Taxisym_poroelasticity_elements.h

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// LIC// ====================================================================
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#ifndef OOMPH_TAXISYM_POROELASTICITY_ELEMENTS_HEADER
#define OOMPH_TAXISYM_POROELASTICITY_ELEMENTS_HEADER
 
// Config header generated by autoconfig
#ifdef HAVE_CONFIG_H
#include <oomph-lib-config.h>
#endif
 
#include "axisym_poroelasticity_elements.h"
#include "../generic/Telements.h"
 
namespace oomph
{
  /// =================================================================
  /// Element which solves the Darcy/linear elasticity equations
  /// using TElements
  /// Geometrically the element is always a six noded triangle.
  /// We use the mid-side nodes to store edge-based flux degrees of
  /// freedom and internal data for the discontinuous pressure
  /// and internal flux dofs.
  /// =================================================================
  template<unsigned ORDER>
  class TAxisymmetricPoroelasticityElement
    : public TElement<2, 3>,
      public AxisymmetricPoroelasticityEquations
  {
  private:
    /// The number of values stored at each node
    static const unsigned Initial_Nvalue[];
 
    ///  Face index associated with edge flux degree of freedom
    static const unsigned Face_index_of_edge_flux[];
 
    /// Conversion scheme from an edge degree of freedom to the node
    /// it's stored at
    static const unsigned Q_edge_conv[];
 
    /// The points along each edge where the fluxes are taken to be
    static const double Flux_interpolation_point[];
 
    /// The internal data index where the internal q degrees of freedom are
    /// stored
    unsigned Q_internal_data_index;
 
    /// The internal data index where the p degrees of freedom are stored
    unsigned P_internal_data_index;
 
    /// Unit normal signs associated with each edge to ensure
    /// inter-element continuity of the flux
    std::vector<short> Sign_edge;
 
  public:
    /// Constructor
    TAxisymmetricPoroelasticityElement();
 
    /// Destructor
    ~TAxisymmetricPoroelasticityElement();
 
    /// Number of values required at node n
    unsigned required_nvalue(const unsigned& n) const
    {
      return Initial_Nvalue[n];
    }
 
    /// Return the face index associated with specified edge
    unsigned face_index_of_edge(const unsigned& j) const
    {
      return (j + 2) % 3;
    }
 
    /// Compute the face element coordinates of the nth flux
    /// interpolation point along specified edge
    void face_local_coordinate_of_flux_interpolation_point(
      const unsigned& edge, const unsigned& n, Vector<double>& s) const
    {
      // Get the location of the n-th flux interpolation point along
      // the edge in terms of the distance along the edge itself
      Vector<double> flux_interpolation_point =
        edge_flux_interpolation_point(edge, n);
 
      // Convert the edge number to the number of the mid-edge node along that
      // edge
      unsigned node_number = Q_edge_conv[edge];
 
      // The edge basis functions are defined in a clockwise manner, so we have
      // to effectively "flip" some coordinates
      switch (node_number)
      {
        case 3:
          s[0] = flux_interpolation_point[0];
          break;
        case 4:
          s[0] = 1.0 - flux_interpolation_point[0];
          break;
        case 5:
          s[0] = flux_interpolation_point[0];
          break;
      }
    }
 
    /// Return the face index associated with j-th edge flux degree of freedom
    unsigned face_index_of_q_edge_basis_fct(const unsigned& j) const
    {
      return Face_index_of_edge_flux[j];
    }
 
    /// Return the nodal index of the j-th solid displacement unknown
    /// [0: r; 1: z]
    unsigned u_index_axisym_poroelasticity(const unsigned& j) const
    {
#ifdef RANGE_CHECKING
      if (j >= 2)
      {
        std::ostringstream error_message;
        error_message << "Range Error: j " << j << " is not in the range (0,1)";
        throw OomphLibError(error_message.str(),
                            OOMPH_CURRENT_FUNCTION,
                            OOMPH_EXCEPTION_LOCATION);
      }
#endif
      return j;
    }
 
