Poisson problem in refineable eighth of a sphere mesh. More...

Inheritance diagram for EighthSpherePoissonProblem< ELEMENT >:

Public Member Functions
	EighthSpherePoissonProblem (PoissonEquations< 3 >::PoissonSourceFctPt source_fct_pt)
	Constructor: Pass pointer to source function. More...

	~EighthSpherePoissonProblem ()
	Destructor: Empty. More...

RefineableEighthSphereMesh< ELEMENT > *	mesh_pt ()

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

void	actions_before_newton_solve ()

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

	EighthSpherePoissonProblem (PoissonEquations< 3 >::PoissonSourceFctPt source_fct_pt)
	Constructor: Pass pointer to source function. More...

	~EighthSpherePoissonProblem ()
	Destructor: Empty. More...

RefineableEighthSphereMesh< ELEMENT > *	mesh_pt ()

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

void	actions_before_adapt ()

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

void	actions_before_newton_solve ()

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

	EighthSpherePoissonProblem (PoissonEquations< 3 >::PoissonSourceFctPt source_fct_pt)
	Constructor: Pass pointer to source function. More...

	~EighthSpherePoissonProblem ()
	Destructor: Empty. More...

RefineableEighthSphereMesh< ELEMENT > *	mesh_pt ()

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

void	actions_before_newton_solve ()

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

	EighthSpherePoissonProblem (PoissonEquations< 3 >::PoissonSourceFctPt source_fct_pt)
	Constructor: Pass pointer to source function. More...

	~EighthSpherePoissonProblem ()
	Destructor: Empty. More...

RefineableEighthSphereMesh< ELEMENT > *	mesh_pt ()

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

void	actions_before_newton_solve ()

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

	EighthSpherePoissonProblem (PoissonEquations< 3 >::PoissonSourceFctPt source_fct_pt, const unsigned &h_power)
	Constructor: Pass pointer to source function. More...

	~EighthSpherePoissonProblem ()
	Destructor: Empty. More...

RefineableEighthSphereMesh< ELEMENT > *	mesh_pt ()

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

void	actions_before_newton_solve ()

void	doc_solution (DocInfo &doc_info, ostream &convergence_file)
	Doc the solution. 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

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
PoissonEquations< 3 >::PoissonSourceFctPt	Source_fct_pt
	Pointer to source function. More...

unsigned	H_power
	Exponent for h scaling. More...

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

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

Public Attributes inherited from oomph::Problem
bool	Shut_up_in_newton_solve

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

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

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

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

virtual void	actions_before_newton_convergence_check ()

virtual void	actions_before_newton_step ()

virtual void	actions_after_newton_step ()

virtual void	actions_before_implicit_timestep ()

virtual void	actions_after_implicit_timestep ()

virtual void	actions_after_implicit_timestep_and_error_estimation ()

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

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

virtual void	actions_before_read_unstructured_meshes ()

virtual void	actions_after_read_unstructured_meshes ()

virtual void	actions_after_change_in_global_parameter (double *const &parameter_pt)

virtual void	actions_after_change_in_bifurcation_parameter ()

virtual void	actions_after_parameter_increase (double *const &parameter_pt)

double &	dof_derivative (const unsigned &i)

double &	dof_current (const unsigned &i)

virtual void	set_initial_condition ()

virtual double	global_temporal_error_norm ()

unsigned	newton_solve_continuation (double *const &parameter_pt)

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

void	calculate_continuation_derivatives (double *const &parameter_pt)

void	calculate_continuation_derivatives (const DoubleVector &z)

void	calculate_continuation_derivatives_fd (double *const &parameter_pt)

bool	does_pointer_correspond_to_problem_data (double *const &parameter_pt)

void	set_consistent_pinned_values_for_continuation ()

