Class definition. More...

Inheritance diagram for UnstructuredPoissonProblem< ELEMENT >:

Public Member Functions
	UnstructuredPoissonProblem ()
	Constructor. More...

	~UnstructuredPoissonProblem ()
	Destructor. More...

void	actions_before_adapt ()
	Actions before adapt. Empty. More...

void	actions_after_adapt ()

void	actions_after_newton_solve ()
	Update after solve (empty) More...

void	actions_before_newton_solve ()
	Update the problem specs before solve: Re-apply boundary conditons. More...

void	doc_solution (const std::string &comment="")
	Doc the solution. More...

	UnstructuredPoissonProblem ()
	Constructor. More...

	~UnstructuredPoissonProblem ()
	Destructor. More...

void	actions_after_newton_solve ()
	Update after solve (empty) More...

void	actions_before_newton_solve ()
	Update the problem specs before solve: Re-apply boundary conditons. More...

void	doc_solution (const std::string &comment="")
	Doc the solution. More...

	UnstructuredPoissonProblem ()
	Constructor. More...

	~UnstructuredPoissonProblem ()
	Destructor. More...

void	actions_before_adapt ()
	Actions before adapt. Empty. More...

void	actions_after_adapt ()

void	actions_after_newton_solve ()
	Update after solve (empty) More...

void	actions_before_newton_solve ()
	Update the problem specs before solve: Re-apply boundary conditons. More...

void	doc_solution (const std::string &comment="")
	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 Member Functions
void	apply_boundary_conditions ()
	Helper function to apply boundary conditions. More...

void	complete_problem_setup ()

void	apply_boundary_conditions ()
	Helper function to apply boundary conditions. More...

void	complete_problem_setup ()

void	apply_boundary_conditions ()
	Helper function to apply boundary conditions. More...

void	complete_problem_setup ()

Private Attributes
DocInfo	Doc_info
	Doc info object for labeling output. More...

RefineableTriangleMesh< ELEMENT > *	My_mesh_pt
	Pointers to specific mesh. More...

ofstream	Trace_file
	Trace file to document norm of solution. More...

TriangleMesh< ELEMENT > *	My_mesh_pt
	Pointers to specific mesh. 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 UnstructuredPoissonProblem< ELEMENT >

Class definition.

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

Constructor & Destructor Documentation

◆ UnstructuredPoissonProblem() [1/3]

template<class ELEMENT >

UnstructuredPoissonProblem< ELEMENT >::UnstructuredPoissonProblem

Constructor.

 {          
  // Intrinsic coordinate along GeomObject
  Vector<double> zeta(1);
  
  // Position vector on GeomObject
  Vector<double> posn(2);
  
  // Ellipse defining the outer boundary
  double x_center = 0.0;
  double y_center = 0.0;
  double A = 1.0;
  double B = 1.0;
  Ellipse * outer_boundary_ellipse_pt = new Ellipse(A,B);
  
  // Pointer to the closed curve that defines the outer boundary
  TriangleMeshClosedCurve* closed_curve_pt=0;
  
  // Build outer boundary as Polygon?
  //---------------------------------
  bool polygon_for_outer_boundary=false;
 #ifdef OUTER_POLYGON
  polygon_for_outer_boundary=true;
 #endif
  if (polygon_for_outer_boundary)
   { 
    // Number of segments that make up the boundary
    unsigned n_seg = 5; 
    double unit_zeta = 0.5*MathematicalConstants::Pi/double(n_seg);
    
    // The boundary is bounded by two distinct boundaries, each
    // represented by its own polyline
    Vector<TriangleMeshCurveSection*> boundary_polyline_pt(2);
    
    // Vertex coordinates on boundary
    Vector<Vector<double> > bound_coords(n_seg+1);
    
    // First part of the boundary 
    //---------------------------
    for(unsigned ipoint=0; ipoint<n_seg+1;ipoint++)
     {
      // Resize the vector 
      bound_coords[ipoint].resize(2);
      
      // Get the coordinates
      zeta[0]=unit_zeta*double(ipoint);
      outer_boundary_ellipse_pt->position(zeta,posn);
      bound_coords[ipoint][0]=posn[0]+x_center;
      bound_coords[ipoint][1]=posn[1]+y_center;
     }
    
    // Build the 1st boundary polyline
    unsigned boundary_id=0;
    boundary_polyline_pt[0]=new TriangleMeshPolyLine(bound_coords,boundary_id);
    
