Class for Refineable PVD equations. More...

#include <refineable_solid_elements.h>

Inheritance diagram for oomph::RefineablePVDEquations< DIM >:

Public Member Functions
	RefineablePVDEquations ()
	Constructor. More...

void	fill_in_generic_contribution_to_residuals_pvd (Vector< double > &residuals, DenseMatrix< double > &jacobian, const unsigned &flag)
	Call the residuals including hanging node cases. More...

void	get_interpolated_values (const unsigned &t, const Vector< double > &s, Vector< double > &values)
	No values are interpolated in this element (pure solid) More...

void	get_interpolated_values (const Vector< double > &s, Vector< double > &values)
	No values are interpolated in this element (pure solid) More...

unsigned	num_Z2_flux_terms ()
	Number of 'flux' terms for Z2 error estimation. More...

void	get_Z2_flux (const Vector< double > &s, Vector< double > &flux)

unsigned	ncont_interpolated_values () const
	Number of continuously interpolated values: 0 (pure solid problem) More...

virtual Node *	solid_pressure_node_pt (const unsigned &l)

void	further_build ()
	Further build function, pass the pointers down to the sons. More...

Public Member Functions inherited from oomph::PVDEquations< DIM >
	PVDEquations ()
	Constructor. More...

void	get_stress (const Vector< double > &s, DenseMatrix< double > &sigma)

void	fill_in_contribution_to_residuals (Vector< double > &residuals)

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

void	output (std::ostream &outfile)
	Output: x,y,[z],xi0,xi1,[xi2],gamma. More...

void	output (std::ostream &outfile, const unsigned &n_plot)
	Output: x,y,[z],xi0,xi1,[xi2],gamma. More...

void	output (FILE *file_pt)
	C-style output: x,y,[z],xi0,xi1,[xi2],gamma. More...

void	output (FILE *file_pt, const unsigned &n_plot)
	Output: x,y,[z],xi0,xi1,[xi2],gamma. More...

void	extended_output (std::ostream &outfile, const unsigned &n_plot)
	Output: x,y,[z],xi0,xi1,[xi2],gamma strain and stress components. More...

Public Member Functions inherited from oomph::PVDEquationsBase< DIM >
	PVDEquationsBase ()

ConstitutiveLaw *&	constitutive_law_pt ()
	Return the constitutive law pointer. More...

const double &	lambda_sq () const
	Access function for timescale ratio (nondim density) More...

double *&	lambda_sq_pt ()
	Access function for pointer to timescale ratio (nondim density) More...

IsotropicGrowthFctPt &	isotropic_growth_fct_pt ()
	Access function: Pointer to isotropic growth function. More...

PrestressFctPt &	prestress_fct_pt ()
	Access function: Pointer to pre-stress function. More...

IsotropicGrowthFctPt	isotropic_growth_fct_pt () const
	Access function: Pointer to isotropic growth function (const version) More...

BodyForceFctPt &	body_force_fct_pt ()
	Access function: Pointer to body force function. More...

BodyForceFctPt	body_force_fct_pt () const
	Access function: Pointer to body force function (const version) More...

void	enable_inertia ()
	Switch on solid inertia. More...

void	disable_inertia ()
	Switch off solid inertia. More...

bool	is_inertia_enabled () const
	Access function to flag that switches inertia on/off (const version) More...

virtual unsigned	npres_solid () const

virtual int	solid_p_local_eqn (const unsigned &i) const

virtual int	solid_p_nodal_index () const

virtual void	pin_elemental_redundant_nodal_solid_pressures ()
	Pin the element's redundant solid pressures (needed for refinement) More...

void	get_strain (const Vector< double > &s, DenseMatrix< double > &strain) const
	Return the strain tensor. More...

void	get_energy (double &pot_en, double &kin_en)
	Get potential (strain) and kinetic energy. More...

void	get_deformed_covariant_basis_vectors (const Vector< double > &s, DenseMatrix< double > &def_covariant_basis)

void	get_principal_stress (const Vector< double > &s, DenseMatrix< double > &principal_stress_vector, Vector< double > &principal_stress)

virtual void	get_isotropic_growth (const unsigned &ipt, const Vector< double > &s, const Vector< double > &xi, double &gamma) const

void	body_force (const Vector< double > &xi, Vector< double > &b) const

unsigned	ndof_types () const
	returns the number of DOF types associated with this element. More...

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

void	enable_evaluate_jacobian_by_fd ()
	Set Jacobian to be evaluated by FD? Else: Analytically. More...

void	disable_evaluate_jacobian_by_fd ()
	Set Jacobian to be evaluated analytically Else: by FD. More...

bool	is_jacobian_evaluated_by_fd () const
	Return the flag indicating whether the jacobian is evaluated by fd. More...

double	prestress (const unsigned &i, const unsigned &j, const Vector< double > xi)

Public Member Functions inherited from oomph::SolidFiniteElement
void	set_lagrangian_dimension (const unsigned &lagrangian_dimension)

virtual bool	has_internal_solid_data ()

	SolidFiniteElement ()
	Constructor: Set defaults. More...

virtual	~SolidFiniteElement ()
	Destructor to clean up any allocated memory. More...

