Inheritance diagram for DeformableFishPoissonProblem< ELEMENT >:

Public Member Functions
	DeformableFishPoissonProblem ()
	Constructor: More...

void	run ()
	Run simulation. More...

ElasticFishMesh< ELEMENT > *	mesh_pt ()
	Access function for the specific mesh. More...

void	doc_solution (DocInfo &doc_info)
	Doc the solution. More...

void	actions_after_newton_solve ()
	Update function (empty) More...

void	actions_before_newton_solve ()

void	actions_after_adapt ()
	Update after adapt: Pin all redundant solid pressure nodes (if required) More...

	DeformableFishPoissonProblem ()
	Constructor: More...

void	run ()
	Run simulation. More...

ElasticFishMesh< ELEMENT > *	mesh_pt ()
	Access function for the specific mesh. More...

void	doc_solution (DocInfo &doc_info)
	Doc the solution. More...

void	actions_after_newton_solve ()
	Update function (empty) More...

void	actions_before_newton_solve ()

void	actions_after_adapt ()
	Update after adapt: Pin all redundant solid pressure nodes (if required) More...

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 ()

Private Attributes
Node *	Doc_node_pt
	Node at which the solution of the Poisson equation is documented. More...

ofstream	Trace_file
	Trace file. More...

Circle *	Fish_back_pt

ElasticallySupportedRingElement *	Fish_back_pt

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

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

Public Attributes inherited from oomph::Problem
bool	Shut_up_in_newton_solve

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

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

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

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

virtual void	actions_before_newton_convergence_check ()

virtual void	actions_before_newton_step ()

virtual void	actions_after_newton_step ()

virtual void	actions_before_implicit_timestep ()

virtual void	actions_after_implicit_timestep ()

virtual void	actions_after_implicit_timestep_and_error_estimation ()

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

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

virtual void	actions_before_read_unstructured_meshes ()

virtual void	actions_after_read_unstructured_meshes ()

virtual void	actions_after_change_in_global_parameter (double *const &parameter_pt)

virtual void	actions_after_change_in_bifurcation_parameter ()

virtual void	actions_after_parameter_increase (double *const &parameter_pt)

double &	dof_derivative (const unsigned &i)

double &	dof_current (const unsigned &i)

virtual void	set_initial_condition ()

virtual double	global_temporal_error_norm ()

unsigned	newton_solve_continuation (double *const &parameter_pt)

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

void	calculate_continuation_derivatives (double *const &parameter_pt)

void	calculate_continuation_derivatives (const DoubleVector &z)

void	calculate_continuation_derivatives_fd (double *const &parameter_pt)

bool	does_pointer_correspond_to_problem_data (double *const &parameter_pt)

void	set_consistent_pinned_values_for_continuation ()

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

std::map< double *, bool >	Calculate_dparameter_analytic

bool	Calculate_hessian_products_analytic

LinearAlgebraDistribution *	Dof_distribution_pt

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

DoubleVectorWithHaloEntries	Element_count_per_dof

double	Relaxation_factor

double	Newton_solver_tolerance

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

unsigned	Nnewton_iter_taken

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

double	Max_residuals

bool	Time_adaptive_newton_crash_on_solve_fail

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

bool	Jacobian_has_been_computed

bool	Problem_is_nonlinear

bool	Pause_at_end_of_sparse_assembly

bool	Doc_time_in_distribute

unsigned	Sparse_assembly_method

unsigned	Sparse_assemble_with_arrays_initial_allocation

unsigned	Sparse_assemble_with_arrays_allocation_increment

Vector< Vector< unsigned > >	Sparse_assemble_with_arrays_previous_allocation

double	Numerical_zero_for_sparse_assembly

double	FD_step_used_in_get_hessian_vector_products

bool	Mass_matrix_reuse_is_enabled

bool	Mass_matrix_has_been_computed

bool	Discontinuous_element_formulation

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

double	Maximum_dt
	Maximum desired dt. More...

double	DTSF_max_increase

double	DTSF_min_decrease

double	Minimum_dt_but_still_proceed

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

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

double	Theta_squared

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

double	Continuation_direction

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

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

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

unsigned	Dof_derivative_offset

unsigned	Dof_current_offset

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

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

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

unsigned	Desired_newton_iterations_ds

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

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

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

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

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

bool	Use_finite_differences_for_continuation_derivatives

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

bool	Always_take_one_newton_step

double	Timestep_reduction_factor_after_nonconvergence

bool	Keep_temporal_error_below_tolerance

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

Detailed Description

template<class ELEMENT>
class DeformableFishPoissonProblem< ELEMENT >

//////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////// Solve Poisson equation on deforming fish-shaped domain. Mesh update via pseudo-elasticity.

