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

#include <solid_elements.h>

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

Public Member Functions

 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...
 
unsigned ngeom_data () const
 Broken assignment operator. More...
 
Data * geom_data_pt (const unsigned &j)
 
void identify_geometric_data (std::set< Data * > &geometric_data_pt)
 
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 assign_nodal_local_eqn_numbers (const bool &store_local_dof_pt)
 
virtual void describe_nodal_local_dofs (std::ostream &out, const std::string &current_string) const
 
Node *& node_pt (const unsigned &n)
 Return a pointer to the local node n. More...
 
Node *const & node_pt (const unsigned &n) const
 Return a pointer to the local node n (const version) More...
 
unsigned nnode () const
 Return the number of nodes. More...
 
virtual unsigned nnode_1d () const
 
double raw_nodal_position (const unsigned &n, const unsigned &i) const
 
double raw_nodal_position (const unsigned &t, const unsigned &n, const unsigned &i) const
 
double raw_dnodal_position_dt (const unsigned &n, const unsigned &i) const
 
double raw_dnodal_position_dt (const unsigned &n, const unsigned &j, const unsigned &i) const
 
double raw_nodal_position_gen (const unsigned &n, const unsigned &k, const unsigned &i) const
 
double raw_nodal_position_gen (const unsigned &t, const unsigned &n, const unsigned &k, const unsigned &i) const
 
double raw_dnodal_position_gen_dt (const unsigned &n, const unsigned &k, const unsigned &i) const
 
double raw_dnodal_position_gen_dt (const unsigned &j, const unsigned &n, const unsigned &k, const unsigned &i) const
 
double nodal_position (const unsigned &n, const unsigned &i) const
 
double nodal_position (const unsigned &t, const unsigned &n, const unsigned &i) const
 
double dnodal_position_dt (const unsigned &n, const unsigned &i) const
 Return the i-th component of nodal velocity: dx/dt at local node n. More...
 
double dnodal_position_dt (const unsigned &n, const unsigned &j, const unsigned &i) const
 
double nodal_position_gen (const unsigned &n, const unsigned &k, const unsigned &i) const
 
double nodal_position_gen (const unsigned &t, const unsigned &n, const unsigned &k, const unsigned &i) const
 
double dnodal_position_gen_dt (const unsigned &n, const unsigned &k, const unsigned &i) const
 
double dnodal_position_gen_dt (const unsigned &j, const unsigned &n, const unsigned &k, const unsigned &i) const
 
virtual void get_dresidual_dnodal_coordinates (RankThreeTensor< double > &dresidual_dnodal_coordinates)
 
virtual void disable_ALE ()
 
virtual void enable_ALE ()
 
virtual unsigned required_nvalue (const unsigned &n) const
 
unsigned nnodal_position_type () const
 
bool has_hanging_nodes () const
 
unsigned nodal_dimension () const
 Return the required Eulerian dimension of the nodes in this element. More...
 
virtual unsigned nvertex_node () const
 
virtual Node * vertex_node_pt (const unsigned &j) const
 
int get_node_number (Node *const &node_pt) const
 
virtual Node * get_node_at_local_coordinate (const Vector< double > &s) const
 
double raw_nodal_value (const unsigned &n, const unsigned &i) const
 
double raw_nodal_value (const unsigned &t, const unsigned &n, const unsigned &i) const
 
double nodal_value (const unsigned &n, const unsigned &i) const
 
double nodal_value (const unsigned &t, const unsigned &n, const unsigned &i) const
 
unsigned dim () const
 
virtual ElementGeometry::ElementGeometry element_geometry () const
 Return the geometry type of the element (either Q or T usually). More...
 
virtual double interpolated_x (const Vector< double > &s, const unsigned &i) const
 Return FE interpolated coordinate x[i] at local coordinate s. More...
 
virtual double interpolated_x (const unsigned &t, const Vector< double > &s, const unsigned &i) const
 
virtual void interpolated_x (const Vector< double > &s, Vector< double > &x) const
 Return FE interpolated position x[] at local coordinate s as Vector. More...
 
virtual void interpolated_x (const unsigned &t, const Vector< double > &s, Vector< double > &x) const
 
virtual double interpolated_dxdt (const Vector< double > &s, const unsigned &i, const unsigned &t)
 
virtual void interpolated_dxdt (const Vector< double > &s, const unsigned &t, Vector< double > &dxdt)
 
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 void identify_field_data_for_interactions (std::set< std::pair< Data *, unsigned >> &paired_field_data)
 
virtual double s_min () const
 Min value of local coordinate. More...
 
virtual double s_max () const
 Max. value of local coordinate. More...
 
double size () const
 
virtual double compute_physical_size () const
 
virtual void point_output_data (const Vector< double > &s, Vector< double > &data)
 
void point_output (std::ostream &outfile, const Vector< double > &s)
 
virtual unsigned nplot_points_paraview (const unsigned &nplot) const
 
virtual unsigned nsub_elements_paraview (const unsigned &nplot) const
 
void output_paraview (std::ofstream &file_out, const unsigned &nplot) const
 
virtual void write_paraview_output_offset_information (std::ofstream &file_out, const unsigned &nplot, unsigned &counter) const
 
virtual void write_paraview_type (std::ofstream &file_out, const unsigned &nplot) const
 
virtual void write_paraview_offsets (std::ofstream &file_out, const unsigned &nplot, unsigned &offset_sum) const
 
virtual unsigned nscalar_paraview () const
 
virtual void scalar_value_paraview (std::ofstream &file_out, const unsigned &i, const unsigned &nplot) const
 
virtual void scalar_value_fct_paraview (std::ofstream &file_out, const unsigned &i, const unsigned &nplot, FiniteElement::SteadyExactSolutionFctPt exact_soln_pt) const
 
virtual void scalar_value_fct_paraview (std::ofstream &file_out, const unsigned &i, const unsigned &nplot, const double &time, FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt) const
 
virtual std::string scalar_name_paraview (const unsigned &i) const
 
virtual void output (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
 

Protected Member Functions

virtual void fill_in_generic_contribution_to_residuals_pvd (Vector< double > &residuals, DenseMatrix< double > &jacobian, const unsigned &flag)
 
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
 
virtual double local_to_lagrangian_mapping_diagonal (const DShape &dpsids, DenseMatrix< double > &jacobian, DenseMatrix< double > &inverse_jacobian) const
 
virtual void assign_solid_local_eqn_numbers (const bool &store_local_dof)
 Assign local equation numbers for the solid equations in the element. More...
 
void describe_solid_local_dofs (std::ostream &out, const std::string &current_string) const
 Classifies dofs locally for solid specific aspects. More...
 
virtual void fill_in_jacobian_from_solid_position_by_fd (Vector< double > &residuals, DenseMatrix< double > &jacobian)
 