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

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

virtual void	get_x_and_xi (const Vector< double > &s, Vector< double > &x_fe, Vector< double > &x, Vector< double > &xi_fe, Vector< double > &xi) const

virtual void	set_macro_elem_pt (MacroElement *macro_elem_pt)

virtual void	set_macro_elem_pt (MacroElement macro_elem_pt, MacroElement undeformed_macro_elem_pt)

void	set_undeformed_macro_elem_pt (MacroElement *undeformed_macro_elem_pt)

MacroElement *	undeformed_macro_elem_pt ()
	Access function to pointer to "undeformed" macro element. More...

double	dshape_lagrangian (const Vector< double > &s, Shape &psi, DShape &dpsidxi) const

virtual double	dshape_lagrangian_at_knot (const unsigned &ipt, Shape &psi, DShape &dpsidxi) const

double	d2shape_lagrangian (const Vector< double > &s, Shape &psi, DShape &dpsidxi, DShape &d2psidxi) const

virtual double	d2shape_lagrangian_at_knot (const unsigned &ipt, Shape &psi, DShape &dpsidxi, DShape &d2psidxi) const

unsigned	lagrangian_dimension () const

unsigned	nnodal_lagrangian_type () const

Node *	construct_node (const unsigned &n)
	Construct the local node n and return a pointer to it. More...

Node *	construct_node (const unsigned &n, TimeStepper *const &time_stepper_pt)

Node *	construct_boundary_node (const unsigned &n)

Node *	construct_boundary_node (const unsigned &n, TimeStepper *const &time_stepper_pt)

virtual void	assign_all_generic_local_eqn_numbers (const bool &store_local_dof_pt)

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

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

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

double	lagrangian_position (const unsigned &n, const unsigned &i) const
	Return i-th Lagrangian coordinate at local node n. More...

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

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

virtual void	interpolated_xi (const Vector< double > &s, Vector< double > &xi) const

virtual void	interpolated_dxids (const Vector< double > &s, DenseMatrix< double > &dxids) const

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

virtual double	J_lagrangian_at_knot (const unsigned &ipt) const

SolidInitialCondition *&	solid_ic_pt ()
	Pointer to object that describes the initial condition. More...

void	enable_solve_for_consistent_newmark_accel ()

void	disable_solve_for_consistent_newmark_accel ()
	Set to reset the problem being solved to be the standard problem. More...

MultiplierFctPt &	multiplier_fct_pt ()

MultiplierFctPt	multiplier_fct_pt () const

virtual void	get_residuals_for_solid_ic (Vector< double > &residuals)

void	fill_in_residuals_for_solid_ic (Vector< double > &residuals)

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

void	fill_in_jacobian_for_newmark_accel (DenseMatrix< double > &jacobian)

void	compute_norm (double &el_norm)

int	position_local_eqn (const unsigned &n, const unsigned &k, const unsigned &j) 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)

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	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	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...

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)

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)

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

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	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 void	compute_norm (Vector< double > &norm)

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::RefineableSolidElement
	RefineableSolidElement ()
	Constructor. More...

virtual	~RefineableSolidElement ()
	Virtual Destructor, delete any allocated storage. More...

void	assign_solid_local_eqn_numbers (const bool &store_local_dof_pt)

unsigned	ngeom_data () const

Data *	geom_data_pt (const unsigned &j)

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

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

bool	is_undeformed_macro_element_used_for_new_lagrangian_coords () const

void	enable_use_of_undeformed_macro_element_for_new_lagrangian_coords ()

void	disable_use_of_undeformed_macro_element_for_new_lagrangian_coords ()

DenseMatrix< int > &	local_position_hang_eqn (Node *const &node_pt)

Public Member Functions inherited from oomph::RefineableElement
	RefineableElement ()

virtual	~RefineableElement ()
	Destructor, delete the allocated storage for the hanging equations. More...

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

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

Tree *	tree_pt ()
	Access function: Pointer to quadtree representation of this element. More...

void	set_tree_pt (Tree *my_tree_pt)
	Set pointer to quadtree representation of this element. More...

virtual unsigned	required_nsons () const

bool	refinement_is_enabled ()
	Flag to indicate suppression of any refinement. More...

void	disable_refinement ()
	Suppress of any refinement for this element. More...

void	enable_refinement ()
	Emnable refinement for this element. More...

template<class ELEMENT >
void	split (Vector< ELEMENT * > &son_pt) const

int	local_hang_eqn (Node *const &node_pt, const unsigned &i)

virtual void	build (Mesh &mesh_pt, Vector< Node > &new_node_pt, bool &was_already_built, std::ofstream &new_nodes_file)=0

void	set_refinement_level (const int &refine_level)
	Set the refinement level. More...

unsigned	refinement_level () const
	Return the Refinement level. More...

void	select_for_refinement ()
	Select the element for refinement. More...

void	deselect_for_refinement ()
	Deselect the element for refinement. More...

void	select_sons_for_unrefinement ()
	Unrefinement will be performed by merging the four sons of this element. More...

void	deselect_sons_for_unrefinement ()

bool	to_be_refined ()
	Has the element been selected for refinement? More...