 
    /// Return the equation number of the j-th edge (flux) degree of freedom
    int q_edge_local_eqn(const unsigned& j) const
    {
#ifdef RANGE_CHECKING
      if (j >= nq_basis_edge())
      {
        std::ostringstream error_message;
        error_message << "Range Error: j " << j << " is not in the range (0,"
                      << nq_basis_edge() - 1 << ")";
        throw OomphLibError(error_message.str(),
                            OOMPH_CURRENT_FUNCTION,
                            OOMPH_EXCEPTION_LOCATION);
      }
#endif
      return this->nodal_local_eqn(q_edge_node_number(j), q_edge_index(j));
    }
 
    /// Return the equation number of the j-th internal degree of freedom
    int q_internal_local_eqn(const unsigned& j) const
    {
#ifdef RANGE_CHECKING
      if (j >= nq_basis_internal())
      {
        std::ostringstream error_message;
        error_message << "Range Error: j " << j << " is not in the range (0,"
                      << nq_basis_internal() - 1 << ")";
        throw OomphLibError(error_message.str(),
                            OOMPH_CURRENT_FUNCTION,
                            OOMPH_EXCEPTION_LOCATION);
      }
#endif
      return internal_local_eqn(q_internal_index(), j);
    }
 
    /// Return vector of pointers to the Data objects that store the
    /// edge flux values
    Vector<Data*> q_edge_data_pt() const
    {
      // It's the mid-side nodes:
      Vector<Data*> data_pt(3);
      data_pt[0] = node_pt(3);
      data_pt[1] = node_pt(4);
      data_pt[2] = node_pt(5);
      return data_pt;
    }
 
    /// Return pointer to the Data object that stores the internal flux values
    Data* q_internal_data_pt() const
    {
      return this->internal_data_pt(Q_internal_data_index);
    }
 
    /// Return the index of the internal data where the q_internal
    /// degrees of freedom are stored
    unsigned q_internal_index() const
    {
      return Q_internal_data_index;
    }
 
    /// Return the nodal index at which the jth edge unknown is stored
    unsigned q_edge_index(const unsigned& j) const
    {
#ifdef RANGE_CHECKING
      if (j >= (nq_basis_edge()))
      {
        std::ostringstream error_message;
        error_message << "Range Error: j " << j << " is not in the range (0,"
                      << nq_basis_edge() - 1 << ")";
        throw OomphLibError(error_message.str(),
                            OOMPH_CURRENT_FUNCTION,
                            OOMPH_EXCEPTION_LOCATION);
      }
#endif
      return j % (ORDER + 1) + 2;
    }
 
    /// Return the number of the node where the jth edge unknown is stored
    unsigned q_edge_node_number(const unsigned& j) const
    {
#ifdef RANGE_CHECKING
      if (j >= (nq_basis_edge()))
      {
        std::ostringstream error_message;
        error_message << "Range Error: j " << j << " is not in the range (0,"
                      << nq_basis_edge() - 1 << ")";
        throw OomphLibError(error_message.str(),
                            OOMPH_CURRENT_FUNCTION,
                            OOMPH_EXCEPTION_LOCATION);
      }
#endif
      return Q_edge_conv[j / (ORDER + 1)];
    }
 
 
    /// Get pointer to node that stores the edge flux dofs for specified edge
    Node* edge_flux_node_pt(const unsigned& edge)
    {
      return node_pt(Q_edge_conv[edge]);
    }
 
    /// Return the values of the j-th edge (flux) degree of freedom
    double q_edge(const unsigned& j) const
    {
#ifdef RANGE_CHECKING
      if (j >= (nq_basis_edge()))
      {
        std::ostringstream error_message;
        error_message << "Range Error: j " << j << " is not in the range (0,"
                      << nq_basis_edge() - 1 << ")";
        throw OomphLibError(error_message.str(),
                            OOMPH_CURRENT_FUNCTION,
                            OOMPH_EXCEPTION_LOCATION);
      }
#endif
      return nodal_value(q_edge_node_number(j), q_edge_index(j));
    }
 
