Demo class solves Poisson problem using Gmsh mesh. More...

Inheritance diagram for TetmeshPoissonProblem< ELEMENT >:

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

	~TetmeshPoissonProblem ()
	Destructor (empty) More...

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

void	actions_after_adapt ()
	Totally new mesh; build elements and apply boundary conditions. More...

void	actions_before_newton_solve ()
	Update the problem specs before solve: (empty) More...

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

void	doc_solution (const unsigned &nplot, DocInfo &doc_info)
	Doc the solution. More...

	TetmeshPoissonProblem ()
	Constructor. More...

	~TetmeshPoissonProblem ()
	Destructor (empty) More...

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

void	actions_after_adapt ()
	Totally new mesh; build elements and apply boundary conditions. More...

void	actions_before_newton_solve ()
	Update the problem specs before solve: (empty) More...

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

void	doc_solution (const unsigned &nplot, DocInfo &doc_info)
	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	complete_problem_setup ()
	Apply BCs and make elements functional. More...

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

void	complete_problem_setup ()
	Apply BCs and make elements functional. More...

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

Private Attributes
RefineableGmshTetMesh< ELEMENT > *	Bulk_mesh_pt
	Bulk mesh. More...

TetMeshFacetedClosedSurface *	Outer_boundary_pt
	Storage for the outer boundary object. More...

Vector< TetMeshFacetedSurface * >	Inner_boundary_pt
	Inner boundary. More...

unsigned	First_boundary_id_for_outer_boundary
	First boundary ID for outer boundary. More...

unsigned	First_disk_boundary_id
	First boundary ID for warped disk. More...

unsigned	Last_disk_boundary_id
	Last boundary ID for warped disk. More...

unsigned	Torus_region_id
	Region ID for torus around edge of warped disk. More...

unsigned	First_disk_with_torus_boundary_id
	First boundary ID for disk that is surrounded by torus. More...

unsigned	Last_disk_with_torus_boundary_id
	Last boundary ID for disk that is surrounded by torus. More...

unsigned	First_torus_boundary_id
	First boundary ID for torus surrounding edge of disk. More...

unsigned	Last_torus_boundary_id
	Last boundary ID for torus surrounding edge of disk. More...

Vector< unsigned >	One_based_boundary_id_for_disk_within_torus

Vector< unsigned >	One_based_boundary_id_for_disk_outside_torus

unsigned	Above_disk_region_id
	Region ID for layer above disk. More...

unsigned	Below_disk_region_id
	Region ID for layer below disk. More...

unsigned	First_disk_with_layers_boundary_id
	First boundary ID for disk with layers. More...

unsigned	Last_disk_with_layers_boundary_id
	Last boundary ID for disk with layers. More...

double	Exact_bounded_volume
	Sanity check: Exact bounded volume. More...

unsigned	First_hollow_cube_boundary_id
	First boundary ID for hollow cube. More...

unsigned	First_cube_region_boundary_id
	First boundary ID for cube region. More...

unsigned	Cube_region_id
	Region ID for cube region. More...

unsigned	Internal_rectangle_boundary_id
	Boundary ID for rectangular facet in main volume. More...

unsigned	Internal_embedded_rectangle_boundary_id
	Boundary ID for rectangular facet embedded in region. More...

double	Exact_volume_of_hole
	Sanity check: Exact volume of hole. More...

double	Exact_volume_of_internal_region
	Sanity check: Exact volume of internal region. 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 TetmeshPoissonProblem< ELEMENT >

Demo class solves Poisson problem using Gmsh mesh.

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

Constructor & Destructor Documentation

◆ TetmeshPoissonProblem() [1/2]

template<class ELEMENT >

TetmeshPoissonProblem< ELEMENT >::TetmeshPoissonProblem

Constructor.

Keep track of (zero-based) IDs

 { 
  
  // OUTER BOUNDARY
  //===============
  
  // Start boundary IDs for outer boundary from some crazy offset
  // (just for testing). By default the one-based boundary IDs go from
  // 1 to 6; let's start from 1001.
  unsigned outer_boundary_id_offset=1000;
  
  //Make the outer boundary object
  Outer_boundary_pt = new CubicTetMeshFacetedSurface(
   Global_Parameters::Box_half_width,
   Global_Parameters::Box_half_length,
   outer_boundary_id_offset);
  
  // Look, we can visualise the faceted surface!
  Outer_boundary_pt->output("outer_faceted_surface.dat");
  
  // First oomph-lib (zero-based!) boundary ID for outer boundary
  First_boundary_id_for_outer_boundary=outer_boundary_id_offset;
  
  // For sanity check:
  Exact_bounded_volume=
   2.0*Global_Parameters::Box_half_width*
   2.0*Global_Parameters::Box_half_width*
   2.0*Global_Parameters::Box_half_length;
  
  
  // INTERNAL BOUNDARIES
  //====================
  
  
  
  // A warped disk
  //--------------
  
  // Warped disk with specified amplitude and wavenumber for warping
  double epsilon=0.1; 
  unsigned n=4;
  double z_offset=0.5;
  WarpedCircularDisk* disk_pt=new WarpedCircularDisk(epsilon,n,z_offset);
  
  // (Half) number of segments used to represent the disk perimeter
  unsigned half_nsegment=30; 
  
  // Start enumeration from here
  unsigned first_one_based_boundary_id=9001; 
  
  // Provide storage for last boundary ID on disk (don't know
  // in advance how many facets (with distinct IDs) the disk
  // is going to be represented by
  unsigned last_one_based_boundary_for_disk_id=0;
  
  // Create faceted representation of warped disk
  DiskTetMeshFacetedSurface* disk_faceted_surface_pt=
   new DiskTetMeshFacetedSurface(disk_pt,
                                 half_nsegment,
                                 first_one_based_boundary_id,
                                 last_one_based_boundary_for_disk_id);
  
