oomph::RefineablePVDEquationsWithPressure< DIM > Class Template Reference

Class for Refineable solid mechanics elements in near-incompressible/ incompressible formulation, so a pressure is included! In this case, the pressure interpolation is discontinuous, a la Crouzeix Raviart. More...

#include <refineable_solid_elements.h>

Inheritance diagram for oomph::RefineablePVDEquationsWithPressure< DIM >:

## Public Member Functions

RefineablePVDEquationsWithPressure ()
Constructor: More...

void fill_in_generic_residual_contribution_pvd_with_pressure (Vector< double > &residuals, DenseMatrix< double > &jacobian, DenseMatrix< double > &mass_matrix, const unsigned &flag)
Add element's contribution to elemental residual vector and/or Jacobian matrix flag=1: compute both flag=0: compute only residual vector. More...

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

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

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

void get_Z2_flux (const Vector< double > &s, Vector< double > &flux)
in strain tensor. More...

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

virtual Nodesolid_pressure_node_pt (const unsigned &l)

void further_build ()
Pass the generic stuff down to the sons. More...

void get_mass_matrix_diagonal (Vector< double > &mass_diag)
Compute the diagonal of the displacement mass matrix for LSC preconditioner. More...

Public Member Functions inherited from oomph::PVDEquationsWithPressure< DIM >
PVDEquationsWithPressure ()
Constructor, by default the element is NOT incompressible. More...

void get_stress (const Vector< double > &s, DenseMatrix< double > &sigma)
Return the 2nd Piola Kirchoff stress tensor, as calculated from the constitutive law at specified local coordinate. More...

bool is_incompressible () const
Return whether the material is incompressible. More...

void set_incompressible ()
Set the material to be incompressible. More...

void set_compressible ()
Set the material to be compressible. More...

virtual double solid_p (const unsigned &l)=0
Return the lth solid pressure. More...

virtual void set_solid_p (const unsigned &l, const double &p_value)=0
Set the lth solid pressure to p_value. More...

void fill_in_contribution_to_residuals (Vector< double > &residuals)
Fill in the residuals. More...

void fill_in_contribution_to_jacobian (Vector< double > &residuals, DenseMatrix< double > &jacobian)
Fill in contribution to Jacobian (either by FD or analytically, for the positional variables; control this via evaluate_jacobian_by_fd(). Note: Jacobian entries arising from derivatives w.r.t. pressure terms are always computed analytically. More...

void fill_in_contribution_to_jacobian_and_mass_matrix (Vector< double > &residuals, DenseMatrix< double > &jacobian, DenseMatrix< double > &mass_matrix)
Fill in contribution to Mass matrix and Jacobian (either by FD or analytically, for the positional variables; control this via evaluate_jacobian_by_fd(). Note: Jacobian entries arising from derivatives w.r.t. pressure terms are always computed analytically. Note that the Jacobian is multiplied by minus one to ensure that the mass matrix is positive semi-definite. More...

double interpolated_solid_p (const Vector< double > &s)
Return the interpolated_solid_pressure. More...

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

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

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

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

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

void get_mass_matrix_diagonal (Vector< double > &mass_diag)
Compute the diagonal of the displacement mass matrix for LSC preconditioner. More...

unsigned ndof_types () const
returns the number of DOF types associated with this element: displacement components and pressure More...

void get_dof_numbers_for_unknowns (std::list< std::pair< unsigned long, unsigned > > &dof_lookup_list) const
Create a list of pairs for all unknowns in this element, so that the first entry in each pair contains the global equation number of the unknown, while the second one contains the number of the "DOF" that this unknown is associated with. (Function can obviously only be called if the equation numbering scheme has been set up.) There are DIM+1 types of DOF: displacement compnents and pressure. More...

Public Member Functions inherited from oomph::PVDEquationsBase< DIM >
PVDEquationsBase ()
Constructor: Set null pointers for constitutive law and for isotropic growth function. Set physical parameter values to default values, enable inertia and set body force to zero. Default evaluation of Jacobian: analytically rather than by FD. More...

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...

IsotropicGrowthFctPtisotropic_growth_fct_pt ()
Access function: Pointer to isotropic growth function. More...

PrestressFctPtprestress_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...

BodyForceFctPtbody_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
Return the number of solid pressure degrees of freedom Default is that there are no solid pressures. More...

virtual int solid_p_local_eqn (const unsigned &i) const
Return the local degree of freedom associated with the i-th solid pressure. Default is that there are none. More...

virtual int solid_p_nodal_index () const
Return the index at which the solid pressure is stored if it is stored at the nodes. If not stored at the nodes this will return a negative number. More...

virtual void unpin_elemental_solid_pressure_dofs ()=0
Unpin all solid pressure dofs in the element. More...

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)
Return the deformed covariant basis vectors at specified local coordinate: def_covariant_basis(i,j) is the j-th component of the i-th basis vector. More...

void get_principal_stress (const Vector< double > &s, DenseMatrix< double > &principal_stress_vector, Vector< double > &principal_stress)
Compute principal stress vectors and (scalar) principal stresses at specified local coordinate. principal_stress_vector(i,j) is the j-th component of the i-th principal stress vector. More...

virtual void get_isotropic_growth (const unsigned &ipt, const Vector< double > &s, const Vector< double > &xi, double &gamma) const
Evaluate isotropic growth function at Lagrangian coordinate xi and/or local coordinate s. (returns 1, i.e. no growth, if no function pointer has been set) This function is virtual to allow overloading in multi-physics problems where the growth function might be determined by another system of equations. More...

void body_force (const Vector< double > &xi, Vector< double > &b) const
Evaluate body force at Lagrangian coordinate xi at present time (returns zero vector if no body force function pointer has been set) More...

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)
Return (i,j)-th component of second Piola Kirchhoff membrane prestress at Lagrangian coordinate xi. More...

Public Member Functions inherited from oomph::SolidFiniteElement
void set_lagrangian_dimension (const unsigned &lagrangian_dimension)
Set the lagrangian dimension of the element — the number of lagrangian coordinates stored at the nodes in the element. More...

virtual bool has_internal_solid_data ()
Return whether there is internal solid data (e.g. discontinuous solid pressure). At present, this is used to report an error in setting initial conditions for ElasticProblems which can't handle such cases. The default is false. More...

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

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

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

double zeta_nodal (const unsigned &n, const unsigned &k, const unsigned &i) const
In a SolidFiniteElement, the "global" intrinsic coordinate of the element when viewed as part of a compound geometric object (a Mesh) is, by default, the Lagrangian coordinate Note the assumption here is that we are always using isoparameteric elements in which the lagrangian coordinate is interpolated by the same shape functions as the eulerian coordinate. More...

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
Eulerian and Lagrangian coordinates as function of the local coordinates: The Eulerian position is returned in FE-interpolated form (x_fe) and then in the form obtained from the "current" MacroElement representation (if it exists – if not, x is the same as x_fe). This allows the Domain/MacroElement- based representation to be used to apply displacement boundary conditions exactly. Ditto for the Lagrangian coordinates returned in xi_fe and xi. (Broken virtual – overload in specific geometric element class if you want to use this functionality.) More...

virtual void set_macro_elem_pt (MacroElement *macro_elem_pt)
Set pointer to MacroElement – overloads generic version and uses the MacroElement also as the default for the "undeformed" configuration. This assignment must be overwritten with set_undeformed_macro_elem_pt(...) if the deformation of the solid body is driven by a deformation of the "current" Domain/MacroElement representation of it's boundary. Can be overloaded in derived classes to perform additional tasks. More...

virtual void set_macro_elem_pt (MacroElement *macro_elem_pt, MacroElement *undeformed_macro_elem_pt)
Set pointers to "current" and "undeformed" MacroElements. Can be overloaded in derived classes to perform additional tasks. More...

void set_undeformed_macro_elem_pt (MacroElement *undeformed_macro_elem_pt)
Set pointer to "undeformed" macro element. Can be overloaded in derived classes to perform additional tasks. More...

MacroElementundeformed_macro_elem_pt ()
Access function to pointer to "undeformed" macro element. More...

double dshape_lagrangian (const Vector< double > &s, Shape &psi, DShape &dpsidxi) const
Calculate shape functions and derivatives w.r.t. Lagrangian coordinates at local coordinate s. Returns the Jacobian of the mapping from Lagrangian to local coordinates. More...

virtual double dshape_lagrangian_at_knot (const unsigned &ipt, Shape &psi, DShape &dpsidxi) const
Return the geometric shape functions and also first derivatives w.r.t. Lagrangian coordinates at ipt-th integration point. More...

double d2shape_lagrangian (const Vector< double > &s, Shape &psi, DShape &dpsidxi, DShape &d2psidxi) const
Compute the geometric shape functions and also first and second derivatives w.r.t. Lagrangian coordinates at local coordinate s; Returns Jacobian of mapping from Lagrangian to local coordinates. Numbering: 1D: d2pidxi(i,0) = 2D: d2psidxi(i,0) = d2psidxi(i,1) = d2psidxi(i,2) = 3D: d2psidxi(i,0) = d2psidxi(i,1) = d2psidxi(i,2) = d2psidxi(i,3) = d2psidxi(i,4) = d2psidxi(i,5) = . More...

virtual double d2shape_lagrangian_at_knot (const unsigned &ipt, Shape &psi, DShape &dpsidxi, DShape &d2psidxi) const
Return the geometric shape functions and also first and second derivatives w.r.t. Lagrangian coordinates at the ipt-th integration point. Returns Jacobian of mapping from Lagrangian to local coordinates. Numbering: 1D: d2pidxi(i,0) = 2D: d2psidxi(i,0) = d2psidxi(i,1) = d2psidxi(i,2) = 3D: d2psidxi(i,0) = d2psidxi(i,1) = d2psidxi(i,2) = d2psidxi(i,3) = d2psidxi(i,4) = d2psidxi(i,5) = . More...

unsigned lagrangian_dimension () const
Return the number of Lagrangian coordinates that the element requires at all nodes. This is by default the elemental dimension. If we ever need any other case, it can be implemented. More...

unsigned nnodal_lagrangian_type () const
Return the number of types of (generalised) nodal Lagrangian coordinates required to interpolate the Lagrangian coordinates in the element. (E.g. 1 for Lagrange-type elements; 2 for Hermite beam elements; 4 for Hermite shell elements). Default value is 1. Needs to be overloaded for any other element. More...

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

Nodeconstruct_node (const unsigned &n, TimeStepper *const &time_stepper_pt)
Construct the local node n and return a pointer to it. Additionally, create storage for ‘history’ values as required by timestepper. More...

Nodeconstruct_boundary_node (const unsigned &n)
Construct the local node n and return a pointer to it. in the case when it is a boundary node; that is it MAY be located on a Mesh boundary. More...