    // Second part of the boundary
    //----------------------------
    unit_zeta*=3.0;
    for(unsigned ipoint=0; ipoint<n_seg+1;ipoint++)
     {
      // Resize the vector 
      bound_coords[ipoint].resize(2);
      
      // Get the coordinates
      zeta[0]=(unit_zeta*double(ipoint))+0.5*MathematicalConstants::Pi;
      outer_boundary_ellipse_pt->position(zeta,posn);
      bound_coords[ipoint][0]=posn[0]+x_center;
      bound_coords[ipoint][1]=posn[1]+y_center;
     }
    
    // Build the 2nd boundary polyline
    boundary_id=1;
    boundary_polyline_pt[1]=new TriangleMeshPolyLine(bound_coords,boundary_id);
    
  
    // Create the triangle mesh polygon for outer boundary
    //----------------------------------------------------
    TriangleMeshPolygon *outer_polygon =
     new TriangleMeshPolygon(boundary_polyline_pt);
  
    // Enable redistribution of polylines
    outer_polygon->
     enable_redistribution_of_segments_between_polylines();
  
    // Set the pointer
    closed_curve_pt = outer_polygon;
  
   }
  // Build outer boundary as curvilinear
  //------------------------------------
  else
   {   
  
    // Provide storage for pointers to the two parts of the curvilinear boundary
    Vector<TriangleMeshCurveSection*> outer_curvilinear_boundary_pt(2);
    
    // First bit
    //----------
    double zeta_start=0.0;
    double zeta_end=MathematicalConstants::Pi;
    unsigned nsegment=5;
    unsigned boundary_id=0;
    outer_curvilinear_boundary_pt[0]=new TriangleMeshCurviLine(
     outer_boundary_ellipse_pt,zeta_start,zeta_end,nsegment,boundary_id);
    
    // Second bit
    //-----------
    zeta_start=MathematicalConstants::Pi;
    zeta_end=2.0*MathematicalConstants::Pi;
    nsegment=8;
    boundary_id=1;
    outer_curvilinear_boundary_pt[1]=new TriangleMeshCurviLine(
     outer_boundary_ellipse_pt,zeta_start,zeta_end,nsegment,boundary_id);
    
    // Combine to curvilinear boundary and define the
    //--------------------------------
    // outer boundary
    //--------------------------------
    closed_curve_pt=
      new TriangleMeshClosedCurve(outer_curvilinear_boundary_pt);
    
   }
  
  
  // Now build the holes
  //====================
  Vector<TriangleMeshClosedCurve*> hole_pt(2);
  
  // Build polygonal hole
  //=====================
  
  // Build first hole: A circle
  x_center = 0.0;
  y_center = 0.5;
  A = 0.1;
  B = 0.1;
  Ellipse* polygon_ellipse_pt=new Ellipse(A,B);
  
  // Number of segments defining upper and lower half of the hole
  unsigned n_seg = 6; 
  double unit_zeta = MathematicalConstants::Pi/double(n_seg);
  
  // This hole is bounded by two distinct boundaries, each
  // represented by its own polyline
  Vector<TriangleMeshCurveSection*> hole_polyline_pt(2);
  
  
  // First boundary of polygonal hole
  //---------------------------------
  
  // Vertex coordinates
  Vector<Vector<double> > bound_hole(n_seg+1);
  for(unsigned ipoint=0; ipoint<n_seg+1;ipoint++)
   {
    // Resize the vector 
    bound_hole[ipoint].resize(2);
    
    // Get the coordinates
    zeta[0]=unit_zeta*double(ipoint);
    polygon_ellipse_pt->position(zeta,posn);
    bound_hole[ipoint][0]=posn[0]+x_center;
    bound_hole[ipoint][1]=posn[1]+y_center;
   }
  
  // Specify the hole boundary id
  unsigned boundary_id=2;
  
  // Build the 1st hole polyline
  hole_polyline_pt[0] = new TriangleMeshPolyLine(bound_hole,boundary_id);
  
  
  // Second boundary of polygonal hole
  //----------------------------------
  for(unsigned ipoint=0; ipoint<n_seg+1;ipoint++)
   {
    // Resize the vector 
    bound_hole[ipoint].resize(2);
    
