RefineableAdvectionDiffusionProblem< ELEMENT > Class Template Reference
+ Inheritance diagram for RefineableAdvectionDiffusionProblem< ELEMENT >:

Public Member Functions

 RefineableAdvectionDiffusionProblem (AdvectionDiffusionEquations< 2 >::AdvectionDiffusionSourceFctPt source_fct_pt, AdvectionDiffusionEquations< 2 >::AdvectionDiffusionWindFctPt wind_fct_pt)
 Constructor: Pass pointer to source and wind functions. More...
 
 ~RefineableAdvectionDiffusionProblem ()
 Destructor. Empty. More...
 
void actions_before_newton_solve ()
 
void actions_after_newton_solve ()
 Update the problem after solve (empty) More...
 
void actions_before_adapt ()
 Actions before adapt: Document the solution. More...
 
void doc_solution ()
 Doc the solution. More...
 
RefineableRectangularQuadMesh< ELEMENT > * mesh_pt ()
 
 RefineableAdvectionDiffusionProblem (AdvectionDiffusionEquations< 2 >::AdvectionDiffusionSourceFctPt source_fct_pt, AdvectionDiffusionEquations< 2 >::AdvectionDiffusionWindFctPt wind_fct_pt)
 Constructor: Pass pointer to source function. More...
 
 ~RefineableAdvectionDiffusionProblem ()
 Destructor (empty) More...
 
void actions_before_newton_solve ()
 
void actions_after_newton_solve ()
 Update the problem after solve (empty) More...
 
void doc_solution (DocInfo &doc_info)
 Doc the solution: doc_info contains labels/output directory etc. More...
 
RefineableRectangularQuadMesh< ELEMENT > * mesh_pt ()
 
 RefineableAdvectionDiffusionProblem (GeneralisedAdvectionDiffusionEquations< 2 >::GeneralisedAdvectionDiffusionWindFctPt wind_fct_pt, GeneralisedAdvectionDiffusionEquations< 2 >::GeneralisedAdvectionDiffusionWindFctPt swim_fct_pt, GeneralisedAdvectionDiffusionEquations< 2 >::GeneralisedAdvectionDiffusionDiffFctPt diff_fct_pt)
 Constructor: Pass pointer to source, wind and diffusivity functions. More...
 
 ~RefineableAdvectionDiffusionProblem ()
 Destructor. Delete the mesh and error estimator. More...
 
void actions_before_newton_solve ()
 Update the problem specs before solve. More...
 
void actions_after_newton_solve ()
 Update the problem after solve (empty) More...
 
void actions_before_adapt ()
 Actions before adapt: Document the solution. More...
 
void doc_solution ()
 Doc the solution. More...
 
RefineableRectangularQuadMesh< ELEMENT > * mesh_pt ()
 
- Public Member Functions inherited from oomph::Problem
virtual void debug_hook_fct (const unsigned &i)
 
void set_analytic_dparameter (double *const &parameter_pt)
 
void unset_analytic_dparameter (double *const &parameter_pt)
 
bool is_dparameter_calculated_analytically (double *const &parameter_pt)
 
void set_analytic_hessian_products ()
 
void unset_analytic_hessian_products ()
 
bool are_hessian_products_calculated_analytically ()
 
void set_pinned_values_to_zero ()
 
bool distributed () const
 
virtual void actions_after_adapt ()
 Actions that are to be performed after a mesh adaptation. More...
 
OomphCommunicator * communicator_pt ()
 access function to the oomph-lib communicator More...
 
const OomphCommunicator * communicator_pt () const
 access function to the oomph-lib communicator, const version More...
 
 Problem ()
 
 Problem (const Problem &dummy)=delete
 Broken copy constructor. More...
 
void operator= (const Problem &)=delete
 Broken assignment operator. More...
 
virtual ~Problem ()
 Virtual destructor to clean up memory. More...
 
Mesh *& mesh_pt ()
 Return a pointer to the global mesh. More...
 
Mesh *const & mesh_pt () const
 Return a pointer to the global mesh (const version) More...
 
Mesh *& mesh_pt (const unsigned &imesh)
 
Mesh *const & mesh_pt (const unsigned &imesh) const
 Return a pointer to the i-th submesh (const version) More...
 
unsigned nsub_mesh () const
 Return number of submeshes. More...
 
unsigned add_sub_mesh (Mesh *const &mesh_pt)
 
void flush_sub_meshes ()
 
void build_global_mesh ()
 
void rebuild_global_mesh ()
 
LinearSolver *& linear_solver_pt ()
 Return a pointer to the linear solver object. More...
 
LinearSolver *const & linear_solver_pt () const
 Return a pointer to the linear solver object (const version) More...
 
LinearSolver *& mass_matrix_solver_for_explicit_timestepper_pt ()
 
LinearSolver * mass_matrix_solver_for_explicit_timestepper_pt () const
 
EigenSolver *& eigen_solver_pt ()
 Return a pointer to the eigen solver object. More...
 
EigenSolver *const & eigen_solver_pt () const
 Return a pointer to the eigen solver object (const version) More...
 
Time *& time_pt ()
 Return a pointer to the global time object. More...
 
Time * time_pt () const
 Return a pointer to the global time object (const version). More...
 
double & time ()
 Return the current value of continuous time. More...
 
double time () const
 Return the current value of continuous time (const version) More...
 