bool	sons_to_be_unrefined ()
	Has the element been selected for unrefinement? More...

virtual void	rebuild_from_sons (Mesh *&mesh_pt)=0

virtual void	unbuild ()

virtual void	deactivate_element ()

virtual bool	nodes_built ()
	Return true if all the nodes have been built, false if not. More...

long	number () const
	Element number (for debugging/plotting) More...

void	set_number (const long &mynumber)
	Set element number (for debugging/plotting) More...

virtual Node *	interpolating_node_pt (const unsigned &n, const int &value_id)

virtual double	local_one_d_fraction_of_interpolating_node (const unsigned &n1d, const unsigned &i, const int &value_id)

virtual Node *	get_interpolating_node_at_local_coordinate (const Vector< double > &s, const int &value_id)

virtual unsigned	ninterpolating_node (const int &value_id)

virtual unsigned	ninterpolating_node_1d (const int &value_id)

virtual void	interpolating_basis (const Vector< double > &s, Shape &psi, const int &value_id) const

virtual void	check_integrity (double &max_error)=0

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

void	assign_nodal_local_eqn_numbers (const bool &store_local_dof_pt)

virtual RefineableElement *	root_element_pt ()

virtual RefineableElement *	father_element_pt () const
	Return a pointer to the father element. More...

void	get_father_at_refinement_level (unsigned &refinement_level, RefineableElement *&father_at_reflevel_pt)

virtual void	initial_setup (Tree *const &adopted_father_pt=0, const unsigned &initial_p_order=0)

virtual void	pre_build (Mesh &mesh_pt, Vector< Node > &new_node_pt)
	Pre-build the element. More...

virtual void	setup_hanging_nodes (Vector< std::ofstream * > &output_stream)

virtual void	further_setup_hanging_nodes ()

void	get_dresidual_dnodal_coordinates (RankThreeTensor< double > &dresidual_dnodal_coordinates)

unsigned	nshape_controlling_nodes ()

std::map< Node *, unsigned >	shape_controlling_node_lookup ()

Public Member Functions inherited from oomph::ElementWithZ2ErrorEstimator
	ElementWithZ2ErrorEstimator ()
	Default empty constructor. More...

	ElementWithZ2ErrorEstimator (const ElementWithZ2ErrorEstimator &)=delete
	Broken copy constructor. More...

void	operator= (const ElementWithZ2ErrorEstimator &)=delete
	Broken assignment operator. More...

virtual unsigned	ncompound_fluxes ()

virtual void	compute_exact_Z2_error (std::ostream &outfile, FiniteElement::SteadyExactSolutionFctPt exact_flux_pt, double &error, double &norm)

virtual void	get_Z2_compound_flux_indices (Vector< unsigned > &flux_index)

virtual unsigned	nvertex_node () const =0
	Number of vertex nodes in the element. More...

virtual Node *	vertex_node_pt (const unsigned &j) const =0

virtual unsigned	nrecovery_order ()=0
	Order of recovery shape functions. More...

virtual double	geometric_jacobian (const Vector< double > &x)

Additional Inherited Members
Public Types inherited from oomph::PVDEquationsBase< DIM >
typedef void(*	IsotropicGrowthFctPt) (const Vector< double > &xi, double &gamma)

typedef double(*	PrestressFctPt) (const unsigned &i, const unsigned &j, const Vector< double > &xi)

typedef void(*	BodyForceFctPt) (const double &t, const Vector< double > &xi, Vector< double > &b)

Public Types inherited from oomph::SolidFiniteElement
typedef double(*	MultiplierFctPt) (const Vector< double > &xi)

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 Member Functions inherited from oomph::PVDEquationsBase< DIM >
static void	pin_redundant_nodal_solid_pressures (const Vector< GeneralisedElement * > &element_pt)

static void	unpin_all_solid_pressure_dofs (const Vector< GeneralisedElement * > &element_pt)
	Unpin all pressure dofs in elements listed in vector. More...

Static Public Member Functions inherited from oomph::RefineableElement
static double &	max_integrity_tolerance ()
	Max. allowed discrepancy in element integrity check. More...

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::PVDEquations< DIM >
void	get_stress (const DenseMatrix< double > &g, const DenseMatrix< double > &G, DenseMatrix< double > &sigma)

void	get_d_stress_dG_upper (const DenseMatrix< double > &g, const DenseMatrix< double > &G, const DenseMatrix< double > &sigma, RankFourTensor< double > &d_sigma_dG)

Protected Member Functions inherited from oomph::SolidFiniteElement
void	fill_in_generic_jacobian_for_solid_ic (Vector< double > &residuals, DenseMatrix< double > &jacobian, const unsigned &flag)

void	set_nnodal_lagrangian_type (const unsigned &nlagrangian_type)

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

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

void	describe_solid_local_dofs (std::ostream &out, const std::string &current_string) const
	Classifies dofs locally for solid specific aspects. More...

void	fill_in_jacobian_from_solid_position_by_fd (DenseMatrix< double > &jacobian)

virtual void	update_before_solid_position_fd ()

virtual void	reset_after_solid_position_fd ()

virtual void	update_in_solid_position_fd (const unsigned &i)

virtual void	reset_in_solid_position_fd (const unsigned &i)

Protected Member Functions inherited from oomph::FiniteElement
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 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

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)

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)

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 Member Functions inherited from oomph::RefineableSolidElement
void	assemble_local_to_lagrangian_jacobian (const DShape &dpsids, DenseMatrix< double > &jacobian) const

void	assemble_local_to_lagrangian_jacobian2 (const DShape &d2psids, DenseMatrix< double > &jacobian2) const

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

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

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

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

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

void	assign_hanging_local_eqn_numbers (const bool &store_local_dof_pt)
	Assign the local equation numbers for hanging node variables. More...

