refineable_advection_diffusion_reaction_elements.h

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// LIC// ====================================================================
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// LIC// multi-physics finite-element library, available
// LIC// at http://www.oomph-lib.org.
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// LIC// Copyright (C) 2006-2024 Matthias Heil and Andrew Hazel
// LIC//
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// LIC//====================================================================
// Header file for elements that solve the advection diffusion equation
// and that can be refined.
 
#ifndef OOMPH_REFINEABLE_ADVECTION_DIFFUSION_REACTION_ELEMENTS_HEADER
#define OOMPH_REFINEABLE_ADVECTION_DIFFUSION_REACTION_ELEMENTS_HEADER
 
// Config header generated by autoconfig
#ifdef HAVE_CONFIG_H
#include <oomph-lib-config.h>
#endif
 
// oomph-lib headers
#include "../generic/refineable_quad_element.h"
#include "../generic/refineable_brick_element.h"
#include "../generic/error_estimator.h"
#include "advection_diffusion_reaction_elements.h"
 
namespace oomph
{
  //======================================================================
  /// A version of the Advection Diffusion Reaction equations that can be
  /// used with non-uniform mesh refinement. In essence, the class overloads
  /// the fill_in_generic_residual_contribution_adv_diff_react()
  /// function so that contributions
  /// from hanging nodes (or alternatively in-compatible function values)
  /// are taken into account.
  //======================================================================
  template<unsigned NREAGENT, unsigned DIM>
  class RefineableAdvectionDiffusionReactionEquations
    : public virtual AdvectionDiffusionReactionEquations<NREAGENT, DIM>,
      public virtual RefineableElement,
      public virtual ElementWithZ2ErrorEstimator
  {
  public:
    /// Empty Constructor
    RefineableAdvectionDiffusionReactionEquations()
      : AdvectionDiffusionReactionEquations<NREAGENT, DIM>(),
        RefineableElement(),
        ElementWithZ2ErrorEstimator()
    {
    }
 
 
    /// Broken copy constructor
    RefineableAdvectionDiffusionReactionEquations(
      const RefineableAdvectionDiffusionReactionEquations<NREAGENT, DIM>&
        dummy) = delete;
 
    /// Broken assignment operator
    void operator=(
      const RefineableAdvectionDiffusionReactionEquations<NREAGENT, DIM>&) =
      delete;
 
    /// Number of 'flux' terms for Z2 error estimation
    unsigned num_Z2_flux_terms()
    {
      return NREAGENT * DIM;
    }
 
    /// Get 'flux' for Z2 error recovery:
    /// Standard flux.from AdvectionDiffusionReaction equations
    void get_Z2_flux(const Vector<double>& s, Vector<double>& flux)
    {
      this->get_flux(s, flux);
    }
 
 
    /// Get the function values c in Vector.
    /// Note: Given the generality of the interface (this function
    /// is usually called from black-box documentation or interpolation
    /// routines), the values Vector sets its own size in here.
    void get_interpolated_values(const Vector<double>& s,
                                 Vector<double>& values)
    {
      // Set size of Vector: c
      values.resize(NREAGENT);
 
      // Find number of nodes
      unsigned n_node = nnode();
 
      // Local shape function
      Shape psi(n_node);
 
      // Find values of shape function
      shape(s, psi);
 
      // Loop over the unknowns
      for (unsigned r = 0; r < NREAGENT; r++)
      {
        unsigned c_nodal_index = this->c_index_adv_diff_react(r);
 
        // Initialise value of c
        values[r] = 0.0;
 
        // Loop over the local nodes and sum
        for (unsigned l = 0; l < n_node; l++)
        {
          values[r] += this->nodal_value(l, c_nodal_index) * psi[l];
        }
      }
    }
 
    /// Get the function values c in Vector.
    /// Note: Given the generality of the interface (this function
    /// is usually called from black-box documentation or interpolation
    /// routines), the values Vector sets its own size in here.
    void get_interpolated_values(const unsigned& t,
                                 const Vector<double>& s,
                                 Vector<double>& values)
    {
      // Set size of Vector:
      values.resize(NREAGENT);
 
      // Find out how many nodes there are
      const unsigned n_node = nnode();
 
      // Shape functions
      Shape psi(n_node);
      shape(s, psi);
 
      // Loop over the reagents
      for (unsigned r = 0; r < NREAGENT; r++)
      {
        // Find the nodal index at which the unknown is stored
        unsigned c_nodal_index = this->c_index_adv_diff_react(r);
 
        // Initialise
        values[r] = 0.0;
 
        // Calculate value
        for (unsigned l = 0; l < n_node; l++)
        {
          values[r] += this->nodal_value(t, l, c_nodal_index) * psi[l];
        }
      }
    }
 
