#include <assembly_handler.h>

Inheritance diagram for oomph::AssemblyHandler:

Public Member Functions
	AssemblyHandler ()
	Empty constructor. More...

virtual unsigned	ndof (GeneralisedElement *const &elem_pt)
	Return the number of degrees of freedom in the element elem_pt. More...

virtual void	dof_vector (GeneralisedElement *const &elem_pt, const unsigned &t, Vector< double > &dof)
	Return vector of dofs at time level t in the element elem_pt. More...

virtual void	dof_pt_vector (GeneralisedElement const &elem_pt, Vector< double > &dof_pt)
	Return vector of pointers to dofs in the element elem_pt. More...

virtual double &	local_problem_dof (Problem *const &problem_pt, const unsigned &t, const unsigned &i)

virtual unsigned long	eqn_number (GeneralisedElement *const &elem_pt, const unsigned &ieqn_local)

virtual void	get_residuals (GeneralisedElement *const &elem_pt, Vector< double > &residuals)
	Return the contribution to the residuals of the element elem_pt. More...

virtual void	get_jacobian (GeneralisedElement *const &elem_pt, Vector< double > &residuals, DenseMatrix< double > &jacobian)

virtual void	get_all_vectors_and_matrices (GeneralisedElement *const &elem_pt, Vector< Vector< double >> &vec, Vector< DenseMatrix< double >> &matrix)

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

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

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

virtual int	bifurcation_type () const

virtual double *	bifurcation_parameter_pt () const

virtual void	get_eigenfunction (Vector< DoubleVector > &eigenfunction)

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

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

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

Detailed Description

A class that is used to define the functions used to assemble the elemental contributions to the residuals vector and Jacobian matrix that define the problem being solved. The main use of this class is to assemble and solve the augmented systems used in bifurcation detection and tracking. The default implementation merely calls the underlying elemental functions with no augmentation.

Constructor & Destructor Documentation

◆ AssemblyHandler()

oomph::AssemblyHandler::AssemblyHandler ( )

inline

Empty constructor.

66 {}

◆ ~AssemblyHandler()

virtual oomph::AssemblyHandler::~AssemblyHandler ( )

inlinevirtual

Empty virtual destructor.

169 {}

Member Function Documentation

◆ bifurcation_parameter_pt()

double * oomph::AssemblyHandler::bifurcation_parameter_pt ( ) const

virtual

Return a pointer to the bifurcation parameter in bifurcation tracking problems

Return the eigenfunction(s) associated with the bifurcation that has been detected in bifurcation tracking problems. Default Broken implementation

Reimplemented in oomph::HopfHandler, oomph::PitchForkHandler, and oomph::FoldHandler.

   {
     std::ostringstream error_stream;
     error_stream << "There is no bifurcation parameter associated with the "
                     "current assembly handler.\n"
                  << "Eigenfunction are only calculated by the Fold, PitchFork "
                     "and Hopf Handlers"
                  << "\n";
  
     throw OomphLibError(
       error_stream.str(), OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION);
     return 0;
   }

References OOMPH_CURRENT_FUNCTION, and OOMPH_EXCEPTION_LOCATION.

Referenced by oomph::Problem::bifurcation_parameter_pt().

◆ bifurcation_type()

virtual int oomph::AssemblyHandler::bifurcation_type ( ) const

inlinevirtual

Return an unsigned integer to indicate whether the handler is a bifurcation tracking handler. The default is zero (not)

Reimplemented in oomph::HopfHandler, oomph::PitchForkHandler, and oomph::FoldHandler.

     {
       return 0;
     }

Referenced by oomph::Problem::adapt(), oomph::Problem::doc_errors(), and oomph::Problem::p_adapt().

◆ dof_pt_vector()

void oomph::AssemblyHandler::dof_pt_vector	(	GeneralisedElement *const &	elem_pt,
		Vector< double * > &	dof_pt
	)

virtual

Return vector of pointers to dofs in the element elem_pt.

Get the vector of pointers to dofs in the element elem_pt Direct call to the function in the element.

   {
     return elem_pt->dof_pt_vector(dof_pt);
   }

References oomph::GeneralisedElement::dof_pt_vector().

