ucd_io.C

Go to the documentation of this file.

// The libMesh Finite Element Library.
// Copyright (C) 2002-2018 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>


// Local includes
#include "libmesh/libmesh_config.h"
#include "libmesh/ucd_io.h"
#include "libmesh/mesh_base.h"
#include "libmesh/face_quad4.h"
#include "libmesh/face_tri3.h"
#include "libmesh/cell_tet4.h"
#include "libmesh/cell_hex8.h"
#include "libmesh/cell_prism6.h"
#include "libmesh/enum_io_package.h"
#include "libmesh/enum_elem_type.h"

#ifdef LIBMESH_HAVE_GZSTREAM
# include "libmesh/ignore_warnings.h" // shadowing in gzstream.h
# include "gzstream.h" // For reading/writing compressed streams
# include "libmesh/restore_warnings.h"
#endif


namespace libMesh
{

// Initialize the static data members by calling the static build functions.
std::map<ElemType, std::string> UCDIO::_writing_element_map = UCDIO::build_writing_element_map();
std::map<std::string, ElemType> UCDIO::_reading_element_map = UCDIO::build_reading_element_map();



// Static function used to build the _writing_element_map.
std::map<ElemType, std::string> UCDIO::build_writing_element_map()
{
  std::map<ElemType, std::string> ret;
  ret[EDGE2]    = "edge";
  ret[TRI3]     = "tri";
  ret[QUAD4]    = "quad";
  ret[TET4]     = "tet";
  ret[HEX8]     = "hex";
  ret[PRISM6]   = "prism";
  ret[PYRAMID5] = "pyramid";
  return ret;
}



// Static function used to build the _reading_element_map.
std::map<std::string, ElemType> UCDIO::build_reading_element_map()
{
  std::map<std::string, ElemType> ret;
  ret["edge"]    = EDGE2;
  ret["tri"]     = TRI3;
  ret["quad"]    = QUAD4;
  ret["tet"]     = TET4;
  ret["hex"]     = HEX8;
  ret["prism"]   = PRISM6;
  ret["pyramid"] = PYRAMID5;
  return ret;
}


void UCDIO::read (const std::string & file_name)
{
  if (file_name.rfind(".gz") < file_name.size())
    {
#ifdef LIBMESH_HAVE_GZSTREAM
      igzstream in_stream (file_name.c_str());
      this->read_implementation (in_stream);
#else
      libmesh_error_msg("ERROR:  You must have the zlib.h header files and libraries to read and write compressed streams.");
#endif
    }

  else
    {
      std::ifstream in_stream (file_name.c_str());
      this->read_implementation (in_stream);
    }
}



void UCDIO::write (const std::string & file_name)
{
  if (file_name.rfind(".gz") < file_name.size())
    {
#ifdef LIBMESH_HAVE_GZSTREAM
      ogzstream out_stream (file_name.c_str());
      this->write_implementation (out_stream);
#else
      libmesh_error_msg("ERROR:  You must have the zlib.h header files and libraries to read and write compressed streams.");
#endif
    }

  else
    {
      std::ofstream out_stream (file_name.c_str());
      this->write_implementation (out_stream);
    }
}



void UCDIO::read_implementation (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);

  // Check input buffer
  libmesh_assert (in.good());

  MeshBase & mesh = MeshInput<MeshBase>::mesh();

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

  this->skip_comment_lines (in, '#');

  unsigned int nNodes=0, nElem=0, dummy=0;

  in >> nNodes   // Read the number of nodes from the stream
     >> nElem    // Read the number of elements from the stream
     >> dummy
     >> dummy
     >> dummy;


  // Read the nodal coordinates. Note that UCD format always
  // stores (x,y,z), and in 2D z=0. We don't need to store this,
  // however.  So, we read in x,y,z for each node and make a point
  // in the proper way based on what dimension we're in
  {
    Point xyz;

    for (unsigned int i=0; i<nNodes; i++)
      {
        libmesh_assert (in.good());

        in >> dummy   // Point number
           >> xyz(0)  // x-coordinate value
           >> xyz(1)  // y-coordinate value
           >> xyz(2); // z-coordinate value

        // Build the node
        mesh.add_point (xyz, i);
      }
  }

  // Read the elements from the stream. Notice that the UCD node-numbering
  // scheme is 1-based, and we just created a 0-based scheme above
  // (which is of course what we want). So, when we read in the nodal
  // connectivity for each element we need to take 1 off the value of
  // each node so that we get the right thing.
  {
    unsigned int material_id=0, node=0;
    std::string type;

    for (unsigned int i=0; i<nElem; i++)
      {
        libmesh_assert (in.good());

        // The cell type can be either tri, quad, tet, hex, or prism.
        in >> dummy        // Cell number, means nothing to us
           >> material_id  // We'll use this for the element subdomain id.
           >> type;        // string describing cell type

        // Convert the UCD type string to a libmesh ElementType
        auto it = _reading_element_map.find(type);
        if (it == _reading_element_map.end())
          libmesh_error_msg("Unsupported element type = " << type);