  // Keep track of the (zero-based) boundary IDs
  First_disk_boundary_id=first_one_based_boundary_id-1;
  Last_disk_boundary_id=last_one_based_boundary_for_disk_id-1;
  
  // Look, we can visualise the faceted surface!
  disk_faceted_surface_pt->output("warped_disk_faceted_surface.dat");
  
  // Add as inner boundary for mesh
  Inner_boundary_pt.push_back(disk_faceted_surface_pt);
  
  
  
  // A warped disk surrounded by a torus
  //------------------------------------
  
  // Radius of torus region
  double r_torus=0.1;
  
  // Warped disk with specified amplitude and wavenumber for warping
  epsilon=0.1;
  n=5;
  
  // Thickness of annular region on disk = radius of torus surrounding the
  // edge
  double h_annulus=r_torus;
  WarpedCircularDiskWithAnnularInternalBoundary* disk2_pt =
   new WarpedCircularDiskWithAnnularInternalBoundary(h_annulus,epsilon,n);
  
  // Number of vertices around perimeter of torus
  unsigned nvertex_torus=20;
  
  // Enumerate the boundaries making up the disk starting with this
  // one-based ID
  unsigned first_one_based_disk_with_torus_boundary_id=
   last_one_based_boundary_for_disk_id+200;
  
  
  // These get returned
  unsigned last_one_based_disk_with_torus_boundary_id=0;
  unsigned first_one_based_torus_boundary_id=0;
  unsigned last_one_based_torus_boundary_id=0;
  
  // One-based region ID for torus
  unsigned one_based_torus_region_id=4;
  
  
  // Build disk with torus around the edge
  DiskWithTorusAroundEdgeTetMeshFacetedSurface* disk_with_torus_pt=
   new DiskWithTorusAroundEdgeTetMeshFacetedSurface(
    disk2_pt,
    half_nsegment,
    r_torus,
    nvertex_torus,
    first_one_based_disk_with_torus_boundary_id,
    one_based_torus_region_id, 
    last_one_based_disk_with_torus_boundary_id,
    first_one_based_torus_boundary_id,
    last_one_based_torus_boundary_id,
    One_based_boundary_id_for_disk_within_torus,
    One_based_boundary_id_for_disk_outside_torus);
  
  
  Torus_region_id=one_based_torus_region_id-1; 
  First_disk_with_torus_boundary_id=
   first_one_based_disk_with_torus_boundary_id-1;
  Last_disk_with_torus_boundary_id=
   last_one_based_disk_with_torus_boundary_id-1;
  First_torus_boundary_id=first_one_based_torus_boundary_id-1;
  Last_torus_boundary_id=last_one_based_torus_boundary_id-1;
  
  // Look, we can visualise the faceted surface!
  disk_with_torus_pt->output("warped_disk_with_torus_faceted_surface.dat");
  
  // Add as inner boundary for mesh
  Inner_boundary_pt.push_back(disk_with_torus_pt);
  
  
  
  // A warped disk bounded by a layer above and below
  //-------------------------------------------------
  
  // Warped disk with specified amplitude and wavenumber for warping
  epsilon=0.1;
  n=6;
  z_offset=-0.5;
  WarpedCircularDisk* disk3_pt=new WarpedCircularDisk(epsilon,n,z_offset);
  
  // Start enumeration from here
  first_one_based_boundary_id=last_one_based_torus_boundary_id+200;
  
  // Provide storage for last boundary ID on disk (don't know
  // in advance how many facets (with distinct IDs) the disk
  // is going to be represented by
  unsigned last_one_based_boundary_for_disk_with_layers_id=0;
  unsigned last_one_based_boundary_id=0;
   
  unsigned one_based_region_id_above_disk=2408;
  unsigned one_based_region_id_below_disk=2409;
  
  
  // Create faceted representation of warped disk
  DiskWithTwoLayersTetMeshFacetedSurface* disk_with_layers_faceted_surface_pt=
   new DiskWithTwoLayersTetMeshFacetedSurface
   (disk3_pt,
    half_nsegment,
    first_one_based_boundary_id,
    one_based_region_id_above_disk,
    one_based_region_id_below_disk,
    last_one_based_boundary_for_disk_with_layers_id,
    last_one_based_boundary_id);
  
  // // Keep track of the (zero-based) boundary IDs
  First_disk_with_layers_boundary_id=first_one_based_boundary_id-1;
  Last_disk_with_layers_boundary_id=
   last_one_based_boundary_for_disk_with_layers_id-1;
  
  // Zero-based region IDs
  Above_disk_region_id=one_based_region_id_above_disk-1; 
  Below_disk_region_id=one_based_region_id_below_disk-1; 
  
  
  // Look, we can visualise the faceted surface!
  disk_with_layers_faceted_surface_pt->output
   ("warped_disk_with_layers_faceted_surface.dat");
  
  // Add as inner boundary for mesh
  Inner_boundary_pt.push_back(disk_with_layers_faceted_surface_pt);
  
  
  // Build the mesh
  //--------------- 
  
  // Initial element volume
  double initial_element_volume=1.0;
  
  // Setup parameters for gmsh
  GmshParameters* gmsh_parameters_pt=
   new GmshParameters(Outer_boundary_pt,
                      Global_Parameters::Gmsh_command_line_invocation);
  
  // Element volume
  gmsh_parameters_pt->element_volume()=initial_element_volume;
  
  
  // Specify inner boundaries
  gmsh_parameters_pt->internal_surface_pt()=Inner_boundary_pt;
  
  // Filename for file in which target element size is stored
  // (for disk-based operation of gmsh)
  gmsh_parameters_pt->stem_for_filename_gmsh_size_transfer()=
   "target_size_on_grid";
  gmsh_parameters_pt->counter_for_filename_gmsh_size_transfer()=0;
  
  // Problem is linear so we don't need to transfer the solution to the
  // new mesh; we keep it on for self-test purposes...
  // gmsh_parameters_pt->disable_projection();
  
  // Redirect gmsh on-screen output
  gmsh_parameters_pt->gmsh_onscreen_output_file_name()=
   "RESLT/gmsh_on_screen_output.dat";
  