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
virtual void assemble_local_to_eulerian_jacobian (const DShape &dpsids, DenseMatrix< double > &jacobian) const
 
virtual void assemble_local_to_eulerian_jacobian2 (const DShape &d2psids, DenseMatrix< double > &jacobian2) const
 
virtual void assemble_eulerian_base_vectors (const DShape &dpsids, DenseMatrix< double > &interpolated_G) const
 
template<unsigned DIM>
double invert_jacobian (const DenseMatrix< double > &jacobian, DenseMatrix< double > &inverse_jacobian) const
 
virtual double invert_jacobian_mapping (const DenseMatrix< double > &jacobian, DenseMatrix< double > &inverse_jacobian) const
 
virtual double local_to_eulerian_mapping (const DShape &dpsids, DenseMatrix< double > &jacobian, DenseMatrix< double > &inverse_jacobian) const
 
double local_to_eulerian_mapping (const DShape &dpsids, DenseMatrix< double > &inverse_jacobian) const
 
virtual double local_to_eulerian_mapping_diagonal (const DShape &dpsids, DenseMatrix< double > &jacobian, DenseMatrix< double > &inverse_jacobian) const
 
virtual void dJ_eulerian_dnodal_coordinates (const DenseMatrix< double > &jacobian, const DShape &dpsids, DenseMatrix< double > &djacobian_dX) const
 
template<unsigned DIM>
void dJ_eulerian_dnodal_coordinates_templated_helper (const DenseMatrix< double > &jacobian, const DShape &dpsids, DenseMatrix< double > &djacobian_dX) const
 
virtual void d_dshape_eulerian_dnodal_coordinates (const double &det_jacobian, const DenseMatrix< double > &jacobian, const DenseMatrix< double > &djacobian_dX, const DenseMatrix< double > &inverse_jacobian, const DShape &dpsids, RankFourTensor< double > &d_dpsidx_dX) const
 
template<unsigned DIM>
void d_dshape_eulerian_dnodal_coordinates_templated_helper (const double &det_jacobian, const DenseMatrix< double > &jacobian, const DenseMatrix< double > &djacobian_dX, const DenseMatrix< double > &inverse_jacobian, const DShape &dpsids, RankFourTensor< double > &d_dpsidx_dX) const
 
virtual void transform_derivatives (const DenseMatrix< double > &inverse_jacobian, DShape &dbasis) const
 
void transform_derivatives_diagonal (const DenseMatrix< double > &inverse_jacobian, DShape &dbasis) const
 
virtual void transform_second_derivatives (const DenseMatrix< double > &jacobian, const DenseMatrix< double > &inverse_jacobian, const DenseMatrix< double > &jacobian2, DShape &dbasis, DShape &d2basis) const
 
template<unsigned DIM>
void transform_second_derivatives_template (const DenseMatrix< double > &jacobian, const DenseMatrix< double > &inverse_jacobian, const DenseMatrix< double > &jacobian2, DShape &dbasis, DShape &d2basis) const
 
template<unsigned DIM>
void transform_second_derivatives_diagonal (const DenseMatrix< double > &jacobian, const DenseMatrix< double > &inverse_jacobian, const DenseMatrix< double > &jacobian2, DShape &dbasis, DShape &d2basis) const
 
virtual void fill_in_jacobian_from_nodal_by_fd (Vector< double > &residuals, DenseMatrix< double > &jacobian)
 
void fill_in_jacobian_from_nodal_by_fd (DenseMatrix< double > &jacobian)
 
virtual void update_before_nodal_fd ()
 
virtual void reset_after_nodal_fd ()
 
virtual void update_in_nodal_fd (const unsigned &i)
 
virtual void reset_in_nodal_fd (const unsigned &i)
 
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)
 

Private Member Functions

void unpin_elemental_solid_pressure_dofs ()
 Unpin all solid pressure dofs – empty as there are no pressures. More...
 

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 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 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
 
- 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
 

Detailed Description

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

A class for elements that solve the equations of solid mechanics, based on the principle of virtual displacements in cartesian coordinates.

Constructor & Destructor Documentation

◆ PVDEquations()

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

Constructor.

443 {}

Member Function Documentation

◆ extended_output()

template<unsigned DIM>
void oomph::PVDEquations< DIM >::extended_output ( std::ostream &  outfile,
const unsigned &  n_plot 
)

Output: x,y,[z],xi0,xi1,[xi2],gamma strain and stress components.

Output: x,y,[z],xi0,xi1,[xi2],gamma and the strain and stress components

753  {
754  Vector<double> x(DIM);
755  Vector<double> xi(DIM);
756  Vector<double> s(DIM);
757  DenseMatrix<double> stress_or_strain(DIM, DIM);
758 
759  // Tecplot header info
760  outfile << this->tecplot_zone_string(n_plot);
761 
762  // Loop over plot points
763  unsigned num_plot_points = this->nplot_points(n_plot);
764  for (unsigned iplot = 0; iplot < num_plot_points; iplot++)
765  {
766  // Get local coordinates of plot point
767  this->get_s_plot(iplot, n_plot, s);
768 
769  // Get Eulerian and Lagrangian coordinates
770  this->interpolated_x(s, x);
771  this->interpolated_xi(s, xi);
772 
773  // Get isotropic growth
774  double gamma;
775  // Dummy integration point
776  unsigned ipt = 0;
777  this->get_isotropic_growth(ipt, s, xi, gamma);
778 
779  // Output the x,y,..
780  for (unsigned i = 0; i < DIM; i++)
781  {
782  outfile << x[i] << " ";
783  }
784 
785  // Output xi0,xi1,..
786  for (unsigned i = 0; i < DIM; i++)
787  {
788  outfile << xi[i] << " ";
789  }
790 
791  // Output growth
792  outfile << gamma << " ";
793 
794  // get the strain
795  this->get_strain(s, stress_or_strain);
796  for (unsigned i = 0; i < DIM; i++)
797  {
798  for (unsigned j = 0; j <= i; j++)
799  {
800  outfile << stress_or_strain(j, i) << " ";
801  }
802  }
803 
804  // get the stress
805  this->get_stress(s, stress_or_strain);
806  for (unsigned i = 0; i < DIM; i++)
807  {
808  for (unsigned j = 0; j <= i; j++)
809  {
810  outfile << stress_or_strain(j, i) << " ";
811  }
812  }
813 
814 
815  outfile << std::endl;
816  }
817 
818 
819  // Write tecplot footer (e.g. FE connectivity lists)
820  this->write_tecplot_zone_footer(outfile, n_plot);
821  outfile << std::endl;
822  }
i
int i
Definition: BiCGSTAB_step_by_step.cpp:9
oomph::FiniteElement::tecplot_zone_string
virtual std::string tecplot_zone_string(const unsigned &nplot) const
Definition: elements.h:3161
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::get_s_plot
virtual void get_s_plot(const unsigned &i, const unsigned &nplot, Vector< double > &s, const bool &shifted_to_interior=false) const
Definition: elements.h:3148
oomph::FiniteElement::nplot_points
virtual unsigned nplot_points(const unsigned &nplot) const
Definition: elements.h:3186
oomph::FiniteElement::write_tecplot_zone_footer
virtual void write_tecplot_zone_footer(std::ostream &outfile, const unsigned &nplot) const
Definition: elements.h:3174
oomph::PVDEquationsBase::get_isotropic_growth
virtual void get_isotropic_growth(const unsigned &ipt, const Vector< double > &s, const Vector< double > &xi, double &gamma) const
Definition: solid_elements.h:267
oomph::PVDEquationsBase::get_strain
void get_strain(const Vector< double > &s, DenseMatrix< double > &strain) const
Return the strain tensor.
Definition: solid_elements.cc:47
oomph::PVDEquations::get_stress
void get_stress(const Vector< double > &s, DenseMatrix< double > &sigma)
Definition: solid_elements.cc:951
oomph::SolidFiniteElement::interpolated_xi
virtual double interpolated_xi(const Vector< double > &s, const unsigned &i) const
Definition: elements.cc:7104
s
RealScalar s
Definition: level1_cplx_impl.h:130
DIM
#define DIM
Definition: linearised_navier_stokes_elements.h:44
mathsFunc::gamma
Mdouble gamma(Mdouble gamma_in)
This is the gamma function returns the true value for the half integer value.
Definition: ExtendedMath.cc:116
plotDoE.x
list x
Definition: plotDoE.py:28
j
std::ptrdiff_t j
Definition: tut_arithmetic_redux_minmax.cpp:2

References DIM, mathsFunc::gamma(), i, j, s, and plotDoE::x.

