Darcy problem. More...

Inheritance diagram for DarcyProblem< ELEMENT >:

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

void	doc_solution (const unsigned &label)
	Post-process results, using unsigned to label files. More...

void	actions_before_newton_solve ()
	Actions before Newton solve (empty) More...

void	doc_shape_functions ()
	Doc shape functions. 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 ()

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

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	create_pressure_elements ()
	Allocate pressure elements on the top surface. More...

void	complete_problem_setup ()
	Complete problem setup. More...

Private Attributes
TriangleMesh< ELEMENT > *	Bulk_mesh_pt
	Pointer to the "bulk" mesh. More...

Mesh *	Surface_mesh_pt
	Mesh of boundary condition elements. More...

std::ofstream	Trace_file
	Trace file for results. 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_after_newton_solve ()

virtual void	actions_before_newton_convergence_check ()

virtual void	actions_before_newton_step ()

virtual void	actions_after_newton_step ()

virtual void	actions_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 DarcyProblem< ELEMENT >

Darcy problem.

Constructor & Destructor Documentation

◆ DarcyProblem()

template<class ELEMENT >

DarcyProblem< ELEMENT >::DarcyProblem

Constructor.

 {
  // Mesh
  //-----
  
  // Closed curve definiting outer boundary
  TriangleMeshClosedCurve *outer_boundary_pt=0;
  
  // Internal boundary to prevent problem with flux B.C.s
  Vector<TriangleMeshOpenCurve*> inner_open_boundary_pt;
  
  Vector<double> zeta(1);
  Vector<double> posn(2);
  
  Ellipse* outer_boundary_ellipse_pt = new Ellipse(1,1);
  
  Vector<TriangleMeshCurveSection*> outer_curvilinear_boundary_pt(2);
  
  // First bit
  double zeta_start = 0.0;
  double zeta_end = MathematicalConstants::Pi;
  unsigned nsegment =
   (unsigned)max(
    3.0,MathematicalConstants::Pi/std::sqrt(TestProblem::Element_area));
  outer_curvilinear_boundary_pt[0] =
   new TriangleMeshCurviLine(outer_boundary_ellipse_pt, zeta_start,
                             zeta_end, nsegment, 0);
  
  // Second bit
  zeta_start = MathematicalConstants::Pi;
  zeta_end = 2.0*MathematicalConstants::Pi;
  nsegment =
   (unsigned)max(
    3.0,MathematicalConstants::Pi/std::sqrt(TestProblem::Element_area));
  outer_curvilinear_boundary_pt[1] =
   new TriangleMeshCurviLine(outer_boundary_ellipse_pt, zeta_start,
                             zeta_end, nsegment, 1);
  
  outer_boundary_pt =
   new TriangleMeshClosedCurve(outer_curvilinear_boundary_pt);
  
  // Target element area for Triangle
  double uniform_element_area = TestProblem::Element_area;
  
  // Use the TriangleMeshParameters object for gathering all
  // the necessary arguments for the TriangleMesh object
  TriangleMeshParameters triangle_mesh_parameters(
    outer_boundary_pt);
  
  // Take the maximum element area
  triangle_mesh_parameters.element_area() =
   uniform_element_area;
  
  
 #ifdef ADAPTIVE
  
  // Build adaptive "bulk" mesh
  Bulk_mesh_pt=new RefineableTriangleMesh<ELEMENT>(triangle_mesh_parameters);
  
  // Create/set error estimator
  Bulk_mesh_pt->spatial_error_estimator_pt()=new Z2ErrorEstimator;
  
  // Choose error tolerances 
  if (TestProblem::Use_point_source_solution)
   {
    Bulk_mesh_pt->min_permitted_error()=0.0001; 
    Bulk_mesh_pt->max_permitted_error()=0.001; 
   }
  else
   {
    Bulk_mesh_pt->min_permitted_error()=1.0e-8;
    Bulk_mesh_pt->max_permitted_error()=1.0e-7;
   }
  
  // Actions before projection
  Bulk_mesh_pt->mesh_update_fct_pt()=&TestProblem::edge_sign_setup<ELEMENT>;
  
