mesh_smoother_laplace.C

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// The libMesh Finite Element Library.
// Copyright (C) 2002-2014 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



// C++ includes
#include <algorithm> // for std::copy, std::sort


// Local includes
#include "libmesh/mesh_smoother_laplace.h"
#include "libmesh/mesh_tools.h"
#include "libmesh/elem.h"
#include "libmesh/unstructured_mesh.h"
#include "libmesh/parallel.h"
#include "libmesh/parallel_ghost_sync.h" // sync_dofobject_data_by_id()
#include "libmesh/parallel_algebra.h" // StandardType<Point>

namespace libMesh
{
// LaplaceMeshSmoother member functions
LaplaceMeshSmoother::LaplaceMeshSmoother(UnstructuredMesh& mesh)
  : MeshSmoother(mesh),
    _initialized(false)
{
}




void LaplaceMeshSmoother::smooth(unsigned int n_iterations)
{
  if (!_initialized)
    this->init();

  // Don't smooth the nodes on the boundary...
  // this would change the mesh geometry which
  // is probably not something we want!
  std::vector<bool> on_boundary;
  MeshTools::find_boundary_nodes(_mesh, on_boundary);

  // Ensure that the find_boundary_nodes() function returned a properly-sized vector
  if (on_boundary.size() != _mesh.n_nodes())
    libmesh_error_msg("MeshTools::find_boundary_nodes() returned incorrect length vector!");

  // We can only update the nodes after all new positions were
  // determined. We store the new positions here
  std::vector<Point> new_positions;

  for (unsigned int n=0; n<n_iterations; n++)
    {
      new_positions.resize(_mesh.n_nodes());

      {
        MeshBase::node_iterator       it     = _mesh.local_nodes_begin();
        const MeshBase::node_iterator it_end = _mesh.local_nodes_end();
        for (; it != it_end; ++it)
          {
            Node* node = *it;

            if (node == NULL)
              libmesh_error_msg("[" << _mesh.processor_id() << "]: Node iterator returned NULL pointer.");

            // leave the boundary intact
            // Only relocate the nodes which are vertices of an element
            // All other entries of _graph (the secondary nodes) are empty
            if (!on_boundary[node->id()] && (_graph[node->id()].size() > 0))
              {
                Point avg_position(0.,0.,0.);

                for (unsigned j=0; j<_graph[node->id()].size(); ++j)
                  {
                    // Will these nodal positions always be available
                    // or will they refer to remote nodes?  To be
                    // careful, we grab a pointer and test it against
                    // NULL.
                    Node* connected_node = _mesh.node_ptr(_graph[node->id()][j]);

                    if (connected_node == NULL)
                      libmesh_error_msg("Error! Libmesh returned NULL pointer for node " << _graph[connected_node->id()][j]);

                    avg_position.add( *connected_node );
                  } // end for(j)

                // Compute the average, store in the new_positions vector
                new_positions[node->id()] = avg_position / static_cast<Real>(_graph[node->id()].size());
              } // end if
          } // end for
      } // end scope


      // now update the node positions (local node positions only)
      {
        MeshBase::node_iterator it           = _mesh.local_nodes_begin();
        const MeshBase::node_iterator it_end = _mesh.local_nodes_end();
        for (; it != it_end; ++it)
          {
            Node* node = *it;

            if (!on_boundary[node->id()] && (_graph[node->id()].size() > 0))
              {
                // Should call Point::op=
                // libMesh::out << "Setting node id " << node->id() << " to position " << new_positions[node->id()];
                _mesh.node(node->id()) = new_positions[node->id()];
              }
          } // end for
      } // end scope

      // Now the nodes which are ghosts on this processor may have been moved on
      // the processors which own them.  So we need to synchronize with our neighbors
      // and get the most up-to-date positions for the ghosts.
      SyncNodalPositions sync_object(_mesh);
      Parallel::sync_dofobject_data_by_id
        (_mesh.comm(), _mesh.nodes_begin(), _mesh.nodes_end(), sync_object);

    } // end for n_iterations

  // finally adjust the second order nodes (those located between vertices)
  // these nodes will be located between their adjacent nodes
  // do this element-wise
  MeshBase::element_iterator       el  = _mesh.active_elements_begin();
  const MeshBase::element_iterator end = _mesh.active_elements_end();

  for (; el != end; ++el)
    {
      // Constant handle for the element
      const Elem* elem = *el;

