Problem class. More...

Inheritance diagram for PMLStructuredCubicHelmholtz< ELEMENT >:

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

	~PMLStructuredCubicHelmholtz ()
	Destructor (empty) More...

void	doc_solution ()
	Doc the solution. More...

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

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

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

void	actions_after_adapt ()
	Actions after adapt:(empty) More...

void	set_gmres_multigrid_solver ()
	Set GMRES preconditioner by multigrid as the linear solver. More...

void	enable_pmls ()
	Enable the PML mapping function for all nodes in the PML region. More...

void	apply_boundary_conditions ()
	Apply boundary conditions. More...

Public Member Functions inherited from oomph::HelmholtzMGProblem
	HelmholtzMGProblem ()
	Constructor. Initialise pointers to coarser and finer levels. More...

virtual	~HelmholtzMGProblem ()
	Destructor (empty) 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
HelmholtzMGProblem *	make_new_problem ()
	Overload the make_new_problem function to return an object of this class. More...

TreeBasedRefineableMeshBase *	mg_bulk_mesh_pt ()

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

ofstream	Trace_file
	Trace file. 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 PMLStructuredCubicHelmholtz< ELEMENT >

Problem class.

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

Constructor & Destructor Documentation

◆ PMLStructuredCubicHelmholtz()

template<class ELEMENT >

PMLStructuredCubicHelmholtz< ELEMENT >::PMLStructuredCubicHelmholtz

Constructor.

Constructor for Helmholtz problem.

 {
  // Indicate that the problem is nonlinear to ensure the residual is
  // calculated at the end of the iteration
  problem_is_nonlinear(true);
  
  // Set the number of Newton iterations to one
  max_newton_iterations()=1;
  
  // Set up solver specific information:
  //------------------------------------
  // If we're choosing to use GMRES & MG as our linear solver
  if (GlobalParameters::Linear_solver_flag==1)
  {
   // Set the solver
   set_gmres_multigrid_solver();
  }
  
  // Open trace file
  Trace_file.open("RESLT/trace.dat");
  
  // Build the mesh using the specified parameters:
  //-----------------------------------------------
  // Build the "bulk" mesh
  Bulk_mesh_pt=new RefineableSimpleCubicMesh<ELEMENT>(
   GlobalParameters::Nx,GlobalParameters::Ny,GlobalParameters::Nz,
   GlobalParameters::Lx,GlobalParameters::Ly,GlobalParameters::Lz);
  
  // Create/set error estimator
  Bulk_mesh_pt->spatial_error_estimator_pt()=new Z2ErrorEstimator;
  
  // Choose error tolerances
  Bulk_mesh_pt->max_permitted_error()=1.0e-03;
  Bulk_mesh_pt->min_permitted_error()=1.0e-06;
  
  // Create the main mesh
  add_sub_mesh(Bulk_mesh_pt);
  
  // Build the entire mesh from its submeshes
  build_global_mesh();
  
  // Complete the build of all elements so they are fully functional: 
  //-----------------------------------------------------------------
  // How many elements in the mesh?
  unsigned n_element=mesh_pt()->nelement();
  
  // Loop over the elements and pass a pointer to the value of k^2
  for (unsigned e=0;e<n_element;e++)
  {
   // Upcast from GeneralisedElement to Helmholtz bulk element
   ELEMENT* el_pt=dynamic_cast<ELEMENT*>(Bulk_mesh_pt->element_pt(e));
  
   // If the upcast was successful
   if (el_pt!=0)
   {
    // Set the wavenumber function pointer
    el_pt->k_squared_pt()=&GlobalParameters::K_squared;
    
    // If we're using Jonathon's new test mapping
    if (GlobalParameters::Enable_test_pml_mapping_flag)
    {
     // Set the PML mapping function
     el_pt->pml_mapping_pt()=GlobalParameters::Test_pml_mapping_pt;
    }
   } // if (el_pt!=0)
  } // for (unsigned e=0;e<n_element;e++)
  
  // Apply the boundary conditions, both in the central region and on the
  // outer boundary (since these nodes are PML nodes)
  apply_boundary_conditions();
  
  // Enable the PML mapping in elements in the PML region
  enable_pmls();
  
  // Setup equation numbering scheme
  assign_eqn_numbers(); 
 } // End of constructor

References e(), GlobalParameters::Enable_test_pml_mapping_flag, GlobalParameters::K_squared, GlobalParameters::Linear_solver_flag, GlobalParameters::Lx, GlobalParameters::Ly, GlobalParameters::Lz, GlobalParameters::Nx, GlobalParameters::Ny, GlobalParameters::Nz, GlobalParameters::Test_pml_mapping_pt, and oomph::Problem_Parameter::Trace_file.

◆ ~PMLStructuredCubicHelmholtz()

template<class ELEMENT >

PMLStructuredCubicHelmholtz< ELEMENT >::~PMLStructuredCubicHelmholtz

Destructor (empty)

Destructor for Helmholtz problem.

 {
  // If we're using GMRES & MG as the linear solver
  if (GlobalParameters::Linear_solver_flag==1)
  {
   // Delete the MG solver pointers
   delete dynamic_cast<HelmholtzFGMRESMG<CRDoubleMatrix>* >
    (linear_solver_pt())->preconditioner_pt();
  
   // Set the pointer to null
   dynamic_cast<HelmholtzFGMRESMG<CRDoubleMatrix>* >
    (linear_solver_pt())->preconditioner_pt()=0;
     
   // Delete the MG solver pointers
   delete linear_solver_pt();
  
   // Set the pointer to null
   linear_solver_pt()=0;    
  }
    
  // Delete the error estimator
  delete Bulk_mesh_pt->spatial_error_estimator_pt();
  
  // Set the pointer to null
  Bulk_mesh_pt->spatial_error_estimator_pt()=0;
  
  // Delete the "bulk" mesh
  delete Bulk_mesh_pt;
  
  // Set the pointer to null
  Bulk_mesh_pt=0;
  
 } // End of ~PMLStructuredCubicHelmholtz

References GlobalParameters::Linear_solver_flag.

Member Function Documentation

◆ actions_after_adapt()

template<class ELEMENT >

void PMLStructuredCubicHelmholtz< ELEMENT >::actions_after_adapt

virtual

Actions after adapt:(empty)

Actions after adapt: Re-apply the boundary conditions.

Reimplemented from oomph::Problem.

 {
  // Complete the build of all elements so they are fully functional: 
  //-----------------------------------------------------------------
  // How many elements in the mesh?
  unsigned n_element=mesh_pt()->nelement();
  
  // Loop over the elements and pass a pointer to the value of k^2
  for (unsigned e=0;e<n_element;e++)
  {
   // Upcast from GeneralisedElement to Helmholtz bulk element
   ELEMENT* el_pt=dynamic_cast<ELEMENT*>(Bulk_mesh_pt->element_pt(e));
  
   // If the upcast was successful
   if (el_pt!=0)
   {
    // Set the wavenumber function pointer
    el_pt->k_squared_pt()=&GlobalParameters::K_squared;
   }
  } // for (unsigned e=0;e<n_element;e++)
  
  // Re-apply boundary conditions
  apply_boundary_conditions();
  
  // Re-enable the PML mapping in elements in the PML region
  enable_pmls();
  
  // Rebuild the mesh
  rebuild_global_mesh();
 } // End of actions_after_adapt

References e(), and GlobalParameters::K_squared.

◆ actions_after_newton_solve()

template<class ELEMENT >

void PMLStructuredCubicHelmholtz< ELEMENT >::actions_after_newton_solve ( )

inlinevirtual

Update the problem specs after solve (empty)

Reimplemented from oomph::Problem.

  {
   // Document the solution
   doc_solution();
  }

◆ actions_before_adapt()

template<class ELEMENT >

void PMLStructuredCubicHelmholtz< ELEMENT >::actions_before_adapt ( )

inlinevirtual

Actions before adapt: (empty)

Reimplemented from oomph::Problem.

296 {}

◆ actions_before_newton_solve()

template<class ELEMENT >

void PMLStructuredCubicHelmholtz< ELEMENT >::actions_before_newton_solve ( )

inlinevirtual

Update the problem specs before solve (empty)

Reimplemented from oomph::Problem.

286 {}

◆ apply_boundary_conditions()

template<class ELEMENT >

void PMLStructuredCubicHelmholtz< ELEMENT >::apply_boundary_conditions

Apply boundary conditions.

 {
  // Find the number of elements in the mesh
  unsigned n_element=Bulk_mesh_pt->nelement();
  
  // Vector to hold the local coordinates of a point in any given element 
  Vector<double> s(3,0.0);
  
  // Vector to hold the (Eulerian) coordinates of a point
  Vector<double> x(3,0.0);
  
  // Vector to hold the real and imaginary part of the solution
  Vector<double> u(2,0.0);
  
  // If the user wishes to silence everything
  if (GlobalParameters::Output_management_flag==3)
  {
   // Store the output stream pointer
   GlobalParameters::Stream_pt=oomph_info.stream_pt();
  
   // Now set the oomph_info stream pointer to the null stream to
   // disable all possible output
   oomph_info.stream_pt()=&oomph_nullstream;
  }
     
  // Loop over the elements in the mesh
  for (unsigned e=0;e<n_element;e++)
  {
   // Upcast from GeneralisedElement to Helmholtz bulk element
   ELEMENT* el_pt=dynamic_cast<ELEMENT*>(Bulk_mesh_pt->element_pt(e));
  
   // If the upcast was successful
   if (el_pt!=0)
   {
    // Get the (Eulerian) coordinates of the centre of the element
    el_pt->get_x(s,x);
  
    // Check if the element lies in the central cube region
    if (GlobalParameters::is_in_pinned_region(x))
    {
     // Calculate the number of nodes in the element
     unsigned nnode=el_pt->nnode();
  
     // Loop over all of the nodes in the element
     for (unsigned i=0;i<nnode;i++)
     {
      // Create a node pointer to store the i-th node in the element
      Node* node_pt=el_pt->node_pt(i);
  
      // Get the spatial position of this node
      for (unsigned k=0;k<3;k++)
      {
       // Store the k-th coordinate value in the vector, x
       x[k]=node_pt->x(k);
      }
  
      // Get the exact solution at this (Eulerian) position
      GlobalParameters::get_simple_exact_u(x,u);
  
      // Make sure each dof at this point is pinned (real and imaginary)
      node_pt->pin(0);
      node_pt->pin(1);
  
      // Set the solution value at this point
      node_pt->set_value(0,u[0]);
      node_pt->set_value(1,u[1]);
     }
    } // if(abs(x[0]-GlobalParameters::Centre) < 0.51 ... 
   } // if (el_pt!=0)
  } // for (unsigned e=0;e<n_element;e++)
         
  // If the user wishes to suppress all output restore the the stream pointer
  if (GlobalParameters::Output_management_flag==3)
  {
   // Now set the oomph_info stream pointer to the null stream to
   // disable all possible output
   oomph_info.stream_pt()=GlobalParameters::Stream_pt;
  }
   
  // Find the number of boundaries in the mesh
  unsigned n_bound=Bulk_mesh_pt->nboundary();
  
  // Loop over all boundaries
  for (unsigned b=0;b<n_bound;b++)
  {
   // Find the number of nodes on the b-th boundary
   unsigned n_node=Bulk_mesh_pt->nboundary_node(b);
  
   // Loop over the nodes on the b-th boundary
   for(unsigned n=0;n<n_node;n++)
   {
    // All of these nodes sides are PMLs so pin to 0
    Node* boundary_node_pt=Bulk_mesh_pt->boundary_node_pt(b,n);
  
