#include <navier_stokes_preconditioners.h>

Inheritance diagram for oomph::FpPressureAdvectionDiffusionProblem< ELEMENT >:

Public Member Functions
	FpPressureAdvectionDiffusionProblem (Mesh navier_stokes_mesh_pt, Problem orig_problem_pt)
	Constructor: Pass Navier-Stokes mesh and pointer to orig problem. More...

void	get_pressure_advection_diffusion_jacobian (CRDoubleMatrix &jacobian)
	Get the pressure advection diffusion Jacobian. More...

void	reset_pin_status ()
	Reset pin status of all values. More...

void	pin_all_non_pressure_dofs (const bool &set_pressure_bc_for_validation=false)

void	validate (DocInfo &doc_info)

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

virtual void	actions_before_adapt ()

virtual void	actions_after_adapt ()
	Actions that are to be performed after a mesh adaptation. More...

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 Attributes
unsigned	Ndim
	The spatial dimension. More...

Problem *	Orig_problem_pt

std::map< Data *, std::vector< int > >	Eqn_number_backup
	Map to store original equation numbers. 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_solve ()

virtual void	actions_after_newton_solve ()

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 oomph::FpPressureAdvectionDiffusionProblem< ELEMENT >

//////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////// Auxiliary Problem that can be used to assemble the pressure advection diffusion matrix needed by the FpPreconditoner

Constructor & Destructor Documentation

◆ FpPressureAdvectionDiffusionProblem()

template<class ELEMENT >

oomph::FpPressureAdvectionDiffusionProblem< ELEMENT >::FpPressureAdvectionDiffusionProblem	(	Mesh *	navier_stokes_mesh_pt,
		Problem *	orig_problem_pt
	)

inline

Constructor: Pass Navier-Stokes mesh and pointer to orig problem.

     {
       // Pass across mesh -- boundary conditions have already
       // been applied and the equations have been enumerated.
       mesh_pt() = navier_stokes_mesh_pt;
  
       // Store pointer to orig problem so we can re-assign the
       // orig eqn numbers when we're done
       Orig_problem_pt = orig_problem_pt;
  
       // Get the spatial dimension
       Ndim = mesh_pt()->finite_element_pt(0)->dim();
  
       // Set new assembly handler
       this->assembly_handler_pt() = new FpPreconditionerAssemblyHandler(Ndim);
     }

References oomph::Problem::assembly_handler_pt(), oomph::FiniteElement::dim(), oomph::Mesh::finite_element_pt(), oomph::Problem::mesh_pt(), oomph::FpPressureAdvectionDiffusionProblem< ELEMENT >::Ndim, and oomph::FpPressureAdvectionDiffusionProblem< ELEMENT >::Orig_problem_pt.

Member Function Documentation

◆ doc_solution()

template<class ELEMENT >

void oomph::FpPressureAdvectionDiffusionProblem< ELEMENT >::doc_solution ( DocInfo & doc_info )

inline

Doc solution (only needed during development – kept alive in case validation is required during code maintenance)

     {
       std::ofstream some_file;
       std::ostringstream filename;
  
       // Number of plot points
       unsigned npts;
       npts = 5;
  
       // Check value of FE solution in first element
       Vector<double> s(Ndim, 0.0);
       Vector<double> x(Ndim);
       double p = dynamic_cast<ELEMENT*>(mesh_pt()->finite_element_pt(0))
                    ->interpolated_p_nst(s);
       dynamic_cast<ELEMENT*>(mesh_pt()->finite_element_pt(0))
         ->interpolated_x(s, x);
  
       // Get offset-free exact solution
       double u_exact = 0;
       PressureAdvectionDiffusionValidation::get_exact_u(x, u_exact);
  
       // Adjust offset
       unsigned nnode = mesh_pt()->nnode();
       for (unsigned j = 0; j < nnode; j++)
       {
         if (mesh_pt()->node_pt(j)->nvalue() == 3)
         {
           *(mesh_pt()->node_pt(j)->value_pt(2)) -= p - u_exact;
         }
       }
  
       // Output solution
       filename << doc_info.directory() << "/fp_soln" << doc_info.number()
                << ".dat";
       some_file.open(filename.str().c_str());
       some_file.precision(20);
       mesh_pt()->output(some_file, npts);
       some_file.close();
  
       filename.str("");
       filename << doc_info.directory() << "/fp_exact_soln" << doc_info.number()
                << ".dat";
       some_file.open(filename.str().c_str());
       some_file.precision(20);
       mesh_pt()->output_fct(
         some_file, npts, PressureAdvectionDiffusionValidation::get_exact_u);
       some_file.close();
     }

References oomph::DocInfo::directory(), MergeRestartFiles::filename, oomph::Mesh::finite_element_pt(), oomph::PressureAdvectionDiffusionValidation::get_exact_u(), j, oomph::Problem::mesh_pt(), oomph::FpPressureAdvectionDiffusionProblem< ELEMENT >::Ndim, oomph::Mesh::nnode(), oomph::Mesh::node_pt(), oomph::DocInfo::number(), oomph::Mesh::output(), oomph::Mesh::output_fct(), p, s, oomph::Data::value_pt(), and plotDoE::x.

