Element for integrating an initial value ODE. More...

#include <ode_elements.h>

Inheritance diagram for oomph::ODEElement:

Public Member Functions
	ODEElement ()
	Default constructor: null any pointers. More...

	ODEElement (TimeStepper time_stepper_pt, SolutionFunctorBase exact_solution_pt)

void	build (TimeStepper time_stepper_pt, SolutionFunctorBase exact_solution_pt)
	Store pointers, create internal data. More...

virtual	~ODEElement ()

unsigned	nvalue () const

virtual void	fill_in_contribution_to_residuals (Vector< double > &residuals)
	Get residuals. More...

virtual void	fill_in_contribution_to_jacobian (Vector< double > &residuals, DenseMatrix< double > &jacobian)

virtual void	fill_in_contribution_to_mass_matrix (Vector< double > &residuals, DenseMatrix< double > &mm)

Vector< double >	exact_solution (const double &t) const
	Exact solution. More...

Vector< double >	derivative_function (const double &t, const Vector< double > &u)
	Exact solution. More...

Public Member Functions inherited from oomph::GeneralisedElement
	GeneralisedElement ()
	Constructor: Initialise all pointers and all values to zero. More...

virtual	~GeneralisedElement ()
	Virtual destructor to clean up any memory allocated by the object. More...

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

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

Data *&	internal_data_pt (const unsigned &i)
	Return a pointer to i-th internal data object. More...

Data *const &	internal_data_pt (const unsigned &i) const
	Return a pointer to i-th internal data object (const version) More...

Data *&	external_data_pt (const unsigned &i)
	Return a pointer to i-th external data object. More...

Data *const &	external_data_pt (const unsigned &i) const
	Return a pointer to i-th external data object (const version) More...

unsigned long	eqn_number (const unsigned &ieqn_local) const

int	local_eqn_number (const unsigned long &ieqn_global) const

unsigned	add_external_data (Data *const &data_pt, const bool &fd=true)

bool	external_data_fd (const unsigned &i) const

void	exclude_external_data_fd (const unsigned &i)

void	include_external_data_fd (const unsigned &i)

void	flush_external_data ()
	Flush all external data. More...

void	flush_external_data (Data *const &data_pt)
	Flush the object addressed by data_pt from the external data array. More...

unsigned	ninternal_data () const
	Return the number of internal data objects. More...

unsigned	nexternal_data () const
	Return the number of external data objects. More...

unsigned	ndof () const
	Return the number of equations/dofs in the element. More...

void	dof_vector (const unsigned &t, Vector< double > &dof)
	Return the vector of dof values at time level t. More...

void	dof_pt_vector (Vector< double * > &dof_pt)
	Return the vector of pointers to dof values. More...

void	set_internal_data_time_stepper (const unsigned &i, TimeStepper *const &time_stepper_pt, const bool &preserve_existing_data)

void	assign_internal_eqn_numbers (unsigned long &global_number, Vector< double * > &Dof_pt)

void	describe_dofs (std::ostream &out, const std::string &current_string) const

virtual void	describe_local_dofs (std::ostream &out, const std::string &current_string) const

void	add_internal_value_pt_to_map (std::map< unsigned, double * > &map_of_value_pt)

virtual void	assign_local_eqn_numbers (const bool &store_local_dof_pt)

virtual void	complete_setup_of_dependencies ()

virtual void	get_residuals (Vector< double > &residuals)

virtual void	get_jacobian (Vector< double > &residuals, DenseMatrix< double > &jacobian)

virtual void	get_mass_matrix (Vector< double > &residuals, DenseMatrix< double > &mass_matrix)

virtual void	get_jacobian_and_mass_matrix (Vector< double > &residuals, DenseMatrix< double > &jacobian, DenseMatrix< double > &mass_matrix)

virtual void	get_dresiduals_dparameter (double *const &parameter_pt, Vector< double > &dres_dparam)

virtual void	get_djacobian_dparameter (double *const &parameter_pt, Vector< double > &dres_dparam, DenseMatrix< double > &djac_dparam)

virtual void	get_djacobian_and_dmass_matrix_dparameter (double *const &parameter_pt, Vector< double > &dres_dparam, DenseMatrix< double > &djac_dparam, DenseMatrix< double > &dmass_matrix_dparam)

virtual void	get_hessian_vector_products (Vector< double > const &Y, DenseMatrix< double > const &C, DenseMatrix< double > &product)

virtual void	get_inner_products (Vector< std::pair< unsigned, unsigned >> const &history_index, Vector< double > &inner_product)

virtual void	get_inner_product_vectors (Vector< unsigned > const &history_index, Vector< Vector< double >> &inner_product_vector)

virtual unsigned	self_test ()

virtual void	compute_norm (Vector< double > &norm)

virtual void	compute_norm (double &norm)

virtual unsigned	ndof_types () const

virtual void	get_dof_numbers_for_unknowns (std::list< std::pair< unsigned long, unsigned >> &dof_lookup_list) const

