libMesh::TetGenIO Class Reference

This class implements reading and writing meshes in the TetGen format. More...

#include <tetgen_io.h>

Inheritance diagram for libMesh::TetGenIO:

Public Member Functions
	TetGenIO (MeshBase &mesh)
	Constructor. More...
	TetGenIO (const MeshBase &mesh)
	Constructor. More...
virtual void	read (const std::string &) override
	This method implements reading a mesh from a specified file in TetGen format. More...
virtual void	write (const std::string &) override
	This method implements writing a mesh to a specified ".poly" file. More...
bool	is_parallel_format () const
	Returns true iff this mesh file format and input class are parallelized, so that all processors can read their share of the data at once. 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 std::vector< Number > &, const std::vector< std::string > &)
	This method implements writing a mesh with nodal data to a specified file where the nodal data and variable names are provided. 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...

Public Attributes
std::vector< std::vector< Real > >	node_attributes
	Data structure to hold node attributes read in from file. More...

Protected Member Functions
MeshBase &	mesh ()
void	set_n_partitions (unsigned int n_parts)
	Sets the number of partitions in the mesh. More...
void	skip_comment_lines (std::istream &in, const char comment_start)
	Reads input from in, skipping all the lines that start with the character comment_start. More...
const MeshBase &	mesh () const
virtual bool	get_add_sides ()

Protected Attributes
std::vector< bool >	elems_of_dimension
	A vector of bools describing what dimension elements have been encountered when reading a mesh. More...
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	read_nodes_and_elem (std::istream &node_stream, std::istream &ele_stream)
	Reads a mesh (nodes & elements) from the file provided through node_stream and ele_stream. More...
void	node_in (std::istream &node_stream)
	Method reads nodes from node_stream and stores them in vector<Node *> nodes in the order they come in. More...
void	element_in (std::istream &ele_stream)
	Method reads elements and stores them in vector<Elem *> elements in the same order as they come in. More...

Private Attributes
std::map< dof_id_type, dof_id_type >	_assign_nodes
	stores new positions of nodes. More...
dof_id_type	_num_nodes
	total number of nodes. More...
dof_id_type	_num_elements
	total number of elements. More...

Detailed Description

This class implements reading and writing meshes in the TetGen format.

Format description: cf. TetGen home page.

Author

Benjamin S. Kirk

Date

2004

Definition at line 47 of file tetgen_io.h.

Constructor & Destructor Documentation

TetGenIO() [1/2]

libMesh::TetGenIO::TetGenIO ( MeshBase &  mesh )

inlineexplicit

Constructor.

Takes a writable reference to a mesh object. This is the constructor required to read a mesh.

Definition at line 138 of file tetgen_io.h.

                                   :
  MeshInput<MeshBase> (mesh),
  MeshOutput<MeshBase>(mesh)
{
}

TetGenIO() [2/2]

libMesh::TetGenIO::TetGenIO ( const MeshBase &  mesh )

inlineexplicit

Constructor.

Takes a read-only reference to a mesh object. This is the constructor required to write a mesh.

Definition at line 147 of file tetgen_io.h.

                                         :
  MeshOutput<MeshBase>(mesh)
{
}

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(), libMesh::STLIO::write(), libMesh::MEDITIO::write_ascii(), libMesh::TecplotIO::write_ascii(), libMesh::GMVIO::write_ascii_new_impl(), and libMesh::GMVIO::write_ascii_old_impl().

{
  return _ascii_precision;
}

element_in()

void libMesh::TetGenIO::element_in ( std::istream &  ele_stream )

private

Method reads elements and stores them in vector<Elem *> elements in the same order as they come in.

Within TetGenMeshInterface, element labels are ignored.

Definition at line 186 of file tetgen_io.C.

References _assign_nodes, _num_elements, libMesh::MeshBase::add_elem(), libMesh::Elem::build_with_id(), libMesh::libmesh_assert(), libMesh::MeshInput< MeshBase >::mesh(), libMesh::MeshInput< MT >::mesh(), n_nodes, libMesh::MeshBase::node_ptr(), libMesh::TET10, and libMesh::TET4.

Referenced by read_nodes_and_elem().