TimeStepper *& time_stepper_pt ()
 
const TimeStepper * time_stepper_pt () const
 
TimeStepper *& time_stepper_pt (const unsigned &i)
 Return a pointer to the i-th timestepper. More...
 
ExplicitTimeStepper *& explicit_time_stepper_pt ()
 Return a pointer to the explicit timestepper. More...
 
unsigned long set_timestepper_for_all_data (TimeStepper *const &time_stepper_pt, const bool &preserve_existing_data=false)
 
virtual void shift_time_values ()
 Shift all values along to prepare for next timestep. More...
 
AssemblyHandler *& assembly_handler_pt ()
 Return a pointer to the assembly handler object. More...
 
AssemblyHandler *const & assembly_handler_pt () const
 Return a pointer to the assembly handler object (const version) More...
 
double & minimum_dt ()
 Access function to min timestep in adaptive timestepping. More...
 
double & maximum_dt ()
 Access function to max timestep in adaptive timestepping. More...
 
unsigned & max_newton_iterations ()
 Access function to max Newton iterations before giving up. More...
 
void problem_is_nonlinear (const bool &prob_lin)
 Access function to Problem_is_nonlinear. More...
 
double & max_residuals ()
 
bool & time_adaptive_newton_crash_on_solve_fail ()
 Access function for Time_adaptive_newton_crash_on_solve_fail. More...
 
double & newton_solver_tolerance ()
 
void add_time_stepper_pt (TimeStepper *const &time_stepper_pt)
 
void set_explicit_time_stepper_pt (ExplicitTimeStepper *const &explicit_time_stepper_pt)
 
void initialise_dt (const double &dt)
 
void initialise_dt (const Vector< double > &dt)
 
Data *& global_data_pt (const unsigned &i)
 Return a pointer to the the i-th global data object. More...
 
void add_global_data (Data *const &global_data_pt)
 
void flush_global_data ()
 
LinearAlgebraDistribution *const & dof_distribution_pt () const
 Return the pointer to the dof distribution (read-only) More...
 
unsigned long ndof () const
 Return the number of dofs. More...
 
unsigned ntime_stepper () const
 Return the number of time steppers. More...
 
unsigned nglobal_data () const
 Return the number of global data values. More...
 
unsigned self_test ()
 Self-test: Check meshes and global data. Return 0 for OK. More...
 
void enable_store_local_dof_pt_in_elements ()
 
void disable_store_local_dof_pt_in_elements ()
 
unsigned long assign_eqn_numbers (const bool &assign_local_eqn_numbers=true)
 
void describe_dofs (std::ostream &out= *(oomph_info.stream_pt())) const
 
void enable_discontinuous_formulation ()
 
void disable_discontinuous_formulation ()
 
void get_dofs (DoubleVector &dofs) const
 
void get_dofs (const unsigned &t, DoubleVector &dofs) const
 Return vector of the t'th history value of all dofs. More...
 
void set_dofs (const DoubleVector &dofs)
 Set the values of the dofs. More...
 
void set_dofs (const unsigned &t, DoubleVector &dofs)
 Set the history values of the dofs. More...
 
void set_dofs (const unsigned &t, Vector< double * > &dof_pt)
 
void add_to_dofs (const double &lambda, const DoubleVector &increment_dofs)
 Add lambda x incremenet_dofs[l] to the l-th dof. More...
 
double * global_dof_pt (const unsigned &i)
 
double & dof (const unsigned &i)
 i-th dof in the problem More...
 
double dof (const unsigned &i) const
 i-th dof in the problem (const version) More...
 
double *& dof_pt (const unsigned &i)
 Pointer to i-th dof in the problem. More...
 
double * dof_pt (const unsigned &i) const
 Pointer to i-th dof in the problem (const version) More...
 
virtual void get_inverse_mass_matrix_times_residuals (DoubleVector &Mres)
 
virtual void get_dvaluesdt (DoubleVector &f)
 
virtual void get_residuals (DoubleVector &residuals)
 Get the total residuals Vector for the problem. More...
 
virtual void get_jacobian (DoubleVector &residuals, DenseDoubleMatrix &jacobian)
 
virtual void get_jacobian (DoubleVector &residuals, CRDoubleMatrix &jacobian)
 
virtual void get_jacobian (DoubleVector &residuals, CCDoubleMatrix &jacobian)
 
virtual void get_jacobian (DoubleVector &residuals, SumOfMatrices &jacobian)
 
void get_fd_jacobian (DoubleVector &residuals, DenseMatrix< double > &jacobian)
 Get the full Jacobian by finite differencing. More...
 
void get_derivative_wrt_global_parameter (double *const &parameter_pt, DoubleVector &result)
 
void get_hessian_vector_products (DoubleVectorWithHaloEntries const &Y, Vector< DoubleVectorWithHaloEntries > const &C, Vector< DoubleVectorWithHaloEntries > &product)
 
void solve_eigenproblem (const unsigned &n_eval, Vector< std::complex< double >> &eigenvalue, Vector< DoubleVector > &eigenvector, const bool &steady=true)
 Solve the eigenproblem. More...
 
void solve_eigenproblem (const unsigned &n_eval, Vector< std::complex< double >> &eigenvalue, const bool &steady=true)
 
virtual void get_eigenproblem_matrices (CRDoubleMatrix &mass_matrix, CRDoubleMatrix &main_matrix, const double &shift=0.0)
 
void assign_eigenvector_to_dofs (DoubleVector &eigenvector)
 Assign the eigenvector passed to the function to the dofs. More...
 
