#include <perturbed_spines.h>

Inheritance diagram for oomph::PerturbedSpineElement< ELEMENT >:

Public Member Functions
	PerturbedSpineElement ()
	Constructor, call the constructor of the base element. More...

	PerturbedSpineElement (FiniteElement *const &element_pt, const int &face_index)
	Constructor used for spine face elements. More...

	~PerturbedSpineElement ()
	Destructor, clean up the storage allocated to the local equation numbers. More...

int	spine_local_eqn (const unsigned &n, const unsigned &i)

virtual int	get_local_eqn_number_corresponding_to_geometric_dofs (const unsigned &n, const unsigned &i)

Public Member Functions inherited from oomph::ElementWithSpecificMovingNodes< ELEMENT, PerturbedSpineNode >
void	describe_local_dofs (std::ostream &out, const std::string &current_string) const

void	describe_local_dofs (std::ostream &out, std::string &curr_str)
	Unique final overrider for describe_dofs. More...

	ElementWithSpecificMovingNodes ()
	Constructor, call the constructor of the base element. More...

	ElementWithSpecificMovingNodes (FiniteElement *const &element_pt, const int &face_index)
	Constructor used for face elements. More...

	~ElementWithSpecificMovingNodes ()
	Empty Destructor,. More...

Node *	construct_node (const unsigned &n)

Node *	construct_node (const unsigned &n, TimeStepper *const &time_stepper_pt)
	Overloaded node allocation for unsteady problems. More...

Node *	construct_boundary_node (const unsigned &n)
	Overload the node assignment routine to assign boundary nodes. More...

Node *	construct_boundary_node (const unsigned &n, TimeStepper *const &time_stepper_pt)
	Overloaded boundary node allocation for unsteady problems. More...

void	complete_setup_of_dependencies ()

void	assign_all_generic_local_eqn_numbers (const bool &store_local_dof_pt)

void	get_jacobian (Vector< double > &residuals, DenseMatrix< double > &jacobian)
	Compute the element's residuals vector and jacobian matrix. More...

void	get_jacobian_and_mass_matrix (Vector< double > &residuals, DenseMatrix< double > &jacobian, DenseMatrix< double > &mass_matrix)
	Compute the element's residuals vector and jacobian matrix. More...

Public Member Functions inherited from oomph::ElementWithMovingNodes
	ElementWithMovingNodes ()
	Constructor. More...

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

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

virtual	~ElementWithMovingNodes ()
	Virtual destructor (clean up and allocated memory) More...

unsigned	ngeom_dof () const
	Number of geometric dofs. More...

int	geometric_data_local_eqn (const unsigned &n, const unsigned &i)

void	assemble_set_of_all_geometric_data (std::set< Data * > &unique_geom_data_pt)
	Return a set of all geometric data associated with the element. More...

void	identify_geometric_data (std::set< Data * > &geometric_data_pt)

bool	are_dresidual_dnodal_coordinates_always_evaluated_by_fd () const
	Return whether shape derivatives are evaluated by fd. More...

void	enable_always_evaluate_dresidual_dnodal_coordinates_by_fd ()

void	disable_always_evaluate_dresidual_dnodal_coordinates_by_fd ()

void	evaluate_shape_derivs_by_direct_fd ()
	Evaluate shape derivatives by direct finite differencing. More...

void	evaluate_shape_derivs_by_chain_rule (const bool &i_know_what_i_am_doing=false)

void	evaluate_shape_derivs_by_fastest_method (const bool &i_know_what_i_am_doing=false)

int &	method_for_shape_derivs ()
	Access to method (enumerated flag) for determination of shape derivs. More...

void	enable_bypass_fill_in_jacobian_from_geometric_data ()
	Bypass the call to fill_in_jacobian_from_geometric_data. More...

void	disable_bypass_fill_in_jacobian_from_geometric_data ()
	Do not bypass the call to fill_in_jacobian_from_geometric_data. More...

bool	is_fill_in_jacobian_from_geometric_data_bypassed () const

unsigned	ngeom_data () const

Public Member Functions inherited from oomph::FiniteElement
void	set_dimension (const unsigned &dim)

void	set_nodal_dimension (const unsigned &nodal_dim)

void	set_nnodal_position_type (const unsigned &nposition_type)
	Set the number of types required to interpolate the coordinate. More...

void	set_n_node (const unsigned &n)

int	nodal_local_eqn (const unsigned &n, const unsigned &i) const

double	dJ_eulerian_at_knot (const unsigned &ipt, Shape &psi, DenseMatrix< double > &djacobian_dX) const

	FiniteElement ()
	Constructor. More...

virtual	~FiniteElement ()

