libMesh::NameBasedIO Class Reference

This class supports simple reads and writes in any libMesh-supported format, by dispatching to one of the other I/O classes based on filename. More...

#include <namebased_io.h>

Inheritance diagram for libMesh::NameBasedIO:

Public Member Functions
	NameBasedIO (const MeshBase &)
	Constructor. More...
	NameBasedIO (MeshBase &)
	Constructor. More...
virtual void	read (const std::string &mesh_file) override
	This method implements reading a mesh from a specified file. More...
virtual void	write (const std::string &mesh_file) override
	This method implements writing a mesh to a specified file. More...
virtual void	write_equation_systems (const std::string &filename, const EquationSystems &es, const std::set< std::string > *system_names=nullptr) override
	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_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	is_parallel_file_format (std::string_view filename)
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_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...

Detailed Description

This class supports simple reads and writes in any libMesh-supported format, by dispatching to one of the other I/O classes based on filename.

Other I/O classes may have more advanced features that are not accessible via this interface.

Author

Roy H. Stogner

Date

2015

Definition at line 44 of file namebased_io.h.

Constructor & Destructor Documentation

NameBasedIO() [1/2]

libMesh::NameBasedIO::NameBasedIO ( 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 110 of file namebased_io.h.

                                               :
  MeshOutput<MeshBase>    (mesh)
{
}

NameBasedIO() [2/2]

libMesh::NameBasedIO::NameBasedIO ( MeshBase &  mesh )

inlineexplicit

Constructor.

Takes a writable reference to a mesh object. This constructor is required to let us read in a mesh.

Definition at line 116 of file namebased_io.h.

                                         :
  MeshInput<MeshBase> (mesh),
  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;
}

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_file_format()

bool libMesh::NameBasedIO::is_parallel_file_format ( std::string_view  filename )

inline

Definition at line 124 of file namebased_io.h.

References libMesh::Quality::name().

Referenced by read(), and write().

{
  return ((name.rfind(".xda") < name.size()) ||
          (name.rfind(".xdr") < name.size()) ||
          (name.rfind(".nem") == name.size() - 4) ||
          (name.rfind(".n") == name.size() - 2) ||
          (name.rfind(".cp") < name.size())
          );
}

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::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(), 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(), 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;
}

read()

void libMesh::NameBasedIO::read ( const std::string &  mesh_file )

overridevirtual

This method implements reading a mesh from a specified file.

Implements libMesh::MeshInput< MeshBase >.

Definition at line 69 of file namebased_io.C.

References libMesh::MeshBase::allow_renumbering(), libMesh::Utility::basename_of(), libMesh::XdrIO::binary(), libMesh::MeshCommunication::broadcast(), is_parallel_file_format(), libMesh::XdrIO::legacy(), libMesh::MeshInput< MT >::mesh(), libMesh::ParallelObject::n_processors(), libMesh::Quality::name(), libMesh::ParallelObject::processor_id(), libMesh::OFFIO::read(), libMesh::AbaqusIO::read(), libMesh::TetGenIO::read(), libMesh::UCDIO::read(), libMesh::GMVIO::read(), libMesh::STLIO::read(), libMesh::UNVIO::read(), libMesh::Nemesis_IO::read(), libMesh::GmshIO::read(), libMesh::DynaIO::read(), libMesh::XdrIO::read(), libMesh::MatlabIO::read(), libMesh::ExodusII_IO::read(), libMesh::CheckpointIO::read(), and libMesh::VTKIO::read().

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

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

  const std::string_view basename = Utility::basename_of(name);

  // See if the file exists.  Perform this check on all processors
  // so that the code is terminated properly in the case that the
  // file does not exist.

