legacy_xdr_io.C

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// The libMesh Finite Element Library.
// Copyright (C) 2002-2016 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 <iostream>
#include <iomanip>

#include <vector>
#include <string>

// Local includes
#include "libmesh/legacy_xdr_io.h"
#include "libmesh/mesh_base.h"
#include "libmesh/mesh_data.h"
#include "libmesh/mesh_tools.h" // MeshTools::n_levels(mesh)
#include "libmesh/parallel.h"   // - which makes write parallel-only
#include "libmesh/cell_hex27.h" // Needed for MGF-style Hex27 meshes
#include "libmesh/boundary_info.h"
#include "libmesh/libmesh_logging.h"
#include "libmesh/xdr_mgf.h"
#include "libmesh/xdr_mesh.h"
#include "libmesh/xdr_mhead.h"
#include "libmesh/xdr_soln.h"
#include "libmesh/xdr_shead.h"

#ifdef LIBMESH_USE_COMPLEX_NUMBERS
#include "libmesh/utility.h"
#endif


namespace libMesh
{






// ------------------------------------------------------------
// LegacyXdrIO members
LegacyXdrIO::LegacyXdrIO (MeshBase & mesh, const bool binary_in) :
  MeshInput<MeshBase> (mesh),
  MeshOutput<MeshBase>(mesh),
  _binary (binary_in)
{
}




LegacyXdrIO::LegacyXdrIO (const MeshBase & mesh, const bool binary_in) :
  MeshOutput<MeshBase>(mesh),
  _binary (binary_in)
{
}




LegacyXdrIO::~LegacyXdrIO ()
{
}




bool & LegacyXdrIO::binary ()
{
  return _binary;
}




bool LegacyXdrIO::binary () const
{
  return _binary;
}



void LegacyXdrIO::read (const std::string & name)
{
  // This is a serial-only process for now;
  // the Mesh should be read on processor 0 and
  // broadcast later
  if (MeshOutput<MeshBase>::mesh().processor_id() != 0)
    return;

  if (this->binary())
    this->read_binary (name);
  else
    this->read_ascii  (name);
}



void LegacyXdrIO::read_mgf (const std::string & name)
{
  if (this->binary())
    this->read_binary (name, LegacyXdrIO::MGF);
  else
    this->read_ascii  (name, LegacyXdrIO::MGF);
}



void LegacyXdrIO::write (const std::string & name)
{
  if (this->binary())
    this->write_binary (name);
  else
    this->write_ascii  (name);
}



void LegacyXdrIO::write_mgf (const std::string & name)
{
  if (this->binary())
    this->write_binary (name, LegacyXdrIO::MGF);
  else
    this->write_ascii  (name, LegacyXdrIO::MGF);
}



void LegacyXdrIO::read_mgf_soln (const std::string & name,
                                 std::vector<Number> & soln,
                                 std::vector<std::string> & var_names) const
{
  libmesh_deprecated();

#ifdef LIBMESH_USE_COMPLEX_NUMBERS

  // buffer for writing separately
  std::vector<Real> real_soln;
  std::vector<Real> imag_soln;

  Utility::prepare_complex_data (soln, real_soln, imag_soln);

  this->read_soln (Utility::complex_filename(name, 0),
                   real_soln,
                   var_names);

  this->read_soln (Utility::complex_filename(name, 1),
                   imag_soln,
                   var_names);

#else

  this->read_soln (name, soln, var_names);

#endif
}



void LegacyXdrIO::write_mgf_soln (const std::string & name,
                                  std::vector<Number> & soln,
                                  std::vector<std::string> & var_names) const
{
  libmesh_deprecated();

#ifdef LIBMESH_USE_COMPLEX_NUMBERS

  // buffer for writing separately
  std::vector<Real> real_soln;
  std::vector<Real> imag_soln;

  Utility::prepare_complex_data (soln, real_soln, imag_soln);

  this->write_soln (Utility::complex_filename(name, 0),
                    real_soln,
                    var_names);

  this->write_soln (Utility::complex_filename(name, 1),
                    imag_soln,
                    var_names);

#else

  this->write_soln (name, soln, var_names);

#endif
}



void LegacyXdrIO::read_ascii (const std::string & name,
                              const LegacyXdrIO::FileFormat originator)
{
  // get a writeable reference to the underlying mesh
  MeshBase & mesh = MeshInput<MeshBase>::mesh();

  // clear any existing mesh data
  mesh.clear();

  // read the mesh
  this->read_mesh (name, originator);
}



#ifndef LIBMESH_HAVE_XDR
void LegacyXdrIO::read_binary (const std::string & name,
                               const LegacyXdrIO::FileFormat)
{

  libMesh::err << "WARNING: Compiled without XDR binary support.\n"
               << "Will try ASCII instead" << std::endl << std::endl;

  this->read_ascii (name);
}
#else
void LegacyXdrIO::read_binary (const std::string & name,
                               const LegacyXdrIO::FileFormat originator)
{
  // get a writeable reference to the underlying mesh
  MeshBase & mesh = MeshInput<MeshBase>::mesh();

  // clear any existing mesh data
  mesh.clear();

  // read the mesh
  this->read_mesh (name, originator);
}
#endif



void LegacyXdrIO::write_ascii (const std::string & name, const LegacyXdrIO::FileFormat originator)
{
  this->write_mesh (name, originator);
}



#ifndef LIBMESH_HAVE_XDR
void LegacyXdrIO::write_binary (const std::string & name, const LegacyXdrIO::FileFormat)
{
  libMesh::err << "WARNING: Compiled without XDR binary support.\n"
               << "Will try ASCII instead" << std::endl << std::endl;

  this->write_ascii (name);
}
#else
void LegacyXdrIO::write_binary (const std::string & name, const LegacyXdrIO::FileFormat originator)
{
  this->write_mesh (name, originator);
}
#endif



void LegacyXdrIO::read_mesh (const std::string & name,
                             const LegacyXdrIO::FileFormat originator,
                             MeshData * mesh_data)
{
  // This is a serial-only process for now;
  // the Mesh should be read on processor 0 and
  // broadcast later
  libmesh_assert_equal_to (MeshOutput<MeshBase>::mesh().processor_id(), 0);

  // get a writeable reference to the mesh
  MeshBase & mesh = MeshInput<MeshBase>::mesh();

  // clear any data in the mesh
  mesh.clear();

  // Keep track of what kinds of elements this file contains
  elems_of_dimension.clear();
  elems_of_dimension.resize(4, false);

  // Create an XdrMESH object.
  XdrMESH m;

  // Create a pointer
  // to an XdrMESH file
  // header.
  XdrMHEAD mh;

  // Open the XDR file for reading.
  // Note 1: Provide an additional argument
  // to specify the dimension.
  //
  // Note 2: Has to do the right thing for
  // both binary and ASCII files.
  m.set_orig_flag(originator);
  m.init((this->binary() ? XdrMGF::DECODE : XdrMGF::R_ASCII), name.c_str(), 0); // mesh files are always number 0 ...

  // From here on, things depend
  // on whether we are reading or
  // writing!  First, we define
  // header variables that may
  // be read OR written.
  unsigned int              n_blocks = 0;
  unsigned int              n_levels = 0;

  if (m.get_orig_flag() == LegacyXdrIO::LIBM)
    n_levels = m.get_num_levels();


  std::vector<ElemType>     etypes;
  std::vector<unsigned int> neeb;

  // Get the information from
  // the header, and place it
  // in the header pointer.
  m.header(&mh);

  // Read information from the
  // file header.  This depends on
  // whether its a libMesh or MGF mesh.
  const int numElem     = mh.getNumEl();
  const int numNodes    = mh.getNumNodes();
  const int totalWeight = mh.getSumWghts();
  const int numBCs      = mh.getNumBCs();