void add_eigenvector_to_dofs (const double &epsilon, const DoubleVector &eigenvector)
 
void store_current_dof_values ()
 Store the current values of the degrees of freedom. More...
 
void restore_dof_values ()
 Restore the stored values of the degrees of freedom. More...
 
void enable_jacobian_reuse ()
 
void disable_jacobian_reuse ()
 Disable recycling of Jacobian in Newton iteration. More...
 
bool jacobian_reuse_is_enabled ()
 Is recycling of Jacobian in Newton iteration enabled? More...
 
bool & use_predictor_values_as_initial_guess ()
 
void newton_solve ()
 Use Newton method to solve the problem. More...
 
void enable_globally_convergent_newton_method ()
 enable globally convergent Newton method More...
 
void disable_globally_convergent_newton_method ()
 disable globally convergent Newton method More...
 
void newton_solve (unsigned const &max_adapt)
 
void steady_newton_solve (unsigned const &max_adapt=0)
 
void copy (Problem *orig_problem_pt)
 
virtual Problem * make_copy ()
 
virtual void read (std::ifstream &restart_file, bool &unsteady_restart)
 
virtual void read (std::ifstream &restart_file)
 
virtual void dump (std::ofstream &dump_file) const
 
void dump (const std::string &dump_file_name) const
 
void delete_all_external_storage ()
 
virtual void symmetrise_eigenfunction_for_adaptive_pitchfork_tracking ()
 
double * bifurcation_parameter_pt () const
 
void get_bifurcation_eigenfunction (Vector< DoubleVector > &eigenfunction)
 
void activate_fold_tracking (double *const &parameter_pt, const bool &block_solve=true)
 
void activate_bifurcation_tracking (double *const &parameter_pt, const DoubleVector &eigenvector, const bool &block_solve=true)
 
void activate_bifurcation_tracking (double *const &parameter_pt, const DoubleVector &eigenvector, const DoubleVector &normalisation, const bool &block_solve=true)
 
void activate_pitchfork_tracking (double *const &parameter_pt, const DoubleVector &symmetry_vector, const bool &block_solve=true)
 
void activate_hopf_tracking (double *const &parameter_pt, const bool &block_solve=true)
 
void activate_hopf_tracking (double *const &parameter_pt, const double &omega, const DoubleVector &null_real, const DoubleVector &null_imag, const bool &block_solve=true)
 
void deactivate_bifurcation_tracking ()
 
void reset_assembly_handler_to_default ()
 Reset the system to the standard non-augemented state. More...
 
double arc_length_step_solve (double *const &parameter_pt, const double &ds, const unsigned &max_adapt=0)
 
double arc_length_step_solve (Data *const &data_pt, const unsigned &data_index, const double &ds, const unsigned &max_adapt=0)
 
void reset_arc_length_parameters ()
 
int & sign_of_jacobian ()
 
void explicit_timestep (const double &dt, const bool &shift_values=true)
 Take an explicit timestep of size dt. More...
 
void unsteady_newton_solve (const double &dt)
 
void unsteady_newton_solve (const double &dt, const bool &shift_values)
 
void unsteady_newton_solve (const double &dt, const unsigned &max_adapt, const bool &first, const bool &shift=true)
 
double doubly_adaptive_unsteady_newton_solve (const double &dt, const double &epsilon, const unsigned &max_adapt, const bool &first, const bool &shift=true)
 
double doubly_adaptive_unsteady_newton_solve (const double &dt, const double &epsilon, const unsigned &max_adapt, const unsigned &suppress_resolve_after_spatial_adapt_flag, const bool &first, const bool &shift=true)
 
double adaptive_unsteady_newton_solve (const double &dt_desired, const double &epsilon)
 
double adaptive_unsteady_newton_solve (const double &dt_desired, const double &epsilon, const bool &shift_values)
 
void assign_initial_values_impulsive ()
 
void assign_initial_values_impulsive (const double &dt)
 
void calculate_predictions ()
 Calculate predictions. More...
 
void enable_mass_matrix_reuse ()
 
void disable_mass_matrix_reuse ()
 
bool mass_matrix_reuse_is_enabled ()
 Return whether the mass matrix is being reused. More...
 
void refine_uniformly (const Vector< unsigned > &nrefine_for_mesh)
 
void refine_uniformly (const Vector< unsigned > &nrefine_for_mesh, DocInfo &doc_info)
 
void refine_uniformly_and_prune (const Vector< unsigned > &nrefine_for_mesh)
 
void refine_uniformly_and_prune (const Vector< unsigned > &nrefine_for_mesh, DocInfo &doc_info)
 
void refine_uniformly (DocInfo &doc_info)
 
void refine_uniformly_and_prune (DocInfo &doc_info)
 
void refine_uniformly ()
 
void refine_uniformly (const unsigned &i_mesh, DocInfo &doc_info)
 Do uniform refinement for submesh i_mesh with documentation. More...
 
void refine_uniformly (const unsigned &i_mesh)
 Do uniform refinement for submesh i_mesh without documentation. More...
 