 #else
  
  // Create the buk mesh
  Bulk_mesh_pt = new TriangleMesh<ELEMENT>(triangle_mesh_parameters);
  
 #endif
  
  // Create mesh of pressure bc elements
  Surface_mesh_pt = new Mesh;
  create_pressure_elements();
  
  // Combine into global mesh
  add_sub_mesh(Bulk_mesh_pt);
  add_sub_mesh(Surface_mesh_pt);
  build_global_mesh();
  
  // Complete problem setup
  complete_problem_setup();
  
  // Assign equation numbers
  oomph_info << "Number of equations: " << assign_eqn_numbers() << std::endl;
  
  
  // Open trace file
  char filename[50];
  sprintf(filename,"%s/trace.dat",TestProblem::Directory.c_str());
  Trace_file.open(filename);
  
 } // end of problem constructor

References TestProblem::Directory, TestProblem::Element_area, oomph::TriangleMeshParameters::element_area(), MergeRestartFiles::filename, max, oomph::oomph_info, oomph::MathematicalConstants::Pi, sqrt(), oomph::Problem_Parameter::Trace_file, TestProblem::Use_point_source_solution, and Eigen::zeta().

Member Function Documentation

◆ actions_before_newton_solve()

template<class ELEMENT >

void DarcyProblem< ELEMENT >::actions_before_newton_solve ( )

inlinevirtual

Actions before Newton solve (empty)

Reimplemented from oomph::Problem.

197 {}

◆ complete_problem_setup()

template<class ELEMENT >

void DarcyProblem< ELEMENT >::complete_problem_setup

private

Complete problem setup.

 {
  // Setup the signs for the fluxes
  TestProblem::edge_sign_setup<ELEMENT>(Bulk_mesh_pt);
  
  // Loop over all elements
  unsigned n_element = Bulk_mesh_pt->nelement();
  for(unsigned e=0;e<n_element;e++)
   {
    ELEMENT* el_pt = dynamic_cast<ELEMENT*>(Bulk_mesh_pt->element_pt(e));
    
    // Set source fcts
    el_pt->source_fct_pt()=TestProblem::source;
    el_pt->mass_source_fct_pt()=TestProblem::mass_source;
   
 #ifdef ADAPTIVE
  
    // Pin dofs at vertex nodes (because they're only used for projection)
    el_pt->pin_superfluous_darcy_dofs();
  
 #endif
  
   } // end of loop over elements
  
  
  // Apply boundary conditions
  //--------------------------
  
  // Get the nodal index at which values representing edge fluxes
  // at flux interpolation points are stored
  ELEMENT *el_pt=dynamic_cast<ELEMENT*>(Bulk_mesh_pt->element_pt(0));
  
  // Where are the values stored?
  unsigned n=el_pt->nedge_flux_interpolation_point();
  Vector<unsigned> q_index(n);
  for (unsigned j=0;j<n;j++)
   {
    q_index[j]=el_pt->q_edge_index(j);
   }
  
  // Coordinate vector
  Vector<double> x(2);
  
  // Impose normal component of flux on lower part of outer boundary
  unsigned ibound=1;
  {
   // Get the number of elements along boundary ibound
   unsigned n_boundary_element=Bulk_mesh_pt->nboundary_element(ibound);
   
   // Loop over the elements along boundary ibound
   for(unsigned e=0;e<n_boundary_element;e++)
    {
     // Upcast the current element to the actual type
     ELEMENT *el_pt=
      dynamic_cast<ELEMENT*>(Bulk_mesh_pt->boundary_element_pt(ibound,e));
     
     // Loop over the edges
     for(unsigned edge=0;edge<3;edge++)
      {
       // Get pointer to node that stores the edge flux dofs for this edge
       Node* nod_pt=el_pt->edge_flux_node_pt(edge);
       
       // Pin/set values for the flux degrees of freedom
       if (nod_pt->is_on_boundary(ibound))
        {
         for (unsigned j=0;j<n;j++)
          {
           nod_pt->pin(q_index[j]);
          }
  
         // Get face index of face associated with edge
         unsigned f=el_pt->face_index_of_edge(edge);
         
