libMesh::MEDITIO Class Reference

This class implements writing meshes in the mesh format used by the MEdit visualization tool developed in the Gamma Project at INRIA Roquencourt. More...

#include <medit_io.h>

Inheritance diagram for libMesh::MEDITIO:

Public Member Functions
	MEDITIO (const MeshBase &)
	Constructor. More...
	MEDITIO (const MeshBase &, unsigned int c)
	Constructor. More...
virtual void	write (const std::string &) override
	This method implements writing a mesh to a specified ".mesh" file. More...
virtual void	write_nodal_data (const std::string &, const std::vector< Number > &, const std::vector< std::string > &) override
	This method implements writing a mesh with nodal data to a specified file where the nodal data and variable names are provided. More...
bool &	binary ()
	Flag indicating whether or not to write a binary file. More...
virtual void	write_equation_systems (const std::string &, const EquationSystems &, const std::set< std::string > *system_names=nullptr)
	This method implements writing a mesh with data to a specified file where the data is taken from the EquationSystems object. More...
virtual void	write_discontinuous_equation_systems (const std::string &, const EquationSystems &, const std::set< std::string > *system_names=nullptr)
	This method implements writing a mesh with discontinuous data to a specified file where the data is taken from the EquationSystems object. More...
virtual void	write_nodal_data (const std::string &, const NumericVector< Number > &, const std::vector< std::string > &)
	This method may be overridden by "parallel" output formats for writing nodal data. More...
virtual void	write_nodal_data (const std::string &, const EquationSystems &, const std::set< std::string > *)
	This method should be overridden by "parallel" output formats for writing nodal data. More...
virtual void	write_nodal_data_discontinuous (const std::string &, const std::vector< Number > &, const std::vector< std::string > &)
	This method implements writing a mesh with discontinuous data to a specified file where the nodal data and variables names are provided. More...
unsigned int &	ascii_precision ()
	Return/set the precision to use when writing ASCII files. More...

Protected Member Functions
const MeshBase &	mesh () const
virtual bool	get_add_sides ()

Protected Attributes
const bool	_is_parallel_format
	Flag specifying whether this format is parallel-capable. More...
const bool	_serial_only_needed_on_proc_0
	Flag specifying whether this format can be written by only serializing the mesh to processor zero. More...

Private Member Functions
void	write_ascii (const std::string &, const std::vector< Number > *=nullptr, const std::vector< std::string > *=nullptr)
	This method implements writing a mesh with nodal data to a specified file where the nodal data and variable names are optionally provided. More...

Private Attributes
bool	_binary
	Flag to write binary data. More...
unsigned int	scalar_idx

Detailed Description

This class implements writing meshes in the mesh format used by the MEdit visualization tool developed in the Gamma Project at INRIA Roquencourt.

For a full description of the mesh format and to obtain the MEdit software see the MEdit home page.

Author

Florian Prill

Date

2004

Definition at line 47 of file medit_io.h.

Constructor & Destructor Documentation

MEDITIO() [1/2]

libMesh::MEDITIO::MEDITIO ( const MeshBase &  mesh_in )

inlineexplicit

Constructor.

Takes a reference to a constant mesh object. This constructor will only allow us to write the mesh.

Definition at line 113 of file medit_io.h.

                                          :
  MeshOutput<MeshBase> (mesh_in),
  _binary (false),
  scalar_idx (0)
{
}

MEDITIO() [2/2]

libMesh::MEDITIO::MEDITIO ( const MeshBase &  mesh_in, unsigned int  c  )

inline

Constructor.

Takes a reference to a constant mesh object. and the desired scalar index for mesh colouring. MEdit seems to understand only one scalar value.

Definition at line 121 of file medit_io.h.

                                                          :
  MeshOutput<MeshBase> (mesh_in),
  _binary    (false),
  scalar_idx (c)
{
}

Member Function Documentation

ascii_precision()

unsigned int & libMesh::MeshOutput< MeshBase >::ascii_precision ( )

inlineinherited

Return/set the precision to use when writing ASCII files.

By default we use numeric_limits<Real>::max_digits10, which should be enough to write out to ASCII and get the exact same Real back when reading in.

Definition at line 269 of file mesh_output.h.

Referenced by libMesh::UNVIO::nodes_out(), libMesh::FroIO::write(), write_ascii(), libMesh::TecplotIO::write_ascii(), libMesh::GMVIO::write_ascii_new_impl(), and libMesh::GMVIO::write_ascii_old_impl().

