Inheritance diagram for TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >:

Public Member Functions
	TwoMeshFluxAdvectionDiffusionProblem (AdvectionDiffusionEquations< 2 >::AdvectionDiffusionSourceFctPt source_fct_pt, AdvectionDiffusionEquations< 2 >::AdvectionDiffusionWindFctPt wind_fct_pt)
	Constructor: Pass pointer to source and wind functions. More...

	~TwoMeshFluxAdvectionDiffusionProblem ()
	Destructor (empty) More...

void	doc_solution (DocInfo &doc_info)
	Doc the solution: doc_info contains labels/output directory etc. More...

	TwoMeshFluxAdvectionDiffusionProblem (AdvectionDiffusionEquations< 2 >::AdvectionDiffusionSourceFctPt source_fct_pt, AdvectionDiffusionEquations< 2 >::AdvectionDiffusionWindFctPt wind_fct_pt)
	Constructor: Pass pointer to source and wind functions. More...

	~TwoMeshFluxAdvectionDiffusionProblem ()
	Destructor (empty) More...

void	doc_solution (DocInfo &doc_info)

Public Member Functions inherited from oomph::Problem
virtual void	debug_hook_fct (const unsigned &i)

void	set_analytic_dparameter (double *const &parameter_pt)

void	unset_analytic_dparameter (double *const &parameter_pt)

bool	is_dparameter_calculated_analytically (double *const &parameter_pt)

void	set_analytic_hessian_products ()

void	unset_analytic_hessian_products ()

bool	are_hessian_products_calculated_analytically ()

void	set_pinned_values_to_zero ()

bool	distributed () const

OomphCommunicator *	communicator_pt ()
	access function to the oomph-lib communicator More...

const OomphCommunicator *	communicator_pt () const
	access function to the oomph-lib communicator, const version More...

	Problem ()

	Problem (const Problem &dummy)=delete
	Broken copy constructor. More...

void	operator= (const Problem &)=delete
	Broken assignment operator. More...

virtual	~Problem ()
	Virtual destructor to clean up memory. More...

Mesh *&	mesh_pt ()
	Return a pointer to the global mesh. More...

Mesh *const &	mesh_pt () const
	Return a pointer to the global mesh (const version) More...

Mesh *&	mesh_pt (const unsigned &imesh)

Mesh *const &	mesh_pt (const unsigned &imesh) const
	Return a pointer to the i-th submesh (const version) More...

unsigned	nsub_mesh () const
	Return number of submeshes. More...

unsigned	add_sub_mesh (Mesh *const &mesh_pt)

void	flush_sub_meshes ()

void	build_global_mesh ()

void	rebuild_global_mesh ()

LinearSolver *&	linear_solver_pt ()
	Return a pointer to the linear solver object. More...

LinearSolver *const &	linear_solver_pt () const
	Return a pointer to the linear solver object (const version) More...

LinearSolver *&	mass_matrix_solver_for_explicit_timestepper_pt ()

LinearSolver *	mass_matrix_solver_for_explicit_timestepper_pt () const

EigenSolver *&	eigen_solver_pt ()
	Return a pointer to the eigen solver object. More...

EigenSolver *const &	eigen_solver_pt () const
	Return a pointer to the eigen solver object (const version) More...

Time *&	time_pt ()
	Return a pointer to the global time object. More...

Time *	time_pt () const
	Return a pointer to the global time object (const version). More...

double &	time ()
	Return the current value of continuous time. More...

double	time () const
	Return the current value of continuous time (const version) More...

TimeStepper *&	time_stepper_pt ()

const TimeStepper *	time_stepper_pt () const

TimeStepper *&	time_stepper_pt (const unsigned &i)
	Return a pointer to the i-th timestepper. More...

ExplicitTimeStepper *&	explicit_time_stepper_pt ()
	Return a pointer to the explicit timestepper. More...

unsigned long	set_timestepper_for_all_data (TimeStepper *const &time_stepper_pt, const bool &preserve_existing_data=false)

virtual void	shift_time_values ()
	Shift all values along to prepare for next timestep. More...

AssemblyHandler *&	assembly_handler_pt ()
	Return a pointer to the assembly handler object. More...

AssemblyHandler *const &	assembly_handler_pt () const
	Return a pointer to the assembly handler object (const version) More...

double &	minimum_dt ()
	Access function to min timestep in adaptive timestepping. More...

double &	maximum_dt ()
	Access function to max timestep in adaptive timestepping. More...

unsigned &	max_newton_iterations ()
	Access function to max Newton iterations before giving up. More...

void	problem_is_nonlinear (const bool &prob_lin)
	Access function to Problem_is_nonlinear. More...

double &	max_residuals ()

bool &	time_adaptive_newton_crash_on_solve_fail ()
	Access function for Time_adaptive_newton_crash_on_solve_fail. More...

double &	newton_solver_tolerance ()

void	add_time_stepper_pt (TimeStepper *const &time_stepper_pt)

void	set_explicit_time_stepper_pt (ExplicitTimeStepper *const &explicit_time_stepper_pt)

void	initialise_dt (const double &dt)

void	initialise_dt (const Vector< double > &dt)

Data *&	global_data_pt (const unsigned &i)
	Return a pointer to the the i-th global data object. More...

void	add_global_data (Data *const &global_data_pt)

void	flush_global_data ()

LinearAlgebraDistribution *const &	dof_distribution_pt () const
	Return the pointer to the dof distribution (read-only) More...

unsigned long	ndof () const
	Return the number of dofs. More...

unsigned	ntime_stepper () const
	Return the number of time steppers. More...

unsigned	nglobal_data () const
	Return the number of global data values. More...