    /// Return the values of the j-th edge (flux) degree of
    /// freedom at time history level t
    double q_edge(const unsigned& t, const unsigned& j) const
    {
#ifdef RANGE_CHECKING
      if (j >= (nq_basis_edge()))
      {
        std::ostringstream error_message;
        error_message << "Range Error: j " << j << " is not in the range (0,"
                      << nq_basis_edge() - 1 << ")";
        throw OomphLibError(error_message.str(),
                            OOMPH_CURRENT_FUNCTION,
                            OOMPH_EXCEPTION_LOCATION);
      }
#endif
      return nodal_value(t, q_edge_node_number(j), q_edge_index(j));
    }
 
    /// Return the values of the internal degree of freedom
    double q_internal(const unsigned& j) const
    {
#ifdef RANGE_CHECKING
      if (j >= nq_basis_internal())
      {
        std::ostringstream error_message;
        error_message << "Range Error: j " << j << " is not in the range (0,"
                      << nq_basis_internal() - 1 << ")";
        throw OomphLibError(error_message.str(),
                            OOMPH_CURRENT_FUNCTION,
                            OOMPH_EXCEPTION_LOCATION);
      }
#endif
      return this->internal_data_pt(q_internal_index())->value(j);
    }
 
    /// Return the value of the j-th internal degree of freedom at
    /// time history level t
    double q_internal(const unsigned& t, const unsigned& j) const
    {
#ifdef RANGE_CHECKING
      if (j >= nq_basis_internal())
      {
        std::ostringstream error_message;
        error_message << "Range Error: j " << j << " is not in the range (0,"
                      << nq_basis_internal() - 1 << ")";
        throw OomphLibError(error_message.str(),
                            OOMPH_CURRENT_FUNCTION,
                            OOMPH_EXCEPTION_LOCATION);
      }
#endif
      return this->internal_data_pt(q_internal_index())->value(t, j);
    }
 
    /// Pin the j-th edge (flux) degree of freedom and set it to specified value
    void pin_q_edge_value(const unsigned& j, const double& value)
    {
      node_pt(q_edge_node_number(j))->pin(q_edge_index(j));
      node_pt(q_edge_node_number(j))->set_value(q_edge_index(j), value);
    }
 
    /// Set the values of the j-th edge (flux) degree of freedom
    void set_q_edge(const unsigned& j, const double& value)
    {
      node_pt(q_edge_node_number(j))->set_value(q_edge_index(j), value);
    }
 
    /// Set the values of the j-th edge (flux) degree of freedom at
    /// time history level t
    void set_q_edge(const unsigned& t, const unsigned& j, const double& value)
    {
      node_pt(q_edge_node_number(j))->set_value(t, q_edge_index(j), value);
    }
 
 
    /// Set the values of the j-th internal degree of freedom
    void set_q_internal(const unsigned& j, const double& value)
    {
      this->internal_data_pt(q_internal_index())->set_value(j, value);
    }
 
    /// Set the values of the j-th internal degree of freedom at
    /// time history level t
    void set_q_internal(const unsigned& t,
                        const unsigned& j,
                        const double& value)
    {
      this->internal_data_pt(q_internal_index())->set_value(t, j, value);
    }
 
    /// Return the number of edge basis functions for flux q
    unsigned nq_basis_edge() const;
 
    /// Return the number of internal basis functions for flux q
    unsigned nq_basis_internal() const;
 
    /// Returns the local form of the q basis at local coordinate s
    void get_q_basis_local(const Vector<double>& s, Shape& q_basis) const;
 
    /// Returns the local form of the q basis and dbasis/ds at local coordinate
    /// s
    void get_div_q_basis_local(const Vector<double>& s,
                               Shape& div_q_basis_ds) const;
 
    /// Returns the number of flux_interpolation points along each
    /// edge of the element
    unsigned nedge_flux_interpolation_point() const;
 
