Porous channel flow on a refineable mesh. More...

Inheritance diagram for RefineablePorousChannelProblem< ELEMENT >:

Public Member Functions
Problem *	make_copy ()
	Make a copy of the problem for using in adaptive bifurcation tracking. More...

	RefineablePorousChannelProblem ()
	Constructor. More...

	~RefineablePorousChannelProblem ()
	Destructor to clean up memory. More...

void	set_boundary_conditions ()
	Set the boundary conditions. More...

void	actions_after_change_in_bifurcation_parameter ()

void	actions_before_implicit_timestep ()
	Update the boundary conditions before next timestep: More...

void	symmetrise_eigenfunction_for_adaptive_pitchfork_tracking ()

void	actions_after_adapt ()

RefineableRectangularQuadMesh< ELEMENT > *	mesh_pt ()

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 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 ()

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_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 RefineablePorousChannelProblem< ELEMENT >

Porous channel flow on a refineable mesh.

Constructor & Destructor Documentation

◆ RefineablePorousChannelProblem()

template<class ELEMENT >

RefineablePorousChannelProblem< ELEMENT >::RefineablePorousChannelProblem

Constructor.

Constructor for RefineablePorousChannel problem.

 {
  //Set the maximum residuals to be large so that the initial 
  //(coarse) problem converges
  Max_residuals = 1000.0;
  
  // Allocate the timestepper -- this constructs the Problem's 
  // time object with a sufficient amount of storage to store the
  // previous timesteps. 
  add_time_stepper_pt(new BDF<2>);
  
  //Number of elements in one unit
  unsigned N=2;
  
  // Domain length in r-direction
  double l_x=Global_Physical_Variables::L;
  
  //Number of elements across
  unsigned n_y = 2*N;
  
  // # of elements in x-direction
  unsigned n_x= static_cast<unsigned>(l_x)*N;
  
  // Build and assign rectangular mesh
  Problem::mesh_pt() = 
   new RefineableRectangularQuadMesh<ELEMENT>(n_x,n_y,0.0,l_x,-1.0,1.0, 
                                              time_stepper_pt());
  
  
  // Set error estimator
  Z2ErrorEstimator* error_estimator_pt=new Z2ErrorEstimator;
  mesh_pt()->spatial_error_estimator_pt()=error_estimator_pt;
  
  //Let this problem be conventional form by setting gamma to zero
  ELEMENT::Gamma[0] = 0.0; //x-momentum
  ELEMENT::Gamma[1] = 0.0; //y-momentum
   
  // Set the boundary conditions for this problem: All nodes are
  // free by default -- just pin the ones that have Dirichlet conditions
  // here. 
  
  unsigned num_bound = mesh_pt()->nboundary();
  
  // Pin all two velocities on boundaries 0 and 2
  for(unsigned ibound=0;ibound<num_bound;ibound = ibound + 2)
   {
    unsigned num_nod= mesh_pt()->nboundary_node(ibound);
    for (unsigned inod=0;inod<num_nod;inod++)
     {
      // Loop over values (u/v velocities)
      for (unsigned i=0;i<2;i++)
       {
        mesh_pt()->boundary_node_pt(ibound,inod)->pin(i); 
       }
     }
   } // end loop over boundaries 0 and 2
   
  // Now pin the x velocity on boundaries 3
  {
   unsigned ibound = 3;
   unsigned num_nod= mesh_pt()->nboundary_node(ibound);
   for (unsigned inod=0;inod<num_nod;inod++)
    {
     // Loop over the theta- and phi-velocities
     mesh_pt()->boundary_node_pt(ibound,inod)->pin(0);
    }
  } 
  // end of set boundary conditions
  
  // Complete the build of all elements so they are fully functional
  //================================================================
  
  //Find number of elements in mesh
  unsigned n_element = mesh_pt()->nelement();
  
  // Loop over the elements to set up element-specific 
  // things that cannot be handled by constructor
  for(unsigned e=0;e<n_element;e++)
   {
    // Upcast from GeneralisedElement to the present element
    ELEMENT* el_pt = dynamic_cast<ELEMENT*>(mesh_pt()->element_pt(e));
  
    //Set the Reynolds number
    el_pt->re_pt() = &Global_Physical_Variables::Re;
    //Set the Womersley number
    el_pt->re_st_pt() = &Global_Physical_Variables::Re;
    
    //The Mesh does not move
    el_pt->disable_ALE();
   } // end loop over elements
  
  // Pin redudant pressure dofs
  RefineableNavierStokesEquations<2>::
   pin_redundant_nodal_pressures(mesh_pt()->element_pt());
  
  // Setup equation numbering scheme
  std::cout <<"Number of equations: " << assign_eqn_numbers() << std::endl; 
  
 } // end_of_constructor

References e(), MeshRefinement::error_estimator_pt, GlobalPhysicalVariables::Gamma, i, oomph::Global_Physical_Variables::L, oomph::Problem::mesh_pt(), N, oomph::RefineableNavierStokesEquations< DIM >::pin_redundant_nodal_pressures(), and oomph::Global_Physical_Variables::Re.

