Public Member Functions | Private Member Functions | List of all members
oomph::RefineablePoissonEquations< DIM > Class Template Reference

#include <refineable_poisson_elements.h>

+ Inheritance diagram for oomph::RefineablePoissonEquations< DIM >:

Public Member Functions

 RefineablePoissonEquations ()
 Constructor, simply call other constructors. More...
 
 RefineablePoissonEquations (const RefineablePoissonEquations< DIM > &dummy)=delete
 Broken copy constructor. More...
 
void operator= (const RefineablePoissonEquations< DIM > &)=delete
 Broken assignment operator. 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)
 Get 'flux' for Z2 error recovery: Standard flux.from Poisson equations. More...
 
void compute_exact_Z2_error (std::ostream &outfile, FiniteElement::SteadyExactSolutionFctPt exact_flux_pt, double &error, double &norm)
 Get error against and norm of exact flux. More...
 
void get_interpolated_values (const Vector< double > &s, Vector< double > &values)
 
void get_interpolated_values (const unsigned &t, const Vector< double > &s, Vector< double > &values)
 
void further_build ()
 Further build: Copy source function pointer from father element. More...
 
- Public Member Functions inherited from oomph::PoissonEquations< DIM >
 PoissonEquations ()
 Constructor (must initialise the Source_fct_pt to null) More...
 
 PoissonEquations (const PoissonEquations &dummy)=delete
 Broken copy constructor. More...
 
void operator= (const PoissonEquations &)=delete
 Broken assignment operator. More...
 
virtual unsigned u_index_poisson () const
 
void point_output_data (const Vector< double > &s, Vector< double > &data)
 
unsigned nscalar_paraview () const
 
void scalar_value_paraview (std::ofstream &file_out, const unsigned &i, const unsigned &nplot) const
 
std::string scalar_name_paraview (const unsigned &i) const
 
void scalar_value_fct_paraview (std::ofstream &file_out, const unsigned &i, const unsigned &nplot, FiniteElement::SteadyExactSolutionFctPt exact_soln_pt) const
 
void output (std::ostream &outfile)
 Output with default number of plot points. More...
 
void output (std::ostream &outfile, const unsigned &n_plot)
 
void output (FILE *file_pt)
 C_style output with default number of plot points. More...
 
void output (FILE *file_pt, const unsigned &n_plot)
 
void output_fct (std::ostream &outfile, const unsigned &n_plot, FiniteElement::SteadyExactSolutionFctPt exact_soln_pt)
 
virtual void output_fct (std::ostream &outfile, const unsigned &n_plot, const double &time, FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt)
 
void compute_norm (double &norm)
 Compute norm of solution: square of the L2 norm. More...
 
void compute_error (std::ostream &outfile, FiniteElement::SteadyExactSolutionFctPt exact_soln_pt, double &error, double &norm)
 Get error against and norm of exact solution. More...
 
void compute_error (std::ostream &outfile, FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt, const double &time, double &error, double &norm)
 Dummy, time dependent error checker. More...
 
PoissonSourceFctPt & source_fct_pt ()
 Access function: Pointer to source function. More...
 
PoissonSourceFctPt source_fct_pt () const
 Access function: Pointer to source function. Const version. More...
 
PoissonSourceFctGradientPt & source_fct_gradient_pt ()
 Access function: Pointer to gradient of source function. More...
 
PoissonSourceFctGradientPt source_fct_gradient_pt () const
 Access function: Pointer to gradient source function. Const version. More...
 
virtual void get_source_poisson (const unsigned &ipt, const Vector< double > &x, double &source) const
 
virtual void get_source_gradient_poisson (const unsigned &ipt, const Vector< double > &x, Vector< double > &gradient) const
 
void get_flux (const Vector< double > &s, Vector< double > &flux) const
 Get flux: flux[i] = du/dx_i. More...
 
void get_dflux_dnodal_u (const Vector< double > &s, Vector< Vector< double >> &dflux_dnodal_u) const
 
void fill_in_contribution_to_residuals (Vector< double > &residuals)
 Add the element's contribution to its residual vector (wrapper) More...
 
void fill_in_contribution_to_jacobian (Vector< double > &residuals, DenseMatrix< double > &jacobian)
 
virtual double interpolated_u_poisson (const Vector< double > &s) const
 
unsigned self_test ()
 Self-test: Return 0 for OK. More...
 