Nodeconstruct_boundary_node (const unsigned &n, TimeStepper *const &time_stepper_pt)
Construct the local node n and return a pointer to it, in the case when the node MAY be located on a boundary. Additionally, create storage for ‘history’ values as required by timestepper. More...

virtual void assign_all_generic_local_eqn_numbers (const bool &store_local_dof_pt)
Overload assign_all_generic_local_equation numbers to include the data associated with solid dofs. It remains virtual so that it can be overloaded by RefineableSolidElements. If the boolean argument is true then the degrees of freedom are stored in Dof_pt. More...

void describe_local_dofs (std::ostream &out, const std::string &current_string) const
Function to describe the local dofs of the element. The ostream specifies the output stream to which the description is written; the string stores the currently assembled output that is ultimately written to the output stream by Data::describe_dofs(...); it is typically built up incrementally as we descend through the call hierarchy of this function when called from Problem::describe_dofs(...) More...

double raw_lagrangian_position (const unsigned &n, const unsigned &i) const
Return i-th Lagrangian coordinate at local node n without using the hanging representation. More...

double raw_lagrangian_position_gen (const unsigned &n, const unsigned &k, const unsigned &i) const
Return Generalised Lagrangian coordinate at local node n. ‘Direction’ i, ‘Type’ k. Does not use the hanging node representation. More...

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
Return Generalised Lagrangian coordinate at local node n. ‘Direction’ i, ‘Type’ k. More...

virtual double interpolated_xi (const Vector< double > &s, const unsigned &i) const
Return i-th FE-interpolated Lagrangian coordinate xi[i] at local coordinate s. More...

virtual void interpolated_xi (const Vector< double > &s, Vector< double > &xi) const
Compute FE interpolated Lagrangian coordinate vector xi[] at local coordinate s as Vector. More...

virtual void interpolated_dxids (const Vector< double > &s, DenseMatrix< double > &dxids) const
Compute derivatives of FE-interpolated Lagrangian coordinates xi with respect to local coordinates: dxids[i][j]=dxi_i/ds_j. More...

virtual void J_lagrangian (const Vector< double > &s) const
Return the Jacobian of mapping from local to Lagrangian coordinates at local position s. NOT YET IMPLEMENTED. More...

virtual double J_lagrangian_at_knot (const unsigned &ipt) const
Return the Jacobian of the mapping from local to Lagrangian coordinates at the ipt-th integration point. NOT YET IMPLEMENTED. More...

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

void enable_solve_for_consistent_newmark_accel ()
Set to alter the problem being solved when assigning the initial conditions for time-dependent problems: solve for the history value that corresponds to the acceleration in the Newmark scheme by demanding that the PDE is satisifed at the initial time. In this case the Jacobian is replaced by the mass matrix. More...

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

MultiplierFctPtmultiplier_fct_pt ()
Access function: Pointer to multiplicator function for assignment of consistent assignement of initial conditions for Newmark scheme. More...

MultiplierFctPt multiplier_fct_pt () const
Access function: Pointer to multiplicator function for assignment of consistent assignement of initial conditions for Newmark scheme (const version) More...

virtual void get_residuals_for_solid_ic (Vector< double > &residuals)
Compute the residuals for the setup of an initial condition. The global equations are: More...

void fill_in_residuals_for_solid_ic (Vector< double > &residuals)
Fill in the residuals for the setup of an initial condition. The global equations are: More...

void fill_in_jacobian_for_solid_ic (Vector< double > &residuals, DenseMatrix< double > &jacobian)
Fill in the residuals and Jacobian for the setup of an initial condition. The global equations are: More...

void fill_in_jacobian_for_newmark_accel (DenseMatrix< double > &jacobian)
Fill in the contributions of the Jacobian matrix for the consistent assignment of the initial "accelerations" in Newmark scheme. In this case the Jacobian is the mass matrix. More...

void compute_norm (double &el_norm)
Calculate the L2 norm of the displacement u=R-r to overload the compute_norm function in the GeneralisedElement base class. More...

int position_local_eqn (const unsigned &n, const unsigned &k, const unsigned &j) const
Access function that returns the local equation number that corresponds to the j-th coordinate of the k-th position-type at the n-th local node. More...

Public Member Functions inherited from oomph::FiniteElement
void set_dimension (const unsigned &dim)
Set the dimension of the element and initially set the dimension of the nodes to be the same as the dimension of the element. More...

void set_nodal_dimension (const unsigned &nodal_dim)
Set the dimension of the nodes in the element. This will typically only be required when constructing FaceElements or in beam and shell type elements where a lower dimensional surface is embedded in a higher dimensional space. More...

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)
Set the number of nodes in the element to n, by resizing the storage for pointers to the Node objects. More...

int nodal_local_eqn (const unsigned &n, const unsigned &i) const
Return the local equation number corresponding to the i-th value at the n-th local node. More...

double dJ_eulerian_at_knot (const unsigned &ipt, Shape &psi, DenseMatrix< double > &djacobian_dX) const
Compute the geometric shape functions (psi) at integration point ipt. Return the determinant of the jacobian of the mapping (detJ). Additionally calculate the derivatives of "detJ" w.r.t. the nodal coordinates. More...

FiniteElement ()
Constructor. More...

virtual ~FiniteElement ()
The destructor cleans up the static memory allocated for shape function storage. Internal and external data get wiped by the GeneralisedElement destructor; nodes get killed in mesh destructor. More...

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
Adjust local coordinates so that they're located inside the element. More...

Compute centre of gravity of all nodes and radius of node that is furthest from it. Used to assess approximately if a point is likely to be contained with an element in locate_zeta-like operations. More...

virtual void local_coordinate_of_node (const unsigned &j, Vector< double > &s) const
Get local coordinates of node j in the element; vector sets its own size (broken virtual) More...

virtual void local_fraction_of_node (const unsigned &j, Vector< double > &s_fraction)
Get the local fraction of the node j in the element A dumb, but correct default implementation is provided. More...

virtual double local_one_d_fraction_of_node (const unsigned &n1d, const unsigned &i)
Get the local fraction of any node in the n-th position in a one dimensional expansion along the i-th local coordinate. More...

MacroElementmacro_elem_pt ()
Access function to pointer to macro element. More...

void get_x (const Vector< double > &s, Vector< double > &x) const
Global coordinates as function of local coordinates. Either via FE representation or via macro-element (if Macro_elem_pt!=0) More...

void get_x (const unsigned &t, const Vector< double > &s, Vector< double > &x)
Global coordinates as function of local coordinates at previous time "level" t (t=0: present; t>0: previous). Either via FE representation of QElement or via macro-element (if Macro_elem_pt!=0). More...

virtual void get_x_from_macro_element (const Vector< double > &s, Vector< double > &x) const
Global coordinates as function of local coordinates using macro element representation. (Broken virtual — this must be overloaded in specific geometric element classes) More...

virtual void get_x_from_macro_element (const unsigned &t, const Vector< double > &s, Vector< double > &x)
Global coordinates as function of local coordinates at previous time "level" t (t=0: present; t>0: previous). using macro element representation (Broken virtual – overload in specific geometric element class if you want to use this functionality.) More...

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
Calculate the geometric shape functions at local coordinate s. This function must be overloaded for each specific geometric element. More...

virtual void shape_at_knot (const unsigned &ipt, Shape &psi) const
Return the geometric shape function at the ipt-th integration point. More...

virtual void dshape_local (const Vector< double > &s, Shape &psi, DShape &dpsids) const
Function to compute the geometric shape functions and derivatives w.r.t. local coordinates at local coordinate s. This function must be overloaded for each specific geometric element. (Broken virtual function — specifies the interface) More...

virtual void dshape_local_at_knot (const unsigned &ipt, Shape &psi, DShape &dpsids) const
Return the geometric shape function and its derivative w.r.t. the local coordinates at the ipt-th integration point. More...

virtual void d2shape_local (const Vector< double > &s, Shape &psi, DShape &dpsids, DShape &d2psids) const
Function to compute the geometric shape functions and also first and second derivatives w.r.t. local coordinates at local coordinate s. This function must be overloaded for each specific geometric element (if required). (Broken virtual function — specifies the interface). Numbering: 1D: d2psids(i,0) = 2D: d2psids(i,0) = d2psids(i,1) = d2psids(i,2) = 3D: d2psids(i,0) = d2psids(i,1) = d2psids(i,2) = d2psids(i,3) = d2psids(i,4) = d2psids(i,5) = . More...

virtual void d2shape_local_at_knot (const unsigned &ipt, Shape &psi, DShape &dpsids, DShape &d2psids) const
Return the geometric shape function and its first and second derivatives w.r.t. the local coordinates at the ipt-th integration point. Numbering: 1D: d2psids(i,0) = 2D: d2psids(i,0) = d2psids(i,1) = d2psids(i,2) = 3D: d2psids(i,0) = d2psids(i,1) = d2psids(i,2) = d2psids(i,3) = d2psids(i,4) = d2psids(i,5) = . More...

virtual double J_eulerian (const Vector< double > &s) const
Return the Jacobian of mapping from local to global coordinates at local position s. More...

virtual double J_eulerian_at_knot (const unsigned &ipt) const
Return the Jacobian of the mapping from local to global coordinates at the ipt-th integration point. More...

void check_J_eulerian_at_knots (bool &passed) const
Check that Jacobian of mapping between local and Eulerian coordinates at all integration points is positive. More...

void check_jacobian (const double &jacobian) const
Helper function used to check for singular or negative Jacobians in the transform from local to global or Lagrangian coordinates. More...

double dshape_eulerian (const Vector< double > &s, Shape &psi, DShape &dpsidx) const
Compute the geometric shape functions and also first derivatives w.r.t. global coordinates at local coordinate s; Returns Jacobian of mapping from global to local coordinates. More...

virtual double dshape_eulerian_at_knot (const unsigned &ipt, Shape &psi, DShape &dpsidx) const
Return the geometric shape functions and also first derivatives w.r.t. global coordinates at the ipt-th integration point. More...

virtual double dshape_eulerian_at_knot (const unsigned &ipt, Shape &psi, DShape &dpsi, DenseMatrix< double > &djacobian_dX, RankFourTensor< double > &d_dpsidx_dX) const
Compute the geometric shape functions (psi) and first derivatives w.r.t. global coordinates (dpsidx) at the ipt-th integration point. Return the determinant of the jacobian of the mapping (detJ). Additionally calculate the derivatives of both "detJ" and "dpsidx" w.r.t. the nodal coordinates. More...

double d2shape_eulerian (const Vector< double > &s, Shape &psi, DShape &dpsidx, DShape &d2psidx) const
Compute the geometric shape functions and also first and second derivatives w.r.t. global coordinates at local coordinate s; Returns Jacobian of mapping from global to local coordinates. Numbering: 1D: d2psidx(i,0) = 2D: d2psidx(i,0) = d2psidx(i,1) = d2psidx(i,2) = 3D: d2psidx(i,0) = d2psidx(i,1) = d2psidx(i,2) = d2psidx(i,3) = d2psidx(i,4) = d2psidx(i,5) = . More...

virtual double d2shape_eulerian_at_knot (const unsigned &ipt, Shape &psi, DShape &dpsidx, DShape &d2psidx) const
Return the geometric shape functions and also first and second derivatives w.r.t. global coordinates at ipt-th integration point. Numbering: 1D: d2psidx(i,0) = 2D: d2psidx(i,0) = d2psidx(i,1) = d2psidx(i,2) = 3D: d2psidx(i,0) = d2psidx(i,1) = d2psidx(i,2) = d2psidx(i,3) = d2psidx(i,4) = d2psidx(i,5) = . More...

virtual void describe_nodal_local_dofs (std::ostream &out, const std::string &current_string) const
Function to describe the local dofs of the element[s]. The ostream specifies the output stream to which the description is written; the string stores the currently assembled output that is ultimately written to the output stream by Data::describe_dofs(...); it is typically built up incrementally as we descend through the call hierarchy of this function when called from Problem::describe_dofs(...) More...

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
Return the number of nodes along one edge of the element Default is to return zero — must be overloaded by geometric elements. More...

double raw_nodal_position (const unsigned &n, const unsigned &i) const
Return the i-th coordinate at local node n. Do not use the hanging node representation. NOTE: Moved to cc file because of a possible compiler bug in gcc (yes, really!). The move to the cc file avoids inlining which appears to cause problems (only) when compiled with gcc and -O3; offensive "illegal read" is in optimised-out section of code and data that is allegedly illegal is readily readable (by other means) just before this function is called so I can't really see how we could possibly be responsible for this... More...

double raw_nodal_position (const unsigned &t, const unsigned &n, const unsigned &i) const
Return the i-th coordinate at local node n, at time level t (t=0: present; t>0: previous time level). Do not use the hanging node representation. More...

double raw_dnodal_position_dt (const unsigned &n, const unsigned &i) const
Return the i-th component of nodal velocity: dx/dt at local node n. Do not use the hanging node representation. More...

double raw_dnodal_position_dt (const unsigned &n, const unsigned &j, const unsigned &i) const
Return the i-th component of j-th derivative of nodal position: d^jx/dt^j at node n. Do not use the hanging node representation. More...

double raw_nodal_position_gen (const unsigned &n, const unsigned &k, const unsigned &i) const
Return the value of the k-th type of the i-th positional variable at the local node n. Do not use the hanging node representation. More...

double raw_nodal_position_gen (const unsigned &t, const unsigned &n, const unsigned &k, const unsigned &i) const
Return the generalised nodal position (type k, i-th variable) at previous timesteps at local node n. Do not use the hanging node representation. More...

double raw_dnodal_position_gen_dt (const unsigned &n, const unsigned &k, const unsigned &i) const
i-th component of time derivative (velocity) of the generalised position, dx(k,i)/dt at local node n. ‘Type’: k; Coordinate direction: i. Do not use the hanging node representation. More...

double raw_dnodal_position_gen_dt (const unsigned &j, const unsigned &n, const unsigned &k, const unsigned &i) const
i-th component of j-th time derivative of the generalised position, dx(k,i)/dt at local node n. ‘Type’: k; Coordinate direction: i. Do not use the hanging node representation. More...

double nodal_position (const unsigned &n, const unsigned &i) const
Return the i-th coordinate at local node n. If the node is hanging, the appropriate interpolation is handled by the position function in the Node class. More...

double nodal_position (const unsigned &t, const unsigned &n, const unsigned &i) const
Return the i-th coordinate at local node n, at time level t (t=0: present; t>0: previous time level) Returns suitably interpolated version for hanging nodes. More...

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
Return the i-th component of j-th derivative of nodal position: d^jx/dt^j at node n. More...

double nodal_position_gen (const unsigned &n, const unsigned &k, const unsigned &i) const
Return the value of the k-th type of the i-th positional variable at the local node n. More...

double nodal_position_gen (const unsigned &t, const unsigned &n, const unsigned &k, const unsigned &i) const
Return the generalised nodal position (type k, i-th variable) at previous timesteps at local node n. More...

double dnodal_position_gen_dt (const unsigned &n, const unsigned &k, const unsigned &i) const
i-th component of time derivative (velocity) of the generalised position, dx(k,i)/dt at local node n. ‘Type’: k; Coordinate direction: i. More...

double dnodal_position_gen_dt (const unsigned &j, const unsigned &n, const unsigned &k, const unsigned &i) const
i-th component of j-th time derivative of the generalised position, dx(k,i)/dt at local node n. ‘Type’: k; Coordinate direction: i. More...

virtual void disable_ALE ()
This is an empty function that establishes a uniform interface for all (derived) elements that involve time-derivatives. Such elements are/should be implemented in ALE form to allow mesh motions. The additional expense associated with the computation of the mesh velocities is, of course, superfluous if the elements are used in problems in which the mesh is stationary. This function should therefore be overloaded in all derived elements that are formulated in ALE form to suppress the computation of the mesh velocities. The user disables the ALE functionality at his/her own risk! If the mesh does move after all, then the results will be wrong. Here we simply issue a warning message stating that the empty function has been called. More...

virtual void enable_ALE ()
(Re-)enable ALE, i.e. take possible mesh motion into account when evaluating the time-derivative. This function is empty and simply establishes a common interface for all derived elements that are formulated in ALE form. More...

virtual unsigned required_nvalue (const unsigned &n) const
Number of values that must be stored at local node n by the element. The default is 0, until over-ridden by a particular element. For example, a Poisson equation requires only one value to be stored at each node; 2D Navier–Stokes equations require two values (velocity components) to be stored at each Node (provided that the pressure interpolation is discontinuous). More...

unsigned nnodal_position_type () const
Return the number of coordinate types that the element requires to interpolate the geometry between the nodes. For Lagrange elements it is 1. More...

bool has_hanging_nodes () const
Return boolean to indicate if any of the element's nodes are geometrically hanging. More...

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

int get_node_number (Node *const &node_pt) const
Return the number of the node *node_pt if this node is in the element, else return -1;. More...

virtual Nodeget_node_at_local_coordinate (const Vector< double > &s) const
If there is a node at this local coordinate, return the pointer to the node. More...

double raw_nodal_value (const unsigned &n, const unsigned &i) const
Return the i-th value stored at local node n but do NOT take hanging nodes into account. More...

double raw_nodal_value (const unsigned &t, const unsigned &n, const unsigned &i) const
Return the i-th value stored at local node n, at time level t (t=0: present; t>0 previous timesteps), but do NOT take hanging nodes into account. More...

double nodal_value (const unsigned &n, const unsigned &i) const
Return the i-th value stored at local node n. Produces suitably interpolated values for hanging nodes. More...

double nodal_value (const unsigned &t, const unsigned &n, const unsigned &i) const
Return the i-th value stored at local node n, at time level t (t=0: present; t>0 previous timesteps). Produces suitably interpolated values for hanging nodes. More...

unsigned dim () const
Return the spatial dimension of the element, i.e. the number of local coordinates required to parametrise its geometry. More...

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
Return FE interpolated coordinate x[i] at local coordinate s at previous timestep t (t=0: present; t>0: previous timestep) More...

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
Return FE interpolated position x[] at local coordinate s at previous timestep t as Vector (t=0: present; t>0: previous timestep) More...

virtual double interpolated_dxdt (const Vector< double > &s, const unsigned &i, const unsigned &t)
Return t-th time-derivative of the i-th FE-interpolated Eulerian coordinate at local coordinate s. More...

virtual void interpolated_dxdt (const Vector< double > &s, const unsigned &t, Vector< double > &dxdt)
Compte t-th time-derivative of the FE-interpolated Eulerian coordinate vector at local coordinate s. More...

void position (const Vector< double > &zeta, Vector< double > &r) const
Return the parametrised position of the FiniteElement in its incarnation as a GeomObject, r(zeta). The position is given by the Eulerian coordinate and the intrinsic coordinate (zeta) is the local coordinate of the element (s). More...

void position (const unsigned &t, const Vector< double > &zeta, Vector< double > &r) const
Return the parametrised position of the FiniteElement in its GeomObject incarnation: r(zeta). The position is given by the Eulerian coordinate and the intrinsic coordinate (zeta) is the local coordinate of the element (s) This version of the function returns the position as a function of time t=0: current time; t>0: previous timestep. Works for t=0 but needs to be overloaded if genuine time-dependence is required. More...

void dposition_dt (const Vector< double > &zeta, const unsigned &t, Vector< double > &drdt)
Return the t-th time derivative of the parametrised position of the FiniteElement in its GeomObject incarnation: . Call the t-th time derivative of the FE-interpolated Eulerian coordinate. More...

void interpolated_zeta (const Vector< double > &s, Vector< double > &zeta) const
Calculate the interpolated value of zeta, the intrinsic coordinate of the element when viewed as a compound geometric object within a Mesh as a function of the local coordinate of the element, s. The default assumption is the zeta is interpolated using the shape functions of the element with the values given by zeta_nodal(). A MacroElement representation of the intrinsic coordinate parametrised by the local coordinate s is used if available. Choosing the MacroElement representation of zeta (Eulerian x by default) allows a correspondence to be established between elements on different Meshes covering the same curvilinear domain in cases where one element is much coarser than the other. More...

void locate_zeta (const Vector< double > &zeta, GeomObject *&geom_object_pt, Vector< double > &s, const bool &use_coordinate_as_initial_guess=false)
For a given value of zeta, the "global" intrinsic coordinate of a mesh of FiniteElements represented as a compound geometric object, find the local coordinate in this element that corresponds to the requested value of zeta. If zeta cannot be located in this element, geom_object_pt is set to NULL. If zeta is located in this element, we return its "this" pointer. By default don't use any value passed in to the local coordinate s as the initial guess in the Newton method. More...

virtual void node_update ()
Update the positions of all nodes in the element using each node update function. The default implementation may be overloaded so that more efficient versions can be written. More...

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
Calculate the size of the element (length, area, volume,...) in Eulerian computational coordinates. Use suitably overloaded compute_physical_size() function to compute the actual size (taking into account factors such as 2pi or radii the integrand) – such function can only be implemented on an equation-by-equation basis. More...

virtual double compute_physical_size () const
Broken virtual function to compute the actual size (taking into account factors such as 2pi or radii the integrand) – such function can only be implemented on an equation-by-equation basis. More...

virtual void point_output_data (const Vector< double > &s, Vector< double > &data)
Virtual function to write the double precision numbers that appear in a single line of output into the data vector. Empty virtual, can be overloaded for specific elements; used e.g. by LineVisualiser. More...

void point_output (std::ostream &outfile, const Vector< double > &s)
Output solution (as defined by point_output_data()) at local cordinates s. More...

virtual unsigned nplot_points_paraview (const unsigned &nplot) const
Return the number of actual plot points for paraview plot with parameter nplot. Broken virtual; can be overloaded in specific elements. More...

virtual unsigned nsub_elements_paraview (const unsigned &nplot) const
Return the number of local sub-elements for paraview plot with parameter nplot. Broken virtual; can be overloaded in specific elements. More...

void output_paraview (std::ofstream &file_out, const unsigned &nplot) const
Paraview output – this outputs the coordinates at the plot points (for parameter nplot) to specified output file. More...

virtual void write_paraview_output_offset_information (std::ofstream &file_out, const unsigned &nplot, unsigned &counter) const
Fill in the offset information for paraview plot. Broken virtual. Needs to be implemented for each new geometric element type; see http://www.vtk.org/VTK/img/file-formats.pdf. More...

virtual void write_paraview_type (std::ofstream &file_out, const unsigned &nplot) const
Return the paraview element type. Broken virtual. Needs to be implemented for each new geometric element type; see http://www.vtk.org/VTK/img/file-formats.pdf. More...

virtual void write_paraview_offsets (std::ofstream &file_out, const unsigned &nplot, unsigned &offset_sum) const
Return the offsets for the paraview sub-elements. Broken virtual. Needs to be implemented for each new geometric element type; see http://www.vtk.org/VTK/img/file-formats.pdf. More...

virtual unsigned nscalar_paraview () const
Number of scalars/fields output by this element. Broken virtual. Needs to be implemented for each new specific element type. More...

virtual void scalar_value_paraview (std::ofstream &file_out, const unsigned &i, const unsigned &nplot) const
Write values of the i-th scalar field at the plot points. Broken virtual. Needs to be implemented for each new specific element type. More...

virtual void scalar_value_fct_paraview (std::ofstream &file_out, const unsigned &i, const unsigned &nplot, FiniteElement::SteadyExactSolutionFctPt exact_soln_pt) const
Write values of the i-th scalar field at the plot points. Broken virtual. Needs to be implemented for each new specific element type. More...