unsigned	self_test ()
	Self-test: Check meshes and global data. Return 0 for OK. More...

void	enable_store_local_dof_pt_in_elements ()

void	disable_store_local_dof_pt_in_elements ()

unsigned long	assign_eqn_numbers (const bool &assign_local_eqn_numbers=true)

void	describe_dofs (std::ostream &out= *(oomph_info.stream_pt())) const

void	enable_discontinuous_formulation ()

void	disable_discontinuous_formulation ()

void	get_dofs (DoubleVector &dofs) const

void	get_dofs (const unsigned &t, DoubleVector &dofs) const
	Return vector of the t'th history value of all dofs. More...

void	set_dofs (const DoubleVector &dofs)
	Set the values of the dofs. More...

void	set_dofs (const unsigned &t, DoubleVector &dofs)
	Set the history values of the dofs. More...

void	set_dofs (const unsigned &t, Vector< double * > &dof_pt)

void	add_to_dofs (const double &lambda, const DoubleVector &increment_dofs)
	Add lambda x incremenet_dofs[l] to the l-th dof. More...

double *	global_dof_pt (const unsigned &i)

double &	dof (const unsigned &i)
	i-th dof in the problem More...

double	dof (const unsigned &i) const
	i-th dof in the problem (const version) More...

double *&	dof_pt (const unsigned &i)
	Pointer to i-th dof in the problem. More...

double *	dof_pt (const unsigned &i) const
	Pointer to i-th dof in the problem (const version) More...

virtual void	get_inverse_mass_matrix_times_residuals (DoubleVector &Mres)

virtual void	get_dvaluesdt (DoubleVector &f)

virtual void	get_residuals (DoubleVector &residuals)
	Get the total residuals Vector for the problem. More...

virtual void	get_jacobian (DoubleVector &residuals, DenseDoubleMatrix &jacobian)

virtual void	get_jacobian (DoubleVector &residuals, CRDoubleMatrix &jacobian)

virtual void	get_jacobian (DoubleVector &residuals, CCDoubleMatrix &jacobian)

virtual void	get_jacobian (DoubleVector &residuals, SumOfMatrices &jacobian)

void	get_fd_jacobian (DoubleVector &residuals, DenseMatrix< double > &jacobian)
	Get the full Jacobian by finite differencing. More...

void	get_derivative_wrt_global_parameter (double *const &parameter_pt, DoubleVector &result)

void	get_hessian_vector_products (DoubleVectorWithHaloEntries const &Y, Vector< DoubleVectorWithHaloEntries > const &C, Vector< DoubleVectorWithHaloEntries > &product)

void	solve_eigenproblem (const unsigned &n_eval, Vector< std::complex< double >> &eigenvalue, Vector< DoubleVector > &eigenvector, const bool &steady=true)
	Solve the eigenproblem. More...

void	solve_eigenproblem (const unsigned &n_eval, Vector< std::complex< double >> &eigenvalue, const bool &steady=true)

virtual void	get_eigenproblem_matrices (CRDoubleMatrix &mass_matrix, CRDoubleMatrix &main_matrix, const double &shift=0.0)

void	assign_eigenvector_to_dofs (DoubleVector &eigenvector)
	Assign the eigenvector passed to the function to the dofs. More...

void	add_eigenvector_to_dofs (const double &epsilon, const DoubleVector &eigenvector)

void	store_current_dof_values ()
	Store the current values of the degrees of freedom. More...

void	restore_dof_values ()
	Restore the stored values of the degrees of freedom. More...

void	enable_jacobian_reuse ()

void	disable_jacobian_reuse ()
	Disable recycling of Jacobian in Newton iteration. More...

bool	jacobian_reuse_is_enabled ()
	Is recycling of Jacobian in Newton iteration enabled? More...

bool &	use_predictor_values_as_initial_guess ()

void	newton_solve ()
	Use Newton method to solve the problem. More...

void	enable_globally_convergent_newton_method ()
	enable globally convergent Newton method More...

void	disable_globally_convergent_newton_method ()
	disable globally convergent Newton method More...

void	newton_solve (unsigned const &max_adapt)

void	steady_newton_solve (unsigned const &max_adapt=0)

void	copy (Problem *orig_problem_pt)

virtual Problem *	make_copy ()

virtual void	read (std::ifstream &restart_file, bool &unsteady_restart)

virtual void	read (std::ifstream &restart_file)

virtual void	dump (std::ofstream &dump_file) const

void	dump (const std::string &dump_file_name) const

void	delete_all_external_storage ()

virtual void	symmetrise_eigenfunction_for_adaptive_pitchfork_tracking ()

double *	bifurcation_parameter_pt () const

void	get_bifurcation_eigenfunction (Vector< DoubleVector > &eigenfunction)

void	activate_fold_tracking (double *const &parameter_pt, const bool &block_solve=true)

void	activate_bifurcation_tracking (double *const &parameter_pt, const DoubleVector &eigenvector, const bool &block_solve=true)

void	activate_bifurcation_tracking (double *const &parameter_pt, const DoubleVector &eigenvector, const DoubleVector &normalisation, const bool &block_solve=true)

void	activate_pitchfork_tracking (double *const &parameter_pt, const DoubleVector &symmetry_vector, const bool &block_solve=true)

void	activate_hopf_tracking (double *const &parameter_pt, const bool &block_solve=true)

void	activate_hopf_tracking (double *const &parameter_pt, const double &omega, const DoubleVector &null_real, const DoubleVector &null_imag, const bool &block_solve=true)

void	deactivate_bifurcation_tracking ()

void	reset_assembly_handler_to_default ()
	Reset the system to the standard non-augemented state. More...