    // Pin the (real) dof at this node
    boundary_node_pt->pin(0);
    
    // Pin the (imaginary) dof at this node
    boundary_node_pt->pin(1);
  
    // Set the solution value at this point (real part)
    boundary_node_pt->set_value(0,0.0);
    
    // Set the solution value at this point (imaginary part)
    boundary_node_pt->set_value(1,0.0);
   }
  } // for(unsigned b=0;b<n_bound;b++)
 } // End of apply_boundary_conditions

References b, e(), GlobalParameters::get_simple_exact_u(), i, GlobalParameters::is_in_pinned_region(), k, n, oomph::oomph_info, oomph::oomph_nullstream, GlobalParameters::Output_management_flag, oomph::Data::pin(), s, oomph::Data::set_value(), GlobalParameters::Stream_pt, oomph::OomphInfo::stream_pt(), plotDoE::x, and oomph::Node::x().

◆ doc_solution()

template<class ELEMENT >

void PMLStructuredCubicHelmholtz< ELEMENT >::doc_solution

Doc the solution.

Doc the solution: doc_info contains labels/output directory etc.

 {
  // Tell the user
  oomph_info << "\nDocumentation step: "
         << GlobalParameters::Doc_info.number() << std::endl;
  
  // Create an output stream
  ofstream some_file;
  
  // Create space for the file name
  char filename[100];
  
  // Number of plot points
  unsigned npts=5;
  
  // Number of plot points in the coarse solution
  unsigned npts_coarse=2;
  
  // Output solution
  //-----------------
  sprintf(filename,"%s/soln%i.dat",
      GlobalParameters::Doc_info.directory().c_str(),
      GlobalParameters::Doc_info.number());
  some_file.open(filename);
  Bulk_mesh_pt->output(some_file,npts);
  some_file.close();
  
  // Ouput exact solution
  //---------------------
  sprintf(filename,"%s/exact_soln%i.dat",
      GlobalParameters::Doc_info.directory().c_str(),
      GlobalParameters::Doc_info.number());
  some_file.open(filename);
  Bulk_mesh_pt->output_fct(some_file,npts,GlobalParameters::simple_exact_u_pt);
  some_file.close();
  
  // Output coarse solution
  //-----------------------
  sprintf(filename,"%s/coarse_soln%i.dat",
      GlobalParameters::Doc_info.directory().c_str(),
      GlobalParameters::Doc_info.number());
  some_file.open(filename);
  Bulk_mesh_pt->output(some_file,npts_coarse);
  some_file.close();
  
  // Compute error
  //--------------
  sprintf(filename,"%s/error%i.dat",
      GlobalParameters::Doc_info.directory().c_str(),
      GlobalParameters::Doc_info.number());
  some_file.open(filename);
  
  //---------------------------------------------------------------------
  // To compute the norm of the error norm we first need to loop over all
  // of the elements in the mesh. Before we compute the norm of the error
  // in any element we need to make sure it doesn't lie in the PML region
  // or in the pinned region
  //--------------------------------------------------------------------- 
  // Variables to hold the L2 norm of the error in the solution
  double error=0.0;
  
  // Variable to hold the L2 norm of the solution
  double norm=0.0;
  
  // Vector to hold the local coordinates of a point in an element
  Vector<double> s(3,0.0);
  
  // Vector to hold the spatial position of a point in an element
  Vector<double> x(3,0.0);
  
  // Store the required coordinate of the inner boundary of the left PML; 
  // in any given direction this will be the value of Pml_thickness
  double left_boundary=GlobalParameters::Pml_thickness;
    
  // Store the required coordinate of the inner boundary of the right
  // PML; in the x-direction this will be the value of Lx-Pml_thickness
  // (or Ly-Pml_thickness in the y-direction and Lz-Pml_thickness in
  // the z-direction) but we assume the PML has the same thickness in
  // all directions
  double right_boundary=GlobalParameters::Lx-GlobalParameters::Pml_thickness;
  
