inf_elem_builder.C

Go to the documentation of this file.

// The libMesh Finite Element Library.
// Copyright (C) 2002-2019 Benjamin S. Kirk, John W. Peterson, Roy H. Stogner
 
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
 
// This library is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
// Lesser General Public License for more details.
 
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 
#include "libmesh/libmesh_config.h"
 
#ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
 
// C++ includes
 
// Local includes
#include "libmesh/inf_elem_builder.h"
#include "libmesh/libmesh_logging.h"
#include "libmesh/mesh_tools.h"
#include "libmesh/face_inf_quad4.h"
#include "libmesh/face_inf_quad6.h"
#include "libmesh/cell_inf_prism6.h"
#include "libmesh/cell_inf_prism12.h"
#include "libmesh/cell_inf_hex8.h"
#include "libmesh/cell_inf_hex16.h"
#include "libmesh/cell_inf_hex18.h"
#include "libmesh/mesh_base.h"
#include "libmesh/remote_elem.h"
 
namespace libMesh
{
 
const Point InfElemBuilder::build_inf_elem(bool be_verbose)
{
  // determine origin automatically,
  // works only if the mesh has no symmetry planes.
  const BoundingBox b_box = MeshTools::create_bounding_box(_mesh);
  Point origin = (b_box.first + b_box.second) / 2;
 
  if (be_verbose && _mesh.processor_id() == 0)
    {
#ifdef DEBUG
      libMesh::out << " Determined origin for Infinite Elements:"
                   << std::endl
                   << "  ";
      origin.write_unformatted(libMesh::out);
      libMesh::out << std::endl;
#endif
    }
 
  // Call the protected implementation function with the
  // automatically determined origin.
  this->build_inf_elem(origin, false, false, false, be_verbose);
 
  // when finished with building the Ifems,
  // it remains to prepare the mesh for use:
  // find neighbors (again), partition (if needed)...
  this->_mesh.prepare_for_use (/*skip_renumber =*/ false);
 
  return origin;
}
 
 
 
 
 
 
 
 
 
 
 
 
const Point InfElemBuilder::build_inf_elem (const InfElemOriginValue & origin_x,
                                            const InfElemOriginValue & origin_y,
                                            const InfElemOriginValue & origin_z,
                                            const bool x_sym,
                                            const bool y_sym,
                                            const bool z_sym,
                                            const bool be_verbose,
                                            std::vector<const Node *> * inner_boundary_nodes)
{
  START_LOG("build_inf_elem()", "InfElemBuilder");
 
  // first determine the origin of the
  // infinite elements.  For this, the
  // origin defaults to the given values,
  // and may be overridden when the user
  // provided values
  Point origin(origin_x.second, origin_y.second, origin_z.second);
 
  // when only _one_ of the origin coordinates is _not_
  // given, we have to determine it on our own
  if ( !origin_x.first || !origin_y.first || !origin_z.first)
    {
      // determine origin
      const BoundingBox b_box = MeshTools::create_bounding_box(_mesh);
      const Point auto_origin = (b_box.first+b_box.second)/2;
 
      // override default values, if necessary
      if (!origin_x.first)
        origin(0) = auto_origin(0);
#if LIBMESH_DIM > 1
      if (!origin_y.first)
        origin(1) = auto_origin(1);
#endif
#if LIBMESH_DIM > 2
      if (!origin_z.first)
        origin(2) = auto_origin(2);
#endif
 
      if (be_verbose)
        {
          libMesh::out << " Origin for Infinite Elements:" << std::endl;
 
          if (!origin_x.first)
            libMesh::out << "  determined x-coordinate" << std::endl;
          if (!origin_y.first)
            libMesh::out << "  determined y-coordinate" << std::endl;
          if (!origin_z.first)
            libMesh::out << "  determined z-coordinate" << std::endl;
 
          libMesh::out << "  coordinates: ";
          origin.write_unformatted(libMesh::out);
          libMesh::out << std::endl;
        }
    }
 
  else if (be_verbose)
 
    {
      libMesh::out << " Origin for Infinite Elements:" << std::endl;
      libMesh::out << "  coordinates: ";
      origin.write_unformatted(libMesh::out);
      libMesh::out << std::endl;
    }
 
 
 
  // Now that we have the origin, check if the user provided an \p
  // inner_boundary_nodes.  If so, we pass a std::set to the actual
  // implementation of the build_inf_elem(), so that we can convert
  // this to the Node * vector
  if (inner_boundary_nodes != nullptr)
    {
      // note that the std::set that we will get
      // from build_inf_elem() uses the index of
      // the element in this->_elements vector,
      // and the second entry is the side index
      // for this element.  Therefore, we do _not_
      // need to renumber nodes and elements
      // prior to building the infinite elements.
      //
      // However, note that this method here uses
      // node id's... Do we need to renumber?
 