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
Write values of the i-th scalar field at the plot points. Broken virtual. Needs to be implemented for each new specific element type. More...

virtual std::string scalar_name_paraview (const unsigned &i) const
Name of the i-th scalar field. Default implementation returns V1 for the first one, V2 for the second etc. Can (should!) be overloaded with more meaningful names in specific elements. More...

virtual void output (const unsigned &t, std::ostream &outfile, const unsigned &n_plot) const
Output the element data at time step t. This is const because it is newly added and so can be done easily. Really all the output(...) functions should be const! More...

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
Get cector of local coordinates of plot point i (when plotting nplot points in each "coordinate direction"). Generally these plot points will be uniformly spaced across the element. The optional final boolean flag (default: false) allows them to be shifted inwards to avoid duplication of plot point points between elements – useful when they are used in locate_zeta, say. More...

virtual std::string tecplot_zone_string (const unsigned &nplot) const
Return string for tecplot zone header (when plotting nplot points in each "coordinate direction") More...

virtual void write_tecplot_zone_footer (std::ostream &outfile, const unsigned &nplot) const
Add tecplot zone "footer" to output stream (when plotting nplot points in each "coordinate direction"). Empty by default – can be used, e.g., to add FE connectivity lists to elements that need it. More...

virtual void write_tecplot_zone_footer (FILE *file_pt, const unsigned &nplot) const
Add tecplot zone "footer" to C-style output. (when plotting nplot points in each "coordinate direction"). Empty by default – can be used, e.g., to add FE connectivity lists to elements that need it. More...

virtual unsigned nplot_points (const unsigned &nplot) const
Return total number of plot points (when plotting nplot points in each "coordinate direction") More...

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)
Given the exact solution this function calculates the norm of the error and that of the exact solution. Version with vectors of norms and errors so that different variables' norms and errors can be returned individually. More...

virtual void compute_error (FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt, const double &time, Vector< double > &error, Vector< double > &norm)
Given the exact solution this function calculates the norm of the error and that of the exact solution. Version with vectors of norms and errors so that different variables' norms and errors can be returned individually. More...

virtual void compute_error (std::ostream &outfile, FiniteElement::SteadyExactSolutionFctPt exact_soln_pt, double &error, double &norm)
Plot the error when compared against a given exact solution . Also calculates the norm of the error and that of the exact solution. More...

virtual void compute_error (std::ostream &outfile, FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt, const double &time, double &error, double &norm)
Plot the error when compared against a given time-dependent exact solution . Also calculates the norm of the error and that of the exact solution. More...

virtual void compute_error (std::ostream &outfile, FiniteElement::SteadyExactSolutionFctPt exact_soln_pt, Vector< double > &error, Vector< double > &norm)
Plot the error when compared against a given exact solution . Also calculates the norm of the error and that of the exact solution. The version with vectors of norms and errors so that different variables' norms and errors can be returned individually. More...

virtual void compute_error (std::ostream &outfile, FiniteElement::UnsteadyExactSolutionFctPt exact_soln_pt, const double &time, Vector< double > &error, Vector< double > &norm)
Plot the error when compared against a given time-dependent exact solution . Also calculates the norm of the error and that of the exact solution. The version with vectors of norms and errors so that different variables' norms and errors can be returned individually. More...

virtual void compute_abs_error (std::ostream &outfile, FiniteElement::SteadyExactSolutionFctPt exact_soln_pt, double &error)
Plot the error when compared against a given exact solution . Also calculates the maximum absolute error. More...

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

void integrate_fct (FiniteElement::UnsteadyExactSolutionFctPt integrand_fct_pt, const double &time, Vector< double > &integral)
Evaluate integral of a Vector-valued, time-dependent function over the element. More...

virtual void build_face_element (const int &face_index, FaceElement *face_element_pt)
Function for building a lower dimensional FaceElement on the specified face of the FiniteElement. The arguments are the index of the face, an integer whose value depends on the particular element type, and a pointer to the FaceElement. More...

virtual unsigned self_test ()
Self-test: Check inversion of element & do self-test for GeneralisedElement. Return 0 if OK. More...

virtual unsigned get_bulk_node_number (const int &face_index, const unsigned &i) const
Get the number of the ith node on face face_index (in the bulk node vector). More...

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
Get a pointer to the function mapping face coordinates to bulk coordinates. More...

virtual BulkCoordinateDerivativesFctPt bulk_coordinate_derivatives_fct_pt (const int &face_index) const
Get a pointer to the derivative of the mapping from face to bulk coordinates. More...

Public Member Functions inherited from oomph::GeneralisedElement
GeneralisedElement() GeneralisedElement (const GeneralisedElement &)=delete
Constructor: Initialise all pointers and all values to zero. 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
Return the global equation number corresponding to the ieqn_local-th local equation number. More...

int local_eqn_number (const unsigned long &ieqn_global) const
Return the local equation number corresponding to the ieqn_global-th global equation number. Returns minus one (-1) if there is no local degree of freedom corresponding to the chosen global equation number. More...

unsigned add_external_data (Data *const &data_pt, const bool &fd=true)
Add a (pointer to an) external data object to the element and return its index (i.e. the index required to obtain it from the access function external_data_pt(...). The optional boolean flag indicates whether the data should be included in the general finite-difference loop when calculating the jacobian. The default value is true, i.e. the data will be included in the finite-differencing. More...

bool external_data_fd (const unsigned &i) const
Return the status of the boolean flag indicating whether the external data is included in the finite difference loop. More...

void exclude_external_data_fd (const unsigned &i)
Set the boolean flag to exclude the external datum from the the finite difference loop when computing the jacobian matrix. More...

void include_external_data_fd (const unsigned &i)
Set the boolean flag to include the external datum in the the finite difference loop when computing the jacobian matrix. More...

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)
Set the timestepper associated with the i-th internal data object. More...

void assign_internal_eqn_numbers (unsigned long &global_number, Vector< double * > &Dof_pt)
Assign the global equation numbers to the internal Data. The arguments are the current highest global equation number (which will be incremented) and a Vector of pointers to the global variables (to which any unpinned values in the internal Data are added). More...

void describe_dofs (std::ostream &out, const std::string &current_string) const
Function to describe the dofs of the element. The ostream specifies the output stream to which the description is written; the string stores the currently assembled output that is ultimately written to the output stream by Data::describe_dofs(...); it is typically built up incrementally as we descend through the call hierarchy of this function when called from Problem::describe_dofs(...) More...

void add_internal_value_pt_to_map (std::map< unsigned, double * > &map_of_value_pt)
Add pointers to the internal data values to map indexed by the global equation number. More...

void add_internal_data_values_to_vector (Vector< double > &vector_of_values)
Add all internal data and time history values to the vector in the internal storage order. More...

void read_internal_data_values_from_vector (const Vector< double > &vector_of_values, unsigned &index)
Read all internal data and time history values from the vector starting from index. On return the index will be set to the value at the end of the data that has been read in. More...

void add_internal_eqn_numbers_to_vector (Vector< long > &vector_of_eqn_numbers)
Add all equation numbers associated with internal data to the vector in the internal storage order. More...

void read_internal_eqn_numbers_from_vector (const Vector< long > &vector_of_eqn_numbers, unsigned &index)
Read all equation numbers associated with internal data from the vector starting from index. On return the index will be set to the value at the end of the data that has been read in. More...

virtual void assign_local_eqn_numbers (const bool &store_local_dof_pt)
Setup the arrays of local equation numbers for the element. If the optional boolean argument is true, then pointers to the associated degrees of freedom are stored locally in the array Dof_pt. More...

virtual void complete_setup_of_dependencies ()
Complete the setup of any additional dependencies that the element may have. Empty virtual function that may be overloaded for specific derived elements. Used, e.g., for elements with algebraic node update functions to determine the "geometric Data", i.e. the Data that affects the element's shape. This function is called (for all elements) at the very beginning of the equation numbering procedure to ensure that all dependencies are accounted for. More...

virtual void get_residuals (Vector< double > &residuals)
Calculate the vector of residuals of the equations in the element. By default initialise the vector to zero and then call the fill_in_contribution_to_residuals() function. Note that this entire function can be overloaded if desired. More...

virtual void get_jacobian (Vector< double > &residuals, DenseMatrix< double > &jacobian)
Calculate the elemental Jacobian matrix "d equation / d variable". More...

virtual void get_mass_matrix (Vector< double > &residuals, DenseMatrix< double > &mass_matrix)
Calculate the residuals and the elemental "mass" matrix, the matrix that multiplies the time derivative terms in a problem. More...

virtual void get_jacobian_and_mass_matrix (Vector< double > &residuals, DenseMatrix< double > &jacobian, DenseMatrix< double > &mass_matrix)
Calculate the residuals and jacobian and elemental "mass" matrix, the matrix that multiplies the time derivative terms. More...

virtual void get_dresiduals_dparameter (double *const &parameter_pt, Vector< double > &dres_dparam)
Calculate the derivatives of the residuals with respect to a parameter. More...

virtual void get_djacobian_dparameter (double *const &parameter_pt, Vector< double > &dres_dparam, DenseMatrix< double > &djac_dparam)
Calculate the derivatives of the elemental Jacobian matrix and residuals with respect to a parameter. More...

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)
Calculate the derivatives of the elemental Jacobian matrix mass matrix and residuals with respect to a parameter. More...

virtual void get_hessian_vector_products (Vector< double > const &Y, DenseMatrix< double > const &C, DenseMatrix< double > &product)
Calculate the product of the Hessian (derivative of Jacobian with respect to all variables) an eigenvector, Y, and other specified vectors, C (d(J_{ij})/d u_{k}) Y_{j} C_{k}. More...

virtual void get_inner_products (Vector< std::pair< unsigned, unsigned > > const &history_index, Vector< double > &inner_product)
Return the vector of inner product of the given pairs of history values. More...

virtual void get_inner_product_vectors (Vector< unsigned > const &history_index, Vector< Vector< double > > &inner_product_vector)
Compute the vectors that when taken as a dot product with other history values give the inner product over the element. More...

virtual void compute_norm (Vector< double > &norm)
Compute norm of solution – broken virtual can be overloaded by element writer to implement whatever norm is desired for the specific element. More...

void set_halo (const unsigned &non_halo_proc_ID)
Label the element as halo and specify processor that holds non-halo counterpart. More...

void set_nonhalo ()
Label the element as not being a halo. More...

bool is_halo () const
Is this element a halo? More...

int non_halo_proc_ID ()
ID of processor ID that holds non-halo counterpart of halo element; negative if not a halo. More...

void set_must_be_kept_as_halo ()
Insist that this element be kept as a halo element during a distribute? More...

void unset_must_be_kept_as_halo ()
Do not insist that this element be kept as a halo element during distribution. More...

bool must_be_kept_as_halo () const
Test whether the element must be kept as a halo element. More...

