gmsh_io.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 <fstream>
#include <set>
#include <cstring> // std::memcpy
#include <numeric>
#include <unordered_map>
#include <cstddef>
 
// Local includes
#include "libmesh/libmesh_config.h"
#include "libmesh/libmesh_logging.h"
#include "libmesh/boundary_info.h"
#include "libmesh/elem.h"
#include "libmesh/gmsh_io.h"
#include "libmesh/mesh_base.h"
#include "libmesh/int_range.h"
#include "libmesh/utility.h" // map_find
 
namespace libMesh
{
 
// Initialize the static data member
GmshIO::ElementMaps GmshIO::_element_maps = GmshIO::build_element_maps();
 
 
 
// Definition of the static function which constructs the ElementMaps object.
GmshIO::ElementMaps GmshIO::build_element_maps()
{
  // Object to be filled up
  ElementMaps em;
 
  // POINT (import only)
  em.in.insert(std::make_pair(15, ElementDefinition(NODEELEM, 15, 0, 1)));
 
  // Add elements with trivial node mappings
  em.add_def(ElementDefinition(EDGE2, 1, 1, 2));
  em.add_def(ElementDefinition(EDGE3, 8, 1, 3));
  em.add_def(ElementDefinition(TRI3, 2, 2, 3));
  em.add_def(ElementDefinition(TRI6, 9, 2, 6));
  em.add_def(ElementDefinition(QUAD4, 3, 2, 4));
  em.add_def(ElementDefinition(QUAD8, 16, 2, 8));
  em.add_def(ElementDefinition(QUAD9, 10, 2, 9));
  em.add_def(ElementDefinition(HEX8, 5, 3, 8));
  em.add_def(ElementDefinition(TET4, 4, 3, 4));
  em.add_def(ElementDefinition(PRISM6, 6, 3, 6));
  em.add_def(ElementDefinition(PYRAMID5, 7, 3, 5));
 
  // Add elements with non-trivial node mappings
 
  // HEX20
  {
    ElementDefinition eledef(HEX20, 17, 3, 20);
    const unsigned int nodes[] = {0,1,2,3,4,5,6,7,8,11,12,9,13,10,14,15,16,19,17,18};
    std::vector<unsigned int>(nodes, nodes+eledef.nnodes).swap(eledef.nodes); // swap trick
    em.add_def(eledef);
  }
 
  // HEX27
  {
    ElementDefinition eledef(HEX27, 12, 3, 27);
    const unsigned int nodes[] = {0,1,2,3,4,5,6,7,8,11,12,9,13,10,14,
                                  15,16,19,17,18,20,21,24,22,23,25,26};
    std::vector<unsigned int>(nodes, nodes+eledef.nnodes).swap(eledef.nodes); // swap trick
    em.add_def(eledef);
  }
 
  // TET10
  {
    ElementDefinition eledef(TET10, 11, 3, 10);
    const unsigned int nodes[] = {0,1,2,3,4,5,6,7,9,8};
    std::vector<unsigned int>(nodes, nodes+eledef.nnodes).swap(eledef.nodes); // swap trick
    em.add_def(eledef);
  }
 
  // PRISM15
  {
    ElementDefinition eledef(PRISM15, 18, 3, 15);
    const unsigned int nodes[] = {0,1,2,3,4,5,6,8,9,7,10,11,12,14,13};
    std::vector<unsigned int>(nodes, nodes+eledef.nnodes).swap(eledef.nodes); // swap trick
    em.add_def(eledef);
  }
 
  // PRISM18
  {
    ElementDefinition eledef(PRISM18, 13, 3, 18);
    const unsigned int nodes[] = {0,1,2,3,4,5,6,8,9,7,10,11,12,14,13,15,17,16};
    std::vector<unsigned int>(nodes, nodes+eledef.nnodes).swap(eledef.nodes); // swap trick
    em.add_def(eledef);
  }
 
  return em;
}
 
 
 
GmshIO::GmshIO (const MeshBase & mesh) :
  MeshOutput<MeshBase>(mesh),
  _binary(false),
  _write_lower_dimensional_elements(true)
{
}
 
 
 
GmshIO::GmshIO (MeshBase & mesh) :
  MeshInput<MeshBase>  (mesh),
  MeshOutput<MeshBase> (mesh),
  _binary (false),
  _write_lower_dimensional_elements(true)
{
}
 
 
 
bool & GmshIO::binary ()
{
  return _binary;
}
 
 
 
bool & GmshIO::write_lower_dimensional_elements ()
{
  return _write_lower_dimensional_elements;
}
 
 
 
void GmshIO::read (const std::string & name)
{
  std::ifstream in (name.c_str());
  this->read_mesh (in);
}
 
 
 
void GmshIO::read_mesh(std::istream & in)
{
  // 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);
 
  libmesh_assert(in.good());
 
  // clear any data in the mesh
  MeshBase & mesh = MeshInput<MeshBase>::mesh();
  mesh.clear();
 
  // some variables
  int format=0, size=0;
  Real version = 1.0;
 
  // Keep track of lower-dimensional blocks which are not BCs, but
  // actually blocks of lower-dimensional elements.
  std::set<subdomain_id_type> lower_dimensional_blocks;
 