  // Not needed, of course, but here to test out the handling
  // of timesteppers
  add_time_stepper_pt(new Steady<1>);
  
 #ifdef DO_TETGEN
  
  // And now build it... 
  Bulk_mesh_pt =
   new RefineableTetgenMesh<ELEMENT>(Outer_boundary_pt,
                                     Inner_boundary_pt,
                                     initial_element_volume,
                                     this->time_stepper_pt());
  
  // Problem is linear so we don't need to transfer the solution to the
  // new mesh; we keep it on for self-test purposes...
  Bulk_mesh_pt->disable_projection();
  
 #else
  
  // And now build it...
  Bulk_mesh_pt = new RefineableGmshTetMesh<ELEMENT>(gmsh_parameters_pt,
                                                    this->time_stepper_pt());
  
 #endif
  
  // Add sub-mesh
  Problem::mesh_pt()=Bulk_mesh_pt;
  
  // Set error estimator for bulk mesh
  Z2ErrorEstimator* error_estimator_pt=new Z2ErrorEstimator;
  Bulk_mesh_pt->spatial_error_estimator_pt()=error_estimator_pt;
  
  // Set targets for spatial adaptivity
  Bulk_mesh_pt->max_permitted_error()=0.0005; 
  Bulk_mesh_pt->min_permitted_error()=0.00001;
  
  // Complete problem setup
  complete_problem_setup();
  
 #ifdef OOMPH_HAS_HYPRE
  
  // Create a new Hypre linear solver
  HypreSolver* hypre_linear_solver_pt = new HypreSolver;
  
  // Set the linear solver for problem
  linear_solver_pt() = hypre_linear_solver_pt;
  
  // Set some solver parameters
  hypre_linear_solver_pt->max_iter() = 100;
  hypre_linear_solver_pt->tolerance() = 1e-10;
  hypre_linear_solver_pt->amg_simple_smoother() = 1;
  hypre_linear_solver_pt->disable_doc_time();
  hypre_linear_solver_pt->enable_hypre_error_messages();
  hypre_linear_solver_pt->amg_print_level() = 0;
  hypre_linear_solver_pt->krylov_print_level() = 0;
  hypre_linear_solver_pt->hypre_method() = HypreSolver::BoomerAMG;
    
 #endif
  
  // Setup equation numbering scheme
  oomph_info <<"Number of equations: " << assign_eqn_numbers() << std::endl; 
  
 }

References oomph::HypreSolver::amg_print_level(), oomph::HypreSolver::amg_simple_smoother(), Global_Parameters::Box_half_length, Global_Parameters::Box_half_width, oomph::GmshParameters::counter_for_filename_gmsh_size_transfer(), oomph::LinearSolver::disable_doc_time(), e(), oomph::GmshParameters::element_volume(), oomph::HypreInterface::enable_hypre_error_messages(), oomph::SarahBL::epsilon, MeshRefinement::error_estimator_pt, Global_Parameters::Gmsh_command_line_invocation, oomph::GmshParameters::gmsh_onscreen_output_file_name(), oomph::HypreSolver::hypre_method(), oomph::GmshParameters::internal_surface_pt(), oomph::HypreSolver::krylov_print_level(), oomph::HypreSolver::max_iter(), n, oomph::oomph_info, oomph::TetMeshFacetedSurface::output(), oomph::GmshParameters::stem_for_filename_gmsh_size_transfer(), and oomph::HypreSolver::tolerance().

◆ ~TetmeshPoissonProblem() [1/2]

template<class ELEMENT >

TetmeshPoissonProblem< ELEMENT >::~TetmeshPoissonProblem ( )

inline

Destructor (empty)

   {
    //Delete the objects
    unsigned nh = Inner_boundary_pt.size();
    for(unsigned h=0;h<nh;++h)
     {
      delete Inner_boundary_pt[h];
     }
    delete Outer_boundary_pt;
   }

◆ TetmeshPoissonProblem() [2/2]

template<class ELEMENT >

TetmeshPoissonProblem< ELEMENT >::TetmeshPoissonProblem ( )

Constructor.

◆ ~TetmeshPoissonProblem() [2/2]

template<class ELEMENT >

TetmeshPoissonProblem< ELEMENT >::~TetmeshPoissonProblem ( )

inline

Destructor (empty)

   {
    //Delete the objects
    unsigned nh = Inner_boundary_pt.size();
    for(unsigned h=0;h<nh;++h)
     {
      delete Inner_boundary_pt[h];
     }
    delete Outer_boundary_pt;
   }

Member Function Documentation

◆ actions_after_adapt() [1/2]

template<class ELEMENT >

void TetmeshPoissonProblem< ELEMENT >::actions_after_adapt ( )

inlinevirtual

Totally new mesh; build elements and apply boundary conditions.

Reimplemented from oomph::Problem.

   {
    // Complete problem setup
    complete_problem_setup();
   }

◆ actions_after_adapt() [2/2]

template<class ELEMENT >

void TetmeshPoissonProblem< ELEMENT >::actions_after_adapt ( )

inlinevirtual

Totally new mesh; build elements and apply boundary conditions.

Reimplemented from oomph::Problem.

   {
    // Complete problem setup
    complete_problem_setup();
   }

◆ actions_after_newton_solve() [1/2]

template<class ELEMENT >

void TetmeshPoissonProblem< ELEMENT >::actions_after_newton_solve ( )

inlinevirtual

Update the problem specs before solve (empty)

Reimplemented from oomph::Problem.

124 {}

◆ actions_after_newton_solve() [2/2]

template<class ELEMENT >

void TetmeshPoissonProblem< ELEMENT >::actions_after_newton_solve ( )

inlinevirtual

Update the problem specs before solve (empty)

Reimplemented from oomph::Problem.