◆ fill_in_contribution_to_jacobian()

template<unsigned DIM>
void oomph::PVDEquations< DIM >::fill_in_contribution_to_jacobian ( Vector< double > &  residuals,
DenseMatrix< double > &  jacobian 
)
inlinevirtual

Fill in contribution to Jacobian (either by FD or analytically, control this via evaluate_jacobian_by_fd()

Reimplemented from oomph::SolidFiniteElement.

Reimplemented in oomph::PseudoSolidNodeUpdateElement< TCrouzeixRaviartElement< 2 >, TPVDBubbleEnrichedElement< 2, 3 > >, oomph::PseudoSolidNodeUpdateElement< TTaylorHoodElement< 2 >, TPVDElement< 2, 3 > >, oomph::PseudoSolidNodeUpdateElement< GeneralisedNewtonianAxisymmetricTTaylorHoodElement, TPVDElement< 2, 3 > >, oomph::PseudoSolidNodeUpdateElement< AxisymmetricTTaylorHoodElement, TPVDElement< 2, 3 > >, and oomph::PseudoSolidNodeUpdateElement< GeneralisedNewtonianTTaylorHoodElement< 2 >, TPVDElement< 2, 3 > >.

461  {
462  // Solve for the consistent acceleration in Newmark scheme?
463  if (this->Solve_for_consistent_newmark_accel_flag)
464  {
465  // Add the contribution to the residuals -- these are the
466  // full residuals of whatever solid equations we're solving
467  this->fill_in_contribution_to_residuals(residuals);
468 
469  // Jacobian is not the Jacobian associated with these
470  // residuals (treating the postions as unknowns)
471  // but the derivatives w.r.t. to the discrete generalised
472  // accelerations in the Newmark scheme -- the Jacobian
473  // is therefore the associated mass matrix, multiplier
474  // by suitable scaling factors
475  this->fill_in_jacobian_for_newmark_accel(jacobian);
476  return;
477  }
478 
479  // Are we assigning a solid initial condition?
480  if (this->Solid_ic_pt != 0)
481  {
482  this->fill_in_jacobian_for_solid_ic(residuals, jacobian);
483  return;
484  }
485 
486 
487  // Use FD
488  if ((this->Evaluate_jacobian_by_fd))
489  {
490  // Add the contribution to the residuals from this element
491  this->fill_in_generic_contribution_to_residuals_pvd(
492  residuals, GeneralisedElement::Dummy_matrix, 0);
493 
494  // Get the solid entries in the jacobian using finite differences
495  this->fill_in_jacobian_from_solid_position_by_fd(jacobian);
496  }
497  // Do it analytically
498  else
499  {
500  fill_in_generic_contribution_to_residuals_pvd(residuals, jacobian, 1);
501  }
502  }
oomph::GeneralisedElement::Dummy_matrix
static DenseMatrix< double > Dummy_matrix
Definition: elements.h:227
oomph::PVDEquationsBase::Evaluate_jacobian_by_fd
bool Evaluate_jacobian_by_fd
Use FD to evaluate Jacobian.
Definition: solid_elements.h:430
oomph::PVDEquations::fill_in_generic_contribution_to_residuals_pvd
virtual void fill_in_generic_contribution_to_residuals_pvd(Vector< double > &residuals, DenseMatrix< double > &jacobian, const unsigned &flag)
Definition: solid_elements.cc:179
oomph::PVDEquations::fill_in_contribution_to_residuals
void fill_in_contribution_to_residuals(Vector< double > &residuals)
Definition: solid_elements.h:451
oomph::SolidFiniteElement::Solve_for_consistent_newmark_accel_flag
bool Solve_for_consistent_newmark_accel_flag
Definition: elements.h:4302
oomph::SolidFiniteElement::Solid_ic_pt
SolidInitialCondition * Solid_ic_pt
Pointer to object that specifies the initial condition.
Definition: elements.h:4131
oomph::SolidFiniteElement::fill_in_jacobian_from_solid_position_by_fd
virtual void fill_in_jacobian_from_solid_position_by_fd(Vector< double > &residuals, DenseMatrix< double > &jacobian)
Definition: elements.cc:6985
oomph::SolidFiniteElement::fill_in_jacobian_for_solid_ic
void fill_in_jacobian_for_solid_ic(Vector< double > &residuals, DenseMatrix< double > &jacobian)
Definition: elements.h:4035
oomph::SolidFiniteElement::fill_in_jacobian_for_newmark_accel
void fill_in_jacobian_for_newmark_accel(DenseMatrix< double > &jacobian)
Definition: elements.cc:7227

References oomph::GeneralisedElement::Dummy_matrix, oomph::PVDEquationsBase< DIM >::Evaluate_jacobian_by_fd, oomph::PVDEquations< DIM >::fill_in_contribution_to_residuals(), oomph::PVDEquations< DIM >::fill_in_generic_contribution_to_residuals_pvd(), oomph::SolidFiniteElement::fill_in_jacobian_for_newmark_accel(), oomph::SolidFiniteElement::fill_in_jacobian_for_solid_ic(), oomph::SolidFiniteElement::fill_in_jacobian_from_solid_position_by_fd(), oomph::SolidFiniteElement::Solid_ic_pt, and oomph::SolidFiniteElement::Solve_for_consistent_newmark_accel_flag.

◆ fill_in_contribution_to_residuals()

template<unsigned DIM>
void oomph::PVDEquations< DIM >::fill_in_contribution_to_residuals ( Vector< double > &  residuals)
inlinevirtual

Fill in the residuals for the solid equations (the discretised principle of virtual displacements)

Reimplemented from oomph::GeneralisedElement.

Reimplemented in oomph::PseudoSolidNodeUpdateElement< TCrouzeixRaviartElement< 2 >, TPVDBubbleEnrichedElement< 2, 3 > >, oomph::PseudoSolidNodeUpdateElement< TTaylorHoodElement< 2 >, TPVDElement< 2, 3 > >, oomph::PseudoSolidNodeUpdateElement< GeneralisedNewtonianAxisymmetricTTaylorHoodElement, TPVDElement< 2, 3 > >, oomph::PseudoSolidNodeUpdateElement< AxisymmetricTTaylorHoodElement, TPVDElement< 2, 3 > >, and oomph::PseudoSolidNodeUpdateElement< GeneralisedNewtonianTTaylorHoodElement< 2 >, TPVDElement< 2, 3 > >.

452  {
453  fill_in_generic_contribution_to_residuals_pvd(
454  residuals, GeneralisedElement::Dummy_matrix, 0);
455  }

References oomph::GeneralisedElement::Dummy_matrix, and oomph::PVDEquations< DIM >::fill_in_generic_contribution_to_residuals_pvd().

Referenced by oomph::PVDEquations< DIM >::fill_in_contribution_to_jacobian(), and QThermalPVDElement< DIM >::fill_in_contribution_to_residuals().

◆ fill_in_generic_contribution_to_residuals_pvd()

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

Compute element residual Vector only (if flag=and/or element Jacobian matrix

Compute the residuals for the discretised principle of virtual displacements.