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

GeomObject (const unsigned &ndim)
Constructor: Pass dimension of geometric object (# of Eulerian coords = # of Lagrangian coords; no time history available/needed) More...

GeomObject (const unsigned &nlagrangian, const unsigned &ndim)
Constructor: pass # of Eulerian and Lagrangian coordinates. No time history available/needed. More...

GeomObject (const unsigned &nlagrangian, const unsigned &ndim, TimeStepper *time_stepper_pt)
Constructor: pass # of Eulerian and Lagrangian coordinates and pointer to time-stepper which is used to handle the position at previous timesteps and allows the evaluation of veloc/acceleration etc. in cases where the GeomData varies with time. More...

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 ()
Access function for pointer to time stepper: Null if object is not time-dependent. More...

TimeSteppertime_stepper_pt () const
Access function for pointer to time stepper: Null if object is not time-dependent. Const version. More...

virtual void position (const double &t, const Vector< double > &zeta, Vector< double > &r) const
Parametrised position on object: r(zeta). Evaluated at the continuous time value, t. More...

virtual void dposition (const Vector< double > &zeta, DenseMatrix< double > &drdzeta) const
Derivative of position Vector w.r.t. to coordinates: = drdzeta(alpha,i). Evaluated at current time. More...

virtual void d2position (const Vector< double > &zeta, RankThreeTensor< double > &ddrdzeta) const
2nd derivative of position Vector w.r.t. to coordinates: = ddrdzeta(alpha,beta,i). Evaluated at current time. More...

virtual void d2position (const Vector< double > &zeta, Vector< double > &r, DenseMatrix< double > &drdzeta, RankThreeTensor< double > &ddrdzeta) const
Posn Vector and its 1st & 2nd derivatives w.r.t. to coordinates: = drdzeta(alpha,i). = ddrdzeta(alpha,beta,i). Evaluated at current time. More...

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

virtual ~SolidElementWithDiagonalMassMatrix ()
Virtual destructor. More...

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

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

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

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

void assign_solid_local_eqn_numbers (const bool &store_local_dof_pt)
Overload the local equation numbers for Data stored as part of solid nodes to include hanging node data. More...

unsigned ngeom_data () const
The number of geometric data affecting a RefineableSolidFiniteElement is the positional Data of all non-hanging nodes plus the geometric Data of all distinct master nodes. Recomputed on the fly. More...

Datageom_data_pt (const unsigned &j)
Return pointer to the j-th Data item that the object's shape depends on: Positional data of non-hanging nodes and positional data of master nodes. Recomputed on the fly. More...

void identify_geometric_data (std::set< Data * > &geometric_data_pt)
Specify Data that affects the geometry of the element by adding the position Data to the set that's passed in. (This functionality is required in FSI problems; set is used to avoid double counting). Refineable version includes hanging nodes. More...

void fill_in_jacobian_from_solid_position_by_fd (Vector< double > &residuals, DenseMatrix< double > &jacobian)
Compute element residual Vector and element Jacobian matrix corresponding to the solid positions. Overloaded version to take the hanging nodes into account. More...

bool is_undeformed_macro_element_used_for_new_lagrangian_coords () const
Return the flag deciding if the Lagrangian coordinates of newly-created interior SolidNodes are to be determined by the father element's undeformed MacroElement representation (if it has one). Default: False as it means that, following a refinement an element is no longer in equilbrium (as the Lagrangian coordinate is determined differently from the Eulerian one). However, basing the Lagrangian coordinates on the undeformed MacroElement can be more stable numerically and for steady problems it's not a big deal either way as the difference between the two formulations only matters at finite resolution so we have no right to say that one is "more correct" than the other... More...

void enable_use_of_undeformed_macro_element_for_new_lagrangian_coords ()
Set the flag deciding if the Lagrangian coordinates of newly-created interior SolidNodes are to be determined by the father element's undeformed MacroElement representation (if it has one). More...

void disable_use_of_undeformed_macro_element_for_new_lagrangian_coords ()
Unset the flag deciding if the Lagrangian coordinates of newly-created interior SolidNodes are to be determined by the father element's undeformed MacroElement representation (if it has one). More...

DenseMatrix< int > & local_position_hang_eqn (Node *const &node_pt)
Access the local equation number of of hanging node variables associated with nodal positions. The function returns a dense matrix that contains all the local equation numbers corresponding to the positional degrees of freedom. More...

Public Member Functions inherited from oomph::RefineableElement
RefineableElement ()
Constructor, calls the FiniteElement constructor and initialises the member data. More...

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...

Treetree_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
Set the number of sons that can be constructed by the element The default is none. More...

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
Split the element into the number of sons to be constructed and return a vector of pointers to the sons. Elements are allocated, but they are not given any properties. The refinement level of the sons is one higher than that of the father elemern. More...

int local_hang_eqn (Node *const &node_pt, const unsigned &i)
Access function that returns the local equation number for the hanging node variables (values stored at master nodes). The local equation number corresponds to the i-th unknown stored at the node addressed by node_pt. More...

virtual void build (Mesh *&mesh_pt, Vector< Node * > &new_node_pt, bool &was_already_built, std::ofstream &new_nodes_file)=0
Interface to function that builds the element: i.e. construct the nodes, assign their positions, apply boundary conditions, etc. The required procedures depend on the geometrical type of the element and must be implemented in specific refineable elements. Any new nodes created during the build process are returned in the vector new_node_pt. More...

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 ()
No unrefinement will be performed by merging the four sons of this element. More...

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
Rebuild the element, e.g. set internal values in line with those of the sons that have now merged. More...

virtual void unbuild ()
Unbuild the element, i.e. mark the nodes that were created during its creation for possible deletion. More...

virtual void deactivate_element ()
Final operations that must be performed when the element is no longer active in the mesh, but still resident in the QuadTree. More...

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 Nodeinterpolating_node_pt (const unsigned &n, const int &value_id)
In mixed elements, different sets of nodes are used to interpolate different unknowns. This function returns the n-th node that interpolates the value_id-th unknown. Default implementation is that all variables use the positional nodes, i.e. isoparametric elements. Note that any overloaded versions of this function MUST provide a set of nodes for the position, which always has the value_id -1. More...

virtual double local_one_d_fraction_of_interpolating_node (const unsigned &n1d, const unsigned &i, const int &value_id)
Return the local one dimensional fraction of the n1d-th node in the direction of the local coordinate s[i] that is used to interpolate the value_id-th continuously interpolated unknown. Default assumes isoparametric interpolation for all unknowns. More...

virtual Nodeget_interpolating_node_at_local_coordinate (const Vector< double > &s, const int &value_id)
Return a pointer to the node that interpolates the value-id-th unknown at local coordinate s. If there is not a node at that position, then return 0. More...

virtual unsigned ninterpolating_node (const int &value_id)
Return the number of nodes that are used to interpolate the value_id-th unknown. Default is to assume isoparametric elements. More...

virtual unsigned ninterpolating_node_1d (const int &value_id)
Return the number of nodes in a one_d direction that are used to interpolate the value_id-th unknown. Default is to assume an isoparametric mapping. More...

virtual void interpolating_basis (const Vector< double > &s, Shape &psi, const int &value_id) const
Return the basis functions that are used to interpolate the value_id-th unknown. By default assume isoparameteric interpolation. More...

virtual void check_integrity (double &max_error)=0
Check the integrity of the element: Continuity of positions values, etc. Essentially, check that the approximation of the functions is consistent when viewed from both sides of the element boundaries Must be overloaded for each different geometric element. More...

void identify_field_data_for_interactions (std::set< std::pair< Data *, unsigned > > &paired_field_data)
The purpose of this function is to identify all possible Data that can affect the fields interpolated by the FiniteElement. This must be overloaded to include data from any hanging nodes correctly. More...

void assign_nodal_local_eqn_numbers (const bool &store_local_dof_pt)
Overload the function that assigns local equation numbers for the Data stored at the nodes so that hanging data is taken into account. More...

virtual RefineableElementroot_element_pt ()
Pointer to the root element in refinement hierarchy (must be implemented in specific elements that do refinement via tree-like refinement structure. Here we provide a default implementation that is appropriate for cases where tree-like refinement doesn't exist or if the element doesn't have root in that tree (i.e. if it's a root itself): We return "this". More...

virtual RefineableElementfather_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)
Return a pointer to the "father" element at the specified refinement level. More...

virtual void initial_setup (Tree *const &adopted_father_pt=0, const unsigned &initial_p_order=0)
Initial setup of the element: e.g. set the appropriate internal p-order. If an adopted father is specified, information from this is used instead of using the father found from the tree. More...

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)
Mark up any hanging nodes that arise as a result of non-uniform refinement. Any hanging nodes will be documented in files addressed by the streams in the vector output_stream, if the streams are open. More...

virtual void further_setup_hanging_nodes ()
Perform additional hanging node procedures for variables that are not interpolated by all nodes (e.g. lower order interpolations for the pressure in Taylor Hood). More...

void get_dresidual_dnodal_coordinates (RankThreeTensor< double > &dresidual_dnodal_coordinates)
Compute derivatives of elemental residual vector with respect to nodal coordinates. Default implementation by FD can be overwritten for specific elements. dresidual_dnodal_coordinates(l,i,j) = d res(l) / dX_{ij} This version is overloaded from the version in FiniteElement and takes hanging nodes into account – j in the above loop loops over all the nodes that actively control the shape of the element (i.e. they are non-hanging or master nodes of hanging nodes in this element). More...

unsigned nshape_controlling_nodes ()
Number of shape-controlling nodes = the number of non-hanging nodes plus the number of master nodes associated with hanging nodes. More...

std::map< Node *, unsigned > shape_controlling_node_lookup ()
Return lookup scheme for unique number associated with any of the nodes that actively control the shape of the element (i.e. they are either non-hanging nodes of this element or master nodes of hanging nodes. More...

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 ()
A stuitable error estimator for a multi-physics elements may require one Z2 error estimate for each field (e.g. velocity and temperature in a fluid convection problem). It is assumed that these error estimates will each use selected flux terms. The number of compound fluxes returns the number of such combinations of the flux terms. Default value is one and all flux terms are combined with equal weight. More...

virtual void compute_exact_Z2_error (std::ostream &outfile, FiniteElement::SteadyExactSolutionFctPt exact_flux_pt, double &error, double &norm)
Plot the error when compared against a given exact flux. Also calculates the norm of the error and that of the exact flux. More...

virtual void get_Z2_compound_flux_indices (Vector< unsigned > &flux_index)
Return the compound flux index of each flux component The default (do nothing behaviour) will mean that all indices remain at the default value zero. More...

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

virtual Nodevertex_node_pt (const unsigned &j) const =0
Pointer to the j-th vertex node in the element. Needed for efficient patch assmbly. More...

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

virtual double geometric_jacobian (const Vector< double > &x)
Return the geometric jacobian (should be overloaded in cylindrical and spherical geometries). Default value one is suitable for Cartesian coordinates. More...