{
  // Check input buffer
  libmesh_assert (ele_stream.good());

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

  // Read the elements from the ele_stream (*.ele file).
  unsigned int element_lab=0, n_nodes=0, region_attribute=0;

  ele_stream >> _num_elements // Read the number of tetrahedrons from the stream.
             >> n_nodes       // Read the number of nodes per tetrahedron from the stream (defaults to 4).
             >> region_attribute; // Read the number of attributes from stream.

  // According to the Tetgen docs for .ele files:
  // http://wias-berlin.de/software/tetgen/1.5/doc/manual/manual006.html#ff_ele
  // region_attribute can either 0 or 1, and specifies whether, for
  // each tetrahedron, there is an extra integer specifying which
  // region it belongs to. Normally, this id matches a value in a
  // corresponding .poly or .smesh file, but here we simply use it to
  // set the subdomain_id of the element in question.
  libmesh_error_msg_if(region_attribute > 1,
                       "Invalid region_attribute " << region_attribute << " specified in .ele file.");

  // Vector that maps Tetgen node numbering to libMesh node numbering. Tet4s are
  // numbered identically, but Tet10s are not.
  static const unsigned int assign_elm_nodes[] = {0, 1, 2, 3, 9, 7, 4, 5, 8, 6};

  for (dof_id_type i=0; i<_num_elements; i++)
    {
      libmesh_assert (ele_stream.good());

      // TetGen only supports Tet4 and Tet10 elements.
      Elem * elem = nullptr;

      if (n_nodes==4)
        elem = mesh.add_elem(Elem::build_with_id(TET4, i));

      else if (n_nodes==10)
        elem = mesh.add_elem(Elem::build_with_id(TET10, i));

      else
        libmesh_error_msg("Elements with " << n_nodes <<
                          " nodes are not supported in the LibMesh tetgen module.");

      libmesh_assert(elem);
      libmesh_assert_equal_to (elem->n_nodes(), n_nodes);

      // The first number on the line is the tetrahedron number. We
      // have previously ignored this, preferring to set our own ids,
      // but this could be changed to respect the Tetgen numbering if
      // desired.
      ele_stream >> element_lab;

      // Read node labels
      for (dof_id_type j=0; j<n_nodes; j++)
        {
          dof_id_type node_label;
          ele_stream >> node_label;

          // Assign node to element
          elem->set_node(assign_elm_nodes[j],
            mesh.node_ptr(_assign_nodes[node_label]));
        }

      // Read the region attribute (if present) and use it to set the subdomain id.
      if (region_attribute)
        {
          unsigned int region;
          ele_stream >> region;

          // Make sure that the id we read can be successfully cast to
          // an integral value of type subdomain_id_type.
          elem->subdomain_id() = cast_int<subdomain_id_type>(region);
        }
    }
}

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; }

is_parallel_format()

bool libMesh::MeshInput< MeshBase >::is_parallel_format ( ) const

inlineinherited

Returns true iff this mesh file format and input class are parallelized, so that all processors can read their share of the data at once.

Definition at line 87 of file mesh_input.h.

References libMesh::MeshInput< MT >::_is_parallel_format.

{ return this->_is_parallel_format; }

mesh() [1/2]

MeshBase & libMesh::MeshInput< MeshBase >::mesh ( )

inlineprotectedinherited

Returns

The object as a writable reference.

Definition at line 178 of file mesh_input.h.