  // For Nemesis files, the name we try to read will have suffixes
  // identifying processor rank
  if (basename.rfind(".nem") == basename.size() - 4 ||
      basename.rfind(".n") == basename.size() - 2)
    {
      std::ostringstream full_name;

      // Find the length of a string which represents the highest processor ID
      full_name << (mymesh.n_processors());
      int field_width = cast_int<int>(full_name.str().size());

      // reset the string stream
      full_name.str("");

      // And build up the full filename
      full_name << name
                << '.' << mymesh.n_processors()
                << '.' << std::setfill('0') << std::setw(field_width) << mymesh.processor_id();

      std::ifstream in (full_name.str().c_str());
      libmesh_error_msg_if(!in.good(), "ERROR: cannot locate specified file:\n\t" << full_name.str());
    }
  else if (basename.rfind(".cp")) {} // Do error checking in the reader
  else
    {
      std::ifstream in (name.c_str());
      libmesh_error_msg_if(!in.good(), "ERROR: cannot locate specified file:\n\t" << name);
    }

  // Look for parallel formats first
  if (is_parallel_file_format(basename))
    {
      // no need to handle bz2 files here -- the Xdr class does that.
      if ((basename.rfind(".xda") < basename.size()) ||
          (basename.rfind(".xdr") < basename.size()))
        {
          XdrIO xdr_io(mymesh);

          // .xda* ==> bzip2/gzip/ASCII flavors
          if (basename.rfind(".xda") < basename.size())
            {
              xdr_io.binary() = false;
              xdr_io.read (name);
            }
          else // .xdr* ==> true binary XDR file
            {
              xdr_io.binary() = true;
              xdr_io.read (name);
            }

          // The xdr_io object gets constructed with legacy() == false.
          // if legacy() == true then it means that a legacy file was detected and
          // thus processor 0 performed the read. We therefore need to broadcast the
          // mesh.  Further, for this flavor of mesh solution data ordering is tied
          // to the node ordering, so we better not reorder the nodes!
          if (xdr_io.legacy())
            {
              mymesh.allow_renumbering(false);
              MeshCommunication().broadcast(mymesh);
            }

          // libHilbert-enabled libMesh builds should construct files
          // with a canonical node ordering, which libHilbert-enabled
          // builds will be able to read in again regardless of any
          // renumbering.  So in that case we're free to renumber.
          // However, if either the writer or the reader of this file
          // don't have libHilbert, then we'll have to skip
          // renumbering because we need the numbering to remain
          // consistent with any solution file we read in next.
#ifdef LIBMESH_HAVE_LIBHILBERT
          // if (!xdr_io.libhilbert_ordering())
          //   skip_renumber_nodes_and_elements = true;
#else
          mymesh.allow_renumbering(false);
#endif
        }
      else if (basename.rfind(".nem") < basename.size() ||
               basename.rfind(".n")   < basename.size())
        Nemesis_IO(mymesh).read (name);
      else if (basename.rfind(".cp") < basename.size())
        {
          if (basename.rfind(".cpa") < basename.size())
            CheckpointIO(mymesh, false).read(name);
          else
            CheckpointIO(mymesh, true).read(name);
        }
    }

  // Serial mesh formats
  else
    {
      // Read the file based on extension.  Only processor 0
      // needs to read the mesh.  It will then broadcast it and
      // the other processors will pick it up
      if (mymesh.processor_id() == 0)
        {
          LOG_SCOPE("read()", "NameBasedIO");

          std::ostringstream pid_suffix;
          pid_suffix << '_' << getpid();
          // Nasty hack for reading/writing zipped files
          std::string new_name = name;
          if (name.rfind(".bz2") == name.size() - 4)
            {
#ifdef LIBMESH_HAVE_BZIP
              new_name.erase(new_name.end() - 4, new_name.end());
              new_name += pid_suffix.str();
              std::string system_string = "bunzip2 -f -k -c ";
              system_string += name + " > " + new_name;
              LOG_SCOPE("system(bunzip2)", "NameBasedIO");
              if (std::system(system_string.c_str()))
                libmesh_file_error(system_string);
#else
              libmesh_error_msg("ERROR: need bzip2/bunzip2 to open .bz2 file " << name);
#endif
            }
          else if (name.rfind(".xz") == name.size() - 3)
            {
#ifdef LIBMESH_HAVE_XZ
              new_name.erase(new_name.end() - 3, new_name.end());
              new_name += pid_suffix.str();
              std::string system_string = "xz -f -d -k -c ";
              system_string += name + " > " + new_name;
              LOG_SCOPE("system(xz -d)", "XdrIO");
              if (std::system(system_string.c_str()))
                libmesh_file_error(system_string);
#else
              libmesh_error_msg("ERROR: need xz to open .xz file " << name);
#endif
            }