- 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 describe_local_dofs (std::ostream &out, const std::string &current_string) const
 
virtual void describe_nodal_local_dofs (std::ostream &out, const std::string &current_string) const
 
virtual void assign_all_generic_local_eqn_numbers (const bool &store_local_dof_pt)
 
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...
 
virtual Node * construct_node (const unsigned &n)
 
virtual Node * construct_node (const unsigned &n, TimeStepper *const &time_stepper_pt)
 
virtual Node * construct_boundary_node (const unsigned &n)
 
virtual Node * construct_boundary_node (const unsigned &n, TimeStepper *const &time_stepper_pt)
 
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_geometric_data (std::set< Data * > &geometric_data_pt)
 
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
 
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 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 void output (const unsigned &t, std::ostream &outfile, const unsigned &n_plot) const
 
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, 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 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)
 
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::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 unsigned ncont_interpolated_values () const =0
 
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 ()
 
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 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)
 

Private Member Functions

void fill_in_generic_residual_contribution_poisson (Vector< double > &residuals, DenseMatrix< double > &jacobian, const unsigned &flag)
 
virtual void get_dresidual_dnodal_coordinates (RankThreeTensor< double > &dresidual_dnodal_coordinates)
 

Additional Inherited Members

- Public Types inherited from oomph::PoissonEquations< DIM >
typedef void(* PoissonSourceFctPt) (const Vector< double > &x, double &f)
 
typedef void(* PoissonSourceFctGradientPt) (const Vector< double > &x, Vector< double > &gradient)
 
- 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::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::PoissonEquations< DIM >
virtual double dshape_and_dtest_eulerian_poisson (const Vector< double > &s, Shape &psi, DShape &dpsidx, Shape &test, DShape &dtestdx) const =0
 
virtual double dshape_and_dtest_eulerian_at_knot_poisson (const unsigned &ipt, Shape &psi, DShape &dpsidx, Shape &test, DShape &dtestdx) const =0
 
virtual double dshape_and_dtest_eulerian_at_knot_poisson (const unsigned &ipt, Shape &psi, DShape &dpsidx, RankFourTensor< double > &d_dpsidx_dX, Shape &test, DShape &dtestdx, RankFourTensor< double > &d_dtestdx_dX, DenseMatrix< double > &djacobian_dX) const =0
 
- 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::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::PoissonEquations< DIM >
PoissonSourceFctPt Source_fct_pt
 Pointer to source function: More...
 
PoissonSourceFctGradientPt Source_fct_gradient_pt
 Pointer to gradient of source function. More...
 
- 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::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::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::RefineablePoissonEquations< DIM >

//////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////// Refineable version of Poisson equations

Constructor & Destructor Documentation

◆ RefineablePoissonEquations() [1/2]

template<unsigned DIM>
oomph::RefineablePoissonEquations< DIM >::RefineablePoissonEquations ( )
inline

Constructor, simply call other constructors.

63  : PoissonEquations<DIM>(),
64  RefineableElement(),
65  ElementWithZ2ErrorEstimator()
66  {
67  }
oomph::ElementWithZ2ErrorEstimator::ElementWithZ2ErrorEstimator
ElementWithZ2ErrorEstimator()
Default empty constructor.
Definition: error_estimator.h:82
oomph::RefineableElement::RefineableElement
RefineableElement()
Definition: refineable_elements.h:188

◆ RefineablePoissonEquations() [2/2]

template<unsigned DIM>
oomph::RefineablePoissonEquations< DIM >::RefineablePoissonEquations ( const RefineablePoissonEquations< DIM > &  dummy)
delete

Broken copy constructor.

Member Function Documentation

◆ compute_exact_Z2_error()

template<unsigned DIM>
void oomph::RefineablePoissonEquations< DIM >::compute_exact_Z2_error ( std::ostream &  outfile,
FiniteElement::SteadyExactSolutionFctPt  exact_flux_pt,
double &  error,
double &  norm 
)
virtual

Get error against and norm of exact flux.

Validate against exact flux. Flux is provided via function pointer. Plot error at a given number of plot points.

Reimplemented from oomph::ElementWithZ2ErrorEstimator.