{
  return _ascii_precision;
}

binary()

bool & libMesh::MEDITIO::binary ( )

inline

Flag indicating whether or not to write a binary file.

Definition at line 130 of file medit_io.h.

References _binary.

Referenced by write(), and write_nodal_data().

{
  return _binary;
}

get_add_sides()

virtual bool libMesh::MeshOutput< MeshBase >::get_add_sides ( )

inlineprotectedvirtualinherited

Returns

Whether or not added sides are expected to be output, to plot SIDE_DISCONTINUOUS data. Subclasses should override this if they are capable of plotting such data.

Reimplemented in libMesh::ExodusII_IO.

Definition at line 176 of file mesh_output.h.

{ return false; }

mesh()

const MeshBase & libMesh::MeshOutput< MeshBase >::mesh ( ) const

inlineprotectedinherited

Returns

The object as a read-only reference.

Definition at line 259 of file mesh_output.h.

References libMesh::libmesh_assert().

Referenced by libMesh::FroIO::write(), libMesh::TecplotIO::write(), write(), libMesh::PostscriptIO::write(), libMesh::EnsightIO::write(), libMesh::TecplotIO::write_ascii(), libMesh::TecplotIO::write_binary(), libMesh::TecplotIO::write_nodal_data(), write_nodal_data(), and libMesh::GnuPlotIO::write_solution().

{
  libmesh_assert(_obj);
  return *_obj;
}

write()

void libMesh::MEDITIO::write ( const std::string &  fname )

overridevirtual

This method implements writing a mesh to a specified ".mesh" file.

Implements libMesh::MeshOutput< MeshBase >.

Definition at line 37 of file medit_io.C.

References binary(), libMesh::MeshOutput< MeshBase >::mesh(), and write_ascii().

Referenced by libMesh::NameBasedIO::write().

{
  if (this->mesh().processor_id() == 0)
    if (!this->binary())
      this->write_ascii  (fname);
}

write_ascii()

void libMesh::MEDITIO::write_ascii ( const std::string &  fname, const std::vector< Number > *  vec = nullptr, const std::vector< std::string > *  solution_names = nullptr  )

private

This method implements writing a mesh with nodal data to a specified file where the nodal data and variable names are optionally provided.

This will write an ASCII file.

Definition at line 59 of file medit_io.C.

References libMesh::MeshOutput< MeshBase >::ascii_precision(), libMesh::MeshTools::Generation::Private::idx(), libMesh::make_range(), libMesh::MeshOutput< MT >::mesh(), libMesh::MeshBase::n_nodes(), n_vars, libMesh::MeshBase::point(), libMesh::QUAD4, libMesh::QUAD9, scalar_idx, libMesh::TET4, and libMesh::TRI3.

Referenced by write(), and write_nodal_data().

{
  // Current lacks in implementation:
  //  (i)   only 3D meshes.
  //  (ii)  only QUAD4, TRI3, TET4 elements, others are omitted !
  //  (iii) no distinction between materials.
  //  (iv)  no vector output, just first scalar as output

  // libmesh_assert three dimensions (should be extended later)
  libmesh_assert_equal_to (MeshOutput<MeshBase>::mesh().mesh_dimension(), 3);

  // Open the output file stream
  std::ofstream out_stream (fname.c_str());

  // Make sure it opened correctly
  if (!out_stream.good())
    libmesh_file_error(fname.c_str());

  // Get a reference to the mesh
  const MeshBase & the_mesh = MeshOutput<MeshBase>::mesh();

  // Begin interfacing with the MEdit data file
  {
    // header:
    out_stream << "MeshVersionFormatted  1\n";
    out_stream << "Dimension  3\n";
    out_stream << "# Mesh generated by libmesh\n\n";

    // write the nodes:
    out_stream << "# Set of mesh vertices\n";
    out_stream << "Vertices\n";
    out_stream << the_mesh.n_nodes() << "\n";

    for (auto v : make_range(the_mesh.n_nodes()))
      out_stream << the_mesh.point(v)(0) << " " << the_mesh.point(v)(1) << " " << the_mesh.point(v)(2) << " 0\n";
  }

  {
    // write the connectivity:
    out_stream << "\n# Set of Polys\n\n";

