geom_obj_with_boundary.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) 2006-2023 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.
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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// The authors may be contacted at oomph-lib@maths.man.ac.uk.
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// LIC//====================================================================
#ifndef OOMPH_GEOM_OBJ_WITH_BOUNDARY_HEADER
#define OOMPH_GEOM_OBJ_WITH_BOUNDARY_HEADER
 
 
// Config header generated by autoconfig
#ifdef HAVE_CONFIG_H
#include <oomph-lib-config.h>
#endif
 
 
// oomph-lib headers
#include "geom_objects.h"
 
 
namespace oomph
{
  //===========================================================================
  /// Base class for upgraded disk-like GeomObject (i.e. 2D surface in 3D space)
  /// with specification of boundaries. The GeomObject's position(...)
  /// function computes the 3D (Eulerian) position vector r as a function of the
  /// 2D intrinsic (Lagrangian) coordinates, zeta, without reference to
  /// any boundaries. This class specifies the boundaries by specifying
  /// a mapping from a 1D intrinsic boundary coordinate, zeta_bound,
  /// to the 2D intrinsic (Lagrangian) coordinates, zeta.
  ///
  /// The class is made functional by provision (in the derived class!) of:
  /// - a pointer to a GeomObject<1,2> that parametrises the 2D intrinisic
  ///   coordinates zeta along boundary b in terms of the 1D boundary
  ///   coordinate, zeta_bound,
  /// - the initial value of the 1D boundary coordinate zeta_bound on boundary
  /// b,
  /// - the final value of the 1D boundary coordinate zeta_bound on boundary b
  /// .
  /// for each of these boundaries. All three containers for these
  /// must be resized (consistently) and populated in the derived class.
  /// Number of boundaries is inferred from their size.
  ///
  /// Class also provides broken virtual function to specify boundary triads,
  /// and various output functions.
  //===========================================================================
  class DiskLikeGeomObjectWithBoundaries : public virtual GeomObject
  {
  public:
    /// Constructor
    DiskLikeGeomObjectWithBoundaries() : GeomObject(2, 3) {}
 
    /// How many boundaries do we have?
    unsigned nboundary() const
    {
      return Boundary_parametrising_geom_object_pt.size();
    }
 
    /// Compute 3D vector of Eulerian coordinates at 1D boundary
    /// coordinate zeta_bound on boundary b:
    void position_on_boundary(const unsigned& b,
                              const double& zeta_bound,
                              Vector<double>& r) const
    {
      Vector<double> zeta(2);
      zeta_on_boundary(b, zeta_bound, zeta);
      position(zeta, r);
    }
 
    /// Compute 2D vector of intrinsic coordinates at 1D boundary
    /// coordinate zeta_bound on boundary b:
    void zeta_on_boundary(const unsigned& b,
                          const double& zeta_bound,
                          Vector<double>& zeta) const
    {
#ifdef PARANOID
      if (Boundary_parametrising_geom_object_pt[b] == 0)
      {
        std::ostringstream error_message;
        error_message << "You must create a <1,2> Geom Object that provides a\n"
                      << "mapping from the 1D boundary coordinate to the 2D\n"
                      << "intrinsic Lagrangian coordinate of disk-like object\n"
                      << std::endl;
        throw OomphLibError(error_message.str(),
                            OOMPH_CURRENT_FUNCTION,
                            OOMPH_EXCEPTION_LOCATION);
      }
      if (Boundary_parametrising_geom_object_pt[b]->nlagrangian() != 1)
      {
        std::ostringstream error_message;
        error_message << "Boundary_parametrising_geom_object_pt must point to\n"
                      << "GeomObject with one Lagrangian coordinate. Yours has "
                      << Boundary_parametrising_geom_object_pt[b]->nlagrangian()
                      << std::endl;
        throw OomphLibError(error_message.str(),
                            OOMPH_CURRENT_FUNCTION,
                            OOMPH_EXCEPTION_LOCATION);
      }
      if (Boundary_parametrising_geom_object_pt[b]->ndim() != 2)
      {
        std::ostringstream error_message;
        error_message << "Boundary_parametrising_geom_object_pt must point to\n"
                      << "GeomObject with two Eulerian coordinates. Yours has "
                      << Boundary_parametrising_geom_object_pt[b]->ndim()
                      << std::endl;
        throw OomphLibError(error_message.str(),
                            OOMPH_CURRENT_FUNCTION,
                            OOMPH_EXCEPTION_LOCATION);
      }
#endif
      Vector<double> zeta_bound_vector(1, zeta_bound);
      Boundary_parametrising_geom_object_pt[b]->position(zeta_bound_vector,
                                                         zeta);
    }
 