Constructor & Destructor Documentation

◆ DeformableFishPoissonProblem() [1/2]

template<class ELEMENT >

DeformableFishPoissonProblem< ELEMENT >::DeformableFishPoissonProblem

Constructor:

Loop over elements and set pointers to source function

 {
  
  // Set coordinates and radius for the circle that will become the fish back
  double x_c=0.5;
  double y_c=0.0;
  double r_back=1.0;
  
  // Build geometric object that will become the deformable fish back
  //GeomObject* fish_back_pt=new ElasticFishBackElement(x_c,y_c,r_back);
  Fish_back_pt=new Circle(x_c,y_c,r_back);
  
  // Build geometric object that specifies the fish back in the
  // undeformed configuration (basically a deep copy of the previous one)
  GeomObject* undeformed_fish_back_pt=new Circle(x_c,y_c,r_back);
  
  // Build fish mesh with geometric object that specifies the deformable
  // and undeformed fish back 
  Problem::mesh_pt()=new ElasticFishMesh<ELEMENT>(Fish_back_pt,
                                                  undeformed_fish_back_pt);
  
  
  // Choose a node at which the solution is documented: Choose
  // the central node that is shared by all four elements in
  // the base mesh because it exists at all refinement levels.
  
  // How many nodes does element 0 have?
  unsigned nnod=mesh_pt()->finite_element_pt(0)->nnode();
  
  // The central node is the last node in element 0:
  Doc_node_pt=mesh_pt()->finite_element_pt(0)->node_pt(nnod-1);
  
  // Doc
  cout << std::endl <<  "Control node is located at: " 
       << Doc_node_pt->x(0) << " " << Doc_node_pt->x(1) << std::endl << std::endl;
  
  
  // Set error estimator
  Z2ErrorEstimator* error_estimator_pt=new Z2ErrorEstimator;
  mesh_pt()->spatial_error_estimator_pt()=error_estimator_pt;
  
  // Change/doc targets for mesh adaptation
  if (CommandLineArgs::Argc>1) 
   {
    mesh_pt()->max_permitted_error()=0.05;
    mesh_pt()->min_permitted_error()=0.005;
   }
  mesh_pt()->doc_adaptivity_targets(cout);
  
  
  // Specify BC/source fct for Poisson problem:
  //-------------------------------------------
  
  // Set the Poisson 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();
  for(unsigned ibound=0;ibound<num_bound;ibound++)
   {
    unsigned num_nod=mesh_pt()->nboundary_node(ibound);
    for (unsigned inod=0;inod<num_nod;inod++)
     {
      mesh_pt()->boundary_node_pt(ibound,inod)->pin(0); 
     }
   }
  
  // Set homogeneous boundary conditions for the Poisson equation 
  // on all boundaries 
  for(unsigned ibound=0;ibound<num_bound;ibound++)
   {
    // Loop over the nodes on boundary
    unsigned num_nod=mesh_pt()->nboundary_node(ibound);
    for (unsigned inod=0;inod<num_nod;inod++)
     {
      mesh_pt()->boundary_node_pt(ibound,inod)->set_value(0,0.0);
     }
   }
  
  unsigned n_element = mesh_pt()->nelement();
  for(unsigned i=0;i<n_element;i++)
   {
    // Upcast from FiniteElement to the present element
    ELEMENT *el_pt = dynamic_cast<ELEMENT*>(mesh_pt()->element_pt(i));
    
    //Set the source function pointer
    el_pt->source_fct_pt() = &ConstSourceForPoisson::get_source;
   }
  
  
  // Specify BC/source fct etc for (pseudo-)Solid problem
  //-----------------------------------------------------
  
  // Pin all nodal positions
  for(unsigned ibound=0;ibound<num_bound;ibound++)
   {
    unsigned num_nod=mesh_pt()->nboundary_node(ibound);
    for (unsigned inod=0;inod<num_nod;inod++)
     {
      for (unsigned i=0;i<2;i++)
       {
        mesh_pt()->boundary_node_pt(ibound,inod)->pin_position(i); 
       }
     }
   }
  
  //Loop over the elements in the mesh to set Solid parameters/function pointers
  for(unsigned i=0;i<n_element;i++)
   {
    //Cast to a solid element
    ELEMENT *el_pt = dynamic_cast<ELEMENT*>(mesh_pt()->element_pt(i));
    
    // Set the constitutive law
    el_pt->constitutive_law_pt() =
     Global_Physical_Variables::Constitutive_law_pt;
   }
  
