Inheritance diagram for RefineableActivatorInhibitorProblem< ELEMENT >:

Public Member Functions
	RefineableActivatorInhibitorProblem ()
	Constructor: Pass pointer to source and wind functions. More...

	~RefineableActivatorInhibitorProblem ()
	Destructor. Empty. More...

void	actions_before_newton_solve ()
	Empty. More...

void	actions_after_newton_solve ()

void	set_initial_condition ()
	Set the initial conditions to be a single "hot" spot. More...

void	timestep (const double &dt, const unsigned &nstep)
	Timestep the problem. More...

RefineableRectangularQuadMesh< ELEMENT > *	mesh_pt ()

	RefineableActivatorInhibitorProblem ()
	Constructor: Pass pointer to source and wind functions. More...

	~RefineableActivatorInhibitorProblem ()
	Destructor. Empty. More...

void	actions_before_newton_solve ()
	Empty. More...

void	actions_after_newton_solve ()

void	actions_before_adapt ()

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

void	set_initial_condition ()

void	complete_problem_setup ()
	Set the elemental properties. More...

void	timestep (const double &dt, const unsigned &nstep)

Public Member Functions inherited from oomph::Problem
virtual void	debug_hook_fct (const unsigned &i)

void	set_analytic_dparameter (double *const &parameter_pt)

void	unset_analytic_dparameter (double *const &parameter_pt)

bool	is_dparameter_calculated_analytically (double *const &parameter_pt)

void	set_analytic_hessian_products ()

void	unset_analytic_hessian_products ()

bool	are_hessian_products_calculated_analytically ()

void	set_pinned_values_to_zero ()

bool	distributed () const

OomphCommunicator *	communicator_pt ()
	access function to the oomph-lib communicator More...

const OomphCommunicator *	communicator_pt () const
	access function to the oomph-lib communicator, const version More...

	Problem ()

	Problem (const Problem &dummy)=delete
	Broken copy constructor. More...

void	operator= (const Problem &)=delete
	Broken assignment operator. More...

virtual	~Problem ()
	Virtual destructor to clean up memory. More...

Mesh *&	mesh_pt ()
	Return a pointer to the global mesh. More...

Mesh *const &	mesh_pt () const
	Return a pointer to the global mesh (const version) More...

Mesh *&	mesh_pt (const unsigned &imesh)

Mesh *const &	mesh_pt (const unsigned &imesh) const
	Return a pointer to the i-th submesh (const version) More...

unsigned	nsub_mesh () const
	Return number of submeshes. More...

unsigned	add_sub_mesh (Mesh *const &mesh_pt)

void	flush_sub_meshes ()

void	build_global_mesh ()

void	rebuild_global_mesh ()

LinearSolver *&	linear_solver_pt ()
	Return a pointer to the linear solver object. More...

LinearSolver *const &	linear_solver_pt () const
	Return a pointer to the linear solver object (const version) More...

LinearSolver *&	mass_matrix_solver_for_explicit_timestepper_pt ()

LinearSolver *	mass_matrix_solver_for_explicit_timestepper_pt () const

EigenSolver *&	eigen_solver_pt ()
	Return a pointer to the eigen solver object. More...

EigenSolver *const &	eigen_solver_pt () const
	Return a pointer to the eigen solver object (const version) More...

Time *&	time_pt ()
	Return a pointer to the global time object. More...

Time *	time_pt () const
	Return a pointer to the global time object (const version). More...

double &	time ()
	Return the current value of continuous time. More...

double	time () const
	Return the current value of continuous time (const version) More...

TimeStepper *&	time_stepper_pt ()

const TimeStepper *	time_stepper_pt () const

TimeStepper *&	time_stepper_pt (const unsigned &i)
	Return a pointer to the i-th timestepper. More...

ExplicitTimeStepper *&	explicit_time_stepper_pt ()
	Return a pointer to the explicit timestepper. More...

unsigned long	set_timestepper_for_all_data (TimeStepper *const &time_stepper_pt, const bool &preserve_existing_data=false)

virtual void	shift_time_values ()
	Shift all values along to prepare for next timestep. More...