Referenced by oomph::FpPressureAdvectionDiffusionProblem< ELEMENT >::validate().

◆ get_pressure_advection_diffusion_jacobian()

template<class ELEMENT >

void oomph::FpPressureAdvectionDiffusionProblem< ELEMENT >::get_pressure_advection_diffusion_jacobian ( CRDoubleMatrix & jacobian )

inline

Get the pressure advection diffusion Jacobian.

     {
       // Pin all non-pressure dofs
       pin_all_non_pressure_dofs();
  
       // Re-assign the equation numbers for all elements in Navier-Stokes mesh
       unsigned n_dof = assign_eqn_numbers();
       oomph_info << "Eqn numbers after pinning veloc dofs: " << n_dof
                  << std::endl;
  
       // Get "Jacobian" of the modified system
       DoubleVector dummy_residuals;
       this->get_jacobian(dummy_residuals, jacobian);
  
       // Reset pin status
       reset_pin_status();
  
       // Reassign equation numbering of original problem
       oomph_info << "Eqn numbers in orig problem after re-assignment: "
                  << Orig_problem_pt->assign_eqn_numbers() << std::endl;
     }

References oomph::Problem::assign_eqn_numbers(), oomph::Problem::get_jacobian(), oomph::oomph_info, oomph::FpPressureAdvectionDiffusionProblem< ELEMENT >::Orig_problem_pt, oomph::FpPressureAdvectionDiffusionProblem< ELEMENT >::pin_all_non_pressure_dofs(), and oomph::FpPressureAdvectionDiffusionProblem< ELEMENT >::reset_pin_status().

◆ pin_all_non_pressure_dofs()

template<class ELEMENT >

void oomph::FpPressureAdvectionDiffusionProblem< ELEMENT >::pin_all_non_pressure_dofs ( const bool & set_pressure_bc_for_validation = false )

inline

Pin all non-pressure dofs and (if boolean flag is set to true also all pressure dofs along domain boundaries – only used for validation)

     {
       // Backup pin status and then pin all non-pressure degrees of freedom
       unsigned nelem = mesh_pt()->nelement();
       for (unsigned e = 0; e < nelem; e++)
       {
         // Get actual element (needed because different elements
         // store nodal pressure in different places)
         ELEMENT* el_pt =
           dynamic_cast<ELEMENT*>(mesh_pt()->finite_element_pt(e));
  
  
 #ifdef PARANOID
         if (el_pt == 0)
         {
           std::ostringstream error_message;
           error_message << "Navier Stokes mesh must contain only Navier Stokes"
                         << "bulk elements\n";
           throw OomphLibError(error_message.str(),
                               OOMPH_CURRENT_FUNCTION,
                               OOMPH_EXCEPTION_LOCATION);
         }
 #endif
  
         // Check if element has internal pressure representation
         // usually discontinuous -- preconditioner doesn't work for that case!
         if (el_pt->p_nodal_index_nst() < 0)
         {
           std::ostringstream error_message;
           error_message << "Cannot use Fp preconditioner with discontinuous\n"
                         << "pressures.\n";
           throw OomphLibError(error_message.str(),
                               OOMPH_CURRENT_FUNCTION,
                               OOMPH_EXCEPTION_LOCATION);
         }
  
         // Loop over internal data and pin the values (having established that
         // pressure dofs aren't amongst those)
         unsigned nint = el_pt->ninternal_data();
         for (unsigned j = 0; j < nint; j++)
         {
           Data* data_pt = el_pt->internal_data_pt(j);
           if (Eqn_number_backup[data_pt].size() == 0)
           {
             unsigned nvalue = data_pt->nvalue();
             Eqn_number_backup[data_pt].resize(nvalue);
             for (unsigned i = 0; i < nvalue; i++)
             {
               // Backup
               Eqn_number_backup[data_pt][i] = data_pt->eqn_number(i);
  
               // Pin everything
               data_pt->pin(i);
             }
           }
         }
  