void p_refine_uniformly (const Vector< unsigned > &nrefine_for_mesh)
 
void p_refine_uniformly (const Vector< unsigned > &nrefine_for_mesh, DocInfo &doc_info)
 
void p_refine_uniformly_and_prune (const Vector< unsigned > &nrefine_for_mesh)
 
void p_refine_uniformly_and_prune (const Vector< unsigned > &nrefine_for_mesh, DocInfo &doc_info)
 
void p_refine_uniformly (DocInfo &doc_info)
 
void p_refine_uniformly_and_prune (DocInfo &doc_info)
 
void p_refine_uniformly ()
 
void p_refine_uniformly (const unsigned &i_mesh, DocInfo &doc_info)
 Do uniform p-refinement for submesh i_mesh with documentation. More...
 
void p_refine_uniformly (const unsigned &i_mesh)
 Do uniform p-refinement for submesh i_mesh without documentation. More...
 
void refine_selected_elements (const Vector< unsigned > &elements_to_be_refined)
 
void refine_selected_elements (const Vector< RefineableElement * > &elements_to_be_refined_pt)
 
void refine_selected_elements (const unsigned &i_mesh, const Vector< unsigned > &elements_to_be_refined)
 
void refine_selected_elements (const unsigned &i_mesh, const Vector< RefineableElement * > &elements_to_be_refined_pt)
 
void refine_selected_elements (const Vector< Vector< unsigned >> &elements_to_be_refined)
 
void refine_selected_elements (const Vector< Vector< RefineableElement * >> &elements_to_be_refined_pt)
 
void p_refine_selected_elements (const Vector< unsigned > &elements_to_be_refined)
 
void p_refine_selected_elements (const Vector< PRefineableElement * > &elements_to_be_refined_pt)
 
void p_refine_selected_elements (const unsigned &i_mesh, const Vector< unsigned > &elements_to_be_refined)
 
void p_refine_selected_elements (const unsigned &i_mesh, const Vector< PRefineableElement * > &elements_to_be_refined_pt)
 
void p_refine_selected_elements (const Vector< Vector< unsigned >> &elements_to_be_refined)
 
void p_refine_selected_elements (const Vector< Vector< PRefineableElement * >> &elements_to_be_refined_pt)
 
unsigned unrefine_uniformly ()
 
unsigned unrefine_uniformly (const unsigned &i_mesh)
 
void p_unrefine_uniformly (DocInfo &doc_info)
 
void p_unrefine_uniformly (const unsigned &i_mesh, DocInfo &doc_info)
 Do uniform p-unrefinement for submesh i_mesh without documentation. More...
 
void adapt (unsigned &n_refined, unsigned &n_unrefined)
 
void adapt ()
 
void p_adapt (unsigned &n_refined, unsigned &n_unrefined)
 
void p_adapt ()
 
void adapt_based_on_error_estimates (unsigned &n_refined, unsigned &n_unrefined, Vector< Vector< double >> &elemental_error)
 
void adapt_based_on_error_estimates (Vector< Vector< double >> &elemental_error)
 
void get_all_error_estimates (Vector< Vector< double >> &elemental_error)
 
void doc_errors (DocInfo &doc_info)
 Get max and min error for all elements in submeshes. More...
 
void doc_errors ()
 Get max and min error for all elements in submeshes. More...
 
void enable_info_in_newton_solve ()
 
void disable_info_in_newton_solve ()
 Disable the output of information when in the newton solver. More...
 
- Public Member Functions inherited from oomph::ExplicitTimeSteppableObject
 ExplicitTimeSteppableObject ()
 Empty constructor. More...
 
 ExplicitTimeSteppableObject (const ExplicitTimeSteppableObject &)=delete
 Broken copy constructor. More...
 
void operator= (const ExplicitTimeSteppableObject &)=delete
 Broken assignment operator. More...
 
virtual ~ExplicitTimeSteppableObject ()
 Empty destructor. More...
 
virtual void actions_before_explicit_stage ()
 
virtual void actions_after_explicit_stage ()
 

Private Attributes

DocInfo Doc_info
 DocInfo object. More...
 
AdvectionDiffusionEquations< 2 >::AdvectionDiffusionSourceFctPt Source_fct_pt
 Pointer to source function. More...
 
AdvectionDiffusionEquations< 2 >::AdvectionDiffusionWindFctPt Wind_fct_pt
 Pointer to wind function. More...
 
GeneralisedAdvectionDiffusionEquations< 2 >::GeneralisedAdvectionDiffusionDiffFctPt Diff_fct_pt
 Pointer to diffusivity function. More...
 
GeneralisedAdvectionDiffusionEquations< 2 >::GeneralisedAdvectionDiffusionWindFctPt Wind_fct_pt
 Pointer to wind function. More...
 
GeneralisedAdvectionDiffusionEquations< 2 >::GeneralisedAdvectionDiffusionWindFctPt Swim_fct_pt
 Pointer to a swimming speed. 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 RefineableAdvectionDiffusionProblem< ELEMENT >

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

/////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////// 2D GeneralisedAdvectionDiffusion problem on a rectangular domain, discretised with refineable 2D QGeneralisedAdvectionDiffusion elements. The specific type of element is specified via the template parameter.

Constructor & Destructor Documentation

◆ RefineableAdvectionDiffusionProblem() [1/3]

template<class ELEMENT >
RefineableAdvectionDiffusionProblem< ELEMENT >::RefineableAdvectionDiffusionProblem ( AdvectionDiffusionEquations< 2 >::AdvectionDiffusionSourceFctPt  source_fct_pt,
AdvectionDiffusionEquations< 2 >::AdvectionDiffusionWindFctPt  wind_fct_pt 
)

Constructor: Pass pointer to source and wind functions.