         // Build a temporary face element from which we'll extract
         // the outer unit normal
         DarcyFaceElement<ELEMENT>* face_el_pt=
          new DarcyFaceElement<ELEMENT>(el_pt,f);   
         
         // Loop over the flux interpolation points
         unsigned n_flux_interpolation_points=
          el_pt->nedge_flux_interpolation_point();
         for(unsigned g=0;g<n_flux_interpolation_points;g++)
          {
           // Get the global coords of the flux_interpolation point
           el_pt->edge_flux_interpolation_point_global(edge,g,x);
           
           // Get the exact solution
           Vector<double> exact_soln(4,0.0);
           TestProblem::exact_soln(x,exact_soln);
  
           // Get unit normal at this flux interpolation point
           Vector<double> s(1);
           el_pt->face_local_coordinate_of_flux_interpolation_point(edge,g,s);
           Vector<double> unit_normal(2);
           face_el_pt->outer_unit_normal(s,unit_normal);
           
 #ifdef PARANOID          
  
           // Sanity check
           Vector<double> x_face(2);
           face_el_pt->interpolated_x(s,x_face);
           if ((x_face[0]-x[0])*(x_face[0]-x[0])+
               (x_face[1]-x[1])*(x_face[1]-x[1])>1.0e-3)
            {
             std::stringstream error;
             error << "Discrepancy in coordinate of flux interpolation point\n"
                   << "(computed by bulk and face elements) for edge " << e 
                   << " and flux int pt " << g << "\n"
                   << "Face thinks node is at: "
                   << x_face[0] << " " << x_face[1] << "\n"
                   << "Bulk thinks node is at: "
                   << x[0] << " " << x[1] << "\n";
             throw OomphLibError(
              error.str(),
              OOMPH_CURRENT_FUNCTION,
              OOMPH_EXCEPTION_LOCATION);
            }
 #endif
           
           // Set the boundary flux
           nod_pt->set_value(q_index[g],
                             exact_soln[0]*unit_normal[0]+
                             exact_soln[1]*unit_normal[1]);
           
          } // End of loop over flux interpolation points
  
         // Don't need face element on that edge any more
         delete face_el_pt;
         
        } // End if for edge on required boundary
      } // End of loop over edges
  
    } // End of loop over boundary elements
  } // End of loop over boundaries
 }

References e(), calibrate::error, TestProblem::exact_soln(), f(), oomph::FaceElement::interpolated_x(), oomph::Node::is_on_boundary(), j, TestProblem::mass_source(), n, OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION, oomph::FaceElement::outer_unit_normal(), oomph::Data::pin(), s, oomph::Data::set_value(), TestProblem::source(), and plotDoE::x.

◆ create_pressure_elements()

template<class ELEMENT >

void DarcyProblem< ELEMENT >::create_pressure_elements

private

Allocate pressure elements on the top surface.

Creat traction elements.

 {
  
  // Upper part of boundary
  unsigned bound=0;
   
  // How many bulk elements are next to that boundary 
  unsigned n_neigh = Bulk_mesh_pt->nboundary_element(bound);
  
  // Now loop over bulk elements and create the face elements
  for(unsigned n=0;n<n_neigh;n++)
   {
    // Create the face element
    DarcyFaceElement<ELEMENT>* pressure_element_pt
     = new DarcyFaceElement<ELEMENT>
     (Bulk_mesh_pt->boundary_element_pt(bound,n),
      Bulk_mesh_pt->face_index_at_boundary(bound,n));
    
    // Add to mesh
    Surface_mesh_pt->add_element_pt(pressure_element_pt);
  
    // Set function pointer
    pressure_element_pt->pressure_fct_pt()=&TestProblem::boundary_pressure;
  
   }
  
 } // end of assign_traction_elements

References TestProblem::boundary_pressure(), n, and oomph::DarcyFaceElement< ELEMENT >::pressure_fct_pt.

◆ doc_shape_functions()

template<class ELEMENT >

void DarcyProblem< ELEMENT >::doc_shape_functions

Doc shape functions.