Referenced by libMesh::GMVIO::_read_one_cell(), libMesh::VTKIO::cells_to_vtk(), libMesh::ExodusII_IO::copy_elemental_solution(), libMesh::Nemesis_IO::copy_elemental_solution(), libMesh::ExodusII_IO::copy_nodal_solution(), element_in(), libMesh::UNVIO::elements_in(), libMesh::UNVIO::elements_out(), libMesh::VTKIO::get_local_node_values(), libMesh::ExodusII_IO::get_sideset_data_indices(), libMesh::UNVIO::groups_in(), node_in(), libMesh::UNVIO::nodes_in(), libMesh::UNVIO::nodes_out(), libMesh::VTKIO::nodes_to_vtk(), libMesh::Nemesis_IO::prepare_to_write_nodal_data(), libMesh::GMVIO::read(), libMesh::STLIO::read(), libMesh::Nemesis_IO::read(), libMesh::XdrIO::read(), libMesh::ExodusII_IO::read(), libMesh::CheckpointIO::read(), libMesh::VTKIO::read(), libMesh::STLIO::read_ascii(), libMesh::CheckpointIO::read_bcs(), libMesh::STLIO::read_binary(), libMesh::CheckpointIO::read_connectivity(), libMesh::ExodusII_IO::read_header(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::UCDIO::read_implementation(), libMesh::UNVIO::read_implementation(), libMesh::GmshIO::read_mesh(), libMesh::DynaIO::read_mesh(), libMesh::CheckpointIO::read_nodes(), libMesh::CheckpointIO::read_nodesets(), libMesh::CheckpointIO::read_remote_elem(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::ExodusII_IO::read_sideset_data(), libMesh::OFFIO::read_stream(), libMesh::MatlabIO::read_stream(), libMesh::CheckpointIO::read_subdomain_names(), libMesh::STLIO::write(), write(), libMesh::Nemesis_IO::write(), libMesh::XdrIO::write(), libMesh::CheckpointIO::write(), libMesh::ExodusII_IO::write(), libMesh::GMVIO::write_ascii_new_impl(), libMesh::GMVIO::write_ascii_old_impl(), libMesh::GMVIO::write_binary(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::Nemesis_IO::write_element_data(), libMesh::ExodusII_IO::write_element_data(), libMesh::ExodusII_IO::write_elemsets(), libMesh::UCDIO::write_header(), libMesh::UCDIO::write_implementation(), libMesh::UCDIO::write_interior_elems(), libMesh::GmshIO::write_mesh(), libMesh::UCDIO::write_nodal_data(), libMesh::VTKIO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data_common(), libMesh::ExodusII_IO::write_nodal_data_discontinuous(), libMesh::UCDIO::write_nodes(), libMesh::CheckpointIO::write_nodesets(), libMesh::XdrIO::write_parallel(), libMesh::GmshIO::write_post(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), libMesh::XdrIO::write_serialized_nodesets(), libMesh::XdrIO::write_serialized_subdomain_names(), libMesh::ExodusII_IO::write_sideset_data(), libMesh::UCDIO::write_soln(), and libMesh::CheckpointIO::write_subdomain_names().

{
  libmesh_error_msg_if(_obj == nullptr, "ERROR: _obj should not be nullptr!");
  return *_obj;
}

mesh() [2/2]

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

{
  libmesh_assert(_obj);
  return *_obj;
}

node_in()

void libMesh::TetGenIO::node_in ( std::istream &  node_stream )

private

Method reads nodes from node_stream and stores them in vector<Node *> nodes in the order they come in.

The original node labels are being stored in the map _assign_nodes in order to assign the elements to the right nodes later.

Definition at line 115 of file tetgen_io.C.

References _assign_nodes, _num_nodes, libMesh::MeshBase::add_point(), libMesh::libmesh_assert(), libMesh::MeshInput< MT >::mesh(), libMesh::MeshInput< MeshBase >::mesh(), node_attributes, and libMesh::Real.

Referenced by read_nodes_and_elem().

{
  // Check input buffer
  libmesh_assert (node_stream.good());

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

  unsigned int dimension=0, nAttributes=0, BoundaryMarkers=0;

  node_stream >> _num_nodes       // Read the number of nodes from the stream
              >> dimension        // Read the dimension from the stream
              >> nAttributes      // Read the number of attributes from stream
              >> BoundaryMarkers; // Read if or not boundary markers are included in *.node (0 or 1)

  // Read the nodal coordinates from the node_stream (*.node file).
  unsigned int node_lab=0;
  Real dummy;

  // If present, make room for node attributes to be stored.
  this->node_attributes.resize(nAttributes);
  for (unsigned i=0; i<nAttributes; ++i)
    this->node_attributes[i].resize(_num_nodes);


  for (unsigned int i=0; i<_num_nodes; i++)
    {
      // Check input buffer
      libmesh_assert (node_stream.good());

      std::array<Real, 3> xyz;

      node_stream >> node_lab  // node number
                  >> xyz[0]    // x-coordinate value
                  >> xyz[1]    // y-coordinate value
                  >> xyz[2];   // z-coordinate value

