#include <ode_problem.h>

Inheritance diagram for oomph::ODEProblem:

Public Member Functions
	ODEProblem ()
	constructor More...

virtual	~ODEProblem ()

virtual void	build (Vector< Mesh * > &bulk_mesh_pt)
	Perform set up of problem. More...

void	my_set_initial_condition (const SolutionFunctorBase &ic)
	Assign initial conditions from function pointer. More...

virtual void	write_additional_trace_headers (std::ofstream &trace_file) const

virtual void	write_additional_trace_data (const unsigned &t_hist, std::ofstream &trace_file) const

virtual double	get_error_norm (const unsigned &t_hist=0) const
	Error norm calculator. More...

Vector< double >	exact_solution (const double &time) const

double	global_temporal_error_norm ()
	Error norm: use abs(error in data). More...

Vector< double >	trace_values (const unsigned &t_hist=0) const

ODEElement *	element_pt ()

const ODEElement *	element_pt () const

TimeStepper *	ts_pt () const

unsigned	nvalue () const

void	output_solution (const unsigned &t, std::ostream &outstream, const unsigned &npoints=2) const

Vector< double >	solution (const unsigned &timestep=0) const

Public Member Functions inherited from oomph::MyProblem
	MyProblem ()
	Default constructor. More...

virtual	~MyProblem ()

double	smart_time_step (double dt, const double &tol)

virtual bool	finished () const

void	get_solver_parameters (SolverParameters &sp)

void	set_solver_parameters (SolverParameters &sp)

bool	explicit_flag ()

bool	is_steady ()

virtual void	actions_before_newton_step ()

unsigned	nnewton_step_this_solve () const

virtual void	actions_before_explicit_stage ()

virtual void	actions_after_explicit_stage ()

virtual void	actions_before_time_integration ()

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_after_implicit_timestep ()

virtual void	actions_before_implicit_timestep ()

virtual void	actions_after_newton_step ()

virtual void	actions_before_newton_solve ()

void	segregated_pin_indices (const Vector< unsigned > &indices)

void	undo_segregated_pinning ()
	Remove pinning set up by segregated_pin_indices. More...

void	check_not_segregated (const char *function) const
	Check that nothing is currently pinned for a segregated solve. More...

void	check_norm_limits ()

double	min_element_size ()
	??ds More...

void	write_trace (const unsigned &t_hist=0)

virtual void	output_solution (std::ofstream &soln_file) const
	Overload to write any problem specific data. More...

virtual void	final_doc_additional () const

virtual void	initial_doc_additional () const

void	initial_doc ()

void	final_doc ()

void	doc_solution (const unsigned &t_hist=0, const std::string &prefix="")

virtual void	doc_boundaries (const std::string &boundary_file_basename) const
	Output nodes with boundary number to csv file. More...

void	output_solution (std::ostream &outstream, const unsigned &npoints=2) const

virtual void	output_exact_solution (const unsigned &t_hist, std::ostream &outstream, const unsigned &npoints=2) const

virtual double	get_solution_norm (const unsigned &t_hist=0) const
	Dummy solution norm calculator (overload in derived classes). More...

virtual bool	should_doc_this_step (const double &dt, const double &time) const

void	set_doc_times (Vector< double > &doc_times)
	Assign a vector of times to output the full solution at. More...

double	lte_norm ()

bool	doc_exact () const

void	dump_current_mm_or_jacobian_residuals (const std::string &label)

IterativeLinearSolver *	iterative_linear_solver_pt () const

const unsigned	dim () const
	Get problem dimension (nodal dimension). More...

virtual std::string	problem_name () const

virtual void	set_up_impulsive_initial_condition ()
	Set all history values/dts to be the same as the present values/dt. More...

virtual void	actions_after_set_initial_condition ()

virtual double	integrate_over_problem (const ElementalFunction func_pt, const Integral quadrature_pt=0) const

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

virtual void	read (std::ifstream &restart_file)

void	output_ltes (const unsigned &t_hist, std::ostream &output) const

Vector< double >	exact_solution (const double &t, const Vector< double > &x) const
	Get exact solution. More...