  // Mapping from physical id -> (physical dim, physical name) pairs.
  // These can refer to either "sidesets" or "subdomains"; we need to
  // wait until the Mesh has been read to know which is which.  Note
  // that we are using 'int' as the key here rather than
  // subdomain_id_type or boundary_id_type, since at this point, it
  // could be either.
  typedef std::pair<unsigned, std::string> GmshPhysical;
  std::map<int, GmshPhysical> gmsh_physicals;
 
  // map to hold the node numbers for translation
  // note the the nodes can be non-consecutive
  std::map<unsigned int, unsigned int> nodetrans;
 
  // Map from entity tag to physical id. The key is a pair with the first
  // item being the dimension of the entity and the second item being
  // the entity tag/id
  std::map<std::pair<unsigned, int>, int> entity_to_physical_id;
 
  // For reading the file line by line
  std::string s;
 
  while (true)
    {
      // Try to read something.  This may set EOF!
      std::getline(in, s);
 
      if (in)
        {
          // Process s...
 
          if (s.find("$MeshFormat") == static_cast<std::string::size_type>(0))
            {
              in >> version >> format >> size;
              if (version < 2.0)
                {
                  // Some notes on gmsh mesh versions:
                  //
                  // Mesh version 2.0 goes back as far as I know.  It's not explicitly
                  // mentioned here: http://www.geuz.org/gmsh/doc/VERSIONS.txt
                  //
                  // As of gmsh-2.4.0:
                  // bumped mesh version format to 2.1 (small change in the $PhysicalNames
                  // section, where the group dimension is now required);
                  // [Since we don't even parse the PhysicalNames section at the time
                  //  of this writing, I don't think this change affects us.]
                  //
                  // Mesh version 2.2 tested by Manav Bhatia; no other
                  // libMesh code changes were required for support
                  //
                  // Mesh version 4.0 is a near complete rewrite of the previous mesh version
                  //
                  libmesh_error_msg("Error: Unknown msh file version " << version);
                }
 
              if (format)
                libmesh_error_msg("Error: Unknown data format for mesh in Gmsh reader.");
            }
 
          // Read and process the "PhysicalNames" section.
          else if (s.find("$PhysicalNames") == static_cast<std::string::size_type>(0))
            {
              // The lines in the PhysicalNames section should look like the following:
              // 2 1 "frac" lower_dimensional_block
              // 2 3 "top"
              // 2 4 "bottom"
              // 3 2 "volume"
 
              // Read in the number of physical groups to expect in the file.
              unsigned int num_physical_groups = 0;
              in >> num_physical_groups;
 
              // Read rest of line including newline character.
              std::getline(in, s);
 
              for (unsigned int i=0; i<num_physical_groups; ++i)
                {
                  // Read an entire line of the PhysicalNames section.
                  std::getline(in, s);
 
                  // Use an istringstream to extract the physical
                  // dimension, physical id, and physical name from
                  // this line.
                  std::istringstream s_stream(s);
                  unsigned phys_dim;
                  int phys_id;
                  std::string phys_name;
                  s_stream >> phys_dim >> phys_id >> phys_name;
 
                  // Not sure if this is true for all Gmsh files, but
                  // my test file has quotes around the phys_name
                  // string.  So let's erase any quotes now...
                  phys_name.erase(std::remove(phys_name.begin(), phys_name.end(), '"'), phys_name.end());
 
                  // Record this ID for later assignment of subdomain/sideset names.
                  gmsh_physicals[phys_id] = std::make_pair(phys_dim, phys_name);
 
                  // If 's' also contains the libmesh-specific string
                  // "lower_dimensional_block", add this block ID to
                  // the list of blocks which are not boundary
                  // conditions.
                  if (s.find("lower_dimensional_block") != std::string::npos)
                    {
                      lower_dimensional_blocks.insert(cast_int<subdomain_id_type>(phys_id));
 
                      // The user has explicitly told us that this
                      // block is a subdomain, so set that association
                      // in the Mesh.
                      mesh.subdomain_name(cast_int<subdomain_id_type>(phys_id)) = phys_name;
                    }
                }
            }
 
          else if (s.find("$Entities") == static_cast<std::string::size_type>(0))
          {
            if (version >= 4.0)
            {
              std::size_t num_point_entities, num_curve_entities, num_surface_entities, num_volume_entities;
              in >> num_point_entities >> num_curve_entities >> num_surface_entities >> num_volume_entities;
 
              for (std::size_t n = 0; n < num_point_entities; ++n)
              {
                int point_tag, physical_tag;
                Real x, y, z;
                std::size_t num_physical_tags;
                in >> point_tag >> x >> y >> z >> num_physical_tags;
                if (num_physical_tags > 1)
                  libmesh_error_msg("Sorry, you cannot currently specify multiple subdomain or " <<
                                    "boundary ids for a given geometric entity");
                else if (num_physical_tags)
                {
                  in >> physical_tag;
                  entity_to_physical_id[std::make_pair(0, point_tag)] = physical_tag;
                }
              }
              for (std::size_t n = 0; n < num_curve_entities; ++n)
              {
                int curve_tag, physical_tag;
                Real minx, miny, minz, maxx, maxy, maxz;
                std::size_t num_physical_tags;
                in >> curve_tag >> minx >> miny >> minz >> maxx >> maxy >> maxz >> num_physical_tags;
                if (num_physical_tags > 1)
                  libmesh_error_msg("I don't believe that we can specify multiple subdomain or " <<
                                    "boundary ids for a given geometric entity");
                else if (num_physical_tags)
                {
                  in >> physical_tag;
                  entity_to_physical_id[std::make_pair(1, curve_tag)] = physical_tag;
                }
 
