Solve the Axisymmetric Navier Stokes equations in a torus. More...

Inheritance diagram for TorusProblem< ELEMENT >:

Public Member Functions
	TorusProblem (const unsigned &max_refinement_level, const double &min_error_target, const double &max_error_target)

void	set_initial_condition ()
	Set the initial conditions: all nodes have zero velocity. More...

void	set_boundary_conditions (const double &time)
	Set boundary conditions on the walls. More...

void	solve_system (const double &dt, const unsigned &nstep)
	Function that is used to run the parameter study. More...

RefineableFullCircleMesh< ELEMENT > *	mesh_pt ()
	Return a pointer to the specific mesh used. More...

void	actions_before_implicit_timestep ()
	Update the problem specs before next timestep: More...

void	actions_after_adapt ()

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 ()

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 ()

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_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 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 TorusProblem< ELEMENT >

Solve the Axisymmetric Navier Stokes equations in a torus.

Constructor & Destructor Documentation

◆ TorusProblem()

template<class ELEMENT >

TorusProblem< ELEMENT >::TorusProblem	(	const unsigned &	max_refinement_level,
		const double &	min_error_target,
		const double &	max_error_target
	)

Constructor taking the maximum refinement level and the minimum and maximum error targets.

Constructor: specify the maximum refinement level, the minimum and maximum error targets

 {
  
  using namespace Global_Physical_Variables;
  
  //Create a timestepper
  add_time_stepper_pt(new BDF<2>);
  
  //Create the domain for the mesh, which consists of a circle of
  //radius Radius and centred at (1/Delta, 0) 
  GeomObject* area_pt = new FilledCircle(1.0/Delta,0.0,Radius);
  
  //Define pi
  const double pi = MathematicalConstants::Pi;
  
  //Set the positions of the angles that divide the outer ring
  //These must be in the range -pi,pi, ordered from smallest to
  //largest
  Vector<double> theta_positions(4);
  theta_positions[0] = -0.75*pi;
  theta_positions[1] = -0.25*pi;
  theta_positions[2] = 0.25*pi;
  theta_positions[3] = 0.75*pi;
  
  //Define the radial fraction of the central box (always halfway
  //along the radius)
  Vector<double> radial_frac(4,0.5);
  
  //Now create the mesh
  Problem::mesh_pt() = new RefineableFullCircleMesh<ELEMENT>(
   area_pt,theta_positions,radial_frac,time_stepper_pt());
  
  // Set error estimator 
  Z2ErrorEstimator* error_estimator_pt=new Z2ErrorEstimator;
  mesh_pt()->spatial_error_estimator_pt()=error_estimator_pt;
  
  // Maximum number of refinements (increase this if you want a finer mesh)
  mesh_pt()->max_refinement_level() = max_refinement_level;
  
  // Error targets for adaptive refinement
  mesh_pt()->max_permitted_error() = max_error_target; 
  mesh_pt()->min_permitted_error() = min_error_target; 
  
  //Build iterative linear solver
  GMRES<CRDoubleMatrix>* iterative_linear_solver_pt = new
   GMRES<CRDoubleMatrix>;
  
  // Set maximum number of iterations
  iterative_linear_solver_pt->max_iter() = 100;
  
  // Set tolerance
  iterative_linear_solver_pt->tolerance() = 1.0e-8;   
  
  NavierStokesSchurComplementPreconditioner* prec_pt = 
   new NavierStokesSchurComplementPreconditioner(this);
  //Set the mesh
  prec_pt->set_navier_stokes_mesh(this->mesh_pt());
  
  //Set the preconditioner
  iterative_linear_solver_pt->preconditioner_pt() = prec_pt;
  
  //Set the linear solver
  this->linear_solver_pt() = iterative_linear_solver_pt;
  
  //Precondition the pressure block with AMG if we have Hypre
 #ifdef OOMPH_HAS_HYPRE
 //Trap because HYPRE can't handle the case when OOMPH_HAS_MPI, but we
 //run in serial
 #ifndef OOMPH_HAS_MPI
  
  //Set up the internal preconditioners
  Preconditioner* P_matrix_preconditioner_pt = new HyprePreconditioner;
  
  // Set parameters for use as preconditioner on Poisson-type problem
  Hypre_default_settings::set_defaults_for_2D_poisson_problem(
   static_cast<HyprePreconditioner*>(P_matrix_preconditioner_pt));
  
  // Use Hypre for the Schur complement block
  prec_pt->set_p_preconditioner(P_matrix_preconditioner_pt);
  
  // Shut up!
  static_cast<HyprePreconditioner*>(P_matrix_preconditioner_pt)->
   disable_doc_time();
 #endif
 #endif
  
 //Set Block diagonal preconditioner for the momentum block
 BlockDiagonalPreconditioner<CRDoubleMatrix>* F_matrix_preconditioner_pt = 
   new BlockDiagonalPreconditioner<CRDoubleMatrix>;
  