AssemblyHandler *&	assembly_handler_pt ()
	Return a pointer to the assembly handler object. More...

AssemblyHandler *const &	assembly_handler_pt () const
	Return a pointer to the assembly handler object (const version) More...

double &	minimum_dt ()
	Access function to min timestep in adaptive timestepping. More...

double &	maximum_dt ()
	Access function to max timestep in adaptive timestepping. More...

unsigned &	max_newton_iterations ()
	Access function to max Newton iterations before giving up. More...

void	problem_is_nonlinear (const bool &prob_lin)
	Access function to Problem_is_nonlinear. More...

double &	max_residuals ()

bool &	time_adaptive_newton_crash_on_solve_fail ()
	Access function for Time_adaptive_newton_crash_on_solve_fail. More...

double &	newton_solver_tolerance ()

void	add_time_stepper_pt (TimeStepper *const &time_stepper_pt)

void	set_explicit_time_stepper_pt (ExplicitTimeStepper *const &explicit_time_stepper_pt)

void	initialise_dt (const double &dt)

void	initialise_dt (const Vector< double > &dt)

Data *&	global_data_pt (const unsigned &i)
	Return a pointer to the the i-th global data object. More...

void	add_global_data (Data *const &global_data_pt)

void	flush_global_data ()

LinearAlgebraDistribution *const &	dof_distribution_pt () const
	Return the pointer to the dof distribution (read-only) More...

unsigned long	ndof () const
	Return the number of dofs. More...

unsigned	ntime_stepper () const
	Return the number of time steppers. More...

unsigned	nglobal_data () const
	Return the number of global data values. More...

unsigned	self_test ()
	Self-test: Check meshes and global data. Return 0 for OK. More...

void	enable_store_local_dof_pt_in_elements ()

void	disable_store_local_dof_pt_in_elements ()

unsigned long	assign_eqn_numbers (const bool &assign_local_eqn_numbers=true)

void	describe_dofs (std::ostream &out= *(oomph_info.stream_pt())) const

void	enable_discontinuous_formulation ()

void	disable_discontinuous_formulation ()

void	get_dofs (DoubleVector &dofs) const

void	get_dofs (const unsigned &t, DoubleVector &dofs) const
	Return vector of the t'th history value of all dofs. More...

void	set_dofs (const DoubleVector &dofs)
	Set the values of the dofs. More...

void	set_dofs (const unsigned &t, DoubleVector &dofs)
	Set the history values of the dofs. More...

void	set_dofs (const unsigned &t, Vector< double * > &dof_pt)

void	add_to_dofs (const double &lambda, const DoubleVector &increment_dofs)
	Add lambda x incremenet_dofs[l] to the l-th dof. More...

double *	global_dof_pt (const unsigned &i)

double &	dof (const unsigned &i)
	i-th dof in the problem More...

double	dof (const unsigned &i) const
	i-th dof in the problem (const version) More...

double *&	dof_pt (const unsigned &i)
	Pointer to i-th dof in the problem. More...

double *	dof_pt (const unsigned &i) const
	Pointer to i-th dof in the problem (const version) More...

virtual void	get_inverse_mass_matrix_times_residuals (DoubleVector &Mres)

virtual void	get_dvaluesdt (DoubleVector &f)

virtual void	get_residuals (DoubleVector &residuals)
	Get the total residuals Vector for the problem. More...

virtual void	get_jacobian (DoubleVector &residuals, DenseDoubleMatrix &jacobian)

virtual void	get_jacobian (DoubleVector &residuals, CRDoubleMatrix &jacobian)

virtual void	get_jacobian (DoubleVector &residuals, CCDoubleMatrix &jacobian)

virtual void	get_jacobian (DoubleVector &residuals, SumOfMatrices &jacobian)

void	get_fd_jacobian (DoubleVector &residuals, DenseMatrix< double > &jacobian)
	Get the full Jacobian by finite differencing. More...