    /// Returns the local coordinate of the jth flux_interpolation point
    /// along specified edge
    Vector<double> edge_flux_interpolation_point(const unsigned& edge,
                                                 const unsigned& j) const
    {
#ifdef RANGE_CHECKING
      if (edge >= 3)
      {
        std::ostringstream error_message;
        error_message << "Range Error: edge " << edge
                      << " is not in the range (0,2)";
        throw OomphLibError(error_message.str(),
                            OOMPH_CURRENT_FUNCTION,
                            OOMPH_EXCEPTION_LOCATION);
      }
      if (j >= nedge_flux_interpolation_point())
      {
        std::ostringstream error_message;
        error_message << "Range Error: j " << j << " is not in the range (0,"
                      << nedge_flux_interpolation_point() - 1 << ")";
        throw OomphLibError(error_message.str(),
                            OOMPH_CURRENT_FUNCTION,
                            OOMPH_EXCEPTION_LOCATION);
      }
#endif
      Vector<double> coord(1);
      coord[0] = (1.0 - sign_edge(edge)) / 2.0 +
                 sign_edge(edge) * Flux_interpolation_point[j];
      return coord;
    }
 
    /// Compute the global coordinates of the jth flux_interpolation
    /// point along specified edge
    void edge_flux_interpolation_point_global(const unsigned& edge,
                                              const unsigned& j,
                                              Vector<double>& x) const
    {
#ifdef RANGE_CHECKING
      if (edge >= 3)
      {
        std::ostringstream error_message;
        error_message << "Range Error: edge " << edge
                      << " is not in the range (0,2)";
        throw OomphLibError(error_message.str(),
                            OOMPH_CURRENT_FUNCTION,
                            OOMPH_EXCEPTION_LOCATION);
      }
      if (j >= nedge_flux_interpolation_point())
      {
        std::ostringstream error_message;
        error_message << "Range Error: j " << j << " is not in the range (0,"
                      << nedge_flux_interpolation_point() - 1 << ")";
        throw OomphLibError(error_message.str(),
                            OOMPH_CURRENT_FUNCTION,
                            OOMPH_EXCEPTION_LOCATION);
      }
#endif
 
      // Get the location of the n-th flux_interpolation point along the
      // edge in terms of the distance along the edge itself
      Vector<double> flux_interpolation_point =
        edge_flux_interpolation_point(edge, j);
 
      // Convert the edge number to the number of the mid-edge node along that
      // edge
      unsigned node_number = Q_edge_conv[edge];
 
      // Storage for the local coords of the flux_interpolation point
      Vector<double> s_flux_interpolation(2, 0);
 
      // The edge basis functions are defined in a clockwise manner, so we have
      // to effectively "flip" the coordinates along edges 0 and 1 to match this
      switch (node_number)
      {
        case 3:
          s_flux_interpolation[0] = 1.0 - flux_interpolation_point[0];
          s_flux_interpolation[1] = flux_interpolation_point[0];
          break;
        case 4:
          s_flux_interpolation[0] = 0.0;
          s_flux_interpolation[1] = 1.0 - flux_interpolation_point[0];
          break;
        case 5:
          s_flux_interpolation[0] = flux_interpolation_point[0];
          s_flux_interpolation[1] = 0.0;
          break;
      }
 
      // Calculate the global coordinates from the local ones
      interpolated_x(s_flux_interpolation, x);
    }
 
    /// Pin the jth internal q value and set it to specified value
    void pin_q_internal_value(const unsigned& j, const double& q)
    {
#ifdef RANGE_CHECKING
      if (j >= nq_basis_internal())
      {
        std::ostringstream error_message;
        error_message << "Range Error: j " << j << " is not in the range (0,"
                      << nq_basis_internal() - 1 << ")";
        throw OomphLibError(error_message.str(),
                            OOMPH_CURRENT_FUNCTION,
                            OOMPH_EXCEPTION_LOCATION);
      }
#endif
      this->internal_data_pt(q_internal_index())->pin(j);
      this->internal_data_pt(q_internal_index())->set_value(j, q);
    }
 