Constructor for AdvectionDiffusion problem: Pass pointer to source function.

168 {
169 
170  // Set output directory
171  Doc_info.set_directory("RESLT");
172 
173  // Setup mesh
174 
175  // # of elements in x-direction
176  unsigned n_x=4;
177 
178  // # of elements in y-direction
179  unsigned n_y=4;
180 
181  // Domain length in x-direction
182  double l_x=1.0;
183 
184  // Domain length in y-direction
185  double l_y=2.0;
186 
187  // Build and assign mesh
188  Problem::mesh_pt() =
189  new RefineableRectangularQuadMesh<ELEMENT>(n_x,n_y,l_x,l_y);
190 
191  // Create/set error estimator
192  mesh_pt()->spatial_error_estimator_pt()=new Z2ErrorEstimator;
193 
194  // Set the boundary conditions for this problem: All nodes are
195  // free by default -- only need to pin the ones that have Dirichlet
196  // conditions here
197  unsigned num_bound = mesh_pt()->nboundary();
198  for(unsigned ibound=0;ibound<num_bound;ibound++)
199  {
200  unsigned num_nod= mesh_pt()->nboundary_node(ibound);
201  for (unsigned inod=0;inod<num_nod;inod++)
202  {
203  mesh_pt()->boundary_node_pt(ibound,inod)->pin(0);
204  }
205  } // end loop over boundaries
206 
207  // Complete the build of all elements so they are fully functional
208 
209  // Loop over the elements to set up element-specific
210  // things that cannot be handled by the (argument-free!) ELEMENT
211  // constructor: Pass pointer to source function
212  unsigned n_element = mesh_pt()->nelement();
213  for(unsigned i=0;i<n_element;i++)
214  {
215  // Upcast from GeneralsedElement to the present element
216  ELEMENT *el_pt = dynamic_cast<ELEMENT*>(mesh_pt()->element_pt(i));
217 
218  //Set the source function pointer
219  el_pt->source_fct_pt() = Source_fct_pt;
220 
221  //Set the wind function pointer
222  el_pt->wind_fct_pt() = Wind_fct_pt;
223 
224  // Set the Peclet number
226  }
227 
228  // Setup equation numbering scheme
229  cout <<"Number of equations: " << assign_eqn_numbers() << std::endl;
230 
231 } // end of constructor
int i
Definition: BiCGSTAB_step_by_step.cpp:9
DocInfo Doc_info
DocInfo object.
Definition: two_d_adv_diff_adapt.cc:147
AdvectionDiffusionEquations< 2 >::AdvectionDiffusionSourceFctPt Source_fct_pt
Pointer to source function.
Definition: two_d_adv_diff_adapt.cc:150
AdvectionDiffusionEquations< 2 >::AdvectionDiffusionWindFctPt Wind_fct_pt
Pointer to wind function.
Definition: two_d_adv_diff_adapt.cc:153
RefineableRectangularQuadMesh< ELEMENT > * mesh_pt()
Definition: two_d_adv_diff_adapt.cc:138
double *& pe_pt()
Pointer to Peclet number.
Definition: advection_diffusion_elements.h:324
AdvectionDiffusionWindFctPt & wind_fct_pt()
Access function: Pointer to wind function.
Definition: advection_diffusion_elements.h:305
void set_directory(const std::string &directory)
Definition: oomph_utilities.cc:298
unsigned long assign_eqn_numbers(const bool &assign_local_eqn_numbers=true)
Definition: problem.cc:1989
Definition: rectangular_quadmesh.template.h:326
Definition: error_estimator.h:266
double Peclet
Peclet number.
Definition: two_d_adv_diff_adapt.cc:50
GeneralisedAxisymAdvectionDiffusionSourceFctPt & source_fct_pt()
Access function: Pointer to source function.
Definition: gen_axisym_advection_diffusion_elements.h:229
Constructor for SteadyAxisymAdvectionDiffusion SteadyAxisymAdvectionDiffusionEquations::SteadyAxisymAdvectionDiffusionWindFctPt wind_fct_pt
Definition: steady_axisym_advection_diffusion.cc:215

References oomph::Problem::assign_eqn_numbers(), RefineableAdvectionDiffusionProblem< ELEMENT >::Doc_info, i, RefineableAdvectionDiffusionProblem< ELEMENT >::mesh_pt(), oomph::AdvectionDiffusionEquations< DIM >::pe_pt(), TanhSolnForAdvectionDiffusion::Peclet, oomph::DocInfo::set_directory(), RefineableAdvectionDiffusionProblem< ELEMENT >::Source_fct_pt, RefineableAdvectionDiffusionProblem< ELEMENT >::Wind_fct_pt, and oomph::AdvectionDiffusionEquations< DIM >::wind_fct_pt().

◆ ~RefineableAdvectionDiffusionProblem() [1/3]

template<class ELEMENT >
RefineableAdvectionDiffusionProblem< ELEMENT >::~RefineableAdvectionDiffusionProblem ( )
inline

Destructor. Empty.