void	get_derivative_wrt_global_parameter (double *const &parameter_pt, DoubleVector &result)

void	get_hessian_vector_products (DoubleVectorWithHaloEntries const &Y, Vector< DoubleVectorWithHaloEntries > const &C, Vector< DoubleVectorWithHaloEntries > &product)

void	solve_eigenproblem (const unsigned &n_eval, Vector< std::complex< double >> &eigenvalue, Vector< DoubleVector > &eigenvector, const bool &steady=true)
	Solve the eigenproblem. More...

void	solve_eigenproblem (const unsigned &n_eval, Vector< std::complex< double >> &eigenvalue, const bool &steady=true)

virtual void	get_eigenproblem_matrices (CRDoubleMatrix &mass_matrix, CRDoubleMatrix &main_matrix, const double &shift=0.0)

void	assign_eigenvector_to_dofs (DoubleVector &eigenvector)
	Assign the eigenvector passed to the function to the dofs. More...

void	add_eigenvector_to_dofs (const double &epsilon, const DoubleVector &eigenvector)

void	store_current_dof_values ()
	Store the current values of the degrees of freedom. More...

void	restore_dof_values ()
	Restore the stored values of the degrees of freedom. More...

void	enable_jacobian_reuse ()

void	disable_jacobian_reuse ()
	Disable recycling of Jacobian in Newton iteration. More...

bool	jacobian_reuse_is_enabled ()
	Is recycling of Jacobian in Newton iteration enabled? More...

bool &	use_predictor_values_as_initial_guess ()

void	newton_solve ()
	Use Newton method to solve the problem. More...

void	enable_globally_convergent_newton_method ()
	enable globally convergent Newton method More...

void	disable_globally_convergent_newton_method ()
	disable globally convergent Newton method More...

void	newton_solve (unsigned const &max_adapt)

void	steady_newton_solve (unsigned const &max_adapt=0)

void	copy (Problem *orig_problem_pt)

virtual Problem *	make_copy ()

virtual void	read (std::ifstream &restart_file, bool &unsteady_restart)

virtual void	read (std::ifstream &restart_file)

virtual void	dump (std::ofstream &dump_file) const

void	dump (const std::string &dump_file_name) const

void	delete_all_external_storage ()

virtual void	symmetrise_eigenfunction_for_adaptive_pitchfork_tracking ()

double *	bifurcation_parameter_pt () const

void	get_bifurcation_eigenfunction (Vector< DoubleVector > &eigenfunction)

void	activate_fold_tracking (double *const &parameter_pt, const bool &block_solve=true)

void	activate_bifurcation_tracking (double *const &parameter_pt, const DoubleVector &eigenvector, const bool &block_solve=true)

void	activate_bifurcation_tracking (double *const &parameter_pt, const DoubleVector &eigenvector, const DoubleVector &normalisation, const bool &block_solve=true)

void	activate_pitchfork_tracking (double *const &parameter_pt, const DoubleVector &symmetry_vector, const bool &block_solve=true)

void	activate_hopf_tracking (double *const &parameter_pt, const bool &block_solve=true)

void	activate_hopf_tracking (double *const &parameter_pt, const double &omega, const DoubleVector &null_real, const DoubleVector &null_imag, const bool &block_solve=true)

void	deactivate_bifurcation_tracking ()

void	reset_assembly_handler_to_default ()
	Reset the system to the standard non-augemented state. More...

double	arc_length_step_solve (double *const &parameter_pt, const double &ds, const unsigned &max_adapt=0)

double	arc_length_step_solve (Data *const &data_pt, const unsigned &data_index, const double &ds, const unsigned &max_adapt=0)

void	reset_arc_length_parameters ()

int &	sign_of_jacobian ()

void	explicit_timestep (const double &dt, const bool &shift_values=true)
	Take an explicit timestep of size dt. More...