double	arc_length_step_solve (double *const &parameter_pt, const double &ds, const unsigned &max_adapt=0)

double	arc_length_step_solve (Data *const &data_pt, const unsigned &data_index, const double &ds, const unsigned &max_adapt=0)

void	reset_arc_length_parameters ()

int &	sign_of_jacobian ()

void	explicit_timestep (const double &dt, const bool &shift_values=true)
	Take an explicit timestep of size dt. More...

void	unsteady_newton_solve (const double &dt)

void	unsteady_newton_solve (const double &dt, const bool &shift_values)

void	unsteady_newton_solve (const double &dt, const unsigned &max_adapt, const bool &first, const bool &shift=true)

double	doubly_adaptive_unsteady_newton_solve (const double &dt, const double &epsilon, const unsigned &max_adapt, const bool &first, const bool &shift=true)

double	doubly_adaptive_unsteady_newton_solve (const double &dt, const double &epsilon, const unsigned &max_adapt, const unsigned &suppress_resolve_after_spatial_adapt_flag, const bool &first, const bool &shift=true)

double	adaptive_unsteady_newton_solve (const double &dt_desired, const double &epsilon)

double	adaptive_unsteady_newton_solve (const double &dt_desired, const double &epsilon, const bool &shift_values)

void	assign_initial_values_impulsive ()

void	assign_initial_values_impulsive (const double &dt)

void	calculate_predictions ()
	Calculate predictions. More...

void	enable_mass_matrix_reuse ()

void	disable_mass_matrix_reuse ()

bool	mass_matrix_reuse_is_enabled ()
	Return whether the mass matrix is being reused. More...

void	refine_uniformly (const Vector< unsigned > &nrefine_for_mesh)

void	refine_uniformly (const Vector< unsigned > &nrefine_for_mesh, DocInfo &doc_info)

void	refine_uniformly_and_prune (const Vector< unsigned > &nrefine_for_mesh)

void	refine_uniformly_and_prune (const Vector< unsigned > &nrefine_for_mesh, DocInfo &doc_info)

void	refine_uniformly (DocInfo &doc_info)

void	refine_uniformly_and_prune (DocInfo &doc_info)

void	refine_uniformly ()

void	refine_uniformly (const unsigned &i_mesh, DocInfo &doc_info)
	Do uniform refinement for submesh i_mesh with documentation. More...

void	refine_uniformly (const unsigned &i_mesh)
	Do uniform refinement for submesh i_mesh without documentation. More...

void	p_refine_uniformly (const Vector< unsigned > &nrefine_for_mesh)

void	p_refine_uniformly (const Vector< unsigned > &nrefine_for_mesh, DocInfo &doc_info)

void	p_refine_uniformly_and_prune (const Vector< unsigned > &nrefine_for_mesh)

void	p_refine_uniformly_and_prune (const Vector< unsigned > &nrefine_for_mesh, DocInfo &doc_info)

void	p_refine_uniformly (DocInfo &doc_info)

void	p_refine_uniformly_and_prune (DocInfo &doc_info)

void	p_refine_uniformly ()

void	p_refine_uniformly (const unsigned &i_mesh, DocInfo &doc_info)
	Do uniform p-refinement for submesh i_mesh with documentation. More...

void	p_refine_uniformly (const unsigned &i_mesh)
	Do uniform p-refinement for submesh i_mesh without documentation. More...

void	refine_selected_elements (const Vector< unsigned > &elements_to_be_refined)

void	refine_selected_elements (const Vector< RefineableElement * > &elements_to_be_refined_pt)

void	refine_selected_elements (const unsigned &i_mesh, const Vector< unsigned > &elements_to_be_refined)

void	refine_selected_elements (const unsigned &i_mesh, const Vector< RefineableElement * > &elements_to_be_refined_pt)

void	refine_selected_elements (const Vector< Vector< unsigned >> &elements_to_be_refined)

void	refine_selected_elements (const Vector< Vector< RefineableElement * >> &elements_to_be_refined_pt)

void	p_refine_selected_elements (const Vector< unsigned > &elements_to_be_refined)

void	p_refine_selected_elements (const Vector< PRefineableElement * > &elements_to_be_refined_pt)

void	p_refine_selected_elements (const unsigned &i_mesh, const Vector< unsigned > &elements_to_be_refined)

void	p_refine_selected_elements (const unsigned &i_mesh, const Vector< PRefineableElement * > &elements_to_be_refined_pt)

void	p_refine_selected_elements (const Vector< Vector< unsigned >> &elements_to_be_refined)

void	p_refine_selected_elements (const Vector< Vector< PRefineableElement * >> &elements_to_be_refined_pt)

unsigned	unrefine_uniformly ()

unsigned	unrefine_uniformly (const unsigned &i_mesh)

void	p_unrefine_uniformly (DocInfo &doc_info)

void	p_unrefine_uniformly (const unsigned &i_mesh, DocInfo &doc_info)
	Do uniform p-unrefinement for submesh i_mesh without documentation. More...

void	adapt (unsigned &n_refined, unsigned &n_unrefined)

void	adapt ()

void	p_adapt (unsigned &n_refined, unsigned &n_unrefined)

void	p_adapt ()

void	adapt_based_on_error_estimates (unsigned &n_refined, unsigned &n_unrefined, Vector< Vector< double >> &elemental_error)

void	adapt_based_on_error_estimates (Vector< Vector< double >> &elemental_error)

void	get_all_error_estimates (Vector< Vector< double >> &elemental_error)

void	doc_errors (DocInfo &doc_info)
	Get max and min error for all elements in submeshes. More...

void	doc_errors ()
	Get max and min error for all elements in submeshes. More...

void	enable_info_in_newton_solve ()

void	disable_info_in_newton_solve ()
	Disable the output of information when in the newton solver. More...