◆ dof_vector()

void oomph::AssemblyHandler::dof_vector	(	GeneralisedElement *const &	elem_pt,
		const unsigned &	t,
		Vector< double > &	dof
	)

virtual

Return vector of dofs at time level t in the element elem_pt.

Get the vector of dofs in the element elem_pt at time level t Direct call to the function in the element.

   {
     return elem_pt->dof_vector(t, dof);
   }

References oomph::GeneralisedElement::dof_vector(), and plotPSD::t.

◆ eqn_number()

unsigned long oomph::AssemblyHandler::eqn_number	(	GeneralisedElement *const &	elem_pt,
		const unsigned &	ieqn_local
	)

virtual

Return the global equation number of the local unknown ieqn_local in elem_pt.

Get the global equation number of the local unknown. Direct call to the function in the element.

Reimplemented in oomph::PeriodicOrbitAssemblyHandler< NNODE_1D >, oomph::HopfHandler, oomph::PitchForkHandler, oomph::FoldHandler, oomph::ParameterDerivativeHandler, oomph::ParallelResidualsHandler, oomph::EigenProblemHandler, and oomph::ExplicitTimeStepHandler.

   {
     return elem_pt->eqn_number(ieqn_local);
   }

References oomph::GeneralisedElement::eqn_number().

◆ get_all_vectors_and_matrices()

void oomph::AssemblyHandler::get_all_vectors_and_matrices	(	GeneralisedElement *const &	elem_pt,
		Vector< Vector< double >> &	vec,
		Vector< DenseMatrix< double >> &	matrix
	)

virtual

Calculate all desired vectors and matrices provided by the element elem_pt.

Calculate all desired vectors and matrices that are required by the element by calling the get_jacobian function

Reimplemented in oomph::ParallelResidualsHandler, oomph::EigenProblemHandler, and oomph::ExplicitTimeStepHandler.

   {
     get_jacobian(elem_pt, vec[0], matrix[0]);
   }

References get_jacobian(), and matrix().

Referenced by oomph::Problem::sparse_assemble_row_or_column_compressed_with_lists(), oomph::Problem::sparse_assemble_row_or_column_compressed_with_maps(), oomph::Problem::sparse_assemble_row_or_column_compressed_with_two_arrays(), oomph::Problem::sparse_assemble_row_or_column_compressed_with_two_vectors(), and oomph::Problem::sparse_assemble_row_or_column_compressed_with_vectors_of_pairs().

◆ get_djacobian_dparameter()

void oomph::AssemblyHandler::get_djacobian_dparameter	(	GeneralisedElement *const &	elem_pt,
		double *const &	parameter_pt,
		Vector< double > &	dres_dparam,
		DenseMatrix< double > &	djac_dparam
	)

virtual

Calculate the derivative of the residuals and jacobian with respect to a parameter

Calculate the derivative of the residuals and jacobian with respect to a parameter by calling the elemental function

Reimplemented in oomph::HopfHandler, oomph::PitchForkHandler, and oomph::FoldHandler.

   {
     elem_pt->get_djacobian_dparameter(parameter_pt, dres_dparam, djac_dparam);
   }

References oomph::GeneralisedElement::get_djacobian_dparameter().

Referenced by oomph::ParameterDerivativeHandler::get_jacobian().

◆ get_dresiduals_dparameter()

void oomph::AssemblyHandler::get_dresiduals_dparameter	(	GeneralisedElement *const &	elem_pt,
		double *const &	parameter_pt,
		Vector< double > &	dres_dparam
	)

virtual

Calculate the derivative of the residuals with respect to a parameter

Calculate the derivative of the residuals with respect to a parameter, by calling the elemental function

Reimplemented in oomph::HopfHandler, oomph::PitchForkHandler, and oomph::FoldHandler.

   {
     elem_pt->get_dresiduals_dparameter(parameter_pt, dres_dparam);
   }

References oomph::GeneralisedElement::get_dresiduals_dparameter().

Referenced by oomph::ParameterDerivativeHandler::get_residuals().