    /// Return the equation number of the j-th pressure degree of freedom
    int p_local_eqn(const unsigned& j) const
    {
#ifdef RANGE_CHECKING
      if (j >= np_basis())
      {
        std::ostringstream error_message;
        error_message << "Range Error: j " << j << " is not in the range (0,"
                      << np_basis() - 1 << ")";
        throw OomphLibError(error_message.str(),
                            OOMPH_CURRENT_FUNCTION,
                            OOMPH_EXCEPTION_LOCATION);
      }
#endif
      return this->internal_local_eqn(P_internal_data_index, j);
    }
 
    /// Return the jth pressure value
    double p_value(const unsigned& j) const
    {
#ifdef RANGE_CHECKING
      if (j >= np_basis())
      {
        std::ostringstream error_message;
        error_message << "Range Error: j " << j << " is not in the range (0,"
                      << np_basis() - 1 << ")";
        throw OomphLibError(error_message.str(),
                            OOMPH_CURRENT_FUNCTION,
                            OOMPH_EXCEPTION_LOCATION);
      }
#endif
      return this->internal_data_pt(P_internal_data_index)->value(j);
    }
 
    /// Return the total number of pressure basis functions
    unsigned np_basis() const;
 
    /// Return the pressure basis
    void get_p_basis(const Vector<double>& s, Shape& p_basis) const;
 
    /// Pin the jth pressure value and set to specified value
    void pin_p_value(const unsigned& j, const double& p)
    {
#ifdef RANGE_CHECKING
      if (j >= np_basis())
      {
        std::ostringstream error_message;
        error_message << "Range Error: j " << j << " is not in the range (0,"
                      << np_basis() - 1 << ")";
        throw OomphLibError(error_message.str(),
                            OOMPH_CURRENT_FUNCTION,
                            OOMPH_EXCEPTION_LOCATION);
      }
#endif
      this->internal_data_pt(P_internal_data_index)->pin(j);
      this->internal_data_pt(P_internal_data_index)->set_value(j, p);
    }
 
    /// Return pointer to the Data object that stores the pressure values
    Data* p_data_pt() const
    {
      return this->internal_data_pt(P_internal_data_index);
    }
 
    /// Set the jth pressure value
    void set_p_value(const unsigned& j, const double& value)
    {
      this->internal_data_pt(P_internal_data_index)->set_value(j, value);
    }
 
    /// Scale the edge basis to allow arbitrary edge mappings
    void scale_basis(Shape& basis) const
    {
      // Storage for the lengths of the edges of the element
      Vector<double> length(3, 0.0);
 
      // Temporary storage for the vertex positions
      double x0, y0, x1, y1;
 
      // loop over the edges of the element and calculate their lengths (in x-y
      // space)
      for (unsigned i = 0; i < 3; i++)
      {
        x0 = this->node_pt(i)->x(0);
        y0 = this->node_pt(i)->x(1);
        x1 = this->node_pt((i + 1) % 3)->x(0);
        y1 = this->node_pt((i + 1) % 3)->x(1);
 
        length[i] = std::sqrt(std::pow(y1 - y0, 2) + std::pow(x1 - x0, 2));
      }
 
      // lengths of the sides of the reference element (in the same order as the
      // basis functions)
      const double ref_length[3] = {std::sqrt(2.0), 1, 1};
 
      // get the number of basis functions associated with the edges
      unsigned n_q_basis_edge = nq_basis_edge();
 
      // rescale the edge basis functions to allow arbitrary edge mappings from
      // element to ref. element
      const unsigned n_index2 = basis.nindex2();
      for (unsigned i = 0; i < n_index2; i++)
      {
        for (unsigned l = 0; l < n_q_basis_edge; l++)
        {
          basis(l, i) *=
            (length[l / (ORDER + 1)] / ref_length[l / (ORDER + 1)]);
        }
      }
    }
 
    /// Accessor for the unit normal sign of edge n (const version)
    const short& sign_edge(const unsigned& n) const
    {
      return Sign_edge[n];
    }
 
    /// Accessor for the unit normal sign of edge n
    short& sign_edge(const unsigned& n)
    {
      return Sign_edge[n];
    }
 
    /// Output with default number of plot points
    void output(std::ostream& outfile)
    {
      AxisymmetricPoroelasticityEquations::output(outfile);
    }
 
