refineable_poisson_elements.cc

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// LIC// ====================================================================
// LIC// This file forms part of oomph-lib, the object-oriented,
// LIC// multi-physics finite-element library, available
// LIC// at http://www.oomph-lib.org.
// LIC//
// LIC// Copyright (C) 2006-2024 Matthias Heil and Andrew Hazel
// LIC//
// LIC// This library is free software; you can redistribute it and/or
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// LIC// License as published by the Free Software Foundation; either
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#include "refineable_poisson_elements.h"
 
 
namespace oomph
{
  //========================================================================
  /// Validate against exact flux.
  /// Flux is provided via function pointer.
  /// Plot error at a given number of plot points.
  //========================================================================
  template<unsigned DIM>
  void RefineablePoissonEquations<DIM>::compute_exact_Z2_error(
    std::ostream& outfile,
    FiniteElement::SteadyExactSolutionFctPt exact_flux_pt,
    double& error,
    double& norm)
  {
    // Initialise
    error = 0.0;
    norm = 0.0;
 
    // Vector of local coordinates
    Vector<double> s(DIM);
 
    // Vector of global coordinates
    Vector<double> x(DIM);
 
    // Find out how many nodes there are in the element
    const unsigned n_node = nnode();
 
    // Allocate storage for shape functions
    Shape psi(n_node);
 
    // Set the value of n_intpt
    const unsigned n_intpt = integral_pt()->nweight();
 
    // Tecplot
    outfile << "ZONE" << std::endl;
 
    // Exact flux Vector (size is DIM)
    Vector<double> exact_flux(DIM);
 
    // Loop over the integration points
    for (unsigned ipt = 0; ipt < n_intpt; ipt++)
    {
      // Assign values of s
      for (unsigned i = 0; i < DIM; i++)
      {
        s[i] = integral_pt()->knot(ipt, i);
      }
 
      // Get the integral weight
      double w = integral_pt()->weight(ipt);
 
      // Get jacobian of mapping
      double J = J_eulerian(s);
 
      // Premultiply the weights and the Jacobian
      double W = w * J;
 
      // Get x position as Vector
      interpolated_x(s, x);
 
      // Allocate storage for FE flux Vector
      Vector<double> fe_flux(DIM);
 
      // Get FE flux as Vector
      get_Z2_flux(s, fe_flux);
 
      // Get exact flux at this point
      (*exact_flux_pt)(x, exact_flux);
 
      // Output x,y,...
      for (unsigned i = 0; i < DIM; i++)
      {
        outfile << x[i] << " ";
      }
 
      // Output exact flux
      for (unsigned i = 0; i < DIM; i++)
      {
        outfile << exact_flux[i] << " ";
      }
 
      // Output error
      for (unsigned i = 0; i < DIM; i++)
      {
        outfile << exact_flux[i] - fe_flux[i] << " ";
      }
      outfile << std::endl;
 
      // Add to RMS error:
      double sum = 0.0;
      double sum2 = 0.0;
      for (unsigned i = 0; i < DIM; i++)
      {
        sum += (fe_flux[i] - exact_flux[i]) * (fe_flux[i] - exact_flux[i]);
        sum2 += exact_flux[i] * exact_flux[i];
      }
      error += sum * W;
      norm += sum2 * W;
 
    } // End of loop over the integration points
  }
 
 
  //========================================================================
  /// Add element's contribution to the elemental
  /// residual vector and/or Jacobian matrix.
  /// flag=1: compute both
  /// flag=0: compute only residual vector
  //========================================================================
  template<unsigned DIM>
  void RefineablePoissonEquations<DIM>::
    fill_in_generic_residual_contribution_poisson(Vector<double>& residuals,
                                                  DenseMatrix<double>& jacobian,
                                                  const unsigned& flag)
  {
    // Find out how many nodes there are in the element
    unsigned n_node = nnode();
 
    // Set up memory for the shape and test functions
    Shape psi(n_node), test(n_node);
    DShape dpsidx(n_node, DIM), dtestdx(n_node, DIM);
 