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

virtual bool	local_coord_is_valid (const Vector< double > &s)
	Broken assignment operator. More...

virtual void	move_local_coord_back_into_element (Vector< double > &s) const

void	get_centre_of_gravity_and_max_radius_in_terms_of_zeta (Vector< double > &cog, double &max_radius) const

virtual void	local_coordinate_of_node (const unsigned &j, Vector< double > &s) const

virtual void	local_fraction_of_node (const unsigned &j, Vector< double > &s_fraction)

virtual double	local_one_d_fraction_of_node (const unsigned &n1d, const unsigned &i)

virtual void	set_macro_elem_pt (MacroElement *macro_elem_pt)

MacroElement *	macro_elem_pt ()
	Access function to pointer to macro element. More...

void	get_x (const Vector< double > &s, Vector< double > &x) const

void	get_x (const unsigned &t, const Vector< double > &s, Vector< double > &x)

virtual void	get_x_from_macro_element (const Vector< double > &s, Vector< double > &x) const

virtual void	get_x_from_macro_element (const unsigned &t, const Vector< double > &s, Vector< double > &x)

virtual void	set_integration_scheme (Integral *const &integral_pt)
	Set the spatial integration scheme. More...

Integral *const &	integral_pt () const
	Return the pointer to the integration scheme (const version) More...

virtual void	shape (const Vector< double > &s, Shape &psi) const =0

virtual void	shape_at_knot (const unsigned &ipt, Shape &psi) const

virtual void	dshape_local (const Vector< double > &s, Shape &psi, DShape &dpsids) const

virtual void	dshape_local_at_knot (const unsigned &ipt, Shape &psi, DShape &dpsids) const

virtual void	d2shape_local (const Vector< double > &s, Shape &psi, DShape &dpsids, DShape &d2psids) const

virtual void	d2shape_local_at_knot (const unsigned &ipt, Shape &psi, DShape &dpsids, DShape &d2psids) const

virtual double	J_eulerian (const Vector< double > &s) const

virtual double	J_eulerian_at_knot (const unsigned &ipt) const

void	check_J_eulerian_at_knots (bool &passed) const

void	check_jacobian (const double &jacobian) const

double	dshape_eulerian (const Vector< double > &s, Shape &psi, DShape &dpsidx) const

virtual double	dshape_eulerian_at_knot (const unsigned &ipt, Shape &psi, DShape &dpsidx) const

virtual double	dshape_eulerian_at_knot (const unsigned &ipt, Shape &psi, DShape &dpsi, DenseMatrix< double > &djacobian_dX, RankFourTensor< double > &d_dpsidx_dX) const

double	d2shape_eulerian (const Vector< double > &s, Shape &psi, DShape &dpsidx, DShape &d2psidx) const

virtual double	d2shape_eulerian_at_knot (const unsigned &ipt, Shape &psi, DShape &dpsidx, DShape &d2psidx) const

virtual void	assign_nodal_local_eqn_numbers (const bool &store_local_dof_pt)

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

Node *&	node_pt (const unsigned &n)
	Return a pointer to the local node n. More...

Node *const &	node_pt (const unsigned &n) const
	Return a pointer to the local node n (const version) More...

unsigned	nnode () const
	Return the number of nodes. More...

virtual unsigned	nnode_1d () const

double	raw_nodal_position (const unsigned &n, const unsigned &i) const

double	raw_nodal_position (const unsigned &t, const unsigned &n, const unsigned &i) const

double	raw_dnodal_position_dt (const unsigned &n, const unsigned &i) const

double	raw_dnodal_position_dt (const unsigned &n, const unsigned &j, const unsigned &i) const

double	raw_nodal_position_gen (const unsigned &n, const unsigned &k, const unsigned &i) const

double	raw_nodal_position_gen (const unsigned &t, const unsigned &n, const unsigned &k, const unsigned &i) const

double	raw_dnodal_position_gen_dt (const unsigned &n, const unsigned &k, const unsigned &i) const

double	raw_dnodal_position_gen_dt (const unsigned &j, const unsigned &n, const unsigned &k, const unsigned &i) const

double	nodal_position (const unsigned &n, const unsigned &i) const

double	nodal_position (const unsigned &t, const unsigned &n, const unsigned &i) const

double	dnodal_position_dt (const unsigned &n, const unsigned &i) const
	Return the i-th component of nodal velocity: dx/dt at local node n. More...