42  {
43  // Initialise
44  error = 0.0;
45  norm = 0.0;
46 
47  // Vector of local coordinates
48  Vector<double> s(DIM);
49 
50  // Vector of global coordinates
51  Vector<double> x(DIM);
52 
53  // Find out how many nodes there are in the element
54  const unsigned n_node = nnode();
55 
56  // Allocate storage for shape functions
57  Shape psi(n_node);
58 
59  // Set the value of n_intpt
60  const unsigned n_intpt = integral_pt()->nweight();
61 
62  // Tecplot
63  outfile << "ZONE" << std::endl;
64 
65  // Exact flux Vector (size is DIM)
66  Vector<double> exact_flux(DIM);
67 
68  // Loop over the integration points
69  for (unsigned ipt = 0; ipt < n_intpt; ipt++)
70  {
71  // Assign values of s
72  for (unsigned i = 0; i < DIM; i++)
73  {
74  s[i] = integral_pt()->knot(ipt, i);
75  }
76 
77  // Get the integral weight
78  double w = integral_pt()->weight(ipt);
79 
80  // Get jacobian of mapping
81  double J = J_eulerian(s);
82 
83  // Premultiply the weights and the Jacobian
84  double W = w * J;
85 
86  // Get x position as Vector
87  interpolated_x(s, x);
88 
89  // Allocate storage for FE flux Vector
90  Vector<double> fe_flux(DIM);
91 
92  // Get FE flux as Vector
93  get_Z2_flux(s, fe_flux);
94 
95  // Get exact flux at this point
96  (*exact_flux_pt)(x, exact_flux);
97 
98  // Output x,y,...
99  for (unsigned i = 0; i < DIM; i++)
100  {
101  outfile << x[i] << " ";
102  }
103 
104  // Output exact flux
105  for (unsigned i = 0; i < DIM; i++)
106  {
107  outfile << exact_flux[i] << " ";
108  }
109 
110  // Output error
111  for (unsigned i = 0; i < DIM; i++)
112  {
113  outfile << exact_flux[i] - fe_flux[i] << " ";
114  }
115  outfile << std::endl;
116 
117  // Add to RMS error:
118  double sum = 0.0;
119  double sum2 = 0.0;
120  for (unsigned i = 0; i < DIM; i++)
121  {
122  sum += (fe_flux[i] - exact_flux[i]) * (fe_flux[i] - exact_flux[i]);
123  sum2 += exact_flux[i] * exact_flux[i];
124  }
125  error += sum * W;
126  norm += sum2 * W;
127 
128  } // End of loop over the integration points
129  }
i
int i
Definition: BiCGSTAB_step_by_step.cpp:9
J
JacobiRotation< float > J
Definition: Jacobi_makeJacobi.cpp:3
w
RowVector3d w
Definition: Matrix_resize_int.cpp:3
oomph::FiniteElement::interpolated_x
virtual double interpolated_x(const Vector< double > &s, const unsigned &i) const
Return FE interpolated coordinate x[i] at local coordinate s.
Definition: elements.cc:3962
oomph::FiniteElement::nnode
unsigned nnode() const
Return the number of nodes.
Definition: elements.h:2210
oomph::FiniteElement::integral_pt
Integral *const & integral_pt() const
Return the pointer to the integration scheme (const version)
Definition: elements.h:1963
oomph::FiniteElement::J_eulerian
virtual double J_eulerian(const Vector< double > &s) const
Definition: elements.cc:4103
oomph::Integral::knot
virtual double knot(const unsigned &i, const unsigned &j) const =0
Return local coordinate s[j] of i-th integration point.
oomph::Integral::nweight
virtual unsigned nweight() const =0
Return the number of integration points of the scheme.
oomph::Integral::weight
virtual double weight(const unsigned &i) const =0
Return weight of i-th integration point.
oomph::RefineablePoissonEquations::get_Z2_flux
void get_Z2_flux(const Vector< double > &s, Vector< double > &flux)
Get 'flux' for Z2 error recovery: Standard flux.from Poisson equations.
Definition: refineable_poisson_elements.h:83
s
RealScalar s
Definition: level1_cplx_impl.h:130
DIM
#define DIM
Definition: linearised_navier_stokes_elements.h:44
calibrate.error
int error
Definition: calibrate.py:297
oomph::QuadTreeNames::W
@ W
Definition: quadtree.h:63
plotDoE.x
list x
Definition: plotDoE.py:28

References DIM, calibrate::error, get_Z2_flux(), i, J, s, w, oomph::QuadTreeNames::W, and plotDoE::x.

◆ fill_in_generic_residual_contribution_poisson()

template<unsigned DIM>
void oomph::RefineablePoissonEquations< DIM >::fill_in_generic_residual_contribution_poisson ( Vector< double > &  residuals,
DenseMatrix< double > &  jacobian,
const unsigned &  flag 
)
privatevirtual

Add element's contribution to elemental residual vector and/or Jacobian matrix flag=1: compute both flag=0: compute only residual vector

Add element's contribution to the elemental residual vector and/or Jacobian matrix. flag=1: compute both flag=0: compute only residual vector

Reimplemented from oomph::PoissonEquations< DIM >.