Public Member Functions inherited from oomph::ExplicitTimeSteppableObject
	ExplicitTimeSteppableObject ()
	Empty constructor. More...

	ExplicitTimeSteppableObject (const ExplicitTimeSteppableObject &)=delete
	Broken copy constructor. More...

void	operator= (const ExplicitTimeSteppableObject &)=delete
	Broken assignment operator. More...

virtual	~ExplicitTimeSteppableObject ()
	Empty destructor. More...

virtual void	actions_before_explicit_stage ()

virtual void	actions_after_explicit_stage ()

Private Member Functions
void	actions_before_newton_solve ()

void	actions_after_newton_solve ()
	Update the problem specs after solve (empty) More...

void	actions_before_adapt ()
	Actions before adapt: Wipe the mesh of prescribed flux elements. More...

void	actions_after_adapt ()
	Actions after adapt: Rebuild the mesh of prescribed flux elements. More...

void	create_flux_elements (const unsigned &b, Mesh const &bulk_mesh_pt, Mesh const &surface_mesh_pt)

void	delete_flux_elements (Mesh *const &surface_mesh_pt)
	Delete Advection Diffusion flux elements and wipe the surface mesh. More...

void	actions_before_newton_solve ()

void	actions_after_newton_solve ()
	Update the problem specs after solve (empty) More...

void	actions_before_adapt ()
	Actions before adapt: Wipe the mesh of prescribed flux elements. More...

void	actions_after_adapt ()
	Actions after adapt: Rebuild the mesh of prescribed flux elements. More...

void	create_flux_elements (const unsigned &b, Mesh const &bulk_mesh_pt, Mesh const &surface_mesh_pt)

void	delete_flux_elements (Mesh *const &surface_mesh_pt)
	Delete Advection Diffusion flux elements and wipe the surface mesh. More...

Private Attributes
RefineableRectangularQuadMesh< ELEMENT > *	Bulk_mesh_pt
	Pointer to the "bulk" mesh. More...

Mesh *	Surface_mesh_pt
	Pointer to the "surface" mesh. More...

AdvectionDiffusionEquations< 2 >::AdvectionDiffusionSourceFctPt	Source_fct_pt
	Pointer to source function. More...

AdvectionDiffusionEquations< 2 >::AdvectionDiffusionWindFctPt	Wind_fct_pt
	Pointer to wind function. More...

Additional Inherited Members
Public Types inherited from oomph::Problem
typedef void(*	SpatialErrorEstimatorFctPt) (Mesh *&mesh_pt, Vector< double > &elemental_error)
	Function pointer for spatial error estimator. More...

typedef void(*	SpatialErrorEstimatorWithDocFctPt) (Mesh *&mesh_pt, Vector< double > &elemental_error, DocInfo &doc_info)
	Function pointer for spatial error estimator with doc. More...

Public Attributes inherited from oomph::Problem
bool	Shut_up_in_newton_solve

Static Public Attributes inherited from oomph::Problem
static bool	Suppress_warning_about_actions_before_read_unstructured_meshes

Protected Types inherited from oomph::Problem
enum	Assembly_method { Perform_assembly_using_vectors_of_pairs , Perform_assembly_using_two_vectors , Perform_assembly_using_maps , Perform_assembly_using_lists , Perform_assembly_using_two_arrays }
	Enumerated flags to determine which sparse assembly method is used. More...

Protected Member Functions inherited from oomph::Problem
unsigned	setup_element_count_per_dof ()

virtual void	sparse_assemble_row_or_column_compressed (Vector< int * > &column_or_row_index, Vector< int * > &row_or_column_start, Vector< double * > &value, Vector< unsigned > &nnz, Vector< double * > &residual, bool compressed_row_flag)

virtual void	actions_before_newton_convergence_check ()

virtual void	actions_before_newton_step ()

virtual void	actions_after_newton_step ()

virtual void	actions_before_implicit_timestep ()

virtual void	actions_after_implicit_timestep ()

virtual void	actions_after_implicit_timestep_and_error_estimation ()

virtual void	actions_before_explicit_timestep ()
	Actions that should be performed before each explicit time step. More...

virtual void	actions_after_explicit_timestep ()
	Actions that should be performed after each explicit time step. More...

virtual void	actions_before_read_unstructured_meshes ()

virtual void	actions_after_read_unstructured_meshes ()

virtual void	actions_after_change_in_global_parameter (double *const &parameter_pt)

virtual void	actions_after_change_in_bifurcation_parameter ()

virtual void	actions_after_parameter_increase (double *const &parameter_pt)

double &	dof_derivative (const unsigned &i)

double &	dof_current (const unsigned &i)

virtual void	set_initial_condition ()

virtual double	global_temporal_error_norm ()

unsigned	newton_solve_continuation (double *const &parameter_pt)

unsigned	newton_solve_continuation (double *const &parameter_pt, DoubleVector &z)

void	calculate_continuation_derivatives (double *const &parameter_pt)

void	calculate_continuation_derivatives (const DoubleVector &z)

void	calculate_continuation_derivatives_fd (double *const &parameter_pt)

bool	does_pointer_correspond_to_problem_data (double *const &parameter_pt)

void	set_consistent_pinned_values_for_continuation ()

Protected Attributes inherited from oomph::Problem
Vector< Problem * >	Copy_of_problem_pt

std::map< double *, bool >	Calculate_dparameter_analytic

bool	Calculate_hessian_products_analytic

LinearAlgebraDistribution *	Dof_distribution_pt

Vector< double * >	Dof_pt
	Vector of pointers to dofs. More...