      // Read and store attributes from the stream.
      for (unsigned int j=0; j<nAttributes; j++)
        node_stream >> node_attributes[j][i];

      // Read (and discard) boundary marker if BoundaryMarker=1.
      // TODO: should we store this somehow?
      if (BoundaryMarkers == 1)
        node_stream >> dummy;

      // Store the new position of the node under its label.
      //_assign_nodes.emplace(node_lab,i);
      _assign_nodes[node_lab] = i;

      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

      // Add this point to the Mesh.
      mesh.add_point(p, i);
    }
}

read()

void libMesh::TetGenIO::read ( const std::string &  name )

overridevirtual

This method implements reading a mesh from a specified file in TetGen format.

Implements libMesh::MeshInput< MeshBase >.

Definition at line 36 of file tetgen_io.C.

References libMesh::Utility::contains(), libMesh::MeshInput< MT >::mesh(), libMesh::Quality::name(), libMesh::out, read_nodes_and_elem(), and libMesh::MeshInput< MeshBase >::skip_comment_lines().

Referenced by libMesh::NameBasedIO::read(), and MeshInputTest::testTetgenIO().

{
  // 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);

  std::string name_node, name_ele, dummy;

  // tetgen only works in 3D
  MeshInput<MeshBase>::mesh().set_mesh_dimension(3);

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

  // Check name for *.node or *.ele extension.
  // Set std::istream for node_stream and ele_stream.
  //
  if (Utility::contains(name, ".node"))
    {
      name_node            = name;
      dummy                = name;
      std::size_t position = dummy.rfind(".node");
      name_ele             = dummy.replace(position, 5, ".ele");
    }
  else if (Utility::contains(name, ".ele"))
    {
      name_ele = name;
      dummy    = name;
      std::size_t position = dummy.rfind(".ele");
      name_node    = dummy.replace(position, 4, ".node");
    }
  else
    libmesh_error_msg("ERROR: Unrecognized file name: " << name);



  // Set the streams from which to read in
  std::ifstream node_stream (name_node.c_str());
  std::ifstream ele_stream  (name_ele.c_str());

  libmesh_error_msg_if(!node_stream.good() || !ele_stream.good(),
                       "Error while opening either "
                       << name_node
                       << " or "
                       << name_ele);

  libMesh::out<< "TetGenIO found the tetgen files to read " <<std::endl;

  // Skip the comment lines at the beginning
  this->skip_comment_lines (node_stream, '#');
  this->skip_comment_lines (ele_stream, '#');

  // Read the nodes and elements from the streams
  this->read_nodes_and_elem (node_stream, ele_stream);
  libMesh::out<< "TetGenIO read in nodes and elements " <<std::endl;
}

read_nodes_and_elem()

void libMesh::TetGenIO::read_nodes_and_elem ( std::istream &  node_stream, std::istream &  ele_stream  )

private

Reads a mesh (nodes & elements) from the file provided through node_stream and ele_stream.

Definition at line 97 of file tetgen_io.C.

References _assign_nodes, _num_elements, _num_nodes, element_in(), and node_in().

Referenced by read().

{
  _num_nodes    = 0;
  _num_elements = 0;

  // Read all the datasets.
  this->node_in    (node_stream);
  this->element_in (ele_stream);

  // some more clean-up
  _assign_nodes.clear();
}

set_n_partitions()

void libMesh::MeshInput< MeshBase >::set_n_partitions ( unsigned int  n_parts )

inlineprotectedinherited

Sets the number of partitions in the mesh.

Typically this gets done by the partitioner, but some parallel file formats begin "pre-partitioned".

Definition at line 101 of file mesh_input.h.

References libMesh::MeshInput< MT >::mesh().

Referenced by libMesh::Nemesis_IO::read(), and libMesh::XdrIO::read_header().

{ this->mesh().set_n_partitions() = n_parts; }

skip_comment_lines()

void libMesh::MeshInput< MeshBase >::skip_comment_lines ( std::istream &  in, const char  comment_start  )

protectedinherited

Reads input from in, skipping all the lines that start with the character comment_start.

Definition at line 187 of file mesh_input.h.

Referenced by read(), and libMesh::UCDIO::read_implementation().