128 {}

◆ actions_before_adapt() [1/2]

template<class ELEMENT >

void TetmeshPoissonProblem< ELEMENT >::actions_before_adapt ( )

inlinevirtual

Actions before adapt (empty)

Reimplemented from oomph::Problem.

111 {}

◆ actions_before_adapt() [2/2]

template<class ELEMENT >

void TetmeshPoissonProblem< ELEMENT >::actions_before_adapt ( )

inlinevirtual

Actions before adapt (empty)

Reimplemented from oomph::Problem.

115 {}

◆ actions_before_newton_solve() [1/2]

template<class ELEMENT >

void TetmeshPoissonProblem< ELEMENT >::actions_before_newton_solve ( )

inlinevirtual

Update the problem specs before solve: (empty)

Reimplemented from oomph::Problem.

121 {}

◆ actions_before_newton_solve() [2/2]

template<class ELEMENT >

void TetmeshPoissonProblem< ELEMENT >::actions_before_newton_solve ( )

inlinevirtual

Update the problem specs before solve: (empty)

Reimplemented from oomph::Problem.

125 {}

◆ apply_boundary_conditions() [1/2]

template<class ELEMENT >

void TetmeshPoissonProblem< ELEMENT >::apply_boundary_conditions

private

Helper function to apply boundary conditions.

 {
  
  
  ofstream pin_file;
  pin_file.open("pinned_nodes.dat");
  
  // Identify boundary ids of pinned nodes
  
  
  Vector<unsigned> pinned_boundary_id;
  for (unsigned ibound=First_disk_boundary_id;
       ibound<=Last_disk_boundary_id;ibound++)
   {
    pinned_boundary_id.push_back(ibound);
   }
  for (unsigned ibound=First_disk_with_torus_boundary_id;
       ibound<=Last_disk_with_torus_boundary_id;ibound++)
   {
    pinned_boundary_id.push_back(ibound);
   }
  for (unsigned ibound=First_disk_with_layers_boundary_id;
       ibound<=Last_disk_with_layers_boundary_id;ibound++)
   {
    pinned_boundary_id.push_back(ibound);
   }
  for (unsigned ibound=First_boundary_id_for_outer_boundary;
       ibound<First_boundary_id_for_outer_boundary+6;ibound++)
   {
    pinned_boundary_id.push_back(ibound);
   }
  
  // Loop over pinned boundaries
  unsigned num_pin_bnd=pinned_boundary_id.size();
  for (unsigned bnd=0;bnd<num_pin_bnd;bnd++)
   {
    unsigned ibound=pinned_boundary_id[bnd];
    unsigned num_nod= Bulk_mesh_pt->nboundary_node(ibound);
    if (num_nod==0)
     {
      std::ostringstream error_message;
      error_message << "No boundary nodes on boundary " 
                    << ibound << "! Something's gone wrong!\n";
      throw OomphLibError(error_message.str(),
                          OOMPH_CURRENT_FUNCTION,
                          OOMPH_EXCEPTION_LOCATION);
     }
    for (unsigned inod=0;inod<num_nod;inod++)
     {
      Bulk_mesh_pt->boundary_node_pt(ibound,inod)->pin(0);
      Vector<double> x(3);
      x[0]=Bulk_mesh_pt->boundary_node_pt(ibound,inod)->x(0);
      x[1]=Bulk_mesh_pt->boundary_node_pt(ibound,inod)->x(1);
      x[2]=Bulk_mesh_pt->boundary_node_pt(ibound,inod)->x(2);
  
      // Zero BC on outer boundary; unit BC elsewhere
      double value=0.0;
      if ((ibound>=First_disk_with_torus_boundary_id)&&
          (ibound<=Last_disk_with_torus_boundary_id))
       {
        value=1.0;
       }
      if ((ibound>=First_disk_boundary_id)&&
          (ibound<=Last_disk_boundary_id))
       {
        value=1.0;
       }
      if ((ibound>=First_disk_with_layers_boundary_id)&&
          (ibound<=Last_disk_with_layers_boundary_id))
       {
        value=1.0;
       }
  
      Bulk_mesh_pt->boundary_node_pt(ibound,inod)->set_value(0,value);
      pin_file << x[0] << " " 
               << x[1] << " " 
               << x[2] << " " 
               << std::endl;
     }
   }
  
  pin_file.close();
  
  
  
 } // end set bc

References OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION, Eigen::value, and plotDoE::x.

◆ apply_boundary_conditions() [2/2]

template<class ELEMENT >

void TetmeshPoissonProblem< ELEMENT >::apply_boundary_conditions ( )

private

Helper function to apply boundary conditions.

◆ complete_problem_setup() [1/2]

template<class ELEMENT >

void TetmeshPoissonProblem< ELEMENT >::complete_problem_setup

private

Apply BCs and make elements functional.

Complete problem setup.

 {
  // Apply bcs
  apply_boundary_conditions();
 }

◆ complete_problem_setup() [2/2]

template<class ELEMENT >

void TetmeshPoissonProblem< ELEMENT >::complete_problem_setup ( )

private

Apply BCs and make elements functional.

◆ doc_solution() [1/2]

template<class ELEMENT >

void TetmeshPoissonProblem< ELEMENT >::doc_solution	(	const unsigned &	nplot,
		DocInfo &	doc_info
	)

Doc the solution.

so if it's very large it's BAAAAAD)

 { 
  
  
  bool do_bulk_output=true;
  if (CommandLineArgs::command_line_flag_has_been_set("--suppress_bulk_output"))
   {
    do_bulk_output=false;
   }
  
  ofstream some_file;
  ofstream some_file2;
  ofstream face_some_file;
  ofstream coarse_some_file;
  char filename[100];
  
  
  // Doc mesh quality (Ratio of max. edge length to min. height,
  sprintf(filename,"%s/mesh_quality%i.dat",
          doc_info.directory().c_str(),
          doc_info.number()); 
  ofstream quality_file;
  quality_file.open(filename);
  if (do_bulk_output) Bulk_mesh_pt->assess_mesh_quality(quality_file);
  quality_file.close();
  