double	dnodal_position_dt (const unsigned &n, const unsigned &j, const unsigned &i) const

double	nodal_position_gen (const unsigned &n, const unsigned &k, const unsigned &i) const

double	nodal_position_gen (const unsigned &t, const unsigned &n, const unsigned &k, const unsigned &i) const

double	dnodal_position_gen_dt (const unsigned &n, const unsigned &k, const unsigned &i) const

double	dnodal_position_gen_dt (const unsigned &j, const unsigned &n, const unsigned &k, const unsigned &i) const

virtual void	get_dresidual_dnodal_coordinates (RankThreeTensor< double > &dresidual_dnodal_coordinates)

virtual void	disable_ALE ()

virtual void	enable_ALE ()

virtual unsigned	required_nvalue (const unsigned &n) const

unsigned	nnodal_position_type () const

bool	has_hanging_nodes () const

unsigned	nodal_dimension () const
	Return the required Eulerian dimension of the nodes in this element. More...

virtual unsigned	nvertex_node () const

virtual Node *	vertex_node_pt (const unsigned &j) const

int	get_node_number (Node *const &node_pt) const

virtual Node *	get_node_at_local_coordinate (const Vector< double > &s) const

double	raw_nodal_value (const unsigned &n, const unsigned &i) const

double	raw_nodal_value (const unsigned &t, const unsigned &n, const unsigned &i) const

double	nodal_value (const unsigned &n, const unsigned &i) const

double	nodal_value (const unsigned &t, const unsigned &n, const unsigned &i) const

unsigned	dim () const

virtual ElementGeometry::ElementGeometry	element_geometry () const
	Return the geometry type of the element (either Q or T usually). More...

virtual double	interpolated_x (const Vector< double > &s, const unsigned &i) const
	Return FE interpolated coordinate x[i] at local coordinate s. More...

virtual double	interpolated_x (const unsigned &t, const Vector< double > &s, const unsigned &i) const

virtual void	interpolated_x (const Vector< double > &s, Vector< double > &x) const
	Return FE interpolated position x[] at local coordinate s as Vector. More...

virtual void	interpolated_x (const unsigned &t, const Vector< double > &s, Vector< double > &x) const

virtual double	interpolated_dxdt (const Vector< double > &s, const unsigned &i, const unsigned &t)

virtual void	interpolated_dxdt (const Vector< double > &s, const unsigned &t, Vector< double > &dxdt)

unsigned	ngeom_data () const

Data *	geom_data_pt (const unsigned &j)

void	position (const Vector< double > &zeta, Vector< double > &r) const

void	position (const unsigned &t, const Vector< double > &zeta, Vector< double > &r) const

void	dposition_dt (const Vector< double > &zeta, const unsigned &t, Vector< double > &drdt)

virtual double	zeta_nodal (const unsigned &n, const unsigned &k, const unsigned &i) const

void	interpolated_zeta (const Vector< double > &s, Vector< double > &zeta) const

void	locate_zeta (const Vector< double > &zeta, GeomObject *&geom_object_pt, Vector< double > &s, const bool &use_coordinate_as_initial_guess=false)

virtual void	node_update ()

virtual void	identify_field_data_for_interactions (std::set< std::pair< Data *, unsigned >> &paired_field_data)

virtual double	s_min () const
	Min value of local coordinate. More...

virtual double	s_max () const
	Max. value of local coordinate. More...

double	size () const

virtual double	compute_physical_size () const

virtual void	point_output_data (const Vector< double > &s, Vector< double > &data)

void	point_output (std::ostream &outfile, const Vector< double > &s)

virtual unsigned	nplot_points_paraview (const unsigned &nplot) const

virtual unsigned	nsub_elements_paraview (const unsigned &nplot) const

void	output_paraview (std::ofstream &file_out, const unsigned &nplot) const

virtual void	write_paraview_output_offset_information (std::ofstream &file_out, const unsigned &nplot, unsigned &counter) const

virtual void	write_paraview_type (std::ofstream &file_out, const unsigned &nplot) const

virtual void	write_paraview_offsets (std::ofstream &file_out, const unsigned &nplot, unsigned &offset_sum) const

virtual unsigned	nscalar_paraview () const

virtual void	scalar_value_paraview (std::ofstream &file_out, const unsigned &i, const unsigned &nplot) const

virtual void	scalar_value_fct_paraview (std::ofstream &file_out, const unsigned &i, const unsigned &nplot, FiniteElement::SteadyExactSolutionFctPt exact_soln_pt) const

virtual void	scalar_value_fct_paraview (std::ofstream &file_out, const unsigned &i, const unsigned &nplot, const double &time, FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt) const

virtual std::string	scalar_name_paraview (const unsigned &i) const

virtual void	output (std::ostream &outfile)

virtual void	output (std::ostream &outfile, const unsigned &n_plot)

virtual void	output (const unsigned &t, std::ostream &outfile, const unsigned &n_plot) const

virtual void	output (FILE *file_pt)

virtual void	output (FILE *file_pt, const unsigned &n_plot)

virtual void	output_fct (std::ostream &outfile, const unsigned &n_plot, FiniteElement::SteadyExactSolutionFctPt exact_soln_pt)
	Output an exact solution over the element. More...