    // count occurrences of output elements:
    int n_tri3  = 0;
    int n_quad4 = 0;
    int n_tet4  = 0;

    for (const auto & elem : the_mesh.active_element_ptr_range())
      {
        if (elem->type() == TRI3)  n_tri3++;
        if (elem->type() == QUAD4) n_quad4++;
        if (elem->type() == QUAD9) n_quad4+=4; // (QUAD9 is written as 4 QUAD4.)
        if (elem->type() == TET4)  n_tet4++;
      }

    // First: write out TRI3 elements:
    out_stream << "Triangles\n";
    out_stream << n_tri3 << "\n";

    for (const auto & elem : the_mesh.active_element_ptr_range())
      if (elem->type() == TRI3)
        out_stream << elem->node_id(0)+1  << " "
                   << elem->node_id(1)+1  << " "
                   << elem->node_id(2)+1  << " 0\n";

    // Second: write out QUAD4 elements:
    out_stream << "Quadrilaterals\n";
    out_stream << n_quad4 << "\n";

    for (const auto & elem : the_mesh.active_element_ptr_range())
      {
        if (elem->type() == QUAD4)
          {
            out_stream << elem->node_id(0)+1  << " "
                       << elem->node_id(1)+1  << " "
                       << elem->node_id(2)+1  << " "
                       << elem->node_id(3)+1  <<" 0\n";
          } // if
        else if (elem->type() == QUAD9)
          {
            out_stream << elem->node_id(0)+1  << " "
                       << elem->node_id(4)+1  << " "
                       << elem->node_id(8)+1  << " "
                       << elem->node_id(7)+1  <<" 0\n";
            out_stream << elem->node_id(7)+1  << " "
                       << elem->node_id(8)+1  << " "
                       << elem->node_id(6)+1  << " "
                       << elem->node_id(3)+1  <<" 0\n";
            out_stream << elem->node_id(4)+1  << " "
                       << elem->node_id(1)+1  << " "
                       << elem->node_id(5)+1  << " "
                       << elem->node_id(8)+1  <<" 0\n";
            out_stream << elem->node_id(8)+1  << " "
                       << elem->node_id(5)+1  << " "
                       << elem->node_id(2)+1  << " "
                       << elem->node_id(6)+1  <<" 0\n";
          }
      }

    // Third: write out TET4 elements:
    out_stream << "Tetrahedra\n";
    out_stream << n_tet4 << "\n";

    for (const auto & elem : the_mesh.active_element_ptr_range())
      if (elem->type() == TET4)
        {
          out_stream << elem->node_id(0)+1  << " "
                     << elem->node_id(1)+1  << " "
                     << elem->node_id(2)+1  << " "
                     << elem->node_id(3)+1  <<" 0\n";
        }
  }
  // end of the out file
  out_stream << '\n' << "# end of file\n";

  // optionally write the data
  if ((solution_names != nullptr) &&
      (vec != nullptr))
    {
      // Open the ".bb" file stream
      std::size_t idx = fname.find_last_of(".");
      std::string bbname = fname.substr(0,idx) + ".bb";

      std::ofstream bbout (bbname.c_str());

      // Make sure it opened correctly
      if (!bbout.good())
        libmesh_file_error(bbname.c_str());

      // Header: 3: 3D mesh, 1: scalar output, 2: node-indexed
      const std::size_t n_vars = solution_names->size();
      bbout << "3 1 " << the_mesh.n_nodes() << " 2\n";
      for (auto n : make_range(the_mesh.n_nodes()))
        bbout << std::setprecision(this->ascii_precision()) << (*vec)[n*n_vars + scalar_idx] << " ";
      bbout << "\n";
    } // endif
}

write_discontinuous_equation_systems()

void libMesh::MeshOutput< MeshBase >::write_discontinuous_equation_systems ( const std::string &  fname, const EquationSystems &  es, const std::set< std::string > *  system_names = nullptr  )

virtualinherited

This method implements writing a mesh with discontinuous data to a specified file where the data is taken from the EquationSystems object.

Definition at line 89 of file mesh_output.C.

References libMesh::EquationSystems::build_discontinuous_solution_vector(), libMesh::EquationSystems::build_variable_names(), libMesh::EquationSystems::get_mesh(), libMesh::libmesh_assert(), and libMesh::out.

Referenced by libMesh::ExodusII_IO::write_timestep_discontinuous().