◆ get_eigenfunction()

void oomph::AssemblyHandler::get_eigenfunction ( Vector< DoubleVector > & eigenfunction )

virtual

Return the eigenfunction(s) associated with the bifurcation that has been detected in bifurcation tracking problems

Return the eigenfunction(s) associated with the bifurcation that has been detected in bifurcation tracking problems. Default Broken implementation

Reimplemented in oomph::HopfHandler, oomph::PitchForkHandler, and oomph::FoldHandler.

   {
     std::ostringstream error_stream;
     error_stream << "There is no eigenfunction associated with the current "
                     "assembly handler.\n"
                  << "Eigenfunction are only calculated by the Fold, PitchFork "
                     "and Hopf Handlers"
                  << "\n";
  
     throw OomphLibError(
       error_stream.str(), OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION);
   }

References OOMPH_CURRENT_FUNCTION, and OOMPH_EXCEPTION_LOCATION.

Referenced by oomph::Problem::get_bifurcation_eigenfunction().

◆ get_hessian_vector_products()

void oomph::AssemblyHandler::get_hessian_vector_products	(	GeneralisedElement *const &	elem_pt,
		Vector< double > const &	Y,
		DenseMatrix< double > const &	C,
		DenseMatrix< double > &	product
	)

virtual

Calculate the product of the Hessian (derivative of Jacobian with respect to all variables) an eigenvector, Y, and other specified vectors, C (d(J_{ij})/d u_{k}) Y_{j} C_{k}

Calculate the product of the Hessian (derivative of Jacobian with respect to all variables) an eigenvector, Y, and other specified vectors, C (d(J_{ij})/d u_{k}) Y_{j} C_{k} At the moment the dof pointer is passed in to enable easy calculation of finite difference default

Reimplemented in oomph::HopfHandler, oomph::PitchForkHandler, and oomph::FoldHandler.

   {
     elem_pt->get_hessian_vector_products(Y, C, product);
   }

References oomph::GeneralisedElement::get_hessian_vector_products(), product(), and Y.

Referenced by oomph::Problem::get_hessian_vector_products().

◆ get_inner_product_vectors()

void oomph::AssemblyHandler::get_inner_product_vectors	(	GeneralisedElement *const &	elem_pt,
		Vector< unsigned > const &	history_index,
		Vector< Vector< double >> &	inner_product_vector
	)

virtual

Compute the vectors that when taken as a dot product with other history values give the inner product over the element

Compute the vectors that when taken as a dot product with other history values give the inner product over the element. In other words if we call get_inner_product_vectors({0,1},output) output[0] will be a vector such that dofs.output[0] gives the inner product of current dofs with themselves.

   {
     elem_pt->get_inner_product_vectors(history_index, inner_product_vector);
   }

References oomph::GeneralisedElement::get_inner_product_vectors().

◆ get_inner_products()

void oomph::AssemblyHandler::get_inner_products	(	GeneralisedElement *const &	elem_pt,
		Vector< std::pair< unsigned, unsigned >> const &	history_index,
		Vector< double > &	inner_product
	)

virtual

Compute the inner products of the given vector of pairs of history values over the element.

========================================================================== Compute the inner products of the given vector of pairs of history values over the element. The values of the index in the pair may be the same.

   {
     elem_pt->get_inner_products(history_index, inner_product);
   }

References oomph::GeneralisedElement::get_inner_products().

◆ get_jacobian()

void oomph::AssemblyHandler::get_jacobian	(	GeneralisedElement *const &	elem_pt,
		Vector< double > &	residuals,
		DenseMatrix< double > &	jacobian
	)

virtual

Calculate the elemental Jacobian matrix "d equation / d variable" for elem_pt.

Calculate the elemental Jacobian matrix "d equation / d variable" by calling the element's get_jacobian function.

Reimplemented in oomph::FpPreconditionerAssemblyHandler, oomph::PeriodicOrbitAssemblyHandler< NNODE_1D >, oomph::HopfHandler, oomph::PitchForkHandler, oomph::FoldHandler, oomph::ParameterDerivativeHandler, oomph::ParallelResidualsHandler, oomph::EigenProblemHandler, and oomph::ExplicitTimeStepHandler.