113 {}

◆ RefineableAdvectionDiffusionProblem() [2/3]

template<class ELEMENT >
RefineableAdvectionDiffusionProblem< ELEMENT >::RefineableAdvectionDiffusionProblem ( AdvectionDiffusionEquations< 2 >::AdvectionDiffusionSourceFctPt  source_fct_pt,
AdvectionDiffusionEquations< 2 >::AdvectionDiffusionWindFctPt  wind_fct_pt 
)

Constructor: Pass pointer to source function.

◆ ~RefineableAdvectionDiffusionProblem() [2/3]

template<class ELEMENT >
RefineableAdvectionDiffusionProblem< ELEMENT >::~RefineableAdvectionDiffusionProblem ( )
inline

Destructor (empty)

107 {}

◆ RefineableAdvectionDiffusionProblem() [3/3]

template<class ELEMENT >
RefineableAdvectionDiffusionProblem< ELEMENT >::RefineableAdvectionDiffusionProblem ( GeneralisedAdvectionDiffusionEquations< 2 >::GeneralisedAdvectionDiffusionWindFctPt  wind_fct_pt,
GeneralisedAdvectionDiffusionEquations< 2 >::GeneralisedAdvectionDiffusionWindFctPt  swim_fct_pt,
GeneralisedAdvectionDiffusionEquations< 2 >::GeneralisedAdvectionDiffusionDiffFctPt  diff_fct_pt 
)

Constructor: Pass pointer to source, wind and diffusivity functions.

Constructor for AdvectionDiffusion problem: Pass pointer to source function.

231  Swim_fct_pt(swim_fct_pt)
232 {
233 
234  // Set output directory
235  Doc_info.set_directory("RESLT");
236 
237  // Setup mesh
238 
239  // # of elements in x-direction
240  unsigned n_x=4;
241 
242  // # of elements in y-direction
243  unsigned n_y=4;
244 
245  // Domain length in x-direction
246  double l_x=1.0;
247 
248  // Domain length in y-direction
249  double l_y=1.0;
250 
251  // Build and assign mesh
252  Problem::mesh_pt() =
253  new RefineableRectangularQuadMesh<ELEMENT>(n_x,n_y,l_x,l_y);
254 
255  // Create/set error estimator
256  mesh_pt()->spatial_error_estimator_pt()=new Z2ErrorEstimator;
257 
258  // Set the boundary conditions for this problem: All nodes are
259  // free by default -- only need to pin the ones that have Dirichlet
260  // conditions here. That is those on the lower wall
261  for(unsigned ibound=0;ibound<1;ibound++)
262  {
263  unsigned num_nod= mesh_pt()->nboundary_node(ibound);
264  for (unsigned inod=0;inod<num_nod;inod++)
265  {
266  mesh_pt()->boundary_node_pt(ibound,inod)->pin(0);
267  mesh_pt()->boundary_node_pt(ibound,inod)->set_value(0,1.0);
268  }
269  } // end loop over boundaries
270 
271  // Complete the build of all elements so they are fully functional
272 
273  // Loop over the elements to set up element-specific
274  // things that cannot be handled by the (argument-free!) ELEMENT
275  // constructor: Pass pointer to source function
276  unsigned n_element = mesh_pt()->nelement();
277  for(unsigned i=0;i<n_element;i++)
278  {
279  // Upcast from GeneralsedElement to the present element
280  ELEMENT *el_pt = dynamic_cast<ELEMENT*>(mesh_pt()->element_pt(i));
281 
282  //Set the diffusivity function pointer
283  el_pt->diff_fct_pt() = Diff_fct_pt;
284 
285  //Set the wind function pointer
286  el_pt->wind_fct_pt() = Wind_fct_pt;
287 
288  //Set the swimming speed
289  el_pt->conserved_wind_fct_pt() = Swim_fct_pt;
290 
291  // Set the Peclet number
293  }
294 
295  // Setup equation numbering scheme
296  cout <<"Number of equations: " << assign_eqn_numbers() << std::endl;
297 
298 } // end of constructor
GeneralisedAdvectionDiffusionEquations< 2 >::GeneralisedAdvectionDiffusionDiffFctPt Diff_fct_pt
Pointer to diffusivity function.
Definition: two_d_variable_diff_adapt.cc:203
GeneralisedAdvectionDiffusionEquations< 2 >::GeneralisedAdvectionDiffusionWindFctPt Swim_fct_pt
Pointer to a swimming speed.
Definition: two_d_variable_diff_adapt.cc:211
GeneralisedAdvectionDiffusionWindFctPt & wind_fct_pt()
Access function: Pointer to wind function.
Definition: gen_advection_diffusion_elements.h:232
double *& pe_pt()
Pointer to Peclet number.
Definition: gen_advection_diffusion_elements.h:279
double Peclet
Peclet number.
Definition: two_d_variable_diff_adapt.cc:50
GeneralisedAxisymAdvectionDiffusionDiffFctPt & diff_fct_pt()
Access function: Pointer to diffusion function.
Definition: gen_axisym_advection_diffusion_elements.h:272

References oomph::Problem::assign_eqn_numbers(), RefineableAdvectionDiffusionProblem< ELEMENT >::Diff_fct_pt, RefineableAdvectionDiffusionProblem< ELEMENT >::Doc_info, i, RefineableAdvectionDiffusionProblem< ELEMENT >::mesh_pt(), oomph::GeneralisedAdvectionDiffusionEquations< DIM >::pe_pt(), RachelsAdvectionDiffusion::Peclet, oomph::DocInfo::set_directory(), RefineableAdvectionDiffusionProblem< ELEMENT >::Swim_fct_pt, RefineableAdvectionDiffusionProblem< ELEMENT >::Wind_fct_pt, and oomph::GeneralisedAdvectionDiffusionEquations< DIM >::wind_fct_pt().