 {
  ofstream some_file;
  char filename[100];
  
  // Coarse solution
  unsigned npts_coarse=2;
  sprintf(filename,"%s/coarse_soln.dat",TestProblem::Directory.c_str());
  some_file.open(filename);
  Bulk_mesh_pt->output(some_file,npts_coarse);
  some_file.close();
  
  // Backup for all values (double counting plenty but I don't care...)
  //-------------------------------------------------------------------
  Vector<double> backed_up_value;
  unsigned nel=Bulk_mesh_pt->nelement();
  for (unsigned e=0;e<nel;e++)
   {
    ELEMENT* el_pt=dynamic_cast<ELEMENT*>(Bulk_mesh_pt->element_pt(e));
  
    // Backup edge-based q values
    unsigned n_q_basis_edge = el_pt->nq_basis_edge();
    for (unsigned j=0;j<n_q_basis_edge;j++)
     {
      backed_up_value.push_back(el_pt->q_edge(j));
     }
  
    // Backup internal q values
    unsigned n_q_basis = el_pt->nq_basis();
    for (unsigned j=n_q_basis_edge;j<n_q_basis;j++)
     {
      backed_up_value.push_back(el_pt->q_internal(j-n_q_basis_edge));
     }
  
    // Backup pressures
    unsigned n_p_basis = el_pt->np_basis();
    for (unsigned j=0;j<n_p_basis;j++)
     {
      backed_up_value.push_back(el_pt->p_value(j));
     }
   }
  
  
  
  // Loop over all elements to wipe
  //-------------------------------
  for (unsigned e=0;e<nel;e++)
   {
    ELEMENT* el_pt=dynamic_cast<ELEMENT*>(Bulk_mesh_pt->element_pt(e));
  
    // Kill edge-based q values
    unsigned n_q_basis_edge = el_pt->nq_basis_edge();
    for (unsigned j=0;j<n_q_basis_edge;j++)
     {
      el_pt->set_q_edge(j,0.0);
     }
  
    // Kill internal q values
    unsigned n_q_basis = el_pt->nq_basis();
    for (unsigned j=n_q_basis_edge;j<n_q_basis;j++)
     {
      el_pt->set_q_internal(j-n_q_basis_edge,0.0);
     }
  
  
    // Kill pressures
    unsigned n_p_basis = el_pt->np_basis();
    for (unsigned j=0;j<n_p_basis;j++)
     {
      el_pt->set_p_value(j,0.0);
     }
   }
  
  
  // Choose a specific element for which we'll switch on all the dofs
  //-----------------------------------------------------------------
  // one by one
  //-----------
  MeshAsGeomObject* mesh_geom_obj_pt=new MeshAsGeomObject(Bulk_mesh_pt); 
  Vector<double> x(2,0.0);
  Vector<double> s(2,0.0);
  
  // Get pointer to GeomObject that contains this point and cast
  GeomObject* geom_obj_pt=0;
  mesh_geom_obj_pt->locate_zeta(x,geom_obj_pt,s); 
  ELEMENT* el_pt=dynamic_cast<ELEMENT*>(geom_obj_pt);
  
  
  // Number of plot points
  unsigned npts=10;
    
  // Doc edge-based q values
  unsigned count_shape_doc=0;
  unsigned n_q_basis_edge = el_pt->nq_basis_edge();
  for (unsigned j=0;j<n_q_basis_edge;j++)
   {
    // Set this dof to one
    el_pt->set_q_edge(j,1.0);
  
    // Get face index of face associated with this flux basis fct
    // and erect face element
    unsigned f=el_pt->face_index_of_q_edge_basis_fct(j);
    DarcyFaceElement<ELEMENT>* face_el_pt=
     new DarcyFaceElement<ELEMENT>(el_pt,f);   
    
    // Get outer unit normal halfway along edge
    Vector<double> s(1,0.5);
    Vector<double> unit_normal(2);
    Vector<double> x(2);
    face_el_pt->outer_unit_normal(s,unit_normal);
    face_el_pt->interpolated_x(s,x);
    delete face_el_pt;
  