void	unsteady_newton_solve (const double &dt)

void	unsteady_newton_solve (const double &dt, const bool &shift_values)

void	unsteady_newton_solve (const double &dt, const unsigned &max_adapt, const bool &first, const bool &shift=true)

double	doubly_adaptive_unsteady_newton_solve (const double &dt, const double &epsilon, const unsigned &max_adapt, const bool &first, const bool &shift=true)

double	doubly_adaptive_unsteady_newton_solve (const double &dt, const double &epsilon, const unsigned &max_adapt, const unsigned &suppress_resolve_after_spatial_adapt_flag, const bool &first, const bool &shift=true)

double	adaptive_unsteady_newton_solve (const double &dt_desired, const double &epsilon)

double	adaptive_unsteady_newton_solve (const double &dt_desired, const double &epsilon, const bool &shift_values)

void	assign_initial_values_impulsive ()

void	assign_initial_values_impulsive (const double &dt)

void	calculate_predictions ()
	Calculate predictions. More...

void	enable_mass_matrix_reuse ()

void	disable_mass_matrix_reuse ()

bool	mass_matrix_reuse_is_enabled ()
	Return whether the mass matrix is being reused. More...

void	refine_uniformly (const Vector< unsigned > &nrefine_for_mesh)

void	refine_uniformly (const Vector< unsigned > &nrefine_for_mesh, DocInfo &doc_info)

void	refine_uniformly_and_prune (const Vector< unsigned > &nrefine_for_mesh)

void	refine_uniformly_and_prune (const Vector< unsigned > &nrefine_for_mesh, DocInfo &doc_info)

void	refine_uniformly (DocInfo &doc_info)

void	refine_uniformly_and_prune (DocInfo &doc_info)

void	refine_uniformly ()

void	refine_uniformly (const unsigned &i_mesh, DocInfo &doc_info)
	Do uniform refinement for submesh i_mesh with documentation. More...

void	refine_uniformly (const unsigned &i_mesh)
	Do uniform refinement for submesh i_mesh without documentation. More...

void	p_refine_uniformly (const Vector< unsigned > &nrefine_for_mesh)

void	p_refine_uniformly (const Vector< unsigned > &nrefine_for_mesh, DocInfo &doc_info)

void	p_refine_uniformly_and_prune (const Vector< unsigned > &nrefine_for_mesh)

void	p_refine_uniformly_and_prune (const Vector< unsigned > &nrefine_for_mesh, DocInfo &doc_info)

void	p_refine_uniformly (DocInfo &doc_info)

void	p_refine_uniformly_and_prune (DocInfo &doc_info)

void	p_refine_uniformly ()

void	p_refine_uniformly (const unsigned &i_mesh, DocInfo &doc_info)
	Do uniform p-refinement for submesh i_mesh with documentation. More...

void	p_refine_uniformly (const unsigned &i_mesh)
	Do uniform p-refinement for submesh i_mesh without documentation. More...

void	refine_selected_elements (const Vector< unsigned > &elements_to_be_refined)

void	refine_selected_elements (const Vector< RefineableElement * > &elements_to_be_refined_pt)

void	refine_selected_elements (const unsigned &i_mesh, const Vector< unsigned > &elements_to_be_refined)

void	refine_selected_elements (const unsigned &i_mesh, const Vector< RefineableElement * > &elements_to_be_refined_pt)

void	refine_selected_elements (const Vector< Vector< unsigned >> &elements_to_be_refined)

void	refine_selected_elements (const Vector< Vector< RefineableElement * >> &elements_to_be_refined_pt)

void	p_refine_selected_elements (const Vector< unsigned > &elements_to_be_refined)

void	p_refine_selected_elements (const Vector< PRefineableElement * > &elements_to_be_refined_pt)

void	p_refine_selected_elements (const unsigned &i_mesh, const Vector< unsigned > &elements_to_be_refined)

void	p_refine_selected_elements (const unsigned &i_mesh, const Vector< PRefineableElement * > &elements_to_be_refined_pt)

void	p_refine_selected_elements (const Vector< Vector< unsigned >> &elements_to_be_refined)

void	p_refine_selected_elements (const Vector< Vector< PRefineableElement * >> &elements_to_be_refined_pt)

unsigned	unrefine_uniformly ()

unsigned	unrefine_uniformly (const unsigned &i_mesh)

void	p_unrefine_uniformly (DocInfo &doc_info)

void	p_unrefine_uniformly (const unsigned &i_mesh, DocInfo &doc_info)
	Do uniform p-unrefinement for submesh i_mesh without documentation. More...

