object, name(), and libMesh::System::QOI::qoi().

Referenced by assemble_qoi().

user_QOI_derivative()

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

virtual

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 _equation_systems, _qoi_evaluate_derivative_function, _qoi_evaluate_derivative_object, name(), and libMesh::System::QOIDerivative::qoi_derivative().

Referenced by assemble_qoi_derivative().

variable()

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

inline

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 _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()(), point_gradient(), point_hessian(), point_value(), read_parallel_data(), read_SCALAR_dofs(), read_serialized_vector(), read_serialized_vectors(), libMesh::PetscDMWrapper::set_point_range_in_section(), write_header(), write_parallel_data(), write_serialized_vector(), and write_serialized_vectors().

variable_group()

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

inline

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 _variable_groups.

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

variable_name()

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

inline

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 _variables.

Referenced by add_variable(), 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(), write_header(), and libMesh::Nemesis_IO_Helper::write_nodal_solution().

variable_number()

unsigned short int libMesh::System::variable_number

(

const std::string &

var

)

const

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 _variable_numbers, _variables, and 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(), 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(), variable_scalar_number(), 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

inline

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 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

inline

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 _variables.

variable_type() [1/2]

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

inline

Returns

The finite element type for variable var.

Definition at line 2243 of file system.h.

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

References _variables, and variable_number().

variable_type() [2/2]

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

inline

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 _variables.

Referenced by add_variable(), 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(), 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

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 _vector_is_adjoint, and libMesh::libmesh_assert().

Referenced by restrict_vectors().

vector_name() [1/2]

const std::string & libMesh::System::vector_name

(

const NumericVector< Number > &

vec_reference

)

const

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(), vectors_begin(), and vectors_end().

vector_name() [2/2]

const std::string & libMesh::System::vector_name

(

const unsigned int

vec_num

)

const

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(), vectors_begin(), and vectors_end().

Referenced by main().

vector_preservation()

bool libMesh::System::vector_preservation

(

const std::string &

vec_name

)

const

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 _vector_projections.

Referenced by libMesh::MemorySolutionHistory::store().

vectors_begin() [1/2]

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

inline

Beginning of vectors container.

Definition at line 2295 of file system.h.

{
  return _vectors.begin();
}

References _vectors.

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

vectors_begin() [2/2]

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

inline

Beginning of vectors container.

Definition at line 2301 of file system.h.

{
  return _vectors.begin();
}

References _vectors.

vectors_end() [1/2]

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

inline

End of vectors container.

Definition at line 2307 of file system.h.

{
  return _vectors.end();
}

References _vectors.

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

vectors_end() [2/2]

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

inline

End of vectors container.

Definition at line 2313 of file system.h.

{
  return _vectors.end();
}

References _vectors.

weighted_sensitivity_adjoint_solve()

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

inlinevirtual

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

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

Returns

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

This method is only implemented in some derived classes.

Reimplemented in libMesh::ImplicitSystem.

Definition at line 2357 of file system.h.

{
  libmesh_not_implemented();
}

weighted_sensitivity_solve()

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

inlinevirtual

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

Returns

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

This method is only implemented in some derived classes.

Reimplemented in libMesh::ImplicitSystem.

Definition at line 2342 of file system.h.

{
  libmesh_not_implemented();
}

write_header()

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

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 _vectors, libMesh::Variable::active_subdomains(), libMesh::Xdr::data(), libMesh::FEType::family, get_mesh(), libMesh::FEType::inf_map, libMesh::libmesh_assert(), n_vars(), n_vectors(), name(), libMesh::ParallelObject::processor_id(), libMesh::FEType::radial_family, variable(), variable_name(), 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

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 _vectors, libMesh::Xdr::data(), libMesh::FEType::family, get_dof_map(), get_mesh(), libMesh::DofObject::invalid_id, libMesh::libmesh_assert(), libMesh::ParallelObject::n_processors(), n_vars(), name(), number(), libMesh::ParallelObject::processor_id(), libMesh::SCALAR, libMesh::DofMap::SCALAR_dof_indices(), solution, libMesh::Variable::type(), 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

private

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(), get_dof_map(), libMesh::ParallelObject::n_processors(), libMesh::ParallelObject::processor_id(), and libMesh::DofMap::SCALAR_dof_indices().

Referenced by write_serialized_vector(), and 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

private

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(), n_vars(), number(), and libMesh::ParallelObject::processor_id().

Referenced by write_serialized_vector(), and write_serialized_vectors().

write_serialized_data()

void libMesh::System::write_serialized_data	(	Xdr &	io,
		const bool	write_additional_data = true
	)		const

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 _vectors, libMesh::Xdr::comment(), name(), libMesh::ParallelObject::processor_id(), solution, and 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

private

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(), get_mesh(), libMesh::libmesh_assert(), libMesh::MeshTools::n_elem(), n_nodes, n_vars(), libMesh::ParallelObject::processor_id(), libMesh::SCALAR, libMesh::NumericVector< T >::size(), variable(), write_SCALAR_dofs(), write_serialized_blocked_dof_objects(), and libMesh::Xdr::writing().