    // Get the coordinates
    zeta[0]=(unit_zeta*double(ipoint))+MathematicalConstants::Pi;
    polygon_ellipse_pt->position(zeta,posn);
    bound_hole[ipoint][0]=posn[0]+x_center;
    bound_hole[ipoint][1]=posn[1]+y_center;
   }
  
  // Specify the hole boundary id
  boundary_id=3;
  
  // Build the 2nd hole polyline
  hole_polyline_pt[1] = new TriangleMeshPolyLine(bound_hole,boundary_id);
  
  
  // Build the polygonal hole 
  //-------------------------
  
  // Inner hole center coordinates
  Vector<double> hole_center(2);
  hole_center[0]=x_center;
  hole_center[1]=y_center;
  
  hole_pt[0] = new TriangleMeshPolygon(hole_polyline_pt, hole_center);
  
  
  // Build curvilinear hole
  //======================
  
  // Build second hole: Another ellipse
  A = 0.2;
  B = 0.1;
  Ellipse* ellipse_pt=new Ellipse(A,B);
  
  // Build the two parts of the curvilinear boundary
  Vector<TriangleMeshCurveSection*> curvilinear_boundary_pt(2);
  
  
  // First part of curvilinear boundary
  //-----------------------------------
  double zeta_start=0.0;
  double zeta_end=MathematicalConstants::Pi;
  unsigned nsegment=10;
  boundary_id=4;
  curvilinear_boundary_pt[0]=new TriangleMeshCurviLine(
   ellipse_pt,zeta_start,zeta_end, 
   nsegment,boundary_id);
  
  // Second part of curvilinear boundary
  //-------------------------------------
  zeta_start=MathematicalConstants::Pi;
  zeta_end=2.0*MathematicalConstants::Pi;
  nsegment=15;
  boundary_id=5;
  curvilinear_boundary_pt[1]=new TriangleMeshCurviLine(
   ellipse_pt,zeta_start,zeta_end, 
   nsegment,boundary_id);
  
  
  // Combine to hole
  //----------------
  Vector<double> hole_coords(2);
  hole_coords[0]=0.0;
  hole_coords[1]=0.0;
  Vector<TriangleMeshClosedCurve*> curvilinear_hole_pt(1);
  hole_pt[1]=
   new TriangleMeshClosedCurve(curvilinear_boundary_pt,
                                                  hole_coords);
  
  // Uncomment this as an exercise to observe how a
  // layer of fine elements get left behind near the boundary
  // once the tanh step has swept past: 
  
  // closed_curve_pt->disable_polyline_refinement();
  // closed_curve_pt->disable_polyline_unrefinement();
  
  // Now build the mesh
  //===================
  
  // Use the TriangleMeshParameters object for helping on the manage of the
  // TriangleMesh parameters
  TriangleMeshParameters triangle_mesh_parameters(closed_curve_pt);
  
  // Specify the closed curve using the TriangleMeshParameters object
  triangle_mesh_parameters.internal_closed_curve_pt() = hole_pt;
  
  // Specify the maximum area element
  double uniform_element_area=0.2;
  triangle_mesh_parameters.element_area() = uniform_element_area;
  
  // Create the mesh
  My_mesh_pt=new 
   RefineableTriangleMesh<ELEMENT>(triangle_mesh_parameters);
  
  // Store as the problem's one and only mesh
  Problem::mesh_pt()=My_mesh_pt;
  
  // Set error estimator for bulk mesh
  Z2ErrorEstimator* error_estimator_pt=new Z2ErrorEstimator;
  My_mesh_pt->spatial_error_estimator_pt()=error_estimator_pt;
  
  // Set element size limits
  My_mesh_pt->max_element_size()=0.2;
  My_mesh_pt->min_element_size()=0.002; 
  
  // Set boundary condition and complete the build of all elements
  complete_problem_setup();
  
  // Open trace file
  char filename[100];
  sprintf(filename,"RESLT/trace.dat");
  Trace_file.open(filename);
  
  // Setup equation numbering scheme
  oomph_info <<"Number of equations: " 
             << this->assign_eqn_numbers() << std::endl;
  
 } // end_of_constructor

References oomph::TriangleMeshParameters::element_area(), MeshRefinement::error_estimator_pt, MergeRestartFiles::filename, oomph::TriangleMeshParameters::internal_closed_curve_pt(), oomph::oomph_info, BiharmonicTestFunctions2::Pi, oomph::Ellipse::position(), oomph::Problem_Parameter::Trace_file, and Eigen::zeta().

