refineable_advection_diffusion_reaction_elements.h

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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) 2006-2022 Matthias Heil and Andrew Hazel
// LIC//
// LIC// This library is free software; you can redistribute it and/or
// LIC// modify it under the terms of the GNU Lesser General Public
// LIC// License as published by the Free Software Foundation; either
// LIC// version 2.1 of the License, or (at your option) any later version.
// LIC//
// LIC// This library is distributed in the hope that it will be useful,
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// LIC// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
// LIC// Lesser General Public License for more details.
// LIC//
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// LIC//
// LIC// The authors may be contacted at oomph-lib@maths.man.ac.uk.
// LIC//
// 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
{
  //======================================================================
  //======================================================================
  template<unsigned NREAGENT, unsigned DIM>
  class RefineableAdvectionDiffusionReactionEquations
    : public virtual AdvectionDiffusionReactionEquations<NREAGENT, DIM>,
      public virtual RefineableElement,
      public virtual ElementWithZ2ErrorEstimator
  {
  public:
    RefineableAdvectionDiffusionReactionEquations()
      : AdvectionDiffusionReactionEquations<NREAGENT, DIM>(),
        RefineableElement(),
        ElementWithZ2ErrorEstimator()
    {
    }
 
 
    RefineableAdvectionDiffusionReactionEquations(
      const RefineableAdvectionDiffusionReactionEquations<NREAGENT, DIM>&
        dummy) = delete;
 
    void operator=(
      const RefineableAdvectionDiffusionReactionEquations<NREAGENT, DIM>&) =
      delete;
 
    unsigned num_Z2_flux_terms()
    {
      return NREAGENT * DIM;
    }
 
    void get_Z2_flux(const Vector<double>& s, Vector<double>& flux)
    {
      this->get_flux(s, flux);
    }
 
 
    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];
        }
      }
    }
 
    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];
        }
      }
    }
 
 
    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:
    void fill_in_generic_residual_contribution_adv_diff_react(
      Vector<double>& residuals,
      DenseMatrix<double>& jacobian,
      DenseMatrix<double>& mass_matrix,
      unsigned flag);
  };
 
 
  //======================================================================
  //======================================================================
  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:
    RefineableQAdvectionDiffusionReactionElement()
      : RefineableElement(),
        RefineableAdvectionDiffusionReactionEquations<NREAGENT, DIM>(),
        RefineableQElement<DIM>(),
        QAdvectionDiffusionReactionElement<NREAGENT, DIM, NNODE_1D>()
    {
    }
 
 
    RefineableQAdvectionDiffusionReactionElement(
      const RefineableQAdvectionDiffusionReactionElement<NREAGENT,
                                                         DIM,
                                                         NNODE_1D>& dummy) =
      delete;
 
    void operator=(
      const RefineableQAdvectionDiffusionReactionElement<NREAGENT,
                                                         DIM,
                                                         NNODE_1D>&) = delete;
 
    unsigned ncont_interpolated_values() const
    {
      return NREAGENT;
    }
 
    unsigned nvertex_node() const
    {
      return QAdvectionDiffusionReactionElement<NREAGENT, DIM, NNODE_1D>::
        nvertex_node();
    }
 
    Node* vertex_node_pt(const unsigned& j) const
    {
      return QAdvectionDiffusionReactionElement<NREAGENT, DIM, NNODE_1D>::
        vertex_node_pt(j);
    }
 
    void rebuild_from_sons(Mesh*& mesh_pt) {}
 
    unsigned nrecovery_order()
    {
      return (NNODE_1D - 1);
    }
 
    void further_setup_hanging_nodes() {}
  };
 
 
 
  //=======================================================================
  //=======================================================================
  template<unsigned NREAGENT, unsigned DIM, unsigned NNODE_1D>
  class FaceGeometry<
    RefineableQAdvectionDiffusionReactionElement<NREAGENT, DIM, NNODE_1D>>
    : public virtual QElement<DIM - 1, NNODE_1D>
  {
  public:
    FaceGeometry() : QElement<DIM - 1, NNODE_1D>() {}
  };
 
} // namespace oomph
 
#endif