    /// Pointer to GeomObject<1,2> that parametrises intrinisc
    /// coordinates along boundary b
    GeomObject* boundary_parametrising_geom_object_pt(const unsigned& b) const
    {
      return Boundary_parametrising_geom_object_pt[b];
    }
 
    /// Initial value of 1D boundary coordinate
    /// zeta_bound on boundary b:
    double zeta_boundary_start(const unsigned& b) const
    {
      return Zeta_boundary_start[b];
    }
 
    /// Final value of 1D boundary coordinate
    /// zeta_bound on boundary b:
    double zeta_boundary_end(const unsigned& b) const
    {
      return Zeta_boundary_end[b];
    }
 
 
    /// Boundary triad on boundary b at boundary coordinate zeta_bound.
    /// Broken virtual.
    virtual void boundary_triad(const unsigned& b,
                                const double& zeta_bound,
                                Vector<double>& r,
                                Vector<double>& tangent,
                                Vector<double>& normal,
                                Vector<double>& binormal)
    {
      std::ostringstream error_message;
      error_message << "Broken virtual function; please implement for your\n"
                    << "derived version of this class!" << std::endl;
      throw OomphLibError(
        error_message.str(), OOMPH_CURRENT_FUNCTION, OOMPH_EXCEPTION_LOCATION);
    }
 
    /// Output boundaries at nplot plot points. Streams:
    /// - two_d_boundaries_file: zeta_0, zeta_1, zeta_bound
    /// - three_d_boundaries_file : x, y, z, zeta_0, zeta_1, zeta_bound
    void output_boundaries(const unsigned& nplot,
                           std::ofstream& two_d_boundaries_file,
                           std::ofstream& three_d_boundaries_file)
    {
      std::ofstream boundaries_tangent_file;
      std::ofstream boundaries_normal_file;
      std::ofstream boundaries_binormal_file;
      output_boundaries_and_triads(nplot,
                                   two_d_boundaries_file,
                                   three_d_boundaries_file,
                                   boundaries_tangent_file,
                                   boundaries_normal_file,
                                   boundaries_binormal_file);
    }
 
 
    /// Output boundaries and triad at nplot plot points. Streams:
    /// - two_d_boundaries_file: zeta_0, zeta_1, zeta_bound
    /// - three_d_boundaries_file : x, y, z, zeta_0, zeta_1, zeta_bound
    /// - boundaries_tangent_file : x, y, z, t_x, t_y, t_z
    /// - boundaries_normal_file  : x, y, z, n_x, n_y, n_z
    /// - boundaries_binormal_file: x, y, z, N_x, N_y, N_z
    void output_boundaries_and_triads(const unsigned& nplot,
                                      std::ofstream& two_d_boundaries_file,
                                      std::ofstream& three_d_boundaries_file,
                                      std::ofstream& boundaries_tangent_file,
                                      std::ofstream& boundaries_normal_file,
                                      std::ofstream& boundaries_binormal_file)
    {
      Vector<double> r(3);
      Vector<double> zeta(2);
      double zeta_bound = 0.0;
      Vector<double> tangent(3);
      Vector<double> normal(3);
      Vector<double> binormal(3);
      unsigned nb = nboundary();
      for (unsigned b = 0; b < nb; b++)
      {
        two_d_boundaries_file << "ZONE" << std::endl;
        three_d_boundaries_file << "ZONE" << std::endl;
        boundaries_tangent_file << "ZONE" << std::endl;
        boundaries_normal_file << "ZONE" << std::endl;
        boundaries_binormal_file << "ZONE" << std::endl;
 
        double zeta_min = zeta_boundary_start(b);
        double zeta_max = zeta_boundary_end(b);
        unsigned n = 100;
        for (unsigned i = 0; i < n; i++)
        {
          zeta_bound =
            zeta_min + (zeta_max - zeta_min) * double(i) / double(n - 1);
          position_on_boundary(b, zeta_bound, r);
          zeta_on_boundary(b, zeta_bound, zeta);
          boundary_triad(b, zeta_bound, r, tangent, normal, binormal);
 
