mesh_smoother_laplace.C

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// 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
 
 
 
// 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>
#include "libmesh/int_range.h"
 
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!
  auto on_boundary = MeshTools::find_boundary_nodes(_mesh);
 
  // Also: don't smooth block bondary nodes
  auto on_block_boundary = MeshTools::find_block_boundary_nodes(_mesh);
 
  // Merge them
  on_boundary.insert(on_block_boundary.begin(), on_block_boundary.end());
 
  // 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.max_node_id());
 
      for (auto & node : _mesh.local_node_ptr_range())
        {
          if (node == nullptr)
            libmesh_error_msg("[" << _mesh.processor_id() << "]: Node iterator returned nullptr.");
 
          // 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.count(node->id()) && (_graph[node->id()].size() > 0))
            {
              Point avg_position(0.,0.,0.);
 
              for (const auto & connected_id : _graph[node->id()])
                {
                  // Will these nodal positions always be available
                  // or will they refer to remote nodes?  This will
                  // fail an assertion in the latter case, which
                  // shouldn't occur if DistributedMesh is working
                  // correctly.
                  const Point & connected_node = _mesh.point(connected_id);
 
                  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
 
 
      // now update the node positions (local node positions only)
      for (auto & node : _mesh.local_node_ptr_range())
        if (!on_boundary.count(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_ref(node->id()) = new_positions[node->id()];
          }
 
      // 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
  for (auto & elem : _mesh.active_element_ptr_range())
    {
      // 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.count(elem->node_id(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_id( elem->second_order_adjacent_vertex(son,v) ) );
 
              _mesh.node_ref(elem->node_id(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 indexed by node id.
        // Each node may be connected to an arbitrary number of other
        // nodes via edges.
        _graph.resize(_mesh.max_node_id());
 
        for (auto & elem : _mesh.active_local_element_ptr_range())
          for (auto s : elem->side_index_range())
            {
              // 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_ptr(s) == nullptr) ||
                  (elem->id() > elem->neighbor_ptr(s)->id()))
                {
                  std::unique_ptr<const Elem> side(elem->build_side_ptr(s));
                  _graph[side->node_id(0)].push_back(side->node_id(1));
                  _graph[side->node_id(1)].push_back(side->node_id(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.max_node_id());
 
        for (auto & elem : _mesh.active_local_element_ptr_range())
          for (auto f : elem->side_index_range()) // Loop over faces
            if ((elem->neighbor_ptr(f) == nullptr) ||
                (elem->id() > elem->neighbor_ptr(f)->id()))
              {
                // We need a full (i.e. non-proxy) element for the face, since we will
                // be looking at its sides as well!
                std::unique_ptr<const Elem> face = elem->build_side_ptr(f, /*proxy=*/false);
 
                for (auto s : face->side_index_range()) // Loop over face's edges
                  {
                    // Here we can use a proxy
                    std::unique_ptr<const Elem> side = face->build_side_ptr(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_id(0)].push_back(side->node_id(1));
                    _graph[side->node_id(1)].push_back(side->node_id(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 (auto & id_vec : _graph)
    {
      // 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(id_vec.begin(), id_vec.end());
      id_vec.erase(std::unique(id_vec.begin(), id_vec.end()), id_vec.end());
    }
 
} // init()
 
 
 
 
void LaplaceMeshSmoother::print_graph(std::ostream & out_stream) const
{
  for (auto i : index_range(_graph))
    {
      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 (const auto & id_vec : _graph)
    {
      // First push back the number of entries for this node
      flat_graph.push_back (cast_int<dof_id_type>(id_vec.size()));
 
      // Then push back all the IDs
      for (const auto & dof : id_vec)
        flat_graph.push_back(dof);
    }
 
  // // 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.max_node_id());
 
  // Our current position in the allgather'd flat_graph
  std::size_t cursor=0;
 
  // There are max_node_id * n_processors entries 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.max_node_id(); ++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 (const auto & dof : copy_of_flat_graph)
  //     graph_stream << dof << " ";
  //   graph_stream << "\n";
  //
  //   // Print the allgather'd grap for verification
  //   for (const auto & dof : flat_graph)
  //     graph_stream << dof << " ";
  //   graph_stream << "\n";
  //
  //   // Print the global non-flat graph
  //   std::swap(_graph, copy_of_graph);
  //   print_graph(graph_stream);
  // }
} // allgather_graph()
 
} // namespace libMesh