    // Set the value of n_intpt
    unsigned n_intpt = integral_pt()->nweight();
 
    // The local index at which the poisson variable is stored
    unsigned u_nodal_index = this->u_index_poisson();
 
    // Integers to store the local equation and unknown numbers
    int local_eqn = 0, local_unknown = 0;
 
    // Local storage for pointers to hang_info objects
    HangInfo *hang_info_pt = 0, *hang_info2_pt = 0;
 
    // Loop over the integration points
    for (unsigned ipt = 0; ipt < n_intpt; ipt++)
    {
      // Get the integral weight
      double w = integral_pt()->weight(ipt);
 
      // Call the derivatives of the shape and test functions
      double J = this->dshape_and_dtest_eulerian_at_knot_poisson(
        ipt, psi, dpsidx, test, dtestdx);
 
      // Premultiply the weights and the Jacobian
      double W = w * J;
 
      // Position and gradient
      Vector<double> interpolated_x(DIM, 0.0);
      Vector<double> interpolated_dudx(DIM, 0.0);
 
      // Calculate function value and derivatives:
      //-----------------------------------------
 
      // Loop over nodes
      for (unsigned l = 0; l < n_node; l++)
      {
        // Get the poisson value from the node
        //(hanging-ness will be taken into account
        double u_value = this->nodal_value(l, u_nodal_index);
 
        // Loop over directions
        for (unsigned j = 0; j < DIM; j++)
        {
          interpolated_x[j] += nodal_position(l, j) * psi(l);
          interpolated_dudx[j] += u_value * dpsidx(l, j);
        }
      }
 
      // Get body force
      double source;
      this->get_source_poisson(ipt, interpolated_x, source);
 
 
      // Assemble residuals and Jacobian
 
      // Loop over the nodes for the test functions
      for (unsigned l = 0; l < n_node; l++)
      {
        // Local variables used to store the number of master nodes and the
        // weight associated with the shape function if the node is hanging
        unsigned n_master = 1;
        double hang_weight = 1.0;
 
        // Local bool (is the node hanging)
        bool is_node_hanging = this->node_pt(l)->is_hanging();
 
        // If the node is hanging, get the number of master nodes
        if (is_node_hanging)
        {
          hang_info_pt = this->node_pt(l)->hanging_pt();
          n_master = hang_info_pt->nmaster();
        }
        // Otherwise there is just one master node, the node itself
        else
        {
          n_master = 1;
        }
 
        // Loop over the master nodes
        for (unsigned m = 0; m < n_master; m++)
        {
          // Get the local equation number and hang_weight
          // If the node is hanging
          if (is_node_hanging)
          {
            // Read out the local equation number from the m-th master node
            local_eqn = this->local_hang_eqn(hang_info_pt->master_node_pt(m),
                                             u_nodal_index);
 
            // Read out the weight from the master node
            hang_weight = hang_info_pt->master_weight(m);
          }
          // If the node is not hanging
          else
          {
            // The local equation number comes from the node itself
            local_eqn = this->nodal_local_eqn(l, u_nodal_index);
 
            // The hang weight is one
            hang_weight = 1.0;
          }
 
          // If the nodal equation is not a boundary condition
          if (local_eqn >= 0)
          {
            // Add body force/source term here
            residuals[local_eqn] += source * test(l) * W * hang_weight;
 
            // The Poisson bit itself
            for (unsigned k = 0; k < DIM; k++)
            {
              residuals[local_eqn] +=
                interpolated_dudx[k] * dtestdx(l, k) * W * hang_weight;
            }
 
            // Calculate the Jacobian
            if (flag)
            {
              // Local variables to store the number of master nodes
              // and the weights associated with each hanging node
              unsigned n_master2 = 1;
              double hang_weight2 = 1.0;
 
              // Loop over the nodes for the variables
              for (unsigned l2 = 0; l2 < n_node; l2++)
              {
                // Local bool (is the node hanging)
                bool is_node2_hanging = this->node_pt(l2)->is_hanging();
 