                // Read to end of line; this captures bounding information that we don't care about
                std::getline(in, s);
              }
              for (std::size_t n = 0; n < num_surface_entities; ++n)
              {
                int surface_tag, physical_tag;
                Real minx, miny, minz, maxx, maxy, maxz;
                std::size_t num_physical_tags;
                in >> surface_tag >> minx >> miny >> minz >> maxx >> maxy >> maxz >> num_physical_tags;
                if (num_physical_tags > 1)
                  libmesh_error_msg("I don't believe that we can specify multiple subdomain or " <<
                                    "boundary ids for a given geometric entity");
                else if (num_physical_tags)
                {
                  in >> physical_tag;
                  entity_to_physical_id[std::make_pair(2, surface_tag)] = physical_tag;
                }
 
                // Read to end of line; this captures bounding information that we don't care about
                std::getline(in, s);
              }
              for (std::size_t n = 0; n < num_volume_entities; ++n)
              {
                int volume_tag, physical_tag;
                Real minx, miny, minz, maxx, maxy, maxz;
                std::size_t num_physical_tags;
                in >> volume_tag >> minx >> miny >> minz >> maxx >> maxy >> maxz >> num_physical_tags;
                if (num_physical_tags > 1)
                  libmesh_error_msg("I don't believe that we can specify multiple subdomain or " <<
                                    "boundary ids for a given geometric entity");
                else if (num_physical_tags)
                {
                  in >> physical_tag;
                  entity_to_physical_id[std::make_pair(3, volume_tag)] = physical_tag;
                }
 
                // Read to end of line; this captures bounding information that we don't care about
                std::getline(in, s);
              }
              // Read the $EndEntities
              std::getline(in, s);
            } // end if (version >= 4.0)
 
            else
              libmesh_error_msg("The Entities block was introduced in mesh version 4.0");
          } // end if $Entities
 
          // read the node block
          else if (s.find("$NOD") == static_cast<std::string::size_type>(0) ||
                   s.find("$NOE") == static_cast<std::string::size_type>(0) ||
                   s.find("$Nodes") == static_cast<std::string::size_type>(0))
          {
            if (version < 4.0)
            {
              unsigned int num_nodes = 0;
              in >> num_nodes;
              mesh.reserve_nodes (num_nodes);
 
              // read in the nodal coordinates and form points.
              Real x, y, z;
              unsigned int id;
 
              // add the nodal coordinates to the mesh
              for (unsigned int i=0; i<num_nodes; ++i)
              {
                in >> id >> x >> y >> z;
                mesh.add_point (Point(x, y, z), i);
                nodetrans[id] = i;
              }
            }
            else
            {
              // Read numEntityBlocks line
              std::size_t num_entities = 0, num_nodes = 0, min_node_tag, max_node_tag;
              in >> num_entities >> num_nodes >> min_node_tag >> max_node_tag;
 
              mesh.reserve_nodes(num_nodes);
 
              std::size_t node_counter = 0;
 
              // Now loop over entities
              for (std::size_t i = 0; i < num_entities; ++i)
              {
                int entity_dim, entity_tag, parametric;
                std::size_t num_nodes_in_block = 0;
                in >> entity_dim >> entity_tag >> parametric >> num_nodes_in_block;
                if (parametric)
                  libmesh_error_msg("We don't currently support reading parametric gmsh entities");
 
                // Read the node tags/ids
                std::size_t gmsh_id;
                for (std::size_t n = 0; n < num_nodes_in_block; ++n)
                {
 
                  in >> gmsh_id;
                  nodetrans[gmsh_id] = node_counter++;
                }
 
                // Read the node coordinates and add the nodes to the mesh
                Real x, y, z;
                for (std::size_t libmesh_id = node_counter - num_nodes_in_block;
                     libmesh_id < node_counter;
                     ++libmesh_id)
                {
                  in >> x >> y >> z;
                  mesh.add_point(Point(x, y, z), libmesh_id);
                }
              }
            }
            // read the $ENDNOD delimiter
            std::getline(in, s);
          }
 
          // Read the element block
          else if (s.find("$ELM") == static_cast<std::string::size_type>(0) ||
                   s.find("$Elements") == static_cast<std::string::size_type>(0))
          {
            // Keep track of element dimensions seen
            std::vector<unsigned> elem_dimensions_seen(3);
 
            if (version < 4.0)
            {
              // For reading the number of elements and the node ids from the stream
              unsigned int
                num_elem = 0,
                node_id = 0;
 
              // read how many elements are there, and reserve space in the mesh
              in >> num_elem;
              mesh.reserve_elem (num_elem);
 
              // As of version 2.2, the format for each element line is:
              // elm-number elm-type number-of-tags < tag > ... node-number-list
              // From the Gmsh docs:
              // * the first tag is the number of the
              //   physical entity to which the element belongs
              // * the second is the number of the elementary geometrical
              //   entity to which the element belongs
              // * the third is the number of mesh partitions to which the element
              //   belongs
              // * The rest of the tags are the partition ids (negative
              //   partition ids indicate ghost cells). A zero tag is
              //   equivalent to no tag. Gmsh and most codes using the
              //   MSH 2 format require at least the first two tags
              //   (physical and elementary tags).
 