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

Static Protected Member Functions inherited from oomph::RefineableElement
static void	check_value_id (const int &n_continuously_interpolated_values, const int &value_id)

Protected Attributes inherited from oomph::PVDEquationsBase< DIM >
IsotropicGrowthFctPt	Isotropic_growth_fct_pt
	Pointer to isotropic growth function. More...

PrestressFctPt	Prestress_fct_pt
	Pointer to prestress function. More...

ConstitutiveLaw *	Constitutive_law_pt
	Pointer to the constitutive law. More...

double *	Lambda_sq_pt
	Timescale ratio (non-dim. density) More...

bool	Unsteady
	Flag that switches inertia on/off. More...

BodyForceFctPt	Body_force_fct_pt
	Pointer to body force function. More...

bool	Evaluate_jacobian_by_fd
	Use FD to evaluate Jacobian. More...

Protected Attributes inherited from oomph::SolidFiniteElement
MacroElement *	Undeformed_macro_elem_pt
	Pointer to the element's "undeformed" macro element (NULL by default) More...

SolidInitialCondition *	Solid_ic_pt
	Pointer to object that specifies the initial condition. More...

bool	Solve_for_consistent_newmark_accel_flag

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

Protected Attributes inherited from oomph::RefineableSolidElement
bool	Use_undeformed_macro_element_for_new_lagrangian_coords

Protected Attributes inherited from oomph::RefineableElement
Tree *	Tree_pt
	A pointer to a general tree object. More...

unsigned	Refine_level
	Refinement level. More...

bool	To_be_refined
	Flag for refinement. More...

bool	Refinement_is_enabled
	Flag to indicate suppression of any refinement. More...

bool	Sons_to_be_unrefined
	Flag for unrefinement. More...

long	Number
	Global element number – for plotting/validation purposes. More...

Static Protected Attributes inherited from oomph::PVDEquationsBase< DIM >
static double	Default_lambda_sq_value = 1.0
	Static default value for timescale ratio (1.0 – for natural scaling) More...

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

Static Protected Attributes inherited from oomph::RefineableElement
static double	Max_integrity_tolerance = 1.0e-8
	Max. allowed discrepancy in element integrity check. More...

Detailed Description

template<unsigned DIM>
class oomph::RefineablePVDEquations< DIM >

Class for Refineable PVD equations.

Constructor & Destructor Documentation

◆ RefineablePVDEquations()

template<unsigned DIM>

oomph::RefineablePVDEquations< DIM >::RefineablePVDEquations ( )

inline

Constructor.

       : PVDEquations<DIM>(),
         RefineableElement(),
         RefineableSolidElement(),
         ElementWithZ2ErrorEstimator()
     {
     }

Member Function Documentation

◆ fill_in_generic_contribution_to_residuals_pvd()

template<unsigned DIM>

void oomph::RefineablePVDEquations< DIM >::fill_in_generic_contribution_to_residuals_pvd	(	Vector< double > &	residuals,
		DenseMatrix< double > &	jacobian,
		const unsigned &	flag
	)

virtual

Call the residuals including hanging node cases.

Residuals for Refineable QPVDElements.

Reimplemented from oomph::PVDEquations< DIM >.

   {
 #ifdef PARANOID
     // Check if the constitutive equation requires the explicit imposition of an
     // incompressibility constraint
     if (this->Constitutive_law_pt->requires_incompressibility_constraint())
     {
       throw OomphLibError("RefineablePVDEquations cannot be used with "
                           "incompressible constitutive laws.",
                           OOMPH_CURRENT_FUNCTION,
                           OOMPH_EXCEPTION_LOCATION);
     }
 #endif
  
     // Simply set up initial condition?
     if (Solid_ic_pt != 0)
     {
       get_residuals_for_solid_ic(residuals);
       return;
     }
  
     // Find out how many nodes there are
     const unsigned n_node = nnode();
  
     // Find out how many positional dofs there are
     const unsigned n_position_type = this->nnodal_position_type();
  
     // Integers to store local equation numbers
     int local_eqn = 0;
  
     // Timescale ratio (non-dim density)
     double lambda_sq = this->lambda_sq();
  
     // Time factor
     double time_factor = 0.0;
     if (lambda_sq > 0)
     {
       time_factor = this->node_pt(0)->position_time_stepper_pt()->weight(2, 0);
     }
  
     // Set up memory for the shape functions
     Shape psi(n_node, n_position_type);
     DShape dpsidxi(n_node, n_position_type, DIM);
  
     // Set the value of n_intpt -- the number of integration points
     const unsigned n_intpt = integral_pt()->nweight();
  