Reimplemented in oomph::RefineablePVDEquations< DIM >, and oomph::RefineableQDPVDElement< DIM, NNODE_1D >.

183  {
184 #ifdef PARANOID
185  // Check if the constitutive equation requires the explicit imposition of an
186  // incompressibility constraint
187  if (this->Constitutive_law_pt->requires_incompressibility_constraint())
188  {
189  throw OomphLibError(
190  "PVDEquations cannot be used with incompressible constitutive laws.",
191  OOMPH_CURRENT_FUNCTION,
192  OOMPH_EXCEPTION_LOCATION);
193  }
194 #endif
195 
196  // Simply set up initial condition?
197  if (this->Solid_ic_pt != 0)
198  {
199  this->fill_in_residuals_for_solid_ic(residuals);
200  return;
201  }
202 
203  // Find out how many nodes there are
204  const unsigned n_node = this->nnode();
205 
206  // Find out how many positional dofs there are
207  const unsigned n_position_type = this->nnodal_position_type();
208 
209  // Set up memory for the shape functions
210  Shape psi(n_node, n_position_type);
211  DShape dpsidxi(n_node, n_position_type, DIM);
212 
213  // Set the value of Nintpt -- the number of integration points
214  const unsigned n_intpt = this->integral_pt()->nweight();
215 
216  // Set the vector to hold the local coordinates in the element
217  Vector<double> s(DIM);
218 
219  // Timescale ratio (non-dim density)
220  double lambda_sq = this->lambda_sq();
221 
222  // Time factor
223  double time_factor = 0.0;
224  if (lambda_sq > 0)
225  {
226  time_factor = this->node_pt(0)->position_time_stepper_pt()->weight(2, 0);
227  }
228 
229  // Integer to store the local equation number
230  int local_eqn = 0;
231 
232  // Loop over the integration points
233  for (unsigned ipt = 0; ipt < n_intpt; ipt++)
234  {
235  // Assign the values of s
236  for (unsigned i = 0; i < DIM; ++i)
237  {
238  s[i] = this->integral_pt()->knot(ipt, i);
239  }
240 
241  // Get the integral weight
242  double w = this->integral_pt()->weight(ipt);
243 
244  // Call the derivatives of the shape functions (and get Jacobian)
245  double J = this->dshape_lagrangian_at_knot(ipt, psi, dpsidxi);
246 
247  // Calculate interpolated values of the derivative of global position
248  // wrt lagrangian coordinates
249  DenseMatrix<double> interpolated_G(DIM);
250 
251  // Setup memory for accelerations
252  Vector<double> accel(DIM);
253 
254  // Initialise to zero
255  for (unsigned i = 0; i < DIM; i++)
256  {
257  // Initialise acclerations
258  accel[i] = 0.0;
259  for (unsigned j = 0; j < DIM; j++)
260  {
261  interpolated_G(i, j) = 0.0;
262  }
263  }
264 
265  // Storage for Lagrangian coordinates (initialised to zero)
266  Vector<double> interpolated_xi(DIM, 0.0);
267 
268  // Calculate displacements and derivatives and lagrangian coordinates
269  for (unsigned l = 0; l < n_node; l++)
270  {
271  // Loop over positional dofs
272  for (unsigned k = 0; k < n_position_type; k++)
273  {
274  double psi_ = psi(l, k);
275  // Loop over displacement components (deformed position)
276  for (unsigned i = 0; i < DIM; i++)
277  {
278  // Calculate the Lagrangian coordinates and the accelerations
279  interpolated_xi[i] += this->lagrangian_position_gen(l, k, i) * psi_;
280 
281  // Only compute accelerations if inertia is switched on
282  if ((lambda_sq > 0.0) && (this->Unsteady))
283  {
284  accel[i] += this->dnodal_position_gen_dt(2, l, k, i) * psi_;
285  }
286 
287  // Loop over derivative directions
288  for (unsigned j = 0; j < DIM; j++)
289  {
290  interpolated_G(j, i) +=
291  this->nodal_position_gen(l, k, i) * dpsidxi(l, k, j);
292  }
293  }
294  }
295  }
296 
297  // Get isotropic growth factor
298  double gamma = 1.0;
299  this->get_isotropic_growth(ipt, s, interpolated_xi, gamma);
300 
301 
302  // Get body force at current time
303  Vector<double> b(DIM);
304  this->body_force(interpolated_xi, b);
305 
306  // We use Cartesian coordinates as the reference coordinate
307  // system. In this case the undeformed metric tensor is always
308  // the identity matrix -- stretched by the isotropic growth
309  double diag_entry = pow(gamma, 2.0 / double(DIM));
310  DenseMatrix<double> g(DIM);
311  for (unsigned i = 0; i < DIM; i++)
312  {
313  for (unsigned j = 0; j < DIM; j++)
314  {
315  if (i == j)
316  {
317  g(i, j) = diag_entry;
318  }
319  else
320  {
321  g(i, j) = 0.0;
322  }
323  }
324  }
325 
326  // Premultiply the undeformed volume ratio (from the isotropic
327  // growth), the weights and the Jacobian
328  double W = gamma * w * J;
329 
330  // Declare and calculate the deformed metric tensor
331  DenseMatrix<double> G(DIM);
332 
333  // Assign values of G
334  for (unsigned i = 0; i < DIM; i++)
335  {
336  // Do upper half of matrix
337  for (unsigned j = i; j < DIM; j++)
338  {
339  // Initialise G(i,j) to zero
340  G(i, j) = 0.0;
341  // Now calculate the dot product
342  for (unsigned k = 0; k < DIM; k++)
343  {
344  G(i, j) += interpolated_G(i, k) * interpolated_G(j, k);
345  }
346  }
347  // Matrix is symmetric so just copy lower half
348  for (unsigned j = 0; j < i; j++)
349  {
350  G(i, j) = G(j, i);
351  }
352  }
353 
354  // Now calculate the stress tensor from the constitutive law
355  DenseMatrix<double> sigma(DIM);
356  get_stress(g, G, sigma);
357 
358  // Add pre-stress
359  for (unsigned i = 0; i < DIM; i++)
360  {
361  for (unsigned j = 0; j < DIM; j++)
362  {
363  sigma(i, j) += this->prestress(i, j, interpolated_xi);
364  }
365  }
366 
367  // Get stress derivative by FD only needed for Jacobian
368  //-----------------------------------------------------
369 
370  // Stress derivative
371  RankFourTensor<double> d_stress_dG(DIM, DIM, DIM, DIM, 0.0);
372  // Derivative of metric tensor w.r.t. to nodal coords
373  RankFiveTensor<double> d_G_dX(
374  n_node, n_position_type, DIM, DIM, DIM, 0.0);
375 
376  // Get Jacobian too?
377  if (flag == 1)
378  {
379  // Derivative of metric tensor w.r.t. to discrete positional dofs
380  // NOTE: Since G is symmetric we only compute the upper triangle
381  // and DO NOT copy the entries across. Subsequent computations
382  // must (and, in fact, do) therefore only operate with upper
383  // triangular entries
384  for (unsigned ll = 0; ll < n_node; ll++)
385  {
386  for (unsigned kk = 0; kk < n_position_type; kk++)
387  {
388  for (unsigned ii = 0; ii < DIM; ii++)
389  {
390  for (unsigned aa = 0; aa < DIM; aa++)
391  {
392  for (unsigned bb = aa; bb < DIM; bb++)
393  {
394  d_G_dX(ll, kk, ii, aa, bb) =
395  interpolated_G(aa, ii) * dpsidxi(ll, kk, bb) +
396  interpolated_G(bb, ii) * dpsidxi(ll, kk, aa);
397  }
398  }
399  }
400  }
401  }
402 
403  // Get the "upper triangular" entries of the derivatives of the stress
404  // tensor with respect to G
405  this->get_d_stress_dG_upper(g, G, sigma, d_stress_dG);
406  }
407 
408  //=====EQUATIONS OF ELASTICITY FROM PRINCIPLE OF VIRTUAL
409  // DISPLACEMENTS========
410 
411  // Loop over the test functions, nodes of the element
412  for (unsigned l = 0; l < n_node; l++)
413  {
414  // Loop of types of dofs
415  for (unsigned k = 0; k < n_position_type; k++)
416  {
417  // Offset for faster access
418  const unsigned offset5 = dpsidxi.offset(l, k);
419 
420  // Loop over the displacement components
421  for (unsigned i = 0; i < DIM; i++)
422  {
423  // Get the equation number
424  local_eqn = this->position_local_eqn(l, k, i);
425 
