libMesh::UCDIO Class Reference

This class implements reading & writing meshes in the AVS's UCD format. More...

#include <ucd_io.h>

Inheritance diagram for libMesh::UCDIO:

Public Member Functions
	UCDIO (MeshBase &mesh)
	Constructor. More...
	UCDIO (const MeshBase &mesh)
	Constructor. More...
virtual void	read (const std::string &) override
	This method implements reading a mesh from a specified file in UCD format. More...
virtual void	write (const std::string &) override
	This method implements writing a mesh to a specified file in UCD format. More...
virtual void	write_nodal_data (const std::string &fname, const std::vector< Number > &soln, const std::vector< std::string > &names) override
	This method implements writing a mesh and solution to a specified file in UCD format. 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 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
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_implementation (std::istream &in_stream)
	The actual implementation of the read function. More...
void	write_implementation (std::ostream &out_stream)
	The actual implementation of the write function. More...
void	write_header (std::ostream &out, const MeshBase &mesh, dof_id_type n_elems, unsigned int n_vars)
	Write UCD format header. More...
void	write_nodes (std::ostream &out, const MeshBase &mesh)
	Write node information. More...
void	write_interior_elems (std::ostream &out, const MeshBase &mesh)
	Write element information. More...
void	write_soln (std::ostream &out, const MeshBase &mesh, const std::vector< std::string > &names, const std::vector< Number > &soln)
	Writes all nodal solution variables. More...

Static Private Member Functions
static std::map< ElemType, std::string >	build_writing_element_map ()
static std::map< std::string, ElemType >	build_reading_element_map ()

Static Private Attributes
static std::map< ElemType, std::string >	_writing_element_map = UCDIO::build_writing_element_map()
static std::map< std::string, ElemType >	_reading_element_map = UCDIO::build_reading_element_map()

Detailed Description

This class implements reading & writing meshes in the AVS's UCD format.

Author

Benjamin S. Kirk

Date

2004

Definition at line 44 of file ucd_io.h.

Constructor & Destructor Documentation

UCDIO() [1/2]

libMesh::UCDIO::UCDIO ( MeshBase &  mesh )

inlineexplicit

Constructor.

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

Definition at line 54 of file ucd_io.h.

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

UCDIO() [2/2]

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

inlineexplicit

Constructor.

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

Definition at line 64 of file ucd_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::MEDITIO::write_ascii(), libMesh::TecplotIO::write_ascii(), libMesh::GMVIO::write_ascii_new_impl(), and libMesh::GMVIO::write_ascii_old_impl().

{
  return _ascii_precision;
}

build_reading_element_map()

std::map< std::string, ElemType > libMesh::UCDIO::build_reading_element_map ( )

staticprivate

Definition at line 70 of file ucd_io.C.

References libMesh::EDGE2, libMesh::HEX8, libMesh::PRISM6, libMesh::PYRAMID5, libMesh::QUAD4, libMesh::TET4, and libMesh::TRI3.

{
  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;
}

build_writing_element_map()

std::map< ElemType, std::string > libMesh::UCDIO::build_writing_element_map ( )

staticprivate

Definition at line 54 of file ucd_io.C.

References libMesh::EDGE2, libMesh::HEX8, libMesh::PRISM6, libMesh::PYRAMID5, libMesh::QUAD4, libMesh::TET4, and libMesh::TRI3.

{
  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;
}

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(), libMesh::TetGenIO::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(), libMesh::TetGenIO::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::Nemesis_IO::read(), libMesh::ExodusII_IO::read(), libMesh::XdrIO::read(), libMesh::CheckpointIO::read(), libMesh::VTKIO::read(), libMesh::CheckpointIO::read_bcs(), libMesh::CheckpointIO::read_connectivity(), libMesh::ExodusII_IO::read_header(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), 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::TetGenIO::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(), write_header(), write_implementation(), write_interior_elems(), libMesh::GmshIO::write_mesh(), 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(), 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(), 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;
}

read()

void libMesh::UCDIO::read ( const std::string &  file_name )

overridevirtual

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

Implements libMesh::MeshInput< MeshBase >.

Definition at line 84 of file ucd_io.C.

References read_implementation().

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

{
  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);
    }
}

read_implementation()

void libMesh::UCDIO::read_implementation ( std::istream &  in_stream )

private

The actual implementation of the read function.

The public read interface simply decides which type of stream to pass the implementation.

Definition at line 126 of file ucd_io.C.

References _reading_element_map, libMesh::MeshBase::add_elem(), libMesh::MeshBase::add_point(), libMesh::Elem::build(), libMesh::MeshInput< MeshBase >::elems_of_dimension, libMesh::libmesh_assert(), libMesh::MeshInput< MeshBase >::mesh(), libMesh::MeshInput< MT >::mesh(), libMesh::MeshBase::mesh_dimension(), libMesh::MeshBase::n_nodes(), libMesh::MeshBase::node_ptr(), libMesh::MeshBase::set_mesh_dimension(), and libMesh::MeshInput< MeshBase >::skip_comment_lines().