Public Types inherited from oomph::PVDEquationsBase< DIM >
typedef void(* IsotropicGrowthFctPt) (const Vector< double > &xi, double &gamma)
Function pointer to function that specifies the isotropic growth as a function of the Lagrangian coordinates FCT(xi,gamma(xi)) – xi is a Vector! More...

typedef double(* PrestressFctPt) (const unsigned &i, const unsigned &j, const Vector< double > &xi)
Function pointer to function that specifies the pre-stress sigma_0(i,j) as a function of the Lagrangian coordinates FCT(i,j,xi) – xi is a Vector! More...

typedef void(* BodyForceFctPt) (const double &t, const Vector< double > &xi, Vector< double > &b)
Function pointer to function that specifies the body force as a function of the Lagrangian coordinates and time FCT(t,xi,b) – xi and b are Vectors! More...

Public Types inherited from oomph::SolidFiniteElement
typedef double(* MultiplierFctPt) (const Vector< double > &xi)
Pointer to function that computes the "multiplier" for the inertia terms in the consistent determination of the initial conditions for Newmark timestepping. More...

Public Types inherited from oomph::FiniteElement
typedef void(* SteadyExactSolutionFctPt) (const Vector< double > &, Vector< double > &)
Function pointer for function that computes vector-valued steady "exact solution" as . More...

typedef void(* UnsteadyExactSolutionFctPt) (const double &, const Vector< double > &, Vector< double > &)
Function pointer for function that computes Vector-valued time-dependent function as . More...

Static Public Member Functions inherited from oomph::PVDEquationsBase< DIM >
static void pin_redundant_nodal_solid_pressures (const Vector< GeneralisedElement * > &element_pt)
Loop over all elements in Vector (which typically contains all the elements in a refineable solid mesh) and pin the nodal solid pressure degrees of freedom that are not being used. Function uses the member function. More...

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

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

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

static bool Accept_negative_jacobian = false
Boolean that if set to true allows a negative jacobian in the transform between global and local coordinates (negative surface area = left-handed coordinate system). More...

static bool Suppress_output_while_checking_for_inverted_elements
Static boolean to suppress output while checking for inverted elements. More...

Static Public Attributes inherited from oomph::GeneralisedElement
Static boolean to suppress warnings about repeated internal data. Defaults to false. More...

Static boolean to suppress warnings about repeated external data. Defaults to true. More...

static double Default_fd_jacobian_step = 1.0e-8
Double used for the default finite difference step in elemental jacobian calculations. More...

Protected Member Functions inherited from oomph::PVDEquationsWithPressure< DIM >
void get_stress (const DenseMatrix< double > &g, const DenseMatrix< double > &G, DenseMatrix< double > &sigma_dev, DenseMatrix< double > &Gcontra, double &gen_dil, double &inv_kappa)
Return the deviatoric part of the 2nd Piola Kirchhoff stress tensor, as calculated from the constitutive law in the nearly incompresible formulation. Also return the contravariant deformed metric tensor, the generalised dilatation, and the inverse of the bulk modulus. More...

void get_d_stress_dG_upper (const DenseMatrix< double > &g, const DenseMatrix< double > &G, const DenseMatrix< double > &sigma, const double &gen_dil, const double &inv_kappa, const double &interpolated_solid_p, RankFourTensor< double > &d_sigma_dG, DenseMatrix< double > &d_gen_dil_dG)
Return the derivative of the deviatoric part of the 2nd Piola Kirchhoff stress tensor, as calculated from the constitutive law in the nearly incompresible formulation. Also return the derivative of the generalised dilatation. More...

virtual void solid_pshape (const Vector< double > &s, Shape &psi) const =0
Return the solid pressure shape functions. More...

void solid_pshape_at_knot (const unsigned &ipt, Shape &psi) const
Return the stored solid shape functions at the knots. More...

void get_stress (const DenseMatrix< double > &g, const DenseMatrix< double > &G, DenseMatrix< double > &sigma_dev, DenseMatrix< double > &Gcontra, double &detG)
Return the deviatoric part of the 2nd Piola Kirchhoff stress tensor, as calculated from the constitutive law in the incompresible formulation. Also return the contravariant deformed metric tensor, and the determinant of the deformed covariant metric tensor (likely to be needed in the incompressibility constraint) More...

void get_d_stress_dG_upper (const DenseMatrix< double > &g, const DenseMatrix< double > &G, const DenseMatrix< double > &sigma, const double &detG, const double &interpolated_solid_p, RankFourTensor< double > &d_sigma_dG, DenseMatrix< double > &d_detG_dG)
Return the derivative of the 2nd Piola Kirchhoff stress tensor, as calculated from the constitutive law in the incompresible formulation. Also return derivative of the determinant of the deformed covariant metric tensor (likely to be needed in the incompressibility constraint) More...

Protected Member Functions inherited from oomph::SolidFiniteElement
void fill_in_generic_jacobian_for_solid_ic (Vector< double > &residuals, DenseMatrix< double > &jacobian, const unsigned &flag)
Helper function to fill in the residuals and (if flag==1) the Jacobian for the setup of an initial condition. The global equations are: More...

void set_nnodal_lagrangian_type (const unsigned &nlagrangian_type)
Set the number of types required to interpolate the Lagrangian coordinates. More...

virtual double local_to_lagrangian_mapping (const DShape &dpsids, DenseMatrix< double > &jacobian, DenseMatrix< double > &inverse_jacobian) const
Calculate the mapping from local to lagrangian coordinates, given the derivatives of the shape functions w.r.t. local coorindates. Return the determinant of the jacobian, the jacobian and inverse jacobian. More...

double local_to_lagrangian_mapping (const DShape &dpsids, DenseMatrix< double > &inverse_jacobian) const
Calculate the mapping from local to lagrangian coordinates, given the derivatives of the shape functions w.r.t. local coordinates, Return only the determinant of the jacobian and the inverse of the mapping (ds/dx) More...

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

void fill_in_jacobian_from_solid_position_by_fd (DenseMatrix< double > &jacobian)
Use finite differences to calculate the Jacobian entries corresponding to the solid positions. More...

virtual void update_before_solid_position_fd ()
Function that is called before the finite differencing of any solid position data. This may be overloaded to update any dependent data before finite differencing takes place. More...

virtual void reset_after_solid_position_fd ()
Function that is call after the finite differencing of the solid position data. This may be overloaded to reset any dependent variables that may have changed during the finite differencing. More...

virtual void update_in_solid_position_fd (const unsigned &i)
Function called within the finite difference loop for the solid position dat after a change in any values in the n-th node. More...

virtual void reset_in_solid_position_fd (const unsigned &i)
Function called within the finite difference loop for solid position data after the values in the i-th node are reset. The default behaviour is to call the update function. More...

Protected Member Functions inherited from oomph::FiniteElement
template<unsigned DIM>
double invert_jacobian (const DenseMatrix< double > &jacobian, DenseMatrix< double > &inverse_jacobian) const
Take the matrix passed as jacobian and return its inverse in inverse_jacobian. This function is templated by the dimension of the element because matrix inversion cannot be written efficiently in a generic manner. More...

virtual double invert_jacobian_mapping (const DenseMatrix< double > &jacobian, DenseMatrix< double > &inverse_jacobian) const
A template-free interface that takes the matrix passed as jacobian and return its inverse in inverse_jacobian. By default the function will use the dimension of the element to call the correct invert_jacobian(..) function. This should be overloaded for efficiency (removal of a switch statement) in specific elements. More...

virtual double local_to_eulerian_mapping (const DShape &dpsids, DenseMatrix< double > &jacobian, DenseMatrix< double > &inverse_jacobian) const
Calculate the mapping from local to Eulerian coordinates, given the derivatives of the shape functions w.r.t. local coordinates. Returns the determinant of the jacobian, the jacobian and inverse jacobian. More...

double local_to_eulerian_mapping (const DShape &dpsids, DenseMatrix< double > &inverse_jacobian) const
Calculate the mapping from local to Eulerian coordinates, given the derivatives of the shape functions w.r.t. local coordinates, Return only the determinant of the jacobian and the inverse of the mapping (ds/dx). More...

virtual void dJ_eulerian_dnodal_coordinates (const DenseMatrix< double > &jacobian, const DShape &dpsids, DenseMatrix< double > &djacobian_dX) const
A template-free interface that calculates the derivative of the jacobian of a mapping with respect to the nodal coordinates X_ij. To do this it requires the jacobian matrix and the derivatives of the shape functions w.r.t. the local coordinates. By default the function will use the dimension of the element to call the correct dJ_eulerian_dnodal_coordinates_templated_helper(..) function. This should be overloaded for efficiency (removal of a switch statement) in specific elements. More...

template<unsigned DIM>
void dJ_eulerian_dnodal_coordinates_templated_helper (const DenseMatrix< double > &jacobian, const DShape &dpsids, DenseMatrix< double > &djacobian_dX) const
Calculate the derivative of the jacobian of a mapping with respect to the nodal coordinates X_ij using the jacobian matrix and the derivatives of the shape functions w.r.t. the local coordinates. This function is templated by the dimension of the element. More...

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
A template-free interface that calculates the derivative w.r.t. the nodal coordinates of the derivative of the shape functions w.r.t. the global eulerian coordinates . I.e. this function calculates. More...

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
Calculate the derivative w.r.t. the nodal coordinates of the derivative of the shape functions w.r.t. the global eulerian coordinates , using the determinant of the jacobian mapping, its derivative w.r.t. the nodal coordinates , the inverse jacobian and the derivatives of the shape functions w.r.t. the local coordinates. The result is returned as a tensor of rank four. Numbering: d_dpsidx_dX(p,q,j,i) = This function is templated by the dimension of the element. More...

virtual void transform_derivatives (const DenseMatrix< double > &inverse_jacobian, DShape &dbasis) const
Convert derivative w.r.t.local coordinates to derivatives w.r.t the coordinates used to assemble the inverse_jacobian passed in the mapping. On entry, dbasis must contain the basis function derivatives w.r.t. the local coordinates; it will contain the derivatives w.r.t. the new coordinates on exit. This is virtual so that it may be overloaded if desired for efficiency reasons. More...

void transform_derivatives_diagonal (const DenseMatrix< double > &inverse_jacobian, DShape &dbasis) const
Convert derivative w.r.t local coordinates to derivatives w.r.t the coordinates used to assemble the inverse jacobian passed in the mapping, assuming that the coordinates are aligned in the direction of the local coordinates. On entry dbasis must contain the derivatives of the basis functions w.r.t. the local coordinates; it will contain the derivatives w.r.t. the new coordinates. are converted into the new using the mapping inverse_jacobian. More...

virtual void transform_second_derivatives (const DenseMatrix< double > &jacobian, const DenseMatrix< double > &inverse_jacobian, const DenseMatrix< double > &jacobian2, DShape &dbasis, DShape &d2basis) const
Convert derivatives and second derivatives w.r.t. local coordiantes to derivatives and second derivatives w.r.t. the coordinates used to assemble the jacobian, inverse jacobian and jacobian2 passed to the function. By default this function will call transform_second_derivatives_template<>(...) using the dimension of the element as the template parameter. It is virtual so that it can be overloaded by a specific element to save using a switch statement. Optionally, the element writer may wish to use the transform_second_derivatives_diagonal<>(...) function On entry dbasis and d2basis must contain the derivatives w.r.t. the local coordinates; on exit they will be the derivatives w.r.t. the transformed coordinates. More...