426  /*IF it's not a boundary condition*/
427  if (local_eqn >= 0)
428  {
429  // Initialise contribution to sum
430  double sum = 0.0;
431 
432  // Acceleration and body force
433  sum += (lambda_sq * accel[i] - b[i]) * psi(l, k);
434 
435  // Stress term
436  for (unsigned a = 0; a < DIM; a++)
437  {
438  unsigned count = offset5;
439  for (unsigned b = 0; b < DIM; b++)
440  {
441  // Add the stress terms to the residuals
442  sum += sigma(a, b) * interpolated_G(a, i) *
443  dpsidxi.raw_direct_access(count);
444  ++count;
445  }
446  }
447  residuals[local_eqn] += W * sum;
448 
449  // Get Jacobian too?
450  if (flag == 1)
451  {
452  // Offset for faster access in general stress loop
453  const unsigned offset1 = d_G_dX.offset(l, k, i);
454 
455  // Loop over the nodes of the element again
456  for (unsigned ll = 0; ll < n_node; ll++)
457  {
458  // Loop of types of dofs again
459  for (unsigned kk = 0; kk < n_position_type; kk++)
460  {
461  // Loop over the displacement components again
462  for (unsigned ii = 0; ii < DIM; ii++)
463  {
464  // Get the number of the unknown
465  int local_unknown = this->position_local_eqn(ll, kk, ii);
466 
467  /*IF it's not a boundary condition*/
468  if (local_unknown >= 0)
469  {
470  // Offset for faster access in general stress loop
471  const unsigned offset2 = d_G_dX.offset(ll, kk, ii);
472  const unsigned offset4 = dpsidxi.offset(ll, kk);
473 
474  // General stress term
475  //--------------------
476  double sum = 0.0;
477  unsigned count1 = offset1;
478  for (unsigned a = 0; a < DIM; a++)
479  {
480  // Bump up direct access because we're only
481  // accessing upper triangle
482  count1 += a;
483  for (unsigned b = a; b < DIM; b++)
484  {
485  double factor = d_G_dX.raw_direct_access(count1);
486  if (a == b) factor *= 0.5;
487 
488  // Offset for faster access
489  unsigned offset3 = d_stress_dG.offset(a, b);
490  unsigned count2 = offset2;
491  unsigned count3 = offset3;
492 
493  for (unsigned aa = 0; aa < DIM; aa++)
494  {
495  // Bump up direct access because we're only
496  // accessing upper triangle
497  count2 += aa;
498  count3 += aa;
499 
500  // Only upper half of derivatives w.r.t. symm
501  // tensor
502  for (unsigned bb = aa; bb < DIM; bb++)
503  {
504  sum += factor *
505  d_stress_dG.raw_direct_access(count3) *
506  d_G_dX.raw_direct_access(count2);
507  ++count2;
508  ++count3;
509  }
510  }
511  ++count1;
512  }
513  }
514 
515  // Multiply by weight and add contribution
516  // (Add directly because this bit is nonsymmetric)
517  jacobian(local_eqn, local_unknown) += sum * W;
518 
519  // Only upper triangle (no separate test for bc as
520  // local_eqn is already nonnegative)
521  if ((i == ii) && (local_unknown >= local_eqn))
522  {
523  // Initialise contribution
524  double sum = 0.0;
525 
526  // Inertia term
527  sum +=
528  lambda_sq * time_factor * psi(ll, kk) * psi(l, k);
529 
530  // Stress term
531  unsigned count4 = offset4;
532  for (unsigned a = 0; a < DIM; a++)
533  {
534  // Cache term
535  const double factor =
536  dpsidxi.raw_direct_access(count4); // ll ,kk
537  ++count4;
538 
539  unsigned count5 = offset5;
540  for (unsigned b = 0; b < DIM; b++)
541  {
542  sum += sigma(a, b) * factor *
543  dpsidxi.raw_direct_access(count5); // l ,k
544  ++count5;
545  }
546  }
547  // Add contribution to jacobian
548  jacobian(local_eqn, local_unknown) += sum * W;
549  // Add to lower triangular section
550  if (local_eqn != local_unknown)
551  {
552  jacobian(local_unknown, local_eqn) += sum * W;
553  }
554  }
555 
556  } // End of if not boundary condition
557  }
558  }
559  }
560  }
561 
562  } // End of if not boundary condition
563 
564  } // End of loop over coordinate directions
565  } // End of loop over type of dof
566  } // End of loop over shape functions
567  } // End of loop over integration points
568  }
G
JacobiRotation< float > G
Definition: Jacobi_makeGivens.cpp:2
J
JacobiRotation< float > J
Definition: Jacobi_makeJacobi.cpp:3
w
RowVector3d w
Definition: Matrix_resize_int.cpp:3
b
Scalar * b
Definition: benchVecAdd.cpp:17
oomph::ConstitutiveLaw::requires_incompressibility_constraint
virtual bool requires_incompressibility_constraint()=0
oomph::FiniteElement::node_pt
Node *& node_pt(const unsigned &n)
Return a pointer to the local node n.
Definition: elements.h:2175
oomph::FiniteElement::nnodal_position_type
unsigned nnodal_position_type() const
Definition: elements.h:2463
oomph::FiniteElement::dnodal_position_gen_dt
double dnodal_position_gen_dt(const unsigned &n, const unsigned &k, const unsigned &i) const
Definition: elements.h:2369
oomph::FiniteElement::nodal_position_gen
double nodal_position_gen(const unsigned &n, const unsigned &k, const unsigned &i) const
Definition: elements.h:2349
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::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::Node::position_time_stepper_pt
TimeStepper *& position_time_stepper_pt()
Return a pointer to the position timestepper.
Definition: nodes.h:1022
oomph::PVDEquationsBase::Unsteady
bool Unsteady
Flag that switches inertia on/off.
Definition: solid_elements.h:421
oomph::PVDEquationsBase::Constitutive_law_pt
ConstitutiveLaw * Constitutive_law_pt
Pointer to the constitutive law.
Definition: solid_elements.h:415
oomph::PVDEquationsBase::prestress
double prestress(const unsigned &i, const unsigned &j, const Vector< double > xi)
Definition: solid_elements.h:393
oomph::PVDEquationsBase::body_force
void body_force(const Vector< double > &xi, Vector< double > &b) const
Definition: solid_elements.h:287
oomph::PVDEquationsBase::lambda_sq
const double & lambda_sq() const
Access function for timescale ratio (nondim density)
Definition: solid_elements.h:108
oomph::PVDEquations::get_d_stress_dG_upper
void get_d_stress_dG_upper(const DenseMatrix< double > &g, const DenseMatrix< double > &G, const DenseMatrix< double > &sigma, RankFourTensor< double > &d_sigma_dG)
Definition: solid_elements.h:569
oomph::SolidFiniteElement::lagrangian_position_gen
double lagrangian_position_gen(const unsigned &n, const unsigned &k, const unsigned &i) const
Definition: elements.h:3912
oomph::SolidFiniteElement::fill_in_residuals_for_solid_ic
void fill_in_residuals_for_solid_ic(Vector< double > &residuals)
Definition: elements.h:4018
oomph::SolidFiniteElement::position_local_eqn
int position_local_eqn(const unsigned &n, const unsigned &k, const unsigned &j) const
Definition: elements.h:4137
oomph::SolidFiniteElement::dshape_lagrangian_at_knot
virtual double dshape_lagrangian_at_knot(const unsigned &ipt, Shape &psi, DShape &dpsidxi) const
Definition: elements.cc:6737
oomph::TimeStepper::weight
virtual double weight(const unsigned &i, const unsigned &j) const
Access function for j-th weight for the i-th derivative.
Definition: timesteppers.h:594
a
const Scalar * a
Definition: level2_cplx_impl.h:32
k
char char char int int * k
Definition: level2_impl.h:374
Eigen::bfloat16_impl::pow
EIGEN_STRONG_INLINE EIGEN_DEVICE_FUNC bfloat16 pow(const bfloat16 &a, const bfloat16 &b)
Definition: BFloat16.h:625
calibrate.sigma
int sigma
Definition: calibrate.py:179
oomph::QuadTreeNames::W
@ W
Definition: quadtree.h:63
OOMPH_EXCEPTION_LOCATION
#define OOMPH_EXCEPTION_LOCATION
Definition: oomph_definitions.h:61
OOMPH_CURRENT_FUNCTION
#define OOMPH_CURRENT_FUNCTION
Definition: oomph_definitions.h:86