         // Now deal with nodal values
         unsigned nnod = el_pt->nnode();
         for (unsigned j = 0; j < nnod; j++)
         {
           Node* nod_pt = el_pt->node_pt(j);
           if (Eqn_number_backup[nod_pt].size() == 0)
           {
             unsigned nvalue = nod_pt->nvalue();
             Eqn_number_backup[nod_pt].resize(nvalue);
             for (unsigned i = 0; i < nvalue; i++)
             {
               // Pin everything apart from the nodal pressure
               // value
               if (int(i) != el_pt->p_nodal_index_nst())
               {
                 // Backup and pin
                 Eqn_number_backup[nod_pt][i] = nod_pt->eqn_number(i);
                 nod_pt->pin(i);
               }
               // Else it's a pressure value
               else
               {
                 // Exclude non-nodal pressure based elements
                 if (el_pt->p_nodal_index_nst() >= 0)
                 {
                   // Backup
                   Eqn_number_backup[nod_pt][i] = nod_pt->eqn_number(i);
                 }
               }
             }
           }
  
           // Set wind
           if (set_pressure_bc_for_validation)
           {
             Vector<double> x(2);
             x[0] = nod_pt->x(0);
             x[1] = nod_pt->x(1);
             Vector<double> u(2);
             PressureAdvectionDiffusionValidation::wind_function(x, u);
             nod_pt->set_value(el_pt->u_index_nst(0), u[0]);
             nod_pt->set_value(el_pt->u_index_nst(1), u[1]);
           }
         }
       }
     }

References e(), oomph::Data::eqn_number(), oomph::FpPressureAdvectionDiffusionProblem< ELEMENT >::Eqn_number_backup, oomph::Mesh::finite_element_pt(), i, j, oomph::Problem::mesh_pt(), oomph::Mesh::nelement(), oomph::Data::nvalue(), OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION, oomph::Data::pin(), oomph::Data::set_value(), size, oomph::PressureAdvectionDiffusionValidation::wind_function(), plotDoE::x, and oomph::Node::x().

Referenced by oomph::FpPressureAdvectionDiffusionProblem< ELEMENT >::get_pressure_advection_diffusion_jacobian(), and oomph::FpPressureAdvectionDiffusionProblem< ELEMENT >::validate().

◆ reset_pin_status()

template<class ELEMENT >

void oomph::FpPressureAdvectionDiffusionProblem< ELEMENT >::reset_pin_status ( )

inline

Reset pin status of all values.

     {
       // Reset pin status for nodes
       unsigned nnod = mesh_pt()->nnode();
       for (unsigned j = 0; j < nnod; j++)
       {
         Node* nod_pt = mesh_pt()->node_pt(j);
         unsigned nval = nod_pt->nvalue();
         for (unsigned i = 0; i < nval; i++)
         {
           nod_pt->eqn_number(i) = Eqn_number_backup[nod_pt][i];
         }
       }
  
       // ... and internal data
       unsigned nelem = mesh_pt()->nelement();
       for (unsigned e = 0; e < nelem; e++)
       {
         // Get actual element
         ELEMENT* el_pt =
           dynamic_cast<ELEMENT*>(mesh_pt()->finite_element_pt(e));
  
  
 #ifdef PARANOID
         if (el_pt == 0)
         {
           std::ostringstream error_message;
           error_message << "Navier Stokes mesh must contain only Navier Stokes"
                         << "bulk elements\n";
           throw OomphLibError(error_message.str(),
                               OOMPH_CURRENT_FUNCTION,
                               OOMPH_EXCEPTION_LOCATION);
         }
 #endif
  
         unsigned nint = el_pt->ninternal_data();
         for (unsigned j = 0; j < nint; j++)
         {
           Data* data_pt = el_pt->internal_data_pt(j);
           unsigned nvalue = data_pt->nvalue();
           for (unsigned i = 0; i < nvalue; i++)
           {
             data_pt->eqn_number(i) = Eqn_number_backup[data_pt][i];
           }
         }
       }
  
       // Free up storage
       Eqn_number_backup.clear();
     }

References e(), oomph::Data::eqn_number(), oomph::FpPressureAdvectionDiffusionProblem< ELEMENT >::Eqn_number_backup, oomph::Mesh::finite_element_pt(), i, j, oomph::Problem::mesh_pt(), oomph::Mesh::nelement(), oomph::Mesh::nnode(), oomph::Mesh::node_pt(), oomph::Data::nvalue(), OOMPH_CURRENT_FUNCTION, and OOMPH_EXCEPTION_LOCATION.