  // Find out how many elements there are in the mesh
  unsigned n_element=Bulk_mesh_pt->nelement();
  
  // Loop over all of the elements in the mesh
  for (unsigned e=0;e<n_element;e++)
  { 
   // Variables to hold the L2 norm of the error in the elemental solution
   double el_error=0.0;
  
   // Variable to hold the L2 norm of the elemental solution
   double el_norm=0.0;
  
   // Upcast from GeneralisedElement to Helmholtz bulk element
   ELEMENT* el_pt=dynamic_cast<ELEMENT*>(Bulk_mesh_pt->element_pt(e));
  
   // If the upcast was successful
   if (el_pt!=0)
   {
    // Get the (Eulerian) coordinates of the centre of the element
    el_pt->get_x(s,x);
  
    // We only take the contribution from this element if it does
    // not lie in the PML region 
    if(x[0]<=left_boundary) continue;
    if(x[0]>=right_boundary) continue;
    if(x[1]<=left_boundary) continue;
    if(x[1]>=right_boundary) continue;
    if(x[2]<=left_boundary) continue;
    if(x[2]>=right_boundary) continue;
  
    // If it's in the (pinned) central region, ignore it 
  
    // Check if the element lies in the central cube region
    if (GlobalParameters::is_in_pinned_region(x))
    {
     // Skip to the next element
     continue;
    }
  
    // Otherwise, compute the L2 norm of the error over this element
    el_pt->compute_error(some_file,
             GlobalParameters::get_simple_exact_u,
             el_error,
             el_norm);
  
    // Update the global error norm value
    error+=el_error;
    
    // Update the global norm value
    norm+=el_norm;
   }
  } // for(unsigned e=0;e<n_element;e++)
  
  // Now close the file
  some_file.close();
  
  // Output the L2 norm of the error and the solution and then output
  // the relative error of the solution
  oomph_info << "\nSolution norm : " << norm
         << "\nAbsolute error: " << error       
         << "\nRelative error: " << error/norm
         << std::endl;
  
  // Write the L2 norm of the solution to the trace file
  Trace_file << norm << std::endl;
  
  // Increment the documentation number
  GlobalParameters::Doc_info.number()++;
 } // End of doc_solution

References GlobalParameters::Doc_info, e(), calibrate::error, MergeRestartFiles::filename, GlobalParameters::get_simple_exact_u(), GlobalParameters::is_in_pinned_region(), GlobalParameters::Lx, oomph::DocInfo::number(), oomph::oomph_info, GlobalParameters::Pml_thickness, s, GlobalParameters::simple_exact_u_pt, oomph::Problem_Parameter::Trace_file, and plotDoE::x.

◆ enable_pmls()

template<class ELEMENT >

void PMLStructuredCubicHelmholtz< ELEMENT >::enable_pmls

Enable the PML mapping function for all nodes in the PML region.

Enable the PML mapping function for each node in the PML region.

 {
  // Find the number of elements in the mesh
  unsigned n_element=Bulk_mesh_pt->nelement();
  
  // Vector to hold the local coordinates of a point in any given element 
  Vector<double> s(3,0.0);
  
  // Vector to hold the (Eulerian) coordinates of a point
  Vector<double> x(3,0.0);
  
  // Vector to hold the real and imaginary part of the solution
  Vector<double> u(2,0.0);
  
  // Store the required coordinate of the inner boundary of the left PML; 
  // in any given direction this will be the value of Pml_thickness
  double left_boundary=GlobalParameters::Pml_thickness;
    
  // Store the required coordinate of the inner boundary of the right
  // PML; in the x-direction this will be the value of Lx-Pml_thickness
  // (or Ly-Pml_thickness in the y-direction and Lz-Pml_thickness in
  // the z-direction) but we assume the PML has the same thickness in
  // all directions
  double right_boundary=GlobalParameters::Lx-GlobalParameters::Pml_thickness;
  