Public Attributes
SolutionFunctorBase *	Exact_solution_pt

bool	Use_fd_jacobian

Additional Inherited Members
Static Public Attributes inherited from oomph::GeneralisedElement
static bool	Suppress_warning_about_repeated_internal_data

static bool	Suppress_warning_about_repeated_external_data = true

static double	Default_fd_jacobian_step = 1.0e-8

Protected Member Functions inherited from oomph::GeneralisedElement
unsigned	add_internal_data (Data *const &data_pt, const bool &fd=true)

bool	internal_data_fd (const unsigned &i) const

void	exclude_internal_data_fd (const unsigned &i)

void	include_internal_data_fd (const unsigned &i)

void	clear_global_eqn_numbers ()

void	add_global_eqn_numbers (std::deque< unsigned long > const &global_eqn_numbers, std::deque< double * > const &global_dof_pt)

virtual void	assign_internal_and_external_local_eqn_numbers (const bool &store_local_dof_pt)

virtual void	assign_all_generic_local_eqn_numbers (const bool &store_local_dof_pt)

virtual void	assign_additional_local_eqn_numbers ()

int	internal_local_eqn (const unsigned &i, const unsigned &j) const

int	external_local_eqn (const unsigned &i, const unsigned &j)

void	fill_in_jacobian_from_internal_by_fd (Vector< double > &residuals, DenseMatrix< double > &jacobian, const bool &fd_all_data=false)

void	fill_in_jacobian_from_internal_by_fd (DenseMatrix< double > &jacobian, const bool &fd_all_data=false)

void	fill_in_jacobian_from_external_by_fd (Vector< double > &residuals, DenseMatrix< double > &jacobian, const bool &fd_all_data=false)

void	fill_in_jacobian_from_external_by_fd (DenseMatrix< double > &jacobian, const bool &fd_all_data=false)

virtual void	update_before_internal_fd ()

virtual void	reset_after_internal_fd ()

virtual void	update_in_internal_fd (const unsigned &i)

virtual void	reset_in_internal_fd (const unsigned &i)

virtual void	update_before_external_fd ()

virtual void	reset_after_external_fd ()

virtual void	update_in_external_fd (const unsigned &i)

virtual void	reset_in_external_fd (const unsigned &i)

virtual void	fill_in_contribution_to_jacobian_and_mass_matrix (Vector< double > &residuals, DenseMatrix< double > &jacobian, DenseMatrix< double > &mass_matrix)

virtual void	fill_in_contribution_to_dresiduals_dparameter (double *const &parameter_pt, Vector< double > &dres_dparam)

virtual void	fill_in_contribution_to_djacobian_dparameter (double *const &parameter_pt, Vector< double > &dres_dparam, DenseMatrix< double > &djac_dparam)

virtual void	fill_in_contribution_to_djacobian_and_dmass_matrix_dparameter (double *const &parameter_pt, Vector< double > &dres_dparam, DenseMatrix< double > &djac_dparam, DenseMatrix< double > &dmass_matrix_dparam)

virtual void	fill_in_contribution_to_hessian_vector_products (Vector< double > const &Y, DenseMatrix< double > const &C, DenseMatrix< double > &product)

virtual void	fill_in_contribution_to_inner_products (Vector< std::pair< unsigned, unsigned >> const &history_index, Vector< double > &inner_product)

virtual void	fill_in_contribution_to_inner_product_vectors (Vector< unsigned > const &history_index, Vector< Vector< double >> &inner_product_vector)

Static Protected Attributes inherited from oomph::GeneralisedElement
static DenseMatrix< double >	Dummy_matrix

static std::deque< double * >	Dof_pt_deque

Detailed Description

Element for integrating an initial value ODE.

Constructor & Destructor Documentation

◆ ODEElement() [1/2]

oomph::ODEElement::ODEElement ( )

inline

Default constructor: null any pointers.