References a, b, Global_Parameters::body_force(), Constitutive::Constitutive_law_pt, DIM, G, mathsFunc::gamma(), i, J, j, k, 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.

Referenced by oomph::PVDEquations< DIM >::fill_in_contribution_to_jacobian(), and oomph::PVDEquations< DIM >::fill_in_contribution_to_residuals().

◆ get_d_stress_dG_upper()

template<unsigned DIM>
void oomph::PVDEquations< DIM >::get_d_stress_dG_upper ( const DenseMatrix< double > &  g,
const DenseMatrix< double > &  G,
const DenseMatrix< double > &  sigma,
RankFourTensor< double > &  d_sigma_dG 
)
inlineprotected

Return the derivatives of the 2nd Piola Kirchhoff stress tensor, as calculated from the constitutive law: Pass metric tensors in the stress free and current configurations and the current value of the the stress tensor.

573  {
574 #ifdef PARANOID
575  // If the pointer to the constitutive law hasn't been set, issue an error
576  if (this->Constitutive_law_pt == 0)
577  {
578  // Write an error message
579  std::string error_message =
580  "Elements derived from PVDEquations must have a constitutive law:\n";
581  error_message +=
582  "set one using the constitutive_law_pt() member function";
583  // Throw the error
584  throw OomphLibError(
585  error_message, OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION);
586  }
587 #endif
588  // Only bother with the symmetric part by passing false as last entry
589  this->Constitutive_law_pt->calculate_d_second_piola_kirchhoff_stress_dG(
590  g, G, sigma, d_sigma_dG, false);
591  }
oomph::ConstitutiveLaw::calculate_d_second_piola_kirchhoff_stress_dG
virtual void calculate_d_second_piola_kirchhoff_stress_dG(const DenseMatrix< double > &g, const DenseMatrix< double > &G, const DenseMatrix< double > &sigma, RankFourTensor< double > &d_sigma_dG, const bool &symmetrize_tensor=true)
Definition: constitutive_laws.cc:352
oomph::Global_string_for_annotation::string
std::string string(const unsigned &i)
Definition: oomph_definitions.cc:286

References oomph::ConstitutiveLaw::calculate_d_second_piola_kirchhoff_stress_dG(), oomph::PVDEquationsBase< DIM >::Constitutive_law_pt, G, OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION, calibrate::sigma, and oomph::Global_string_for_annotation::string().

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

◆ get_stress() [1/2]

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

Return the 2nd Piola Kirchhoff stress tensor, as calculated from the constitutive law: Pass metric tensors in the stress free and current configurations.

546  {
547 #ifdef PARANOID
548  // If the pointer to the constitutive law hasn't been set, issue an error
549  if (this->Constitutive_law_pt == 0)
550  {
551  // Write an error message
552  std::string error_message =
553  "Elements derived from PVDEquations must have a constitutive law:\n";
554  error_message +=
555  "set one using the constitutive_law_pt() member function";
556  // Throw the error
557  throw OomphLibError(
558  error_message, OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION);
559  }
560 #endif
561  this->Constitutive_law_pt->calculate_second_piola_kirchhoff_stress(
562  g, G, sigma);
563  }
oomph::ConstitutiveLaw::calculate_second_piola_kirchhoff_stress
virtual void calculate_second_piola_kirchhoff_stress(const DenseMatrix< double > &g, const DenseMatrix< double > &G, DenseMatrix< double > &sigma)=0

References oomph::ConstitutiveLaw::calculate_second_piola_kirchhoff_stress(), oomph::PVDEquationsBase< DIM >::Constitutive_law_pt, G, OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION, calibrate::sigma, and oomph::Global_string_for_annotation::string().

◆ get_stress() [2/2]

template<unsigned DIM>
void oomph::PVDEquations< DIM >::get_stress ( const Vector< double > &  s,
DenseMatrix< double > &  sigma 
)
virtual

Return the 2nd Piola Kirchoff stress tensor, as calculated from the constitutive law at specified local coordinate

Compute the contravariant second Piola Kirchoff stress at a given local coordinate. Note: this replicates a lot of code that is already coontained in get_residuals() but without sacrificing efficiency (re-computing the shape functions several times) or creating helper functions with horrendous interfaces (to pass all the functions which shouldn't be recomputed) about this is unavoidable.

Implements oomph::PVDEquationsBase< DIM >.