virtual void	output_fct (std::ostream &outfile, const unsigned &n_plot, const double &time, FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt)
	Output a time-dependent exact solution over the element. More...

virtual void	output_fct (std::ostream &outfile, const unsigned &n_plot, const double &time, const SolutionFunctorBase &exact_soln) const
	Output a time-dependent exact solution over the element. More...

virtual void	get_s_plot (const unsigned &i, const unsigned &nplot, Vector< double > &s, const bool &shifted_to_interior=false) const

virtual std::string	tecplot_zone_string (const unsigned &nplot) const

virtual void	write_tecplot_zone_footer (std::ostream &outfile, const unsigned &nplot) const

virtual void	write_tecplot_zone_footer (FILE *file_pt, const unsigned &nplot) const

virtual unsigned	nplot_points (const unsigned &nplot) const

virtual void	compute_error (FiniteElement::SteadyExactSolutionFctPt exact_soln_pt, double &error, double &norm)
	Calculate the norm of the error and that of the exact solution. More...

virtual void	compute_error (FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt, const double &time, double &error, double &norm)
	Calculate the norm of the error and that of the exact solution. More...

virtual void	compute_error (FiniteElement::SteadyExactSolutionFctPt exact_soln_pt, Vector< double > &error, Vector< double > &norm)

virtual void	compute_error (FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt, const double &time, Vector< double > &error, Vector< double > &norm)

virtual void	compute_error (std::ostream &outfile, FiniteElement::SteadyExactSolutionFctPt exact_soln_pt, double &error, double &norm)

virtual void	compute_error (std::ostream &outfile, FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt, const double &time, double &error, double &norm)

virtual void	compute_error (std::ostream &outfile, FiniteElement::SteadyExactSolutionFctPt exact_soln_pt, Vector< double > &error, Vector< double > &norm)

virtual void	compute_error (std::ostream &outfile, FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt, const double &time, Vector< double > &error, Vector< double > &norm)

virtual void	compute_abs_error (std::ostream &outfile, FiniteElement::SteadyExactSolutionFctPt exact_soln_pt, double &error)

void	integrate_fct (FiniteElement::SteadyExactSolutionFctPt integrand_fct_pt, Vector< double > &integral)
	Integrate Vector-valued function over element. More...

void	integrate_fct (FiniteElement::UnsteadyExactSolutionFctPt integrand_fct_pt, const double &time, Vector< double > &integral)
	Integrate Vector-valued time-dep function over element. More...

virtual void	build_face_element (const int &face_index, FaceElement *face_element_pt)

virtual unsigned	self_test ()

virtual unsigned	get_bulk_node_number (const int &face_index, const unsigned &i) const

virtual int	face_outer_unit_normal_sign (const int &face_index) const
	Get the sign of the outer unit normal on the face given by face_index. More...

virtual unsigned	nnode_on_face () const

void	face_node_number_error_check (const unsigned &i) const
	Range check for face node numbers. More...

virtual CoordinateMappingFctPt	face_to_bulk_coordinate_fct_pt (const int &face_index) const

virtual BulkCoordinateDerivativesFctPt	bulk_coordinate_derivatives_fct_pt (const int &face_index) const

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

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	get_residuals (Vector< double > &residuals)

virtual void	get_mass_matrix (Vector< double > &residuals, 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 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 Member Functions inherited from oomph::GeomObject
	GeomObject ()
	Default constructor. More...

	GeomObject (const unsigned &ndim)

	GeomObject (const unsigned &nlagrangian, const unsigned &ndim)

	GeomObject (const unsigned &nlagrangian, const unsigned &ndim, TimeStepper *time_stepper_pt)

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

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

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

unsigned	nlagrangian () const
	Access function to # of Lagrangian coordinates. More...

unsigned	ndim () const
	Access function to # of Eulerian coordinates. More...

void	set_nlagrangian_and_ndim (const unsigned &n_lagrangian, const unsigned &n_dim)
	Set # of Lagrangian and Eulerian coordinates. More...