              // read the elements
              for (unsigned int iel=0; iel<num_elem; ++iel)
              {
                unsigned int
                  id, type,
                  physical=1, elementary=1,
                  nnodes=0, ntags;
 
                // Note: tag has to be an int because it could be negative,
                // see above.
                int tag;
 
                if (version <= 1.0)
                  in >> id >> type >> physical >> elementary >> nnodes;
 
                else
                {
                  in >> id >> type >> ntags;
 
                  if (ntags > 2)
                    libmesh_do_once(libMesh::err << "Warning, ntags=" << ntags << ", but we currently only support reading 2 flags." << std::endl;);
 
                  for (unsigned int j = 0; j < ntags; j++)
                  {
                    in >> tag;
                    if (j == 0)
                      physical = tag;
                    else if (j == 1)
                      elementary = tag;
                  }
                }
 
                // Get a reference to the ElementDefinition, throw an error if not found.
                const GmshIO::ElementDefinition & eletype =
                  libmesh_map_find(_element_maps.in, type);
 
                // If we read nnodes, make sure it matches the number in eletype.nnodes
                if (nnodes != 0 && nnodes != eletype.nnodes)
                  libmesh_error_msg("nnodes = " << nnodes << " and eletype.nnodes = " << eletype.nnodes << " do not match.");
 
                // Assign the value from the eletype object.
                nnodes = eletype.nnodes;
 
                // Don't add 0-dimensional "point" elements to the
                // Mesh.  They should *always* be treated as boundary
                // "nodeset" data.
                if (eletype.dim > 0)
                {
                  // Record this element dimension as being "seen".
                  // We will treat all elements with dimension <
                  // max(dimension) as specifying boundary conditions,
                  // but we won't know what max_elem_dimension_seen is
                  // until we read the entire file.
                  elem_dimensions_seen[eletype.dim-1] = 1;
 
                  // Add the element to the mesh
                  {
                    Elem * elem = Elem::build(eletype.type).release();
                    elem->set_id(iel);
                    elem = mesh.add_elem(elem);
 
                    // Make sure that the libmesh element we added has nnodes nodes.
                    if (elem->n_nodes() != nnodes)
                      libmesh_error_msg("Number of nodes for element " \
                                        << id \
                                        << " of type " << eletype.type \
                                        << " (Gmsh type " << type \
                                        << ") does not match Libmesh definition. " \
                                        << "I expected " << elem->n_nodes() \
                                        << " nodes, but got " << nnodes);
 
                    // Add node pointers to the elements.
                    // If there is a node translation table, use it.
                    if (eletype.nodes.size() > 0)
                      for (unsigned int i=0; i<nnodes; i++)
                      {
                        in >> node_id;
                        elem->set_node(eletype.nodes[i]) = mesh.node_ptr(nodetrans[node_id]);
                      }
                    else
                    {
                      for (unsigned int i=0; i<nnodes; i++)
                      {
                        in >> node_id;
                        elem->set_node(i) = mesh.node_ptr(nodetrans[node_id]);
                      }
                    }
 
                    // Finally, set the subdomain ID to physical.  If this is a lower-dimension element, this ID will
                    // eventually go into the Mesh's BoundaryInfo object.
                    elem->subdomain_id() = static_cast<subdomain_id_type>(physical);
                  }
                }
 
                // Handle 0-dimensional elements (points) by adding
                // them to the BoundaryInfo object with
                // boundary_id == physical.
                else
                {
                  // This seems like it should always be the same
                  // number as the 'id' we already read in on this
                  // line.  At least it was in the example gmsh
                  // file I had...
                  in >> node_id;
                  mesh.get_boundary_info().add_node
                    (nodetrans[node_id],
                     static_cast<boundary_id_type>(physical));
                }
              } // element loop
            } // end if (version < 4.0)
 
            else
            {
              std::size_t num_entity_blocks = 0, num_elem = 0, min_element_tag, max_element_tag;
 
              // Read entity information
              in >> num_entity_blocks >> num_elem >> min_element_tag >> max_element_tag;
 
              mesh.reserve_elem(num_elem);
 
              std::size_t iel = 0;
 
              // Loop over entity blocks
              for (std::size_t i = 0; i < num_entity_blocks; ++i)
              {
                int entity_dim, entity_tag;
                unsigned int element_type;
                std::size_t num_elems_in_block = 0;
                in >> entity_dim >> entity_tag >> element_type >> num_elems_in_block;
 
                // Get a reference to the ElementDefinition
                const GmshIO::ElementDefinition & eletype =
                  libmesh_map_find(_element_maps.in, element_type);
 
                // Don't add 0-dimensional "point" elements to the
                // Mesh.  They should *always* be treated as boundary
                // "nodeset" data.
                if (eletype.dim > 0)
                {
                  // Record this element dimension as being "seen".
                  // We will treat all elements with dimension <
                  // max(dimension) as specifying boundary conditions,
                  // but we won't know what max_elem_dimension_seen is
                  // until we read the entire file.
                  elem_dimensions_seen[eletype.dim-1] = 1;
 
                  // Loop over elements with dim > 0
                  for (std::size_t n = 0; n < num_elems_in_block; ++n)
                  {
                    Elem * elem = Elem::build(eletype.type).release();
                    elem->set_id(iel++);
                    elem = mesh.add_elem(elem);
 
                    std::size_t gmsh_element_id;
                    in >> gmsh_element_id;
 