  
  // Output elements adjacent to outer boundary
  //-------------------------------------------
  sprintf(filename,"%s/elements_next_to_outer_boundary%i.dat",
          doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  for (unsigned ibound=First_boundary_id_for_outer_boundary;
       ibound<First_boundary_id_for_outer_boundary+6;ibound++)
   {
    unsigned n_el=Bulk_mesh_pt->nboundary_element(ibound);
    for (unsigned e=0;e<n_el;e++)
     {
      if (do_bulk_output) 
       {
        Bulk_mesh_pt->boundary_element_pt(ibound,e)->
         output(some_file,nplot);
       }
     }
   }
  some_file.close();
  
  
  // Output boundary coordinates on outer boundary
  //-----------------------------------------------
  sprintf(filename,"%s/boundary_coordinates_outer_boundary%i.dat",
          doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  for (unsigned ibound=First_boundary_id_for_outer_boundary;
       ibound<First_boundary_id_for_outer_boundary+6;ibound++)
   {
    Bulk_mesh_pt->Mesh::template 
     doc_boundary_coordinates<ELEMENT>(ibound,some_file);
   }
  some_file.close();
  
  // Output boundary coordinates on outer boundary
  //-----------------------------------------------
  unsigned n_b=Bulk_mesh_pt->nboundary();
  oomph_info << "number of boundaries in bulk mesh: " << n_b << std::endl;
  sprintf(filename,"%s/boundary_coordinates%i.dat",
          doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  for (unsigned ibound=0;ibound<n_b;ibound++)
   {
    if (Bulk_mesh_pt->boundary_coordinate_exists(ibound))
     {
      Bulk_mesh_pt->Mesh::template 
       doc_boundary_coordinates<ELEMENT>(ibound,some_file);
     }
   }
  some_file.close();
  
  
  // Output boundaries
  //------------------
  sprintf(filename,"%s/boundaries%i.dat",doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  Bulk_mesh_pt->output_boundaries(some_file);
  some_file.close();
  
  
  // Output volumes and areas
  //-------------------------
  std::ofstream volumes_and_areas_file;
  sprintf(filename,"%s/volumes%i.dat",doc_info.directory().c_str(),
          doc_info.number());
  volumes_and_areas_file.open(filename);
  
  
  // Output bulk elements in torus region
  //-------------------------------------
  double volume_in_torus_region=0.0;
  sprintf(filename,"%s/soln_in_torus_region%i.dat",doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  unsigned region_id=Torus_region_id;
  unsigned n_el=Bulk_mesh_pt->nregion_element(region_id);
  for (unsigned e=0;e<n_el;e++)
   {
    if (do_bulk_output) 
     {
      Bulk_mesh_pt->region_element_pt(region_id,e)->output(some_file,nplot);
     }
    volume_in_torus_region+=Bulk_mesh_pt->
     region_element_pt(region_id,e)->size();
   }
  some_file.close();
  
  // Output bulk elements above disk
  //--------------------------------
  double volume_in_above_disk_region=0.0;
  sprintf(filename,"%s/soln_in_above_disk_region%i.dat",
          doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  region_id=Above_disk_region_id;
  n_el=Bulk_mesh_pt->nregion_element(region_id);
  for (unsigned e=0;e<n_el;e++)
   {
    if (do_bulk_output) 
     {
      Bulk_mesh_pt->region_element_pt(region_id,e)->output(some_file,nplot);
     }
    volume_in_above_disk_region+=Bulk_mesh_pt->
     region_element_pt(region_id,e)->size();
   }
  some_file.close();
  
  
  // Output bulk elements below disk
  //--------------------------------
  double volume_in_below_disk_region=0.0;
  sprintf(filename,"%s/soln_in_below_disk_region%i.dat",
          doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  region_id=Above_disk_region_id;
  n_el=Bulk_mesh_pt->nregion_element(region_id);
  for (unsigned e=0;e<n_el;e++)
   {
    if (do_bulk_output) 
     {
      Bulk_mesh_pt->region_element_pt(region_id,e)->output(some_file,nplot);
     }
    volume_in_below_disk_region+=Bulk_mesh_pt->
     region_element_pt(region_id,e)->size();
   }
  some_file.close();
  
  // Output bulk elements in region 0
  //--------------------------------- 
  double volume_in_region0=0.0;
  sprintf(filename,"%s/soln_in_zero_region%i.dat",doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  region_id=0;
  n_el=Bulk_mesh_pt->nregion_element(region_id);
  for (unsigned e=0;e<n_el;e++)
   {
    if (do_bulk_output) 
     {
      Bulk_mesh_pt->region_element_pt(region_id,e)->output(some_file,nplot);
     }
    volume_in_region0+= Bulk_mesh_pt->region_element_pt(region_id,e)->size();
    }
  some_file.close();
  
  
  // Get total mesh volume
  double total_mesh_volume=0.0;
  n_el=Bulk_mesh_pt->nelement();
  for (unsigned e=0;e<n_el;e++)
   {
    total_mesh_volume+=Bulk_mesh_pt->finite_element_pt(e)->size();
   }
  
  
  // Check volumes:
  oomph_info << "Error in total region volume balance: " <<
   abs(total_mesh_volume-(volume_in_above_disk_region+
                          volume_in_below_disk_region+
                          volume_in_torus_region+
                          volume_in_region0))/total_mesh_volume*100.0 
             << " % " << std::endl;
  
  oomph_info << "Error in above/below disk region volume balance: " <<
   abs(volume_in_above_disk_region-volume_in_below_disk_region)/
   volume_in_above_disk_region*100.0 << " % " << std::endl;
  
  
  // Attach face elements to boundary of torus
  //------------------------------------------
  sprintf(filename,"%s/face_elements_on_boundary_of_torus%i.dat",
          doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  double torus_surface_area=0.0;
  region_id=Torus_region_id;
  for (unsigned b=First_torus_boundary_id;
       b<=Last_torus_boundary_id;b++)
   {
    unsigned nel=Bulk_mesh_pt->nboundary_element_in_region(b,region_id);
    for (unsigned e=0;e<nel;e++)
     {
      FiniteElement* el_pt=
       Bulk_mesh_pt->boundary_element_in_region_pt(b,region_id,e);
      