          two_d_boundaries_file << zeta[0] << " " << zeta[1] << " "
                                << zeta_bound << " " << std::endl;
 
          three_d_boundaries_file << r[0] << " " << r[1] << " " << r[2] << " "
                                  << zeta[0] << " " << zeta[1] << " "
                                  << zeta_bound << " " << std::endl;
 
          boundaries_tangent_file << r[0] << " " << r[1] << " " << r[2] << " "
                                  << tangent[0] << " " << tangent[1] << " "
                                  << tangent[2] << " " << std::endl;
 
          boundaries_normal_file << r[0] << " " << r[1] << " " << r[2] << " "
                                 << normal[0] << " " << normal[1] << " "
                                 << normal[2] << " " << std::endl;
 
          boundaries_binormal_file << r[0] << " " << r[1] << " " << r[2] << " "
                                   << binormal[0] << " " << binormal[1] << " "
                                   << binormal[2] << " " << std::endl;
        }
      }
    }
 
 
    /// Specify intrinsic coordinates of a point within a specified
    /// region  -- region ID, r, should be positive.
    void add_region_coordinates(const unsigned& r,
                                Vector<double>& zeta_in_region)
    {
      // Verify if not using the default region number (zero)
      if (r == 0)
      {
        std::ostringstream error_message;
        error_message
          << "Please use another region id different from zero.\n"
          << "It is internally used as the default region number.\n";
        throw OomphLibError(error_message.str(),
                            OOMPH_CURRENT_FUNCTION,
                            OOMPH_EXCEPTION_LOCATION);
      }
      // Need two coordinates
      unsigned n = zeta_in_region.size();
      if (n != 2)
      {
        std::ostringstream error_message;
        error_message << "Vector specifying zeta coordinates of point in\n"
                      << "region has be length 2; yours has length " << n
                      << std::endl;
        throw OomphLibError(error_message.str(),
                            OOMPH_CURRENT_FUNCTION,
                            OOMPH_EXCEPTION_LOCATION);
      }
 
      // First check if the region with the specified id does not already exist
      std::map<unsigned, Vector<double>>::iterator it;
      it = Zeta_in_region.find(r);
 
      // If it is already a region defined with that id throw an error
      if (it != Zeta_in_region.end())
      {
        std::ostringstream error_message;
        error_message << "The region id (" << r << ") that you are using for"
                      << "defining\n"
                      << "your region is already in use. Use another\n"
                      << "region id and verify that you are not re-using\n"
                      << " previously defined regions ids.\n"
                      << std::endl;
        OomphLibWarning(error_message.str(),
                        OOMPH_CURRENT_FUNCTION,
                        OOMPH_EXCEPTION_LOCATION);
      }
 
      // If it does not exist then create the map
      Zeta_in_region[r] = zeta_in_region;
    }
 
    /// Return map that stores zeta coordinates of points that identify regions
    std::map<unsigned, Vector<double>> zeta_in_region() const
    {
      return Zeta_in_region;
    }
 
  protected:
    /// Storage for initial value of 1D boundary coordinate
    /// on boundary b:
    Vector<double> Zeta_boundary_start;
 
    /// Storage for final value of 1D boundary coordinate
    /// on boundary b:
    Vector<double> Zeta_boundary_end;
 
    /// Pointer to GeomObject<1,2> that parametrises intrinisc
    /// coordinates along boundary b; essentially provides a wrapper to
    /// zeta_on_boundary(...)
    Vector<GeomObject*> Boundary_parametrising_geom_object_pt;
 
    /// Map to store zeta coordinates of points that identify regions
    std::map<unsigned, Vector<double>> Zeta_in_region;
  };
 
 
  /// //////////////////////////////////////////////////////////////////
  /// //////////////////////////////////////////////////////////////////
  /// //////////////////////////////////////////////////////////////////
 
 
  //=========================================================================
  /// Warped disk in 3d: zeta[0]=x; zeta[1]=y (so it doesn't have
  /// coordinate singularities), with specification of two boundaries (b=0,1)
  /// that turn the whole thing into a circular disk.
  //=========================================================================
  class WarpedCircularDisk : public DiskLikeGeomObjectWithBoundaries
  {
  public:
    /// Constructor. Pass amplitude and azimuthal wavenumber of
    /// warping as arguments. Can specify vertical offset as final, optional
    /// argument.
    WarpedCircularDisk(const double& epsilon,
                       const unsigned& n,
                       const double& z_offset = 0.0)
      : Epsilon(epsilon), N(n), Z_offset(z_offset)
    {
      // How many boundaries do we have?
      unsigned nb = 2;
      Boundary_parametrising_geom_object_pt.resize(nb);
      Zeta_boundary_start.resize(nb, 0.0);
      Zeta_boundary_end.resize(nb, 0.0);
 
      // GeomObject<1,2> representing the first boundary
      Boundary_parametrising_geom_object_pt[0] = new Ellipse(1.0, 1.0);
      Zeta_boundary_start[0] = 0.0;
      Zeta_boundary_end[0] = MathematicalConstants::Pi;
 
      // GeomObject<1,2> representing the second boundary
      Boundary_parametrising_geom_object_pt[1] = new Ellipse(1.0, 1.0);
      Zeta_boundary_start[1] = MathematicalConstants::Pi;
      Zeta_boundary_end[1] = 2.0 * MathematicalConstants::Pi;
    }
 
    /// Empty default constructor.
    WarpedCircularDisk()
    {
      throw OomphLibError("Don't call default constructor!",
                          OOMPH_CURRENT_FUNCTION,
                          OOMPH_EXCEPTION_LOCATION);
    }
 
 
    /// Broken copy constructor
    WarpedCircularDisk(const WarpedCircularDisk& dummy) = delete;
 
    /// Broken assignment operator
    void operator=(const WarpedCircularDisk&) = delete;
 
    /// Destructor
    virtual ~WarpedCircularDisk()
    {
      unsigned n = nboundary();
      for (unsigned b = 0; b < n; b++)
      {
        delete Boundary_parametrising_geom_object_pt[b];
        Boundary_parametrising_geom_object_pt[b] = 0;
      }
    }
 
    /// Access fct to amplitude of disk warping
    double& epsilon()
    {
      return Epsilon;
    }
 
    /// Position Vector at Lagrangian coordinate zeta
    void position(const Vector<double>& zeta, Vector<double>& r) const
    {
      // Position Vector
      r[0] = zeta[0];
      r[1] = zeta[1];
      double radius = sqrt(r[0] * r[0] + r[1] * r[1]);
      double phi = atan2(r[1], r[0]);
      r[2] = Z_offset + w(radius, phi);
    }
 
 
    /// Parametrised position on object: r(zeta). Evaluated at
    /// previous timestep. t=0: current time; t>0: previous
    /// timestep. Object is steady so calls time-independent version
    void position(const unsigned& t,
                  const Vector<double>& zeta,
                  Vector<double>& r) const
    {
      position(zeta, r);
    }
 
 
    /// Boundary triad on boundary b at boundary coordinate zeta_bound
    void boundary_triad(const unsigned& b,
                        const double& zeta_bound,
                        Vector<double>& r,
                        Vector<double>& tangent,
                        Vector<double>& normal,
                        Vector<double>& binormal)
    {
      double phi = zeta_bound;
 
      // Position Vector
      r[0] = cos(phi);
      r[1] = sin(phi);
      r[2] = Z_offset + w(1.0, phi);
 
      Vector<double> dr_dr(3);
      dr_dr[0] = cos(phi);
      dr_dr[1] = sin(phi);
      dr_dr[2] = dwdr(1.0, phi);
      double inv_norm = 1.0 / sqrt(dr_dr[0] * dr_dr[0] + dr_dr[1] * dr_dr[1] +
                                   dr_dr[2] * dr_dr[2]);
 
      normal[0] = dr_dr[0] * inv_norm;
      normal[1] = dr_dr[1] * inv_norm;
      normal[2] = dr_dr[2] * inv_norm;
 
      Vector<double> dr_dphi(3);
      dr_dphi[0] = -sin(phi);
      dr_dphi[1] = cos(phi);
      dr_dphi[2] = dwdphi(1.0, phi);
 
      inv_norm = 1.0 / sqrt(dr_dphi[0] * dr_dphi[0] + dr_dphi[1] * dr_dphi[1] +
                            dr_dphi[2] * dr_dphi[2]);
 
      tangent[0] = dr_dphi[0] * inv_norm;
      tangent[1] = dr_dphi[1] * inv_norm;
      tangent[2] = dr_dphi[2] * inv_norm;
 
      binormal[0] = tangent[1] * normal[2] - tangent[2] * normal[1];
      binormal[1] = tangent[2] * normal[0] - tangent[0] * normal[2];
      binormal[2] = tangent[0] * normal[1] - tangent[1] * normal[0];
    }
 
  private:
    /// Vertical deflection
    double w(const double& r, const double& phi) const
    {
      return Epsilon * cos(double(N) * phi) * pow(r, 2);
    }
 