                    // Get the remainer of the line that includes the nodes ids
                    std::getline(in, s);
                    std::istringstream is(s);
                    std::size_t local_node_counter = 0, gmsh_node_id;
                    while (is >> gmsh_node_id)
                    {
                      // Add node pointers to the elements.
                      // If there is a node translation table, use it.
                      if (eletype.nodes.size() > 0)
                          elem->set_node(eletype.nodes[local_node_counter++]) =
                            mesh.node_ptr(nodetrans[gmsh_node_id]);
                      else
                          elem->set_node(local_node_counter++) = mesh.node_ptr(nodetrans[gmsh_node_id]);
                    }
 
                    // Make sure that the libmesh element we added has nnodes nodes.
                    if (elem->n_nodes() != local_node_counter)
                      libmesh_error_msg("Number of nodes for element " \
                                        << gmsh_element_id \
                                        << " of type " << eletype.type \
                                        << " (Gmsh type " << element_type \
                                        << ") does not match Libmesh definition. " \
                                        << "I expected " << elem->n_nodes() \
                                        << " nodes, but got " << local_node_counter);
 
 
                    // Finally, set the subdomain ID to physical.  If this is a lower-dimension element, this ID will
                    // eventually go into the Mesh's BoundaryInfo object.
                    elem->subdomain_id() = static_cast<subdomain_id_type>(
                      entity_to_physical_id[std::make_pair(entity_dim, entity_tag)]);
 
                  } // end for (loop over elements in entity block)
                } // end if (eletype.dim > 0)
 
                else
                {
                  for (std::size_t n = 0; n < num_elems_in_block; ++n)
                  {
                    std::size_t gmsh_element_id, gmsh_node_id;
                    in >> gmsh_element_id;
                    in >> gmsh_node_id;
                    mesh.get_boundary_info().add_node(
                      nodetrans[gmsh_node_id],
                      static_cast<boundary_id_type>(entity_to_physical_id[
                                                      std::make_pair(entity_dim, entity_tag)]));
                  } // end for (loop over elements in entity block)
                } // end if (eletype.dim == 0)
              } // end for (loop over entity blocks)
            } // end if (version >= 4.0)
 
            // read the $ENDELM delimiter
            std::getline(in, s);
 
            // Record the max and min element dimension seen while reading the file.
            unsigned char
              max_elem_dimension_seen=1,
              min_elem_dimension_seen=3;
 
            for (auto i : index_range(elem_dimensions_seen))
              if (elem_dimensions_seen[i])
              {
                // Debugging
                // libMesh::out << "Seen elements of dimension " << i+1 << std::endl;
                max_elem_dimension_seen =
                  std::max(max_elem_dimension_seen, cast_int<unsigned char>(i+1));
                min_elem_dimension_seen =
                  std::min(min_elem_dimension_seen, cast_int<unsigned char>(i+1));
              }
 
            // Debugging:
            // libMesh::out << "max_elem_dimension_seen=" << max_elem_dimension_seen << std::endl;
            // libMesh::out << "min_elem_dimension_seen=" << min_elem_dimension_seen << std::endl;
 
 
            // How many different element dimensions did we see while reading from file?
            unsigned n_dims_seen = std::accumulate(elem_dimensions_seen.begin(),
                                                   elem_dimensions_seen.end(),
                                                   static_cast<unsigned>(0),
                                                   std::plus<unsigned>());
 
 
            // Set mesh_dimension based on the largest element dimension seen.
            mesh.set_mesh_dimension(max_elem_dimension_seen);
 
            // Now that we know the maximum element dimension seen,
            // we know whether the physical names are subdomain
            // names or sideset names.
            for (const auto & pr : gmsh_physicals)
            {
              // Extract data
              int phys_id = pr.first;
              unsigned phys_dim = pr.second.first;
              const std::string & phys_name = pr.second.second;
 
              // If the physical's dimension matches the largest
              // dimension we've seen, it's a subdomain name.
              if (phys_dim == max_elem_dimension_seen)
                mesh.subdomain_name(cast_int<subdomain_id_type>(phys_id)) = phys_name;
 
              // Otherwise, if it's not a lower-dimensional
              // block, it's a sideset name.
              else if (phys_dim < max_elem_dimension_seen &&
                       !lower_dimensional_blocks.count(cast_int<boundary_id_type>(phys_id)))
                mesh.get_boundary_info().sideset_name(cast_int<boundary_id_type>(phys_id)) = phys_name;
            }
 
            if (n_dims_seen > 1)
            {
              // Store lower-dimensional elements in a map sorted
              // by Elem::key().  We use a multimap for two reasons:
              // 1.) The hash function is not guaranteed to be
              // unique, so different lower-dimensional elements
              // could theoretically hash to the same value,
              // although this is pretty unlikely.
              // 2.) The Gmsh file may contain multiple
              // lower-dimensional elements for a single side in
              // order to implement multiple boundary ids for a
              // single side.  These lower-dimensional elements
              // will all hash to the same value, and we need to
              // be able to store all of them.
              typedef std::unordered_multimap<dof_id_type, Elem *> provide_container_t;
              provide_container_t provide_bcs;
 