     // Set the vector to hold the local coordinates in the element
     Vector<double> s(DIM);
  
     // Loop over the integration points
     for (unsigned ipt = 0; ipt < n_intpt; ipt++)
     {
       // Assign the values of s
       for (unsigned i = 0; i < DIM; ++i)
       {
         s[i] = integral_pt()->knot(ipt, i);
       }
  
       // Get the integral weight
       double w = integral_pt()->weight(ipt);
  
       // Call the derivatives of the shape functions (and get Jacobian)
       double J = dshape_lagrangian_at_knot(ipt, psi, dpsidxi);
  
       // Calculate interpolated values of the derivative of global position
       // wrt lagrangian coordinates
       DenseMatrix<double> interpolated_G(DIM, DIM, 0.0);
  
       // Setup memory for accelerations
       Vector<double> accel(DIM, 0.0);
  
       // Storage for Lagrangian coordinates (initialised to zero)
       Vector<double> interpolated_xi(DIM, 0.0);
  
       // Calculate displacements and derivatives and lagrangian coordinates
       for (unsigned l = 0; l < n_node; l++)
       {
         // Loop over positional dofs
         for (unsigned k = 0; k < n_position_type; k++)
         {
           double psi_ = psi(l, k);
           // Loop over displacement components (deformed position)
           for (unsigned i = 0; i < DIM; i++)
           {
             // Calculate the Lagrangian coordinates and the accelerations
             interpolated_xi[i] += lagrangian_position_gen(l, k, i) * psi_;
  
             // Only compute accelerations if inertia is switched on
             // otherwise the timestepper might not be able to
             // work out dx_gen_dt(2,...)
             if ((lambda_sq > 0.0) && (this->Unsteady))
             {
               accel[i] += dnodal_position_gen_dt(2, l, k, i) * psi_;
             }
  
             // Loop over derivative directions
             for (unsigned j = 0; j < DIM; j++)
             {
               interpolated_G(j, i) +=
                 this->nodal_position_gen(l, k, i) * dpsidxi(l, k, j);
             }
           }
         }
       }
  
       // Get isotropic growth factor
       double gamma = 1.0;
       this->get_isotropic_growth(ipt, s, interpolated_xi, gamma);
  
       // Get body force at current time
       Vector<double> b(DIM);
       this->body_force(interpolated_xi, b);
  
       // We use Cartesian coordinates as the reference coordinate
       // system. In this case the undeformed metric tensor is always
       // the identity matrix -- stretched by the isotropic growth
       double diag_entry = pow(gamma, 2.0 / double(DIM));
       DenseMatrix<double> g(DIM);
       for (unsigned i = 0; i < DIM; i++)
       {
         for (unsigned j = 0; j < DIM; j++)
         {
           if (i == j)
           {
             g(i, j) = diag_entry;
           }
           else
           {
             g(i, j) = 0.0;
           }
         }
       }
  
       // Premultiply the undeformed volume ratio (from the isotropic
       // growth), the weights and the Jacobian
       double W = gamma * w * J;
  
       // Declare and calculate the deformed metric tensor
       DenseMatrix<double> G(DIM);
  
       // Assign values of G
       for (unsigned i = 0; i < DIM; i++)
       {
         // Do upper half of matrix
         for (unsigned j = i; j < DIM; j++)
         {
           // Initialise G(i,j) to zero
           G(i, j) = 0.0;
           // Now calculate the dot product
           for (unsigned k = 0; k < DIM; k++)
           {
             G(i, j) += interpolated_G(i, k) * interpolated_G(j, k);
           }
         }
         // Matrix is symmetric so just copy lower half
         for (unsigned j = 0; j < i; j++)
         {
           G(i, j) = G(j, i);
         }
       }
  
       // Now calculate the stress tensor from the constitutive law
       DenseMatrix<double> sigma(DIM);
       this->get_stress(g, G, sigma);
  
       // Get stress derivative by FD only needed for Jacobian
       //-----------------------------------------------------
  
       // Stress derivative
       RankFourTensor<double> d_stress_dG(DIM, DIM, DIM, DIM, 0.0);
       // Derivative of metric tensor w.r.t. to nodal coords
       RankFiveTensor<double> d_G_dX(
         n_node, n_position_type, DIM, DIM, DIM, 0.0);
  
       // Get Jacobian too?
       if (flag == 1)
       {
         // Derivative of metric tensor w.r.t. to discrete positional dofs
         // NOTE: Since G is symmetric we only compute the upper triangle
         //       and DO NOT copy the entries across. Subsequent computations
         //       must (and, in fact, do) therefore only operate with upper
         //       triangular entries
         for (unsigned ll = 0; ll < n_node; ll++)
         {
           for (unsigned kk = 0; kk < n_position_type; kk++)
           {
             for (unsigned ii = 0; ii < DIM; ii++)
             {
               for (unsigned aa = 0; aa < DIM; aa++)
               {
                 for (unsigned bb = aa; bb < DIM; bb++)
                 {
                   d_G_dX(ll, kk, ii, aa, bb) =
                     interpolated_G(aa, ii) * dpsidxi(ll, kk, bb) +
                     interpolated_G(bb, ii) * dpsidxi(ll, kk, aa);
                 }
               }
             }
           }
         }
  