DoubleVectorWithHaloEntries	Element_count_per_dof

double	Relaxation_factor

double	Newton_solver_tolerance

unsigned	Max_newton_iterations
	Maximum number of Newton iterations. More...

unsigned	Nnewton_iter_taken

Vector< double >	Max_res
	Maximum residuals at start and after each newton iteration. More...

double	Max_residuals

bool	Time_adaptive_newton_crash_on_solve_fail

bool	Jacobian_reuse_is_enabled
	Is re-use of Jacobian in Newton iteration enabled? Default: false. More...

bool	Jacobian_has_been_computed

bool	Problem_is_nonlinear

bool	Pause_at_end_of_sparse_assembly

bool	Doc_time_in_distribute

unsigned	Sparse_assembly_method

unsigned	Sparse_assemble_with_arrays_initial_allocation

unsigned	Sparse_assemble_with_arrays_allocation_increment

Vector< Vector< unsigned > >	Sparse_assemble_with_arrays_previous_allocation

double	Numerical_zero_for_sparse_assembly

double	FD_step_used_in_get_hessian_vector_products

bool	Mass_matrix_reuse_is_enabled

bool	Mass_matrix_has_been_computed

bool	Discontinuous_element_formulation

double	Minimum_dt
	Minimum desired dt: if dt falls below this value, exit. More...

double	Maximum_dt
	Maximum desired dt. More...

double	DTSF_max_increase

double	DTSF_min_decrease

double	Minimum_dt_but_still_proceed

bool	Scale_arc_length
	Boolean to control whether arc-length should be scaled. More...

double	Desired_proportion_of_arc_length
	Proportion of the arc-length to taken by the parameter. More...

double	Theta_squared

int	Sign_of_jacobian
	Storage for the sign of the global Jacobian. More...

double	Continuation_direction

double	Parameter_derivative
	Storage for the derivative of the global parameter wrt arc-length. More...

double	Parameter_current
	Storage for the present value of the global parameter. More...

bool	Use_continuation_timestepper
	Boolean to control original or new storage of dof stuff. More...

unsigned	Dof_derivative_offset

unsigned	Dof_current_offset

Vector< double >	Dof_derivative
	Storage for the derivative of the problem variables wrt arc-length. More...

Vector< double >	Dof_current
	Storage for the present values of the variables. More...

double	Ds_current
	Storage for the current step value. More...

unsigned	Desired_newton_iterations_ds

double	Minimum_ds
	Minimum desired value of arc-length. More...

bool	Bifurcation_detection
	Boolean to control bifurcation detection via determinant of Jacobian. More...

bool	Bisect_to_find_bifurcation
	Boolean to control wheter bisection is used to located bifurcation. More...

bool	First_jacobian_sign_change
	Boolean to indicate whether a sign change has occured in the Jacobian. More...

bool	Arc_length_step_taken
	Boolean to indicate whether an arc-length step has been taken. More...

bool	Use_finite_differences_for_continuation_derivatives

OomphCommunicator *	Communicator_pt
	The communicator for this problem. More...

bool	Always_take_one_newton_step

double	Timestep_reduction_factor_after_nonconvergence

bool	Keep_temporal_error_below_tolerance

Static Protected Attributes inherited from oomph::Problem
static ContinuationStorageScheme	Continuation_time_stepper
	Storage for the single static continuation timestorage object. More...

Detailed Description

template<class ELEMENT>
class TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >

2D AdvectionDiffusion problem on rectangular domain, discretised with 2D QAdvectionDiffusion elements. Flux boundary conditions are applied along boundary 1 (the boundary where x=L). The specific type of element is specified via the template parameter.

Constructor & Destructor Documentation

◆ TwoMeshFluxAdvectionDiffusionProblem() [1/2]

template<class ELEMENT >

TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::TwoMeshFluxAdvectionDiffusionProblem	(	AdvectionDiffusionEquations< 2 >::AdvectionDiffusionSourceFctPt	source_fct_pt,
		AdvectionDiffusionEquations< 2 >::AdvectionDiffusionWindFctPt	wind_fct_pt
	)

Constructor: Pass pointer to source and wind functions.

Constructor for AdvectionDiffusion problem: Pass pointer to source and wind functions.

  :  Source_fct_pt(source_fct_pt), Wind_fct_pt(wind_fct_pt)
 { 
  // Setup "bulk" mesh
  
  // # of elements in x-direction
  unsigned n_x=4;
  
  // # of elements in y-direction
  unsigned n_y=4;
  
  // Domain length in x-direction
  double l_x=1.0;
  
  // Domain length in y-direction
  double l_y=2.0;
  
  // Build "bulk" mesh
  Bulk_mesh_pt=new RefineableRectangularQuadMesh<ELEMENT>(n_x,n_y,l_x,l_y);
  
  // Create/set error estimator
  Bulk_mesh_pt->spatial_error_estimator_pt()=new Z2ErrorEstimator;
  
  // Create "surface mesh" that will contain only the prescribed-flux 
  // elements. The constructor just creates the mesh without
  // giving it any elements, nodes, etc.
  Surface_mesh_pt = new Mesh;
  
  // Create prescribed-flux elements from all elements that are 
  // adjacent to boundary 1, but add them to a separate mesh.
  // Note that this is exactly the same function as used in the 
  // single mesh version of the problem, we merely pass different Mesh pointers.
  create_flux_elements(1,Bulk_mesh_pt,Surface_mesh_pt);
  
  // Add the two sub meshes to the problem
  add_sub_mesh(Bulk_mesh_pt);
  add_sub_mesh(Surface_mesh_pt);
  
  // Combine all submeshes into a single Mesh
  build_global_mesh();
  