 
      // Form the list of faces of elements which finally
      // will tell us which nodes should receive boundary
      // conditions (to form the std::vector<const Node *>)
      std::set<std::pair<dof_id_type,
                         unsigned int>> inner_faces;
 
 
      // build infinite elements
      this->build_inf_elem(origin,
                           x_sym, y_sym, z_sym,
                           be_verbose,
                           &inner_faces);
 
      if (be_verbose)
        {
          this->_mesh.print_info();
          libMesh::out << "Data pre-processing:" << std::endl
                       << " convert the <int,int> list to a Node * list..."
                       << std::endl;
        }
 
      // First use a std::vector<dof_id_type> that holds
      // the global node numbers.  Then sort this vector,
      // so that it can be made unique (no multiple occurrence
      // of a node), and then finally insert the Node * in
      // the vector inner_boundary_nodes.
      //
      // Reserve memory for the vector<> with
      // 4 times the size of the number of elements in the
      // std::set. This is a good bet for Quad4 face elements.
      // For higher-order elements, this probably _has_ to lead
      // to additional allocations...
      // Practice has to show how this affects performance.
      std::vector<dof_id_type> inner_boundary_node_numbers;
      inner_boundary_node_numbers.reserve(4*inner_faces.size());
 
      // Now transform the set of pairs to a list of (possibly
      // duplicate) global node numbers.
      for (const auto & p : inner_faces)
        {
          // build a full-ordered side element to get _all_ the base nodes
          std::unique_ptr<Elem> side(this->_mesh.elem_ref(p.first).build_side_ptr(p.second));
 
          // insert all the node numbers in inner_boundary_node_numbers
          for (const Node & node : side->node_ref_range())
            inner_boundary_node_numbers.push_back(node.id());
        }
 
 
      // inner_boundary_node_numbers now still holds multiple entries of
      // node numbers.  So first sort, then unique the vector.
      // Note that \p std::unique only puts the new ones in
      // front, while to leftovers are not deleted.  Instead,
      // it returns a pointer to the end of the unique range.
      //TODO:[BSK] int_ibn_size_before is not the same type as unique_size!
#ifndef NDEBUG
      const std::size_t ibn_size_before = inner_boundary_node_numbers.size();
#endif
      std::sort (inner_boundary_node_numbers.begin(), inner_boundary_node_numbers.end());
      auto unique_end =
        std::unique (inner_boundary_node_numbers.begin(), inner_boundary_node_numbers.end());
 
      std::size_t unique_size = std::distance(inner_boundary_node_numbers.begin(), unique_end);
      libmesh_assert_less_equal (unique_size, ibn_size_before);
 
      // Finally, create const Node * in the inner_boundary_nodes
      // vector.  Reserve, not resize (otherwise, the push_back
      // would append the interesting nodes, while nullptr-nodes
      // live in the resize'd area...
      inner_boundary_nodes->reserve (unique_size);
      inner_boundary_nodes->clear();
 
      for (const auto & dof : as_range(inner_boundary_node_numbers.begin(), unique_end))
        {
          const Node * node = this->_mesh.node_ptr(dof);
          inner_boundary_nodes->push_back(node);
        }
 
      if (be_verbose)
        libMesh::out << "  finished identifying " << unique_size
                     << " target nodes." << std::endl;
    }
 
  else
 
    {
      // There are no inner boundary nodes, so simply build the infinite elements
      this->build_inf_elem(origin, x_sym, y_sym, z_sym, be_verbose);
    }
 
 
  STOP_LOG("build_inf_elem()", "InfElemBuilder");
 
  // when finished with building the Ifems,
  // it remains to prepare the mesh for use:
  // find neighbors again, partition (if needed)...
  this->_mesh.prepare_for_use (/*skip_renumber =*/ false);
 
  return origin;
}
 
 
 