        // Build the required type and release it into our custody.
        Elem * elem = Elem::build(it->second).release();

        for (unsigned int n=0; n<elem->n_nodes(); n++)
          {
            libmesh_assert (in.good());

            in >> node; // read the current node
            node -= 1;  // UCD is 1-based, so subtract

            libmesh_assert_less (node, mesh.n_nodes());

            // assign the node
            elem->set_node(n) = mesh.node_ptr(node);
          }

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

        // Set the element's subdomain ID based on the material_id.
        elem->subdomain_id() = cast_int<subdomain_id_type>(material_id);

        // Add the element to the mesh
        elem->set_id(i);
        mesh.add_elem (elem);
      }

    // 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
  }
}



void UCDIO::write_implementation (std::ostream & out_stream)
{
  libmesh_assert (out_stream.good());

  const MeshBase & mesh = MeshOutput<MeshBase>::mesh();

  // UCD doesn't work any dimension except 3?
  if (mesh.mesh_dimension() != 3)
    libmesh_error_msg("Error: Can't write boundary elements for meshes of dimension less than 3. " \
                      << "Mesh dimension = " << mesh.mesh_dimension());

  // Write header
  this->write_header(out_stream, mesh, mesh.n_elem(), 0);

  // Write the node coordinates
  this->write_nodes(out_stream, mesh);

  // Write the elements
  this->write_interior_elems(out_stream, mesh);
}



void UCDIO::write_header(std::ostream & out_stream,
                         const MeshBase & mesh,
                         dof_id_type n_elems,
                         unsigned int n_vars)
{
  libmesh_assert (out_stream.good());
  // TODO: We could print out the libmesh revision used to write this file here.
  out_stream << "# For a description of the UCD format see the AVS Developer's guide.\n"
             << "#\n";

  // Write the mesh info
  out_stream << mesh.n_nodes() << " "
             << n_elems  << " "
             << n_vars << " "
             << " 0 0\n";
}



void UCDIO::write_nodes(std::ostream & out_stream,
                        const MeshBase & mesh)
{
  // 1-based node number for UCD
  unsigned int n=1;

  // Write the node coordinates
  for (auto & node : mesh.node_ptr_range())
    {
      libmesh_assert (out_stream.good());

      out_stream << n++ << "\t";
      node->write_unformatted(out_stream);
    }
}



void UCDIO::write_interior_elems(std::ostream & out_stream,
                                 const MeshBase & mesh)
{
  // 1-based element number for UCD
  unsigned int e=1;

  // Write element information
  for (const auto & elem : mesh.element_ptr_range())
    {
      libmesh_assert (out_stream.good());

      // Look up the corresponding UCD element type in the static map.
      const ElemType etype = elem->type();
      auto it = _writing_element_map.find(etype);
      if (it == _writing_element_map.end())
        libmesh_error_msg("Error: Unsupported ElemType " << etype << " for UCDIO.");

      // Write the element's subdomain ID as the UCD "material_id".
      out_stream << e++ << " " << elem->subdomain_id() << " " << it->second << "\t";
      elem->write_connectivity(out_stream, UCD);
    }
}



void UCDIO::write_nodal_data(const std::string & fname,
                             const std::vector<Number> & soln,
                             const std::vector<std::string> & names)
{
  const MeshBase & mesh = MeshOutput<MeshBase>::mesh();

  const dof_id_type n_elem = mesh.n_elem();

  // Only processor 0 does the writing
  if (mesh.processor_id())
    return;

  std::ofstream out_stream(fname.c_str());

  // UCD doesn't work in 1D
  libmesh_assert (mesh.mesh_dimension() != 1);

  // Write header
  this->write_header(out_stream,mesh,n_elem,
                     cast_int<unsigned int>(names.size()));

  // Write the node coordinates
  this->write_nodes(out_stream, mesh);

  // Write the elements
  this->write_interior_elems(out_stream, mesh);

  // Write the solution
  this->write_soln(out_stream, mesh, names, soln);
}



void UCDIO::write_soln(std::ostream & out_stream,
                       const MeshBase & mesh,
                       const std::vector<std::string> & names,
                       const std::vector<Number> & soln)
{
  libmesh_assert (out_stream.good());

  // First write out how many variables and how many components per variable
  out_stream << names.size();
  for (std::size_t i = 0; i < names.size(); i++)
    {
      libmesh_assert (out_stream.good());
      // Each named variable has only 1 component
      out_stream << " 1";
    }
  out_stream << std::endl;

  // Now write out variable names and units. Since we don't store units
  // We just write out dummy.
  for (const auto & name : names)
    {
      libmesh_assert (out_stream.good());
      out_stream << name << ", dummy" << std::endl;
    }

  // Now, for each node, write out the solution variables.
  // We use a 1-based node numbering for UCD.
  std::size_t nv = names.size();
  for (std::size_t n = 1; n <= mesh.n_nodes(); n++)
    {
      libmesh_assert (out_stream.good());
      out_stream << n;

      for (std::size_t var = 0; var != nv; var++)
        {
          std::size_t idx = nv*(n-1) + var;

          out_stream << " " << soln[idx];
        }
      out_stream << std::endl;
    }
}

} // namespace libMesh