  // If a libMesh-type mesh, read the augmented mesh information
  if ((m.get_orig_flag() == LegacyXdrIO::DEAL) || (m.get_orig_flag() == LegacyXdrIO::LIBM))
    {
      // Read augmented header
      n_blocks = mh.get_n_blocks();

      etypes.resize(n_blocks);
      mh.get_block_elt_types(etypes);

      mh.get_num_elem_each_block(neeb);
    }



  // Read the connectivity
  std::vector<int> conn;

  // Now that we know the
  // number of nodes and elements,
  // we can resize the
  // appropriate vectors if we are
  // reading information in.
  mesh.reserve_nodes (numNodes);
  mesh.reserve_elem  (numElem);

  // Each element stores two extra
  // locations: one which tells
  // what type of element it is,
  // and one which tells how many
  // nodes it has. Therefore,
  // the total number of nodes
  // (totalWeight) must be augmented
  // by 2 times the number of elements
  // in order to read in the entire
  // connectivity array.

  // Note: This section now depends on
  // whether we are reading an old-style libMesh,
  // MGF, or a new-style libMesh mesh.
  if (m.get_orig_flag() == LegacyXdrIO::DEAL)
    {
      conn.resize(totalWeight);
      m.Icon(&conn[0], 1, totalWeight);
    }

  else if (m.get_orig_flag() == LegacyXdrIO::MGF)
    {
      conn.resize(totalWeight+(2*numElem));
      m.Icon(&conn[0], 1, totalWeight+(2*numElem));
    }

  else if (m.get_orig_flag() == LegacyXdrIO::LIBM)
    {
      conn.resize(totalWeight);
      m.Icon(&conn[0], 1, totalWeight);
    }

  else
    {
      // I don't know what type of mesh it is.
      libmesh_error_msg("Unrecognized flag " << m.get_orig_flag());
    }

  // read in the nodal coordinates and form points.
  {
    std::vector<Real> coords(numNodes*3); // Always use three coords per node
    m.coord(&coords[0], 3, numNodes);



    // Form Nodes out of
    // the coordinates.  If the
    // MeshData object is active,
    // add the nodes and ids also
    // to its map.
    for (int innd=0; innd<numNodes; ++innd)
      {
        Node * node = mesh.add_point (Point(coords[0+innd*3],
                                            coords[1+innd*3],
                                            coords[2+innd*3]), innd);

        if (mesh_data != libmesh_nullptr)
          if (mesh_data->active())
            {
              // add the id to the MeshData, so that
              // it knows the foreign id, even when
              // the underlying mesh got re-numbered,
              // refined, elements/nodes added...
              mesh_data->add_foreign_node_id(node, innd);
            }
      }
  }



  // Build the elements.
  // Note: If the originator was MGF, we don't
  // have to do much checking ...
  // all the elements are Hex27.
  // If the originator was
  // this code, we have to loop over
  // et and neeb to read in all the
  // elements correctly.
  //
  // (This used to be before the coords block, but it
  // had to change now that elements store pointers to
  // nodes.  The nodes must exist before we assign them to
  // the elements. BSK, 1/13/2003)
  if ((m.get_orig_flag() == LegacyXdrIO::DEAL) || (m.get_orig_flag() == LegacyXdrIO::LIBM))
    {
      // This map keeps track of elements we've previously
      // constructed, to avoid O(n) lookup times for parent pointers
      // and to enable elements to be added in ascending ID order
      std::map<unsigned int, Elem *> parents;

      {
        unsigned int lastConnIndex = 0;
        unsigned int lastFaceIndex = 0;

        // Keep track of Element ids in MGF-style meshes;
        unsigned int next_elem_id = 0;

        for (unsigned int level=0; level<=n_levels; level++)
          {
            for (unsigned int idx=0; idx<n_blocks; idx++)
              {
                for (unsigned int e=lastFaceIndex; e<lastFaceIndex+neeb[level*n_blocks+idx]; e++)
                  {
                    // Build a temporary element of the right type, so we know how
                    // connectivity entries will be on the line for this element.
                    UniquePtr<Elem> temp_elem = Elem::build(etypes[idx]);

                    // A pointer to the element which will eventually be added to the mesh.
                    Elem * elem;