TimeStepper *&	time_stepper_pt ()

TimeStepper *	time_stepper_pt () const

virtual void	position (const double &t, const Vector< double > &zeta, Vector< double > &r) const

virtual void	dposition (const Vector< double > &zeta, DenseMatrix< double > &drdzeta) const

virtual void	d2position (const Vector< double > &zeta, RankThreeTensor< double > &ddrdzeta) const

virtual void	d2position (const Vector< double > &zeta, Vector< double > &r, DenseMatrix< double > &drdzeta, RankThreeTensor< double > &ddrdzeta) const

Public Member Functions inherited from oomph::PerturbedSpineFiniteElement
	PerturbedSpineFiniteElement ()
	Empty constructor. More...

virtual	~PerturbedSpineFiniteElement ()
	Emtpty virtual destructor. More...

Private Member Functions
void	complete_setup_of_dependencies ()
	Construct and fill the node_update_data vector. More...

Private Attributes
unsigned *	PerturbedSpine_geometric_index

Additional Inherited Members
Public Types inherited from oomph::ElementWithMovingNodes
enum	{ Shape_derivs_by_chain_rule , Shape_derivs_by_direct_fd , Shape_derivs_by_fastest_method }
	Public enumeration to choose method for computing shape derivatives. More...

Public Types inherited from oomph::FiniteElement
typedef void(*	SteadyExactSolutionFctPt) (const Vector< double > &, Vector< double > &)

typedef void(*	UnsteadyExactSolutionFctPt) (const double &, const Vector< double > &, Vector< double > &)

Static Public Attributes inherited from oomph::FiniteElement
static double	Tolerance_for_singular_jacobian = 1.0e-16
	Tolerance below which the jacobian is considered singular. More...

static bool	Accept_negative_jacobian = false

static bool	Suppress_output_while_checking_for_inverted_elements

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::ElementWithMovingNodes
virtual void	get_dnodal_coordinates_dgeom_dofs (RankThreeTensor< double > &dnodal_coordinates_dgeom_dofs)

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

void	fill_in_jacobian_from_geometric_data (DenseMatrix< double > &jacobian)

Protected Member Functions inherited from oomph::FiniteElement
virtual void	assemble_local_to_eulerian_jacobian (const DShape &dpsids, DenseMatrix< double > &jacobian) const

virtual void	assemble_local_to_eulerian_jacobian2 (const DShape &d2psids, DenseMatrix< double > &jacobian2) const

virtual void	assemble_eulerian_base_vectors (const DShape &dpsids, DenseMatrix< double > &interpolated_G) const

template<unsigned DIM>
double	invert_jacobian (const DenseMatrix< double > &jacobian, DenseMatrix< double > &inverse_jacobian) const

virtual double	invert_jacobian_mapping (const DenseMatrix< double > &jacobian, DenseMatrix< double > &inverse_jacobian) const

virtual double	local_to_eulerian_mapping (const DShape &dpsids, DenseMatrix< double > &jacobian, DenseMatrix< double > &inverse_jacobian) const

double	local_to_eulerian_mapping (const DShape &dpsids, DenseMatrix< double > &inverse_jacobian) const

virtual double	local_to_eulerian_mapping_diagonal (const DShape &dpsids, DenseMatrix< double > &jacobian, DenseMatrix< double > &inverse_jacobian) const

virtual void	dJ_eulerian_dnodal_coordinates (const DenseMatrix< double > &jacobian, const DShape &dpsids, DenseMatrix< double > &djacobian_dX) const

template<unsigned DIM>
void	dJ_eulerian_dnodal_coordinates_templated_helper (const DenseMatrix< double > &jacobian, const DShape &dpsids, DenseMatrix< double > &djacobian_dX) const

virtual void	d_dshape_eulerian_dnodal_coordinates (const double &det_jacobian, const DenseMatrix< double > &jacobian, const DenseMatrix< double > &djacobian_dX, const DenseMatrix< double > &inverse_jacobian, const DShape &dpsids, RankFourTensor< double > &d_dpsidx_dX) const

template<unsigned DIM>
void	d_dshape_eulerian_dnodal_coordinates_templated_helper (const double &det_jacobian, const DenseMatrix< double > &jacobian, const DenseMatrix< double > &djacobian_dX, const DenseMatrix< double > &inverse_jacobian, const DShape &dpsids, RankFourTensor< double > &d_dpsidx_dX) const

virtual void	transform_derivatives (const DenseMatrix< double > &inverse_jacobian, DShape &dbasis) const

void	transform_derivatives_diagonal (const DenseMatrix< double > &inverse_jacobian, DShape &dbasis) const

virtual void	transform_second_derivatives (const DenseMatrix< double > &jacobian, const DenseMatrix< double > &inverse_jacobian, const DenseMatrix< double > &jacobian2, DShape &dbasis, DShape &d2basis) const

template<unsigned DIM>
void	transform_second_derivatives_template (const DenseMatrix< double > &jacobian, const DenseMatrix< double > &inverse_jacobian, const DenseMatrix< double > &jacobian2, DShape &dbasis, DShape &d2basis) const

template<unsigned DIM>
void	transform_second_derivatives_diagonal (const DenseMatrix< double > &jacobian, const DenseMatrix< double > &inverse_jacobian, const DenseMatrix< double > &jacobian2, DShape &dbasis, DShape &d2basis) const