 
 
 
 
 
 
// The actual implementation of building elements.
void InfElemBuilder::build_inf_elem(const Point & origin,
                                    const bool x_sym,
                                    const bool y_sym,
                                    const bool z_sym,
                                    const bool be_verbose,
                                    std::set<std::pair<dof_id_type,
                                    unsigned int>> * inner_faces)
{
  if (be_verbose)
    {
#ifdef DEBUG
      libMesh::out << " Building Infinite Elements:" << std::endl;
      libMesh::out << "  updating element neighbor tables..." << std::endl;
#else
      libMesh::out << " Verbose mode disabled in non-debug mode." << std::endl;
#endif
    }
 
 
  // update element neighbors
  this->_mesh.find_neighbors();
 
  LOG_SCOPE("build_inf_elem()", "InfElemBuilder");
 
  // A set for storing element number, side number pairs.
  // pair.first == element number, pair.second == side number
  std::set<std::pair<dof_id_type,unsigned int>> faces;
  std::set<std::pair<dof_id_type,unsigned int>> ofaces;
 
  // A set for storing node numbers on the outer faces.
  std::set<dof_id_type> onodes;
 
  // The distance to the farthest point in the mesh from the origin
  Real max_r=0.;
 
  // The index of the farthest point in the mesh from the origin
  int max_r_node = -1;
 
#ifdef DEBUG
  if (be_verbose)
    {
      libMesh::out << "  collecting boundary sides";
      if (x_sym || y_sym || z_sym)
        libMesh::out << ", skipping sides in symmetry planes..." << std::endl;
      else
        libMesh::out << "..." << std::endl;
    }
#endif
 
  // Iterate through all elements and sides, collect indices of all active
  // boundary sides in the faces set. Skip sides which lie in symmetry planes.
  // Later, sides of the inner boundary will be sorted out.
  for (const auto & elem : _mesh.active_element_ptr_range())
    for (auto s : elem->side_index_range())
      if (elem->neighbor_ptr(s) == nullptr)
        {
          // note that it is safe to use the Elem::side() method,
          // which gives a non-full-ordered element
          std::unique_ptr<Elem> side(elem->build_side_ptr(s));
 
          // bool flags for symmetry detection
          bool sym_side=false;
          bool on_x_sym=true;
          bool on_y_sym=true;
          bool on_z_sym=true;
 
 
          // Loop over the nodes to check whether they are on the symmetry planes,
          // and therefore sufficient to use a non-full-ordered side element
          for (const Node & node : side->node_ref_range())
            {
              const dof_id_type node_id = node.id();
              const Point dist_from_origin =
                this->_mesh.point(node_id) - origin;
 
              if (x_sym)
                if (std::abs(dist_from_origin(0)) > 1.e-3)
                  on_x_sym=false;
 
              if (y_sym)
                if (std::abs(dist_from_origin(1)) > 1.e-3)
                  on_y_sym=false;
 
              if (z_sym)
                if (std::abs(dist_from_origin(2)) > 1.e-3)
                  on_z_sym=false;
 
              //       if (x_sym)
              // if (std::abs(dist_from_origin(0)) > 1.e-6)
              //   on_x_sym=false;
 
              //       if (y_sym)
              // if (std::abs(dist_from_origin(1)) > 1.e-6)
              //   on_y_sym=false;
 
              //       if (z_sym)
              // if (std::abs(dist_from_origin(2)) > 1.e-6)
              //   on_z_sym=false;
 
              //find the node most distant from origin
 
              Real r = dist_from_origin.norm();
              if (r > max_r)
                {
                  max_r = r;
                  max_r_node=node_id;
                }
 
            }
 
          sym_side = (x_sym && on_x_sym) || (y_sym && on_y_sym) || (z_sym && on_z_sym);
 
          if (!sym_side)
            faces.insert( std::make_pair(elem->id(), s) );
 
        } // neighbor(s) == nullptr
 
 
 
 
 