Referenced by write_serialized_data().

write_serialized_vectors()

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

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(), get_mesh(), libMesh::libmesh_assert(), libMesh::MeshBase::n_elem(), libMesh::MeshTools::n_elem(), n_nodes, libMesh::MeshBase::n_nodes(), n_vars(), libMesh::ParallelObject::processor_id(), libMesh::SCALAR, variable(), write_SCALAR_dofs(), 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

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 get_mesh(), mesh, n_vars(), number(), and libMesh::NumericVector< T >::set().

Member Data Documentation

_active

bool libMesh::System::_active

private

Flag stating if the system is active or not.

Definition at line 1977 of file system.h.

Referenced by activate(), active(), and deactivate().

_additional_data_written

unsigned int libMesh::System::_additional_data_written

private

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 read_header(), read_legacy_data(), read_parallel_data(), and read_serialized_data().

_assemble_system_function

void(* libMesh::System::_assemble_system_function) (EquationSystems &es, const std::string &name)

private

Function that assembles the system.

Definition at line 1885 of file system.h.

Referenced by attach_assemble_function(), attach_assemble_object(), user_assembly(), and ~System().

_assemble_system_object

Assembly* libMesh::System::_assemble_system_object

private

Object that assembles the system.

Definition at line 1891 of file system.h.

Referenced by attach_assemble_function(), attach_assemble_object(), user_assembly(), and ~System().

_basic_system_only

bool libMesh::System::_basic_system_only

private

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 init(), and set_basic_system_only().

_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)

private

Function to impose constraints.

Definition at line 1896 of file system.h.

Referenced by attach_constraint_function(), attach_constraint_object(), user_constrain(), and ~System().

_constrain_system_object

Constraint* libMesh::System::_constrain_system_object

private

Object that constrains the system.

Definition at line 1902 of file system.h.

Referenced by attach_constraint_function(), attach_constraint_object(), user_constrain(), and ~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().

_dof_map

std::unique_ptr<DofMap> libMesh::System::_dof_map

private

Data structure describing the relationship between nodes, variables, etc...

and degrees of freedom.

Definition at line 1934 of file system.h.

Referenced by add_vector(), calculate_norm(), clear(), current_solution(), get_dof_map(), init_data(), n_constrained_dofs(), n_dofs(), n_local_constrained_dofs(), n_local_dofs(), restrict_vectors(), and 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

private

Constant reference to the EquationSystems object used for the simulation.

Definition at line 1940 of file system.h.

Referenced by get_equation_systems(), user_assembly(), user_constrain(), user_initialization(), user_QOI(), and user_QOI_derivative().

_hide_output

bool libMesh::System::_hide_output

private

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 hide_output().

_identify_variable_groups

bool libMesh::System::_identify_variable_groups

private

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

Defaults to true.

Definition at line 2027 of file system.h.

Referenced by identify_variable_groups().

_init_system_function

void(* libMesh::System::_init_system_function) (EquationSystems &es, const std::string &name)

private

Function that initializes the system.

Definition at line 1874 of file system.h.

Referenced by attach_init_function(), attach_init_object(), user_initialization(), and ~System().

_init_system_object

Initialization* libMesh::System::_init_system_object

private

Object that initializes the system.

Definition at line 1880 of file system.h.

Referenced by attach_init_function(), attach_init_object(), user_initialization(), and ~System().

_is_initialized

bool libMesh::System::_is_initialized

private

true when additional vectors and variables do not require immediate initialization, false otherwise.

Definition at line 2021 of file system.h.

Referenced by add_vector(), clear(), compare(), init_data(), and is_initialized().

_mesh

MeshBase& libMesh::System::_mesh

private

Constant reference to the mesh data structure used for the simulation.

Definition at line 1946 of file system.h.

Referenced by calculate_norm(), get_mesh(), and reinit_constraints().

_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().

_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)

private

Function to evaluate quantity of interest derivative.

Definition at line 1919 of file system.h.

Referenced by attach_QOI_derivative(), attach_QOI_derivative_object(), user_QOI_derivative(), and ~System().

_qoi_evaluate_derivative_object

QOIDerivative* libMesh::System::_qoi_evaluate_derivative_object

private

Object to compute derivatives of quantities of interest.

Definition at line 1928 of file system.h.

Referenced by attach_QOI_derivative(), attach_QOI_derivative_object(), user_QOI_derivative(), and ~System().

_qoi_evaluate_function

void(* libMesh::System::_qoi_evaluate_function) (EquationSystems &es, const std::string &name, const QoISet &qoi_indices)

private

Function to evaluate quantity of interest.

Definition at line 1907 of file system.h.

Referenced by attach_QOI_function(), attach_QOI_object(), user_QOI(), and ~System().

_qoi_evaluate_object

QOI* libMesh::System::_qoi_evaluate_object

private

Object to compute quantities of interest.

Definition at line 1914 of file system.h.

Referenced by attach_QOI_function(), attach_QOI_object(), user_QOI(), and ~System().