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

std::map< double *, bool >	Calculate_dparameter_analytic

bool	Calculate_hessian_products_analytic

LinearAlgebraDistribution *	Dof_distribution_pt

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

DoubleVectorWithHaloEntries	Element_count_per_dof

double	Relaxation_factor

double	Newton_solver_tolerance

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

unsigned	Nnewton_iter_taken

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

double	Max_residuals

bool	Time_adaptive_newton_crash_on_solve_fail

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

bool	Jacobian_has_been_computed

bool	Problem_is_nonlinear

bool	Pause_at_end_of_sparse_assembly

bool	Doc_time_in_distribute

unsigned	Sparse_assembly_method

unsigned	Sparse_assemble_with_arrays_initial_allocation

unsigned	Sparse_assemble_with_arrays_allocation_increment

Vector< Vector< unsigned > >	Sparse_assemble_with_arrays_previous_allocation

double	Numerical_zero_for_sparse_assembly

double	FD_step_used_in_get_hessian_vector_products

bool	Mass_matrix_reuse_is_enabled

bool	Mass_matrix_has_been_computed

bool	Discontinuous_element_formulation

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

double	Maximum_dt
	Maximum desired dt. More...

double	DTSF_max_increase

double	DTSF_min_decrease

double	Minimum_dt_but_still_proceed

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

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

double	Theta_squared

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

double	Continuation_direction

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

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

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

unsigned	Dof_derivative_offset

unsigned	Dof_current_offset

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

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

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

unsigned	Desired_newton_iterations_ds

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

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

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

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

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

bool	Use_finite_differences_for_continuation_derivatives

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

bool	Always_take_one_newton_step

double	Timestep_reduction_factor_after_nonconvergence

bool	Keep_temporal_error_below_tolerance

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

Detailed Description

template<class ELEMENT>
class EighthSpherePoissonProblem< ELEMENT >

Poisson problem in refineable eighth of a sphere mesh.

///////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////

Constructor & Destructor Documentation

◆ EighthSpherePoissonProblem() [1/5]

template<class ELEMENT >

EighthSpherePoissonProblem< ELEMENT >::EighthSpherePoissonProblem ( PoissonEquations< 3 >::PoissonSourceFctPt source_fct_pt )

Constructor: Pass pointer to source function.

Constructor for Poisson problem on eighth of a sphere mesh.

Create mesh for sphere of radius 5

                                                         : 
          Source_fct_pt(source_fct_pt)
 { 
  
  // Setup parameters for exact tanh solution
  // Steepness of step
  TanhSolnForPoisson::Alpha=50.0;
  
  double radius=5.0; 
  Problem::mesh_pt() = new RefineableEighthSphereMesh<ELEMENT>(radius);
  
  // Set error estimator 
  Z2ErrorEstimator* error_estimator_pt=new Z2ErrorEstimator;
  mesh_pt()->spatial_error_estimator_pt()=error_estimator_pt;
  
  // Adjust error targets for adaptive refinement
  if (CommandLineArgs::Argc>1)
   {
    // Validation: Relax tolerance to get nonuniform refinement during
    // first step
    mesh_pt()->max_permitted_error()=0.7;
    mesh_pt()->min_permitted_error()=0.5;
   }
  else
   {
    mesh_pt()->max_permitted_error()=0.01;
    mesh_pt()->min_permitted_error()=0.001;
   } // end adjustment
  
  //Doc the mesh boundaries
  ofstream some_file;
  some_file.open("boundaries.dat");
  mesh_pt()->output_boundaries(some_file);
  some_file.close();
  
  // Set the boundary conditions for this problem: All nodes are
  // free by default -- just pin the ones that have Dirichlet conditions
  // here (all the nodes on the boundary)
  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); 
     }
   } // end of pinning
  
  
  //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 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() = Source_fct_pt;
   }
  
  // Setup equation numbering 
  cout <<"Number of equations: " << assign_eqn_numbers() << std::endl; 
  
 } // end of constructor

References TanhSolnForPoisson::Alpha, oomph::CommandLineArgs::Argc, oomph::Problem::assign_eqn_numbers(), MeshRefinement::error_estimator_pt, i, EighthSpherePoissonProblem< ELEMENT >::mesh_pt(), UniformPSDSelfTest::radius, and EighthSpherePoissonProblem< ELEMENT >::Source_fct_pt.

◆ ~EighthSpherePoissonProblem() [1/5]

template<class ELEMENT >

EighthSpherePoissonProblem< ELEMENT >::~EighthSpherePoissonProblem ( )

inline

Destructor: Empty.