          if (basename.rfind(".mat") < basename.size())
            MatlabIO(mymesh).read(new_name);

          else if (basename.rfind(".ucd") < basename.size())
            UCDIO(mymesh).read (new_name);

          else if ((basename.rfind(".off")  < basename.size()) ||
                   (basename.rfind(".ogl")  < basename.size()) ||
                   (basename.rfind(".oogl") < basename.size()))
            OFFIO(mymesh).read (new_name);

          else if (basename.rfind(".unv") < basename.size())
            UNVIO(mymesh).read (new_name);

          else if ((basename.rfind(".node")  < basename.size()) ||
                   (basename.rfind(".ele")   < basename.size()))
            TetGenIO(mymesh).read (new_name);

          else if (basename.rfind(".exd") < basename.size() ||
                   basename.rfind(".e") < basename.size())
            ExodusII_IO(mymesh).read (new_name);

          else if (basename.rfind(".msh") < basename.size())
            GmshIO(mymesh).read (new_name);

          else if (basename.rfind(".gmv") < basename.size())
            GMVIO(mymesh).read (new_name);

          else if (basename.rfind(".stl") < basename.size())
            STLIO(mymesh).read (new_name);

          else if (basename.rfind(".pvtu") < basename.size() ||
                   basename.rfind(".vtu") < basename.size())
            VTKIO(mymesh).read(new_name);

          else if (basename.rfind(".inp") < basename.size())
            AbaqusIO(mymesh).read(new_name);

          else if ((basename.rfind(".bext")  < basename.size()) ||
                   (basename.rfind(".bxt")   < basename.size()))
            DynaIO(mymesh).read (new_name);

          else if (basename.rfind(".bez")  < basename.size())
            DynaIO(mymesh, false).read (new_name);

          else
            {
              libmesh_error_msg(" ERROR: Unrecognized file extension: " \
                                << name                                 \
                                << "\n   I understand the following:\n\n" \
                                << "     *.bext -- Bezier files in DYNA format\n" \
                                << "     *.bez  -- Bezier DYNA files, omit spline nodes\n" \
                                << "     *.bxt  -- Bezier files in DYNA format\n" \
                                << "     *.cpa  -- libMesh Checkpoint ASCII format\n" \
                                << "     *.cpr  -- libMesh Checkpoint binary format\n" \
                                << "     *.e    -- Sandia's ExodusII format\n" \
                                << "     *.exd  -- Sandia's ExodusII format\n" \
                                << "     *.gmv  -- LANL's General Mesh Viewer format\n" \
                                << "     *.inp  -- Abaqus .inp format\n" \
                                << "     *.mat  -- Matlab triangular ASCII file\n" \
                                << "     *.n    -- Sandia's Nemesis format\n" \
                                << "     *.nem  -- Sandia's Nemesis format\n" \
                                << "     *.off  -- OOGL OFF surface format\n" \
                                << "     *.ogl  -- OOGL OFF surface format\n" \
                                << "     *.oogl -- OOGL OFF surface format\n" \
                                << "     *.pvtu -- Paraview VTK format\n" \
                                << "     *.stl  -- STereoLithography triangulation format\n" \
                                << "     *.ucd  -- AVS's ASCII UCD format\n" \
                                << "     *.unv  -- I-deas Universal format\n" \
                                << "     *.vtu  -- Paraview VTK format\n" \
                                << "     *.xda  -- libMesh ASCII format\n" \
                                << "     *.xdr  -- libMesh binary format\n" \
                                << "     *.gz   -- any above format gzipped\n" \
                                << "     *.bz2  -- any above format bzip2'ed\n" \
                                << "     *.xz   -- any above format xzipped\n" \
                                );
            }

          // If we temporarily decompressed a file, remove the
          // uncompressed version
          if (name.rfind(".bz2") == name.size() - 4)
            std::remove(new_name.c_str());
          if (name.rfind(".xz") == name.size() - 3)
            std::remove(new_name.c_str());
        }

      // Send the mesh & bcs (which are now only on processor 0) to the other
      // processors
      MeshCommunication().broadcast (mymesh);
    }
}

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 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::NameBasedIO::write ( const std::string &  mesh_file )

overridevirtual

This method implements writing a mesh to a specified file.