◆ ~RefineablePorousChannelProblem()

template<class ELEMENT >

RefineablePorousChannelProblem< ELEMENT >::~RefineablePorousChannelProblem

Destructor to clean up memory.

Destructor for RefineablePorousChannel problem.

 { 
  //Kill the error estimator
  delete mesh_pt()->spatial_error_estimator_pt();
  //Kill the mesh
  delete mesh_pt();
  //Kill the timestepper
  delete time_stepper_pt();
 } // end_of_destructor

Member Function Documentation

◆ actions_after_adapt()

template<class ELEMENT >

void RefineablePorousChannelProblem< 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
    RefineableNavierStokesEquations<2>::
     unpin_all_pressure_dofs(mesh_pt()->element_pt());
    
    // Pin redudant pressure dofs
    RefineableNavierStokesEquations<2>::
     pin_redundant_nodal_pressures(mesh_pt()->element_pt());
    
    //Reset the boundary conditions
    set_boundary_conditions();
   }

References oomph::RefineableNavierStokesEquations< DIM >::pin_redundant_nodal_pressures(), and oomph::RefineableNavierStokesEquations< DIM >::unpin_all_pressure_dofs().

◆ actions_after_change_in_bifurcation_parameter()

template<class ELEMENT >

void RefineablePorousChannelProblem< ELEMENT >::actions_after_change_in_bifurcation_parameter ( )

inlinevirtual

No actions are required after the change in bifurcation parameter. This overloads the default which calls actions before and after newton solve.

Reimplemented from oomph::Problem.

141 {}

◆ actions_before_implicit_timestep()

template<class ELEMENT >

void RefineablePorousChannelProblem< ELEMENT >::actions_before_implicit_timestep ( )

inlinevirtual

Update the boundary conditions before next timestep:

Reimplemented from oomph::Problem.

144 {set_boundary_conditions();}

◆ make_copy()

template<class ELEMENT >

Problem* RefineablePorousChannelProblem< ELEMENT >::make_copy ( )

inlinevirtual

Make a copy of the problem for using in adaptive bifurcation tracking.

Reimplemented from oomph::Problem.

   {
    //Make a copy based on the current parameters
    return(new RefineablePorousChannelProblem<ELEMENT>());
   }

◆ mesh_pt()

template<class ELEMENT >

RefineableRectangularQuadMesh<ELEMENT>* RefineablePorousChannelProblem< ELEMENT >::mesh_pt ( )

inline

   {
    // Upcast from pointer to the Mesh base class to the specific 
    // element type that we're using here.
    return dynamic_cast<RefineableRectangularQuadMesh<ELEMENT>*>(
     Problem::mesh_pt());
   }

References oomph::Problem::mesh_pt().

◆ set_boundary_conditions()

template<class ELEMENT >

void RefineablePorousChannelProblem< ELEMENT >::set_boundary_conditions

Set the boundary conditions.

Actions before timestep: update the domain, then reset the boundary conditions for the current time.

 {
  // Get current time
  const double time=time_pt()->time();
  
  
  //Find number of nodes on top row
  unsigned n_node = mesh_pt()->nboundary_node(2);
  
  //Set the value of a perturbation
  double epsilon = 0.1;
  
  //Loop over the nodes on the top row and set their u and v velocities
  //We are going to add a small time-dependent perturbation
  //to the velocity and also allow the posibility for an initial 
  //symmetry-breaking perturbation
  for(unsigned i=0;i<n_node;i++)
   {
    //Top row
    double u = 1.0 + epsilon*time*exp(-time);
    
    mesh_pt()->boundary_node_pt(2,i)->set_value(0,0.0);
    mesh_pt()->boundary_node_pt(2,i)->set_value(1,u);
   }
  
  //Find number of nodes on bottom row
  n_node = mesh_pt()->nboundary_node(0);
  
  for(unsigned i=0;i<n_node;i++)
   {
    //Bottom row
    double u =  -1.0 + epsilon*time*exp(-time);
  
    mesh_pt()->boundary_node_pt(0,i)->set_value(0,0.0);
    mesh_pt()->boundary_node_pt(0,i)->set_value(1,u);
   }
  
 } // end of actions_before_implicit_timestep

References oomph::SarahBL::epsilon, Eigen::bfloat16_impl::exp(), and i.

◆ symmetrise_eigenfunction_for_adaptive_pitchfork_tracking()

template<class ELEMENT >

void RefineablePorousChannelProblem< ELEMENT >::symmetrise_eigenfunction_for_adaptive_pitchfork_tracking ( )

inlinevirtual

Hacky function to symmetrise the problem The idea is to sort all nodes in the mesh lexicographically Then we can loop over all nodes with the same x value and apply the appropriate symmetry conditions.

Reimplemented from oomph::Problem.