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

void	fill_in_jacobian_from_nodal_by_fd (DenseMatrix< double > &jacobian)

virtual void	update_before_nodal_fd ()

virtual void	reset_after_nodal_fd ()

virtual void	update_in_nodal_fd (const unsigned &i)

virtual void	reset_in_nodal_fd (const unsigned &i)

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

template<>
double	invert_jacobian (const DenseMatrix< double > &jacobian, DenseMatrix< double > &inverse_jacobian) const
	Zero-d specialisation of function to calculate inverse of jacobian mapping. More...

template<>
double	invert_jacobian (const DenseMatrix< double > &jacobian, DenseMatrix< double > &inverse_jacobian) const
	One-d specialisation of function to calculate inverse of jacobian mapping. More...

template<>
double	invert_jacobian (const DenseMatrix< double > &jacobian, DenseMatrix< double > &inverse_jacobian) const
	Two-d specialisation of function to calculate inverse of jacobian mapping. More...

template<>
double	invert_jacobian (const DenseMatrix< double > &jacobian, DenseMatrix< double > &inverse_jacobian) const

template<>
void	dJ_eulerian_dnodal_coordinates_templated_helper (const DenseMatrix< double > &jacobian, const DShape &dpsids, DenseMatrix< double > &djacobian_dX) const

template<>
void	dJ_eulerian_dnodal_coordinates_templated_helper (const DenseMatrix< double > &jacobian, const DShape &dpsids, DenseMatrix< double > &djacobian_dX) const

template<>
void	dJ_eulerian_dnodal_coordinates_templated_helper (const DenseMatrix< double > &jacobian, const DShape &dpsids, DenseMatrix< double > &djacobian_dX) const

template<>
void	dJ_eulerian_dnodal_coordinates_templated_helper (const DenseMatrix< double > &jacobian, const DShape &dpsids, DenseMatrix< double > &djacobian_dX) const

template<>
void	d_dshape_eulerian_dnodal_coordinates_templated_helper (const double &det_jacobian, const DenseMatrix< double > &jacobian, const DenseMatrix< double > &djacobian_dX, const DenseMatrix< double > &inverse_jacobian, const DShape &dpsids, RankFourTensor< double > &d_dpsidx_dX) const

template<>
void	d_dshape_eulerian_dnodal_coordinates_templated_helper (const double &det_jacobian, const DenseMatrix< double > &jacobian, const DenseMatrix< double > &djacobian_dX, const DenseMatrix< double > &inverse_jacobian, const DShape &dpsids, RankFourTensor< double > &d_dpsidx_dX) const

template<>
void	d_dshape_eulerian_dnodal_coordinates_templated_helper (const double &det_jacobian, const DenseMatrix< double > &jacobian, const DenseMatrix< double > &djacobian_dX, const DenseMatrix< double > &inverse_jacobian, const DShape &dpsids, RankFourTensor< double > &d_dpsidx_dX) const

template<>
void	d_dshape_eulerian_dnodal_coordinates_templated_helper (const double &det_jacobian, const DenseMatrix< double > &jacobian, const DenseMatrix< double > &djacobian_dX, const DenseMatrix< double > &inverse_jacobian, const DShape &dpsids, RankFourTensor< double > &d_dpsidx_dX) const

template<>
void	transform_second_derivatives_template (const DenseMatrix< double > &jacobian, const DenseMatrix< double > &inverse_jacobian, const DenseMatrix< double > &jacobian2, DShape &dbasis, DShape &d2basis) const

template<>
void	transform_second_derivatives_template (const DenseMatrix< double > &jacobian, const DenseMatrix< double > &inverse_jacobian, const DenseMatrix< double > &jacobian2, DShape &dbasis, DShape &d2basis) const

template<>
void	transform_second_derivatives_diagonal (const DenseMatrix< double > &jacobian, const DenseMatrix< double > &inverse_jacobian, const DenseMatrix< double > &jacobian2, DShape &dbasis, DShape &d2basis) const

template<>
void	transform_second_derivatives_diagonal (const DenseMatrix< double > &jacobian, const DenseMatrix< double > &inverse_jacobian, const DenseMatrix< double > &jacobian2, DShape &dbasis, DShape &d2basis) const

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_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)

virtual void	fill_in_contribution_to_residuals (Vector< double > &residuals)

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_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)

Protected Attributes inherited from oomph::ElementWithMovingNodes
Vector< Data * >	Geom_data_pt

Protected Attributes inherited from oomph::FiniteElement
MacroElement *	Macro_elem_pt
	Pointer to the element's macro element (NULL by default) More...