                    // New-style libMesh mesh
                    if (m.get_orig_flag() == LegacyXdrIO::LIBM)
                      {
                        unsigned int self_ID   = conn[lastConnIndex + temp_elem->n_nodes()];

#ifdef LIBMESH_ENABLE_AMR
                        unsigned int parent_ID = conn[lastConnIndex + temp_elem->n_nodes()+1];

                        if (level > 0)
                          {
                            // Do a linear search for the parent
                            Elem * my_parent;

                            // Search for parent in the parents map (log(n))
                            START_LOG("log(n) search for parent", "LegacyXdrIO::read_mesh");
                            std::map<unsigned int, Elem *>::iterator it = parents.find(parent_ID);
                            STOP_LOG("log(n) search for parent", "LegacyXdrIO::read_mesh");

                            // If the parent was not previously added, we cannot continue.
                            if (it == parents.end())
                              libmesh_error_msg("Parent element with ID " << parent_ID << " not found.");

                            // Set the my_parent pointer
                            my_parent = (*it).second;

                            // my_parent is now INACTIVE, since he has children
                            my_parent->set_refinement_flag(Elem::INACTIVE);

                            // Now that we know the parent, build the child
                            elem = Elem::build(etypes[idx],my_parent).release();

                            // The new child is marked as JUST_REFINED
                            elem->set_refinement_flag(Elem::JUST_REFINED);

                            // Tell the parent about his new child
                            my_parent->add_child(elem);

                            // sanity check
                            libmesh_assert_equal_to (my_parent->type(), elem->type());
                          }

                        // Add level-0 elements to the mesh
                        else
#endif // #ifdef LIBMESH_ENABLE_AMR
                          {
                            elem = Elem::build(etypes[idx]).release();
                          }

                        // Assign the newly-added element's ID so that future
                        // children which may be added can find it correctly.
                        elem->set_id() = self_ID;

                        // Add this element to the map, it may be a parent for a future element
                        START_LOG("insert elem into map", "LegacyXdrIO::read_mesh");
                        parents[self_ID] = elem;
                        STOP_LOG("insert elem into map", "LegacyXdrIO::read_mesh");
                      }

                    // MGF-style meshes
                    else
                      {
                        elem = Elem::build(etypes[idx]).release();
                        elem->set_id(next_elem_id++);

                        elems_of_dimension[elem->dim()] = true;

                        mesh.add_elem(elem);
                      }

                    // Add elements with the same id as in libMesh.
                    // Provided the data files that MeshData reads
                    // were only written with MeshData, then this
                    // should work properly.  This is an inline
                    // function, so that for disabled MeshData, this
                    // should not induce too much cost
                    if (mesh_data != libmesh_nullptr)
                      mesh_data->add_foreign_elem_id (elem, e);

                    // Set the node pointers of the newly-created element
                    for (unsigned int innd=0; innd < elem->n_nodes(); innd++)
                      {
                        elem->set_node(innd) = mesh.node_ptr(conn[innd+lastConnIndex]);
                      }

                    lastConnIndex += (m.get_orig_flag() == LegacyXdrIO::LIBM) ? (elem->n_nodes()+2) : elem->n_nodes();
                  }
                lastFaceIndex += neeb[idx];
              }
          }
      }

      if (m.get_orig_flag() == LegacyXdrIO::LIBM)
        {
          {
            // Iterate in ascending elem ID order
            unsigned int next_elem_id = 0;
            for (std::map<unsigned int, Elem *>::iterator i =
                   parents.begin();
                 i != parents.end(); ++i)
              {
                Elem * elem = i->second;
                if (elem)
                  {
                    elem->set_id(next_elem_id++);

                    elems_of_dimension[elem->dim()] = true;

                    mesh.add_elem(elem);
                  }
                else
                  // We can probably handle this, but we don't expect it
                  libmesh_error_msg("Unexpected NULL elem encountered while reading libmesh XDR file.");
              }
          }
        }
    }

  // MGF-style (1) Hex27 mesh
  else if (m.get_orig_flag() == LegacyXdrIO::MGF)
    {