143  {
144  // Find out how many nodes there are in the element
145  unsigned n_node = nnode();
146 
147  // Set up memory for the shape and test functions
148  Shape psi(n_node), test(n_node);
149  DShape dpsidx(n_node, DIM), dtestdx(n_node, DIM);
150 
151  // Set the value of n_intpt
152  unsigned n_intpt = integral_pt()->nweight();
153 
154  // The local index at which the poisson variable is stored
155  unsigned u_nodal_index = this->u_index_poisson();
156 
157  // Integers to store the local equation and unknown numbers
158  int local_eqn = 0, local_unknown = 0;
159 
160  // Local storage for pointers to hang_info objects
161  HangInfo *hang_info_pt = 0, *hang_info2_pt = 0;
162 
163  // Loop over the integration points
164  for (unsigned ipt = 0; ipt < n_intpt; ipt++)
165  {
166  // Get the integral weight
167  double w = integral_pt()->weight(ipt);
168 
169  // Call the derivatives of the shape and test functions
170  double J = this->dshape_and_dtest_eulerian_at_knot_poisson(
171  ipt, psi, dpsidx, test, dtestdx);
172 
173  // Premultiply the weights and the Jacobian
174  double W = w * J;
175 
176  // Position and gradient
177  Vector<double> interpolated_x(DIM, 0.0);
178  Vector<double> interpolated_dudx(DIM, 0.0);
179 
180  // Calculate function value and derivatives:
181  //-----------------------------------------
182 
183  // Loop over nodes
184  for (unsigned l = 0; l < n_node; l++)
185  {
186  // Get the poisson value from the node
187  //(hanging-ness will be taken into account
188  double u_value = this->nodal_value(l, u_nodal_index);
189 
190  // Loop over directions
191  for (unsigned j = 0; j < DIM; j++)
192  {
193  interpolated_x[j] += nodal_position(l, j) * psi(l);
194  interpolated_dudx[j] += u_value * dpsidx(l, j);
195  }
196  }
197 
198  // Get body force
199  double source;
200  this->get_source_poisson(ipt, interpolated_x, source);
201 
202 
203  // Assemble residuals and Jacobian
204 
205  // Loop over the nodes for the test functions
206  for (unsigned l = 0; l < n_node; l++)
207  {
208  // Local variables used to store the number of master nodes and the
209  // weight associated with the shape function if the node is hanging
210  unsigned n_master = 1;
211  double hang_weight = 1.0;
212 
213  // Local bool (is the node hanging)
214  bool is_node_hanging = this->node_pt(l)->is_hanging();
215 
216  // If the node is hanging, get the number of master nodes
217  if (is_node_hanging)
218  {
219  hang_info_pt = this->node_pt(l)->hanging_pt();
220  n_master = hang_info_pt->nmaster();
221  }
222  // Otherwise there is just one master node, the node itself
223  else
224  {
225  n_master = 1;
226  }
227 
228  // Loop over the master nodes
229  for (unsigned m = 0; m < n_master; m++)
230  {
231  // Get the local equation number and hang_weight
232  // If the node is hanging
233  if (is_node_hanging)
234  {
235  // Read out the local equation number from the m-th master node
236  local_eqn = this->local_hang_eqn(hang_info_pt->master_node_pt(m),
237  u_nodal_index);
238 
239  // Read out the weight from the master node
240  hang_weight = hang_info_pt->master_weight(m);
241  }
242  // If the node is not hanging
243  else
244  {
245  // The local equation number comes from the node itself
246  local_eqn = this->nodal_local_eqn(l, u_nodal_index);
247 
248  // The hang weight is one
249  hang_weight = 1.0;
250  }
251 
252  // If the nodal equation is not a boundary condition
253  if (local_eqn >= 0)
254  {
255  // Add body force/source term here
256  residuals[local_eqn] += source * test(l) * W * hang_weight;
257 
258  // The Poisson bit itself
259  for (unsigned k = 0; k < DIM; k++)
260  {
261  residuals[local_eqn] +=
262  interpolated_dudx[k] * dtestdx(l, k) * W * hang_weight;
263  }
264 
265  // Calculate the Jacobian
266  if (flag)
267  {
268  // Local variables to store the number of master nodes
269  // and the weights associated with each hanging node
270  unsigned n_master2 = 1;