void	adapt (unsigned &n_refined, unsigned &n_unrefined)

void	adapt ()

void	p_adapt (unsigned &n_refined, unsigned &n_unrefined)

void	p_adapt ()

void	adapt_based_on_error_estimates (unsigned &n_refined, unsigned &n_unrefined, Vector< Vector< double >> &elemental_error)

void	adapt_based_on_error_estimates (Vector< Vector< double >> &elemental_error)

void	get_all_error_estimates (Vector< Vector< double >> &elemental_error)

void	doc_errors (DocInfo &doc_info)
	Get max and min error for all elements in submeshes. More...

void	doc_errors ()
	Get max and min error for all elements in submeshes. More...

void	enable_info_in_newton_solve ()

void	disable_info_in_newton_solve ()
	Disable the output of information when in the newton solver. More...

Public Member Functions inherited from oomph::ExplicitTimeSteppableObject
	ExplicitTimeSteppableObject ()
	Empty constructor. More...

	ExplicitTimeSteppableObject (const ExplicitTimeSteppableObject &)=delete
	Broken copy constructor. More...

void	operator= (const ExplicitTimeSteppableObject &)=delete
	Broken assignment operator. More...

virtual	~ExplicitTimeSteppableObject ()
	Empty destructor. More...

virtual void	actions_before_explicit_stage ()

virtual void	actions_after_explicit_stage ()

Private Attributes
double	Dt
	Storage for the timestep. More...

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

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

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

Public Attributes inherited from oomph::Problem
bool	Shut_up_in_newton_solve

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

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

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

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

virtual void	actions_before_newton_convergence_check ()

virtual void	actions_before_newton_step ()

virtual void	actions_after_newton_step ()

virtual void	actions_before_implicit_timestep ()

virtual void	actions_after_implicit_timestep ()

virtual void	actions_after_implicit_timestep_and_error_estimation ()

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

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

virtual void	actions_before_read_unstructured_meshes ()

virtual void	actions_after_read_unstructured_meshes ()

virtual void	actions_after_change_in_global_parameter (double *const &parameter_pt)

virtual void	actions_after_change_in_bifurcation_parameter ()

virtual void	actions_after_parameter_increase (double *const &parameter_pt)

double &	dof_derivative (const unsigned &i)

double &	dof_current (const unsigned &i)

virtual 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 RefineableActivatorInhibitorProblem< ELEMENT >

2D ActivatorInhibitor problem on rectangular domain, discretised with refineable 2D QActivatorInhibitor elements. The specific type of element is specified via the template parameter.

Constructor & Destructor Documentation

◆ RefineableActivatorInhibitorProblem() [1/2]

template<class ELEMENT >

RefineableActivatorInhibitorProblem< ELEMENT >::RefineableActivatorInhibitorProblem

Constructor: Pass pointer to source and wind functions.

Constructor for ActivatorInhibitor problem.

                                       : Dt(0.1)
 { 
  //Allocate the timestepper 
  add_time_stepper_pt(new BDF<2>);
  
  // Setup initial mesh
  
  // # of elements in x-direction
  unsigned n_x=4;
  
  // # of elements in y-direction
  unsigned n_y=4;
  
  // Domain length in x-direction
  double l_x=10.0;
  
  // Domain length in y-direction
  double l_y=10.0;
  
  // Build and assign mesh
  Problem::mesh_pt() = 
   new RefineableRectangularQuadMesh<ELEMENT>(
    n_x,n_y,l_x,l_y,Problem::time_stepper_pt());
  