    /// Deriv of vertical deflection w.r.t. radius
    double dwdr(const double& r, const double& phi) const
    {
      return Epsilon * cos(double(N) * phi) * 2.0 * r;
    }
 
    /// Deriv of vertical deflection w.r.t. angle
    double dwdphi(const double& r, const double& phi) const
    {
      return -Epsilon * double(N) * sin(double(N) * phi) * pow(r, 2);
    }
 
    /// Amplitude of non-axisymmetric deformation
    double Epsilon;
 
    /// Wavenumber of non-axisymmetric deformation
    unsigned N;
 
    /// Vertical offset
    double Z_offset;
  };
 
  /// //////////////////////////////////////////////////////////////////
  /// //////////////////////////////////////////////////////////////////
  /// //////////////////////////////////////////////////////////////////
 
 
  //=========================================================================
  /// Warped disk in 3d: zeta[0]=x; zeta[1]=y (so it doesn't have
  /// coordinate singularities), with specification of two boundaries (b=0,1)
  /// that turn the whole thing into a circular disk. In addition
  /// has two internal boundaries (b=2,3), a distance h_annulus from
  /// the outer edge. Annual (outer) region is region 1.
  //=========================================================================
  class WarpedCircularDiskWithAnnularInternalBoundary
    : public virtual WarpedCircularDisk
  {
  public:
    /// Constructor. Pass amplitude and azimuthal wavenumber of
    /// warping as arguments. Can specify vertical offset as final, optional
    /// argument.
    WarpedCircularDiskWithAnnularInternalBoundary(const double& h_annulus,
                                                  const double& epsilon,
                                                  const unsigned& n,
                                                  const double& z_offset = 0.0)
      : WarpedCircularDisk(epsilon, n, z_offset), H_annulus(h_annulus)
    {
      // We have two more boundaries!
      Boundary_parametrising_geom_object_pt.resize(4);
      Zeta_boundary_start.resize(4);
      Zeta_boundary_end.resize(4);
 
      // Radius of the internal annular boundary
      double r_annulus = 1.0 - h_annulus;
 
      // GeomObject<1,2> representing the third boundary
      Boundary_parametrising_geom_object_pt[2] =
        new Ellipse(r_annulus, r_annulus);
      Zeta_boundary_start[2] = 0.0;
      Zeta_boundary_end[2] = MathematicalConstants::Pi;
 
      // GeomObject<1,2> representing the fourth boundary
      Boundary_parametrising_geom_object_pt[3] =
        new Ellipse(r_annulus, r_annulus);
      Zeta_boundary_start[3] = MathematicalConstants::Pi;
      Zeta_boundary_end[3] = 2.0 * MathematicalConstants::Pi;
 
      // Region 1 is the annular region; identify it by a point in
      // this region.
      unsigned r = 1;
      Vector<double> zeta_in_region(2);
      zeta_in_region[0] = 0.0;
      zeta_in_region[0] = 1.0 - 0.5 * h_annulus;
      add_region_coordinates(r, zeta_in_region);
    }
 
    /// Broken copy constructor
    WarpedCircularDiskWithAnnularInternalBoundary(
      const WarpedCircularDiskWithAnnularInternalBoundary& dummy) = delete;
 
    /// Broken assignment operator
    void operator=(const WarpedCircularDiskWithAnnularInternalBoundary&) =
      delete;
 
    /// Destructor (empty; cleanup happens in base class)
    virtual ~WarpedCircularDiskWithAnnularInternalBoundary() {}
 
 
    /// Thickness of annular region (distance of internal boundary
    /// from outer edge of unit circle)
    double h_annulus() const
    {
      return H_annulus;
    }
 
  protected:
    /// Thickness of annular region (distance of internal boundary
    /// from outer edge of unit circle)
    double H_annulus;
  };
 
 
} // namespace oomph
 
#endif