              // 1st loop over active elements - get info about lower-dimensional elements.
              for (auto & elem : mesh.active_element_ptr_range())
                if (elem->dim() < max_elem_dimension_seen &&
                    !lower_dimensional_blocks.count(elem->subdomain_id()))
                {
                  // To be consistent with the previous
                  // GmshIO behavior, add all the
                  // lower-dimensional elements' nodes to
                  // the Mesh's BoundaryInfo object with the
                  // lower-dimensional element's subdomain
                  // ID.
                  for (auto n : elem->node_index_range())
                    mesh.get_boundary_info().add_node(elem->node_id(n),
                                                      elem->subdomain_id());
 
                  // Store this elem in a quickly-searchable
                  // container to use it to assign boundary
                  // conditions later.
                  provide_bcs.insert(std::make_pair(elem->key(), elem));
                }
 
              // 2nd loop over active elements - use lower dimensional element data to set BCs for higher dimensional elements
              for (auto & elem : mesh.active_element_ptr_range())
                if (elem->dim() == max_elem_dimension_seen)
                {
                  // This is a max-dimension element that
                  // may require BCs.  For each of its
                  // sides, including internal sides, we'll
                  // see if one more more lower-dimensional elements
                  // provides boundary information for it.
                  // Note that we have not yet called
                  // find_neighbors(), so we can't use
                  // elem->neighbor(sn) in this algorithm...
                  for (auto sn : elem->side_index_range())
                    for (const auto & pr : as_range(provide_bcs.equal_range(elem->key(sn))))
                    {
                      // For each side side in the provide_bcs multimap...
                      // Construct the side for hash verification.
                      std::unique_ptr<Elem> side (elem->build_side_ptr(sn));
 
                      // Construct the lower-dimensional element to compare to the side.
                      Elem * lower_dim_elem = pr.second;
 
                      // This was a hash, so it might not be perfect.  Let's verify...
                      if (*lower_dim_elem == *side)
                      {
                        // Add the lower-dimensional
                        // element's subdomain_id as a
                        // boundary_id for the
                        // higher-dimensional element.
                        boundary_id_type bid = cast_int<boundary_id_type>(lower_dim_elem->subdomain_id());
                        mesh.get_boundary_info().add_side(elem, sn, bid);
                      }
                    }
                }
 
              // 3rd loop over active elements - Remove the lower-dimensional elements
              for (auto & elem : mesh.active_element_ptr_range())
                if (elem->dim() < max_elem_dimension_seen &&
                    !lower_dimensional_blocks.count(elem->subdomain_id()))
                  mesh.delete_elem(elem);
            } // end if (n_dims_seen > 1)
          } // if $ELM
 
          continue;
        } // if (in)
 
 
      // If !in, check to see if EOF was set.  If so, break out
      // of while loop.
      if (in.eof())
        break;
 
      // If !in and !in.eof(), stream is in a bad state!
      libmesh_error_msg("Stream is bad! Perhaps the file does not exist?");
 
    } // while true
}
 
 
 
void GmshIO::write (const std::string & name)
{
  if (MeshOutput<MeshBase>::mesh().processor_id() == 0)
    {
      // Open the output file stream
      std::ofstream out_stream (name.c_str());
 
      // Make sure it opened correctly
      if (!out_stream.good())
        libmesh_file_error(name.c_str());
 
      this->write_mesh (out_stream);
    }
}
 
 
 
void GmshIO::write_nodal_data (const std::string & fname,
                               const std::vector<Number> & soln,
                               const std::vector<std::string> & names)
{
  LOG_SCOPE("write_nodal_data()", "GmshIO");
 
  if (MeshOutput<MeshBase>::mesh().processor_id() == 0)
    this->write_post  (fname, &soln, &names);
}
 
 
 
void GmshIO::write_mesh (std::ostream & out_stream)
{
  // Be sure that the stream is valid.
  libmesh_assert (out_stream.good());
 
  // Get a const reference to the mesh
  const MeshBase & mesh = MeshOutput<MeshBase>::mesh();
 
  // If requested, write out lower-dimensional elements for
  // element-side-based boundary conditions.
  std::size_t n_boundary_faces = 0;
  if (this->write_lower_dimensional_elements())
    n_boundary_faces = mesh.get_boundary_info().n_boundary_conds();
 
  // Note: we are using version 2.0 of the gmsh output format.
 
  // Write the file header.
  out_stream << "$MeshFormat\n";
  out_stream << "2.0 0 " << sizeof(Real) << '\n';
  out_stream << "$EndMeshFormat\n";
 
  // write the nodes in (n x y z) format
  out_stream << "$Nodes\n";
  out_stream << mesh.n_nodes() << '\n';
 
  for (auto v : IntRange<unsigned int>(0, mesh.n_nodes()))
    out_stream << mesh.node_ref(v).id()+1 << " "
               << mesh.node_ref(v)(0) << " "
               << mesh.node_ref(v)(1) << " "
               << mesh.node_ref(v)(2) << '\n';
  out_stream << "$EndNodes\n";
 
  {
    // write the connectivity
    out_stream << "$Elements\n";
    out_stream << mesh.n_active_elem() + n_boundary_faces << '\n';
 
    // loop over the elements
    for (const auto & elem : mesh.active_element_ptr_range())
      {
        // Get a reference to the ElementDefinition object
        const ElementDefinition & eletype =
          libmesh_map_find(_element_maps.out, elem->type());
 
        // The element mapper better not require any more nodes
        // than are present in the current element!
        libmesh_assert_less_equal (eletype.nodes.size(), elem->n_nodes());
 