  // Create/set error estimator
  mesh_pt()->spatial_error_estimator_pt()=new Z2ErrorEstimator;
   
  //Totally free (zero-flux) boundary conditions, so we do nothing
  
  // Complete the build of all elements so they are fully functional 
  
  // Loop over the elements to set up element-specific 
  // things that cannot be handled by the (argument-free!) ELEMENT 
  // constructor: Pass pointer to source function
  unsigned n_element = mesh_pt()->nelement();
  for(unsigned i=0;i<n_element;i++)
   {
    // Upcast from GeneralsedElement to the present element
    ELEMENT *elem_pt = dynamic_cast<ELEMENT*>(mesh_pt()->element_pt(i));
    
    //Set the timescales
    elem_pt->tau_pt() = &GlobalVariables::Tau;
  
    //Set the diffusion coefficients
    elem_pt->diff_pt() = &GlobalVariables::D;
  
    //Set the reaction terms
    elem_pt->reaction_fct_pt() = &GlobalVariables::activator_inhibitor_reaction;
  
     //And their derivatives
    elem_pt->reaction_deriv_fct_pt() = 
     &GlobalVariables::activator_inhibitor_reaction_derivative;
  
   }
  
  // Setup equation numbering scheme
  cout <<"Number of equations: " << assign_eqn_numbers() << std::endl; 
  
 } // end of constructor

References GlobalVariables::activator_inhibitor_reaction(), GlobalVariables::activator_inhibitor_reaction_derivative(), oomph::Problem::add_time_stepper_pt(), oomph::Problem::assign_eqn_numbers(), GlobalVariables::D, i, RefineableActivatorInhibitorProblem< ELEMENT >::mesh_pt(), and GlobalVariables::Tau.

◆ ~RefineableActivatorInhibitorProblem() [1/2]

template<class ELEMENT >

RefineableActivatorInhibitorProblem< ELEMENT >::~RefineableActivatorInhibitorProblem ( )

inline

Destructor. Empty.

91 {}

◆ RefineableActivatorInhibitorProblem() [2/2]

template<class ELEMENT >

RefineableActivatorInhibitorProblem< ELEMENT >::RefineableActivatorInhibitorProblem ( )

Constructor: Pass pointer to source and wind functions.

◆ ~RefineableActivatorInhibitorProblem() [2/2]

template<class ELEMENT >

RefineableActivatorInhibitorProblem< ELEMENT >::~RefineableActivatorInhibitorProblem ( )

inline

Destructor. Empty.

   {
    //Delete the mesh
    delete My_mesh_pt; My_mesh_pt=0;
    //Delete the timestepper
    delete this->time_stepper_pt(); this->time_stepper_pt() = 0;
   }

Member Function Documentation

◆ actions_after_adapt()

template<class ELEMENT >

void RefineableActivatorInhibitorProblem< ELEMENT >::actions_after_adapt ( )

inlinevirtual

Actions that are to be performed after a mesh adaptation.

Reimplemented from oomph::Problem.

   {
    complete_problem_setup();
   }

◆ actions_after_newton_solve() [1/2]

template<class ELEMENT >

void RefineableActivatorInhibitorProblem< ELEMENT >::actions_after_newton_solve ( )

inlinevirtual

Any actions that are to be performed after a complete Newton solve, e.g. post processing. CAREFUL: This step should (and if the FD-based LinearSolver FD_LU is used, must) only update values that are pinned!

Reimplemented from oomph::Problem.

97 {}

◆ actions_after_newton_solve() [2/2]

template<class ELEMENT >

void RefineableActivatorInhibitorProblem< ELEMENT >::actions_after_newton_solve ( )

inlinevirtual

Any actions that are to be performed after a complete Newton solve, e.g. post processing. CAREFUL: This step should (and if the FD-based LinearSolver FD_LU is used, must) only update values that are pinned!

Reimplemented from oomph::Problem.