◆ ~UnstructuredPoissonProblem() [1/3]

template<class ELEMENT >

UnstructuredPoissonProblem< ELEMENT >::~UnstructuredPoissonProblem ( )

inline

Destructor.

99 {};

◆ UnstructuredPoissonProblem() [2/3]

template<class ELEMENT >

UnstructuredPoissonProblem< ELEMENT >::UnstructuredPoissonProblem ( )

Constructor.

◆ ~UnstructuredPoissonProblem() [2/3]

template<class ELEMENT >

UnstructuredPoissonProblem< ELEMENT >::~UnstructuredPoissonProblem ( )

inline

Destructor.

99 {};

◆ UnstructuredPoissonProblem() [3/3]

template<class ELEMENT >

UnstructuredPoissonProblem< ELEMENT >::UnstructuredPoissonProblem ( )

Constructor.

◆ ~UnstructuredPoissonProblem() [3/3]

template<class ELEMENT >

UnstructuredPoissonProblem< ELEMENT >::~UnstructuredPoissonProblem ( )

inline

Destructor.

100 {};

Member Function Documentation

◆ actions_after_adapt() [1/2]

template<class ELEMENT >

void UnstructuredPoissonProblem< ELEMENT >::actions_after_adapt ( )

inlinevirtual

Actions after adapt: Setup the problem again – remember that the mesh has been completely rebuilt and its element's don't have any pointers to source fcts etc. yet

Reimplemented from oomph::Problem.

   {
    complete_problem_setup();
   }

◆ actions_after_adapt() [2/2]

template<class ELEMENT >

void UnstructuredPoissonProblem< ELEMENT >::actions_after_adapt ( )

inlinevirtual

Actions after adapt: Setup the problem again – remember that the mesh has been completely rebuilt and its element's don't have any pointers to source fcts etc. yet

Reimplemented from oomph::Problem.

   {
    complete_problem_setup();
   }

◆ actions_after_newton_solve() [1/3]

template<class ELEMENT >

void UnstructuredPoissonProblem< ELEMENT >::actions_after_newton_solve ( )

inlinevirtual

Update after solve (empty)

Reimplemented from oomph::Problem.

114 {}

◆ actions_after_newton_solve() [2/3]

template<class ELEMENT >

void UnstructuredPoissonProblem< ELEMENT >::actions_after_newton_solve ( )

inlinevirtual

Update after solve (empty)

Reimplemented from oomph::Problem.

102 {}

◆ actions_after_newton_solve() [3/3]

template<class ELEMENT >

void UnstructuredPoissonProblem< ELEMENT >::actions_after_newton_solve ( )

inlinevirtual

Update after solve (empty)

Reimplemented from oomph::Problem.

115 {}

◆ actions_before_adapt() [1/2]

template<class ELEMENT >

void UnstructuredPoissonProblem< ELEMENT >::actions_before_adapt ( )

inlinevirtual

Actions before adapt. Empty.

Reimplemented from oomph::Problem.

102 {}

◆ actions_before_adapt() [2/2]

template<class ELEMENT >

void UnstructuredPoissonProblem< ELEMENT >::actions_before_adapt ( )

inlinevirtual

Actions before adapt. Empty.

Reimplemented from oomph::Problem.

103 {}

◆ actions_before_newton_solve() [1/3]

template<class ELEMENT >

void UnstructuredPoissonProblem< ELEMENT >::actions_before_newton_solve ( )

inlinevirtual

Update the problem specs before solve: Re-apply boundary conditons.

Reimplemented from oomph::Problem.

   {
    apply_boundary_conditions();
   }

◆ actions_before_newton_solve() [2/3]

template<class ELEMENT >

void UnstructuredPoissonProblem< ELEMENT >::actions_before_newton_solve ( )

inlinevirtual

Update the problem specs before solve: Re-apply boundary conditons.

Reimplemented from oomph::Problem.

   {
    apply_boundary_conditions();
   }

◆ actions_before_newton_solve() [3/3]

template<class ELEMENT >

void UnstructuredPoissonProblem< ELEMENT >::actions_before_newton_solve ( )

inlinevirtual

Update the problem specs before solve: Re-apply boundary conditons.

Reimplemented from oomph::Problem.

   {
    apply_boundary_conditions();
   }

◆ apply_boundary_conditions() [1/3]

template<class ELEMENT >

void UnstructuredPoissonProblem< ELEMENT >::apply_boundary_conditions

private

Helper function to apply boundary conditions.