  // Pin the redundant solid pressures (if any)
  PVDEquationsBase<2>::pin_redundant_nodal_solid_pressures(
   mesh_pt()->element_pt());
  
  
  //Attach the boundary conditions to the mesh
  cout << assign_eqn_numbers() << std::endl; 
  
  // Refine the problem uniformly (this automatically passes the
  // function pointers/parameters to the finer elements
  refine_uniformly();
  
  // The non-pinned positions of the newly SolidNodes will have been
  // determined by interpolation. Update all solid nodes based on 
  // the Mesh's Domain/MacroElement representation.
  bool update_all_solid_nodes=true;
  mesh_pt()->node_update(update_all_solid_nodes);
  
  // Now set the Eulerian equal to the Lagrangian coordinates
  mesh_pt()->set_lagrangian_nodal_coordinates();
  
 } 

References oomph::CommandLineArgs::Argc, Global_Physical_Variables::Constitutive_law_pt, MeshRefinement::error_estimator_pt, ConstSourceForPoisson::get_source(), and i.

◆ DeformableFishPoissonProblem() [2/2]

template<class ELEMENT >

DeformableFishPoissonProblem< ELEMENT >::DeformableFishPoissonProblem ( )

Constructor:

Member Function Documentation

◆ actions_after_adapt() [1/2]

template<class ELEMENT >

void DeformableFishPoissonProblem< ELEMENT >::actions_after_adapt ( )

inlinevirtual

Update after adapt: Pin all redundant solid pressure nodes (if required)

Reimplemented from oomph::Problem.

   { 
    // Pin the redundant solid pressures (if any)
    PVDEquationsBase<2>::pin_redundant_nodal_solid_pressures(
     mesh_pt()->element_pt());
   }

◆ actions_after_adapt() [2/2]

template<class ELEMENT >

void DeformableFishPoissonProblem< ELEMENT >::actions_after_adapt ( )

inlinevirtual

Update after adapt: Pin all redundant solid pressure nodes (if required)

Reimplemented from oomph::Problem.

   { 
    // Pin the redundant solid pressures (if any)
    PVDEquationsBase<2>::pin_redundant_nodal_solid_pressures(
     mesh_pt()->element_pt());
   }

◆ actions_after_newton_solve() [1/2]

template<class ELEMENT >

void DeformableFishPoissonProblem< ELEMENT >::actions_after_newton_solve ( )

inlinevirtual

Update function (empty)

Reimplemented from oomph::Problem.

196 {}

◆ actions_after_newton_solve() [2/2]

template<class ELEMENT >

void DeformableFishPoissonProblem< ELEMENT >::actions_after_newton_solve ( )

inlinevirtual

Update function (empty)

Reimplemented from oomph::Problem.

199 {}

◆ actions_before_newton_solve() [1/2]

template<class ELEMENT >

void DeformableFishPoissonProblem< ELEMENT >::actions_before_newton_solve ( )

inlinevirtual

Update before solve: We're dealing with a static problem so the nodal positions before the next solve merely serve as initial conditions. For meshes that are very strongly refined near the boundary, the update of the displacement boundary conditions (which only moves the SolidNodes on the boundary), can lead to strongly distorted meshes. This can cause the Newton method to fail --> the overall method is actually more robust if we use the nodal positions as determined by the Domain/MacroElement- based mesh update as initial guesses.

Reimplemented from oomph::Problem.

   { 
    bool update_all_solid_nodes=true;
    mesh_pt()->node_update(update_all_solid_nodes);
  
    // Now set the Eulerian equal to the Lagrangian coordinates
    mesh_pt()->set_lagrangian_nodal_coordinates();
  
   }   

◆ actions_before_newton_solve() [2/2]

template<class ELEMENT >

void DeformableFishPoissonProblem< ELEMENT >::actions_before_newton_solve ( )

inlinevirtual

Update before solve: We're dealing with a static problem so the nodal positions before the next solve merely serve as initial conditions. For meshes that are very strongly refined near the boundary, the update of the displacement boundary conditions (which only moves the SolidNodes on the boundary), can lead to strongly distorted meshes. This can cause the Newton method to fail --> the overall method is actually more robust if we use the nodal positions as determined by the Domain/MacroElement- based mesh update as initial guesses.

Reimplemented from oomph::Problem.

   { 
    bool update_all_solid_nodes=true;
    mesh_pt()->node_update(update_all_solid_nodes);
   }   

◆ doc_solution() [1/2]

template<class ELEMENT >

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

Doc the solution.