         // Get the "upper triangular"
         // entries of the derivatives of the stress tensor with
         // respect to G
         this->get_d_stress_dG_upper(g, G, sigma, d_stress_dG);
       }
  
  
       // Add pre-stress
       for (unsigned i = 0; i < DIM; i++)
       {
         for (unsigned j = 0; j < DIM; j++)
         {
           sigma(i, j) += this->prestress(i, j, interpolated_xi);
         }
       }
  
       //=====EQUATIONS OF ELASTICITY FROM PRINCIPLE OF VIRTUAL
       // DISPLACEMENTS========
  
  
       // Default setting for non-hanging node
       unsigned n_master = 1;
       double hang_weight = 1.0;
  
       // Loop over the test functions, nodes of the element
       for (unsigned l = 0; l < n_node; l++)
       {
         // Get pointer to local node l
         Node* local_node_pt = node_pt(l);
  
         // Cache hang status
         bool is_hanging = local_node_pt->is_hanging();
  
         // If the node is a hanging node
         if (is_hanging)
         {
           n_master = local_node_pt->hanging_pt()->nmaster();
         }
         // Otherwise the node is its own master
         else
         {
           n_master = 1;
         }
  
  
         // Storage for local equation numbers at node indexed by
         // type and direction
         DenseMatrix<int> position_local_eqn_at_node(n_position_type, DIM);
  
         // Loop over the master nodes
         for (unsigned m = 0; m < n_master; m++)
         {
           if (is_hanging)
           {
             // Find the equation numbers
             position_local_eqn_at_node = local_position_hang_eqn(
               local_node_pt->hanging_pt()->master_node_pt(m));
  
             // Find the hanging node weight
             hang_weight = local_node_pt->hanging_pt()->master_weight(m);
           }
           else
           {
             // Loop of types of dofs
             for (unsigned k = 0; k < n_position_type; k++)
             {
               // Loop over the displacement components
               for (unsigned i = 0; i < DIM; i++)
               {
                 position_local_eqn_at_node(k, i) = position_local_eqn(l, k, i);
               }
             }
  
             // Hang weight is one
             hang_weight = 1.0;
           }
  
           // Loop of types of dofs
           for (unsigned k = 0; k < n_position_type; k++)
           {
             // Offset for faster access
             const unsigned offset5 = dpsidxi.offset(l, k);
  
             // Loop over the displacement components
             for (unsigned i = 0; i < DIM; i++)
             {
               local_eqn = position_local_eqn_at_node(k, i);
  
               /*IF it's not a boundary condition*/
               if (local_eqn >= 0)
               {
                 // Initialise the contribution
                 double sum = 0.0;
  
                 // Acceleration and body force
                 sum += (lambda_sq * accel[i] - b[i]) * psi(l, k);
  
                 // Stress term
                 for (unsigned a = 0; a < DIM; a++)
                 {
                   unsigned count = offset5;
                   for (unsigned b = 0; b < DIM; b++)
                   {
                     // Add the stress terms to the residuals
                     sum += sigma(a, b) * interpolated_G(a, i) *
                            dpsidxi.raw_direct_access(count);
                     ++count;
                   }
                 }
                 residuals[local_eqn] += W * sum * hang_weight;
  
  
                 // Get Jacobian too?
                 if (flag == 1)
                 {
                   // Offset for faster access in general stress loop
                   const unsigned offset1 = d_G_dX.offset(l, k, i);
  
                   // Default setting for non-hanging node
                   unsigned nn_master = 1;
                   double hhang_weight = 1.0;
  
                   // Loop over the nodes of the element again
                   for (unsigned ll = 0; ll < n_node; ll++)
                   {
                     // Get pointer to local node ll
                     Node* llocal_node_pt = node_pt(ll);
  
                     // Cache hang status
                     bool iis_hanging = llocal_node_pt->is_hanging();
  
                     // If the node is a hanging node
                     if (iis_hanging)
                     {
                       nn_master = llocal_node_pt->hanging_pt()->nmaster();
                     }
                     // Otherwise the node is its own master
                     else
                     {
                       nn_master = 1;
                     }
  
  
                     // Storage for local unknown numbers at node indexed by
                     // type and direction
                     DenseMatrix<int> position_local_unk_at_node(n_position_type,
                                                                 DIM);
  
                     // Loop over the master nodes
                     for (unsigned mm = 0; mm < nn_master; mm++)
                     {
                       if (iis_hanging)
                       {
                         // Find the unknown numbers
                         position_local_unk_at_node = local_position_hang_eqn(
                           llocal_node_pt->hanging_pt()->master_node_pt(mm));
  
                         // Find the hanging node weight
                         hhang_weight =
                           llocal_node_pt->hanging_pt()->master_weight(mm);
                       }
                       else
                       {
                         // Loop of types of dofs
                         for (unsigned kk = 0; kk < n_position_type; kk++)
                         {
                           // Loop over the displacement components
                           for (unsigned ii = 0; ii < DIM; ii++)
                           {
                             position_local_unk_at_node(kk, ii) =
                               position_local_eqn(ll, kk, ii);
                           }
                         }
  