Referenced by oomph::FpPressureAdvectionDiffusionProblem< ELEMENT >::get_pressure_advection_diffusion_jacobian(), and oomph::FpPressureAdvectionDiffusionProblem< ELEMENT >::validate().

◆ validate()

template<class ELEMENT >

void oomph::FpPressureAdvectionDiffusionProblem< ELEMENT >::validate ( DocInfo & doc_info )

inline

Validate pressure advection diffusion problem and doc exact and computed solution in directory specified in DocInfo object

     {
       oomph_info << "\n\n==============================================\n\n";
       oomph_info << "Doing validation for pressure adv diff problem\n";
  
       // Choose exact solution
       PressureAdvectionDiffusionValidation::Flag = 1;
  
       // Pin all non-pressure dofs and pressure dofs along boundaries for
       // validation
       bool set_pressure_bc_for_validation = true;
       pin_all_non_pressure_dofs(set_pressure_bc_for_validation);
  
  
       // Set Peclet number
       PressureAdvectionDiffusionValidation::Peclet =
         dynamic_cast<NavierStokesEquations<2>*>(mesh_pt()->element_pt(0))->re();
  
       // Loop over all elements and set source function pointer
       unsigned nel = mesh_pt()->nelement();
       for (unsigned e = 0; e < nel; e++)
       {
         dynamic_cast<NavierStokesEquations<2>*>(mesh_pt()->element_pt(e))
           ->source_fct_for_pressure_adv_diff() =
           &PressureAdvectionDiffusionValidation::source_function;
       }
  
       // Re-assign the equation numbers for all elements in Navier-Stokes mesh
       oomph_info << "Eqn numbers after pinning veloc dofs: "
                  << assign_eqn_numbers() << std::endl;
  
       // Attach Robin BC elements
       unsigned nbound = mesh_pt()->nboundary();
       if (PressureAdvectionDiffusionValidation::Flag == 1)
       {
         // Loop over all boundaries of Navier Stokes mesh
         for (unsigned b = 0; b < nbound; b++)
         {
           // How many bulk elements are adjacent to boundary b?
           unsigned n_element = mesh_pt()->nboundary_element(b);
  
           // Loop over the bulk elements adjacent to boundary b?
           for (unsigned e = 0; e < n_element; e++)
           {
             TemplateFreeNavierStokesEquationsBase* bulk_elem_pt =
               dynamic_cast<TemplateFreeNavierStokesEquationsBase*>(
                 mesh_pt()->boundary_element_pt(b, e));
  
             // What is the index of the face of the bulk element e on bondary b
             int face_index = mesh_pt()->face_index_at_boundary(b, e);
  
             // Build face element
             bulk_elem_pt->build_fp_press_adv_diff_robin_bc_element(face_index);
  
           } // end of loop over bulk elements adjacent to boundary b
         }
       }
  
  
       // Loop over all elements and set source function pointer
       std::ofstream outfile;
       outfile.open("robin_elements.dat");
       for (unsigned e = 0; e < nel; e++)
       {
         dynamic_cast<NavierStokesEquations<2>*>(mesh_pt()->element_pt(e))
           ->output_pressure_advection_diffusion_robin_elements(outfile);
       }
       outfile.close();
  
       // Solve it
       newton_solve();
  
       // And output the solution...
       doc_solution(doc_info);
  
       // Kill Robin BC elements
       if (PressureAdvectionDiffusionValidation::Flag == 1)
       {
         // Loop over all boundaries of Navier Stokes mesh
         for (unsigned b = 0; b < nbound; b++)
         {
           // How many bulk elements are adjacent to boundary b?
           unsigned n_element = mesh_pt()->nboundary_element(b);
  
           // Loop over the bulk elements adjacent to boundary b?
           for (unsigned e = 0; e < n_element; e++)
           {
             TemplateFreeNavierStokesEquationsBase* bulk_elem_pt =
               dynamic_cast<TemplateFreeNavierStokesEquationsBase*>(
                 mesh_pt()->boundary_element_pt(b, e));
  
             // Kill associated Robin elements
             bulk_elem_pt->delete_pressure_advection_diffusion_robin_elements();
  
           } // end of loop over bulk elements adjacent to boundary b
         }
       }
  
       // Reset pin status
       reset_pin_status();
  
       // Reassign equation numbering of original problem
       oomph_info << "Eqn numbers in orig problem after re-assignment: "
                  << Orig_problem_pt->assign_eqn_numbers() << std::endl;
  
  
       oomph_info << "Done validation for pressure adv diff problem\n";
       oomph_info << "\n\n==============================================\n\n";
     }