141 {}

◆ EighthSpherePoissonProblem() [2/5]

template<class ELEMENT >

EighthSpherePoissonProblem< ELEMENT >::EighthSpherePoissonProblem ( PoissonEquations< 3 >::PoissonSourceFctPt source_fct_pt )

Constructor: Pass pointer to source function.

◆ ~EighthSpherePoissonProblem() [2/5]

template<class ELEMENT >

EighthSpherePoissonProblem< ELEMENT >::~EighthSpherePoissonProblem ( )

inline

Destructor: Empty.

142 {}

◆ EighthSpherePoissonProblem() [3/5]

template<class ELEMENT >

EighthSpherePoissonProblem< ELEMENT >::EighthSpherePoissonProblem ( PoissonEquations< 3 >::PoissonSourceFctPt source_fct_pt )

Constructor: Pass pointer to source function.

◆ ~EighthSpherePoissonProblem() [3/5]

template<class ELEMENT >

EighthSpherePoissonProblem< ELEMENT >::~EighthSpherePoissonProblem ( )

inline

Destructor: Empty.

149 {}

◆ EighthSpherePoissonProblem() [4/5]

template<class ELEMENT >

EighthSpherePoissonProblem< ELEMENT >::EighthSpherePoissonProblem ( PoissonEquations< 3 >::PoissonSourceFctPt source_fct_pt )

Constructor: Pass pointer to source function.

◆ ~EighthSpherePoissonProblem() [4/5]

template<class ELEMENT >

EighthSpherePoissonProblem< ELEMENT >::~EighthSpherePoissonProblem ( )

inline

Destructor: Empty.

   {
    delete mesh_pt()->spatial_error_estimator_pt();
    delete Problem::mesh_pt();
   }

◆ EighthSpherePoissonProblem() [5/5]

template<class ELEMENT >

EighthSpherePoissonProblem< ELEMENT >::EighthSpherePoissonProblem	(	PoissonEquations< 3 >::PoissonSourceFctPt	source_fct_pt,
		const unsigned &	h_power
	)

Constructor: Pass pointer to source function.

◆ ~EighthSpherePoissonProblem() [5/5]

template<class ELEMENT >

EighthSpherePoissonProblem< ELEMENT >::~EighthSpherePoissonProblem ( )

inline

Destructor: Empty.

143 {}

Member Function Documentation

◆ actions_after_adapt()

template<class ELEMENT >

void EighthSpherePoissonProblem< ELEMENT >::actions_after_adapt ( )

inlinevirtual

Actions that are to be performed after a mesh adaptation.

Reimplemented from oomph::Problem.

   {
    //Doc the mesh boundaries
    ofstream some_file;
    some_file.open("boundaries_end.dat");
    mesh_pt()->output_boundaries(some_file);
    some_file.close();
   }

◆ actions_after_newton_solve() [1/5]

template<class ELEMENT >

void EighthSpherePoissonProblem< ELEMENT >::actions_after_newton_solve ( )

inlinevirtual

Update the problem specs after solve (empty)

Reimplemented from oomph::Problem.

151 {}

◆ actions_after_newton_solve() [2/5]

template<class ELEMENT >

void EighthSpherePoissonProblem< ELEMENT >::actions_after_newton_solve ( )

inlinevirtual

Update the problem specs after solve (empty)

Reimplemented from oomph::Problem.

163 {}

◆ actions_after_newton_solve() [3/5]

template<class ELEMENT >

void EighthSpherePoissonProblem< ELEMENT >::actions_after_newton_solve ( )

inlinevirtual

Update the problem specs after solve (empty)

Reimplemented from oomph::Problem.

159 {}

◆ actions_after_newton_solve() [4/5]

template<class ELEMENT >

void EighthSpherePoissonProblem< ELEMENT >::actions_after_newton_solve ( )

inlinevirtual

Update the problem specs after solve (empty)

Reimplemented from oomph::Problem.

157 {}

◆ actions_after_newton_solve() [5/5]

template<class ELEMENT >

void EighthSpherePoissonProblem< ELEMENT >::actions_after_newton_solve ( )

inlinevirtual

Update the problem specs after solve (empty)

Reimplemented from oomph::Problem.

