Inheritance diagram for PredatorPreyElement:

Public Member Functions
	PredatorPreyElement ()

const double &	lambda () const

const double &	mu () const

double *&	lambda_pt ()

double *&	mu_pt ()

void	fill_in_contribution_to_residuals (Vector< double > &residuals)
	Add the element's contribution to its residual vector (wrapper) More...

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

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

void	fill_in_generic_residual_contribution (Vector< double > &residuals, DenseMatrix< double > &jacobian, DenseMatrix< double > &mass_matrix, unsigned flag)

void	output (ostream &output)

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

Private Attributes
double *	Lambda_pt

double *	Mu_pt

unsigned	Internal_index

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_mass_matrix (Vector< double > &residuals, 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

Constructor & Destructor Documentation

◆ PredatorPreyElement()

PredatorPreyElement::PredatorPreyElement ( )

inline

   {
    Internal_index = this->add_internal_data(new Data(3));
   }

Member Function Documentation

◆ fill_in_contribution_to_jacobian()

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

inlinevirtual

Add the element's contribution to its residual vector and element Jacobian matrix (wrapper)

Reimplemented from oomph::GeneralisedElement.

   {
    //Call the generic routine with the flag set to 1
    fill_in_generic_residual_contribution(residuals,
                                          jacobian,
                                          GeneralisedElement::Dummy_matrix,1);
   }

◆ fill_in_contribution_to_jacobian_and_mass_matrix()

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

inlinevirtual

Add the element's contribution to its residuals vector, jacobian matrix and mass matrix

Reimplemented from oomph::GeneralisedElement.

   {
    //Call the generic routine with the flag set to 2
    fill_in_generic_residual_contribution(residuals,jacobian,mass_matrix,2);
   }

◆ fill_in_contribution_to_residuals()

void PredatorPreyElement::fill_in_contribution_to_residuals ( Vector< double > & residuals )

inlinevirtual

Add the element's contribution to its residual vector (wrapper)

Reimplemented from oomph::GeneralisedElement.

   {
    //Call the generic residuals function with flag set to 0
    //using a dummy matrix arguments
    fill_in_generic_residual_contribution(
     residuals,GeneralisedElement::Dummy_matrix,
     GeneralisedElement::Dummy_matrix,0);
   }

◆ fill_in_generic_residual_contribution()

void PredatorPreyElement::fill_in_generic_residual_contribution	(	Vector< double > &	residuals,
		DenseMatrix< double > &	jacobian,
		DenseMatrix< double > &	mass_matrix,
		unsigned	flag
	)

inline

Calculate the elemental contributions to the global residual vector for the weak form of the Poisson equation

   {
    //Set the mass matrix
    if(flag==2)
     {
      for(unsigned i=0;i<3;i++) {mass_matrix(i,i) = 1.0;}
     }
  
     //Get the value of the parameter
     double lam = lambda();
     double m = mu();
  
     //Get the values of the unknowns
     double u[3];
     for(unsigned i=0;i<3;i++) 
      {u[i] = internal_data_pt(Internal_index)->value(i);}
  
     unsigned local_eqn = internal_local_eqn(Internal_index,0);
     residuals[local_eqn] = u[0]*(1.0-u[0]) - m*u[0]*u[1];
     
     if(flag)
      {
       unsigned local_unknown = internal_local_eqn(Internal_index,0);
       jacobian(local_eqn,local_unknown) = 1.0 - 2.0*u[0] - m*u[1];
       
       local_unknown = internal_local_eqn(Internal_index,1);
       jacobian(local_eqn,local_unknown) = -m*u[0];
      }
  
  
     local_eqn = internal_local_eqn(Internal_index,1);
     residuals[local_eqn] = 
      -0.25*u[1] + m*u[0]*u[1] - 3.0*u[1]*u[2] - lam*(1.0 - exp(-5.0*u[1]));
  
     if(flag)
      {
       unsigned local_unknown = internal_local_eqn(Internal_index,0);
       jacobian(local_eqn,local_unknown) =
        m*u[1];
  
       local_unknown = internal_local_eqn(Internal_index,1);
       jacobian(local_eqn,local_unknown) =
        -0.25 + m*u[0] - 3.0*u[2] - lam*5.0*exp(-5.0*u[1]);
  
       local_unknown = internal_local_eqn(Internal_index,2);
       jacobian(local_eqn,local_unknown) = -3.0*u[1];
      }
  
     local_eqn = internal_local_eqn(Internal_index,2);
     residuals[local_eqn]  =
      -0.5*u[2] + 3.0*u[1]*u[2];
  
     if(flag)
      {
       unsigned local_unknown = internal_local_eqn(Internal_index,1);
       jacobian(local_eqn,local_unknown) = 3.0*u[2];
  
       local_unknown = internal_local_eqn(Internal_index,2);
       jacobian(local_eqn,local_unknown) = -0.5 + 3.0*u[1];
      }
  
    } //End of function

References Eigen::bfloat16_impl::exp(), i, lambda, m, and Global_Parameters::mu.

◆ lambda()

const double& PredatorPreyElement::lambda ( ) const

inline

70 {return *Lambda_pt;}

PredatorPreyElement::Lambda_pt

double * Lambda_pt

Definition: hopf.cc:56

References Global_Physical_Variables::Lambda_pt.

◆ lambda_pt()

double* & PredatorPreyElement::lambda_pt ( )

inline

75 {return Lambda_pt;}

References Global_Physical_Variables::Lambda_pt.

◆ mu()

const double& PredatorPreyElement::mu ( ) const

inline

72 {return *Mu_pt;}

PredatorPreyElement::Mu_pt

double * Mu_pt

Definition: hopf.cc:58

References Global_Physical_Variables::Mu_pt.

◆ mu_pt()

double* & PredatorPreyElement::mu_pt ( )

inline

77 {return Mu_pt;}

References Global_Physical_Variables::Mu_pt.

◆ output()

void PredatorPreyElement::output ( ostream & output )

inline

    {
     for(unsigned n=0;n<3;n++)
      {
       output << this->internal_data_pt(Internal_index)->value(n) << " ";
      }
     output << std::endl;
    } //End of function

References n, and output().

Member Data Documentation

◆ Internal_index

unsigned PredatorPreyElement::Internal_index

private

◆ Lambda_pt

double* PredatorPreyElement::Lambda_pt

private

◆ Mu_pt

double* PredatorPreyElement::Mu_pt

private

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

hopf.cc

Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ PredatorPreyElement()

Member Function Documentation

◆ fill_in_contribution_to_jacobian()

◆ fill_in_contribution_to_jacobian_and_mass_matrix()

◆ fill_in_contribution_to_residuals()

◆ fill_in_generic_residual_contribution()

◆ lambda()

◆ lambda_pt()

◆ mu()

◆ mu_pt()

◆ output()

Member Data Documentation

◆ Internal_index

◆ Lambda_pt

◆ Mu_pt