 
    ///  Further build: Copy all pointers from the father
    /// element
    void further_build()
    {
      RefineableAdvectionDiffusionReactionEquations<NREAGENT, DIM>*
        cast_father_element_pt = dynamic_cast<
          RefineableAdvectionDiffusionReactionEquations<NREAGENT, DIM>*>(
          this->father_element_pt());
 
      // Set the values of the pointers from the father
      this->Source_fct_pt = cast_father_element_pt->source_fct_pt();
      this->Wind_fct_pt = cast_father_element_pt->wind_fct_pt();
      this->Reaction_fct_pt = cast_father_element_pt->reaction_fct_pt();
      this->Reaction_deriv_fct_pt =
        cast_father_element_pt->reaction_deriv_fct_pt();
 
      this->Diff_pt = cast_father_element_pt->diff_pt();
      this->Tau_pt = cast_father_element_pt->tau_pt();
 
      // Set the value of the ALE flag
      this->ALE_is_disabled = cast_father_element_pt->ALE_is_disabled;
    }
 
  protected:
    /// Add the element's contribution to the elemental residual vector
    /// and/or Jacobian matrix
    /// flag=1: compute both
    /// flag=0: compute only residual vector
    void fill_in_generic_residual_contribution_adv_diff_react(
      Vector<double>& residuals,
      DenseMatrix<double>& jacobian,
      DenseMatrix<double>& mass_matrix,
      unsigned flag);
  };
 
 
  //======================================================================
  /// Refineable version of QAdvectionDiffusionReactionElement.
  /// Inherit from the standard QAdvectionDiffusionReactionElement and the
  /// appropriate refineable geometric element and the refineable equations.
  //======================================================================
  template<unsigned NREAGENT, unsigned DIM, unsigned NNODE_1D>
  class RefineableQAdvectionDiffusionReactionElement
    : public QAdvectionDiffusionReactionElement<NREAGENT, DIM, NNODE_1D>,
      public virtual RefineableAdvectionDiffusionReactionEquations<NREAGENT,
                                                                   DIM>,
      public virtual RefineableQElement<DIM>
  {
  public:
    /// Empty Constructor:
    RefineableQAdvectionDiffusionReactionElement()
      : RefineableElement(),
        RefineableAdvectionDiffusionReactionEquations<NREAGENT, DIM>(),
        RefineableQElement<DIM>(),
        QAdvectionDiffusionReactionElement<NREAGENT, DIM, NNODE_1D>()
    {
    }
 
 
    /// Broken copy constructor
    RefineableQAdvectionDiffusionReactionElement(
      const RefineableQAdvectionDiffusionReactionElement<NREAGENT,
                                                         DIM,
                                                         NNODE_1D>& dummy) =
      delete;
 
    /// Broken assignment operator
    void operator=(
      const RefineableQAdvectionDiffusionReactionElement<NREAGENT,
                                                         DIM,
                                                         NNODE_1D>&) = delete;
 
    /// Number of continuously interpolated values: NREAGENT
    unsigned ncont_interpolated_values() const
    {
      return NREAGENT;
    }
 
    /// Number of vertex nodes in the element
    unsigned nvertex_node() const
    {
      return QAdvectionDiffusionReactionElement<NREAGENT, DIM, NNODE_1D>::
        nvertex_node();
    }
 
    /// Pointer to the j-th vertex node in the element
    Node* vertex_node_pt(const unsigned& j) const
    {
      return QAdvectionDiffusionReactionElement<NREAGENT, DIM, NNODE_1D>::
        vertex_node_pt(j);
    }
 
    /// Rebuild from sons: empty
    void rebuild_from_sons(Mesh*& mesh_pt) {}
 
    /// Order of recovery shape functions for Z2 error estimation:
    /// Same order as shape functions.
    unsigned nrecovery_order()
    {
      return (NNODE_1D - 1);
    }
 
    ///  Perform additional hanging node procedures for variables
    /// that are not interpolated by all nodes. Empty.
    void further_setup_hanging_nodes() {}
  };
 
  /// /////////////////////////////////////////////////////////////////////
  /// /////////////////////////////////////////////////////////////////////
  /// /////////////////////////////////////////////////////////////////////
 
 
  //=======================================================================
  /// Face geometry for the RefineableQuadAdvectionDiffusionReactionElement
  /// elements: The spatial dimension of the face elements is one lower than
  /// that of the bulk element but they have the same number of points along
  /// their 1D edges.
  //=======================================================================
  template<unsigned NREAGENT, unsigned DIM, unsigned NNODE_1D>
  class FaceGeometry<
    RefineableQAdvectionDiffusionReactionElement<NREAGENT, DIM, NNODE_1D>>
    : public virtual QElement<DIM - 1, NNODE_1D>
  {
  public:
    /// Constructor: Call the constructor for the
    /// appropriate lower-dimensional QElement
    FaceGeometry() : QElement<DIM - 1, NNODE_1D>() {}
  };
 
} // namespace oomph
 
#endif