    // Plot
    sprintf(filename,"%s/q_shape_fct%i.dat",TestProblem::Directory.c_str(),
            count_shape_doc++);
    some_file.open(filename);
    unsigned nel=Bulk_mesh_pt->nelement();
    for (unsigned e=0;e<nel;e++)
     {
      dynamic_cast<ELEMENT*>(Bulk_mesh_pt->element_pt(e))->
       output(some_file,npts);
     }
    some_file.close();
  
  
    sprintf(filename,"%s/outer_unit_normal%i.dat",
            TestProblem::Directory.c_str(),j);
    some_file.open(filename);
    some_file << x[0] << " " 
              << x[1] << " " 
              << unit_normal[0] << " " 
              << unit_normal[1] << " " 
              << std::endl;
    some_file.close();
  
  
    sprintf(filename,"%s/flux_interpolation_point%i.dat",
            TestProblem::Directory.c_str(),j);
    some_file.open(filename);
    Vector<double> flux_interpolation_point(2);
    el_pt->edge_flux_interpolation_point_global(j,flux_interpolation_point);
    some_file << flux_interpolation_point[0] << " " 
              << flux_interpolation_point[1] << " " 
              << 1.0 << " " 
              << std::endl;
    some_file.close();
  
    sprintf(filename,"%s/q_shape_fct_with_project%i.dat",
            TestProblem::Directory.c_str(),j);
    some_file.open(filename);
    for (unsigned e=0;e<nel;e++)
     {
      dynamic_cast<ELEMENT*>(Bulk_mesh_pt->element_pt(e))->
       output_with_projected_flux(some_file,npts,unit_normal);
     }
    some_file.close();
  
    // Reset
    el_pt->set_q_edge(j,0.0);
   }
  
  // Doc internal q values
  unsigned n_q_basis = el_pt->nq_basis();
  for (unsigned j=n_q_basis_edge;j<n_q_basis;j++)
   {
    el_pt->set_q_internal(j-n_q_basis_edge,1.0);
    sprintf(filename,"%s/q_shape_fct%i.dat",
            TestProblem::Directory.c_str(),
            count_shape_doc++);
    some_file.open(filename);
    unsigned nel=Bulk_mesh_pt->nelement();
    for (unsigned e=0;e<nel;e++)
     {
      dynamic_cast<ELEMENT*>(Bulk_mesh_pt->element_pt(e))->
       output(some_file,npts);
     }
    some_file.close();
    el_pt->set_q_internal(j-n_q_basis_edge,0.0);
   }
  
  // Doc pressures
  count_shape_doc=0;
  unsigned n_p_basis = el_pt->np_basis();
  for (unsigned j=0;j<n_p_basis;j++)
   {
    el_pt->set_p_value(j,1.0);
    sprintf(filename,"%s/p_shape_fct%i.dat",
            TestProblem::Directory.c_str(),
            count_shape_doc++);
    some_file.open(filename);
    unsigned nel=Bulk_mesh_pt->nelement();
    for (unsigned e=0;e<nel;e++)
     {
      dynamic_cast<ELEMENT*>(Bulk_mesh_pt->element_pt(e))->
       output(some_file,npts);
     }
    some_file.close();
    el_pt->set_p_value(j,0.0);
   }
  
  
  
  // Restore dofs
  unsigned count=0;
  for (unsigned e=0;e<nel;e++)
   {
    ELEMENT* el_pt=dynamic_cast<ELEMENT*>(Bulk_mesh_pt->element_pt(e));
  
    // Reset edge-based q values
    unsigned n_q_basis_edge = el_pt->nq_basis_edge();
    for (unsigned j=0;j<n_q_basis_edge;j++)
     {
      el_pt->set_q_edge(j,backed_up_value[count]);
      count++;
     }
  
    // Reset internal q values
    unsigned n_q_basis = el_pt->nq_basis();
    for (unsigned j=n_q_basis_edge;j<n_q_basis;j++)
     {
      el_pt->set_q_internal(j-n_q_basis_edge,backed_up_value[count]);
      count++;
     }
  
  
    // Reset pressures
    unsigned n_p_basis = el_pt->np_basis();
    for (unsigned j=0;j<n_p_basis;j++)
     {
      el_pt->set_p_value(j,backed_up_value[count]);
      count++;
     }
   }
 } 

References TestProblem::Directory, e(), f(), MergeRestartFiles::filename, oomph::FaceElement::interpolated_x(), j, oomph::MeshAsGeomObject::locate_zeta(), oomph::FaceElement::outer_unit_normal(), oomph::output(), s, and plotDoE::x.