    /// Output FE representation of soln: x,y,u1,u2,div_q,p at
    /// Nplot^DIM plot points
    void output(std::ostream& outfile, const unsigned& Nplot)
    {
      AxisymmetricPoroelasticityEquations::output(outfile, Nplot);
    }
 
 
    /// Number of vertex nodes in the element
    unsigned nvertex_node() const
    {
      return TElement<2, 3>::nvertex_node();
    }
 
    /// Pointer to the j-th vertex node in the element
    Node* vertex_node_pt(const unsigned& j) const
    {
      return TElement<2, 3>::vertex_node_pt(j);
    }
 
    /// Recovery order for Z2 error estimator
    unsigned nrecovery_order()
    {
      return 2; // need to experiment with this...
    }
 
  protected:
    /// Returns the geometric basis, and the u, p and divergence basis
    /// functions and test functions at local coordinate s
    double shape_basis_test_local(const Vector<double>& s,
                                  Shape& psi,
                                  DShape& dpsi,
                                  Shape& u_basis,
                                  Shape& u_test,
                                  DShape& du_basis_dx,
                                  DShape& du_test_dx,
                                  Shape& q_basis,
                                  Shape& q_test,
                                  Shape& p_basis,
                                  Shape& p_test,
                                  Shape& div_q_basis_ds,
                                  Shape& div_q_test_ds) const
    {
      const unsigned n_q_basis = this->nq_basis();
 
      Shape q_basis_local(n_q_basis, 2);
      this->get_q_basis_local(s, q_basis_local);
      this->get_p_basis(s, p_basis);
      this->get_div_q_basis_local(s, div_q_basis_ds);
 
      double J = this->transform_basis(s, q_basis_local, psi, dpsi, q_basis);
 
      // u_basis consists of the normal Lagrangian shape functions
      u_basis = psi;
      du_basis_dx = dpsi;
 
      u_test = psi;
      du_test_dx = dpsi;
 
      q_test = q_basis;
      p_test = p_basis;
      div_q_test_ds = div_q_basis_ds;
 
      return J;
    }
 
    /// Returns the geometric basis, and the u, p and divergence basis
    /// functions and test functions at integration point ipt
    double shape_basis_test_local_at_knot(const unsigned& ipt,
                                          Shape& psi,
                                          DShape& dpsi,
                                          Shape& u_basis,
                                          Shape& u_test,
                                          DShape& du_basis_dx,
                                          DShape& du_test_dx,
                                          Shape& q_basis,
                                          Shape& q_test,
                                          Shape& p_basis,
                                          Shape& p_test,
                                          Shape& div_q_basis_ds,
                                          Shape& div_q_test_ds) const
    {
      Vector<double> s(2);
      for (unsigned i = 0; i < 2; i++)
      {
        s[i] = this->integral_pt()->knot(ipt, i);
      }
 
      return shape_basis_test_local(s,
                                    psi,
                                    dpsi,
                                    u_basis,
                                    u_test,
                                    du_basis_dx,
                                    du_test_dx,
                                    q_basis,
                                    q_test,
                                    p_basis,
                                    p_test,
                                    div_q_basis_ds,
                                    div_q_test_ds);
    }
  };
 
 
  //================================================================
  /// Face geometry for TAxisymmetricPoroelasticityElement<0>
  //================================================================
  template<>
  class FaceGeometry<TAxisymmetricPoroelasticityElement<0>>
    : public virtual TElement<1, 3>
  {
  public:
    /// Constructor: Call constructor of base
    FaceGeometry() : TElement<1, 3>() {}
  };
 
 
  //================================================================
  /// Face geometry for TAxisymmetricPoroelasticityElement<1>
  //================================================================
  template<>
  class FaceGeometry<TAxisymmetricPoroelasticityElement<1>>
    : public virtual TElement<1, 3>
  {
  public:
    /// Constructor: Call constructor of base class
    FaceGeometry() : TElement<1, 3>() {}
  };
 
 
} // namespace oomph
 
#endif