953  {
954  // Find out how many nodes there are
955  unsigned n_node = this->nnode();
956 
957  // Find out how many positional dofs there are
958  unsigned n_position_type = this->nnodal_position_type();
959 
960  // Set up memory for the shape functions
961  Shape psi(n_node, n_position_type);
962  DShape dpsidxi(n_node, n_position_type, DIM);
963 
964  // Call the derivatives of the shape functions (ignore Jacobian)
965  (void)this->dshape_lagrangian(s, psi, dpsidxi);
966 
967  // Lagrangian coordinates
968  Vector<double> xi(DIM);
969  this->interpolated_xi(s, xi);
970 
971  // Get isotropic growth factor
972  double gamma;
973  // Dummy integration point
974  unsigned ipt = 0;
975  this->get_isotropic_growth(ipt, s, xi, gamma);
976 
977  // We use Cartesian coordinates as the reference coordinate
978  // system. In this case the undeformed metric tensor is always
979  // the identity matrix -- stretched by the isotropic growth
980  double diag_entry = pow(gamma, 2.0 / double(DIM));
981  DenseMatrix<double> g(DIM);
982  for (unsigned i = 0; i < DIM; i++)
983  {
984  for (unsigned j = 0; j < DIM; j++)
985  {
986  if (i == j)
987  {
988  g(i, j) = diag_entry;
989  }
990  else
991  {
992  g(i, j) = 0.0;
993  }
994  }
995  }
996 
997 
998  // Calculate interpolated values of the derivative of global position
999  // wrt lagrangian coordinates
1000  DenseMatrix<double> interpolated_G(DIM);
1001 
1002  // Initialise to zero
1003  for (unsigned i = 0; i < DIM; i++)
1004  {
1005  for (unsigned j = 0; j < DIM; j++)
1006  {
1007  interpolated_G(i, j) = 0.0;
1008  }
1009  }
1010 
1011  // Calculate displacements and derivatives
1012  for (unsigned l = 0; l < n_node; l++)
1013  {
1014  // Loop over positional dofs
1015  for (unsigned k = 0; k < n_position_type; k++)
1016  {
1017  // Loop over displacement components (deformed position)
1018  for (unsigned i = 0; i < DIM; i++)
1019  {
1020  // Loop over derivative directions
1021  for (unsigned j = 0; j < DIM; j++)
1022  {
1023  interpolated_G(j, i) +=
1024  this->nodal_position_gen(l, k, i) * dpsidxi(l, k, j);
1025  }
1026  }
1027  }
1028  }
1029 
1030  // Declare and calculate the deformed metric tensor
1031  DenseMatrix<double> G(DIM);
1032  // Assign values of G
1033  for (unsigned i = 0; i < DIM; i++)
1034  {
1035  // Do upper half of matrix
1036  // Note that j must be signed here for the comparison test to work
1037  // Also i must be cast to an int
1038  for (int j = (DIM - 1); j >= static_cast<int>(i); j--)
1039  {
1040  // Initialise G(i,j) to zero
1041  G(i, j) = 0.0;
1042  // Now calculate the dot product
1043  for (unsigned k = 0; k < DIM; k++)
1044  {
1045  G(i, j) += interpolated_G(i, k) * interpolated_G(j, k);
1046  }
1047  }
1048  // Matrix is symmetric so just copy lower half
1049  for (int j = (i - 1); j >= 0; j--)
1050  {
1051  G(i, j) = G(j, i);
1052  }
1053  }
1054 
1055  // Now calculate the stress tensor from the constitutive law
1056  get_stress(g, G, sigma);
1057  }
oomph::SolidFiniteElement::dshape_lagrangian
double dshape_lagrangian(const Vector< double > &s, Shape &psi, DShape &dpsidxi) const
Definition: elements.cc:6710

References DIM, G, mathsFunc::gamma(), i, j, k, Eigen::bfloat16_impl::pow(), s, and calibrate::sigma.

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

◆ output() [1/4]

template<unsigned DIM>
void oomph::PVDEquations< DIM >::output ( FILE *  file_pt)
inlinevirtual

C-style output: x,y,[z],xi0,xi1,[xi2],gamma.

Reimplemented from oomph::FiniteElement.

Reimplemented in oomph::TPVDBubbleEnrichedElement< DIM, NNODE_1D >, oomph::TPVDElement< DIM, NNODE_1D >, oomph::HermitePVDElement< DIM >, oomph::QPVDElement< DIM, NNODE_1D >, oomph::QPVDElement< DIM, 3 >, oomph::PseudoSolidNodeUpdateElement< TCrouzeixRaviartElement< 2 >, TPVDBubbleEnrichedElement< 2, 3 > >, oomph::PseudoSolidNodeUpdateElement< TTaylorHoodElement< 2 >, TPVDElement< 2, 3 > >, oomph::PseudoSolidNodeUpdateElement< GeneralisedNewtonianAxisymmetricTTaylorHoodElement, TPVDElement< 2, 3 > >, oomph::PseudoSolidNodeUpdateElement< AxisymmetricTTaylorHoodElement, TPVDElement< 2, 3 > >, and oomph::PseudoSolidNodeUpdateElement< GeneralisedNewtonianTTaylorHoodElement< 2 >, TPVDElement< 2, 3 > >.

518  {
519  unsigned n_plot = 5;
520  output(file_pt, n_plot);
521  }
oomph::PVDEquations::output
void output(std::ostream &outfile)
Output: x,y,[z],xi0,xi1,[xi2],gamma.
Definition: solid_elements.h:506

References oomph::PVDEquations< DIM >::output().

◆ output() [2/4]

template<unsigned DIM>
void oomph::PVDEquations< DIM >::output ( FILE *  file_pt,
const unsigned &  n_plot 
)
virtual

Output: x,y,[z],xi0,xi1,[xi2],gamma.

C-style output: x,y,[z],xi0,xi1,[xi2],gamma.

Reimplemented from oomph::FiniteElement.

Reimplemented in oomph::TPVDBubbleEnrichedElement< DIM, NNODE_1D >, oomph::TPVDElement< DIM, NNODE_1D >, oomph::HermitePVDElement< DIM >, oomph::QPVDElement< DIM, NNODE_1D >, oomph::QPVDElement< DIM, 3 >, oomph::PseudoSolidNodeUpdateElement< TCrouzeixRaviartElement< 2 >, TPVDBubbleEnrichedElement< 2, 3 > >, oomph::PseudoSolidNodeUpdateElement< TTaylorHoodElement< 2 >, TPVDElement< 2, 3 > >, oomph::PseudoSolidNodeUpdateElement< GeneralisedNewtonianAxisymmetricTTaylorHoodElement, TPVDElement< 2, 3 > >, oomph::PseudoSolidNodeUpdateElement< AxisymmetricTTaylorHoodElement, TPVDElement< 2, 3 > >, and oomph::PseudoSolidNodeUpdateElement< GeneralisedNewtonianTTaylorHoodElement< 2 >, TPVDElement< 2, 3 > >.