◆ ~RefineableAdvectionDiffusionProblem() [3/3]

template<class ELEMENT >
RefineableAdvectionDiffusionProblem< ELEMENT >::~RefineableAdvectionDiffusionProblem ( )
inline

Destructor. Delete the mesh and error estimator.

164  {
165  delete this->mesh_pt();
166  }

Member Function Documentation

◆ actions_after_newton_solve() [1/3]

template<class ELEMENT >
void RefineableAdvectionDiffusionProblem< ELEMENT >::actions_after_newton_solve ( )
inlinevirtual

Update the problem after solve (empty)

Reimplemented from oomph::Problem.

120 {}

◆ actions_after_newton_solve() [2/3]

template<class ELEMENT >
void RefineableAdvectionDiffusionProblem< ELEMENT >::actions_after_newton_solve ( )
inlinevirtual

Update the problem after solve (empty)

Reimplemented from oomph::Problem.

114 {}

◆ actions_after_newton_solve() [3/3]

template<class ELEMENT >
void RefineableAdvectionDiffusionProblem< ELEMENT >::actions_after_newton_solve ( )
inlinevirtual

Update the problem after solve (empty)

Reimplemented from oomph::Problem.

172 {}

◆ actions_before_adapt() [1/2]

template<class ELEMENT >
void RefineableAdvectionDiffusionProblem< ELEMENT >::actions_before_adapt ( )
inlinevirtual

Actions before adapt: Document the solution.

Reimplemented from oomph::Problem.

124  {
125  // Doc the solution
126  doc_solution();
127 
128  // Increment label for output files
129  Doc_info.number()++;
130  }
void doc_solution()
Doc the solution.
Definition: two_d_adv_diff_adapt.cc:277
unsigned & number()
Number used (e.g.) for labeling output files.
Definition: oomph_utilities.h:554

References GlobalParameters::Doc_info, and oomph::DocInfo::number().

◆ actions_before_adapt() [2/2]

template<class ELEMENT >
void RefineableAdvectionDiffusionProblem< ELEMENT >::actions_before_adapt ( )
inlinevirtual

Actions before adapt: Document the solution.

Reimplemented from oomph::Problem.

176  {
177  // Doc the solution
178  doc_solution();
179 
180  // Increment label for output files
181  Doc_info.number()++;
182  }

References GlobalParameters::Doc_info, and oomph::DocInfo::number().

◆ actions_before_newton_solve() [1/3]

template<class ELEMENT >
void RefineableAdvectionDiffusionProblem< ELEMENT >::actions_before_newton_solve
virtual

Update the problem specs before solve: Reset boundary conditions to the values from the tanh solution.

Update the problem specs before solve: (Re-)set boundary conditions to the values from the tanh solution.

Update the problem specs before solve: (Re-)set boundary conditions to the values from the exact solution.

Reimplemented from oomph::Problem.

240 {
241  // How many boundaries are there?
242  unsigned num_bound = mesh_pt()->nboundary();
243 
244  //Loop over the boundaries
245  for(unsigned ibound=0;ibound<num_bound;ibound++)
246  {
247  // How many nodes are there on this boundary?
248  unsigned num_nod=mesh_pt()->nboundary_node(ibound);
249 
250  // Loop over the nodes on boundary
251  for (unsigned inod=0;inod<num_nod;inod++)
252  {
253  // Get pointer to node
254  Node* nod_pt=mesh_pt()->boundary_node_pt(ibound,inod);
255 
256  // Extract nodal coordinates from node:
257  Vector<double> x(2);
258  x[0]=nod_pt->x(0);
259  x[1]=nod_pt->x(1);
260 
261  // Compute the value of the exact solution at the nodal point
262  Vector<double> u(1);
264 
265  // Assign the value to the one (and only) nodal value at this node
266  nod_pt->set_value(0,u[0]);
267  }
268  }
269 } // end of actions before solve
void set_value(const unsigned &i, const double &value_)
Definition: nodes.h:271
Definition: nodes.h:906
double & x(const unsigned &i)
Return the i-th nodal coordinate.
Definition: nodes.h:1060
void get_exact_u(const Vector< double > &x, Vector< double > &u)
Exact solution as a Vector.
Definition: two_d_adv_diff_adapt.cc:59
list x
Definition: plotDoE.py:28

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

◆ actions_before_newton_solve() [2/3]

template<class ELEMENT >
void RefineableAdvectionDiffusionProblem< ELEMENT >::actions_before_newton_solve ( )
virtual

Update the problem specs before solve: Reset boundary conditions to the values from the exact solution.

Reimplemented from oomph::Problem.

◆ actions_before_newton_solve() [3/3]

template<class ELEMENT >
void RefineableAdvectionDiffusionProblem< ELEMENT >::actions_before_newton_solve ( )
inlinevirtual

Update the problem specs before solve.

Reimplemented from oomph::Problem.

169 {}

◆ doc_solution() [1/3]

template<class ELEMENT >
void RefineableAdvectionDiffusionProblem< ELEMENT >::doc_solution

Doc the solution.