      // What is the index of the face of the bulk element at the boundary
      int face_index = Bulk_mesh_pt->
       face_index_at_boundary_in_region(b,region_id,e);
      
      // Build the corresponding flux jump element
      PoissonFluxElement<ELEMENT>* flux_element_pt 
       = new PoissonFluxElement<ELEMENT>(el_pt,face_index);
      
      // Get surface area
      torus_surface_area+=flux_element_pt->size();
      
      // Output
      flux_element_pt->output(some_file);
      
      // ...and we're done!
      delete flux_element_pt;
     }
   }
  some_file.close();
  oomph_info << "Torus surface area: " <<  torus_surface_area << std::endl;
  
  
  // Attach face elements to part of disk inside torus
  //--------------------------------------------------
  sprintf(filename,"%s/face_elements_on_disk_in_torus%i.dat",
          doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  double disk_in_torus_surface_area=0.0;
  region_id=Torus_region_id;
  unsigned nb=One_based_boundary_id_for_disk_within_torus.size();
  for (unsigned i=0;i<nb;i++)
   {
    unsigned b=One_based_boundary_id_for_disk_within_torus[i]-1;
    unsigned nel=Bulk_mesh_pt->nboundary_element_in_region(b,region_id);
    for (unsigned e=0;e<nel;e++)
     {
      FiniteElement* el_pt=
       Bulk_mesh_pt->boundary_element_in_region_pt(b,region_id,e);
      
      // What is the index of the face of the bulk element at the boundary
      int face_index = Bulk_mesh_pt->
       face_index_at_boundary_in_region(b,region_id,e);
      
      // Build the corresponding flux jump element
      PoissonFluxElement<ELEMENT>* flux_element_pt 
       = new PoissonFluxElement<ELEMENT>(el_pt,face_index);
      
      // Get surface area
      disk_in_torus_surface_area+=flux_element_pt->size();
      
      // Output
      flux_element_pt->output(some_file);
      
      // ...and we're done!
      delete flux_element_pt;
     }
   }
  some_file.close();
  oomph_info << "Disk in torus surface area: "
             <<  disk_in_torus_surface_area << std::endl;
  
  
  // Attach face elements to part of disk outside torus
  //--------------------------------------------------
  sprintf(filename,"%s/face_elements_on_disk_outside_torus%i.dat",
          doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  double disk_outside_torus_surface_area=0.0;
  region_id=0; 
  nb=One_based_boundary_id_for_disk_outside_torus.size();
  for (unsigned i=0;i<nb;i++)
   {
    unsigned b=One_based_boundary_id_for_disk_outside_torus[i]-1;
    unsigned nel=Bulk_mesh_pt->nboundary_element_in_region(b,region_id);
    for (unsigned e=0;e<nel;e++)
     {
      FiniteElement* el_pt=
       Bulk_mesh_pt->boundary_element_in_region_pt(b,region_id,e);
      
      // What is the index of the face of the bulk element at the boundary
      int face_index = Bulk_mesh_pt->
       face_index_at_boundary_in_region(b,region_id,e);
      
      // Build the corresponding flux jump element
      PoissonFluxElement<ELEMENT>* flux_element_pt 
       = new PoissonFluxElement<ELEMENT>(el_pt,face_index);
      
      // Get surface area
      disk_outside_torus_surface_area+=flux_element_pt->size();
      
      // Output
      flux_element_pt->output(some_file);
      
      // ...and we're done!
      delete flux_element_pt;
     }
   }
  some_file.close();
  oomph_info << "Disk outside torus surface area: "
             <<  disk_outside_torus_surface_area << std::endl;
  
  oomph_info << "Total surface area of disk with torus: "
             <<  disk_in_torus_surface_area+disk_outside_torus_surface_area 
             << std::endl;
  
  
  // Attach face elements to free-standing disk
  //-------------------------------------------
  sprintf(filename,"%s/face_elements_on_free_standing_disk%i.dat",
          doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  double free_standing_disk_surface_area=0.0;
  region_id=0; 
  for (unsigned b=First_disk_boundary_id;
       b<Last_disk_boundary_id;b++)
   {
    unsigned nel=Bulk_mesh_pt->nboundary_element_in_region(b,region_id);
    for (unsigned e=0;e<nel;e++)
     {
      FiniteElement* el_pt=
       Bulk_mesh_pt->boundary_element_in_region_pt(b,region_id,e);
      
      // What is the index of the face of the bulk element at the boundary
      int face_index = Bulk_mesh_pt->
       face_index_at_boundary_in_region(b,region_id,e);
      
      // Build the corresponding flux jump element
      PoissonFluxElement<ELEMENT>* flux_element_pt 
       = new PoissonFluxElement<ELEMENT>(el_pt,face_index);
      
      // Get surface area
      free_standing_disk_surface_area+=flux_element_pt->size();
      
      // Output
      flux_element_pt->output(some_file);
      
      // ...and we're done!
      delete flux_element_pt;
     }
   }
  some_file.close();
  oomph_info << "Free-standing disk surface area: "
             << free_standing_disk_surface_area << std::endl;
  
  
  // Attach face elements to disk surrounded by layers: above
  //---------------------------------------------------------
  sprintf(filename,"%s/face_elements_on_disk_upper_layer%i.dat",
          doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  double disk_upper_layer_surface_area=0.0;
  region_id=Above_disk_region_id;
  for (unsigned b=First_disk_with_layers_boundary_id;
       b<=Last_disk_with_layers_boundary_id;b++)
   {
    unsigned nel=Bulk_mesh_pt->nboundary_element_in_region(b,region_id);
    for (unsigned e=0;e<nel;e++)
     {
      FiniteElement* el_pt=
       Bulk_mesh_pt->boundary_element_in_region_pt(b,region_id,e);
      