271  double hang_weight2 = 1.0;
272 
273  // Loop over the nodes for the variables
274  for (unsigned l2 = 0; l2 < n_node; l2++)
275  {
276  // Local bool (is the node hanging)
277  bool is_node2_hanging = this->node_pt(l2)->is_hanging();
278 
279  // If the node is hanging, get the number of master nodes
280  if (is_node2_hanging)
281  {
282  hang_info2_pt = this->node_pt(l2)->hanging_pt();
283  n_master2 = hang_info2_pt->nmaster();
284  }
285  // Otherwise there is one master node, the node itself
286  else
287  {
288  n_master2 = 1;
289  }
290 
291  // Loop over the master nodes
292  for (unsigned m2 = 0; m2 < n_master2; m2++)
293  {
294  // Get the local unknown and weight
295  // If the node is hanging
296  if (is_node2_hanging)
297  {
298  // Read out the local unknown from the master node
299  local_unknown = this->local_hang_eqn(
300  hang_info2_pt->master_node_pt(m2), u_nodal_index);
301 
302  // Read out the hanging weight from the master node
303  hang_weight2 = hang_info2_pt->master_weight(m2);
304  }
305  // If the node is not hanging
306  else
307  {
308  // The local unknown number comes from the node
309  local_unknown = this->nodal_local_eqn(l2, u_nodal_index);
310 
311  // The hang weight is one
312  hang_weight2 = 1.0;
313  }
314 
315  // If the unknown is not pinned
316  if (local_unknown >= 0)
317  {
318  // Add contribution to Elemental Matrix
319  for (unsigned i = 0; i < DIM; i++)
320  {
321  jacobian(local_eqn, local_unknown) +=
322  dpsidx(l2, i) * dtestdx(l, i) * W * hang_weight *
323  hang_weight2;
324  }
325  }
326  } // End of loop over master nodes
327  } // End of loop over nodes
328  } // End of Jacobian calculation
329 
330  } // End of case when residual equation is not pinned
331  } // End of loop over master nodes for residual
332  } // End of loop over nodes
333 
334  } // End of loop over integration points
335  }
m2
MatrixType m2(n_dims)
oomph::FiniteElement::node_pt
Node *& node_pt(const unsigned &n)
Return a pointer to the local node n.
Definition: elements.h:2175
oomph::FiniteElement::nodal_value
double nodal_value(const unsigned &n, const unsigned &i) const
Definition: elements.h:2593
oomph::FiniteElement::nodal_local_eqn
int nodal_local_eqn(const unsigned &n, const unsigned &i) const
Definition: elements.h:1432
oomph::FiniteElement::nodal_position
double nodal_position(const unsigned &n, const unsigned &i) const
Definition: elements.h:2317
oomph::Node::hanging_pt
HangInfo *const & hanging_pt() const
Definition: nodes.h:1228
oomph::Node::is_hanging
bool is_hanging() const
Test whether the node is geometrically hanging.
Definition: nodes.h:1285
oomph::PoissonEquations::get_source_poisson
virtual void get_source_poisson(const unsigned &ipt, const Vector< double > &x, double &source) const
Definition: poisson_elements.h:309
oomph::PoissonEquations::u_index_poisson
virtual unsigned u_index_poisson() const
Definition: poisson_elements.h:85
oomph::PoissonEquations::dshape_and_dtest_eulerian_at_knot_poisson
virtual double dshape_and_dtest_eulerian_at_knot_poisson(const unsigned &ipt, Shape &psi, DShape &dpsidx, Shape &test, DShape &dtestdx) const =0
oomph::RefineableElement::local_hang_eqn
int local_hang_eqn(Node *const &node_pt, const unsigned &i)
Definition: refineable_elements.h:278
m
int * m
Definition: level2_cplx_impl.h:294
k
char char char int int * k
Definition: level2_impl.h:374
Eigen::test
squared absolute sa ArrayBase::abs2 DOXCOMMA MatrixBase::cwiseAbs2 sa Eigen::abs2 DOXCOMMA Eigen::pow DOXCOMMA ArrayBase::square nearest sa Eigen::floor DOXCOMMA Eigen::ceil DOXCOMMA ArrayBase::round nearest integer not less than the given sa Eigen::floor DOXCOMMA ArrayBase::ceil not a number test
Definition: GlobalFunctions.h:109
TestProblem::source
void source(const Vector< double > &x, Vector< double > &f)
Source function.
Definition: unstructured_two_d_circle.cc:46
test
Definition: indexed_view.cpp:20
j
std::ptrdiff_t j
Definition: tut_arithmetic_redux_minmax.cpp:2