  // Set the boundary conditions for this problem: All nodes are
  // free by default -- just pin the ones that have Dirichlet conditions
  // here. 
  unsigned n_bound = Bulk_mesh_pt->nboundary();
  for(unsigned b=0;b<n_bound;b++)
   {
    //Leave nodes on boundary 1 free
    if (b!=1)
     {
      unsigned n_node = Bulk_mesh_pt->nboundary_node(b);
      for (unsigned n=0;n<n_node;n++)
       {
        Bulk_mesh_pt->boundary_node_pt(b,n)->pin(0); 
       }
     }
   }
  
  // Complete the build of all elements so they are fully functional
  
  // Loop over the AdvectionDiffusion bulk elements to set up element-specific 
  // things that cannot be handled by constructor: Pass pointer to 
  // source function
  unsigned n_element = Bulk_mesh_pt->nelement();
  for(unsigned e=0;e<n_element;e++)
   {
    // Upcast from GeneralisedElement to AdvectionDiffusion bulk element
    ELEMENT *el_pt = dynamic_cast<ELEMENT*>(Bulk_mesh_pt->element_pt(e));
  
    //Set the source function pointer
    el_pt->source_fct_pt() = Source_fct_pt;
  
    //Set the wind function pointer
    el_pt->wind_fct_pt() = Wind_fct_pt;
  
    // Set the Peclet number
    el_pt->pe_pt() = &TanhSolnForAdvectionDiffusion::Peclet;
   }
  
  // Loop over the flux elements to pass pointer to prescribed flux function
  n_element=Surface_mesh_pt->nelement();
  for(unsigned e=0;e<n_element;e++)
   {
    // Upcast from GeneralisedElement to AdvectionDiffusion flux element
    AdvectionDiffusionFluxElement<ELEMENT> *el_pt = 
     dynamic_cast< AdvectionDiffusionFluxElement<ELEMENT>*>(
      Surface_mesh_pt->element_pt(e));
  
    // Set the pointer to the prescribed flux function
    el_pt->flux_fct_pt() = 
     &TanhSolnForAdvectionDiffusion::prescribed_flux_on_fixed_x_boundary;
   }
  
  // Setup equation numbering scheme
  cout <<"Number of equations: " << assign_eqn_numbers() << std::endl; 
  
 } // end of constructor

References oomph::Problem::add_sub_mesh(), oomph::Problem::assign_eqn_numbers(), b, oomph::Problem::build_global_mesh(), TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::Bulk_mesh_pt, TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::create_flux_elements(), e(), oomph::Mesh::element_pt(), oomph::AdvectionDiffusionFluxElement< ELEMENT >::flux_fct_pt(), n, oomph::Mesh::nelement(), oomph::AdvectionDiffusionEquations< DIM >::pe_pt(), TanhSolnForAdvectionDiffusion::Peclet, TanhSolnForAdvectionDiffusion::prescribed_flux_on_fixed_x_boundary(), TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::Source_fct_pt, TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::Surface_mesh_pt, TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::Wind_fct_pt, and oomph::AdvectionDiffusionEquations< DIM >::wind_fct_pt().

◆ ~TwoMeshFluxAdvectionDiffusionProblem() [1/2]

template<class ELEMENT >

TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::~TwoMeshFluxAdvectionDiffusionProblem ( )

inline

Destructor (empty)

130 {}

◆ TwoMeshFluxAdvectionDiffusionProblem() [2/2]

template<class ELEMENT >

TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::TwoMeshFluxAdvectionDiffusionProblem	(	AdvectionDiffusionEquations< 2 >::AdvectionDiffusionSourceFctPt	source_fct_pt,
		AdvectionDiffusionEquations< 2 >::AdvectionDiffusionWindFctPt	wind_fct_pt
	)

Constructor: Pass pointer to source and wind functions.

◆ ~TwoMeshFluxAdvectionDiffusionProblem() [2/2]

template<class ELEMENT >

TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::~TwoMeshFluxAdvectionDiffusionProblem ( )

inline

Destructor (empty)

130 {}

Member Function Documentation

◆ actions_after_adapt() [1/2]

template<class ELEMENT >

void TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::actions_after_adapt

privatevirtual

Actions after adapt: Rebuild the mesh of prescribed flux elements.

Reimplemented from oomph::Problem.

 {
  // Create prescribed-flux elements from all elements that are 
  // adjacent to boundary 1 and add them to surfac mesh
  create_flux_elements(1,Bulk_mesh_pt,Surface_mesh_pt);
  
  // Rebuild the global mesh
  rebuild_global_mesh();
  
  // Loop over the flux elements to pass pointer to prescribed flux function
  unsigned n_element=Surface_mesh_pt->nelement();
  for(unsigned e=0;e<n_element;e++)
   {
    // Upcast from GeneralisedElement to Advection Diffusion flux element
    AdvectionDiffusionFluxElement<ELEMENT> *el_pt = 
     dynamic_cast< AdvectionDiffusionFluxElement<ELEMENT>*>(
      Surface_mesh_pt->element_pt(e));
    
    // Set the pointer to the prescribed flux function
    el_pt->flux_fct_pt() = 
     &TanhSolnForAdvectionDiffusion::prescribed_flux_on_fixed_x_boundary;
   }
  
  // Doc refinement levels in bulk mesh
  unsigned min_refinement_level;
  unsigned max_refinement_level;
  Bulk_mesh_pt->get_refinement_levels(min_refinement_level,
                                      max_refinement_level); 
  cout << "Min/max. refinement levels in bulk mesh: " 
       << min_refinement_level << " " 
       << max_refinement_level << std::endl;
  
 } // end of actions_after_adapt

References e(), oomph::AdvectionDiffusionFluxElement< ELEMENT >::flux_fct_pt(), and TanhSolnForAdvectionDiffusion::prescribed_flux_on_fixed_x_boundary().