{
  LOG_SCOPE("write_discontinuous_equation_systems()", "MeshOutput");

  // We may need to gather and/or renumber a DistributedMesh to output
  // it, making that const qualifier in our constructor a dirty lie
  MT & my_mesh = const_cast<MT &>(*_obj);

  // If we're asked to write data that's associated with a different
  // mesh, output files full of garbage are the result.
  libmesh_assert_equal_to(&es.get_mesh(), _obj);

  // A non-renumbered mesh may not have a contiguous numbering, and
  // that needs to be fixed before we can build a solution vector.
  if (my_mesh.max_elem_id() != my_mesh.n_elem() ||
      my_mesh.max_node_id() != my_mesh.n_nodes())
    {
      // If we were allowed to renumber then we should have already
      // been properly renumbered...
      libmesh_assert(!my_mesh.allow_renumbering());

      libmesh_do_once(libMesh::out <<
                      "Warning:  This MeshOutput subclass only supports meshes which are contiguously renumbered!"
                      << std::endl;);

      my_mesh.allow_renumbering(true);

      my_mesh.renumber_nodes_and_elements();

      // Not sure what good going back to false will do here, the
      // renumbering horses have already left the barn...
      my_mesh.allow_renumbering(false);
    }

  MeshSerializer serialize(const_cast<MT &>(*_obj), !_is_parallel_format, _serial_only_needed_on_proc_0);

  // Build the list of variable names that will be written.
  std::vector<std::string> names;
  es.build_variable_names  (names, nullptr, system_names);

  if (!_is_parallel_format)
    {
      // Build the nodal solution values & get the variable
      // names from the EquationSystems object
      std::vector<Number> soln;
      es.build_discontinuous_solution_vector (soln, system_names,
                                              nullptr, false, /* defaults */
                                              this->get_add_sides());

      this->write_nodal_data_discontinuous (fname, soln, names);
    }
  else // _is_parallel_format
    {
      libmesh_not_implemented();
    }
}

write_equation_systems()

void libMesh::MeshOutput< MeshBase >::write_equation_systems ( const std::string &  fname, const EquationSystems &  es, const std::set< std::string > *  system_names = nullptr  )

virtualinherited

This method implements writing a mesh with data to a specified file where the data is taken from the EquationSystems object.

Reimplemented in libMesh::NameBasedIO.

Definition at line 31 of file mesh_output.C.

References libMesh::EquationSystems::build_solution_vector(), libMesh::EquationSystems::build_variable_names(), libMesh::EquationSystems::get_mesh(), libMesh::libmesh_assert(), and libMesh::out.

Referenced by libMesh::Nemesis_IO::write_timestep(), and libMesh::ExodusII_IO::write_timestep().

{
  LOG_SCOPE("write_equation_systems()", "MeshOutput");

  // We may need to gather and/or renumber a DistributedMesh to output
  // it, making that const qualifier in our constructor a dirty lie
  MT & my_mesh = const_cast<MT &>(*_obj);

  // If we're asked to write data that's associated with a different
  // mesh, output files full of garbage are the result.
  libmesh_assert_equal_to(&es.get_mesh(), _obj);

  // A non-parallel format, non-renumbered mesh may not have a contiguous
  // numbering, and that needs to be fixed before we can build a solution vector.
  if (!_is_parallel_format &&
      (my_mesh.max_elem_id() != my_mesh.n_elem() ||
       my_mesh.max_node_id() != my_mesh.n_nodes()))
    {
      // If we were allowed to renumber then we should have already
      // been properly renumbered...
      libmesh_assert(!my_mesh.allow_renumbering());

      libmesh_do_once(libMesh::out <<
                      "Warning:  This MeshOutput subclass only supports meshes which are contiguously renumbered!"
                      << std::endl;);

      my_mesh.allow_renumbering(true);

      my_mesh.renumber_nodes_and_elements();

      // Not sure what good going back to false will do here, the
      // renumbering horses have already left the barn...
      my_mesh.allow_renumbering(false);
    }

  if (!_is_parallel_format)
    {
      MeshSerializer serialize(const_cast<MT &>(*_obj), !_is_parallel_format, _serial_only_needed_on_proc_0);

      // Build the list of variable names that will be written.
      std::vector<std::string> names;
      es.build_variable_names  (names, nullptr, system_names);

      // Build the nodal solution values & get the variable
      // names from the EquationSystems object
      std::vector<Number> soln;
      es.build_solution_vector (soln, system_names,
                                this->get_add_sides());

      this->write_nodal_data (fname, soln, names);
    }
  else // _is_parallel_format
    this->write_nodal_data (fname, es, system_names);
}

write_nodal_data() [1/3]

void libMesh::MEDITIO::write_nodal_data ( const std::string &  fname, const std::vector< Number > &  soln, const std::vector< std::string > &  names  )

overridevirtual

This method implements writing a mesh with nodal data to a specified file where the nodal data and variable names are provided.