                         // Hang weight is one
                         hhang_weight = 1.0;
                       }
  
  
                       // Loop of types of dofs again
                       for (unsigned kk = 0; kk < n_position_type; kk++)
                       {
                         // Loop over the displacement components again
                         for (unsigned ii = 0; ii < DIM; ii++)
                         {
                           // Get the number of the unknown
                           int local_unknown =
                             position_local_unk_at_node(kk, ii);
  
  
                           /*IF it's not a boundary condition*/
                           if (local_unknown >= 0)
                           {
                             // Offset for faster access in general stress loop
                             const unsigned offset2 = d_G_dX.offset(ll, kk, ii);
                             const unsigned offset4 = dpsidxi.offset(ll, kk);
  
  
                             // General stress term
                             //--------------------
                             double sum = 0.0;
                             unsigned count1 = offset1;
                             for (unsigned a = 0; a < DIM; a++)
                             {
                               // Bump up direct access because we're only
                               // accessing upper triangle
                               count1 += a;
                               for (unsigned b = a; b < DIM; b++)
                               {
                                 double factor =
                                   d_G_dX.raw_direct_access(count1);
                                 if (a == b) factor *= 0.5;
  
                                 // Offset for faster access
                                 unsigned offset3 = d_stress_dG.offset(a, b);
                                 unsigned count2 = offset2;
                                 unsigned count3 = offset3;
  
                                 for (unsigned aa = 0; aa < DIM; aa++)
                                 {
                                   // Bump up direct access because we're only
                                   // accessing upper triangle
                                   count2 += aa;
                                   count3 += aa;
  
                                   // Only upper half of derivatives w.r.t.
                                   // symm tensor
                                   for (unsigned bb = aa; bb < DIM; bb++)
                                   {
                                     sum +=
                                       factor *
                                       d_stress_dG.raw_direct_access(count3) *
                                       d_G_dX.raw_direct_access(count2);
                                     ++count2;
                                     ++count3;
                                   }
                                 }
                                 ++count1;
                               }
                             }
  
                             // Multiply by weight and add contribution
                             // (Add directly because this bit is nonsymmetric)
                             jacobian(local_eqn, local_unknown) +=
                               sum * W * hang_weight * hhang_weight;
  
                             // Only upper triangle (no separate test for bc as
                             // local_eqn is already nonnegative)
                             if ((i == ii) && (local_unknown >= local_eqn))
                             {
                               // Initialise the contribution
                               double sum = 0.0;
  
                               // Inertia term
                               sum += lambda_sq * time_factor * psi(ll, kk) *
                                      psi(l, k);
  
                               // Stress term
                               unsigned count4 = offset4;
                               for (unsigned a = 0; a < DIM; a++)
                               {
                                 // Cache term
                                 const double factor =
                                   dpsidxi.raw_direct_access(count4); // ll ,kk
                                 ++count4;
  
                                 unsigned count5 = offset5;
                                 for (unsigned b = 0; b < DIM; b++)
                                 {
                                   sum +=
                                     sigma(a, b) * factor *
                                     dpsidxi.raw_direct_access(count5); // l  ,k
                                   ++count5;
                                 }
                               }
  
                               // Multiply by weights to form contribution
                               double sym_entry =
                                 sum * W * hang_weight * hhang_weight;
                               // Add contribution to jacobian
                               jacobian(local_eqn, local_unknown) += sym_entry;
                               // Add to lower triangular entries
                               if (local_eqn != local_unknown)
                               {
                                 jacobian(local_unknown, local_eqn) += sym_entry;
                               }
                             }
                           } // End of if not boundary condition
                         }
                       }
                     }
                   }
                 }
  
               } // End of if not boundary condition
  
             } // End of loop over coordinate directions
           } // End of loop over type of dof
         } // End of loop over master nodes
       } // End of loop over nodes
     } // End of loop over integration points
   }

References a, b, Global_Parameters::body_force(), Constitutive::Constitutive_law_pt, DIM, G, mathsFunc::gamma(), oomph::Node::hanging_pt(), i, oomph::Node::is_hanging(), J, j, k, m, oomph::HangInfo::master_node_pt(), oomph::HangInfo::master_weight(), oomph::HangInfo::nmaster(), oomph::RankFourTensor< T >::offset(), oomph::DShape::offset(), oomph::RankFiveTensor< T >::offset(), OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION, Eigen::bfloat16_impl::pow(), oomph::RankFourTensor< T >::raw_direct_access(), oomph::RankFiveTensor< T >::raw_direct_access(), oomph::DShape::raw_direct_access(), oomph::ConstitutiveLaw::requires_incompressibility_constraint(), s, calibrate::sigma, w, and oomph::QuadTreeNames::W.

◆ further_build()

template<unsigned DIM>

void oomph::RefineablePVDEquations< DIM >::further_build ( )

inlinevirtual

Further build function, pass the pointers down to the sons.

Reimplemented from oomph::RefineableSolidElement.