◆ actions_after_adapt() [2/2]

template<class ELEMENT >

void TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::actions_after_adapt ( )

privatevirtual

Actions after adapt: Rebuild the mesh of prescribed flux elements.

Reimplemented from oomph::Problem.

◆ actions_after_newton_solve() [1/2]

template<class ELEMENT >

void TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::actions_after_newton_solve ( )

inlineprivatevirtual

Update the problem specs after solve (empty)

Reimplemented from oomph::Problem.

144 {}

◆ actions_after_newton_solve() [2/2]

template<class ELEMENT >

void TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::actions_after_newton_solve ( )

inlineprivatevirtual

Update the problem specs after solve (empty)

Reimplemented from oomph::Problem.

144 {}

◆ actions_before_adapt() [1/2]

template<class ELEMENT >

void TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::actions_before_adapt

privatevirtual

Actions before adapt: Wipe the mesh of prescribed flux elements.

Reimplemented from oomph::Problem.

 {
  // Kill the flux elements and wipe surface mesh
  delete_flux_elements(Surface_mesh_pt);
  
  // Rebuild the global mesh
  rebuild_global_mesh();
 } // end of actions_before_adapt

◆ actions_before_adapt() [2/2]

template<class ELEMENT >

void TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::actions_before_adapt ( )

privatevirtual

Actions before adapt: Wipe the mesh of prescribed flux elements.

Reimplemented from oomph::Problem.

◆ actions_before_newton_solve() [1/2]

template<class ELEMENT >

void TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::actions_before_newton_solve

privatevirtual

Update the problem specs before solve: Reset boundary conditions to the values from the exact solution.

Reimplemented from oomph::Problem.

 {
  // How many boundaries are in the bulk mesh?
  unsigned n_bound = Bulk_mesh_pt->nboundary();
  
  //Loop over the boundaries in the bulk mesh
  for(unsigned i=0;i<n_bound;i++)
   {
    // Only update the Dirichlet conditions!
    if (i!=1)
     {
      // How many nodes are there on this boundary?
      unsigned n_node = Bulk_mesh_pt->nboundary_node(i);
      
      // Loop over the nodes on boundary
      for (unsigned n=0;n<n_node;n++)
       {
        // Get pointer to node
        Node* nod_pt=Bulk_mesh_pt->boundary_node_pt(i,n);
        
        // Extract nodal coordinates from node:
        Vector<double> x(2);
        x[0]=nod_pt->x(0);
        x[1]=nod_pt->x(1);
        
        // Compute the value of the exact solution at the nodal point
        Vector<double> u(1);
        TanhSolnForAdvectionDiffusion::get_exact_u(x,u);
        
        // Assign the value to the one (and only) nodal value at this node
        nod_pt->set_value(0,u[0]);
       }
     }
   } 
 } // end of actions before solve

References TanhSolnForAdvectionDiffusion::get_exact_u(), i, n, oomph::Data::set_value(), plotDoE::x, and oomph::Node::x().

◆ actions_before_newton_solve() [2/2]

template<class ELEMENT >

void TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::actions_before_newton_solve ( )

privatevirtual

Update the problem specs before solve: Reset boundary conditions to the values from the exact solution.

Reimplemented from oomph::Problem.

◆ create_flux_elements() [1/2]

template<class ELEMENT >

void TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::create_flux_elements	(	const unsigned &	b,
		Mesh *const &	bulk_mesh_pt,
		Mesh *const &	surface_mesh_pt
	)

private

Create Advection Diffusion flux elements on boundary b of the Mesh pointed to by bulk_mesh_pt and add them to the Mesh object pointed to by surface_mesh_pt

Create AdvectionDiffusion Flux Elements on the b-th boundary of the Mesh object pointed to by bulk_mesh_pt and add the elements to the Mesh object pointeed to by surface_mesh_pt.

 {
  // How many bulk elements are adjacent to boundary b?
  unsigned n_element = bulk_mesh_pt->nboundary_element(b);
  
  // Loop over the bulk elements adjacent to boundary b?
  for(unsigned e=0;e<n_element;e++)
   {
    // Get pointer to the bulk element that is adjacent to boundary b
    ELEMENT* bulk_elem_pt = dynamic_cast<ELEMENT*>(
     bulk_mesh_pt->boundary_element_pt(b,e));
    
    // Find the index of the face of element e along boundary b
    int face_index = bulk_mesh_pt->face_index_at_boundary(b,e);
  
    // Build the corresponding prescribed-flux element
    AdvectionDiffusionFluxElement<ELEMENT>* flux_element_pt = new 
    AdvectionDiffusionFluxElement<ELEMENT>(bulk_elem_pt,face_index);
  
    //Add the prescribed-flux element to the surface mesh
    surface_mesh_pt->add_element_pt(flux_element_pt);
  
   } //end of loop over bulk elements adjacent to boundary b
  
 } // end of create_flux_elements

References oomph::Mesh::add_element_pt(), b, oomph::Mesh::boundary_element_pt(), e(), oomph::Mesh::face_index_at_boundary(), and oomph::Mesh::nboundary_element().

Referenced by TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::TwoMeshFluxAdvectionDiffusionProblem().

◆ create_flux_elements() [2/2]

template<class ELEMENT >

void TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::create_flux_elements	(	const unsigned &	b,
		Mesh *const &	bulk_mesh_pt,
		Mesh *const &	surface_mesh_pt
	)

private

Create Advection Diffusion flux elements on boundary b of the Mesh pointed to by bulk_mesh_pt and add them to the Mesh object pointed to by surface_mesh_pt

◆ delete_flux_elements() [1/2]

template<class ELEMENT >

void TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::delete_flux_elements ( Mesh *const & surface_mesh_pt )

private

Delete Advection Diffusion flux elements and wipe the surface mesh.