References DIM, i, J, j, k, m, m2(), oomph::HangInfo::master_node_pt(), oomph::HangInfo::master_weight(), oomph::HangInfo::nmaster(), TestProblem::source(), Eigen::test, w, and oomph::QuadTreeNames::W.

◆ further_build()

template<unsigned DIM>
void oomph::RefineablePoissonEquations< DIM >::further_build ( )
inlinevirtual

Further build: Copy source function pointer from father element.

Reimplemented from oomph::RefineableElement.

Reimplemented in oomph::PRefineableQPoissonElement< DIM >.

157  {
158  this->Source_fct_pt = dynamic_cast<RefineablePoissonEquations<DIM>*>(
159  this->father_element_pt())
160  ->source_fct_pt();
161  }
oomph::PoissonEquations::Source_fct_pt
PoissonSourceFctPt Source_fct_pt
Pointer to source function:
Definition: poisson_elements.h:523
oomph::PoissonEquations::source_fct_pt
PoissonSourceFctPt & source_fct_pt()
Access function: Pointer to source function.
Definition: poisson_elements.h:281
oomph::RefineableElement::father_element_pt
virtual RefineableElement * father_element_pt() const
Return a pointer to the father element.
Definition: refineable_elements.h:539

References oomph::RefineableElement::father_element_pt(), oomph::PoissonEquations< DIM >::source_fct_pt(), and oomph::PoissonEquations< DIM >::Source_fct_pt.

Referenced by oomph::PRefineableQPoissonElement< DIM >::further_build().

◆ get_dresidual_dnodal_coordinates()

template<unsigned DIM>
void oomph::RefineablePoissonEquations< DIM >::get_dresidual_dnodal_coordinates ( RankThreeTensor< double > &  dresidual_dnodal_coordinates)
privatevirtual

Compute derivatives of elemental residual vector with respect to nodal coordinates. Overwrites default implementation in FiniteElement base class. dresidual_dnodal_coordinates(l,i,j) = d res(l) / dX_{ij}

Compute derivatives of elemental residual vector with respect to nodal coordinates (fully analytical). dresidual_dnodal_coordinates(l,i,j) = d res(l) / dX_{ij} Overloads the FD-based version in the FE base class.

Reimplemented from oomph::RefineableElement.