630  {
631  // Set output Vector
632  Vector<double> s(DIM);
633  Vector<double> x(DIM);
634  Vector<double> xi(DIM);
635 
636  switch (DIM)
637  {
638  case 2:
639 
640  // Tecplot header info
641  // outfile << "ZONE I=" << n_plot << ", J=" << n_plot << std::endl;
642  fprintf(file_pt, "ZONE I=%i, J=%i\n", n_plot, n_plot);
643 
644  // Loop over element nodes
645  for (unsigned l2 = 0; l2 < n_plot; l2++)
646  {
647  s[1] = -1.0 + l2 * 2.0 / (n_plot - 1);
648  for (unsigned l1 = 0; l1 < n_plot; l1++)
649  {
650  s[0] = -1.0 + l1 * 2.0 / (n_plot - 1);
651 
652  // Get Eulerian and Lagrangian coordinates
653  this->interpolated_x(s, x);
654  this->interpolated_xi(s, xi);
655 
656  // Get isotropic growth
657  double gamma;
658  // Dummy integration point
659  unsigned ipt = 0;
660  this->get_isotropic_growth(ipt, s, xi, gamma);
661 
662  // Output the x,y,..
663  for (unsigned i = 0; i < DIM; i++)
664  {
665  // outfile << x[i] << " ";
666  fprintf(file_pt, "%g ", x[i]);
667  }
668  // Output xi0,xi1,..
669  for (unsigned i = 0; i < DIM; i++)
670  {
671  // outfile << xi[i] << " ";
672  fprintf(file_pt, "%g ", xi[i]);
673  }
674  // Output growth
675  // outfile << gamma << " ";
676  // outfile << std::endl;
677  fprintf(file_pt, "%g \n", gamma);
678  }
679  }
680  // outfile << std::endl;
681  fprintf(file_pt, "\n");
682 
683  break;
684 
685  case 3:
686 
687  // Tecplot header info
688  // outfile << "ZONE I=" << n_plot << ", J=" << n_plot << std::endl;
689  fprintf(file_pt, "ZONE I=%i, J=%i, K=%i \n", n_plot, n_plot, n_plot);
690 
691  // Loop over element nodes
692  for (unsigned l3 = 0; l3 < n_plot; l3++)
693  {
694  s[2] = -1.0 + l3 * 2.0 / (n_plot - 1);
695  for (unsigned l2 = 0; l2 < n_plot; l2++)
696  {
697  s[1] = -1.0 + l2 * 2.0 / (n_plot - 1);
698  for (unsigned l1 = 0; l1 < n_plot; l1++)
699  {
700  s[0] = -1.0 + l1 * 2.0 / (n_plot - 1);
701 
702  // Get Eulerian and Lagrangian coordinates
703  this->interpolated_x(s, x);
704  this->interpolated_xi(s, xi);
705 
706  // Get isotropic growth
707  double gamma;
708  // Dummy integration point
709  unsigned ipt = 0;
710  this->get_isotropic_growth(ipt, s, xi, gamma);
711 
712  // Output the x,y,z
713  for (unsigned i = 0; i < DIM; i++)
714  {
715  // outfile << x[i] << " ";
716  fprintf(file_pt, "%g ", x[i]);
717  }
718  // Output xi0,xi1,xi2
719  for (unsigned i = 0; i < DIM; i++)
720  {
721  // outfile << xi[i] << " ";
722  fprintf(file_pt, "%g ", xi[i]);
723  }
724  // Output growth
725  // outfile << gamma << " ";
726  // outfile << std::endl;
727  fprintf(file_pt, "%g \n", gamma);
728  }
729  }
730  }
731  // outfile << std::endl;
732  fprintf(file_pt, "\n");
733 
734  break;
735 
736  default:
737  std::ostringstream error_message;
738  error_message << "No output routine for PVDEquations<" << DIM
739  << "> elements -- write it yourself!" << std::endl;
740  throw OomphLibError(error_message.str(),
741  OOMPH_CURRENT_FUNCTION,
742  OOMPH_EXCEPTION_LOCATION);
743  }
744  }

References DIM, mathsFunc::gamma(), i, OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION, s, and plotDoE::x.

◆ output() [3/4]

template<unsigned DIM>
void oomph::PVDEquations< DIM >::output ( std::ostream &  outfile)
inlinevirtual

Output: x,y,[z],xi0,xi1,[xi2],gamma.

Reimplemented from oomph::FiniteElement.

Reimplemented in oomph::TPVDBubbleEnrichedElement< DIM, NNODE_1D >, oomph::TPVDElement< DIM, NNODE_1D >, oomph::HermitePVDElement< DIM >, oomph::QPVDElement< DIM, NNODE_1D >, oomph::QPVDElement< DIM, 3 >, oomph::PseudoSolidNodeUpdateElement< TCrouzeixRaviartElement< 2 >, TPVDBubbleEnrichedElement< 2, 3 > >, oomph::PseudoSolidNodeUpdateElement< TTaylorHoodElement< 2 >, TPVDElement< 2, 3 > >, oomph::PseudoSolidNodeUpdateElement< GeneralisedNewtonianAxisymmetricTTaylorHoodElement, TPVDElement< 2, 3 > >, oomph::PseudoSolidNodeUpdateElement< AxisymmetricTTaylorHoodElement, TPVDElement< 2, 3 > >, and oomph::PseudoSolidNodeUpdateElement< GeneralisedNewtonianTTaylorHoodElement< 2 >, TPVDElement< 2, 3 > >.

507  {
508  unsigned n_plot = 5;
509  output(outfile, n_plot);
510  }

Referenced by oomph::PVDEquations< DIM >::output(), oomph::QPVDElement< DIM, NNODE_1D >::output(), oomph::TPVDElement< DIM, NNODE_1D >::output(), and oomph::TPVDBubbleEnrichedElement< DIM, NNODE_1D >::output().

◆ output() [4/4]

template<unsigned DIM>
void oomph::PVDEquations< DIM >::output ( std::ostream &  outfile,
const unsigned &  n_plot 
)
virtual

Output: x,y,[z],xi0,xi1,[xi2],gamma.

Reimplemented from oomph::FiniteElement.

Reimplemented in oomph::TPVDBubbleEnrichedElement< DIM, NNODE_1D >, oomph::TPVDElement< DIM, NNODE_1D >, oomph::HermitePVDElement< DIM >, oomph::QPVDElement< DIM, NNODE_1D >, oomph::QPVDElement< DIM, 3 >, oomph::PseudoSolidNodeUpdateElement< TCrouzeixRaviartElement< 2 >, TPVDBubbleEnrichedElement< 2, 3 > >, oomph::PseudoSolidNodeUpdateElement< TTaylorHoodElement< 2 >, TPVDElement< 2, 3 > >, oomph::PseudoSolidNodeUpdateElement< GeneralisedNewtonianAxisymmetricTTaylorHoodElement, TPVDElement< 2, 3 > >, oomph::PseudoSolidNodeUpdateElement< AxisymmetricTTaylorHoodElement, TPVDElement< 2, 3 > >, and oomph::PseudoSolidNodeUpdateElement< GeneralisedNewtonianTTaylorHoodElement< 2 >, TPVDElement< 2, 3 > >.

576  {
577  Vector<double> x(DIM);
578  Vector<double> xi(DIM);
579  Vector<double> s(DIM);
580 
581  // Tecplot header info
582  outfile << this->tecplot_zone_string(n_plot);
583 
584  // Loop over plot points
585  unsigned num_plot_points = this->nplot_points(n_plot);
586  for (unsigned iplot = 0; iplot < num_plot_points; iplot++)
587  {
588  // Get local coordinates of plot point
589  this->get_s_plot(iplot, n_plot, s);
590 
591  // Get Eulerian and Lagrangian coordinates
592  this->interpolated_x(s, x);
593  this->interpolated_xi(s, xi);
594 
595  // Get isotropic growth
596  double gamma;
597  // Dummy integration point
598  unsigned ipt = 0;
599  this->get_isotropic_growth(ipt, s, xi, gamma);
600 
601  // Output the x,y,..
602  for (unsigned i = 0; i < DIM; i++)
603  {
604  outfile << x[i] << " ";
605  }
606 
607  // Output xi0,xi1,..
608  for (unsigned i = 0; i < DIM; i++)
609  {
610  outfile << xi[i] << " ";
611  }
612 
613  // Output growth
614  outfile << gamma;
615  outfile << std::endl;
616  }
617 
618 
619  // Write tecplot footer (e.g. FE connectivity lists)
620  this->write_tecplot_zone_footer(outfile, n_plot);
621  outfile << std::endl;
622  }

References DIM, mathsFunc::gamma(), i, s, and plotDoE::x.

◆ unpin_elemental_solid_pressure_dofs()

template<unsigned DIM>
void oomph::PVDEquations< DIM >::unpin_elemental_solid_pressure_dofs ( )
inlineprivatevirtual

Unpin all solid pressure dofs – empty as there are no pressures.

Implements oomph::PVDEquationsBase< DIM >.

596 {}
The documentation for this class was generated from the following files: