element_with_external_element.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) 2006-2024 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
// LIC// version 2.1 of the License, or (at your option) any later version.
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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 the class
// ElementWithExternalElement which stores pointers to external elements
 
// Include guards to prevent multiple inclusion of the header
#ifndef OOMPH_ELEMENT_WITH_EXTERNAL_ELEMENT_HEADER
#define OOMPH_ELEMENT_WITH_EXTERNAL_ELEMENT_HEADER
 
// Config header generated by autoconfig
#ifdef HAVE_CONFIG_H
#include <oomph-lib-config.h>
#endif
 
// Oomph-lib headers
#include "elements.h"
 
namespace oomph
{
  //========================================================================
  /// This is a base class for all elements that require external sources
  /// (e.g. FSI, multi-domain problems such as Helmholtz, multi-mesh
  ///  Boussinesq convection, etc.).  It provides storage for the source
  /// element and corresponding local coordinate at each integration point,
  /// and allows use of locate_zeta to obtain such source elements. In
  /// addition separate storage is allocated for all field data in the
  /// external elements and all geometric data that can affect the field
  /// data in the external elements. Generic finite difference routines
  /// are provided to calculate entries in the Jacobian from the data
  /// of the external elements.
  //========================================================================
  class ElementWithExternalElement : public virtual FiniteElement
  {
  public:
    /// Constructor. Initialise member data and pointers to data
    /// associated with the external elements to zero.
    ElementWithExternalElement()
      : FiniteElement(),
        Add_external_interaction_data(true),
        Add_external_geometric_data(true),
        External_interaction_field_data_pt(0),
        External_interaction_geometric_data_pt(0),
        Ninteraction(0),
        Nintpt(0),
        Nexternal_element_storage(0),
        Nexternal_interaction_field_data(0),
        Nexternal_interaction_geometric_data(0),
        External_element_pt(0),
        External_element_local_coord(0),
        External_interaction_field_data_index(0),
        External_interaction_field_data_local_eqn(0),
        External_interaction_geometric_data_index(0),
        External_interaction_geometric_data_local_eqn(0)
    {
    }
 
    /// The destructor, clean up any allocated memory
    virtual ~ElementWithExternalElement();
 
    /// Broken copy constructor
    ElementWithExternalElement(const ElementWithExternalElement&) = delete;
 
    /// Broken assignment operator
    void operator=(const ElementWithExternalElement&) = delete;
 
    /// Helper function to check if storage has actually been allocated
    bool storage_has_been_allocated() const
    {
      // If either of the storage arrays is zero, then storage has not
      // yet been allocated. Both arrays are allocated at once, so
      // if one is zero both will (should) be
      if ((External_element_pt == 0) || (External_element_local_coord == 0))
      {
        return false;
      }
      else
      {
        return true;
      }
    }
 
    /// Access function to source element for specified interaction
    /// index at specified integration point
    FiniteElement*& external_element_pt(const unsigned& interaction_index,
                                        const unsigned& ipt)
    {
#ifdef PARANOID
      check_storage_allocated();
#endif
#ifdef RANGE_CHECKING
      range_check(interaction_index, ipt);
#endif
      // Return the appropriate entry in the storage array
      return External_element_pt[Nintpt * interaction_index + ipt];
    }
 
    /// Access function to source element, const version
    FiniteElement* const& external_element_pt(const unsigned& interaction_index,
                                              const unsigned& ipt) const
    {
#ifdef PARANOID
      check_storage_allocated();
#endif
#ifdef RANGE_CHECKING
      range_check(interaction_index, ipt);
#endif
      // Return the appropriate entry in the storage array
      return External_element_pt[Nintpt * interaction_index + ipt];
    }
 
    /// Access function to get source element's local coords for
    /// specified interaction index at specified integration point
    Vector<double>& external_element_local_coord(
      const unsigned& interaction_index, const unsigned& ipt)
    {
#ifdef PARANOID
      check_storage_allocated();
#endif
#ifdef RANGE_CHECKING
      range_check(interaction_index, ipt);
#endif
      return External_element_local_coord[Nintpt * interaction_index + ipt];
    }
 
    /// Access function to get source element's coords, const version
    Vector<double> const& external_element_local_coord(
      const unsigned& interaction_index, const unsigned& ipt) const
    {
#ifdef PARANOID
      check_storage_allocated();
#endif
#ifdef RANGE_CHECKING
      range_check(interaction_index, ipt);
#endif
      return External_element_local_coord[Nintpt * interaction_index + ipt];
    }
 
 
    /// Output by plotting vector from integration point to
    /// corresponding point in external element for specified interaction
    /// index
    void output_external_elements(std::ostream& outfile,
                                  const unsigned& interaction_index);
 
    /// Initialise storage for pointers to external elements and their
    /// local coordinates. This must be called before any of
    /// the access functions are used.
    void initialise_external_element_storage();
 
    /// Flush the storage for external elements
    void flush_all_external_element_storage();
 
    /// Set the number of interactions in the element
    /// This function is usually called in the specific element's constructor
    inline void set_ninteraction(const unsigned& n_interaction)
    {
      Ninteraction = n_interaction;
    }
 
    /// Return the number of interactions in the element
    unsigned ninteraction() const
    {
      return Ninteraction;
    }
 
    /// Function that must return all the data involved
    /// in the desired interactions from the external element
    virtual void identify_all_field_data_for_external_interaction(
      Vector<std::set<FiniteElement*>> const& external_elements_pt,
      std::set<std::pair<Data*, unsigned>>& paired_interaction_data);
 
    /// Function that must return all geometric data involved
    /// in the desired interactions from the external element
    virtual void identify_all_geometric_data_for_external_interaction(
      Vector<std::set<FiniteElement*>> const& external_elements_pt,
      std::set<Data*>& external_geometric_data_pt);
 
    /// Return the number of Data items that affect the
    /// external interactions in this element.
    /// This includes e.g. fluid velocities
    /// and pressures in adjacent fluid elements in an FSI problem
    unsigned nexternal_interaction_field_data() const
    {
      return Nexternal_interaction_field_data;
    }
 
    /// Return vector of pointers to the field Data objects that
    /// affect the interactions on the element.
    Vector<Data*> external_interaction_field_data_pt() const
    {
      // Find out how many external field data there are
      const unsigned n_external_interaction_field_data =
        nexternal_interaction_field_data();
      // Create and populate  a temporary vector
      Vector<Data*> temp_data(n_external_interaction_field_data);
      for (unsigned i = 0; i < n_external_interaction_field_data; i++)
      {
        temp_data[i] = External_interaction_field_data_pt[i];
      }
      // Return the temporary data
      return temp_data;
    }
 
 
    /// Return the number of geometric Data items that affect the
    /// external interactions in this element: i.e. any geometric Data
    /// in the problem that affects the nodal positions in the
    /// external elements.
    unsigned nexternal_interaction_geometric_data() const
    {
      return Nexternal_interaction_geometric_data;
    }
 
    /// Are we including external geometric data in the element's Jacobian
    bool add_external_geometric_data()
    {
      return Add_external_geometric_data;
    }
 
    /// Are we including external data in the element's Jacobian
    bool add_external_interaction_data()
    {
      return Add_external_interaction_data;
    }
 
    /// Return vector of pointers to the geometric Data objects that
    /// affect the interactions on the element.
    Vector<Data*> external_interaction_geometric_data_pt() const
    {
      // Find out how many external field data there are
      const unsigned n_external_interaction_geometric_data =
        nexternal_interaction_geometric_data();
      // Create and populate  a temporary vector
      Vector<Data*> temp_data(n_external_interaction_geometric_data);
      for (unsigned i = 0; i < n_external_interaction_geometric_data; i++)
      {
        temp_data[i] = External_interaction_geometric_data_pt[i];
      }
      // Return the temporary data
      return temp_data;
    }
 
    /// Do not include any external geometric data when computing
    /// the element's Jacobian. This function should be
    /// called if the external element does not move and/or if
    /// the "source term" does not depend on spatial derivatives
    /// of the field computed by the other element.
    void ignore_external_geometric_data()
    {
      Add_external_geometric_data = false;
    }
 
    /// Do not include any external interaction data when computing
    /// the element's Jacobian
    void ignore_external_interaction_data()
    {
      Add_external_interaction_data = false;
    }
 
    /// Do include external geometric data when computing
    /// the element's Jacobian. This function should be called
    /// to re-enable inclusion of external geometric data.
    void include_external_geometric_data()
    {
      Add_external_geometric_data = true;
    }
 
    /// Do include external geometric data when computing the element's
    /// Jacobian This function should be called
    /// to re-enable inclusion of external interaction data
    void include_external_interaction_data()
    {
      Add_external_interaction_data = true;
    }
 
    /// Is the external geometric data taken into account when forming
    /// the Jacobian?
    bool external_geometric_data_is_included() const
    {
      return Add_external_geometric_data;
    }
 
    /// 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(...)
    void describe_local_dofs(std::ostream& out,
                             const std::string& curr_string) const;
 
  protected:
    /// Overload the assign internal and external local equation
    /// number scheme so that the interaction data is taken into account
    void assign_internal_and_external_local_eqn_numbers(
      const bool& store_local_dof_pt)
    {
      // Call the external stuff first so that it is near the front of the
      // list for fast searches when using indexing by global dof for
      // analytic calculation of interaction blocks.
      this->assign_external_interaction_data_local_eqn_numbers(
        store_local_dof_pt);
      // Now call the underlying equation numbering
      GeneralisedElement::assign_internal_and_external_local_eqn_numbers(
        store_local_dof_pt);
    }
 
    /// Assign the local equation numbers for those
    /// Data values involved in the external interactions that
    /// affect the residuals of the element
    void assign_external_interaction_data_local_eqn_numbers(
      const bool& store_local_dof_pt);
 
 
    /// Calculate the contributions to the jacobian from all external
    /// interaction degrees of freedom (geometric and field data) in
    /// the external element using finite differences.
    /// This version of the function assumes that the residuals vector has
    /// already been calculated.
    void fill_in_jacobian_from_external_interaction_by_fd(
      Vector<double>& residuals, DenseMatrix<double>& jacobian)
    {
      // Get the contribution from the external field data
      fill_in_jacobian_from_external_interaction_field_by_fd(residuals,
                                                             jacobian);
      // Get the contribution from the external geometric data
      fill_in_jacobian_from_external_interaction_geometric_by_fd(residuals,
                                                                 jacobian);
    }
 
    /// Calculate the contributions to the jacobian from all enternal
    /// interaction degrees of freedom (geometric and field data) in
    /// the external element using finite differences. This version computes
    /// the residuals vector before calculating the jacobian terms.
    void fill_in_jacobian_from_external_interaction_by_fd(
      DenseMatrix<double>& jacobian)
    {
      const unsigned n_dof = this->ndof();
      // Allocate storage for the residuals
      Vector<double> residuals(n_dof, 0.0);
      // Get the residuals for the entire element
      get_residuals(residuals);
      // Call the jacobian calculation
      fill_in_jacobian_from_external_interaction_by_fd(residuals, jacobian);
    }
 
 
    /// Calculate the contributions to the jacobian from the external
    /// interaction degrees of freedom associated with fields interpolated by
    /// the external element using finite differences.
    /// This version of the function assumes that the residuals vector has
    /// already been calculated.
    void fill_in_jacobian_from_external_interaction_field_by_fd(
      Vector<double>& residuals, DenseMatrix<double>& jacobian);
 
    /// Calculate the contributions to the jacobian from the enternal
    /// interaction degrees of freedom associated with fields interpolated by
    /// the external element using finite differences. This version computes
    /// the residuals vector before calculating the jacobian terms.
    void fill_in_jacobian_from_external_interaction_field_by_fd(
      DenseMatrix<double>& jacobian)
    {
      const unsigned n_dof = this->ndof();
      // Allocate storage for the residuals
      Vector<double> residuals(n_dof, 0.0);
      // Get the residuals for the entire element
      get_residuals(residuals);
      // Call the jacobian calculation
      fill_in_jacobian_from_external_interaction_field_by_fd(residuals,
                                                             jacobian);
    }
 
    /// Calculate the contributions to the jacobian from the external
    /// interaction degrees of freedom associated with the geometry of
    /// the external elements using finite differences.
    /// This version of the function assumes that the residuals vector has
    /// already been calculated.
    void fill_in_jacobian_from_external_interaction_geometric_by_fd(
      Vector<double>& residuals, DenseMatrix<double>& jacobian);
 
    /// Calculate the contributions to the jacobian from the
    /// external
    /// interaction degrees of freedom associated with the geometry of
    /// the external elements using finite differences. This version computes
    /// the residuals vector before calculating the jacobian terms.
    void fill_in_jacobian_from_external_interaction_geometric_by_fd(
      DenseMatrix<double>& jacobian)
    {
      const unsigned n_dof = this->ndof();
      // Allocate storage for the residuals
      Vector<double> residuals(n_dof, 0.0);
      // Get the residuals for the entire element
      get_residuals(residuals);
      // Call the jacobian calculation
      fill_in_jacobian_from_external_interaction_geometric_by_fd(residuals,
                                                                 jacobian);
    }
 
    /// Fill in the element's contribution to the Jacobian matrix
    /// and the residual vector: Done by finite differencing the
    /// residual vector w.r.t. all nodal, internal, external and load Data.
    void fill_in_contribution_to_jacobian(Vector<double>& residuals,
                                          DenseMatrix<double>& jacobian)
    {
      // Add the contribution to the residuals
      fill_in_contribution_to_residuals(residuals);
      // Allocate storage for the full residuals  (residuals of entire element)
      const unsigned n_dof = this->ndof();
      Vector<double> full_residuals(n_dof);
      // Get the residuals for the entire element
      get_residuals(full_residuals);
      // Add the internal and external by finite differences
      fill_in_jacobian_from_internal_by_fd(full_residuals, jacobian);
      fill_in_jacobian_from_external_by_fd(full_residuals, jacobian);
      fill_in_jacobian_from_nodal_by_fd(full_residuals, jacobian);
      fill_in_jacobian_from_external_interaction_by_fd(full_residuals,
                                                       jacobian);
    }
 
 
    /// Function that is called before the finite differencing of
    /// any external interaction data associated with external fields.
    /// This may be overloaded to update any dependent
    /// data before finite differencing takes place.
    virtual inline void update_before_external_interaction_field_fd() {}
 
    /// Function that is call after the finite differencing of
    /// the external interaction data associated with external fields
    /// This may be overloaded to reset any dependent
    /// variables that may have changed during the finite differencing.
    virtual inline void reset_after_external_interaction_field_fd() {}
 
    /// Function called within the finite difference loop for
    /// external interaction data after a change in any values in the i-th
    /// external interaction data object associated with external fields.
    virtual inline void update_in_external_interaction_field_fd(
      const unsigned& i)
    {
    }
 
    /// Function called within the finite difference loop for
    /// external interaction data after the values in the
    /// i-th external interaction data object associated with external fields
    /// are reset. The default behaviour is to call the update function.
    virtual inline void reset_in_external_interaction_field_fd(
      const unsigned& i)
    {
      update_in_external_interaction_field_fd(i);
    }
 
 
    /// Function that is called before the finite differencing of
    /// any external interaction data associated with external geometry.
    /// This may be overloaded to update any dependent
    /// data before finite differencing takes place.
    virtual inline void update_before_external_interaction_geometric_fd() {}
 
    /// Function that is call after the finite differencing of
    /// the external interaction data associated with external geometry.
    /// This may be overloaded to reset any dependent
    /// variables that may have changed during the finite differencing.
    virtual inline void reset_after_external_interaction_geometric_fd() {}
 
    /// Function called within the finite difference loop for
    /// external interaction data after a change in any values in the i-th
    /// external interaction data object associated with external geometry.
    virtual inline void update_in_external_interaction_geometric_fd(
      const unsigned& i)
    {
    }
 
    /// Function called within the finite difference loop for
    /// external interaction data after the values in the
    /// i-th external interaction data object associated with external geometry
    /// are reset. The default behaviour is to call the update function.
    virtual inline void reset_in_external_interaction_geometric_fd(
      const unsigned& i)
    {
      update_in_external_interaction_geometric_fd(i);
    }
 
    /// Boolean flag to indicate whether to include the external data
    bool Add_external_interaction_data;
 
    /// Boolean flag to indicate whether to include the external geometric data
    bool Add_external_geometric_data;
 
    /// / Storage for pointers to external field Data that affect the
    /// interactions in the elemenet
    Data** External_interaction_field_data_pt;
 
    /// / Storage for pointers to external geometric Data that affect the
    /// interactions in the elemenet
    Data** External_interaction_geometric_data_pt;
 
  private:
    /// Helper function to check that storage has actually been allocated
    void check_storage_allocated() const
    {
      // If either of the storage arrays is zero, then storage has not
      // yet been allocated. Both arrays are allocated at once, so
      // if one is zero both will (should) be
      if ((External_element_pt == 0) || (External_element_local_coord == 0))
      {
        std::ostringstream error_stream;
        error_stream
          << "Storage for the external elements has not been allocated.\n"
          << "initialise_external_element_storage() must be called.\n"
          << "This tends to be done automatically during the multi-domain\n"
          << "setup procedures -- you're most likely to get this error\n"
          << "because you have not specified the number of interactions\n"
          << "that your ElementWithExternalElement is involved in.\n"
          << "You ought to specify this with a call to\n\n"
          << "     ElementWithExternalElement::set_ninteraction(...)\n\n";
        throw OomphLibError(
          error_stream.str(), OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION);
      }
    }
 
    /// Helper function for range checking in the access functions
    void range_check(const unsigned& interaction_index,
                     const unsigned& ipt) const
    {
      // Boolean flag used to indicate range error
      bool range_error = false;
      // String for the error message
      std::ostringstream error_message;
      // If there is a range error in the interaction index
      if (interaction_index >= Ninteraction)
      {
        error_message << "Range Error: Interaction " << interaction_index
                      << " is not in the range (0," << Ninteraction - 1 << ")";
        // There has been a range error
        range_error = true;
      }
 
      // If there is a range error in the integration point
      if (ipt >= Nintpt)
      {
        error_message << "Range Error: Integration point " << ipt
                      << " is not in the range (0," << Nintpt - 1 << ")";
        range_error = true;
      }
 
 
      // If there has been a range error report it
      if (range_error)
      {
        throw OomphLibError(error_message.str(),
                            OOMPH_CURRENT_FUNCTION,
                            OOMPH_EXCEPTION_LOCATION);
      }
    }
 
    /// Number of interactions
    unsigned Ninteraction;
 
    /// Number of intergation point in the element
    unsigned Nintpt;
 
    /// Number of entries in the external element storage schemes
    /// (Nintergation_pt * Ninteraction)
    unsigned Nexternal_element_storage;
 
    /// Number of external interaction field data
    unsigned Nexternal_interaction_field_data;
 
    /// Number of external interaction geometric data
    unsigned Nexternal_interaction_geometric_data;
 
 
    /// Storage for pointers to elements that provide contributions
    /// to the residuals of the current element. Potentially a different
    /// element contributes to each integration point.
    FiniteElement** External_element_pt;
 
    ///  Storage for vectors of local coordinates in
    /// external elements that correspond to the appropriate integration
    /// / point.
    Vector<double>* External_element_local_coord;
 
    /// Storage for the index of the values in the external field data
    /// that affect the interactions in the element
    unsigned* External_interaction_field_data_index;
 
    /// Storage for the local equation number associated with the
    /// external field data the affect the interactions in the element
    int* External_interaction_field_data_local_eqn;
 
    /// Storage for the index of the values in the external
    /// geometric data
    /// that affect the interactions in the element
    unsigned* External_interaction_geometric_data_index;
 
    /// Storage for the local equation number associated with the
    /// external geometric data the affect the interactions in the element
    int* External_interaction_geometric_data_local_eqn;
  };
} // namespace oomph
 
#endif