     {
       RefineablePVDEquations<DIM>* cast_father_element_pt =
         dynamic_cast<RefineablePVDEquations<DIM>*>(this->father_element_pt());
  
       // Do whatever needs to be done in the base class
       RefineableSolidElement::further_build();
  
       // Set pointer to isotropic growth function
       this->Isotropic_growth_fct_pt =
         cast_father_element_pt->isotropic_growth_fct_pt();
  
       // Set pointer to body force function
       this->Body_force_fct_pt = cast_father_element_pt->body_force_fct_pt();
  
       // Set pointer to the contitutive law
       this->Constitutive_law_pt = cast_father_element_pt->constitutive_law_pt();
  
       // Set the timescale ratio (non-dim. density)
       this->Lambda_sq_pt = cast_father_element_pt->lambda_sq_pt();
  
       // Set the flag that switches inertia on/off
       this->Unsteady = cast_father_element_pt->is_inertia_enabled();
  
       // Evaluation of Jacobian by same method as father
       this->Evaluate_jacobian_by_fd =
         cast_father_element_pt->is_jacobian_evaluated_by_fd();
     }

Referenced by oomph::RefineableQDPVDElement< DIM, NNODE_1D >::further_build().

◆ get_interpolated_values() [1/2]

template<unsigned DIM>

void oomph::RefineablePVDEquations< DIM >::get_interpolated_values	(	const unsigned &	t,
		const Vector< double > &	s,
		Vector< double > &	values
	)

inlinevirtual

No values are interpolated in this element (pure solid)

Implements oomph::RefineableElement.

     {
       values.clear();
     }

◆ get_interpolated_values() [2/2]

template<unsigned DIM>

void oomph::RefineablePVDEquations< DIM >::get_interpolated_values	(	const Vector< double > &	s,
		Vector< double > &	values
	)

inlinevirtual

No values are interpolated in this element (pure solid)

Reimplemented from oomph::RefineableElement.

     {
       values.clear();
     }

◆ get_Z2_flux()

template<unsigned DIM>

void oomph::RefineablePVDEquations< DIM >::get_Z2_flux	(	const Vector< double > &	s,
		Vector< double > &	flux
	)

inlinevirtual

Get 'flux' for Z2 error recovery: Upper triangular entries in strain tensor.

Implements oomph::ElementWithZ2ErrorEstimator.

     {
 #ifdef PARANOID
       unsigned num_entries = DIM + ((DIM * DIM) - DIM) / 2;
       if (flux.size() != num_entries)
       {
         std::ostringstream error_message;
         error_message << "The flux vector has the wrong number of entries, "
                       << flux.size() << ", whereas it should be " << num_entries
                       << std::endl;
         throw OomphLibError(error_message.str(),
                             OOMPH_CURRENT_FUNCTION,
                             OOMPH_EXCEPTION_LOCATION);
       }
 #endif
  
       // Get strain matrix
       DenseMatrix<double> strain(DIM);
       this->get_strain(s, strain);
  
       // Pack into flux Vector
       unsigned icount = 0;
  
       // Start with diagonal terms
       for (unsigned i = 0; i < DIM; i++)
       {
         flux[icount] = strain(i, i);
         icount++;
       }
  
       // Off diagonals row by row
       for (unsigned i = 0; i < DIM; i++)
       {
         for (unsigned j = i + 1; j < DIM; j++)
         {
           flux[icount] = strain(i, j);
           icount++;
         }
       }
     }

References DIM, ProblemParameters::flux(), oomph::PVDEquationsBase< DIM >::get_strain(), i, j, OOMPH_CURRENT_FUNCTION, and OOMPH_EXCEPTION_LOCATION.

◆ ncont_interpolated_values()

template<unsigned DIM>

unsigned oomph::RefineablePVDEquations< DIM >::ncont_interpolated_values ( ) const

inlinevirtual

Number of continuously interpolated values: 0 (pure solid problem)

Implements oomph::RefineableElement.

     {
       return 0;
     }

◆ num_Z2_flux_terms()

template<unsigned DIM>

unsigned oomph::RefineablePVDEquations< DIM >::num_Z2_flux_terms ( )

inlinevirtual

Number of 'flux' terms for Z2 error estimation.

Implements oomph::ElementWithZ2ErrorEstimator.

     {
       // DIM Diagonal strain rates and DIM*(DIM-1)/2 off diagonal terms
       return DIM + DIM * (DIM - 1) / 2;
     }

References DIM.

◆ solid_pressure_node_pt()

template<unsigned DIM>

virtual Node* oomph::RefineablePVDEquations< DIM >::solid_pressure_node_pt ( const unsigned & l )

inlinevirtual

     {
       return 0;
     }

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

Public Member Functions

Additional Inherited Members

Detailed Description

template<unsigned DIM> class oomph::RefineablePVDEquations< DIM >

Constructor & Destructor Documentation

◆ RefineablePVDEquations()

Member Function Documentation

◆ fill_in_generic_contribution_to_residuals_pvd()

◆ further_build()

◆ get_interpolated_values() [1/2]

◆ get_interpolated_values() [2/2]

◆ get_Z2_flux()

◆ ncont_interpolated_values()

◆ num_Z2_flux_terms()

◆ solid_pressure_node_pt()

template<unsigned DIM>
class oomph::RefineablePVDEquations< DIM >