#ifdef DEBUG
      if (mesh_data != libmesh_nullptr)
        if (mesh_data->active())
          libmesh_error_msg("ERROR: MeshData not implemented for MGF-style mesh.");
#endif

      for (int ielm=0; ielm < numElem; ++ielm)
        {
          Elem * elem = new Hex27;
          elem->set_id(ielm);

          elems_of_dimension[elem->dim()] = true;

          mesh.add_elem(elem);

          for (int innd=0; innd < 27; ++innd)
            elem->set_node(innd) = mesh.node_ptr(conn[innd+2+(27+2)*ielm]);
        }
    }

  // Set the mesh dimension to the largest encountered for an element
  for (unsigned char i=0; i!=4; ++i)
    if (elems_of_dimension[i])
      mesh.set_mesh_dimension(i);

#if LIBMESH_DIM < 3
  if (mesh.mesh_dimension() > LIBMESH_DIM)
    libmesh_error_msg("Cannot open dimension "              \
                      << mesh.mesh_dimension()                          \
                      << " mesh file when configured without "          \
                      << mesh.mesh_dimension()                          \
                      << "D support." );
#endif

  // tell the MeshData object that we are finished
  // reading data
  if (mesh_data != libmesh_nullptr)
    mesh_data->close_foreign_id_maps ();

  // Free memory used in
  // the connectivity
  // vector.
  conn.clear();


  // If we are reading,
  // read in the BCs
  // from the mesh file,
  // otherwise write the
  // boundary conditions
  // if the BoundaryInfo
  // object exists.
  if (numBCs > 0)
    {
      std::vector<int> bcs(numBCs*3);

      // Read the BCs from the XDR file
      m.BC(&bcs[0], numBCs);

      // Add to the boundary_info
      for (int ibc=0; ibc < numBCs; ibc++)
        mesh.get_boundary_info().add_side
          (cast_int<dof_id_type>(bcs[0+ibc*3]),
           cast_int<unsigned short>(bcs[1+ibc*3]),
           cast_int<boundary_id_type>(bcs[2+ibc*3]));
    }
}



void LegacyXdrIO::write_mesh (const std::string & name,
                              const LegacyXdrIO::FileFormat originator)
{
  // get a read-only reference to the mesh
  const MeshBase & mesh = MeshOutput<MeshBase>::mesh();

  // n_levels is a parallel-only method
  libmesh_parallel_only(mesh.comm());
  const unsigned int          n_levels = MeshTools::n_levels(mesh);

  // The Legacy Xdr IO code only works if we have a serialized mesh
  libmesh_assert (mesh.is_serial());

  // In which case only processor 0 needs to do any writing
  if (MeshOutput<MeshBase>::mesh().processor_id() != 0)
    return;

  // Create an XdrMESH object.
  XdrMESH m;

  // Create a pointer
  // to an XdrMESH file
  // header.
  XdrMHEAD mh;

  // Open the XDR file for writing.
  // Note 1: Provide an additional argument
  // to specify the dimension.
  //
  // Note 2: Has to do the right thing for
  // both binary and ASCII files.
  m.set_orig_flag(originator);

  // From here on, things depend
  // on whether we are reading or
  // writing!  First, we define
  // header variables that may
  // be read OR written.
  std::vector<unsigned int> neeb;
  std::vector<ElemType> etypes;


  int n_non_subactive = 0;
  int non_subactive_weight = 0;

  // This map will associate
  // the distance from the beginning of the set
  // to each node ID with the node ID itself.
  std::map<dof_id_type, dof_id_type> node_map;

  {
    // For each non-subactive element:
    // 1.) Increment the number of non subactive elements
    // 2.) Accumulate the total weight
    // 3.) Add the node ids to a set of non subactive node ids
    std::set<dof_id_type> not_subactive_node_ids;
    MeshBase::const_element_iterator el = mesh.elements_begin();
    const MeshBase::const_element_iterator end_el = mesh.elements_end();
    for( ; el != end_el; ++el)
      {
        const Elem * elem = (*el);
        if(!elem->subactive())
          {
            n_non_subactive++;
            non_subactive_weight += elem->n_nodes();

            for (unsigned int n=0; n<elem->n_nodes(); ++n)
              not_subactive_node_ids.insert(elem->node(n));
          }
      }