Implements libMesh::MeshOutput< MeshBase >.

Definition at line 303 of file namebased_io.C.

References TIMPI::Communicator::barrier(), libMesh::Utility::basename_of(), TIMPI::Communicator::broadcast(), libMesh::ParallelObject::comm(), libMesh::err, is_parallel_file_format(), libMesh::MeshOutput< MT >::mesh(), libMesh::MeshBase::n_partitions(), libMesh::Quality::name(), libMesh::GMVIO::partitioning(), libMesh::ParallelObject::processor_id(), libMesh::FroIO::write(), libMesh::TecplotIO::write(), libMesh::STLIO::write(), libMesh::MEDITIO::write(), libMesh::GMVIO::write(), libMesh::TetGenIO::write(), libMesh::UCDIO::write(), libMesh::UNVIO::write(), libMesh::Nemesis_IO::write(), libMesh::GmshIO::write(), libMesh::XdrIO::write(), libMesh::VTKIO::write(), libMesh::CheckpointIO::write(), and libMesh::ExodusII_IO::write().

Referenced by libMesh::UnstructuredMesh::find_neighbors(), and libMesh::UnstructuredMesh::write().

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

  const std::string_view basename = Utility::basename_of(name);

  // parallel formats are special -- they may choose to write
  // separate files, let's not try to handle the zipping here.
  if (is_parallel_file_format(basename))
    {
      // no need to handle bz2 files here -- the Xdr class does that.
      if (basename.rfind(".xda") < basename.size())
        XdrIO(mymesh).write(name);

      else if (basename.rfind(".xdr") < basename.size())
        XdrIO(mymesh,true).write(name);

      else if (basename.rfind(".nem") < basename.size() ||
               basename.rfind(".n")   < basename.size())
        Nemesis_IO(mymesh).write(name);

      else if (basename.rfind(".cpa") < basename.size())
        CheckpointIO(mymesh,false).write(name);

      else if (basename.rfind(".cpr") < basename.size())
        CheckpointIO(mymesh,true).write(name);

      else
        libmesh_error_msg("Couldn't deduce filetype for " << name);
    }

  // serial file formats
  else
    {
      // Nasty hack for reading/writing zipped files
      std::string new_name = name;
      int pid_0 = 0;
      if (mymesh.processor_id() == 0)
        pid_0 = getpid();
      mymesh.comm().broadcast(pid_0);
      std::ostringstream pid_suffix;
      pid_suffix << '_' << pid_0;

      if (name.rfind(".bz2") == name.size() - 4)
        {
          new_name.erase(new_name.end() - 4, new_name.end());
          new_name += pid_suffix.str();
        }
      else if (name.rfind(".xz") == name.size() - 3)
        {
          new_name.erase(new_name.end() - 3, new_name.end());
          new_name += pid_suffix.str();
        }

      // New scope so that io will close before we try to zip the file
      {
        // Write the file based on extension
        if (basename.rfind(".dat") < basename.size())
          TecplotIO(mymesh).write (new_name);

        else if (basename.rfind(".plt") < basename.size())
          TecplotIO(mymesh,true).write (new_name);

        else if (basename.rfind(".ucd") < basename.size())
          UCDIO (mymesh).write (new_name);

        else if (basename.rfind(".gmv") < basename.size())
          if (mymesh.n_partitions() > 1)
            GMVIO(mymesh).write (new_name);
          else
            {
              GMVIO io(mymesh);
              io.partitioning() = false;
              io.write (new_name);
            }