  // Loop over the elements in the mesh
  for (unsigned e=0;e<n_element;e++)
  {
   // Upcast from GeneralisedElement to Helmholtz bulk element
   ELEMENT* el_pt=dynamic_cast<ELEMENT*>(Bulk_mesh_pt->element_pt(e));
  
   // If the upcast was successful
   if (el_pt!=0)
   {
    // If we're using Jonathon's new test mapping
    if (GlobalParameters::Enable_test_pml_mapping_flag)
    {
     // Set the PML mapping function
     el_pt->pml_mapping_pt()=GlobalParameters::Test_pml_mapping_pt;
    }
   
    // Get the (Eulerian) coordinates of the centre of the element
    el_pt->get_x(s,x);
    
    // If it's in the left (x-direction) PML region
    if (x[0]<=left_boundary)
     el_pt->enable_pml(0,left_boundary,0.0);
  
    // If it's in the right (x-direction) PML region
    if (x[0]>=right_boundary)
     el_pt->enable_pml(0,right_boundary,GlobalParameters::Lx);
  
    // If it's in the left (y-direction) PML region
    if (x[1]<=left_boundary)
     el_pt->enable_pml(1,left_boundary,0.0);
  
    // If it's in the right (y-direction) PML region
    if (x[1]>=right_boundary)
     el_pt->enable_pml(1,right_boundary,GlobalParameters::Ly);
  
    // If it's in the left (z-direction) PML region
    if (x[2]<=left_boundary)
     el_pt->enable_pml(2,left_boundary,0.0);
  
    // If it's in the right (z-direction) PML region
    if (x[2]>=right_boundary)
     el_pt->enable_pml(2,right_boundary,GlobalParameters::Lz);
   }
  } // for (unsigned e=0;e<n_element;e++)
 } // End of enable_pmls

References e(), GlobalParameters::Enable_test_pml_mapping_flag, GlobalParameters::Lx, GlobalParameters::Ly, GlobalParameters::Lz, GlobalParameters::Pml_thickness, s, GlobalParameters::Test_pml_mapping_pt, and plotDoE::x.

◆ make_new_problem()

template<class ELEMENT >

HelmholtzMGProblem* PMLStructuredCubicHelmholtz< ELEMENT >::make_new_problem ( )

inlineprivatevirtual

Overload the make_new_problem function to return an object of this class.

Implements oomph::HelmholtzMGProblem.

  {
   // Return a new problem pointer
   return new PMLStructuredCubicHelmholtz<ELEMENT>;
  }

◆ mg_bulk_mesh_pt()

template<class ELEMENT >

TreeBasedRefineableMeshBase* PMLStructuredCubicHelmholtz< ELEMENT >::mg_bulk_mesh_pt ( )

inlineprivatevirtual

Overload the mg_bulk_mesh_pt function to return a pointer to the "refineable" portion of the mesh

Implements oomph::HelmholtzMGProblem.

  {
   // Return the pointer to the bulk mesh
   return Bulk_mesh_pt;
  }

◆ set_gmres_multigrid_solver()

template<class ELEMENT >

void PMLStructuredCubicHelmholtz< ELEMENT >::set_gmres_multigrid_solver

Set GMRES preconditioner by multigrid as the linear solver.

Build and set GMRES preconditioner by multigrid as the linear solver.

 {
  // Create linear solver
  HelmholtzFGMRESMG<CRDoubleMatrix>* solver_pt=
   new HelmholtzFGMRESMG<CRDoubleMatrix>;
  
  // Set the number of iterations
  solver_pt->max_iter()=200;
  
  // Set the tolerance (to ensure the Newton solver converges in one step)
  solver_pt->tolerance()=1.0e-10;
    
  // If the user wishes to document the convergence information
  if (GlobalParameters::Doc_convergence_flag)
  {
   // Create a file to record the convergence history
   solver_pt->open_convergence_history_file_stream("RESLT/conv.dat");
  }
  