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

void	set_analytic_dparameter (double *const &parameter_pt)

void	unset_analytic_dparameter (double *const &parameter_pt)

bool	is_dparameter_calculated_analytically (double *const &parameter_pt)

void	set_analytic_hessian_products ()

void	unset_analytic_hessian_products ()

bool	are_hessian_products_calculated_analytically ()

void	set_pinned_values_to_zero ()

bool	distributed () const

virtual void	actions_before_adapt ()

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

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

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

	Problem ()

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

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

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

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

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

Mesh *&	mesh_pt (const unsigned &imesh)

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

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

unsigned	add_sub_mesh (Mesh *const &mesh_pt)

void	flush_sub_meshes ()

void	build_global_mesh ()

void	rebuild_global_mesh ()

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

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

LinearSolver *&	mass_matrix_solver_for_explicit_timestepper_pt ()

LinearSolver *	mass_matrix_solver_for_explicit_timestepper_pt () const

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

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

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

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

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

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

TimeStepper *&	time_stepper_pt ()

const TimeStepper *	time_stepper_pt () const

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

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

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

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

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

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

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

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

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

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

double &	max_residuals ()

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

double &	newton_solver_tolerance ()

void	add_time_stepper_pt (TimeStepper *const &time_stepper_pt)

void	set_explicit_time_stepper_pt (ExplicitTimeStepper *const &explicit_time_stepper_pt)

void	initialise_dt (const double &dt)

void	initialise_dt (const Vector< double > &dt)

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

void	add_global_data (Data *const &global_data_pt)

void	flush_global_data ()

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

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

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

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

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

void	enable_store_local_dof_pt_in_elements ()

void	disable_store_local_dof_pt_in_elements ()

unsigned long	assign_eqn_numbers (const bool &assign_local_eqn_numbers=true)

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

void	enable_discontinuous_formulation ()

void	disable_discontinuous_formulation ()

void	get_dofs (DoubleVector &dofs) const

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

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

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

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

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

double *	global_dof_pt (const unsigned &i)

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

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

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

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

virtual void	get_inverse_mass_matrix_times_residuals (DoubleVector &Mres)

virtual void	get_dvaluesdt (DoubleVector &f)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

void	enable_jacobian_reuse ()

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

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

bool &	use_predictor_values_as_initial_guess ()

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

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

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

void	newton_solve (unsigned const &max_adapt)

void	steady_newton_solve (unsigned const &max_adapt=0)

void	copy (Problem *orig_problem_pt)

virtual Problem *	make_copy ()

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

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...

Public Attributes
bool	Use_fd_jacobian

Public Attributes inherited from oomph::MyProblem
MyDocInfo	Doc_info

unsigned	Output_precision

unsigned	N_steps_taken

double	Total_step_time

std::string	Trace_filename

std::string	Info_filename

double	Error_norm_limit

double	Solution_norm_limit

bool	Disable_mass_matrix_solver_optimisations

bool	Always_write_trace
	Should we output to trace file every step? More...

bool	Want_doc_exact
	Should we try to output exact solution? More...

bool	Should_doc_boundaries
	Should we output the locations of the boundary nodes? More...

bool	Dump
	Should we dump ready for a restart? More...

bool	Output_ltes
	Should we output the local truncation error at each node as well? More...

bool	Output_predictor_values
	Should we output the predicted values too? More...

bool	Output_initial_condition
	Should we write output for initial conditions as though they are time steps as well? More...

SolutionFunctorBase *	Exact_solution_pt
	Function pointer for exact solution. More...

Public Attributes inherited from oomph::Problem
bool	Shut_up_in_newton_solve

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...

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

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

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

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

virtual void	actions_after_newton_solve ()

virtual void	actions_before_newton_convergence_check ()

virtual void	actions_after_implicit_timestep_and_error_estimation ()

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 ()

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::MyProblem
const std::string	Trace_seperator

double	Dummy_doc_data

unsigned	Dim

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...

Constructor & Destructor Documentation

◆ ODEProblem()

oomph::ODEProblem::ODEProblem ( )

inline

constructor

   {
    // Don't output to trace file every step, often too many steps
    Always_write_trace = false;
  
    Use_fd_jacobian = false;
   }

References oomph::MyProblem::Always_write_trace, and Use_fd_jacobian.

◆ ~ODEProblem()

virtual oomph::ODEProblem::~ODEProblem ( )

inlinevirtual

69 {}

Member Function Documentation

◆ build()

virtual void oomph::ODEProblem::build ( Vector< Mesh * > & bulk_mesh_pt )

inlinevirtual

Perform set up of problem.

Reimplemented from oomph::MyProblem.

   {
    // Call the underlying build
    MyProblem::build(bulk_mesh_pt);
  
    // Set up the global mesh
    build_global_mesh();
  
    element_pt()->Use_fd_jacobian = Use_fd_jacobian;
  
    // assign equation numbers
    this->assign_eqn_numbers();
    oomph_info << "Number of equations: " << ndof() << std::endl;
   }

References oomph::Problem::assign_eqn_numbers(), oomph::MyProblem::build(), oomph::Problem::build_global_mesh(), element_pt(), oomph::Problem::ndof(), oomph::oomph_info, Use_fd_jacobian, and oomph::ODEElement::Use_fd_jacobian.

