ucd_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
 
 
// 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"
#include "libmesh/int_range.h"
#include "libmesh/utility.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
 
// C++ includes
#include <array>
#include <fstream>
 
 
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
  {
    for (unsigned int i=0; i<nNodes; i++)
      {
        libmesh_assert (in.good());
 
        std::array<Real, 3> xyz;
 
        in >> dummy   // Point number
           >> xyz[0]  // x-coordinate value
           >> xyz[1]  // y-coordinate value
           >> xyz[2]; // z-coordinate value
 
        Point p(xyz[0]);
#if LIBMESH_DIM > 1
        p(1) = xyz[1];
#else
        libmesh_assert_equal_to(xyz[1], 0);
#endif
#if LIBMESH_DIM > 2
        p(2) = xyz[2];
#else
        libmesh_assert_equal_to(xyz[2], 0);
#endif
 
        // Build the node
        mesh.add_point (p, 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 ElemType
        ElemType et = libmesh_map_find(_reading_element_map, type);
 
        // Build the required type and release it into our custody.
        Elem * elem = Elem::build(et).release();
 
        for (auto n : elem->node_index_range())
          {
            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.
      std::string elem_string = libmesh_map_find(_writing_element_map, elem->type());
 
      // Write the element's subdomain ID as the UCD "material_id".
      out_stream << e++ << " " << elem->subdomain_id() << " " << elem_string << "\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, ns = names.size(); i < ns; 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 (auto n : IntRange<std::size_t>(1, mesh.n_nodes()))
    {
      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