    // Now that the set is built, most of the hard work is done.  We build
    // the map next and let the set go out of scope.
    std::set<dof_id_type>::iterator it = not_subactive_node_ids.begin();
    const std::set<dof_id_type>::iterator end = not_subactive_node_ids.end();
    dof_id_type cnt=0;
    for (; it!=end; ++it)
      node_map[*it] = cnt++;
  }


  const int numElem = n_non_subactive;
  const int numBCs  =
    cast_int<int>(mesh.get_boundary_info().n_boundary_conds());

  // Fill the etypes vector with all of the element types found in the mesh
  MeshTools::elem_types(mesh, etypes);

  // store number of elements in each block at each refinement level
  neeb.resize((n_levels+1)*etypes.size());

  // Store a variable for the number of element types
  const unsigned int n_el_types =
    cast_int<unsigned int>(etypes.size());

  m.set_num_levels(n_levels);

  // The last argument is zero because mesh files are always number 0 ...
  m.init((this->binary() ? XdrMGF::ENCODE : XdrMGF::W_ASCII), name.c_str(), 0);

  // Loop over all levels and all element types to set the entries of neeb
  for(unsigned int level=0; level<=n_levels; level++)
    for (unsigned int el_type=0; el_type<n_el_types; el_type++)
      neeb[level*n_el_types + el_type] =
        MeshTools::n_non_subactive_elem_of_type_at_level(mesh, etypes[el_type], level);
  // gotta change this function name!!!


  // Now we check to see if we're doing
  // MGF-style headers or libMesh-style
  // "augmented" headers.  An
  // augmented header contains
  // information about mesh blocks,
  // allowing us to optimize storage
  // and minimize IO requirements
  // for these meshes.
  if ((m.get_orig_flag() == LegacyXdrIO::DEAL) || (m.get_orig_flag() == LegacyXdrIO::LIBM))
    {
      mh.set_n_blocks(cast_int<unsigned int>(etypes.size()));
      mh.set_block_elt_types(etypes);
      mh.set_num_elem_each_block(neeb);
    }
  else
    libmesh_assert_equal_to (etypes.size(), 1);

  mh.setNumEl(numElem);
  mh.setNumNodes(cast_int<int>(node_map.size()));
  mh.setStrSize(65536);

  // set a local variable for the total weight of the mesh
  int totalWeight =0;

  if (m.get_orig_flag() == LegacyXdrIO::DEAL)  // old-style LibMesh
    totalWeight=MeshTools::total_weight(mesh);

  else if (m.get_orig_flag() == LegacyXdrIO::MGF) // MGF-style
    totalWeight = MeshTools::total_weight(mesh)+2*numElem;

  else if (m.get_orig_flag() == LegacyXdrIO::LIBM) // new-style LibMesh
    totalWeight = non_subactive_weight+2*numElem;

  else
    libmesh_error_msg("Unrecognized flag " << m.get_orig_flag());

  // Set the total weight in the header
  mh.setSumWghts(totalWeight);

  mh.setNumBCs(numBCs);
  mh.setId("Id String");       // You can put whatever you want, it will be ignored
  mh.setTitle("Title String"); // You can put whatever you want, it will be ignored

  // Put the information
  // in the XDR file.
  m.header(&mh);


  // Write the connectivity
  {
    std::vector<int> conn;
    LegacyXdrIO::FileFormat orig_type = m.get_orig_flag();

    // Resize the connectivity vector to hold all the connectivity for the mesh
    conn.resize(totalWeight);

    unsigned int lastConnIndex = 0;
    unsigned int nn = 0;

