libMesh::MeshOutput< MT > Class Template Reference

This class defines an abstract interface for Mesh output. More...

#include <mesh_output.h>

Public Member Functions
virtual	~MeshOutput ()
	Destructor. More...
virtual void	write (const std::string &)=0
	This method implements writing a mesh to a specified file. More...
virtual void	write_equation_systems (const std::string &, const EquationSystems &, const std::set< std::string > *system_names=nullptr)
	This method implements writing a mesh with data to a specified file where the data is taken from the EquationSystems object. More...
virtual void	write_discontinuous_equation_systems (const std::string &, const EquationSystems &, const std::set< std::string > *system_names=nullptr)
	This method implements writing a mesh with discontinuous data to a specified file where the data is taken from the EquationSystems object. More...
virtual void	write_nodal_data (const std::string &, const 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_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...
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...
unsigned int &	ascii_precision ()
	Return/set the precision to use when writing ASCII files. More...

Protected Member Functions
	MeshOutput (const bool is_parallel_format=false, const bool serial_only_needed_on_proc_0=false)
	Default constructor. More...
	MeshOutput (const MT &, const bool is_parallel_format=false, const bool serial_only_needed_on_proc_0=false)
	Constructor. More...
const MT &	mesh () const
virtual bool	get_add_sides ()

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

Private Attributes
const MT *const	_obj
	A pointer to a constant object. More...
unsigned int	_ascii_precision
	Precision to use when writing ASCII files. More...

Detailed Description

template<class MT>
class libMesh::MeshOutput< MT >

This class defines an abstract interface for Mesh output.

Specific classes derived from this class actually implement writing various mesh formats.

Author

Benjamin S. Kirk

Date

2004

Definition at line 53 of file mesh_output.h.

Constructor & Destructor Documentation

MeshOutput() [1/2]

template<class MT >

libMesh::MeshOutput< MT >::MeshOutput ( const bool  is_parallel_format = false, const bool  serial_only_needed_on_proc_0 = false  )

inlineexplicitprotected

Default constructor.

Will set the _obj to nullptr, effectively rendering this object useless.

Definition at line 219 of file mesh_output.h.

                                                                                                  :
  _is_parallel_format(is_parallel_format),
  _serial_only_needed_on_proc_0(serial_only_needed_on_proc_0),
  _obj(nullptr),
  _ascii_precision (std::numeric_limits<Real>::max_digits10)
{}

MeshOutput() [2/2]

template<class MT>

libMesh::MeshOutput< MT >::MeshOutput ( const MT &  obj, const bool  is_parallel_format = false, const bool  serial_only_needed_on_proc_0 = false  )

inlineexplicitprotected

Constructor.

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

Definition at line 230 of file mesh_output.h.

                                                                                                                  :
  _is_parallel_format(is_parallel_format),
  _serial_only_needed_on_proc_0(serial_only_needed_on_proc_0),
  _obj (&obj),
  _ascii_precision (std::numeric_limits<Real>::max_digits10)
{
  if (!_is_parallel_format && !this->mesh().is_serial())
    {
      if (this->mesh().processor_id() == 0)
        {
          libmesh_do_once(libMesh::out <<
                          "Warning:  This MeshOutput subclass only supports meshes which have been serialized!"
                          << std::endl;);
        }
    }
}

~MeshOutput()

template<class MT >

libMesh::MeshOutput< MT >::~MeshOutput ( )

inlinevirtual

Destructor.

Definition at line 251 of file mesh_output.h.

{
}

Member Function Documentation

ascii_precision()

template<class MT >

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

inline

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.

{
  return _ascii_precision;
}

get_add_sides()

template<class MT>

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

inlineprotectedvirtual

Returns

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

Reimplemented in libMesh::ExodusII_IO.

Definition at line 176 of file mesh_output.h.

{ return false; }

mesh()

template<class MT >

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

inlineprotected

Returns

The object as a read-only reference.

Definition at line 259 of file mesh_output.h.