153 {}

◆ actions_before_adapt()

template<class ELEMENT >

void EighthSpherePoissonProblem< ELEMENT >::actions_before_adapt ( )

inlinevirtual

Actions that are to be performed before a mesh adaptation. These might include removing any additional elements, such as traction boundary elements before the adaptation.

Reimplemented from oomph::Problem.

160 {}

◆ actions_before_newton_solve() [1/5]

template<class ELEMENT >

void EighthSpherePoissonProblem< ELEMENT >::actions_before_newton_solve ( )

inlinevirtual

Update the problem specs before solve: Set Dirchlet boundary conditions from exact solution.

Reimplemented from oomph::Problem.

  {
   //Loop over the boundaries
   unsigned num_bound = mesh_pt()->nboundary();
   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++)
     {
      Node* nod_pt=mesh_pt()->boundary_node_pt(ibound,inod);
      double u;
      Vector<double> x(3);
      x[0]=nod_pt->x(0);
      x[1]=nod_pt->x(1);
      x[2]=nod_pt->x(2);
      TanhSolnForPoisson::get_exact_u(x,u);
      nod_pt->set_value(0,u);
     }
    }
  }

References TanhSolnForPoisson::get_exact_u(), oomph::Data::set_value(), plotDoE::x, and oomph::Node::x().

◆ actions_before_newton_solve() [2/5]

template<class ELEMENT >

void EighthSpherePoissonProblem< ELEMENT >::actions_before_newton_solve ( )

inlinevirtual

Update the problem specs before solve: Set Dirchlet boundary conditions from exact solution.

Reimplemented from oomph::Problem.

  {
   //Loop over the boundaries
   unsigned num_bound = mesh_pt()->nboundary();
   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++)
     {
      Node* nod_pt=mesh_pt()->boundary_node_pt(ibound,inod);
      // Pin
      nod_pt->pin(0);
      // Set value
      double u;
      Vector<double> x(3);
      x[0]=nod_pt->x(0);
      x[1]=nod_pt->x(1);
      x[2]=nod_pt->x(2);
      TanhSolnForPoisson::get_exact_u(x,u);
      nod_pt->set_value(0,u);
     }
    }
  }

References TanhSolnForPoisson::get_exact_u(), oomph::Data::pin(), oomph::Data::set_value(), plotDoE::x, and oomph::Node::x().

◆ actions_before_newton_solve() [3/5]

template<class ELEMENT >

void EighthSpherePoissonProblem< ELEMENT >::actions_before_newton_solve ( )

inlinevirtual

Update the problem specs before solve: Set Dirchlet boundary conditions from exact solution.

Reimplemented from oomph::Problem.

  {
   //Loop over the boundaries
   unsigned num_bound = mesh_pt()->nboundary();
   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++)
     {
      Node* nod_pt=mesh_pt()->boundary_node_pt(ibound,inod);
      double u;
      Vector<double> x(3);
      x[0]=nod_pt->x(0);
      x[1]=nod_pt->x(1);
      x[2]=nod_pt->x(2);
      TanhSolnForPoisson::get_exact_u(x,u);
      nod_pt->set_value(0,u);
     }
    }
  }

References TanhSolnForPoisson::get_exact_u(), oomph::Data::set_value(), plotDoE::x, and oomph::Node::x().

◆ actions_before_newton_solve() [4/5]

template<class ELEMENT >

void EighthSpherePoissonProblem< ELEMENT >::actions_before_newton_solve ( )

inlinevirtual

Update the problem specs before solve: Set Dirchlet boundary conditions from exact solution.

Reimplemented from oomph::Problem.

  {
   //Loop over the boundaries
   unsigned num_bound = mesh_pt()->nboundary();
   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++)
     {
      Node* nod_pt=mesh_pt()->boundary_node_pt(ibound,inod);
      double u;
      Vector<double> x(3);
      x[0]=nod_pt->x(0);
      x[1]=nod_pt->x(1);
      x[2]=nod_pt->x(2);
      TanhSolnForPoisson::get_exact_u(x,u);
      nod_pt->set_value(0,u);
     }
    }
  }

References TanhSolnForPoisson::get_exact_u(), oomph::Data::set_value(), plotDoE::x, and oomph::Node::x().