Referenced by read().

{
  // 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.
        auto elem = Elem::build(et);

        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 (std::move(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
    libmesh_error_msg_if(mesh.mesh_dimension() > LIBMESH_DIM,
                         "Cannot open dimension "
                         << mesh.mesh_dimension()
                         << " mesh file when configured without "
                         << mesh.mesh_dimension()
                         << "D support.");
#endif
  }
}

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 libMesh::TetGenIO::read(), and 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::UCDIO::write ( const std::string &  file_name )

overridevirtual

This method implements writing a mesh to a specified file in UCD format.

Implements libMesh::MeshOutput< MeshBase >.

Definition at line 105 of file ucd_io.C.

References write_implementation().

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

{
  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);
    }
}

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_header()

void libMesh::UCDIO::write_header ( std::ostream &  out, const MeshBase &  mesh, dof_id_type  n_elems, unsigned int  n_vars  )

private

Write UCD format header.

Definition at line 274 of file ucd_io.C.

References libMesh::libmesh_assert(), libMesh::MeshInput< MeshBase >::mesh(), libMesh::MeshBase::n_nodes(), and n_vars.

Referenced by write_implementation(), and write_nodal_data().

{
  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";
}

write_implementation()

void libMesh::UCDIO::write_implementation ( std::ostream &  out_stream )

private

The actual implementation of the write function.

The public write interface simply decides which type of stream to pass the implementation.

Definition at line 251 of file ucd_io.C.

References libMesh::libmesh_assert(), libMesh::MeshInput< MeshBase >::mesh(), libMesh::MeshOutput< MT >::mesh(), libMesh::MeshBase::mesh_dimension(), libMesh::MeshBase::n_elem(), write_header(), write_interior_elems(), and write_nodes().

Referenced by write().

{
  libmesh_assert (out_stream.good());

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

  // UCD doesn't work any dimension except 3?
  libmesh_error_msg_if(mesh.mesh_dimension() != 3,
                       "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);
}

write_interior_elems()

void libMesh::UCDIO::write_interior_elems ( std::ostream &  out, const MeshBase &  mesh  )

private

Write element information.

Definition at line 311 of file ucd_io.C.

References _writing_element_map, libMesh::libmesh_assert(), libMesh::MeshInput< MeshBase >::mesh(), and libMesh::UCD.

Referenced by write_implementation(), and write_nodal_data().

{
  // 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);
    }
}

write_nodal_data() [1/3]

void libMesh::UCDIO::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 and solution to a specified file in UCD format.

This is internally called by MeshOutput::write_equation_systems

Reimplemented from libMesh::MeshOutput< MeshBase >.

Definition at line 333 of file ucd_io.C.

References libMesh::libmesh_assert(), libMesh::MeshInput< MeshBase >::mesh(), libMesh::MeshOutput< MT >::mesh(), libMesh::MeshBase::mesh_dimension(), libMesh::MeshTools::n_elem(), libMesh::MeshBase::n_elem(), libMesh::ParallelObject::processor_id(), write_header(), write_interior_elems(), write_nodes(), and write_soln().

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

{
  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);
}

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(); }

write_nodes()

void libMesh::UCDIO::write_nodes ( std::ostream &  out, const MeshBase &  mesh  )

private

Write node information.

Definition at line 293 of file ucd_io.C.

References libMesh::libmesh_assert(), and libMesh::MeshInput< MeshBase >::mesh().

Referenced by write_implementation(), and write_nodal_data().

{
  // 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);
    }
}

write_soln()

void libMesh::UCDIO::write_soln ( std::ostream &  out, const MeshBase &  mesh, const std::vector< std::string > &  names, const std::vector< Number > &  soln  )

private

Writes all nodal solution variables.

Definition at line 366 of file ucd_io.C.

References libMesh::MeshTools::Generation::Private::idx(), libMesh::libmesh_assert(), libMesh::MeshInput< MeshBase >::mesh(), libMesh::MeshBase::n_nodes(), and libMesh::Quality::name().

Referenced by write_nodal_data().

{
  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;
    }
}

Member Data Documentation

_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().

_reading_element_map

std::map< std::string, ElemType > libMesh::UCDIO::_reading_element_map = UCDIO::build_reading_element_map()

staticprivate

Definition at line 145 of file ucd_io.h.

Referenced by read_implementation().

_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.

_writing_element_map

std::map< ElemType, std::string > libMesh::UCDIO::_writing_element_map = UCDIO::build_writing_element_map()

staticprivate

Definition at line 141 of file ucd_io.h.

Referenced by write_interior_elems().

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(), read_implementation(), libMesh::UNVIO::read_implementation(), and libMesh::XdrIO::read_serialized_connectivity().

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

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