{
  char c, line[256];

  while (in.get(c), c==comment_start)
    in.getline (line, 255);

  // put back first character of
  // first non-comment line
  in.putback (c);
}

write()

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

overridevirtual

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

".poly" files defines so called Piecewise Linear Complex (PLC).

Implements libMesh::MeshOutput< MeshBase >.

Definition at line 270 of file tetgen_io.C.

References libMesh::Utility::contains(), libMesh::make_range(), libMesh::MeshInput< MeshBase >::mesh(), libMesh::MeshOutput< MT >::mesh(), libMesh::MeshBase::n_elem(), libMesh::MeshBase::n_nodes(), and libMesh::MeshBase::point().

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

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

  libmesh_error_msg_if(!Utility::contains(fname, ".poly"),
                       "ERROR: Unrecognized file name: " << fname);

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

  // Begin interfacing with the .poly file
  {
    // header:
    out_stream << "# poly file output generated by libmesh\n"
               << mesh.n_nodes() << " 3 0 0\n";

    // write the nodes:
    for (auto v : make_range(mesh.n_nodes()))
      out_stream << v << " "
                 << mesh.point(v)(0) << " "
                 << mesh.point(v)(1) << " "
                 << mesh.point(v)(2) << "\n";
  }

  {
    // write the connectivity:
    out_stream << "# Facets:\n"
               << mesh.n_elem() << " 0\n";

    for (const auto & elem : mesh.active_element_ptr_range())
      out_stream << "1\n3 " // no. of facet polygons
        //  << elem->n_nodes() << " "
                 << elem->node_id(0)   << " "
                 << elem->node_id(1)   << " "
                 << elem->node_id(2)   << "\n";
  }

  // end of the file
  out_stream << "0\n"; // no holes output!
  out_stream << "\n\n# end of file\n";
}

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::ExodusII_IO, and 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().

{
  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]

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

inlinevirtualinherited

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

Reimplemented in libMesh::ExodusII_IO, libMesh::Nemesis_IO, libMesh::GmshIO, libMesh::NameBasedIO, libMesh::VTKIO, libMesh::UCDIO, libMesh::GMVIO, libMesh::MEDITIO, libMesh::GnuPlotIO, and libMesh::TecplotIO.

Definition at line 109 of file mesh_output.h.

  { libmesh_not_implemented(); }

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

_assign_nodes

std::map<dof_id_type,dof_id_type> libMesh::TetGenIO::_assign_nodes

private

stores new positions of nodes.

Used when reading.

Definition at line 120 of file tetgen_io.h.

Referenced by element_in(), node_in(), and read_nodes_and_elem().

_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().

_num_elements

dof_id_type libMesh::TetGenIO::_num_elements

private

total number of elements.

Primarily used when reading.

Definition at line 130 of file tetgen_io.h.

Referenced by element_in(), and read_nodes_and_elem().

_num_nodes

dof_id_type libMesh::TetGenIO::_num_nodes

private

total number of nodes.

Primarily used when reading.

Definition at line 125 of file tetgen_io.h.

Referenced by node_in(), and read_nodes_and_elem().

_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.

elems_of_dimension

std::vector<bool> libMesh::MeshInput< MeshBase >::elems_of_dimension

protectedinherited

A vector of bools describing what dimension elements have been encountered when reading a mesh.

Definition at line 107 of file mesh_input.h.

Referenced by libMesh::GMVIO::_read_one_cell(), libMesh::UNVIO::elements_in(), libMesh::UNVIO::max_elem_dimension_seen(), libMesh::AbaqusIO::max_elem_dimension_seen(), libMesh::AbaqusIO::read(), libMesh::GMVIO::read(), libMesh::Nemesis_IO::read(), libMesh::ExodusII_IO::read(), libMesh::VTKIO::read(), libMesh::AbaqusIO::read_elements(), libMesh::UCDIO::read_implementation(), libMesh::UNVIO::read_implementation(), and libMesh::XdrIO::read_serialized_connectivity().

node_attributes

std::vector<std::vector<Real> > libMesh::TetGenIO::node_attributes

Data structure to hold node attributes read in from file.

What you do with these is up to you!

Definition at line 82 of file tetgen_io.h.

Referenced by node_in().

---

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

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