 
  //  If a boundary side has one node on the outer boundary,
  //  all points of this side are on the outer boundary.
  //  Start with the node most distant from origin, which has
  //  to be on the outer boundary, then recursively find all
  //  sides and nodes connected to it. Found sides are moved
  //  from faces to ofaces, nodes are collected in onodes.
  //  Here, the search is done iteratively, because, depending on
  //  the mesh, a very high level of recursion might be necessary.
  if (max_r_node >= 0)
    // include the possibility of the 1st element being most far away.
    // Only the case of no outer boundary is to be excluded.
    onodes.insert(max_r_node);
 
 
  {
    auto face_it = faces.begin();
    auto face_end = faces.end();
    unsigned int facesfound=0;
    while (face_it != face_end) {
      std::pair<dof_id_type, unsigned int> p = *face_it;
 
      // This has to be a full-ordered side element,
      // since we need the correct n_nodes,
      std::unique_ptr<Elem> side(this->_mesh.elem_ref(p.first).build_side_ptr(p.second));
 
      bool found=false;
      for (const Node & node : side->node_ref_range())
        if (onodes.count(node.id()))
          {
            found=true;
            break;
          }
 
      // If a new oface is found, include its nodes in onodes
      if (found)
        {
          for (const Node & node : side->node_ref_range())
            onodes.insert(node.id());
 
          ofaces.insert(p);
          face_it = faces.erase(face_it); // increment is done here
 
          facesfound++;
        }
 
      else
        ++face_it; // increment is done here
 
      // If at least one new oface was found in this cycle,
      // do another search cycle.
      if (facesfound>0 && face_it == faces.end())
        {
          facesfound = 0;
          face_it    = faces.begin();
        }
    }
  }
 
 
#ifdef DEBUG
  if (be_verbose)
    libMesh::out << "  found "
                 << faces.size()
                 << " inner and "
                 << ofaces.size()
                 << " outer boundary faces"
                 << std::endl;
#endif
 
  // When the user provided a non-null pointer to
  // inner_faces, that implies he wants to have
  // this std::set.  For now, simply copy the data.
  if (inner_faces != nullptr)
    *inner_faces = faces;
 
  // free memory, clear our local variable, no need
  // for it any more.
  faces.clear();
 
 
  // outer_nodes maps onodes to their duplicates
  std::map<dof_id_type, Node *> outer_nodes;
 
  // We may need to pick our own object ids in parallel
  dof_id_type old_max_node_id = _mesh.max_node_id();
  dof_id_type old_max_elem_id = _mesh.max_elem_id();
 
  // Likewise with our unique_ids
#ifdef LIBMESH_ENABLE_UNIQUE_ID
  unique_id_type old_max_unique_id = _mesh.parallel_max_unique_id();
#endif
 
  // for each boundary node, add an outer_node with
  // double distance from origin.
  for (const auto & dof : onodes)
    {
      Point p = (Point(this->_mesh.point(dof)) * 2) - origin;
      if (_mesh.is_serial())
        {
          // Add with a default id in serial
          outer_nodes[dof]=this->_mesh.add_point(p);
        }
      else
        {
          // Pick a unique id in parallel
          Node & bnode = _mesh.node_ref(dof);
          dof_id_type new_id = bnode.id() + old_max_node_id;
          Node * new_node =
            this->_mesh.add_point(p, new_id,
                                  bnode.processor_id());
#ifdef LIBMESH_ENABLE_UNIQUE_ID
          new_node->set_unique_id() = old_max_unique_id + bnode.id();
#endif
          outer_nodes[dof] = new_node;
        }
    }
 
 
#ifdef DEBUG
  // for verbose, remember n_elem
  dof_id_type n_conventional_elem = this->_mesh.n_elem();
#endif
 
 
  // build Elems based on boundary side type
  for (auto & p : ofaces)
    {
      Elem & belem = this->_mesh.elem_ref(p.first);
 
      // build a full-ordered side element to get the base nodes
      std::unique_ptr<Elem> side(belem.build_side_ptr(p.second));
 
      // create cell depending on side type, assign nodes,
      // use braces to force scope.
      bool is_higher_order_elem = false;
 
      Elem * el;
      switch(side->type())
        {
          // 3D infinite elements
          // TRIs
        case TRI3:
          el=new InfPrism6;
          break;
 
        case TRI6:
          el=new InfPrism12;
          is_higher_order_elem = true;
          break;
 