     {
       Exact_solution_pt = 0;
  
       Use_fd_jacobian = false;
     }

References Exact_solution_pt, and Use_fd_jacobian.

◆ ODEElement() [2/2]

oomph::ODEElement::ODEElement	(	TimeStepper *	time_stepper_pt,
		SolutionFunctorBase *	exact_solution_pt
	)

inline

Constructor: Pass time stepper and a solution function pointer, then build the element.

     {
       build(time_stepper_pt, exact_solution_pt);
     }

References build().

◆ ~ODEElement()

virtual oomph::ODEElement::~ODEElement ( )

inlinevirtual

74 {}

Member Function Documentation

◆ build()

void oomph::ODEElement::build	(	TimeStepper *	time_stepper_pt,
		SolutionFunctorBase *	exact_solution_pt
	)

inline

Store pointers, create internal data.

     {
       Exact_solution_pt = exact_solution_pt;
  
       Vector<double> exact = this->exact_solution(0);
       unsigned nvalue = exact.size();
  
       add_internal_data(new Data(time_stepper_pt, nvalue));
  
       Use_fd_jacobian = false;
     }

References oomph::GeneralisedElement::add_internal_data(), exact_solution(), Exact_solution_pt, nvalue(), and Use_fd_jacobian.

Referenced by ODEElement().

◆ derivative_function()

Vector<double> oomph::ODEElement::derivative_function	(	const double &	t,
		const Vector< double > &	u
	)

inline

Exact solution.

     {
 #ifdef PARANOID
       if (Exact_solution_pt == 0)
       {
         throw OomphLibError("No derivative function",
                             OOMPH_EXCEPTION_LOCATION,
                             OOMPH_CURRENT_FUNCTION);
       }
 #endif
       Vector<double> dummy_x;
       return Exact_solution_pt->derivative(t, dummy_x, u);
     }

References oomph::SolutionFunctorBase::derivative(), Exact_solution_pt, OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION, and plotPSD::t.

Referenced by oomph::IMRODEElement::fill_in_contribution_to_residuals(), and fill_in_contribution_to_residuals().

◆ exact_solution()

Vector<double> oomph::ODEElement::exact_solution ( const double & t ) const

inline

Exact solution.

     {
 #ifdef PARANOID
       if (Exact_solution_pt == 0)
       {
         throw OomphLibError("No exact solution function",
                             OOMPH_EXCEPTION_LOCATION,
                             OOMPH_CURRENT_FUNCTION);
       }
 #endif
       Vector<double> dummy_x;
       return (*Exact_solution_pt)(t, dummy_x);
     }

References Exact_solution_pt, OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION, and plotPSD::t.

Referenced by build(), and oomph::ODEProblem::exact_solution().

◆ fill_in_contribution_to_jacobian()

virtual void oomph::ODEElement::fill_in_contribution_to_jacobian	(	Vector< double > &	residuals,
		DenseMatrix< double > &	jacobian
	)

inlinevirtual

Add the elemental contribution to the jacobian matrix. and the residuals vector. Note that this function will NOT initialise the residuals vector or the jacobian matrix. It must be called after the residuals vector and jacobian matrix have been initialised to zero. The default is to use finite differences to calculate the jacobian

Reimplemented from oomph::GeneralisedElement.

Reimplemented in oomph::IMRODEElement.

     {
       // Get residuals
       fill_in_contribution_to_residuals(residuals);
  
       if (Exact_solution_pt->have_jacobian() && !Use_fd_jacobian)
       {
         // get df/du jacobian
         double t = internal_data_pt(0)->time_stepper_pt()->time();
         Vector<double> dummy, u(nvalue(), 0.0);
         internal_data_pt(0)->value(u);
         Exact_solution_pt->jacobian(t, dummy, u, jacobian);
  
         // We need jacobian of residual = f - dudt so subtract diagonal
         // (dudt)/du term.
         const double a = internal_data_pt(0)->time_stepper_pt()->weight(1, 0);
         const unsigned n = nvalue();
         for (unsigned i = 0; i < n; i++)
         {
           jacobian(i, i) -= a;
         }
       }
       else
       {
         // Use FD for jacobian
         GeneralisedElement::fill_in_jacobian_from_internal_by_fd(
           residuals, jacobian, true);
       }
     }

References a, Exact_solution_pt, fill_in_contribution_to_residuals(), oomph::GeneralisedElement::fill_in_jacobian_from_internal_by_fd(), oomph::SolutionFunctorBase::have_jacobian(), i, oomph::GeneralisedElement::internal_data_pt(), oomph::SolutionFunctorBase::jacobian(), n, nvalue(), plotPSD::t, oomph::TimeStepper::time(), oomph::Data::time_stepper_pt(), Use_fd_jacobian, oomph::Data::value(), and oomph::TimeStepper::weight().