◆ element_pt() [1/2]

ODEElement* oomph::ODEProblem::element_pt ( )

inline

170 {return checked_dynamic_cast<ODEElement*>(mesh_pt()->element_pt(0));}

oomph::Problem::mesh_pt

Mesh *& mesh_pt()

Return a pointer to the global mesh.

Definition: problem.h:1280

References oomph::Problem::mesh_pt().

Referenced by build(), element_pt(), exact_solution(), nvalue(), and ts_pt().

◆ element_pt() [2/2]

const ODEElement* oomph::ODEProblem::element_pt ( ) const

inline

173 {return checked_dynamic_cast<ODEElement*>(mesh_pt()->element_pt(0));}

References element_pt(), and oomph::Problem::mesh_pt().

◆ exact_solution()

Vector<double> oomph::ODEProblem::exact_solution ( const double & time ) const

inline

   {
    ODEElement* el_pt = checked_dynamic_cast<ODEElement*>
     (mesh_pt()->element_pt(0));
    return el_pt->exact_solution(time);
   }

References element_pt(), oomph::ODEElement::exact_solution(), oomph::Problem::mesh_pt(), and oomph::Problem::time().

Referenced by get_error_norm(), and write_additional_trace_data().

◆ get_error_norm()

virtual double oomph::ODEProblem::get_error_norm ( const unsigned & t_hist = 0 ) const

inlinevirtual

Error norm calculator.

Reimplemented from oomph::MyProblem.

   {
    Vector<double> val = trace_values(t_hist);
    Vector<double> exact = exact_solution(time_pt()->time(t_hist));
  
    return VectorHelpers::two_norm(VectorHelpers::vector_diff(val, exact));
   }

References exact_solution(), oomph::Problem::time(), oomph::Problem::time_pt(), trace_values(), oomph::VectorHelpers::two_norm(), calibrate::val, and oomph::VectorHelpers::vector_diff().

◆ global_temporal_error_norm()

double oomph::ODEProblem::global_temporal_error_norm ( )

inlinevirtual

Error norm: use abs(error in data).

Reimplemented from oomph::Problem.

   {
    Data* dat_pt=mesh_pt()->element_pt(0)->internal_data_pt(0);
  
    return std::abs(ts_pt()->temporal_error_in_value(dat_pt, 0));
   }

References abs(), oomph::Mesh::element_pt(), oomph::GeneralisedElement::internal_data_pt(), oomph::Problem::mesh_pt(), and ts_pt().

◆ my_set_initial_condition()

void oomph::ODEProblem::my_set_initial_condition ( const SolutionFunctorBase & ic )

inlinevirtual

Assign initial conditions from function pointer.

Reimplemented from oomph::MyProblem.

   {
    // Loop over current & previous timesteps
    const unsigned nprev_values = time_stepper_pt()->nprev_values();
    for(unsigned t=0; t<nprev_values+1; t++)
    {
     double time = time_pt()->time(t);
  
     std::cout << "setting IC at time =" << time << std::endl;
  
     // Get + set the (only) value
     Vector<double> dummy(nvalue(), 1.0);
     Vector<double> values = ic(time, dummy);
  
     for(unsigned j=0, nj=nvalue(); j<nj; j++)
     {
      mesh_pt()->element_pt(0)->internal_data_pt(0)
       ->set_value(t, j, values[j]);
     }
    }
  
    actions_after_set_initial_condition();
   }

References oomph::MyProblem::actions_after_set_initial_condition(), oomph::Mesh::element_pt(), oomph::GeneralisedElement::internal_data_pt(), j, oomph::Problem::mesh_pt(), oomph::TimeStepper::nprev_values(), nvalue(), oomph::Data::set_value(), plotPSD::t, oomph::Problem::time(), oomph::Time::time(), oomph::Problem::time_pt(), and oomph::Problem::time_stepper_pt().

◆ nvalue()

unsigned oomph::ODEProblem::nvalue ( ) const

inline

   {
    return element_pt()->nvalue();
   }

References element_pt(), and oomph::ODEElement::nvalue().

Referenced by my_set_initial_condition(), and solution().

◆ output_solution()

void oomph::ODEProblem::output_solution	(	const unsigned &	t,
		std::ostream &	outstream,
		const unsigned &	npoints = `2`
	)		const

inlinevirtual

Standard output function: loop over all elements in all meshes and output.

Reimplemented from oomph::MyProblem.