 {
  ofstream some_file;
  char filename[100];
  
  // Number of plot points
  unsigned npts = 5; 
  
  // Call output function for all elements
  sprintf(filename,"%s/soln%i.dat",doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  mesh_pt()->output(some_file,npts);
  some_file.close();
  
  
  // Write vertical position of the fish back, and solution at 
  // control node to trace file
  Trace_file 
   << static_cast<Circle*>(mesh_pt()->fish_back_pt())->y_c()
   << " " << Doc_node_pt->value(0) << std::endl;
  
 }

References oomph::DocInfo::directory(), MergeRestartFiles::filename, oomph::DocInfo::number(), and oomph::Problem_Parameter::Trace_file.

◆ doc_solution() [2/2]

template<class ELEMENT >

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

Doc the solution.

◆ mesh_pt() [1/2]

template<class ELEMENT >

ElasticFishMesh<ELEMENT>* DeformableFishPoissonProblem< ELEMENT >::mesh_pt ( )

inline

Access function for the specific mesh.

190 {return dynamic_cast<ElasticFishMesh<ELEMENT>*>(Problem::mesh_pt());}

◆ mesh_pt() [2/2]

template<class ELEMENT >

ElasticFishMesh<ELEMENT>* DeformableFishPoissonProblem< ELEMENT >::mesh_pt ( )

inline

Access function for the specific mesh.

193 {return dynamic_cast<ElasticFishMesh<ELEMENT>*>(Problem::mesh_pt());}

◆ run() [1/2]

template<class ELEMENT >

void DeformableFishPoissonProblem< ELEMENT >::run

Run simulation.

Run the problem.

 {
  
  // Output
  DocInfo doc_info;
  
  // Set output directory
  doc_info.set_directory("RESLT");
  
  // Step number
  doc_info.number()=0;
  
  // Open trace file
  char filename[100];
  sprintf(filename,"%s/trace.dat",doc_info.directory().c_str());
  Trace_file.open(filename);
  
  Trace_file << "VARIABLES=\"y<sub>circle</sub>\",\"u<sub>control</sub>\""
             << std::endl;
  
   //Parameter incrementation
  unsigned nstep=5; 
  for(unsigned i=0;i<nstep;i++)
   {
    //Solve the problem with Newton's method, allowing for up to 2
    //rounds of adaptation
    newton_solve(2);
  
    // Doc solution
    doc_solution(doc_info);
    doc_info.number()++;
  
    // Increment width of fish domain
    Fish_back_pt->y_c()+=0.3;
   }
  
 }

References oomph::DocInfo::directory(), MergeRestartFiles::filename, i, oomph::DocInfo::number(), oomph::DocInfo::set_directory(), and oomph::Problem_Parameter::Trace_file.

◆ run() [2/2]

template<class ELEMENT >

void DeformableFishPoissonProblem< ELEMENT >::run ( )

Run simulation.

Member Data Documentation

◆ Doc_node_pt

template<class ELEMENT >

Node * DeformableFishPoissonProblem< ELEMENT >::Doc_node_pt

private

Node at which the solution of the Poisson equation is documented.

◆ Fish_back_pt [1/2]

template<class ELEMENT >

Circle* DeformableFishPoissonProblem< ELEMENT >::Fish_back_pt

private

◆ Fish_back_pt [2/2]

template<class ELEMENT >

ElasticallySupportedRingElement* DeformableFishPoissonProblem< ELEMENT >::Fish_back_pt

private

◆ Trace_file

template<class ELEMENT >

ofstream DeformableFishPoissonProblem< ELEMENT >::Trace_file

private

Trace file.

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

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

template<class ELEMENT> class DeformableFishPoissonProblem< ELEMENT >

Constructor & Destructor Documentation

◆ DeformableFishPoissonProblem() [1/2]

◆ DeformableFishPoissonProblem() [2/2]

Member Function Documentation

◆ actions_after_adapt() [1/2]

◆ actions_after_adapt() [2/2]

◆ actions_after_newton_solve() [1/2]

◆ actions_after_newton_solve() [2/2]

◆ actions_before_newton_solve() [1/2]

◆ actions_before_newton_solve() [2/2]

◆ doc_solution() [1/2]

◆ doc_solution() [2/2]

◆ mesh_pt() [1/2]

◆ mesh_pt() [2/2]

◆ run() [1/2]

◆ run() [2/2]

Member Data Documentation

◆ Doc_node_pt

◆ Fish_back_pt [1/2]

◆ Fish_back_pt [2/2]

◆ Trace_file

template<class ELEMENT>
class DeformableFishPoissonProblem< ELEMENT >