Reimplemented from libMesh::MeshOutput< MeshBase >.

Definition at line 46 of file medit_io.C.

References binary(), libMesh::MeshOutput< MeshBase >::mesh(), and write_ascii().

Referenced by libMesh::NameBasedIO::write_nodal_data().

{
  LOG_SCOPE("write_nodal_data()", "MEDITIO");

  if (this->mesh().processor_id() == 0)
    if (!this->binary())
      this->write_ascii  (fname, &soln, &names);
}

write_nodal_data() [2/3]

void libMesh::MeshOutput< MeshBase >::write_nodal_data ( const std::string &  fname, const NumericVector< Number > &  parallel_soln, const std::vector< std::string > &  names  )

virtualinherited

This method may be overridden by "parallel" output formats for writing nodal data.

Instead of getting a localized copy of the nodal solution vector, it is passed a NumericVector of type=PARALLEL which is in node-major order i.e. (u0,v0,w0, u1,v1,w1, u2,v2,w2, u3,v3,w3, ...) and contains n_nodes*n_vars total entries. Then, it is up to the individual I/O class to extract the required solution values from this vector and write them in parallel.

If not implemented, localizes the parallel vector into a std::vector and calls the other version of this function.

Reimplemented in libMesh::Nemesis_IO.

Definition at line 149 of file mesh_output.C.

References libMesh::NumericVector< T >::localize().

{
  // This is the fallback implementation for parallel I/O formats that
  // do not yet implement proper writing in parallel, and instead rely
  // on the full solution vector being available on all processors.
  std::vector<Number> soln;
  parallel_soln.localize(soln);
  this->write_nodal_data(fname, soln, names);
}

write_nodal_data() [3/3]

void libMesh::MeshOutput< MeshBase >::write_nodal_data ( const std::string &  fname, const EquationSystems &  es, const std::set< std::string > *  system_names  )

virtualinherited

This method should be overridden by "parallel" output formats for writing nodal data.

Instead of getting a localized copy of the nodal solution vector, it directly uses EquationSystems current_local_solution vectors to look up nodal values.

If not implemented, reorders the solutions into a nodal-only NumericVector and calls the above version of this function.

Reimplemented in libMesh::Nemesis_IO.

Definition at line 162 of file mesh_output.C.

References libMesh::EquationSystems::build_parallel_solution_vector(), and libMesh::EquationSystems::build_variable_names().

{
  std::vector<std::string> names;
  es.build_variable_names  (names, nullptr, system_names);

  std::unique_ptr<NumericVector<Number>> parallel_soln =
    es.build_parallel_solution_vector(system_names);

  this->write_nodal_data (fname, *parallel_soln, names);
}

write_nodal_data_discontinuous()

virtual void libMesh::MeshOutput< MeshBase >::write_nodal_data_discontinuous ( const std::string &  , const std::vector< Number > &  , const std::vector< std::string > &    )

inlinevirtualinherited

This method implements writing a mesh with discontinuous data to a specified file where the nodal data and variables names are provided.

Reimplemented in libMesh::ExodusII_IO.

Definition at line 118 of file mesh_output.h.

  { libmesh_not_implemented(); }

Member Data Documentation

_binary

bool libMesh::MEDITIO::_binary

private

Flag to write binary data.

Definition at line 103 of file medit_io.h.

Referenced by binary().

_is_parallel_format

const bool libMesh::MeshOutput< MeshBase >::_is_parallel_format

protectedinherited

Flag specifying whether this format is parallel-capable.

If this is false (default) I/O is only permitted when the mesh has been serialized.

Definition at line 184 of file mesh_output.h.

Referenced by libMesh::FroIO::write(), libMesh::PostscriptIO::write(), and libMesh::EnsightIO::write().

_serial_only_needed_on_proc_0

const bool libMesh::MeshOutput< MeshBase >::_serial_only_needed_on_proc_0

protectedinherited

Flag specifying whether this format can be written by only serializing the mesh to processor zero.

If this is false (default) the mesh will be serialized to all processors

Definition at line 193 of file mesh_output.h.

scalar_idx

unsigned int libMesh::MEDITIO::scalar_idx

private

Definition at line 105 of file medit_io.h.

Referenced by write_ascii().

---

The documentation for this class was generated from the following files:

• include/mesh/medit_io.h
• src/mesh/medit_io.C