 // Set mesh
 F_matrix_preconditioner_pt->add_mesh(this->mesh_pt());
  
 //Use AMG on the momentum blocks if we have Hypre 
 #ifdef OOMPH_HAS_HYPRE
 //Trap because HYPRE can't handle the case when 
 //OOMPH_HAS_MPI, but we run in serial
 #ifndef OOMPH_HAS_MPI
  dynamic_cast<BlockDiagonalPreconditioner<CRDoubleMatrix>* >
   (F_matrix_preconditioner_pt)->set_subsidiary_preconditioner_function
   (Hypre_Subsidiary_Preconditioner_Helper::set_hypre_preconditioner);
 #endif
 #endif
   
  // Use Hypre for momentum block 
  prec_pt->set_f_preconditioner(F_matrix_preconditioner_pt);
  
  //Loop over all the (fluid) elements 
  unsigned n_element = mesh_pt()->nelement();
  for(unsigned e=0;e<n_element;e++)
   {
    //Cast to the particular element type, this is necessary because
    //the base elements don't have the member functions that we're about
    //to call!
    ELEMENT *el_pt = dynamic_cast<ELEMENT*>(mesh_pt()->element_pt(e));
  
    //There is no need for ALE
    el_pt->disable_ALE();
  
    //Set the Reynolds number for each element 
    //(yes we could have different Reynolds number in each element!!)
    el_pt->re_pt() = &Re;
    //Set the product of Reynolds and Strouhal numbers
    el_pt->re_st_pt() = &Re;
   }
  
  //Let this problem be conventional form by setting gamma to zero
  ELEMENT::Gamma[0] = 0.0; //r-momentum
  ELEMENT::Gamma[1] = 0.0; //z-momentum
  
  //Set the boundary conditions (no slip on the torus walls)
  //Loop over the nodes on the (only) mesh boundary
  unsigned n_boundary_node = mesh_pt()->nboundary_node(0);
  for(unsigned n=0;n<n_boundary_node;n++)
   {
    //Pin all three velocity components on the wall
    for(unsigned i=0;i<3;i++)
     {
      mesh_pt()->boundary_node_pt(0,n)->pin(i);
     }
   }
  
  // Pin redudant pressure dofs
  RefineableAxisymmetricNavierStokesEquations::
   pin_redundant_nodal_pressures(mesh_pt()->element_pt());
  
  //Pin a single pressure value 
  dynamic_cast<ELEMENT*>(mesh_pt()->element_pt(0))->fix_pressure(0,0.0);
  
  //Setup all the equation numbering and look-up schemes 
  std::cout << assign_eqn_numbers() << std::endl; 
 }

References oomph::GeneralPurposeBlockPreconditioner< MATRIX >::add_mesh(), Global_Physical_Variables::Delta, e(), MeshRefinement::error_estimator_pt, GlobalPhysicalVariables::Gamma, i, oomph::IterativeLinearSolver::max_iter(), n, constants::pi, BiharmonicTestFunctions2::Pi, oomph::IterativeLinearSolver::preconditioner_pt(), Global_Physical_Variables::Radius, GlobalPhysicalVariables::Re, oomph::Hypre_default_settings::set_defaults_for_2D_poisson_problem(), oomph::NavierStokesSchurComplementPreconditioner::set_f_preconditioner(), oomph::NavierStokesSchurComplementPreconditioner::set_navier_stokes_mesh(), oomph::NavierStokesSchurComplementPreconditioner::set_p_preconditioner(), and oomph::IterativeLinearSolver::tolerance().

Member Function Documentation

◆ actions_after_adapt()

template<class ELEMENT >

void TorusProblem< ELEMENT >::actions_after_adapt ( )

inlinevirtual

After adaptation: Pin pressure again (the previously pinned value might have disappeared) and pin redudant pressure dofs.

Reimplemented from oomph::Problem.

   {
    // Unpin all pressure dofs
    RefineableAxisymmetricNavierStokesEquations::
     unpin_all_pressure_dofs(mesh_pt()->element_pt());
    
    // Pin redudant pressure dofs
    RefineableAxisymmetricNavierStokesEquations::
     pin_redundant_nodal_pressures(mesh_pt()->element_pt());
    
    //Pin a single pressure value 
    dynamic_cast<ELEMENT*>(mesh_pt()->element_pt(0))->fix_pressure(0,0.0);
   }

◆ actions_before_implicit_timestep()

template<class ELEMENT >

void TorusProblem< ELEMENT >::actions_before_implicit_timestep ( )

inlinevirtual

Update the problem specs before next timestep:

Reimplemented from oomph::Problem.

157 {set_boundary_conditions(time());}

TorusProblem::set_boundary_conditions

void set_boundary_conditions(const double &time)

Set boundary conditions on the walls.

Definition: torus.cc:342

oomph::Problem::time

double & time()

Return the current value of continuous time.