                // If the node is hanging, get the number of master nodes
                if (is_node2_hanging)
                {
                  hang_info2_pt = this->node_pt(l2)->hanging_pt();
                  n_master2 = hang_info2_pt->nmaster();
                }
                // Otherwise there is one master node, the node itself
                else
                {
                  n_master2 = 1;
                }
 
                // Loop over the master nodes
                for (unsigned m2 = 0; m2 < n_master2; m2++)
                {
                  // Get the local unknown and weight
                  // If the node is hanging
                  if (is_node2_hanging)
                  {
                    // Read out the local unknown from the master node
                    local_unknown = this->local_hang_eqn(
                      hang_info2_pt->master_node_pt(m2), u_nodal_index);
 
                    // Read out the hanging weight from the master node
                    hang_weight2 = hang_info2_pt->master_weight(m2);
                  }
                  // If the node is not hanging
                  else
                  {
                    // The local unknown number comes from the node
                    local_unknown = this->nodal_local_eqn(l2, u_nodal_index);
 
                    // The hang weight is one
                    hang_weight2 = 1.0;
                  }
 
                  // If the unknown is not pinned
                  if (local_unknown >= 0)
                  {
                    // Add contribution to Elemental Matrix
                    for (unsigned i = 0; i < DIM; i++)
                    {
                      jacobian(local_eqn, local_unknown) +=
                        dpsidx(l2, i) * dtestdx(l, i) * W * hang_weight *
                        hang_weight2;
                    }
                  }
                } // End of loop over master nodes
              } // End of loop over nodes
            } // End of Jacobian calculation
 
          } // End of case when residual equation is not pinned
        } // End of loop over master nodes for residual
      } // End of loop over nodes
 
    } // End of loop over integration points
  }
 
 
  //======================================================================
  /// Compute derivatives of elemental residual vector with respect
  /// to nodal coordinates (fully analytical).
  /// dresidual_dnodal_coordinates(l,i,j) = d res(l) / dX_{ij}
  /// Overloads the FD-based version in the FE base class.
  //======================================================================
  template<unsigned DIM>
  void RefineablePoissonEquations<DIM>::get_dresidual_dnodal_coordinates(
    RankThreeTensor<double>& dresidual_dnodal_coordinates)
  {
    // Determine number of nodes in element
    const unsigned n_node = nnode();
 
    // Set up memory for the shape and test functions
    Shape psi(n_node), test(n_node);
    DShape dpsidx(n_node, DIM), dtestdx(n_node, DIM);
 
    // Get number of shape controlling nodes
    const unsigned n_shape_controlling_node = nshape_controlling_nodes();
 
    // Deriatives of shape fct derivatives w.r.t. nodal coords
    RankFourTensor<double> d_dpsidx_dX(
      DIM, n_shape_controlling_node, n_node, DIM);
    RankFourTensor<double> d_dtestdx_dX(
      DIM, n_shape_controlling_node, n_node, DIM);
 
    // Derivative of Jacobian of mapping w.r.t. to nodal coords
    DenseMatrix<double> dJ_dX(DIM, n_shape_controlling_node);
 
    // Derivatives of derivative of u w.r.t. nodal coords
    RankThreeTensor<double> d_dudx_dX(DIM, n_shape_controlling_node, DIM);
 
    // Source function and its gradient
    double source;
    Vector<double> d_source_dx(DIM);
 
    // Index at which the poisson unknown is stored
    const unsigned u_nodal_index = this->u_index_poisson();
 
    // Determine the number of integration points
    const unsigned n_intpt = integral_pt()->nweight();
 
    // Integer to store the local equation number
    int local_eqn = 0;
 
    // Local storage for pointers to hang_info object
    HangInfo* hang_info_pt = 0;
 
    // Loop over the integration points
    for (unsigned ipt = 0; ipt < n_intpt; ipt++)
    {
      // Get the integral weight
      double w = integral_pt()->weight(ipt);
 