    // Loop over levels and types again, write connectivity information to conn.
    for (unsigned int level=0; level<=n_levels; level++)
      for (unsigned int idx=0; idx<etypes.size(); idx++)
        {
          nn = lastConnIndex = 0;

          for (unsigned int e=0; e<mesh.n_elem(); e++)
            if ((mesh.elem(e)->type()  == etypes[idx]) &&
                (mesh.elem(e)->level() == level)       &&
                !mesh.elem(e)->subactive())
              {
                int nstart=0;

                if (orig_type == LegacyXdrIO::DEAL)
                  nn = mesh.elem(e)->n_nodes();

                else if (orig_type == LegacyXdrIO::MGF)
                  {
                    nstart=2; // ignore the 27 and 0 entries
                    nn = mesh.elem(e)->n_nodes()+2;
                    conn[lastConnIndex + 0] = 27;
                    conn[lastConnIndex + 1] = 0;
                  }

                else if (orig_type == LegacyXdrIO::LIBM) // LIBMESH format
                  nn = mesh.elem(e)->n_nodes() + 2;

                else
                  libmesh_error_msg("Unrecognized orig_type = " << orig_type);

                // Loop over the connectivity entries for this element and write to conn.
                START_LOG("set connectivity", "LegacyXdrIO::write_mesh");
                const unsigned int loopmax = (orig_type==LegacyXdrIO::LIBM) ? nn-2 : nn;
                for (unsigned int n=nstart; n<loopmax; n++)
                  {
                    unsigned int connectivity_value=0;

                    // old-style Libmesh and MGF meshes
                    if (orig_type != LegacyXdrIO::LIBM)
                      connectivity_value = mesh.elem(e)->node(n-nstart);

                    // new-style libMesh meshes: compress the connectivity entries to account for
                    // subactive nodes that will not be in the mesh we write out.
                    else
                      {
                        std::map<dof_id_type, dof_id_type>::iterator pos =
                          node_map.find(mesh.elem(e)->node(n-nstart));

                        libmesh_assert (pos != node_map.end());

                        connectivity_value = (*pos).second;
                      }
                    conn[lastConnIndex + n] = connectivity_value;
                  }
                STOP_LOG("set connectivity", "LegacyXdrIO::write_mesh");

                // In the case of an adaptive mesh, set last 2 entries to this ID and parent ID
                if (orig_type == LegacyXdrIO::LIBM)
                  {
                    int self_ID = mesh.elem(e)->id();
                    int parent_ID = -1;
                    if(level != 0)
                      parent_ID = mesh.elem(e)->parent()->id();

                    // Self ID is the second-to-last entry, Parent ID is the last
                    // entry on each connectivity line
                    conn[lastConnIndex+nn-2] = self_ID;
                    conn[lastConnIndex+nn-1] = parent_ID;
                  }

                lastConnIndex += nn;
              }

          // Send conn to the XDR file.  If there are no elements of this level and type,
          // then nn will be zero, and we there is no connectivity to write.
          if (nn != 0)
            m.Icon(&conn[0], nn, lastConnIndex/nn);
        }
  }

  // create the vector of coords and send
  // it to the XDR file.
  {
    std::vector<Real> coords;

    coords.resize(3*node_map.size());
    int lastIndex=0;

    std::map<dof_id_type,dof_id_type>::iterator it = node_map.begin();
    const std::map<dof_id_type,dof_id_type>::iterator end = node_map.end();
    for (; it != end; ++it)
      {
        const Point & p = mesh.node((*it).first);

        coords[lastIndex+0] = p(0);
        coords[lastIndex+1] = p(1);
        coords[lastIndex+2] = p(2);
        lastIndex += 3;
      }

    // Put the nodes in the XDR file
    m.coord(&coords[0], 3, cast_int<int>(node_map.size()));
  }


  // write the
  // boundary conditions
  // if the BoundaryInfo
  // object exists.
  if (numBCs > 0)
    {
      std::vector<int> bcs(numBCs*3);

      //libMesh::out << "numBCs=" << numBCs << std::endl;