Definition: problem.cc:11531

◆ mesh_pt()

template<class ELEMENT >

RefineableFullCircleMesh<ELEMENT>* TorusProblem< ELEMENT >::mesh_pt ( )

inline

Return a pointer to the specific mesh used.

154 {return dynamic_cast<RefineableFullCircleMesh<ELEMENT>*>(Problem::mesh_pt());}

◆ set_boundary_conditions()

template<class ELEMENT >

void TorusProblem< ELEMENT >::set_boundary_conditions ( const double & time )

Set boundary conditions on the walls.

Set the boundary conditions as a function of time we are going to spin up the torus

 {
  //NOTE: The default value of all parameters is zero, so we need only 
  //set the values that are non-zero on the boundary, i.e. the swirl
  
  //Loop over the nodes on the boundary
  unsigned n_boundary_node = mesh_pt()->nboundary_node(0);
  //Loop over the nodes on the boundary
  for(unsigned n=0;n<n_boundary_node;n++)
   {
    //Get the radial values
    double r = mesh_pt()->boundary_node_pt(0,n)->x(0);
    //Set the value of the w-velocity
    //Fast(ish) spin-up
    mesh_pt()->boundary_node_pt(0,n)->set_value(2,r*(1.0 - exp(-20.0*time)));
   }
 }

References Eigen::bfloat16_impl::exp(), n, and UniformPSDSelfTest::r.

◆ set_initial_condition()

template<class ELEMENT >

void TorusProblem< ELEMENT >::set_initial_condition ( )

inlinevirtual

Set the initial conditions: all nodes have zero velocity.

Reimplemented from oomph::Problem.

   {
    const unsigned n_node = mesh_pt()->nnode();
    for(unsigned n=0;n<n_node;n++)
     {
      for(unsigned i=0;i<3;i++)
       {
        mesh_pt()->node_pt(n)->set_value(i,0.0);
       }
     }
   }

References i, and n.

◆ solve_system()

template<class ELEMENT >

void TorusProblem< ELEMENT >::solve_system	(	const double &	dt,
		const unsigned &	nstep
	)

Function that is used to run the parameter study.

Solve the system for a number of different values of the Reynolds number.

 {
  using namespace Global_Physical_Variables;
  
  //Open a trace file
  ofstream trace("time_trace.dat");
  
  //Define a string that we can set to be the name of the output file
  char filename[100];
  //Define an output filestream
  ofstream file;
  
  //Set the Reynolds number
  Re = 1000.0;
  
  //Set an impulsive start from rest
  assign_initial_values_impulsive(dt);
  
  //Output intital data
  trace << time() << " " << mesh_pt()->boundary_node_pt(0,0)->value(2) 
        << " " << mesh_pt()->node_pt(0)->value(0) 
        << " " << mesh_pt()->node_pt(0)->value(1) 
        << " " << mesh_pt()->node_pt(0)->value(2) << std::endl;
  
  //Increase the maximum value of the residuals to get
  //past the first few steps
  Max_residuals = 50.0;
  
  //Now perform the first timestep with 2 steps of refinement
  unsteady_newton_solve(dt,2,true);
  
  trace << time() << " " << mesh_pt()->boundary_node_pt(0,0)->value(2) 
        << " " << mesh_pt()->node_pt(0)->value(0) 
        << " " << mesh_pt()->node_pt(0)->value(1) 
        << " " << mesh_pt()->node_pt(0)->value(2) << std::endl;
  
  //Output data after the first timestep
  //Create the filename, including the array index
  sprintf(filename,"soln_Re%g_t%g.dat",Re,time());
  //Actually, write the data
  file.open(filename);
  mesh_pt()->output(file,5);
  file.close();
  
  //Now do the other steps with only one adaptation per step
  for(unsigned n=1;n<nstep;n++)
   {
    //Solve the problem
    unsteady_newton_solve(dt,1,false);
  
    trace << time() << " " << mesh_pt()->boundary_node_pt(0,0)->value(2) 
          << " " << mesh_pt()->node_pt(0)->value(0) 
          << " " << mesh_pt()->node_pt(0)->value(1) 
          << " " << mesh_pt()->node_pt(0)->value(2) << std::endl;
   
    //Output data at each step
    //Create the filename, including the array index
    sprintf(filename,"soln_Re%g_t%g.dat",Re,time());
    //Actually, write the data
    file.open(filename);
    mesh_pt()->output(file,5);
    file.close();
   }
  
  //Close the trace file
  trace.close();
 }

References MergeRestartFiles::filename, n, and GlobalPhysicalVariables::Re.

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

torus.cc

Public Member Functions

Additional Inherited Members

Detailed Description

template<class ELEMENT> class TorusProblem< ELEMENT >

Constructor & Destructor Documentation

◆ TorusProblem()

Member Function Documentation

◆ actions_after_adapt()

◆ actions_before_implicit_timestep()

◆ mesh_pt()

◆ set_boundary_conditions()

◆ set_initial_condition()

◆ solve_system()

template<class ELEMENT>
class TorusProblem< ELEMENT >