103 {}

◆ actions_before_adapt()

template<class ELEMENT >

void RefineableActivatorInhibitorProblem< ELEMENT >::actions_before_adapt ( )

inlinevirtual

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

Reimplemented from oomph::Problem.

106 {}

◆ actions_before_newton_solve() [1/2]

template<class ELEMENT >

void RefineableActivatorInhibitorProblem< ELEMENT >::actions_before_newton_solve ( )

inlinevirtual

Empty.

Reimplemented from oomph::Problem.

94 {}

◆ actions_before_newton_solve() [2/2]

template<class ELEMENT >

void RefineableActivatorInhibitorProblem< ELEMENT >::actions_before_newton_solve ( )

inlinevirtual

Empty.

Reimplemented from oomph::Problem.

100 {}

◆ complete_problem_setup()

template<class ELEMENT >

void RefineableActivatorInhibitorProblem< ELEMENT >::complete_problem_setup

Set the elemental properties.

 {
  
  // Loop over the elements to set up element-specific 
  // things that cannot be handled by the (argument-free!) ELEMENT 
  // constructor: Pass pointer to source function
  unsigned n_element = mesh_pt()->nelement();
  for(unsigned i=0;i<n_element;i++)
   {
    // Upcast from GeneralsedElement to the present element
    ELEMENT *elem_pt = dynamic_cast<ELEMENT*>(mesh_pt()->element_pt(i));
    
    //Set the timescales
    elem_pt->tau_pt() = &GlobalVariables::Tau;
  
    //Set the diffusion coefficients
    elem_pt->diff_pt() = &GlobalVariables::D;
  
    //Set the reaction terms
    elem_pt->reaction_fct_pt() = &GlobalVariables::activator_inhibitor_reaction;
  
     //And their derivatives
    elem_pt->reaction_deriv_fct_pt() = 
     &GlobalVariables::activator_inhibitor_reaction_derivative;
  
   }
  
  
 }

References GlobalVariables::activator_inhibitor_reaction(), GlobalVariables::activator_inhibitor_reaction_derivative(), GlobalVariables::D, i, and GlobalVariables::Tau.

◆ mesh_pt()

template<class ELEMENT >

RefineableRectangularQuadMesh<ELEMENT>* RefineableActivatorInhibitorProblem< ELEMENT >::mesh_pt ( )

inline

Overloaded version of the problem's access function to the mesh. Recasts the pointer to the base Mesh object to the actual mesh type.

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

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

◆ set_initial_condition() [1/2]

template<class ELEMENT >

void RefineableActivatorInhibitorProblem< ELEMENT >::set_initial_condition

virtual

Set the initial conditions to be a single "hot" spot.

Reimplemented from oomph::Problem.

 {
  //Set the number of hot spots
  const unsigned n_spot = 1;
  //Set the centre of the hot spot
  const double centre_x[n_spot] = {6.0};
  const double centre_y[n_spot] = {7.0};
  
  //Set the initial concentrations of the reagents --- the homogeneous state
  //Plus an exponential hot spot
  unsigned n_node = mesh_pt()->nnode();
  //Loop over the nodes
  for(unsigned n=0;n<n_node;n++)
   {
    //Local pointer to the node
    Node* nod_pt = mesh_pt()->node_pt(n);
    //Get the absolute value of A
    double a13 = pow(std::abs(GlobalVariables::A),(1.0/3.0));
  
    //Set the value of the inhibitor from the homogeneous solution
    nod_pt->set_value(0,a13*(1.0-a13*a13));
    
    //Set a localised hot spot by making an exponential
    //hump in the activator
    double x = nod_pt->x(0);    double y = nod_pt->x(1);
    double spot = 0.0;
  
    for(unsigned s=0; s<n_spot; s++)
     {
      //Find the square distance from the centre of the 
      //hot spot
      double r2 = (x - centre_x[s])*(x - centre_x[s]) + 
                  (y - centre_y[s])*(y - centre_y[s]);
      
      //Add an exponential hump to the value of the spot variable
      spot += 2.0*exp(-2.0*r2);
     }
    