◆ actions_before_newton_solve() [5/5]

template<class ELEMENT >

void EighthSpherePoissonProblem< ELEMENT >::actions_before_newton_solve ( )

inlinevirtual

Update the problem specs before solve: Set Dirchlet boundary conditions from exact solution.

Reimplemented from oomph::Problem.

  {
   //Loop over the boundaries
   unsigned num_bound = mesh_pt()->nboundary();
   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++)
     {
      Node* nod_pt=mesh_pt()->boundary_node_pt(ibound,inod);
      double u;
      Vector<double> x(3);
      x[0]=nod_pt->x(0);
      x[1]=nod_pt->x(1);
      x[2]=nod_pt->x(2);
      TanhSolnForPoisson::get_exact_u(x,u);
      nod_pt->set_value(0,u);
     }
    }
  }

References TanhSolnForPoisson::get_exact_u(), oomph::Data::set_value(), plotDoE::x, and oomph::Node::x().

◆ doc_solution() [1/5]

template<class ELEMENT >

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

Doc the solution.

 {
  ofstream some_file;
  char filename[100];
  
  // Number of plot points
  unsigned npts;
  npts=5; 
  
  
  // Output solution 
  //-----------------
  sprintf(filename,"%s/soln%i.dat",doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  mesh_pt()->output(some_file,npts);
  some_file.close();
  
  
  // Output exact solution 
  //----------------------
  sprintf(filename,"%s/exact_soln%i.dat",doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  mesh_pt()->output_fct(some_file,npts,TanhSolnForPoisson::get_exact_u); 
  some_file.close();
  
  
  // Doc error
  //----------
  double error,norm;
  sprintf(filename,"%s/error%i.dat",doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  mesh_pt()->compute_error(some_file,TanhSolnForPoisson::get_exact_u,
                           error,norm); 
  some_file.close();
  cout << "error: " << sqrt(error) << std::endl; 
  cout << "norm : " << sqrt(norm) << std::endl << std::endl;
  
 } // end of doc

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

◆ doc_solution() [2/5]

template<class ELEMENT >

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

Doc the solution.

◆ doc_solution() [3/5]

template<class ELEMENT >

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

Doc the solution.

◆ doc_solution() [4/5]

template<class ELEMENT >

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

Doc the solution.

◆ doc_solution() [5/5]

template<class ELEMENT >

void EighthSpherePoissonProblem< ELEMENT >::doc_solution	(	DocInfo &	doc_info,
		ostream &	convergence_file
	)

Doc the solution.

 {
  ofstream some_file;
  char filename[100];
  
  // Number of plot points
  unsigned npts;
  npts=5; 
  
  
  
  // Switch on full validation during self test
  if (CommandLineArgs::Argc>1)
   {
  
    // Output boundaries
    //------------------
    sprintf(filename,"%s/boundaries.dat",doc_info.directory().c_str());
    some_file.open(filename);
    mesh_pt()->output_boundaries(some_file);
    some_file.close();
  
    // Output solution 
    //-----------------
    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();
    
    
    // Output exact solution 
    //----------------------
    sprintf(filename,"%s/exact_soln%i.dat",doc_info.directory().c_str(),
            doc_info.number());
    some_file.open(filename);
    mesh_pt()->output_fct(some_file,npts,TanhSolnForPoisson::get_exact_u); 
    some_file.close();
   }
  
  
  // Doc error
  //----------
  double error,norm;
  sprintf(filename,"%s/error%i.dat",doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  mesh_pt()->compute_error(some_file,TanhSolnForPoisson::get_exact_u,
                           error,norm); 
  some_file.close();
  cout << "error: " << sqrt(error) << std::endl; 
  cout << "norm : " << sqrt(norm) << std::endl << std::endl;
  
  double log_h=log(1.0/double(pow(2.0,int(H_power))));
  convergence_file << log_h << " "  
                   << log(sqrt(error)) << " ";
  
  unsigned nnode_1d=mesh_pt()->finite_element_pt(0)->nnode_1d();
  switch (nnode_1d)
   {
   case 2:
    convergence_file << 2.0*log_h+4.0 << " ";
    break;
  
   case 3:
    convergence_file << 3.0*log_h+4.0 << " ";
    break;
  
   case 4:
    convergence_file << 4.0*log_h+4.0 << " ";
    break;
  
   default:
    throw OomphLibError("Never get here",
                        OOMPH_CURRENT_FUNCTION,
                        OOMPH_EXCEPTION_LOCATION);
   }
  
   convergence_file << sqrt(norm) << std::endl;
  
  
 } // end of doc

References oomph::CommandLineArgs::Argc, oomph::DocInfo::directory(), calibrate::error, MergeRestartFiles::filename, TanhSolnForPoisson::get_exact_u(), Eigen::bfloat16_impl::log(), oomph::DocInfo::number(), OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION, Eigen::ArrayBase< Derived >::pow(), and sqrt().