◆ fill_in_contribution_to_mass_matrix()

virtual void oomph::ODEElement::fill_in_contribution_to_mass_matrix	(	Vector< double > &	residuals,
		DenseMatrix< double > &	mass_matrix
	)

inlinevirtual

Add the elemental contribution to the mass matrix matrix. and the residuals vector. Note that this function should NOT initialise the residuals vector or the mass matrix. It must be called after the residuals vector and jacobian matrix have been initialised to zero. The default is deliberately broken

Add the elemental contribution to the mass matrix and the residuals vector. Note that this function will NOT initialise the residuals vector or the mass matrix. It must be called after the residuals vector and jacobian matrix have been initialised to zero. The default is deliberately broken.

Reimplemented from oomph::GeneralisedElement.

     {
       fill_in_contribution_to_residuals(residuals);
       for (unsigned j = 0, nj = nvalue(); j < nj; j++)
       {
         mm(j, j) = 1;
       }
     }

References fill_in_contribution_to_residuals(), j, and nvalue().

◆ fill_in_contribution_to_residuals()

virtual void oomph::ODEElement::fill_in_contribution_to_residuals ( Vector< double > & residuals )

inlinevirtual

Get residuals.

Reimplemented from oomph::GeneralisedElement.

Reimplemented in oomph::IMRODEElement.

     {
       // Get pointer to one-and-only internal data object
       Data* dat_pt = internal_data_pt(0);
  
       // Get it's values
       Vector<double> u(nvalue(), 0.0);
       dat_pt->value(u);
  
       // Get time stepper
       TimeStepper* time_stepper_pt = dat_pt->time_stepper_pt();
  
       // Get continuous time
       double t = time_stepper_pt->time();
  
       Vector<double> deriv = derivative_function(t, u);
       for (unsigned j = 0, nj = deriv.size(); j < nj; j++)
       {
         // Get dudt approximation from time stepper
         double dudt = time_stepper_pt->time_derivative(1, dat_pt, j);
  
         // Residual is difference between the exact derivative and our
         // time stepper's derivative estimate.
         residuals[j] = deriv[j] - dudt;
       }
     }

References derivative_function(), oomph::GeneralisedElement::internal_data_pt(), j, nvalue(), plotPSD::t, oomph::TimeStepper::time(), oomph::TimeStepper::time_derivative(), oomph::Data::time_stepper_pt(), and oomph::Data::value().

Referenced by fill_in_contribution_to_jacobian(), and fill_in_contribution_to_mass_matrix().

◆ nvalue()

unsigned oomph::ODEElement::nvalue ( ) const

inline

     {
       return internal_data_pt(0)->nvalue();
     }

References oomph::GeneralisedElement::internal_data_pt(), and oomph::Data::nvalue().

Referenced by build(), oomph::IMRODEElement::fill_in_contribution_to_jacobian(), fill_in_contribution_to_jacobian(), fill_in_contribution_to_mass_matrix(), fill_in_contribution_to_residuals(), oomph::ODEProblem::nvalue(), and oomph::IMRODEElement::time_interpolate_u().

Member Data Documentation

◆ Exact_solution_pt

SolutionFunctorBase* oomph::ODEElement::Exact_solution_pt

Referenced by build(), derivative_function(), exact_solution(), oomph::IMRODEElement::fill_in_contribution_to_jacobian(), fill_in_contribution_to_jacobian(), and ODEElement().

◆ Use_fd_jacobian

bool oomph::ODEElement::Use_fd_jacobian

Referenced by build(), oomph::ODEProblem::build(), oomph::IMRODEElement::fill_in_contribution_to_jacobian(), fill_in_contribution_to_jacobian(), and ODEElement().

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

ode_elements.h

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ODEElement() [1/2]

◆ ODEElement() [2/2]

◆ ~ODEElement()

Member Function Documentation

◆ build()

◆ derivative_function()

◆ exact_solution()

◆ fill_in_contribution_to_jacobian()

◆ fill_in_contribution_to_mass_matrix()

◆ fill_in_contribution_to_residuals()

◆ nvalue()

Member Data Documentation

◆ Exact_solution_pt

◆ Use_fd_jacobian