   {
    // Create a temporary vector to store the exact solution
    Vector<double> output_vector=solution(t);
  
    // Vector length
    unsigned output_vector_length=output_vector.size();
    
    // Output the vector (to the command window)
    if (output_vector_length==0)
    {
     std::cout << Trace_seperator << "[]";
    }
    else
    {
     std::cout << Trace_seperator << "[" << output_vector[0];
     if (output_vector_length>1)
     {
      for (unsigned i=1;i<output_vector_length;i++)
      {
       std::cout << ", " << output_vector[i];
      }
     }
     std::cout << "]";
    }
  
    // Output the vector (to outstream)
    if (output_vector_length==0)
    {
     outstream << Trace_seperator << "[]";
    }
    else
    {
     outstream << Trace_seperator << "[" << output_vector[0];
     if (output_vector_length>1)
     {
      for (unsigned i=1;i<output_vector_length;i++)
      {
       outstream << ", " << output_vector[i];
      }
     }
     outstream << "]";
    }
       
    // npoints is ignored
   }

References i, output_vector(), solution(), plotPSD::t, and oomph::MyProblem::Trace_seperator.

◆ solution()

Vector<double> oomph::ODEProblem::solution ( const unsigned & timestep = 0 ) const

inline

   {
    Data* dat_pt=mesh_pt()->element_pt(0)->internal_data_pt(0);
    Vector<double> solution(nvalue(), 0.0);
    dat_pt->value(timestep, solution);
    return solution;
   }

References oomph::Mesh::element_pt(), oomph::GeneralisedElement::internal_data_pt(), oomph::Problem::mesh_pt(), nvalue(), and oomph::Data::value().

Referenced by output_solution(), and trace_values().

◆ trace_values()

Vector<double> oomph::ODEProblem::trace_values ( const unsigned & t_hist = 0 ) const

inlinevirtual

Reimplemented from oomph::MyProblem.

   {
    return solution(t_hist);
   }

References solution().

Referenced by get_error_norm().

◆ ts_pt()

TimeStepper* oomph::ODEProblem::ts_pt ( ) const

inline

   {
    return element_pt()->internal_data_pt(0)->time_stepper_pt();
   }

References element_pt(), oomph::GeneralisedElement::internal_data_pt(), and oomph::Data::time_stepper_pt().

Referenced by global_temporal_error_norm().

◆ write_additional_trace_data()

virtual void oomph::ODEProblem::write_additional_trace_data	(	const unsigned &	t_hist,
		std::ofstream &	trace_file
	)		const

inlinevirtual

Overload to write problem specific data into trace file. Note: don't add any line endings, seperate data with the Trace_seperator string (BEFORE each data entry).

Reimplemented from oomph::MyProblem.

   {
    // Create a temporary vector to store the exact solution
    Vector<double> output_vector=exact_solution(time_pt()->time(t_hist));
  
    // Output the vector
    unsigned output_vector_length=output_vector.size();
    if (output_vector_length==0)
    {
     trace_file << Trace_seperator << "[]";
    }
    else
    {
     trace_file << Trace_seperator << "[" << output_vector[0];
     if (output_vector_length>1)
     {
      for (unsigned i=1;i<output_vector_length;i++)
      {
       trace_file << ", " << output_vector[i];
      }
     }
     trace_file << "]";
    }
   }

References exact_solution(), i, output_vector(), oomph::Problem::time(), oomph::Problem::time_pt(), and oomph::MyProblem::Trace_seperator.

◆ write_additional_trace_headers()

virtual void oomph::ODEProblem::write_additional_trace_headers ( std::ofstream & trace_file ) const

inlinevirtual

Overload to write problem specific headers into trace file. Note: don't add any line endings, seperate headers with the Trace_seperator string (BEFORE each data entry).

Reimplemented from oomph::MyProblem.

   {
    trace_file << Trace_seperator << "exact";
   }

References oomph::MyProblem::Trace_seperator.

Member Data Documentation

◆ Use_fd_jacobian

bool oomph::ODEProblem::Use_fd_jacobian

Referenced by build(), and ODEProblem().

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

ode_problem.h

Public Member Functions

Public Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ ODEProblem()

◆ ~ODEProblem()

Member Function Documentation

◆ build()

◆ element_pt() [1/2]

◆ element_pt() [2/2]

◆ exact_solution()

◆ get_error_norm()

◆ global_temporal_error_norm()

◆ my_set_initial_condition()

◆ nvalue()

◆ output_solution()

◆ solution()

◆ trace_values()

◆ ts_pt()

◆ write_additional_trace_data()

◆ write_additional_trace_headers()

Member Data Documentation

◆ Use_fd_jacobian