        else if (basename.rfind(".exd") < basename.size() ||
                 basename.rfind(".e") < basename.size())
          ExodusII_IO(mymesh).write(new_name);

        else if (basename.rfind(".unv") < basename.size())
          UNVIO(mymesh).write (new_name);

        else if (basename.rfind(".mesh") < basename.size())
          MEDITIO(mymesh).write (new_name);

        else if (basename.rfind(".poly") < basename.size())
          TetGenIO(mymesh).write (new_name);

        else if (basename.rfind(".msh") < basename.size())
          GmshIO(mymesh).write (new_name);

        else if (basename.rfind(".fro") < basename.size())
          FroIO(mymesh).write (new_name);

        else if (basename.rfind(".pvtu") < basename.size())
          VTKIO(mymesh).write (name);

        else if (basename.rfind(".stl") < basename.size())
          STLIO(mymesh).write (new_name);

        else
          {
            libMesh::err
              << " ERROR: Unrecognized file extension: " << name
              << "\n   I understand the following:\n\n"
              << "     *.cpa   -- libMesh ASCII checkpoint format\n"
              << "     *.cpr   -- libMesh binary checkpoint format,\n"
              << "     *.dat   -- Tecplot ASCII file\n"
              << "     *.e     -- Sandia's ExodusII format\n"
              << "     *.exd   -- Sandia's ExodusII format\n"
              << "     *.fro   -- ACDL's surface triangulation file\n"
              << "     *.gmv   -- LANL's GMV (General Mesh Viewer) format\n"
              << "     *.mesh  -- MEdit mesh format\n"
              << "     *.msh   -- GMSH ASCII file\n"
              << "     *.n     -- Sandia's Nemesis format\n"
              << "     *.nem   -- Sandia's Nemesis format\n"
              << "     *.plt   -- Tecplot binary file\n"
              << "     *.poly  -- TetGen ASCII file\n"
              << "     *.pvtu  -- VTK (paraview-readable) format\n"
              << "     *.stl   -- STereoLithography triangulation format\n" \
              << "     *.ucd   -- AVS's ASCII UCD format\n"
              << "     *.unv   -- I-deas Universal format\n"
              << "     *.xda   -- libMesh ASCII format\n"
              << "     *.xdr   -- libMesh binary format,\n"
              << std::endl
              << "\n Exiting without writing output\n";
          }
      }

      // Nasty hack for reading/writing zipped files
      if (name.rfind(".bz2") == name.size() - 4)
        {
          LOG_SCOPE("system(bzip2)", "NameBasedIO");
          if (mymesh.processor_id() == 0)
            {
              std::string system_string = "bzip2 -f -c ";
              system_string += new_name + " > " + name;
              if (std::system(system_string.c_str()))
                libmesh_file_error(system_string);
              std::remove(new_name.c_str());
            }
          mymesh.comm().barrier();
        }
      if (name.rfind(".xz") == name.size() - 3)
        {
          LOG_SCOPE("system(xz)", "NameBasedIO");
          if (mymesh.processor_id() == 0)
            {
              std::string system_string = "xz -f -c ";
              system_string += new_name + " > " + name;
              if (std::system(system_string.c_str()))
                libmesh_file_error(system_string);
              std::remove(new_name.c_str());
            }
          mymesh.comm().barrier();
        }
    }
}

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::NameBasedIO::write_equation_systems ( const std::string &  filename, const EquationSystems &  es, const std::set< std::string > *  system_names = nullptr  )

overridevirtual

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

We override the default MeshOutput::write_equation_systems because it only outputs nodal data by default, whereas we want to output a proper restart file if the requested filename is an XDA or XDR type.

Reimplemented from libMesh::MeshOutput< MeshBase >.

Definition at line 530 of file namebased_io.C.

References libMesh::Utility::basename_of(), libMesh::ENCODE, libMesh::WRITE, libMesh::EquationSystems::write(), libMesh::EquationSystems::WRITE_ADDITIONAL_DATA, libMesh::EquationSystems::WRITE_DATA, and libMesh::MeshOutput< MT >::write_equation_systems().