      // What is the index of the face of the bulk element at the boundary
      int face_index = Bulk_mesh_pt->
       face_index_at_boundary_in_region(b,region_id,e);
      
      // Build the corresponding flux jump element
      PoissonFluxElement<ELEMENT>* flux_element_pt 
       = new PoissonFluxElement<ELEMENT>(el_pt,face_index);
      
      // Get surface area
      disk_upper_layer_surface_area+=flux_element_pt->size();
      
      // Output
      flux_element_pt->output(some_file);
      
      // ...and we're done!
      delete flux_element_pt;
     }
   }
  some_file.close();
  oomph_info << "Disk upper layer surface area: "
             <<  disk_upper_layer_surface_area << std::endl;
  
  
  // Attach face elements to disk surrounded by layers: below
  //---------------------------------------------------------
  sprintf(filename,"%s/face_elements_on_disk_lower_layer%i.dat",
          doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  double disk_lower_layer_surface_area=0.0;
  region_id=Below_disk_region_id;
  for (unsigned b=First_disk_with_layers_boundary_id;
       b<=Last_disk_with_layers_boundary_id;b++)
   {
    unsigned nel=Bulk_mesh_pt->nboundary_element_in_region(b,region_id);
    for (unsigned e=0;e<nel;e++)
     {
      FiniteElement* el_pt=
       Bulk_mesh_pt->boundary_element_in_region_pt(b,region_id,e);
      
      // What is the index of the face of the bulk element at the boundary
      int face_index = Bulk_mesh_pt->
       face_index_at_boundary_in_region(b,region_id,e);
      
      // Build the corresponding flux jump element
      PoissonFluxElement<ELEMENT>* flux_element_pt 
       = new PoissonFluxElement<ELEMENT>(el_pt,face_index);
      
      // Get surface area
      disk_lower_layer_surface_area+=flux_element_pt->size();
      
      // Output
      flux_element_pt->output(some_file);
      
      // ...and we're done!
      delete flux_element_pt;
     }
   }
  some_file.close();
  oomph_info << "Disk lower layer surface area: "
             <<  disk_lower_layer_surface_area << std::endl;
  
  
  // Doc volumes and areas
  volumes_and_areas_file << volume_in_above_disk_region << " " 
                         << volume_in_below_disk_region << " " 
                         << volume_in_torus_region << " " 
                         << total_mesh_volume << " " 
                         << volume_in_region0 << " "
                         << torus_surface_area << " " 
                         << disk_in_torus_surface_area << " " 
                         << disk_outside_torus_surface_area << " " 
                         << disk_upper_layer_surface_area << " " 
                         << disk_lower_layer_surface_area << " " 
                         << free_standing_disk_surface_area << " " 
                         << std::endl;
  volumes_and_areas_file.close();
  
  
  // Output solution
  //----------------
  sprintf(filename,"%s/soln%i.dat",doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  if (do_bulk_output) Bulk_mesh_pt->output(some_file,nplot);
  some_file.close();
  
  // Output solution showing element outlines
  //-----------------------------------------
  sprintf(filename,"%s/coarse_soln%i.dat",doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  if (do_bulk_output) Bulk_mesh_pt->output(some_file,2);
  some_file.close();
  
  
  // Get norm of solution
  //---------------------
  sprintf(filename,"%s/norm%i.dat",doc_info.directory().c_str(),
          doc_info.number());
  some_file.open(filename);
  double norm_soln=0.0;
  Bulk_mesh_pt->compute_norm(norm_soln);  
  some_file << sqrt(norm_soln) << std::endl;
  oomph_info << "Norm of computed solution: "   << sqrt(norm_soln)  << endl;
  some_file.close();
  
 } // end of doc

References abs(), b, oomph::CommandLineArgs::command_line_flag_has_been_set(), oomph::DocInfo::directory(), e(), MergeRestartFiles::filename, i, nb, oomph::DocInfo::number(), oomph::oomph_info, oomph::PoissonFluxElement< ELEMENT >::output(), output(), oomph::FiniteElement::size(), and sqrt().

◆ doc_solution() [2/2]

template<class ELEMENT >

void TetmeshPoissonProblem< ELEMENT >::doc_solution	(	const unsigned &	nplot,
		DocInfo &	doc_info
	)

Doc the solution.

Member Data Documentation

◆ Above_disk_region_id

template<class ELEMENT >

unsigned TetmeshPoissonProblem< ELEMENT >::Above_disk_region_id

private

Region ID for layer above disk.

◆ Below_disk_region_id

template<class ELEMENT >

unsigned TetmeshPoissonProblem< ELEMENT >::Below_disk_region_id

private

Region ID for layer below disk.

◆ Bulk_mesh_pt

template<class ELEMENT >

RefineableGmshTetMesh< ELEMENT > * TetmeshPoissonProblem< ELEMENT >::Bulk_mesh_pt

private

Bulk mesh.

◆ Cube_region_id

template<class ELEMENT >

unsigned TetmeshPoissonProblem< ELEMENT >::Cube_region_id

private

Region ID for cube region.

◆ Exact_bounded_volume

template<class ELEMENT >

double TetmeshPoissonProblem< ELEMENT >::Exact_bounded_volume

private

Sanity check: Exact bounded volume.

◆ Exact_volume_of_hole

template<class ELEMENT >

double TetmeshPoissonProblem< ELEMENT >::Exact_volume_of_hole

private

Sanity check: Exact volume of hole.

◆ Exact_volume_of_internal_region

template<class ELEMENT >

double TetmeshPoissonProblem< ELEMENT >::Exact_volume_of_internal_region

private

Sanity check: Exact volume of internal region.

◆ First_boundary_id_for_outer_boundary

template<class ELEMENT >

unsigned TetmeshPoissonProblem< ELEMENT >::First_boundary_id_for_outer_boundary

private

First boundary ID for outer boundary.