   {
    //Find the number of nodes
    const unsigned n_node = this->mesh_pt()->nnode();
    //Allocate storage for the nodes
    Vector<Node*> local_nodes_pt(n_node);
    //Load the nodes into the local copy
    for(unsigned n=0;n<n_node;n++)
     {
      local_nodes_pt[n] = this->mesh_pt()->node_pt(n);
     }
  
    //Now let's sort the nodes lexicographically
    std::sort(local_nodes_pt.begin(),local_nodes_pt.end(),
              CompareNodes());
  
    //The nodes are now sorted, we proceed to find all nodes 
    //in a column (same x location)
    //Storage for start and end of the column
    unsigned column_start=0, column_end = 0;
    //Find the x-location of the first node
    double x = local_nodes_pt[0]->x(0);
    //Find the number of values stored at the nodes 
    //(ASSUMED TO BE THE SAME FOR ALL NODES)
    unsigned n_value = local_nodes_pt[0]->nvalue();
    //Specify the symmetries of the u,v and p components
    int symm[3] = {-1,1,-1};
  
    //Loop over all other nodes
    for(unsigned n=1;n<n_node;n++)
     {
      //If the x-location has changed, then we
      //know all nodes in the column
      if(std::abs(local_nodes_pt[n]->x(0)-x) > 1.0e-14)
       {
        //Set the end of the previous column
        column_end = n-1;
        //Find the number of entries in the column
        unsigned n_entries = (column_end - column_start + 1);
        
        //Storage for "half" the number of nodes
        unsigned n_half=0;
        //Boolean to indicate whether there is an odd (or even) number of nodes
        bool odd = false;
  
        //Is the number of entries odd  (remainder mod 2 is non-zero)
        if(n_entries%2)
         {
          //Find the number of nodes in the half-domain
          n_half = (n_entries - 1)/2;
          odd = true;
         }
        //Otherwise the number is even
        else
         {
          n_half = n_entries/2;
         }
  
        //Loop over the variables stored at every node
        for(unsigned i=0;i<n_value;i++)
         {
          //If the symmetry is odd
          //The idea is to take the average of the sum of the absolute values 
          //located symmetrically about the centreline and set the new values
          //to be +average and -average, preserving the signs.
          if(symm[i]==-1)
           {
            //Set the middle to zero if we have an odd number of nodes
            if(odd) {local_nodes_pt[column_start+n_half]->set_value(i,0.0);}
            //Loop over the half-width
            for(unsigned n=0;n<n_half;n++)
             {
              //Get the values of the node
              Node* node1_pt = local_nodes_pt[column_start+n];
              Node* node2_pt = local_nodes_pt[column_end-n];
              double val1 = node1_pt->value(i);
              double val2 = node2_pt->value(i);
  
              //If the "lower value" is negative,
              //the "upper value" should be positive
              if(val1 < 0)
               {
                //Find the average of the absolute values
                //and set new values preserving the sign
                double average = 0.5*(val2-val1);
                val1 = -average; val2 = average;
               }
              //Otherwise the "lower value" is positive
              //the "upper value" is negative
              else if(val1 > 0)
               {
                //Find the average of the absolute values
                //and set new values preserving the sign
                double average = 0.5*(val1 - val2);
                val1 = average; val2 = -average;
               }
              //Otherwise both values should be zero
              else
               {
                val1 = val2 = 0.0;
               }
  
              //Set the values stored at the nodes
              node1_pt->set_value(i,val1);
              node2_pt->set_value(i,val2);
             }
           }
          //Otherwise the required symmetry is even
          //The idea is to take the simple average of the two values
          //located symmetrically about the midplane
          else
           {
            //Loop over the half-width
            for(unsigned n=0;n<n_half;n++)
             {
              //Get the values stored at the node
              Node* node1_pt = local_nodes_pt[column_start+n];
              Node* node2_pt = local_nodes_pt[column_end-n];
              double val1 = node1_pt->value(i);
              double val2 = node2_pt->value(i);
              //Find the average of the two values
              double average = 0.5*(val1+val2);
              //Set the new values to the average
              val1 = val2 = average;
              //Now actually set the values stored at the node
              node1_pt->set_value(i,val1);
              node2_pt->set_value(i,val2);
             }
           }
         }
        
        //Finally, set the new column start
        column_start = n; column_end=n;
        //Set the new x-location of the column
        x = local_nodes_pt[column_start]->x(0);
       }
     }
   }

References abs(), i, n, oomph::Data::set_value(), symm(), oomph::Node::value(), and plotDoE::x.

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

adaptive_pitchfork.cc

Public Member Functions

Additional Inherited Members

Detailed Description

template<class ELEMENT> class RefineablePorousChannelProblem< ELEMENT >

Constructor & Destructor Documentation

◆ RefineablePorousChannelProblem()

◆ ~RefineablePorousChannelProblem()

Member Function Documentation

◆ actions_after_adapt()

◆ actions_after_change_in_bifurcation_parameter()

◆ actions_before_implicit_timestep()

◆ make_copy()

◆ mesh_pt()

◆ set_boundary_conditions()

◆ symmetrise_eigenfunction_for_adaptive_pitchfork_tracking()

template<class ELEMENT>
class RefineablePorousChannelProblem< ELEMENT >