      // Call the derivatives of the shape/test functions, as well as the
      // derivatives of these w.r.t. nodal coordinates and the derivative
      // of the jacobian of the mapping w.r.t. nodal coordinates
      const double J = this->dshape_and_dtest_eulerian_at_knot_poisson(
        ipt, psi, dpsidx, d_dpsidx_dX, test, dtestdx, d_dtestdx_dX, dJ_dX);
 
      // Calculate local values
      // Allocate and initialise to zero
      Vector<double> interpolated_x(DIM, 0.0);
      Vector<double> interpolated_dudx(DIM, 0.0);
 
      // Calculate function value and derivatives:
      // -----------------------------------------
      // Loop over nodes
      for (unsigned l = 0; l < n_node; l++)
      {
        // Get the nodal value of the Poisson unknown
        double u_value = nodal_value(l, u_nodal_index);
 
        // Loop over directions
        for (unsigned i = 0; i < DIM; i++)
        {
          interpolated_x[i] += nodal_position(l, i) * psi(l);
          interpolated_dudx[i] += u_value * dpsidx(l, i);
        }
      }
 
      // Calculate derivative of du/dx_i w.r.t. nodal positions X_{pq}
 
      // Loop over shape controlling nodes
      for (unsigned q = 0; q < n_shape_controlling_node; q++)
      {
        // Loop over coordinate directions
        for (unsigned p = 0; p < DIM; p++)
        {
          for (unsigned i = 0; i < DIM; i++)
          {
            double aux = 0.0;
            for (unsigned j = 0; j < n_node; j++)
            {
              aux += nodal_value(j, u_nodal_index) * d_dpsidx_dX(p, q, j, i);
            }
            d_dudx_dX(p, q, i) = aux;
          }
        }
      }
 
      // Get source function
      this->get_source_poisson(ipt, interpolated_x, source);
 
      // Get gradient of source function
      this->get_source_gradient_poisson(ipt, interpolated_x, d_source_dx);
 
      //   std::map<Node*,unsigned>
      //   local_shape_controlling_node_lookup=shape_controlling_node_lookup();
 
      // Assemble d res_{local_eqn} / d X_{pq}
      // -------------------------------------
 
      // Loop over the nodes for the test functions
      for (unsigned l = 0; l < n_node; l++)
      {
        // Local variables used to store the number of master nodes and the
        // weight associated with the shape function if the node is hanging
        unsigned n_master = 1;
        double hang_weight = 1.0;
 
        // Local bool (is the node hanging)
        bool is_node_hanging = this->node_pt(l)->is_hanging();
 
        // If the node is hanging, get the number of master nodes
        if (is_node_hanging)
        {
          hang_info_pt = this->node_pt(l)->hanging_pt();
          n_master = hang_info_pt->nmaster();
        }
        // Otherwise there is just one master node, the node itself
        else
        {
          n_master = 1;
        }
 
        // Loop over the master nodes
        for (unsigned m = 0; m < n_master; m++)
        {
          // Get the local equation number and hang_weight
          // If the node is hanging
          if (is_node_hanging)
          {
            // Read out the local equation number from the m-th master node
            local_eqn = this->local_hang_eqn(hang_info_pt->master_node_pt(m),
                                             u_nodal_index);
 
            // Read out the weight from the master node
            hang_weight = hang_info_pt->master_weight(m);
          }
          // If the node is not hanging
          else
          {
            // The local equation number comes from the node itself
            local_eqn = this->nodal_local_eqn(l, u_nodal_index);
            // The hang weight is one
            hang_weight = 1.0;
          }
 
          // If the nodal equation is not a boundary condition
          if (local_eqn >= 0)
          {
            // Loop over coordinate directions
            for (unsigned p = 0; p < DIM; p++)
            {
              // Loop over shape controlling nodes
              for (unsigned q = 0; q < n_shape_controlling_node; q++)
              {
                double sum = source * test(l) * dJ_dX(p, q) +
                             d_source_dx[p] * test(l) * psi(q) * J;
 
                for (unsigned i = 0; i < DIM; i++)
                {
                  sum += interpolated_dudx[i] * (dtestdx(l, i) * dJ_dX(p, q) +
                                                 d_dtestdx_dX(p, q, l, i) * J) +
                         d_dudx_dX(p, q, i) * dtestdx(l, i) * J;
                }
 