        // elements ids are 1 based in Gmsh
        out_stream << elem->id()+1 << " ";
        // element type
        out_stream << eletype.gmsh_type;
 
        // write the number of tags (3) and their values:
        // 1 (physical entity)
        // 2 (geometric entity)
        // 3 (partition entity)
        out_stream << " 3 "
                   << static_cast<unsigned int>(elem->subdomain_id())
                   << " 0 "
                   << elem->processor_id()+1
                   << " ";
 
        // if there is a node translation table, use it
        if (eletype.nodes.size() > 0)
          for (auto i : elem->node_index_range())
            out_stream << elem->node_id(eletype.nodes[i])+1 << " "; // gmsh is 1-based
        // otherwise keep the same node order
        else
          for (auto i : elem->node_index_range())
            out_stream << elem->node_id(i)+1 << " ";                  // gmsh is 1-based
        out_stream << "\n";
      } // element loop
  }
 
  {
    // A counter for writing surface elements to the Gmsh file
    // sequentially.  We start numbering them with a number strictly
    // larger than the largest element ID in the mesh.  Note: the
    // MeshBase docs say "greater than or equal to" the maximum
    // element id in the mesh, so technically we might need a +1 here,
    // but all of the implementations return an ID strictly greater
    // than the largest element ID in the Mesh.
    unsigned int e_id = mesh.max_elem_id();
 
    // loop over the elements, writing out boundary faces
    if (n_boundary_faces)
      {
        // Build a list of (elem, side, bc) tuples.
        auto bc_triples = mesh.get_boundary_info().build_side_list();
 
        // Loop over these lists, writing data to the file.
        for (const auto & t : bc_triples)
          {
            const Elem & elem = mesh.elem_ref(std::get<0>(t));
 
            std::unique_ptr<const Elem> side = elem.build_side_ptr(std::get<1>(t));
 
            // consult the export element table
            const GmshIO::ElementDefinition & eletype =
              libmesh_map_find(_element_maps.out, side->type());
 
            // The element mapper better not require any more nodes
            // than are present in the current element!
            libmesh_assert_less_equal (eletype.nodes.size(), side->n_nodes());
 
            // elements ids are 1-based in Gmsh
            out_stream << e_id+1 << " ";
 
            // element type
            out_stream << eletype.gmsh_type;
 
            // write the number of tags:
            // 1 (physical entity)
            // 2 (geometric entity)
            // 3 (partition entity)
            out_stream << " 3 "
                       << std::get<2>(t)
                       << " 0 "
                       << elem.processor_id()+1
                       << " ";
 
            // if there is a node translation table, use it
            if (eletype.nodes.size() > 0)
              for (auto i : side->node_index_range())
                out_stream << side->node_id(eletype.nodes[i])+1 << " "; // gmsh is 1-based
 
            // otherwise keep the same node order
            else
              for (auto i : side->node_index_range())
                out_stream << side->node_id(i)+1 << " ";                // gmsh is 1-based
 
            // Go to the next line
            out_stream << "\n";
 
            // increment this index too...
            ++e_id;
          }
      }
 
    out_stream << "$EndElements\n";
  }
}
 
 
 
void GmshIO::write_post (const std::string & fname,
                         const std::vector<Number> * v,
                         const std::vector<std::string> * solution_names)
{
 
  // Should only do this on processor 0!
  libmesh_assert_equal_to (MeshOutput<MeshBase>::mesh().processor_id(), 0);
 
  // Create an output stream
  std::ofstream out_stream(fname.c_str());
 
  // Make sure it opened correctly
  if (!out_stream.good())
    libmesh_file_error(fname.c_str());
 
  // create a character buffer
  char buf[80];
 
  // Get a constant reference to the mesh.
  const MeshBase & mesh = MeshOutput<MeshBase>::mesh();
 
  //  write the data
  if ((solution_names != nullptr) && (v != nullptr))
    {
      const unsigned int n_vars =
        cast_int<unsigned int>(solution_names->size());
 
      if (!(v->size() == mesh.n_nodes()*n_vars))
        libMesh::err << "ERROR: v->size()=" << v->size()
                     << ", mesh.n_nodes()=" << mesh.n_nodes()
                     << ", n_vars=" << n_vars
                     << ", mesh.n_nodes()*n_vars=" << mesh.n_nodes()*n_vars
                     << "\n";
 
      libmesh_assert_equal_to (v->size(), mesh.n_nodes()*n_vars);
 
      // write the header
      out_stream << "$PostFormat\n";
      if (this->binary())
        out_stream << "1.2 1 " << sizeof(double) << "\n";
      else
        out_stream << "1.2 0 " << sizeof(double) << "\n";
      out_stream << "$EndPostFormat\n";
 
      // Loop over the elements to see how much of each type there are
      unsigned int n_points=0, n_lines=0, n_triangles=0, n_quadrangles=0,
        n_tetrahedra=0, n_hexahedra=0, n_prisms=0, n_pyramids=0;
      unsigned int n_scalar=0, n_vector=0, n_tensor=0;
      unsigned int nb_text2d=0, nb_text2d_chars=0, nb_text3d=0, nb_text3d_chars=0;
 