347  {
348  // Determine number of nodes in element
349  const unsigned n_node = nnode();
350 
351  // Set up memory for the shape and test functions
352  Shape psi(n_node), test(n_node);
353  DShape dpsidx(n_node, DIM), dtestdx(n_node, DIM);
354 
355  // Get number of shape controlling nodes
356  const unsigned n_shape_controlling_node = nshape_controlling_nodes();
357 
358  // Deriatives of shape fct derivatives w.r.t. nodal coords
359  RankFourTensor<double> d_dpsidx_dX(
360  DIM, n_shape_controlling_node, n_node, DIM);
361  RankFourTensor<double> d_dtestdx_dX(
362  DIM, n_shape_controlling_node, n_node, DIM);
363 
364  // Derivative of Jacobian of mapping w.r.t. to nodal coords
365  DenseMatrix<double> dJ_dX(DIM, n_shape_controlling_node);
366 
367  // Derivatives of derivative of u w.r.t. nodal coords
368  RankThreeTensor<double> d_dudx_dX(DIM, n_shape_controlling_node, DIM);
369 
370  // Source function and its gradient
371  double source;
372  Vector<double> d_source_dx(DIM);
373 
374  // Index at which the poisson unknown is stored
375  const unsigned u_nodal_index = this->u_index_poisson();
376 
377  // Determine the number of integration points
378  const unsigned n_intpt = integral_pt()->nweight();
379 
380  // Integer to store the local equation number
381  int local_eqn = 0;
382 
383  // Local storage for pointers to hang_info object
384  HangInfo* hang_info_pt = 0;
385 
386  // Loop over the integration points
387  for (unsigned ipt = 0; ipt < n_intpt; ipt++)
388  {
389  // Get the integral weight
390  double w = integral_pt()->weight(ipt);
391 
392  // Call the derivatives of the shape/test functions, as well as the
393  // derivatives of these w.r.t. nodal coordinates and the derivative
394  // of the jacobian of the mapping w.r.t. nodal coordinates
395  const double J = this->dshape_and_dtest_eulerian_at_knot_poisson(
396  ipt, psi, dpsidx, d_dpsidx_dX, test, dtestdx, d_dtestdx_dX, dJ_dX);
397 
398  // Calculate local values
399  // Allocate and initialise to zero
400  Vector<double> interpolated_x(DIM, 0.0);
401  Vector<double> interpolated_dudx(DIM, 0.0);
402 
403  // Calculate function value and derivatives:
404  // -----------------------------------------
405  // Loop over nodes
406  for (unsigned l = 0; l < n_node; l++)
407  {
408  // Get the nodal value of the Poisson unknown
409  double u_value = nodal_value(l, u_nodal_index);
410 
411  // Loop over directions
412  for (unsigned i = 0; i < DIM; i++)
413  {
414  interpolated_x[i] += nodal_position(l, i) * psi(l);
415  interpolated_dudx[i] += u_value * dpsidx(l, i);
416  }
417  }
418 
419  // Calculate derivative of du/dx_i w.r.t. nodal positions X_{pq}
420 
421  // Loop over shape controlling nodes
422  for (unsigned q = 0; q < n_shape_controlling_node; q++)
423  {
424  // Loop over coordinate directions
425  for (unsigned p = 0; p < DIM; p++)
426  {
427  for (unsigned i = 0; i < DIM; i++)
428  {
429  double aux = 0.0;
430  for (unsigned j = 0; j < n_node; j++)
431  {
432  aux += nodal_value(j, u_nodal_index) * d_dpsidx_dX(p, q, j, i);
433  }
434  d_dudx_dX(p, q, i) = aux;
435  }
436  }
437  }
438 
439  // Get source function
440  this->get_source_poisson(ipt, interpolated_x, source);
441 
442  // Get gradient of source function
443  this->get_source_gradient_poisson(ipt, interpolated_x, d_source_dx);
444 
445  // std::map<Node*,unsigned>
446  // local_shape_controlling_node_lookup=shape_controlling_node_lookup();
447 
448  // Assemble d res_{local_eqn} / d X_{pq}
449  // -------------------------------------
450 
451  // Loop over the nodes for the test functions
452  for (unsigned l = 0; l < n_node; l++)
453  {
454  // Local variables used to store the number of master nodes and the
455  // weight associated with the shape function if the node is hanging
456  unsigned n_master = 1;
457  double hang_weight = 1.0;
458 
459  // Local bool (is the node hanging)
460  bool is_node_hanging = this->node_pt(l)->is_hanging();
461 
462  // If the node is hanging, get the number of master nodes
463  if (is_node_hanging)
464  {
465  hang_info_pt = this->node_pt(l)->hanging_pt();
466  n_master = hang_info_pt->nmaster();
467  }
468  // Otherwise there is just one master node, the node itself
469  else
470  {
471  n_master = 1;
472  }
473 
474  // Loop over the master nodes
475  for (unsigned m = 0; m < n_master; m++)
476  {
477  // Get the local equation number and hang_weight
478  // If the node is hanging
479  if (is_node_hanging)
480  {
481  // Read out the local equation number from the m-th master node
482  local_eqn = this->local_hang_eqn(hang_info_pt->master_node_pt(m),
483  u_nodal_index);
484 
485  // Read out the weight from the master node
486  hang_weight = hang_info_pt->master_weight(m);
487  }
488  // If the node is not hanging
489  else
490  {
491  // The local equation number comes from the node itself
492  local_eqn = this->nodal_local_eqn(l, u_nodal_index);
493  // The hang weight is one
494  hang_weight = 1.0;
495  }
496 
497  // If the nodal equation is not a boundary condition
498  if (local_eqn >= 0)
499  {
500  // Loop over coordinate directions
501  for (unsigned p = 0; p < DIM; p++)
502  {
503  // Loop over shape controlling nodes
504  for (unsigned q = 0; q < n_shape_controlling_node; q++)
505  {
506  double sum = source * test(l) * dJ_dX(p, q) +
507  d_source_dx[p] * test(l) * psi(q) * J;
508 
509  for (unsigned i = 0; i < DIM; i++)
510  {
511  sum += interpolated_dudx[i] * (dtestdx(l, i) * dJ_dX(p, q) +
512  d_dtestdx_dX(p, q, l, i) * J) +
513  d_dudx_dX(p, q, i) * dtestdx(l, i) * J;
514  }
515 
516  // Multiply through by integration weight
517  dresidual_dnodal_coordinates(local_eqn, p, q) +=
518  sum * w * hang_weight;
519  }
520  }
521  }
522  }
523  }
524  } // End of loop over integration points
525  }
p
float * p
Definition: Tutorial_Map_using.cpp:9
oomph::PoissonEquations::get_source_gradient_poisson
virtual void get_source_gradient_poisson(const unsigned &ipt, const Vector< double > &x, Vector< double > &gradient) const
Definition: poisson_elements.h:331
oomph::RefineableElement::nshape_controlling_nodes
unsigned nshape_controlling_nodes()
Definition: refineable_elements.h:627
Eigen::numext::q
EIGEN_DEVICE_FUNC const Scalar & q
Definition: SpecialFunctionsImpl.h:2019

References DIM, i, J, j, m, oomph::HangInfo::master_node_pt(), oomph::HangInfo::master_weight(), oomph::HangInfo::nmaster(), p, Eigen::numext::q, TestProblem::source(), Eigen::test, and w.