    //Set the value of the activator
    nod_pt->set_value(1,-a13 + spot);
   }
  
  //Document the initial solution
  ofstream filename("input.dat");
  mesh_pt()->output(filename,5);
  filename.close();
  
  //Set the initial values impulsive
  assign_initial_values_impulsive(Dt);
 } 

References GlobalVariables::A, abs(), ProblemParameters::Dt, Eigen::bfloat16_impl::exp(), MergeRestartFiles::filename, n, Eigen::ArrayBase< Derived >::pow(), s, oomph::Data::set_value(), plotDoE::x, oomph::Node::x(), and y.

◆ set_initial_condition() [2/2]

template<class ELEMENT >

void RefineableActivatorInhibitorProblem< ELEMENT >::set_initial_condition ( )

virtual

Set initial condition (incl previous timesteps). We need to establish this interface because I.C. needs to be reset when problem is adapted during the first timestep.

Reimplemented from oomph::Problem.

◆ timestep() [1/2]

template<class ELEMENT >

void RefineableActivatorInhibitorProblem< ELEMENT >::timestep	(	const double &	dt,
		const unsigned &	nstep
	)

Timestep the problem.

 {
  //Set the problem's Dt for the inital condition bit
  Dt = dt;
  
  //One uniform refinement so that we stand a chance of getting 
  //something
  this->refine_uniformly();
  //Maximum adaptation for the first timestep
  unsigned max_adapt = 2;
  
  //Take the first timestep
  bool first = true;
  
  //Set the initial condition
  set_initial_condition();
  
  //Solve the first step
  unsteady_newton_solve(dt,max_adapt,first);
  {
   unsigned i=0;
   char file1[100];
   sprintf(file1,"step%i.dat",i+1);
   ofstream out1(file1);
   mesh_pt()->output(out1,5);
   out1.close();
  }
  
  //Now set so that only one round of adaptation is performed each timestep
  max_adapt = 1;
  first = false;
  
  //Loop over possibilities
  for(unsigned i=1;i<nstep;i++)
   {
    unsteady_newton_solve(dt,max_adapt,first);
    char file1[100];
    sprintf(file1,"step%i.dat",i+1);
    ofstream out1(file1);
    mesh_pt()->output(out1,5);
    out1.close();
   }
 }

References ProblemParameters::Dt, and i.

◆ timestep() [2/2]

template<class ELEMENT >

void RefineableActivatorInhibitorProblem< ELEMENT >::timestep	(	const double &	dt,
		const unsigned &	nstep
	)

Member Data Documentation

◆ Dt

template<class ELEMENT >

double RefineableActivatorInhibitorProblem< ELEMENT >::Dt

private

Storage for the timestep.

◆ My_mesh_pt

template<class ELEMENT >

RefineableTriangleMesh<ELEMENT>* RefineableActivatorInhibitorProblem< ELEMENT >::My_mesh_pt

private

Pointers to specific mesh.

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

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

template<class ELEMENT> class RefineableActivatorInhibitorProblem< ELEMENT >

Constructor & Destructor Documentation

◆ RefineableActivatorInhibitorProblem() [1/2]

◆ ~RefineableActivatorInhibitorProblem() [1/2]

◆ RefineableActivatorInhibitorProblem() [2/2]

◆ ~RefineableActivatorInhibitorProblem() [2/2]

Member Function Documentation

◆ actions_after_adapt()

◆ actions_after_newton_solve() [1/2]

◆ actions_after_newton_solve() [2/2]

◆ actions_before_adapt()

◆ actions_before_newton_solve() [1/2]

◆ actions_before_newton_solve() [2/2]

◆ complete_problem_setup()

◆ mesh_pt()

◆ set_initial_condition() [1/2]

◆ set_initial_condition() [2/2]

◆ timestep() [1/2]

◆ timestep() [2/2]

Member Data Documentation

◆ Dt

◆ My_mesh_pt

template<class ELEMENT>
class RefineableActivatorInhibitorProblem< ELEMENT >