Referenced by main().

{
  // XDA/XDR require a separate code path, and currently only support
  // writing complete restarts
  if (!system_names)
    {
      const std::string_view basename =
        Utility::basename_of(filename);

      if (basename.rfind(".xda") < basename.size())
        {
          es.write(filename,WRITE,
                   EquationSystems::WRITE_DATA |
                   EquationSystems::WRITE_ADDITIONAL_DATA);
          return;
        }
      else if (basename.rfind(".xdr") < basename.size())
        {
          es.write(filename,ENCODE,
                   EquationSystems::WRITE_DATA |
                   EquationSystems::WRITE_ADDITIONAL_DATA);
          return;
        }
    }

  // Other formats just use the default "write nodal values" path
  MeshOutput<MeshBase>::write_equation_systems
    (filename, es, system_names);
}

write_nodal_data() [1/3]

void libMesh::NameBasedIO::write_nodal_data ( const std::string &  name, const std::vector< Number > &  v, const std::vector< std::string > &  vn  )

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 464 of file namebased_io.C.

References libMesh::err, libMesh::MeshOutput< MT >::mesh(), libMesh::MeshBase::n_subdomains(), libMesh::Quality::name(), libMesh::GMVIO::partitioning(), libMesh::TecplotIO::write_nodal_data(), libMesh::MEDITIO::write_nodal_data(), libMesh::GMVIO::write_nodal_data(), libMesh::UCDIO::write_nodal_data(), libMesh::VTKIO::write_nodal_data(), libMesh::GmshIO::write_nodal_data(), libMesh::Nemesis_IO::write_nodal_data(), and libMesh::ExodusII_IO::write_nodal_data().

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

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

  // Write the file based on extension
  if (name.rfind(".dat") < name.size())
    TecplotIO(mymesh).write_nodal_data (name, v, vn);

  else if (name.rfind(".exd") < name.size() ||
           name.rfind(".e") < name.size())
    ExodusII_IO(mymesh).write_nodal_data(name, v, vn);

  else if (name.rfind(".gmv") < name.size())
    {
      if (mymesh.n_subdomains() > 1)
        GMVIO(mymesh).write_nodal_data (name, v, vn);
      else
        {
          GMVIO io(mymesh);
          io.partitioning() = false;
          io.write_nodal_data (name, v, vn);
        }
    }

  else if (name.rfind(".mesh") < name.size())
    MEDITIO(mymesh).write_nodal_data (name, v, vn);

  else if (name.rfind(".msh") < name.size())
    GmshIO(mymesh).write_nodal_data (name, v, vn);

  else if (name.rfind(".nem") < name.size() ||
           name.rfind(".n")   < name.size())
    Nemesis_IO(mymesh).write_nodal_data(name, v, vn);

  else if (name.rfind(".plt") < name.size())
    TecplotIO(mymesh,true).write_nodal_data (name, v, vn);

  else if (name.rfind(".pvtu") < name.size())
    VTKIO(mymesh).write_nodal_data (name, v, vn);

  else if (name.rfind(".ucd") < name.size())
    UCDIO (mymesh).write_nodal_data (name, v, vn);

  else
    {
      libMesh::err
        << " ERROR: Unrecognized file extension: " << name
        << "\n   I understand the following:\n\n"
        << "     *.dat  -- Tecplot ASCII file\n"
        << "     *.e    -- Sandia's ExodusII format\n"
        << "     *.exd  -- Sandia's ExodusII format\n"
        << "     *.gmv  -- LANL's GMV (General Mesh Viewer) format\n"
        << "     *.mesh -- MEdit mesh format\n"
        << "     *.msh  -- GMSH ASCII file\n"
        << "     *.n    -- Sandia's Nemesis format\n"
        << "     *.nem  -- Sandia's Nemesis format\n"
        << "     *.plt  -- Tecplot binary file\n"
        << "     *.pvtu -- Paraview VTK file\n"
        << "     *.ucd  -- AVS's ASCII UCD format\n"
        << "\n Exiting without writing output\n";
    }
}

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

_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.

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().

---

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

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