◆ get_interpolated_values() [1/2]

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

Get the function value u in Vector. Note: Given the generality of the interface (this function is usually called from black-box documentation or interpolation routines), the values Vector sets its own size in here.

Implements oomph::RefineableElement.

135  {
136  if (t != 0)
137  {
138  std::string error_message =
139  "Time-dependent version of get_interpolated_values() ";
140  error_message += "not implemented for this element \n";
141  throw OomphLibError(
142  error_message,
143  "RefineablePoissonEquations::get_interpolated_values()",
144  OOMPH_EXCEPTION_LOCATION);
145  }
146  else
147  {
148  // Make sure that we call this particular object's steady
149  // get_interpolated_values (it could get overloaded lower down)
150  RefineablePoissonEquations<DIM>::get_interpolated_values(s, values);
151  }
152  }
oomph::RefineablePoissonEquations::get_interpolated_values
void get_interpolated_values(const Vector< double > &s, Vector< double > &values)
Definition: refineable_poisson_elements.h:99
oomph::Global_string_for_annotation::string
std::string string(const unsigned &i)
Definition: oomph_definitions.cc:286
plotPSD.t
t
Definition: plotPSD.py:36
OOMPH_EXCEPTION_LOCATION
#define OOMPH_EXCEPTION_LOCATION
Definition: oomph_definitions.h:61

References oomph::RefineablePoissonEquations< DIM >::get_interpolated_values(), OOMPH_EXCEPTION_LOCATION, s, oomph::Global_string_for_annotation::string(), and plotPSD::t.

◆ get_interpolated_values() [2/2]

template<unsigned DIM>
void oomph::RefineablePoissonEquations< DIM >::get_interpolated_values ( const Vector< double > &  s,
Vector< double > &  values 
)
inlinevirtual

Get the function value u in Vector. Note: Given the generality of the interface (this function is usually called from black-box documentation or interpolation routines), the values Vector sets its own size in here.

Reimplemented from oomph::RefineableElement.

101  {
102  // Set size of Vector: u
103  values.resize(1);
104 
105  // Find number of nodes
106  unsigned n_node = nnode();
107 
108  // Local shape function
109  Shape psi(n_node);
110 
111  // Find values of shape function
112  shape(s, psi);
113 
114  // Initialise value of u
115  values[0] = 0.0;
116 
117  // Find the index at which the poisson unknown is stored
118  unsigned u_nodal_index = this->u_index_poisson();
119 
120  // Loop over the local nodes and sum up the values
121  for (unsigned l = 0; l < n_node; l++)
122  {
123  values[0] += this->nodal_value(l, u_nodal_index) * psi[l];
124  }
125  }
oomph::FiniteElement::shape
virtual void shape(const Vector< double > &s, Shape &psi) const =0

References oomph::FiniteElement::nnode(), oomph::FiniteElement::nodal_value(), s, oomph::FiniteElement::shape(), and oomph::PoissonEquations< DIM >::u_index_poisson().

Referenced by oomph::RefineablePoissonEquations< DIM >::get_interpolated_values().

◆ get_Z2_flux()

template<unsigned DIM>
void oomph::RefineablePoissonEquations< DIM >::get_Z2_flux ( const Vector< double > &  s,
Vector< double > &  flux 
)
inlinevirtual

Get 'flux' for Z2 error recovery: Standard flux.from Poisson equations.

Implements oomph::ElementWithZ2ErrorEstimator.

84  {
85  this->get_flux(s, flux);
86  }
oomph::PoissonEquations::get_flux
void get_flux(const Vector< double > &s, Vector< double > &flux) const
Get flux: flux[i] = du/dx_i.
Definition: poisson_elements.h:364
ProblemParameters::flux
void flux(const double &time, const Vector< double > &x, double &flux)
Get flux applied along boundary x=0.
Definition: pretend_melt.cc:59

References ProblemParameters::flux(), and oomph::PoissonEquations< DIM >::get_flux().

◆ num_Z2_flux_terms()

template<unsigned DIM>
unsigned oomph::RefineablePoissonEquations< DIM >::num_Z2_flux_terms ( )
inlinevirtual

Number of 'flux' terms for Z2 error estimation.

Implements oomph::ElementWithZ2ErrorEstimator.

78  {
79  return DIM;
80  }

References DIM.

◆ operator=()

template<unsigned DIM>
void oomph::RefineablePoissonEquations< DIM >::operator= ( const RefineablePoissonEquations< DIM > &  )
delete

Broken assignment operator.

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