 {
  
  // Loop over all boundary nodes
  unsigned nbound=this->My_mesh_pt->nboundary();
  for(unsigned ibound=0;ibound<nbound;ibound++)
   {
    unsigned num_nod=this->My_mesh_pt->nboundary_node(ibound);
    for (unsigned inod=0;inod<num_nod;inod++)
     {
      // Get node
      Node* nod_pt=this->My_mesh_pt->boundary_node_pt(ibound,inod);
      
      // Extract nodal coordinates from node:
      Vector<double> x(2);
      x[0]=nod_pt->x(0);
      x[1]=nod_pt->x(1);
      
      // Compute the value of the exact solution at the nodal point
      Vector<double> u(1);
      TanhSolnForPoisson::get_exact_u(x,u);
      
      // Assign the value to the one (and only) nodal value at this node
      nod_pt->set_value(0,u[0]);
     }
   } 
  
 } // end set bc

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

◆ apply_boundary_conditions() [2/3]

template<class ELEMENT >

void UnstructuredPoissonProblem< ELEMENT >::apply_boundary_conditions ( )

private

Helper function to apply boundary conditions.

◆ apply_boundary_conditions() [3/3]

template<class ELEMENT >

void UnstructuredPoissonProblem< ELEMENT >::apply_boundary_conditions ( )

private

Helper function to apply boundary conditions.

◆ complete_problem_setup() [1/3]

template<class ELEMENT >

void UnstructuredPoissonProblem< ELEMENT >::complete_problem_setup

private

Helper function to (re-)set boundary condition and complete the build of all elements

Set boundary condition exactly, and complete the build of all elements

 {   
  
  // Set the boundary conditions for problem: All nodes are
  // free by default -- just pin the ones that have Dirichlet conditions
  // here. 
  unsigned nbound=My_mesh_pt->nboundary();
  for(unsigned ibound=0;ibound<nbound;ibound++)
   {
    unsigned num_nod=My_mesh_pt->nboundary_node(ibound);
    for (unsigned inod=0;inod<num_nod;inod++)
     {
      // Get node
      Node* nod_pt=My_mesh_pt->boundary_node_pt(ibound,inod);
      
      // Pin one-and-only unknown value
      nod_pt->pin(0);
     }   
   } // end loop over boundaries
  
  
  // Complete the build of all elements so they are fully functional
  unsigned n_element = My_mesh_pt->nelement();
  for(unsigned e=0;e<n_element;e++)
   {
    // Upcast from GeneralisedElement to the present element
    ELEMENT* el_pt = dynamic_cast<ELEMENT*>(My_mesh_pt->element_pt(e));
    
    //Set the source function pointer
    el_pt->source_fct_pt() = &TanhSolnForPoisson::get_source;
   }
  
  // Re-apply Dirichlet boundary conditions (projection ignores
  // boundary conditions!)
  apply_boundary_conditions();
 }

References e(), TanhSolnForPoisson::get_source(), and oomph::Data::pin().

◆ complete_problem_setup() [2/3]

template<class ELEMENT >

void UnstructuredPoissonProblem< ELEMENT >::complete_problem_setup ( )

private

Helper function to (re-)set boundary condition and complete the build of all elements

◆ complete_problem_setup() [3/3]

template<class ELEMENT >

void UnstructuredPoissonProblem< ELEMENT >::complete_problem_setup ( )

private

Helper function to (re-)set boundary condition and complete the build of all elements

◆ doc_solution() [1/3]

template<class ELEMENT >

void UnstructuredPoissonProblem< ELEMENT >::doc_solution ( const std::string & comment = "" )

Doc the solution.

 { 
  ofstream some_file;
  char filename[100];
  
  // Number of plot points
  unsigned npts;
  npts=5; 
  
  sprintf(filename,"RESLT/soln%i.dat",Doc_info.number());
  some_file.open(filename);
  this->My_mesh_pt->output(some_file,npts); 
  some_file << "TEXT X = 22, Y = 92, CS=FRAME T = \"" 
            << comment << "\"\n";
  some_file.close();
  
  // Output exact solution 
  //----------------------
  sprintf(filename,"RESLT/exact_soln%i.dat",Doc_info.number());
  some_file.open(filename);
  My_mesh_pt->output_fct(some_file,npts,TanhSolnForPoisson::get_exact_u); 
  some_file.close();
  