          // QUADs
        case QUAD4:
          el=new InfHex8;
          break;
 
        case QUAD8:
          el=new InfHex16;
          is_higher_order_elem = true;
          break;
 
        case QUAD9:
          el=new InfHex18;
 
          // the method of assigning nodes (which follows below)
          // omits in the case of QUAD9 the bubble node; therefore
          // we assign these first by hand here.
          el->set_node(16) = side->node_ptr(8);
          el->set_node(17) = outer_nodes[side->node_id(8)];
          is_higher_order_elem=true;
          break;
 
          // 2D infinite elements
        case EDGE2:
          el=new InfQuad4;
          break;
 
        case EDGE3:
          el=new InfQuad6;
          el->set_node(4) = side->node_ptr(2);
          break;
 
          // 1D infinite elements not supported
        default:
          libMesh::out << "InfElemBuilder::build_inf_elem(Point, bool, bool, bool, bool): "
                       << "invalid face element "
                       << std::endl;
          continue;
        }
 
      const unsigned int n_base_vertices = side->n_vertices();
 
      // On a distributed mesh, manually assign unique ids to the new
      // element, and make sure any RemoteElem neighbor links are set.
      if (!_mesh.is_serial())
        {
          el->processor_id() = belem.processor_id();
 
          // We'd better not have elements with more than 6 sides
          libmesh_assert_less_equal(el->n_sides(), 6);
          el->set_id (belem.id() * 6 + p.second + old_max_elem_id);
 
#ifdef LIBMESH_ENABLE_UNIQUE_ID
          el->set_unique_id() = old_max_unique_id + old_max_node_id + belem.id();
#endif
 
          // If we have a remote neighbor on a boundary element side
          if (belem.dim() > 1)
            for (auto s : belem.side_index_range())
              if (belem.neighbor_ptr(s) == remote_elem)
                {
                  // Find any corresponding infinite element side
                  std::unique_ptr<const Elem> remote_side(belem.build_side_ptr(s));
 
                  for (auto inf_s : el->side_index_range())
                    {
                      // The base side 0 shares all vertices but isn't
                      // remote
                      if (!inf_s)
                        continue;
 
                      // But another side, one which shares enough
                      // vertices to show it's the same side, is.
                      unsigned int n_shared_vertices = 0;
                      for (unsigned int i = 0; i != n_base_vertices; ++i)
                        for (auto & node : remote_side->node_ref_range())
                          if (side->node_ptr(i) == &node &&
                              el->is_node_on_side(i,inf_s))
                            ++n_shared_vertices;
 
                      if (n_shared_vertices + 1 >= belem.dim())
                        {
                          el->set_neighbor
                            (inf_s, const_cast<RemoteElem *>(remote_elem));
                          break;
                        }
                    }
                }
        }
 
      // assign vertices to the new infinite element
      for (unsigned int i=0; i<n_base_vertices; i++)
        {
          el->set_node(i                ) = side->node_ptr(i);
          el->set_node(i+n_base_vertices) = outer_nodes[side->node_id(i)];
        }
 
 
      // when this is a higher order element,
      // assign also the nodes in between
      if (is_higher_order_elem)
        {
          // n_safe_base_nodes is the number of nodes in \p side
          // that may be safely assigned using below for loop.
          // Actually, n_safe_base_nodes is _identical_ with el->n_vertices(),
          // since for QUAD9, the 9th node was already assigned above
          const unsigned int n_safe_base_nodes   = el->n_vertices();
 
          for (unsigned int i=n_base_vertices; i<n_safe_base_nodes; i++)
            {
              el->set_node(i+n_base_vertices)   = side->node_ptr(i);
              el->set_node(i+n_safe_base_nodes) =
                outer_nodes[side->node_id(i)];
            }
        }
 
 
      // add infinite element to mesh
      this->_mesh.add_elem(el);
    } // for
 
 
#ifdef DEBUG
  _mesh.libmesh_assert_valid_parallel_ids();
 
  if (be_verbose)
    libMesh::out << "  added "
                 << this->_mesh.n_elem() - n_conventional_elem
                 << " infinite elements and "
                 << onodes.size()
                 << " nodes to the mesh"
                 << std::endl
                 << std::endl;
#endif
}
 
} // namespace libMesh
 
 
 
 
 
#endif // LIBMESH_ENABLE_INFINITE_ELEMENTS