◆ First_cube_region_boundary_id

template<class ELEMENT >

unsigned TetmeshPoissonProblem< ELEMENT >::First_cube_region_boundary_id

private

First boundary ID for cube region.

◆ First_disk_boundary_id

template<class ELEMENT >

unsigned TetmeshPoissonProblem< ELEMENT >::First_disk_boundary_id

private

First boundary ID for warped disk.

◆ First_disk_with_layers_boundary_id

template<class ELEMENT >

unsigned TetmeshPoissonProblem< ELEMENT >::First_disk_with_layers_boundary_id

private

First boundary ID for disk with layers.

◆ First_disk_with_torus_boundary_id

template<class ELEMENT >

unsigned TetmeshPoissonProblem< ELEMENT >::First_disk_with_torus_boundary_id

private

First boundary ID for disk that is surrounded by torus.

◆ First_hollow_cube_boundary_id

template<class ELEMENT >

unsigned TetmeshPoissonProblem< ELEMENT >::First_hollow_cube_boundary_id

private

First boundary ID for hollow cube.

◆ First_torus_boundary_id

template<class ELEMENT >

unsigned TetmeshPoissonProblem< ELEMENT >::First_torus_boundary_id

private

First boundary ID for torus surrounding edge of disk.

◆ Inner_boundary_pt

template<class ELEMENT >

Vector< TetMeshFacetedSurface * > TetmeshPoissonProblem< ELEMENT >::Inner_boundary_pt

private

Inner boundary.

◆ Internal_embedded_rectangle_boundary_id

template<class ELEMENT >

unsigned TetmeshPoissonProblem< ELEMENT >::Internal_embedded_rectangle_boundary_id

private

Boundary ID for rectangular facet embedded in region.

◆ Internal_rectangle_boundary_id

template<class ELEMENT >

unsigned TetmeshPoissonProblem< ELEMENT >::Internal_rectangle_boundary_id

private

Boundary ID for rectangular facet in main volume.

◆ Last_disk_boundary_id

template<class ELEMENT >

unsigned TetmeshPoissonProblem< ELEMENT >::Last_disk_boundary_id

private

Last boundary ID for warped disk.

◆ Last_disk_with_layers_boundary_id

template<class ELEMENT >

unsigned TetmeshPoissonProblem< ELEMENT >::Last_disk_with_layers_boundary_id

private

Last boundary ID for disk with layers.

◆ Last_disk_with_torus_boundary_id

template<class ELEMENT >

unsigned TetmeshPoissonProblem< ELEMENT >::Last_disk_with_torus_boundary_id

private

Last boundary ID for disk that is surrounded by torus.

◆ Last_torus_boundary_id

template<class ELEMENT >

unsigned TetmeshPoissonProblem< ELEMENT >::Last_torus_boundary_id

private

Last boundary ID for torus surrounding edge of disk.

◆ One_based_boundary_id_for_disk_outside_torus

template<class ELEMENT >

Vector<unsigned> TetmeshPoissonProblem< ELEMENT >::One_based_boundary_id_for_disk_outside_torus

private

Storage for one-based boundary IDs for boundaries on disk outside the torus region

◆ One_based_boundary_id_for_disk_within_torus

template<class ELEMENT >

Vector<unsigned> TetmeshPoissonProblem< ELEMENT >::One_based_boundary_id_for_disk_within_torus

private

Storage for one-based boundary IDs for boundaries on disk within the torus region

◆ Outer_boundary_pt

template<class ELEMENT >

TetMeshFacetedClosedSurface * TetmeshPoissonProblem< ELEMENT >::Outer_boundary_pt

private

Storage for the outer boundary object.

◆ Torus_region_id

template<class ELEMENT >

unsigned TetmeshPoissonProblem< ELEMENT >::Torus_region_id

private

Region ID for torus around edge of warped disk.

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 TetmeshPoissonProblem< ELEMENT >

Constructor & Destructor Documentation

◆ TetmeshPoissonProblem() [1/2]

◆ ~TetmeshPoissonProblem() [1/2]

◆ TetmeshPoissonProblem() [2/2]

◆ ~TetmeshPoissonProblem() [2/2]

Member Function Documentation

◆ actions_after_adapt() [1/2]

◆ actions_after_adapt() [2/2]

◆ actions_after_newton_solve() [1/2]

◆ actions_after_newton_solve() [2/2]

◆ actions_before_adapt() [1/2]

◆ actions_before_adapt() [2/2]

◆ actions_before_newton_solve() [1/2]

◆ actions_before_newton_solve() [2/2]

◆ apply_boundary_conditions() [1/2]

◆ apply_boundary_conditions() [2/2]

◆ complete_problem_setup() [1/2]

◆ complete_problem_setup() [2/2]

◆ doc_solution() [1/2]

◆ doc_solution() [2/2]

Member Data Documentation

◆ Above_disk_region_id

◆ Below_disk_region_id

◆ Bulk_mesh_pt

◆ Cube_region_id

◆ Exact_bounded_volume

◆ Exact_volume_of_hole

◆ Exact_volume_of_internal_region

◆ First_boundary_id_for_outer_boundary

◆ First_cube_region_boundary_id

◆ First_disk_boundary_id

◆ First_disk_with_layers_boundary_id

◆ First_disk_with_torus_boundary_id

◆ First_hollow_cube_boundary_id

◆ First_torus_boundary_id

◆ Inner_boundary_pt

◆ Internal_embedded_rectangle_boundary_id

◆ Internal_rectangle_boundary_id

◆ Last_disk_boundary_id

◆ Last_disk_with_layers_boundary_id

◆ Last_disk_with_torus_boundary_id

◆ Last_torus_boundary_id

◆ One_based_boundary_id_for_disk_outside_torus

◆ One_based_boundary_id_for_disk_within_torus

◆ Outer_boundary_pt

◆ Torus_region_id

template<class ELEMENT>
class TetmeshPoissonProblem< ELEMENT >