  // Output boundaries
  //------------------
  sprintf(filename,"RESLT/boundaries%i.dat",Doc_info.number());
  some_file.open(filename);
  My_mesh_pt->output_boundaries(some_file);
  some_file.close();
  
  
  // Doc error and return of the square of the L2 error
  //---------------------------------------------------
  double error,norm,dummy_error,zero_norm;
  sprintf(filename,"RESLT/error%i.dat",Doc_info.number());
  some_file.open(filename);
  My_mesh_pt->compute_error(some_file,TanhSolnForPoisson::get_exact_u,
                            error,norm); 
  
  My_mesh_pt->compute_error(some_file,TanhSolnForPoisson::zero,
                            dummy_error,zero_norm); 
  some_file.close();
  
  // Doc L2 error and norm of solution
  oomph_info << "\nNorm of error   : " << sqrt(error) << std::endl; 
  oomph_info << "Norm of exact solution: " << sqrt(norm) << std::endl;
  oomph_info << "Norm of computed solution: " << sqrt(dummy_error) << std::endl;
  Trace_file << sqrt(norm) << " " << sqrt(dummy_error) << std::endl;
  
  // Increment the doc_info number
  Doc_info.number()++;
  
 } // end of doc

References GlobalParameters::Doc_info, calibrate::error, MergeRestartFiles::filename, TanhSolnForPoisson::get_exact_u(), oomph::DocInfo::number(), oomph::oomph_info, sqrt(), oomph::Problem_Parameter::Trace_file, and TanhSolnForPoisson::zero().

◆ doc_solution() [2/3]

template<class ELEMENT >

void UnstructuredPoissonProblem< ELEMENT >::doc_solution ( const std::string & comment = "" )

Doc the solution.

◆ doc_solution() [3/3]

template<class ELEMENT >

void UnstructuredPoissonProblem< ELEMENT >::doc_solution ( const std::string & comment = "" )

Doc the solution.

Member Data Documentation

◆ Doc_info

template<class ELEMENT >

DocInfo UnstructuredPoissonProblem< ELEMENT >::Doc_info

private

Doc info object for labeling output.

◆ My_mesh_pt [1/2]

template<class ELEMENT >

RefineableTriangleMesh< ELEMENT > * UnstructuredPoissonProblem< ELEMENT >::My_mesh_pt

private

Pointers to specific mesh.

◆ My_mesh_pt [2/2]

template<class ELEMENT >

TriangleMesh<ELEMENT>* UnstructuredPoissonProblem< ELEMENT >::My_mesh_pt

private

Pointers to specific mesh.

◆ Trace_file

template<class ELEMENT >

ofstream UnstructuredPoissonProblem< ELEMENT >::Trace_file

private

Trace file to document norm of solution.

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

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

template<class ELEMENT> class UnstructuredPoissonProblem< ELEMENT >

Constructor & Destructor Documentation

◆ UnstructuredPoissonProblem() [1/3]

◆ ~UnstructuredPoissonProblem() [1/3]

◆ UnstructuredPoissonProblem() [2/3]

◆ ~UnstructuredPoissonProblem() [2/3]

◆ UnstructuredPoissonProblem() [3/3]

◆ ~UnstructuredPoissonProblem() [3/3]

Member Function Documentation

◆ actions_after_adapt() [1/2]

◆ actions_after_adapt() [2/2]

◆ actions_after_newton_solve() [1/3]

◆ actions_after_newton_solve() [2/3]

◆ actions_after_newton_solve() [3/3]

◆ actions_before_adapt() [1/2]

◆ actions_before_adapt() [2/2]

◆ actions_before_newton_solve() [1/3]

◆ actions_before_newton_solve() [2/3]

◆ actions_before_newton_solve() [3/3]

◆ apply_boundary_conditions() [1/3]

◆ apply_boundary_conditions() [2/3]

◆ apply_boundary_conditions() [3/3]

◆ complete_problem_setup() [1/3]

◆ complete_problem_setup() [2/3]

◆ complete_problem_setup() [3/3]

◆ doc_solution() [1/3]

◆ doc_solution() [2/3]

◆ doc_solution() [3/3]

Member Data Documentation

◆ Doc_info

◆ My_mesh_pt [1/2]

◆ My_mesh_pt [2/2]

◆ Trace_file

template<class ELEMENT>
class UnstructuredPoissonProblem< ELEMENT >