◆ mesh_pt() [1/5]

template<class ELEMENT >

RefineableEighthSphereMesh<ELEMENT>* EighthSpherePoissonProblem< ELEMENT >::mesh_pt ( )

inline

Overload generic access function by one that returns a pointer to the specific mesh

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

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

◆ mesh_pt() [2/5]

template<class ELEMENT >

RefineableEighthSphereMesh<ELEMENT>* EighthSpherePoissonProblem< ELEMENT >::mesh_pt ( )

inline

Overload generic access function by one that returns a pointer to the specific mesh

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

◆ mesh_pt() [3/5]

template<class ELEMENT >

RefineableEighthSphereMesh<ELEMENT>* EighthSpherePoissonProblem< ELEMENT >::mesh_pt ( )

inline

Overload generic access function by one that returns a pointer to the specific mesh

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

◆ mesh_pt() [4/5]

template<class ELEMENT >

RefineableEighthSphereMesh<ELEMENT>* EighthSpherePoissonProblem< ELEMENT >::mesh_pt ( )

inline

Overload generic access function by one that returns a pointer to the specific mesh

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

◆ mesh_pt() [5/5]

template<class ELEMENT >

RefineableEighthSphereMesh<ELEMENT>* EighthSpherePoissonProblem< ELEMENT >::mesh_pt ( )

inline

Overload generic access function by one that returns a pointer to the specific mesh

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

Member Data Documentation

◆ H_power

template<class ELEMENT >

unsigned EighthSpherePoissonProblem< ELEMENT >::H_power

private

Exponent for h scaling.

◆ Source_fct_pt

template<class ELEMENT >

PoissonEquations< 3 >::PoissonSourceFctPt EighthSpherePoissonProblem< ELEMENT >::Source_fct_pt

private

Pointer to source function.

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

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 EighthSpherePoissonProblem< ELEMENT >

Constructor & Destructor Documentation

◆ EighthSpherePoissonProblem() [1/5]

◆ ~EighthSpherePoissonProblem() [1/5]

◆ EighthSpherePoissonProblem() [2/5]

◆ ~EighthSpherePoissonProblem() [2/5]

◆ EighthSpherePoissonProblem() [3/5]

◆ ~EighthSpherePoissonProblem() [3/5]

◆ EighthSpherePoissonProblem() [4/5]

◆ ~EighthSpherePoissonProblem() [4/5]

◆ EighthSpherePoissonProblem() [5/5]

◆ ~EighthSpherePoissonProblem() [5/5]

Member Function Documentation

◆ actions_after_adapt()

◆ actions_after_newton_solve() [1/5]

◆ actions_after_newton_solve() [2/5]

◆ actions_after_newton_solve() [3/5]

◆ actions_after_newton_solve() [4/5]

◆ actions_after_newton_solve() [5/5]

◆ actions_before_adapt()

◆ actions_before_newton_solve() [1/5]

◆ actions_before_newton_solve() [2/5]

◆ actions_before_newton_solve() [3/5]

◆ actions_before_newton_solve() [4/5]

◆ actions_before_newton_solve() [5/5]

◆ doc_solution() [1/5]

◆ doc_solution() [2/5]

◆ doc_solution() [3/5]

◆ doc_solution() [4/5]

◆ doc_solution() [5/5]

◆ mesh_pt() [1/5]

◆ mesh_pt() [2/5]

◆ mesh_pt() [3/5]

◆ mesh_pt() [4/5]

◆ mesh_pt() [5/5]

Member Data Documentation

◆ H_power

◆ Source_fct_pt

template<class ELEMENT>
class EighthSpherePoissonProblem< ELEMENT >