_solution_projection

bool libMesh::System::_solution_projection

private

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 project_solution_on_reinit(), and restrict_vectors().

_sys_name

const std::string libMesh::System::_sys_name

private

A name associated with this system.

Definition at line 1951 of file system.h.

Referenced by compare(), and name().

_sys_number

const unsigned int libMesh::System::_sys_number

private

The number associated with this system.

Definition at line 1956 of file system.h.

Referenced by number().

_variable_groups

std::vector<VariableGroup> libMesh::System::_variable_groups

private

The VariableGroup in this System.

Definition at line 1966 of file system.h.

Referenced by add_variable(), add_variables(), n_variable_groups(), and variable_group().

_variable_numbers

std::map<std::string, unsigned short int> libMesh::System::_variable_numbers

private

The variable numbers corresponding to user-specified names, useful for name-based lookups.

Definition at line 1972 of file system.h.

Referenced by add_variable(), add_variables(), clear(), get_all_variable_numbers(), has_variable(), and variable_number().

_variables

std::vector<Variable> libMesh::System::_variables

private

The Variable in this System.

Definition at line 1961 of file system.h.

Referenced by add_variable(), add_variables(), clear(), n_components(), n_vars(), variable(), variable_name(), variable_number(), variable_scalar_number(), and variable_type().

_vector_is_adjoint

std::map<std::string, int> libMesh::System::_vector_is_adjoint

private

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 add_vector(), clear(), remove_vector(), set_vector_as_adjoint(), and vector_is_adjoint().

_vector_projections

std::map<std::string, bool> libMesh::System::_vector_projections

private

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 add_vector(), clear(), remove_vector(), restrict_vectors(), set_vector_preservation(), and vector_preservation().

_vector_types

std::map<std::string, ParallelType> libMesh::System::_vector_types

private

Holds the type of a vector.

Definition at line 2002 of file system.h.

Referenced by add_vector(), clear(), init_data(), remove_vector(), and restrict_vectors().

_vectors

std::map<std::string, NumericVector<Number> * > libMesh::System::_vectors

private

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 add_vector(), clear(), compare(), get_vector(), have_vector(), init_data(), n_vectors(), read_legacy_data(), read_parallel_data(), read_serialized_data(), remove_vector(), request_vector(), restrict_vectors(), vectors_begin(), vectors_end(), write_header(), write_parallel_data(), and write_serialized_data().

_written_var_indices

std::vector<unsigned int> libMesh::System::_written_var_indices

private

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 read_header(), read_legacy_data(), read_parallel_data(), read_serialized_blocked_dof_objects(), and read_serialized_vector().

adjoint_already_solved

bool libMesh::System::adjoint_already_solved

private

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 is_adjoint_already_solved(), and set_adjoint_already_solved().

assemble_before_solve

bool libMesh::System::assemble_before_solve

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(), disable_cache(), main(), libMesh::RBConstruction::RBConstruction(), libMesh::RBSCMConstruction::RBSCMConstruction(), libMesh::ImplicitSystem::sensitivity_solve(), libMesh::CondensedEigenSystem::solve(), libMesh::EigenSystem::solve(), and libMesh::LinearImplicitSystem::solve().

current_local_solution

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

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(), clear(), libMesh::Problem_Interface::computeF(), libMesh::Problem_Interface::computeJacobian(), libMesh::Problem_Interface::computePreconditioner(), current_solution(), DMlibMeshFunction(), DMlibMeshJacobian(), libMesh::AdjointRefinementEstimator::estimate_error(), libMesh::ExactErrorEstimator::estimate_error(), 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(), point_gradient(), point_hessian(), point_value(), libMesh::FEMContext::pre_fe_reinit(), re_update(), reinit(), 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(), update(), and libMesh::Nemesis_IO_Helper::write_nodal_solution().

extra_quadrature_order

int libMesh::System::extra_quadrature_order

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().

qoi

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

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(), n_qois(), CoupledSystem::postprocess(), libMesh::ImplicitSystem::qoi_parameter_hessian(), and libMesh::ImplicitSystem::qoi_parameter_hessian_vector_product().

solution

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

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(), clear(), 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(), 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(), re_update(), read_legacy_data(), read_parallel_data(), libMesh::TransientRBConstruction::read_riesz_representors_from_files(), libMesh::RBConstruction::read_riesz_representors_from_files(), read_serialized_data(), reinit(), 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(), update(), 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(), write_parallel_data(), libMesh::TransientRBConstruction::write_riesz_representors_to_files(), libMesh::RBConstruction::write_riesz_representors_to_files(), and write_serialized_data().

time

Real libMesh::System::time

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()(), reinit_constraints(), libMesh::MemorySolutionHistory::retrieve(), libMesh::TwostepTimeSolver::solve(), and libMesh::MemorySolutionHistory::store().

use_fixed_solution

bool libMesh::System::use_fixed_solution

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().

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

• include/systems/system.h
• src/systems/system.C
• src/systems/system_io.C
• src/systems/system_projection.C