      {
        for (const auto & elem : mesh.active_element_ptr_range())
          {
            const ElemType elemtype = elem->type();
 
            switch (elemtype)
              {
              case EDGE2:
              case EDGE3:
              case EDGE4:
                {
                  n_lines += 1;
                  break;
                }
              case TRI3:
              case TRI6:
                {
                  n_triangles += 1;
                  break;
                }
              case QUAD4:
              case QUAD8:
              case QUAD9:
                {
                  n_quadrangles += 1;
                  break;
                }
              case TET4:
              case TET10:
                {
                  n_tetrahedra += 1;
                  break;
                }
              case HEX8:
              case HEX20:
              case HEX27:
                {
                  n_hexahedra += 1;
                  break;
                }
              case PRISM6:
              case PRISM15:
              case PRISM18:
                {
                  n_prisms += 1;
                  break;
                }
              case PYRAMID5:
                {
                  n_pyramids += 1;
                  break;
                }
              default:
                libmesh_error_msg("ERROR: Nonexistent element type " << elem->type());
              }
          }
      }
 
      // create a view for each variable
      for (unsigned int ivar=0; ivar < n_vars; ivar++)
        {
          std::string varname = (*solution_names)[ivar];
 
          // at the moment, we just write out scalar quantities
          // later this should be made configurable through
          // options to the writer class
          n_scalar = 1;
 
          // write the variable as a view, and the number of time steps
          out_stream << "$View\n" << varname << " " << 1 << "\n";
 
          // write how many of each geometry type are written
          out_stream << n_points * n_scalar << " "
                     << n_points * n_vector << " "
                     << n_points * n_tensor << " "
                     << n_lines * n_scalar << " "
                     << n_lines * n_vector << " "
                     << n_lines * n_tensor << " "
                     << n_triangles * n_scalar << " "
                     << n_triangles * n_vector << " "
                     << n_triangles * n_tensor << " "
                     << n_quadrangles * n_scalar << " "
                     << n_quadrangles * n_vector << " "
                     << n_quadrangles * n_tensor << " "
                     << n_tetrahedra * n_scalar << " "
                     << n_tetrahedra * n_vector << " "
                     << n_tetrahedra * n_tensor << " "
                     << n_hexahedra * n_scalar << " "
                     << n_hexahedra * n_vector << " "
                     << n_hexahedra * n_tensor << " "
                     << n_prisms * n_scalar << " "
                     << n_prisms * n_vector << " "
                     << n_prisms * n_tensor << " "
                     << n_pyramids * n_scalar << " "
                     << n_pyramids * n_vector << " "
                     << n_pyramids * n_tensor << " "
                     << nb_text2d << " "
                     << nb_text2d_chars << " "
                     << nb_text3d << " "
                     << nb_text3d_chars << "\n";
 
          // if binary, write a marker to identify the endianness of the file
          if (this->binary())
            {
              const int one = 1;
              std::memcpy(buf, &one, sizeof(int));
              out_stream.write(buf, sizeof(int));
            }
 
          // the time steps (there is just 1 at the moment)
          if (this->binary())
            {
              double one = 1;
              std::memcpy(buf, &one, sizeof(double));
              out_stream.write(buf, sizeof(double));
            }
          else
            out_stream << "1\n";
 
          // Loop over the elements and write out the data
          for (const auto & elem : mesh.active_element_ptr_range())
            {
              const unsigned int nv = elem->n_vertices();
              // this is quite crappy, but I did not invent that file format!
              for (unsigned int d=0; d<3; d++)  // loop over the dimensions
                {
                  for (unsigned int n=0; n < nv; n++)   // loop over vertices
                    {
                      const Point & vertex = elem->point(n);
                      if (this->binary())
                        {
#if defined(LIBMESH_DEFAULT_TRIPLE_PRECISION) || defined(LIBMESH_DEFAULT_QUADRUPLE_PRECISION)
                          libmesh_warning("Gmsh binary writes use only double precision!");
#endif
                          double tmp = double(vertex(d));
                          std::memcpy(buf, &tmp, sizeof(double));
                          out_stream.write(reinterpret_cast<char *>(buf), sizeof(double));
                        }
                      else
                        out_stream << vertex(d) << " ";
                    }
                  if (!this->binary())
                    out_stream << "\n";
                }
 
              // now finally write out the data
              for (unsigned int i=0; i < nv; i++)   // loop over vertices
                if (this->binary())
                  {
#ifdef LIBMESH_USE_COMPLEX_NUMBERS
                    libMesh::out << "WARNING: Gmsh::write_post does not fully support "
                                 << "complex numbers. Will only write the real part of "
                                 << "variable " << varname << std::endl;
#endif
                    double tmp = double(libmesh_real((*v)[elem->node_id(i)*n_vars + ivar]));
                    std::memcpy(buf, &tmp, sizeof(double));
                    out_stream.write(reinterpret_cast<char *>(buf), sizeof(double));
                  }
                else
                  {
#ifdef LIBMESH_USE_COMPLEX_NUMBERS
                    libMesh::out << "WARNING: Gmsh::write_post does not fully support "
                                 << "complex numbers. Will only write the real part of "
                                 << "variable " << varname << std::endl;
#endif
                    out_stream << libmesh_real((*v)[elem->node_id(i)*n_vars + ivar]) << "\n";
                  }
            }
          if (this->binary())
            out_stream << "\n";
          out_stream << "$EndView\n";
 
        } // end variable loop (writing the views)
    }
}
 
} // namespace libMesh