◆ doc_solution()

template<class ELEMENT >

void DarcyProblem< ELEMENT >::doc_solution ( const unsigned & label )

Post-process results, using unsigned to label files.

Write the solution and exact solution to file, and calculate the error.

 {
  ofstream some_file;
  char filename[100];
  
  
  // Output computed solution
  //-------------------------
  unsigned npts=5;
  sprintf(filename,"%s/soln%i.dat",TestProblem::Directory.c_str(),label);
  some_file.open(filename);
  Bulk_mesh_pt->output(some_file,npts);
  some_file.close();
  
  
  // Output coarse solution
  //-----------------------
  unsigned npts_coarse=2;
  sprintf(filename,"%s/coarse_soln%i.dat",TestProblem::Directory.c_str(),label);
  some_file.open(filename);
  Bulk_mesh_pt->output(some_file,npts_coarse);
  some_file.close();
  
  // Output exact solution
  //----------------------
  sprintf(filename,"%s/exact_soln%i.dat",TestProblem::Directory.c_str(),label);
  some_file.open(filename);
  Bulk_mesh_pt->output_fct(some_file,
                             npts,
                             TestProblem::exact_soln);
  some_file.close();
  
  // Output boundary condition elements
  //-----------------------------------
  sprintf(filename,"%s/bc_elements%i.dat",TestProblem::Directory.c_str(),label);
  some_file.open(filename);
  Surface_mesh_pt->output(some_file,npts);
  some_file.close();
  
  // Doc error
  //----------
  Vector<double> norm(2,0.0);
  Vector<double> error(2,0.0);
  sprintf(filename,"%s/error%i.dat",TestProblem::Directory.c_str(),label);
   some_file.open(filename);
  Bulk_mesh_pt->compute_error(some_file,
                              TestProblem::exact_soln,
                              error,norm);
  some_file.close();
  
  // Doc error norm:
  cout << std::endl;
  cout << "Norm of exact q : " << sqrt(norm[0]) << std::endl;
  cout << "Norm of exact p : " << sqrt(norm[1]) << std::endl << std::endl;
  
  cout << "Norm of q error : " << sqrt(error[0]) << std::endl;
  cout << "Norm of p error : " << sqrt(error[1]) << std::endl;
  cout << std::endl << std::endl;
  
  Trace_file << ndof() << " "
             << sqrt(error[0]) << " "
             << sqrt(error[1]) << " "
             << TestProblem::Element_area << " "
             << sqrt(norm[0]) << " "
             << sqrt(norm[1]) << std::endl;
 }

References TestProblem::Directory, TestProblem::Element_area, calibrate::error, TestProblem::exact_soln(), MergeRestartFiles::filename, UniformPSDSelfTest::label, sqrt(), and oomph::Problem_Parameter::Trace_file.

Member Data Documentation

◆ Bulk_mesh_pt

template<class ELEMENT >

TriangleMesh<ELEMENT>* DarcyProblem< ELEMENT >::Bulk_mesh_pt

private

Pointer to the "bulk" mesh.

◆ Surface_mesh_pt

template<class ELEMENT >

Mesh* DarcyProblem< ELEMENT >::Surface_mesh_pt

private

Mesh of boundary condition elements.

◆ Trace_file

template<class ELEMENT >

std::ofstream DarcyProblem< ELEMENT >::Trace_file

private

Trace file for results.

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

unstructured_two_d_circle.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

template<class ELEMENT> class DarcyProblem< ELEMENT >

Constructor & Destructor Documentation

◆ DarcyProblem()

Member Function Documentation

◆ actions_before_newton_solve()

◆ complete_problem_setup()

◆ create_pressure_elements()

◆ doc_shape_functions()

◆ doc_solution()

Member Data Documentation

◆ Bulk_mesh_pt

◆ Surface_mesh_pt

◆ Trace_file

template<class ELEMENT>
class DarcyProblem< ELEMENT >