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
Convert derivatives and second derivatives w.r.t. local coordinates to derivatives and second derivatives w.r.t. the coordinates used to asssmble the jacobian, inverse jacobian and jacobian2 passed in the mapping. This is templated by dimension because the method of calculation varies significantly with the dimension. On entry dbasis and d2basis must contain the derivatives w.r.t. the local coordinates; on exit they will be the derivatives w.r.t. the transformed coordinates. More...

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
Convert derivatives and second derivatives w.r.t. local coordinates to derivatives and second derivatives w.r.t. the coordinates used to asssmble the jacobian, inverse jacobian and jacobian2 passed in the mapping. This version of the function assumes that the local coordinates are aligned with the global coordinates, i.e. the jacobians are diagonal On entry dbasis and d2basis must contain the derivatives w.r.t. the local coordinates; on exit they will be the derivatives w.r.t. the transformed coordinates. More...

void fill_in_jacobian_from_nodal_by_fd (DenseMatrix< double > &jacobian)
Calculate the contributions to the jacobian from the nodal degrees of freedom using finite differences. This version computes the residuals vector before calculating the jacobian terms. More...

virtual void update_before_nodal_fd ()
Function that is called before the finite differencing of any nodal data. This may be overloaded to update any dependent data before finite differencing takes place. More...

virtual void reset_after_nodal_fd ()
Function that is call after the finite differencing of the nodal data. This may be overloaded to reset any dependent variables that may have changed during the finite differencing. More...

virtual void update_in_nodal_fd (const unsigned &i)
Function called within the finite difference loop for nodal data after a change in the i-th nodal value. More...

virtual void reset_in_nodal_fd (const unsigned &i)
Function called within the finite difference loop for nodal data after the i-th nodal values is reset. The default behaviour is to call the update function. More...

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
Three-d specialisation of function to calculate inverse of jacobian mapping. More...

template<>
void dJ_eulerian_dnodal_coordinates_templated_helper (const DenseMatrix< double > &jacobian, const DShape &dpsids, DenseMatrix< double > &djacobian_dX) const
Zero-d specialisation of function to calculate the derivative of the jacobian of a mapping with respect to the nodal coordinates X_ij. More...

template<>
void dJ_eulerian_dnodal_coordinates_templated_helper (const DenseMatrix< double > &jacobian, const DShape &dpsids, DenseMatrix< double > &djacobian_dX) const
One-d specialisation of function to calculate the derivative of the jacobian of a mapping with respect to the nodal coordinates X_ij. More...

template<>
void dJ_eulerian_dnodal_coordinates_templated_helper (const DenseMatrix< double > &jacobian, const DShape &dpsids, DenseMatrix< double > &djacobian_dX) const
Two-d specialisation of function to calculate the derivative of the jacobian of a mapping with respect to the nodal coordinates X_ij. More...

template<>
void dJ_eulerian_dnodal_coordinates_templated_helper (const DenseMatrix< double > &jacobian, const DShape &dpsids, DenseMatrix< double > &djacobian_dX) const
Three-d specialisation of function to calculate the derivative of the jacobian of a mapping with respect to the nodal coordinates X_ij. More...

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
Zero-d specialisation of function to calculate the derivative w.r.t. the nodal coordinates of the derivative of the shape functions w.r.t. the global eulerian coordinates . More...

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
One-d specialisation of function to calculate the derivative w.r.t. the nodal coordinates of the derivative of the shape functions w.r.t. the global eulerian coordinates . More...

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
Two-d specialisation of function to calculate the derivative w.r.t. the nodal coordinates of the derivative of the shape functions w.r.t. the global eulerian coordinates . More...

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
Three-d specialisation of function to calculate the derivative w.r.t. the nodal coordinates of the derivative of the shape functions w.r.t. the global eulerian coordinates . More...

template<>
void transform_second_derivatives_template (const DenseMatrix< double > &jacobian, const DenseMatrix< double > &inverse_jacobian, const DenseMatrix< double > &jacobian2, DShape &dbasis, DShape &d2basis) const
Convert derivatives and second derivatives w.r.t local coordinates to derivatives w.r.t. the coordinates used to assemble the jacobian, inverse_jacobian and jacobian 2 passed. This must be specialised for each dimension, otherwise it gets very ugly Specialisation to one dimension. More...

template<>
void transform_second_derivatives_template (const DenseMatrix< double > &jacobian, const DenseMatrix< double > &inverse_jacobian, const DenseMatrix< double > &jacobian2, DShape &dbasis, DShape &d2basis) const
Convert derivatives and second derivatives w.r.t local coordinates to derivatives w.r.t. the coordinates used to assemble the jacobian, inverse_jacobian and jacobian 2 passed. This must be specialised for each dimension, otherwise it gets very ugly. Specialisation to two spatial dimensions. More...

template<>
void transform_second_derivatives_diagonal (const DenseMatrix< double > &jacobian, const DenseMatrix< double > &inverse_jacobian, const DenseMatrix< double > &jacobian2, DShape &dbasis, DShape &d2basis) const
Convert derivatives and second derivatives w.r.t local coordinates to derivatives w.r.t. the coordinates used to assemble the jacobian, inverse_jacobian and jacobian 2 passed. This must be specialised for each dimension, otherwise it gets very ugly Specialisation to one dimension. More...

template<>
void transform_second_derivatives_diagonal (const DenseMatrix< double > &jacobian, const DenseMatrix< double > &inverse_jacobian, const DenseMatrix< double > &jacobian2, DShape &dbasis, DShape &d2basis) const
Convert second derivatives w.r.t. local coordinates to second derivatives w.r.t. the coordinates passed in the tensor coordinate. Specialised to two spatial dimension. More...

Protected Member Functions inherited from oomph::GeneralisedElement
unsigned add_internal_data (Data *const &data_pt, const bool &fd=true)
Add a (pointer to an) internal data object to the element and return the index required to obtain it from the access function internal_data_pt(). The boolean indicates whether the datum should be included in the general finite-difference loop when calculating the jacobian. The default value is true, i.e. the data will be included in the finite differencing. More...

bool internal_data_fd (const unsigned &i) const
Return the status of the boolean flag indicating whether the internal data is included in the finite difference loop. More...

void exclude_internal_data_fd (const unsigned &i)
Set the boolean flag to exclude the internal datum from the finite difference loop when computing the jacobian matrix. More...

void include_internal_data_fd (const unsigned &i)
Set the boolean flag to include the internal datum in the finite difference loop when computing the jacobian matrix. More...

void clear_global_eqn_numbers ()
Clear the storage for the global equation numbers and pointers to dofs (if stored) More...

void add_global_eqn_numbers (std::deque< unsigned long > const &global_eqn_numbers, std::deque< double * > const &global_dof_pt)
Add the contents of the queue global_eqn_numbers to the local storage for the local-to-global translation scheme. It is essential that the entries in the queue are added IN ORDER i.e. from the front. More...

virtual void assign_internal_and_external_local_eqn_numbers (const bool &store_local_dof_pt)
Assign the local equation numbers for the internal and external Data This must be called after the global equation numbers have all been assigned. It is virtual so that it can be overloaded by ElementWithExternalElements so that any external data from the external elements in included in the numbering scheme. If the boolean argument is true then pointers to the dofs will be stored in Dof_pt. More...

Setup any additional look-up schemes for local equation numbers. Examples of use include using local storage to refer to explicit degrees of freedom. The additional memory cost of such storage may or may not be offset by fast local access. More...

int internal_local_eqn (const unsigned &i, const unsigned &j) const
Return the local equation number corresponding to the j-th value stored at the i-th internal data. More...

int external_local_eqn (const unsigned &i, const unsigned &j)
Return the local equation number corresponding to the j-th value stored at the i-th external data. More...

void fill_in_jacobian_from_internal_by_fd (Vector< double > &residuals, DenseMatrix< double > &jacobian, const bool &fd_all_data=false)
Calculate the contributions to the jacobian from the internal degrees of freedom using finite differences. This version of the function assumes that the residuals vector has already been calculated. If the boolean argument is true, the finite differencing will be performed for all internal data, irrespective of the information in Data_fd. The default value (false) uses the information in Data_fd to selectively difference only certain data. More...

void fill_in_jacobian_from_internal_by_fd (DenseMatrix< double > &jacobian, const bool &fd_all_data=false)
Calculate the contributions to the jacobian from the internal degrees of freedom using finite differences. This version computes the residuals vector before calculating the jacobian terms. If the boolean argument is true, the finite differencing will be performed for all internal data, irrespective of the information in Data_fd. The default value (false) uses the information in Data_fd to selectively difference only certain data. More...

void fill_in_jacobian_from_external_by_fd (Vector< double > &residuals, DenseMatrix< double > &jacobian, const bool &fd_all_data=false)
Calculate the contributions to the jacobian from the external degrees of freedom using finite differences. This version of the function assumes that the residuals vector has already been calculated. If the boolean argument is true, the finite differencing will be performed for all external data, irrespective of the information in Data_fd. The default value (false) uses the information in Data_fd to selectively difference only certain data. More...

void fill_in_jacobian_from_external_by_fd (DenseMatrix< double > &jacobian, const bool &fd_all_data=false)
Calculate the contributions to the jacobian from the external degrees of freedom using finite differences. This version computes the residuals vector before calculating the jacobian terms. If the boolean argument is true, the finite differencing will be performed for all internal data, irrespective of the information in Data_fd. The default value (false) uses the information in Data_fd to selectively difference only certain data. More...

virtual void update_before_internal_fd ()
Function that is called before the finite differencing of any internal data. This may be overloaded to update any dependent data before finite differencing takes place. More...

virtual void reset_after_internal_fd ()
Function that is call after the finite differencing of the internal data. This may be overloaded to reset any dependent variables that may have changed during the finite differencing. More...

virtual void update_in_internal_fd (const unsigned &i)
Function called within the finite difference loop for internal data after a change in any values in the i-th internal data object. More...

virtual void reset_in_internal_fd (const unsigned &i)
Function called within the finite difference loop for internal data after the values in the i-th external data object are reset. The default behaviour is to call the update function. More...

virtual void update_before_external_fd ()
Function that is called before the finite differencing of any external data. This may be overloaded to update any dependent data before finite differencing takes place. More...

virtual void reset_after_external_fd ()
Function that is call after the finite differencing of the external data. This may be overloaded to reset any dependent variables that may have changed during the finite differencing. More...

virtual void update_in_external_fd (const unsigned &i)
Function called within the finite difference loop for external data after a change in any values in the i-th external data object. More...

virtual void reset_in_external_fd (const unsigned &i)
Function called within the finite difference loop for external data after the values in the i-th external data object are reset. The default behaviour is to call the update function. More...

virtual void fill_in_contribution_to_mass_matrix (Vector< double > &residuals, DenseMatrix< double > &mass_matrix)
Add the elemental contribution to the mass matrix matrix. and the residuals vector. Note that this function should NOT initialise the residuals vector or the mass matrix. It must be called after the residuals vector and jacobian matrix have been initialised to zero. The default is deliberately broken. More...

virtual void fill_in_contribution_to_dresiduals_dparameter (double *const &parameter_pt, Vector< double > &dres_dparam)
Add the elemental contribution to the derivatives of the residuals with respect to a parameter. This function should NOT initialise any entries and must be called after the entries have been initialised to zero The default implementation is to use finite differences to calculate the derivatives. More...

virtual void fill_in_contribution_to_djacobian_dparameter (double *const &parameter_pt, Vector< double > &dres_dparam, DenseMatrix< double > &djac_dparam)
Add the elemental contribution to the derivatives of the elemental Jacobian matrix and residuals with respect to a parameter. This function should NOT initialise any entries and must be called after the entries have been initialised to zero The default implementation is to use finite differences to calculate the derivatives. More...