Protected Attributes inherited from oomph::GeomObject
unsigned	NLagrangian
	Number of Lagrangian (intrinsic) coordinates. More...

unsigned	Ndim
	Number of Eulerian coordinates. More...

TimeStepper *	Geom_object_time_stepper_pt

Static Protected Attributes inherited from oomph::FiniteElement
static const unsigned	Default_Initial_Nvalue = 0
	Default value for the number of values at a node. More...

static const double	Node_location_tolerance = 1.0e-14

static const unsigned	N2deriv [] = {0, 1, 3, 6}

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

static std::deque< double * >	Dof_pt_deque

Detailed Description

template<class ELEMENT>
class oomph::PerturbedSpineElement< ELEMENT >

The PerturbedSpineElement<ELEMENT> class takes an existing element as a template parameter and adds the necessary additional functionality to allow the element to be update using the method of spines. A vector of pointers to spines and storage for the local equation numbers associated with the spines are added to the element.

Constructor & Destructor Documentation

◆ PerturbedSpineElement() [1/2]

template<class ELEMENT >

oomph::PerturbedSpineElement< ELEMENT >::PerturbedSpineElement ( )

inline

Constructor, call the constructor of the base element.

                          : 
   ElementWithSpecificMovingNodes<ELEMENT,PerturbedSpineNode>(),  
   PerturbedSpineFiniteElement(),
   PerturbedSpine_geometric_index(0) {}

◆ PerturbedSpineElement() [2/2]

template<class ELEMENT >

oomph::PerturbedSpineElement< ELEMENT >::PerturbedSpineElement	(	FiniteElement *const &	element_pt,
		const int &	face_index
	)

inline

Constructor used for spine face elements.

                                               : 
   ElementWithSpecificMovingNodes<ELEMENT,PerturbedSpineNode>(element_pt,
                                                              face_index),
   PerturbedSpineFiniteElement(),
   PerturbedSpine_geometric_index(0) {}

◆ ~PerturbedSpineElement()

template<class ELEMENT >

oomph::PerturbedSpineElement< ELEMENT >::~PerturbedSpineElement ( )

inline

Destructor, clean up the storage allocated to the local equation numbers.

   {
    if(PerturbedSpine_geometric_index) 
     {
      delete[] PerturbedSpine_geometric_index;
     }
   }

References oomph::PerturbedSpineElement< ELEMENT >::PerturbedSpine_geometric_index.

Member Function Documentation

◆ complete_setup_of_dependencies()

template<class ELEMENT >

void oomph::PerturbedSpineElement< ELEMENT >::complete_setup_of_dependencies

privatevirtual

Construct and fill the node_update_data vector.

Complete the setup of additional dependencies. Overloads empty virtual function in GeneralisedElement to determine the "geometric Data", i.e. the Data that affects the element's shape. This function is called (for all elements) at the very beginning of the equation numbering procedure to ensure that all dependencies are accounted for.

////////////////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////////////// ////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////

Reimplemented from oomph::GeneralisedElement.

 {
  // Call function of underlying element
  ElementWithSpecificMovingNodes<ELEMENT,PerturbedSpineNode>::
   complete_setup_of_dependencies();
  
  // Sort out the perturbed spine index stuff
  // Find the data that correspond to spine heights
  {
   const unsigned n_node = this->nnode();
  
   // Allocate memory
   if(PerturbedSpine_geometric_index)
    {
     delete[] PerturbedSpine_geometric_index;
    }
   PerturbedSpine_geometric_index = new unsigned[n_node];
   
   // Now loop over data and find out where it fits
   for(unsigned n=0;n<n_node;n++)
    {
     // Find pointer to the perturbed spine
     PerturbedSpine* const perturbedspine_pt =
      static_cast<PerturbedSpineNode*>(this->node_pt(n))->perturbed_spine_pt();
  
     // If there is a spine then find the pointer to the data
     if(perturbedspine_pt)
      {
       // Find the pointer to the data
       Data* perturbed_spine_height_data_pt =
        perturbedspine_pt->height_pt();
       
       // Now find the index of the corresponding perturbed spine
       const unsigned n_node_update_data = this->ngeom_data();
       for(unsigned i=0;i<n_node_update_data;i++)
        {
         if(this->Geom_data_pt[i]==perturbed_spine_height_data_pt)
          {
           PerturbedSpine_geometric_index[n] = i;
           break;
          }
        }
      }
     // Otherwise issue a warning
     else
      {
       // Set the spine_geometric_index out of range,
       // which will cause the spine_local_eqn to return a pinned value
       PerturbedSpine_geometric_index[n] = this->ngeom_data();
      }
    }
  }
  
 } // End of complete_setup_of_dependencies

References oomph::ElementWithSpecificMovingNodes< ELEMENT, NODE_TYPE >::complete_setup_of_dependencies(), oomph::PerturbedSpine::height_pt(), i, and n.