      //libMesh::out << "Preparing to write boundary conditions." << std::endl;
      std::vector<dof_id_type> elem_list;
      std::vector<unsigned short int> side_list;
      std::vector<boundary_id_type> elem_id_list;

      mesh.get_boundary_info().build_side_list (elem_list, side_list, elem_id_list);

      for (int ibc=0;  ibc<numBCs; ibc++)
        {
          bcs[0+ibc*3] = elem_list[ibc];
          bcs[1+ibc*3] = side_list[ibc];
          bcs[2+ibc*3] = elem_id_list[ibc];
        }

      // Put the BCs in the XDR file
      m.BC(&bcs[0], numBCs);
    }
}



void LegacyXdrIO::read_soln (const std::string & name,
                             std::vector<Real> & soln,
                             std::vector<std::string> & var_names) const
{
  // Create an XdrSOLN object.
  XdrSOLN s;

  // Create an XdrSHEAD object.
  XdrSHEAD sh;

  // Open the XDR file for
  // reading or writing.
  // Note 1: Provide an additional argument
  // to specify the dimension.
  //
  // Note 2: Has to do the right thing for
  // both binary and ASCII files.
  s.init((this->binary() ? XdrMGF::DECODE : XdrMGF::R_ASCII), name.c_str(), 0); // mesh files are always number 0 ...

  // From here on, things depend
  // on whether we are reading or
  // writing!  First, we define
  // header variables that may
  // be read OR written.
  int         numVar      = 0;
  int         numNodes    = 0;
  const char * varNames;

  // Get the information from
  // the header, and place it
  // in the header pointer.
  s.header(&sh);

  // Read information from the
  // file header.  This depends on
  // whether its a libMesh or MGF mesh.
  numVar   = sh.getWrtVar();
  numNodes = sh.getNumNodes();
  varNames = sh.getVarTitle();

  // Get the variable names
  {
    var_names.resize(numVar);

    const char * p = varNames;

    for (int i=0; i<numVar; i++)
      {
        var_names[i] = p;
        p += std::strlen(p) + 1;
      }
  }

  // Read the soln vector
  soln.resize(numVar*numNodes);

  s.values(&soln[0], numNodes);
}



void LegacyXdrIO::write_soln (const std::string & name,
                              std::vector<Real> & soln,
                              std::vector<std::string> & var_names) const
{
  // get a read-only reference to the mesh
  const MeshBase & mesh = MeshOutput<MeshBase>::mesh();

  // Create an XdrSOLN object.
  XdrSOLN s;

  // Create an XdrSHEAD object.
  XdrSHEAD sh;

  // Open the XDR file for
  // reading or writing.
  // Note 1: Provide an additional argument
  // to specify the dimension.
  //
  // Note 2: Has to do the right thing for
  // both binary and ASCII files.
  s.init((this->binary() ? XdrMGF::ENCODE : XdrMGF::W_ASCII), name.c_str(), 0); // mesh files are always number 0 ...

  // Build the header
  sh.setWrtVar(cast_int<int>(var_names.size()));
  sh.setNumVar(cast_int<int>(var_names.size()));
  sh.setNumNodes(cast_int<int>(mesh.n_nodes()));
  sh.setNumBCs(cast_int<int>(mesh.get_boundary_info().n_boundary_conds()));
  sh.setMeshCnt(0);
  sh.setKstep(0);
  sh.setTime(0.);
  sh.setStrSize(65536);
  sh.setId("Id String");               // Ignored
  sh.setTitle("Title String");          // Ignored
  sh.setUserTitle("User Title String"); // Ignored

  // create the variable array
  {
    std::string var_title;

    for (unsigned int var=0; var<var_names.size(); var++)
      {
        for (unsigned int c=0; c<var_names[var].size(); c++)
          var_title += var_names[var][c];

        var_title += '\0';
      }

    sh.setVarTitle(var_title.c_str(), cast_int<int>(var_title.size()));
  }

  // Put the informationin the XDR file.
  s.header(&sh); // Needs to work for both types of file

  // Write the solution vector
  libmesh_assert_equal_to (soln.size(), var_names.size()*mesh.n_nodes());

  s.values(&soln[0], mesh.n_nodes());
}

} // namespace libMesh