Referenced by libMesh::VTKIO::cells_to_vtk(), libMesh::TecplotIO::elem_dimension(), libMesh::UNVIO::elements_out(), libMesh::VTKIO::get_local_node_values(), libMesh::ExodusII_IO::get_sideset_data_indices(), libMesh::UNVIO::nodes_out(), libMesh::VTKIO::nodes_to_vtk(), libMesh::Nemesis_IO::prepare_to_write_nodal_data(), libMesh::ExodusII_IO::read_sideset_data(), libMesh::FroIO::write(), libMesh::PostscriptIO::write(), libMesh::TetGenIO::write(), libMesh::Nemesis_IO::write(), libMesh::XdrIO::write(), libMesh::CheckpointIO::write(), libMesh::ExodusII_IO::write(), libMesh::MEDITIO::write_ascii(), libMesh::TecplotIO::write_ascii(), libMesh::GMVIO::write_ascii_new_impl(), libMesh::GMVIO::write_ascii_old_impl(), libMesh::TecplotIO::write_binary(), libMesh::GMVIO::write_binary(), libMesh::CheckpointIO::write_connectivity(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::Nemesis_IO::write_element_data(), libMesh::ExodusII_IO::write_element_data(), libMesh::ExodusII_IO::write_element_data_from_discontinuous_nodal_data(), libMesh::ExodusII_IO::write_elemsets(), libMesh::EnsightIO::write_geometry_ascii(), libMesh::UCDIO::write_implementation(), 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::CheckpointIO::write_nodes(), libMesh::CheckpointIO::write_nodesets(), libMesh::XdrIO::write_parallel(), libMesh::GmshIO::write_post(), libMesh::EnsightIO::write_scalar_ascii(), 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::GnuPlotIO::write_solution(), libMesh::CheckpointIO::write_subdomain_names(), and libMesh::EnsightIO::write_vector_ascii().

{
  libmesh_assert(_obj);
  return *_obj;
}

write()

template<class MT>

virtual void libMesh::MeshOutput< MT >::write ( const std::string &  )

pure virtual

This method implements writing a mesh to a specified file.

Note that writes may be buffered for efficiency, and so may not reach disk until after the file has been closed, which happens when the MeshOutput object is destructed.

Implemented in libMesh::ExodusII_IO, libMesh::CheckpointIO, libMesh::VTKIO, libMesh::EnsightIO, libMesh::XdrIO, libMesh::GmshIO, libMesh::UNVIO, libMesh::Nemesis_IO, libMesh::UCDIO, libMesh::TetGenIO, libMesh::NameBasedIO, libMesh::PostscriptIO, libMesh::GMVIO, libMesh::MEDITIO, libMesh::GnuPlotIO, libMesh::TecplotIO, and libMesh::FroIO.

write_discontinuous_equation_systems()

template<class MT >

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

virtual

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.

{
  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()

template<class MT >

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

virtual

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.

Referenced by libMesh::RBConstruction::enrich_basis_from_rhs_terms(), main(), libMesh::ErrorVector::plot_error(), scale_mesh_and_plot(), MeshInputTest::testExodusWriteElementDataFromDiscontinuousNodalData(), PeriodicBCTest::testPeriodicBC(), MeshInputTest::testSingleElementImpl(), WriteVecAndScalar::testWriteExodus(), WriteVecAndScalar::testWriteNemesis(), transform_mesh_and_plot(), libMesh::TransientRBConstruction::truth_solve(), libMesh::RBConstruction::truth_solve(), libMesh::NameBasedIO::write_equation_systems(), and write_output().

{
  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]

template<class MT>

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

inlinevirtual

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]

template<class MT >

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

virtual

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.

{
  // 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]

template<class MT >

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

virtual

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.

{
  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()

template<class MT>

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

inlinevirtual

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

_ascii_precision

template<class MT>

unsigned int libMesh::MeshOutput< MT >::_ascii_precision

private

Precision to use when writing ASCII files.

Definition at line 207 of file mesh_output.h.

_is_parallel_format

template<class MT>

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

protected

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.

_obj

template<class MT>

const MT* const libMesh::MeshOutput< MT >::_obj

private

A pointer to a constant object.

This allows us to write the object to file.

Definition at line 202 of file mesh_output.h.

_serial_only_needed_on_proc_0

template<class MT>

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

protected

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.

---

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

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