278 {
279 
280  ofstream some_file;
281  char filename[100];
282 
283  // Number of plot points: npts x npts
284  unsigned npts=5;
285 
286  // Output solution
287  //-----------------
288  sprintf(filename,"%s/soln%i.dat",Doc_info.directory().c_str(),
289  Doc_info.number());
290  some_file.open(filename);
291  mesh_pt()->output(some_file,npts);
292  some_file.close();
293 
294  // Output exact solution
295  //----------------------
296  sprintf(filename,"%s/exact_soln%i.dat",Doc_info.directory().c_str(),
297  Doc_info.number());
298  some_file.open(filename);
299  mesh_pt()->output_fct(some_file,npts,TanhSolnForAdvectionDiffusion::get_exact_u);
300  some_file.close();
301 
302  // Doc error and return of the square of the L2 error
303  //---------------------------------------------------
304  double error,norm;
305  sprintf(filename,"%s/error%i.dat",Doc_info.directory().c_str(),
306  Doc_info.number());
307  some_file.open(filename);
308  mesh_pt()->compute_error(some_file,TanhSolnForAdvectionDiffusion::get_exact_u,
309  error,norm);
310  some_file.close();
311 
312  // Doc L2 error and norm of solution
313  cout << "\nNorm of error : " << sqrt(error) << std::endl;
314  cout << "Norm of solution: " << sqrt(norm) << std::endl << std::endl;
315 
316 } // end of doc
AnnoyingScalar sqrt(const AnnoyingScalar &x)
Definition: AnnoyingScalar.h:134
std::string directory() const
Output directory.
Definition: oomph_utilities.h:524
string filename
Definition: MergeRestartFiles.py:39
int error
Definition: calibrate.py:297

References oomph::DocInfo::directory(), GlobalParameters::Doc_info, calibrate::error, MergeRestartFiles::filename, TanhSolnForAdvectionDiffusion::get_exact_u(), oomph::DocInfo::number(), and sqrt().

◆ doc_solution() [2/3]

template<class ELEMENT >
void RefineableAdvectionDiffusionProblem< ELEMENT >::doc_solution ( )

Doc the solution.

◆ doc_solution() [3/3]

template<class ELEMENT >
void RefineableAdvectionDiffusionProblem< ELEMENT >::doc_solution ( DocInfo &  doc_info)

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

Doc the solution. DocInfo object stores flags/labels for where the output gets written to

256 {
257 
258  ofstream some_file;
259  char filename[100];
260 
261  // Number of plot points: npts x npts
262  unsigned npts=5;
263 
264  // Output solution
265  //-----------------
266  sprintf(filename,"%s/soln%i.dat",doc_info.directory().c_str(),
267  doc_info.number());
268  some_file.open(filename);
269  mesh_pt()->output(some_file,npts);
270  some_file.close();
271 
272 } // end of doc

References oomph::DocInfo::directory(), MergeRestartFiles::filename, and oomph::DocInfo::number().

◆ mesh_pt() [1/3]

template<class ELEMENT >
RefineableRectangularQuadMesh<ELEMENT>* RefineableAdvectionDiffusionProblem< 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.

139  {
140  return dynamic_cast<RefineableRectangularQuadMesh<ELEMENT>*>(
141  Problem::mesh_pt());
142  }

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

◆ mesh_pt() [2/3]

template<class ELEMENT >
RefineableRectangularQuadMesh<ELEMENT>* RefineableAdvectionDiffusionProblem< 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.

124  {
125  return dynamic_cast<RefineableRectangularQuadMesh<ELEMENT>*>(
126  Problem::mesh_pt());
127  }

◆ mesh_pt() [3/3]

template<class ELEMENT >
RefineableRectangularQuadMesh<ELEMENT>* RefineableAdvectionDiffusionProblem< 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.

191  {
192  return dynamic_cast<RefineableRectangularQuadMesh<ELEMENT>*>(
193  Problem::mesh_pt());
194  }

Member Data Documentation

◆ Diff_fct_pt

template<class ELEMENT >
GeneralisedAdvectionDiffusionEquations<2>:: GeneralisedAdvectionDiffusionDiffFctPt RefineableAdvectionDiffusionProblem< ELEMENT >::Diff_fct_pt
private

◆ Doc_info

template<class ELEMENT >
DocInfo RefineableAdvectionDiffusionProblem< ELEMENT >::Doc_info
private

◆ Source_fct_pt

template<class ELEMENT >
AdvectionDiffusionEquations< 2 >::AdvectionDiffusionSourceFctPt RefineableAdvectionDiffusionProblem< ELEMENT >::Source_fct_pt
private

◆ Swim_fct_pt

template<class ELEMENT >
GeneralisedAdvectionDiffusionEquations<2>:: GeneralisedAdvectionDiffusionWindFctPt RefineableAdvectionDiffusionProblem< ELEMENT >::Swim_fct_pt
private

◆ Wind_fct_pt [1/2]

template<class ELEMENT >
AdvectionDiffusionEquations< 2 >::AdvectionDiffusionWindFctPt RefineableAdvectionDiffusionProblem< ELEMENT >::Wind_fct_pt
private

◆ Wind_fct_pt [2/2]

template<class ELEMENT >
GeneralisedAdvectionDiffusionEquations<2>:: GeneralisedAdvectionDiffusionWindFctPt RefineableAdvectionDiffusionProblem< ELEMENT >::Wind_fct_pt
private

Pointer to wind function.


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