◆ get_local_eqn_number_corresponding_to_geometric_dofs()

template<class ELEMENT >

virtual int oomph::PerturbedSpineElement< ELEMENT >::get_local_eqn_number_corresponding_to_geometric_dofs	(	const unsigned &	n,
		const unsigned &	i
	)

inlinevirtual

Return the local equation number associated with the i-th ‘height’ of the n-th local perturbed spine

  {
   return this->spine_local_eqn(n,i);
  }

References i, and oomph::PerturbedSpineElement< ELEMENT >::spine_local_eqn().

◆ spine_local_eqn()

template<class ELEMENT >

int oomph::PerturbedSpineElement< ELEMENT >::spine_local_eqn	(	const unsigned &	n,
		const unsigned &	i
	)

inline

Return the local equation number corresponding to the i-th component of the "height" of the perturbed spine at the n-th node

   {
 #ifdef RANGE_CHECKING
    const unsigned n_node = this->nnode();
    if(n >= n_node)
     {
      std::ostringstream error_message;
      error_message << "Range Error:  Node number " << n
                    << " is not in the range (0,"
                    << n_node-1 << ")";
      throw OomphLibError(error_message.str(),
                          "PerturbedSpineElement::spine_local_eqn()",
                          OOMPH_EXCEPTION_LOCATION);
     }
 #endif
  
 #ifdef PARANOID
    // The perturbed spine "height" only has two components
    if(i>=2)
     {
      std::ostringstream error_message;
      error_message << "Perturbed spines only have two height components:"
                    << "\nComponent i=" << i
                    << " is not in the range (0,2)";
      throw OomphLibError(error_message.str(),
                          "PerturbedSpineElement::spine_local_eqn()",
                          OOMPH_EXCEPTION_LOCATION);
     }
    // If there is no spine then you can't get the local equation
    if(PerturbedSpine_geometric_index[n]==this->ngeom_data())
     {
      std::ostringstream error_stream;
      error_stream 
       << "PerturbedSpineNode " << n << " does not have a PerturbedSpine\n"
       << "attached, so you can't get its local equation number. Check that\n"
       << "the Mesh is correctly associating PerturbedSpines with is Nodes\n";
      throw OomphLibError(error_stream.str(),
                          "PerturbedSpineElement<ELEMENT>::spine_local_eqn()",
                          OOMPH_EXCEPTION_LOCATION);
     }
 #endif
    return this->geometric_data_local_eqn(PerturbedSpine_geometric_index[n],i);
   }

References oomph::ElementWithMovingNodes::geometric_data_local_eqn(), i, n, oomph::ElementWithMovingNodes::ngeom_data(), oomph::FiniteElement::nnode(), OOMPH_EXCEPTION_LOCATION, and oomph::PerturbedSpineElement< ELEMENT >::PerturbedSpine_geometric_index.

Referenced by oomph::PerturbedSpineElement< ELEMENT >::get_local_eqn_number_corresponding_to_geometric_dofs(), and oomph::PerturbedSpineLinearisedAxisymmetricFluidInterfaceElement< ELEMENT >::kinematic_local_eqn().

Member Data Documentation

◆ PerturbedSpine_geometric_index

template<class ELEMENT >

unsigned* oomph::PerturbedSpineElement< ELEMENT >::PerturbedSpine_geometric_index

private

Array to hold the index of the geometric data associated with the spine height of the spine that affects the n-th node

Referenced by oomph::PerturbedSpineElement< ELEMENT >::spine_local_eqn(), and oomph::PerturbedSpineElement< ELEMENT >::~PerturbedSpineElement().

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

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

template<class ELEMENT> class oomph::PerturbedSpineElement< ELEMENT >

Constructor & Destructor Documentation

◆ PerturbedSpineElement() [1/2]

◆ PerturbedSpineElement() [2/2]

◆ ~PerturbedSpineElement()

Member Function Documentation

◆ complete_setup_of_dependencies()

◆ get_local_eqn_number_corresponding_to_geometric_dofs()

◆ spine_local_eqn()

Member Data Documentation

◆ PerturbedSpine_geometric_index

template<class ELEMENT>
class oomph::PerturbedSpineElement< ELEMENT >