      // get the second order nodes (son)
      // their element indices start at n_vertices and go to n_nodes
      const unsigned int son_begin = elem->n_vertices();
      const unsigned int son_end   = elem->n_nodes();

      // loop over all second order nodes (son)
      for (unsigned int son=son_begin; son<son_end; son++)
        {
          // Don't smooth second-order nodes which are on the boundary
          if (!on_boundary[elem->node(son)])
            {
              const unsigned int n_adjacent_vertices =
                elem->n_second_order_adjacent_vertices(son);

              // calculate the new position which is the average of the
              // position of the adjacent vertices
              Point avg_position(0,0,0);
              for (unsigned int v=0; v<n_adjacent_vertices; v++)
                avg_position +=
                  _mesh.point( elem->node( elem->second_order_adjacent_vertex(son,v) ) );

              _mesh.node(elem->node(son)) = avg_position / n_adjacent_vertices;
            }
        }
    }
}





void LaplaceMeshSmoother::init()
{
  switch (_mesh.mesh_dimension())
    {

      // TODO:[BSK] Fix this to work for refined meshes...  I think
      // the implementation was done quickly for Damien, who did not have
      // refined grids.  Fix it here and in the original Mesh member.

    case 2: // Stolen directly from build_L_graph in mesh_base.C
      {
        // Initialize space in the graph.  It is n_nodes long.  Each
        // node may be connected to an arbitrary number of other nodes
        // via edges.
        _graph.resize(_mesh.n_nodes());

        MeshBase::element_iterator       el  = _mesh.active_local_elements_begin();
        const MeshBase::element_iterator end = _mesh.active_local_elements_end();

        for (; el != end; ++el)
          {
            // Constant handle for the element
            const Elem* elem = *el;

            for (unsigned int s=0; s<elem->n_neighbors(); s++)
              {
                // Only operate on sides which are on the
                // boundary or for which the current element's
                // id is greater than its neighbor's.
                // Sides get only built once.
                if ((elem->neighbor(s) == NULL) ||
                    (elem->id() > elem->neighbor(s)->id()))
                  {
                    UniquePtr<Elem> side(elem->build_side(s));
                    _graph[side->node(0)].push_back(side->node(1));
                    _graph[side->node(1)].push_back(side->node(0));
                  }
              }
          }
        _initialized = true;
        break;
      } // case 2

    case 3: // Stolen blatantly from build_L_graph in mesh_base.C
      {
        // Initialize space in the graph.
        _graph.resize(_mesh.n_nodes());

        MeshBase::element_iterator       el  = _mesh.active_local_elements_begin();
        const MeshBase::element_iterator end = _mesh.active_local_elements_end();

        for (; el != end; ++el)
          {
            // Shortcut notation for simplicity
            const Elem* elem = *el;

            for (unsigned int f=0; f<elem->n_neighbors(); f++) // Loop over faces
              if ((elem->neighbor(f) == NULL) ||
                  (elem->id() > elem->neighbor(f)->id()))
                {
                  // We need a full (i.e. non-proxy) element for the face, since we will
                  // be looking at its sides as well!
                  UniquePtr<Elem> face = elem->build_side(f, /*proxy=*/false);

                  for (unsigned int s=0; s<face->n_neighbors(); s++) // Loop over face's edges
                    {
                      // Here we can use a proxy
                      UniquePtr<Elem> side = face->build_side(s);

                      // At this point, we just insert the node numbers
                      // again.  At the end we'll call sort and unique
                      // to make sure there are no duplicates
                      _graph[side->node(0)].push_back(side->node(1));
                      _graph[side->node(1)].push_back(side->node(0));
                    }
                }
          }

        _initialized = true;
        break;
      } // case 3

    default:
      libmesh_error_msg("At this time it is not possible to smooth a dimension " << _mesh.mesh_dimension() << "mesh.  Aborting...");
    }

  // Done building graph from local elements.  Let's now allgather the
  // graph so that it is available on all processors for the actual
  // smoothing operation?
  this->allgather_graph();