Delete Advection Diffusion Flux Elements and wipe the surface mesh.

 {
  // How many surface elements are in the surface mesh
  unsigned n_element = surface_mesh_pt->nelement();
  
  // Loop over the surface elements
  for(unsigned e=0;e<n_element;e++)
   {
    // Kill surface element
    delete surface_mesh_pt->element_pt(e);
   }
  
  // Wipe the mesh
  surface_mesh_pt->flush_element_and_node_storage();
  
 } // end of delete_flux_elements

References e(), oomph::Mesh::element_pt(), oomph::Mesh::flush_element_and_node_storage(), and oomph::Mesh::nelement().

◆ delete_flux_elements() [2/2]

template<class ELEMENT >

void TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::delete_flux_elements ( Mesh *const & surface_mesh_pt )

private

Delete Advection Diffusion flux elements and wipe the surface mesh.

◆ doc_solution() [1/2]

template<class ELEMENT >

void TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::doc_solution ( DocInfo & doc_info )

Doc the solution: doc_info contains labels/output directory etc.

Doc the solution. DocInfo object stores flags/labels for where the output gets written to

 { 
  
  // Doc refinement levels in bulk mesh
  unsigned min_refinement_level;
  unsigned max_refinement_level;
  Bulk_mesh_pt->get_refinement_levels(min_refinement_level,
                                      max_refinement_level); 
  cout << "Ultimate min/max. refinement levels in bulk mesh : " 
       << min_refinement_level << " " 
       << max_refinement_level << std::endl;
  
  ofstream some_file;
  char filename[100];
  
  // Number of plot points
  unsigned npts;
  npts=5; 
  
  // Output solution 
  //-----------------
  sprintf(filename,"%s/soln%i.dat",doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  Bulk_mesh_pt->output(some_file,npts);
  some_file.close();
  
  // Output exact solution 
  //----------------------
  sprintf(filename,"%s/exact_soln%i.dat",doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  Bulk_mesh_pt->output_fct(some_file,npts,TanhSolnForAdvectionDiffusion::get_exact_u); 
  some_file.close();
  
  
  // Doc error and return of the square of the L2 error
  //---------------------------------------------------
  double error,norm;
  sprintf(filename,"%s/error%i.dat",doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  Bulk_mesh_pt->compute_error(some_file,TanhSolnForAdvectionDiffusion::get_exact_u,
                                error,norm); 
  some_file.close();
  
  // Doc L2 error and norm of solution
  cout << "\nNorm of error   : " << sqrt(error) << std::endl; 
  cout << "Norm of solution: " << sqrt(norm) << std::endl << std::endl;
  
  
 } // end of doc

References oomph::DocInfo::directory(), calibrate::error, MergeRestartFiles::filename, TanhSolnForAdvectionDiffusion::get_exact_u(), oomph::DocInfo::number(), and sqrt().

◆ doc_solution() [2/2]

template<class ELEMENT >

void TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::doc_solution ( DocInfo & doc_info )

Doc the solution. DocInfo object stores flags/labels for where the output gets written to

Member Data Documentation

◆ Bulk_mesh_pt

template<class ELEMENT >

RefineableRectangularQuadMesh< ELEMENT > * TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::Bulk_mesh_pt

private

Pointer to the "bulk" mesh.

Referenced by TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::TwoMeshFluxAdvectionDiffusionProblem().

◆ Source_fct_pt

template<class ELEMENT >

AdvectionDiffusionEquations< 2 >::AdvectionDiffusionSourceFctPt TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::Source_fct_pt

private

Pointer to source function.

Referenced by TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::TwoMeshFluxAdvectionDiffusionProblem().

◆ Surface_mesh_pt

template<class ELEMENT >

Mesh * TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::Surface_mesh_pt

private

Pointer to the "surface" mesh.

Referenced by TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::TwoMeshFluxAdvectionDiffusionProblem().

◆ Wind_fct_pt

template<class ELEMENT >

AdvectionDiffusionEquations< 2 >::AdvectionDiffusionWindFctPt TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::Wind_fct_pt

private

Pointer to wind function.

Referenced by TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >::TwoMeshFluxAdvectionDiffusionProblem().

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

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

template<class ELEMENT> class TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >

Constructor & Destructor Documentation

◆ TwoMeshFluxAdvectionDiffusionProblem() [1/2]

◆ ~TwoMeshFluxAdvectionDiffusionProblem() [1/2]

◆ TwoMeshFluxAdvectionDiffusionProblem() [2/2]

◆ ~TwoMeshFluxAdvectionDiffusionProblem() [2/2]

Member Function Documentation

◆ actions_after_adapt() [1/2]

◆ actions_after_adapt() [2/2]

◆ actions_after_newton_solve() [1/2]

◆ actions_after_newton_solve() [2/2]

◆ actions_before_adapt() [1/2]

◆ actions_before_adapt() [2/2]

◆ actions_before_newton_solve() [1/2]

◆ actions_before_newton_solve() [2/2]

◆ create_flux_elements() [1/2]

◆ create_flux_elements() [2/2]

◆ delete_flux_elements() [1/2]

◆ delete_flux_elements() [2/2]

◆ doc_solution() [1/2]

◆ doc_solution() [2/2]

Member Data Documentation

◆ Bulk_mesh_pt

◆ Source_fct_pt

◆ Surface_mesh_pt

◆ Wind_fct_pt

template<class ELEMENT>
class TwoMeshFluxAdvectionDiffusionProblem< ELEMENT >