                // Multiply through by integration weight
                dresidual_dnodal_coordinates(local_eqn, p, q) +=
                  sum * w * hang_weight;
              }
            }
          }
        }
      }
    } // End of loop over integration points
  }
 
  /// Get error against and norm of exact solution
  template<unsigned DIM>
  void PRefineableQPoissonElement<DIM>::compute_energy_error(
    std::ostream& outfile,
    FiniteElement::SteadyExactSolutionFctPt exact_grad_pt,
    double& error,
    double& norm)
  {
    // Initialise
    error = 0.0;
    norm = 0.0;
 
    // Vector of local coordinates
    Vector<double> s(DIM);
 
    // Vector for coordintes
    Vector<double> x(DIM);
 
    // Set the value of n_intpt
    unsigned n_intpt = this->integral_pt()->nweight();
 
    // Setup output structure: Conversion is fishy but it's only output...
    unsigned nplot;
    if (DIM == 1)
    {
      nplot = n_intpt;
    }
    else
    {
      nplot = unsigned(pow(n_intpt, 1.0 / double(DIM)));
    }
 
    // Tecplot header info
    outfile << this->tecplot_zone_string(nplot);
 
    // Exact gradient Vector
    Vector<double> exact_grad(DIM);
 
    // Loop over the integration points
    for (unsigned ipt = 0; ipt < n_intpt; ipt++)
    {
      // Assign values of s
      for (unsigned i = 0; i < DIM; i++)
      {
        s[i] = this->integral_pt()->knot(ipt, i);
      }
 
      // Get the integral weight
      double w = this->integral_pt()->weight(ipt);
 
      // Get jacobian of mapping
      double J = this->J_eulerian(s);
 
      // Premultiply the weights and the Jacobian
      double W = w * J;
 
      // Get x position as Vector
      this->interpolated_x(s, x);
 
      // Get FE du/dx
      Vector<double> dudx_fe(DIM);
      PoissonEquations<DIM>::get_flux(s, dudx_fe);
 
      // Get exact gradient at this point
      (*exact_grad_pt)(x, exact_grad);
 
      // Output x,y,...,error
      for (unsigned i = 0; i < DIM; i++)
      {
        outfile << x[i] << " ";
      }
      for (unsigned i = 0; i < DIM; i++)
      {
        outfile << exact_grad[i] << " " << exact_grad[i] - dudx_fe[i]
                << std::endl;
      }
 
      // Add to error and norm
      for (unsigned i = 0; i < DIM; i++)
      {
        norm += exact_grad[i] * exact_grad[i] * W;
        error +=
          (exact_grad[i] - dudx_fe[i]) * (exact_grad[i] - dudx_fe[i]) * W;
      }
    }
  }
 
  template<unsigned DIM>
  void PRefineableQPoissonElement<DIM>::further_build()
  {
    if (this->tree_pt()->father_pt() != 0)
    {
      // Needed to set the source function pointer (if there is a father)
      RefineablePoissonEquations<DIM>::further_build();
    }
    // Now do the PRefineableQElement further_build()
    PRefineableQElement<DIM>::further_build();
  }
 
 
  //====================================================================
  // Force build of templates
  //====================================================================
  template class RefineableQPoissonElement<1, 2>;
  template class RefineableQPoissonElement<1, 3>;
  template class RefineableQPoissonElement<1, 4>;
 
  template class RefineableQPoissonElement<2, 2>;
  template class RefineableQPoissonElement<2, 3>;
  template class RefineableQPoissonElement<2, 4>;
 
  template class RefineableQPoissonElement<3, 2>;
  template class RefineableQPoissonElement<3, 3>;
  template class RefineableQPoissonElement<3, 4>;
 
  template class PRefineableQPoissonElement<1>;
  template class PRefineableQPoissonElement<2>;
  template class PRefineableQPoissonElement<3>;
 
} // namespace oomph