  // Create linear solver 
  linear_solver_pt()=solver_pt;
  
  // This preconditioner uses multigrid on the block version of the full
  // matrix. 2 V-cycles will be used here per preconditioning step
  HelmholtzMGPreconditioner<3>* prec_pt=new HelmholtzMGPreconditioner<3>(this);
  
  // Set preconditioner
  solver_pt->preconditioner_pt()=prec_pt;
   
  // Set the shift
  prec_pt->alpha_shift()=GlobalParameters::Alpha_shift;
    
  // If the user wants to use damped Jacobi on every level as a smoother
  if (GlobalParameters::Pre_smoother_flag==1)
  {
   // Set the pre-smoother factory function
   prec_pt->set_pre_smoother_factory_function
    (Smoother_Factory_Function_Helper::set_pre_smoother);
  }
  
  // If the user wants to use damped Jacobi on every level as a smoother
  if (GlobalParameters::Post_smoother_flag==1)
  {
   // Set the post-smoother factory function
   prec_pt->set_post_smoother_factory_function
    (Smoother_Factory_Function_Helper::set_post_smoother);
  }
  
  // Suppress certain timings
  if (GlobalParameters::Output_management_flag==1)
  {
   prec_pt->disable_doc_time();
  }
  else if (GlobalParameters::Output_management_flag==2)
  {
   prec_pt->disable_v_cycle_output();
  }
  else if (GlobalParameters::Output_management_flag==3)
  {
   prec_pt->disable_output();
  }
 } // End of set_gmres_multigrid_solver

References GlobalParameters::Alpha_shift, oomph::HelmholtzMGPreconditioner< DIM >::alpha_shift(), oomph::HelmholtzMGPreconditioner< DIM >::disable_doc_time(), oomph::HelmholtzMGPreconditioner< DIM >::disable_output(), oomph::HelmholtzMGPreconditioner< DIM >::disable_v_cycle_output(), GlobalParameters::Doc_convergence_flag, oomph::IterativeLinearSolver::max_iter(), oomph::IterativeLinearSolver::open_convergence_history_file_stream(), GlobalParameters::Output_management_flag, GlobalParameters::Post_smoother_flag, GlobalParameters::Pre_smoother_flag, oomph::IterativeLinearSolver::preconditioner_pt(), Smoother_Factory_Function_Helper::set_post_smoother(), oomph::HelmholtzMGPreconditioner< DIM >::set_post_smoother_factory_function(), Smoother_Factory_Function_Helper::set_pre_smoother(), oomph::HelmholtzMGPreconditioner< DIM >::set_pre_smoother_factory_function(), and oomph::IterativeLinearSolver::tolerance().

Member Data Documentation

◆ Bulk_mesh_pt

template<class ELEMENT >

RefineableSimpleCubicMesh<ELEMENT>* PMLStructuredCubicHelmholtz< ELEMENT >::Bulk_mesh_pt

private

Pointer to the "bulk" mesh.

◆ Trace_file

template<class ELEMENT >

ofstream PMLStructuredCubicHelmholtz< ELEMENT >::Trace_file

private

Trace file.

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

structured_cubic_point_source.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

template<class ELEMENT> class PMLStructuredCubicHelmholtz< ELEMENT >

Constructor & Destructor Documentation

◆ PMLStructuredCubicHelmholtz()

◆ ~PMLStructuredCubicHelmholtz()

Member Function Documentation

◆ actions_after_adapt()

◆ actions_after_newton_solve()

◆ actions_before_adapt()

◆ actions_before_newton_solve()

◆ apply_boundary_conditions()

◆ doc_solution()

◆ enable_pmls()

◆ make_new_problem()

◆ mg_bulk_mesh_pt()

◆ set_gmres_multigrid_solver()

Member Data Documentation

◆ Bulk_mesh_pt

◆ Trace_file

template<class ELEMENT>
class PMLStructuredCubicHelmholtz< ELEMENT >