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)
Add the elemental contribution to the derivative of the jacobian matrix, mass matrix and the residuals vector with respect to the passed parameter. Note that this function should NOT initialise any entries. It must be called after the residuals vector and matrices have been initialised to zero. More...

virtual void fill_in_contribution_to_hessian_vector_products (Vector< double > const &Y, DenseMatrix< double > const &C, DenseMatrix< double > &product)
Fill in contribution to the product of the Hessian (derivative of Jacobian with respect to all variables) an eigenvector, Y, and other specified vectors, C (d(J_{ij})/d u_{k}) Y_{j} C_{k}. More...

virtual void fill_in_contribution_to_inner_products (Vector< std::pair< unsigned, unsigned > > const &history_index, Vector< double > &inner_product)
Fill in the contribution to the inner products between given pairs of history values. More...

virtual void fill_in_contribution_to_inner_product_vectors (Vector< unsigned > const &history_index, Vector< Vector< double > > &inner_product_vector)
Fill in the contributions to the vectors that when taken as dot product with other history values give the inner product over the element. More...

Protected Member Functions inherited from oomph::RefineableSolidElement
void assemble_local_to_lagrangian_jacobian (const DShape &dpsids, DenseMatrix< double > &jacobian) const
Assemble the jacobian matrix for the mapping from local to lagrangian coordinates, given the derivatives of the shape function Overload the standard version to use the hanging information for the lagrangian coordinates. More...

void assemble_local_to_lagrangian_jacobian2 (const DShape &d2psids, DenseMatrix< double > &jacobian2) const
Assemble the the "jacobian" matrix of second derivatives, given the second derivatives of the shape functions w.r.t. local coordinates Overload the standard version to use the hanging information for the lagrangian coordinates. More...

double local_to_lagrangian_mapping_diagonal (const DShape &dpsids, DenseMatrix< double > &jacobian, DenseMatrix< double > &inverse_jacobian) const
Calculate the mapping from local to Lagrangian coordinates given the derivatives of the shape functions w.r.t the local coorindates. assuming that the coordinates are aligned in the direction of the local coordinates, i.e. there are no cross terms and the jacobian is diagonal. This function returns the determinant of the jacobian, the jacobian and the inverse jacobian. More...

Protected Member Functions inherited from oomph::RefineableElement
void assemble_local_to_eulerian_jacobian (const DShape &dpsids, DenseMatrix< double > &jacobian) const
Assemble the jacobian matrix for the mapping from local to Eulerian coordinates, given the derivatives of the shape function w.r.t the local coordinates. Overload the standard version to use the hanging information for the Eulerian coordinates. More...

void assemble_local_to_eulerian_jacobian2 (const DShape &d2psids, DenseMatrix< double > &jacobian2) const
Assemble the the "jacobian" matrix of second derivatives of the mapping from local to Eulerian coordinates, given the second derivatives of the shape functions w.r.t. local coordinates. Overload the standard version to use the hanging information for the Eulerian coordinates. More...

void assemble_eulerian_base_vectors (const DShape &dpsids, DenseMatrix< double > &interpolated_G) const
Assemble the covariant Eulerian base vectors, assuming that the derivatives of the shape functions with respect to the local coordinates have already been constructed. Overload the standard version to account for hanging nodes. More...

double local_to_eulerian_mapping_diagonal (const DShape &dpsids, DenseMatrix< double > &jacobian, DenseMatrix< double > &inverse_jacobian) const
Calculate the mapping from local to Eulerian coordinates given the derivatives of the shape functions w.r.t the local coordinates. assuming that the coordinates are aligned in the direction of the local coordinates, i.e. there are no cross terms and the jacobian is diagonal. This funciton returns the determinant of the jacobian, the jacobian and the inverse jacobian. Overload the standard version to take hanging info into account. More...

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)
Calculate the contributions to the jacobian from the nodal degrees of freedom using finite differences. This version is overloaded to take hanging node information into account. More...

Static Protected Member Functions inherited from oomph::RefineableElement
static void check_value_id (const int &n_continuously_interpolated_values, const int &value_id)
Static helper function that is used to check that the value_id is in range. More...

Protected Attributes inherited from oomph::PVDEquationsWithPressure< DIM >
bool Incompressible
Boolean to determine whether the solid is incompressible or not. More...

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...

ConstitutiveLawConstitutive_law_pt
Pointer to the constitutive law. More...

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

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
MacroElementUndeformed_macro_elem_pt
Pointer to the element's "undeformed" macro element (NULL by default) More...

SolidInitialConditionSolid_ic_pt
Pointer to object that specifies the initial condition. More...

bool Solve_for_consistent_newmark_accel_flag
Flag to indicate which system of equations to solve when assigning initial conditions for time-dependent problems. If true, solve for the history value that corresponds to the acceleration in the Newmark scheme by demanding that the PDE is satisifed at the initial time. In this case the Jacobian is replaced by the mass matrix. More...

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

Protected Attributes inherited from oomph::GeneralisedElement
int Non_halo_proc_ID
Non-halo processor ID for Data; -1 if it's not a halo. More...

bool Must_be_kept_as_halo
Does this element need to be kept as a halo element during a distribute? More...

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

unsigned Ndim
Number of Eulerian coordinates. More...

TimeStepperGeom_object_time_stepper_pt

Protected Attributes inherited from oomph::RefineableSolidElement
bool Use_undeformed_macro_element_for_new_lagrangian_coords
Flag deciding if the Lagrangian coordinates of newly-created interior SolidNodes are to be determined by the father element's undeformed MacroElement representation (if it has one). Default: False as it means that, following a refinement an element is no longer in equilbrium (as the Lagrangian coordinate is determined differently from the Eulerian one). However, basing the Lagrangian coordinates on the undeformed MacroElement can be more stable numerically and for steady problems it's not a big deal either way as the difference between the two formulations only matters at finite resolution so we have no right to say that one is "more correct" than the other... More...

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

unsigned Refine_level
Refinement level. More...

bool To_be_refined
Flag for refinement. More...

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

bool Sons_to_be_unrefined
Flag for unrefinement. More...

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

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

Static Protected Attributes inherited from oomph::FiniteElement
static const unsigned Default_Initial_Nvalue = 0
Default return value for required_nvalue(n) which gives the number of "data" values required by the element at node n; for example, solving a Poisson equation would required only one "data" value at each node. The defaults is set to zero, because a general element is problem-less. More...

static const double Node_location_tolerance = 1.0e-14
Default value for the tolerance to be used when locating nodes via local coordinates. More...

static const unsigned N2deriv [] = {0, 1, 3, 6}
Static array that holds the number of second derivatives as a function of the dimension of the element. More...

Static Protected Attributes inherited from oomph::GeneralisedElement
static DenseMatrix< double > Dummy_matrix
Empty dense matrix used as a dummy argument to combined residual and jacobian functions in the case when only the residuals are being assembled. More...

static std::deque< double * > Dof_pt_deque
Static storage for deque used to add_global_equation_numbers when pointers to the dofs in each element are not required. More...

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::RefineablePVDEquationsWithPressure< DIM >

Class for Refineable solid mechanics elements in near-incompressible/ incompressible formulation, so a pressure is included! In this case, the pressure interpolation is discontinuous, a la Crouzeix Raviart.

Definition at line 280 of file refineable_solid_elements.h.

## ◆ RefineablePVDEquationsWithPressure()

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

Constructor:

Definition at line 287 of file refineable_solid_elements.h.

## ◆ fill_in_generic_residual_contribution_pvd_with_pressure()

template<unsigned DIM>
 void oomph::RefineablePVDEquationsWithPressure< DIM >::fill_in_generic_residual_contribution_pvd_with_pressure ( Vector< double > & residuals, DenseMatrix< double > & jacobian, DenseMatrix< double > & mass_matrix, const unsigned & flag )
virtual

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

Fill in element's contribution to the elemental residual vector and/or Jacobian matrix. flag=0: compute only residual vector flag=1: compute both, fully analytically flag=2: compute both, using FD for the derivatives w.r.t. to the discrete displacment dofs. flag=3: compute residuals, jacobian (full analytic) and mass matrix flag=4: compute residuals, jacobian (FD for derivatives w.r.t. displacements) and mass matrix.

Reimplemented from oomph::PVDEquationsWithPressure< DIM >.

Definition at line 675 of file refineable_solid_elements.cc.

## ◆ further_build()

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

## ◆ get_interpolated_values() [1/2]

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

No values are interpolated in this element (pure solid)

Implements oomph::RefineableElement.

Reimplemented in oomph::RefineableQPVDElementWithContinuousPressure< DIM >.

Definition at line 306 of file refineable_solid_elements.h.

## ◆ get_interpolated_values() [2/2]

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

No values are interpolated in this element (pure solid)

Reimplemented from oomph::RefineableElement.

Reimplemented in oomph::RefineableQPVDElementWithContinuousPressure< DIM >.

Definition at line 314 of file refineable_solid_elements.h.

## ◆ get_mass_matrix_diagonal()

template<unsigned DIM>
 void oomph::RefineablePVDEquationsWithPressure< DIM >::get_mass_matrix_diagonal ( Vector< double > & mass_diag )
virtual

Compute the diagonal of the displacement mass matrix for LSC preconditioner.

Compute the diagonal of the velocity mass matrix for LSC preconditioner.

Implements oomph::SolidElementWithDiagonalMassMatrix.

Definition at line 551 of file refineable_solid_elements.cc.

## ◆ get_Z2_flux()

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

in strain tensor.

Implements oomph::ElementWithZ2ErrorEstimator.

Definition at line 330 of file refineable_solid_elements.h.

References oomph::PVDEquationsBase< DIM >::get_strain(), and i.

## ◆ ncont_interpolated_values()

template<unsigned DIM>
 unsigned oomph::RefineablePVDEquationsWithPressure< DIM >::ncont_interpolated_values ( ) const
inlinevirtual

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

Implements oomph::RefineableElement.

Definition at line 373 of file refineable_solid_elements.h.

## ◆ num_Z2_flux_terms()

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

Number of 'flux' terms for Z2 error estimation.

Implements oomph::ElementWithZ2ErrorEstimator.

Definition at line 321 of file refineable_solid_elements.h.

## ◆ solid_pressure_node_pt()

template<unsigned DIM>
 virtual Node * oomph::RefineablePVDEquationsWithPressure< DIM >::solid_pressure_node_pt ( const unsigned & l )
inlinevirtual

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