  // In 3D, it's possible for > 2 processor partitions to meet
  // at a single edge, while in 2D only 2 processor partitions
  // share an edge.  Therefore the allgather'd graph in 3D may
  // now have duplicate entries and we need to remove them so
  // they don't foul up the averaging algorithm employed by the
  // Laplace smoother.
  for (unsigned i=0; i<_graph.size(); ++i)
    {
      // The std::unique algorithm removes duplicate *consecutive* elements from a range,
      // so it only makes sense to call it on a sorted range...
      std::sort(_graph[i].begin(), _graph[i].end());
      _graph[i].erase(std::unique(_graph[i].begin(), _graph[i].end()), _graph[i].end());
    }

} // init()




void LaplaceMeshSmoother::print_graph(std::ostream& out_stream) const
{
  for (unsigned int i=0; i<_graph.size(); ++i)
    {
      out_stream << i << ": ";
      std::copy(_graph[i].begin(),
                _graph[i].end(),
                std::ostream_iterator<unsigned>(out_stream, " "));
      out_stream << std::endl;
    }
}



void LaplaceMeshSmoother::allgather_graph()
{
  // The graph data structure is not well-suited for parallel communication,
  // so copy the graph into a single vector defined by:
  // NA A_0 A_1 ... A_{NA} | NB B_0 B_1 ... B_{NB} | NC C_0 C_1 ... C_{NC}
  // where:
  // * NA is the number of graph connections for node A
  // * A_0, A_1, etc. are the IDs connected to node A
  std::vector<dof_id_type> flat_graph;

  // Reserve at least enough space for each node to have zero entries
  flat_graph.reserve(_graph.size());

  for (std::size_t i=0; i<_graph.size(); ++i)
    {
      // First push back the number of entries for this node
      flat_graph.push_back (cast_int<dof_id_type>(_graph[i].size()));

      // Then push back all the IDs
      for (std::size_t j=0; j<_graph[i].size(); ++j)
        flat_graph.push_back(_graph[i][j]);
    }

  // // A copy of the flat graph (for printing only, delete me later)
  // std::vector<unsigned> copy_of_flat_graph(flat_graph);

  // Use the allgather routine to combine all the flat graphs on all processors
  _mesh.comm().allgather(flat_graph);

  // Now reconstruct _graph from the allgathered flat_graph.

  // // (Delete me later, the copy is just for printing purposes.)
  // std::vector<std::vector<unsigned > > copy_of_graph(_graph);

  // Make sure the old graph is cleared out
  _graph.clear();
  _graph.resize(_mesh.n_nodes());

  // Our current position in the allgather'd flat_graph
  std::size_t cursor=0;

  // There are n_nodes * n_processors vectors to read in total
  for (processor_id_type p=0; p<_mesh.n_processors(); ++p)
    for (dof_id_type node_ctr=0; node_ctr<_mesh.n_nodes(); ++node_ctr)
      {
        // Read the number of entries for this node, move cursor
        std::size_t n_entries = flat_graph[cursor++];

        // Reserve space for that many more entries, then push back
        _graph[node_ctr].reserve(_graph[node_ctr].size() + n_entries);

        // Read all graph connections for this node, move the cursor each time
        // Note: there might be zero entries but that's fine
        for (std::size_t i=0; i<n_entries; ++i)
          _graph[node_ctr].push_back(flat_graph[cursor++]);
      }


  //    // Print local graph to uniquely named file (debugging)
  //    {
  //      // Generate unique filename for this processor
  //      std::ostringstream oss;
  //      oss << "graph_filename_" << _mesh.processor_id() << ".txt";
  //      std::ofstream graph_stream(oss.str().c_str());
  //
  //      // Print the local non-flat graph
  //      std::swap(_graph, copy_of_graph);
  //      print_graph(graph_stream);
  //
  //      // Print the (local) flat graph for verification
  //      for (std::size_t i=0; i<copy_of_flat_graph.size(); ++i)
  //graph_stream << copy_of_flat_graph[i] << " ";
  //      graph_stream << "\n";
  //
  //      // Print the allgather'd grap for verification
  //      for (std::size_t i=0; i<flat_graph.size(); ++i)
  //graph_stream << flat_graph[i] << " ";
  //      graph_stream << "\n";
  //
  //      // Print the global non-flat graph
  //      std::swap(_graph, copy_of_graph);
  //      print_graph(graph_stream);
  //    }
} // allgather_graph()

} // namespace libMesh