   {
     elem_pt->get_jacobian(residuals, jacobian);
   }

References oomph::GeneralisedElement::get_jacobian().

Referenced by get_all_vectors_and_matrices(), oomph::Problem::get_hessian_vector_products(), oomph::Problem::get_jacobian(), oomph::ParallelResidualsHandler::get_jacobian(), print_elemental_jacobian(), oomph::HSL_MA42::solve(), and oomph::HSL_MA42::solve_for_one_dof().

◆ get_residuals()

void oomph::AssemblyHandler::get_residuals	(	GeneralisedElement *const &	elem_pt,
		Vector< double > &	residuals
	)

virtual

Return the contribution to the residuals of the element elem_pt.

Get the residuals by calling the underlying element's residuals directly.

Reimplemented in oomph::FpPreconditionerAssemblyHandler, oomph::PeriodicOrbitAssemblyHandler< NNODE_1D >, oomph::HopfHandler, oomph::PitchForkHandler, oomph::FoldHandler, oomph::ParameterDerivativeHandler, oomph::ParallelResidualsHandler, oomph::EigenProblemHandler, and oomph::ExplicitTimeStepHandler.

   {
     elem_pt->get_residuals(residuals);
   }

References oomph::GeneralisedElement::get_residuals().

Referenced by oomph::ParallelResidualsHandler::get_all_vectors_and_matrices(), oomph::Problem::get_residuals(), and oomph::ParallelResidualsHandler::get_residuals().

◆ local_problem_dof()

double & oomph::AssemblyHandler::local_problem_dof	(	Problem *const &	problem_pt,
		const unsigned &	t,
		const unsigned &	i
	)

virtual

Return the t-th level of storage associated with the i-th (local) dof stored in the problem

   {
     return *(problem_pt->dof_pt(i) + t);
   }

References oomph::Problem::dof_pt(), i, and plotPSD::t.

◆ ndof()

unsigned oomph::AssemblyHandler::ndof ( GeneralisedElement *const & elem_pt )

virtual

Return the number of degrees of freedom in the element elem_pt.

Get the number of elemental degrees of freedom. Direct call to the function in the element.

Reimplemented in oomph::PeriodicOrbitAssemblyHandler< NNODE_1D >, oomph::HopfHandler, oomph::PitchForkHandler, oomph::FoldHandler, oomph::ParameterDerivativeHandler, oomph::ParallelResidualsHandler, oomph::EigenProblemHandler, and oomph::ExplicitTimeStepHandler.

   {
     return elem_pt->ndof();
   }

References oomph::GeneralisedElement::ndof().

Referenced by oomph::Problem::get_hessian_vector_products(), oomph::Problem::get_jacobian(), oomph::Problem::get_residuals(), oomph::ParallelResidualsHandler::ndof(), oomph::ParameterDerivativeHandler::ndof(), oomph::PitchForkHandler::PitchForkHandler(), print_elemental_jacobian(), oomph::HSL_MA42::reorder_elements(), oomph::Problem::setup_element_count_per_dof(), oomph::HSL_MA42::solve(), oomph::HSL_MA42::solve_for_one_dof(), oomph::Problem::sparse_assemble_row_or_column_compressed_with_lists(), oomph::Problem::sparse_assemble_row_or_column_compressed_with_maps(), oomph::Problem::sparse_assemble_row_or_column_compressed_with_two_arrays(), oomph::Problem::sparse_assemble_row_or_column_compressed_with_two_vectors(), and oomph::Problem::sparse_assemble_row_or_column_compressed_with_vectors_of_pairs().

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

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ AssemblyHandler()

◆ ~AssemblyHandler()

Member Function Documentation

◆ bifurcation_parameter_pt()

◆ bifurcation_type()

◆ dof_pt_vector()

◆ dof_vector()

◆ eqn_number()

◆ get_all_vectors_and_matrices()

◆ get_djacobian_dparameter()

◆ get_dresiduals_dparameter()

◆ get_eigenfunction()

◆ get_hessian_vector_products()

◆ get_inner_product_vectors()

◆ get_inner_products()

◆ get_jacobian()

◆ get_residuals()

◆ local_problem_dof()

◆ ndof()