libMesh::VTKIO Class Reference

#include <vtk_io.h>

Inheritance diagram for libMesh::VTKIO:

Classes
struct	ElementMaps

Public Member Functions
	VTKIO (MeshBase &mesh)
	VTKIO (const MeshBase &mesh)
virtual void	write_nodal_data (const std::string &, const std::vector< Number > &, const std::vector< std::string > &) override
virtual void	read (const std::string &) override
virtual void	write (const std::string &) override
void	set_compression (bool b)
vtkUnstructuredGrid *	get_vtk_grid ()
virtual void	write_equation_systems (const std::string &, const EquationSystems &, const std::set< std::string > *system_names=nullptr)
virtual void	write_discontinuous_equation_systems (const std::string &, const EquationSystems &, const std::set< std::string > *system_names=nullptr)
virtual void	write_nodal_data (const std::string &, const NumericVector< Number > &, const std::vector< std::string > &)
virtual void	write_nodal_data_discontinuous (const std::string &, const std::vector< Number > &, const std::vector< std::string > &)
unsigned int &	ascii_precision ()

Protected Member Functions
MeshBase &	mesh ()
void	set_n_partitions (unsigned int n_parts)
void	skip_comment_lines (std::istream &in, const char comment_start)
const MeshBase &	mesh () const

Protected Attributes
std::vector< bool >	elems_of_dimension
const bool	_is_parallel_format
const bool	_serial_only_needed_on_proc_0

Private Member Functions
void	nodes_to_vtk ()
void	cells_to_vtk ()

Static Private Member Functions
static ElementMaps	build_element_maps ()

Private Attributes
vtkSmartPointer< vtkUnstructuredGrid >	_vtk_grid
bool	_compress
std::map< dof_id_type, dof_id_type >	_local_node_map

Static Private Attributes
static ElementMaps	_element_maps = VTKIO::build_element_maps()

Detailed Description

This class implements reading and writing meshes in the VTK format. Format description: cf. VTK home page.

This class will not have any functionality unless VTK is detected during configure and hence LIBMESH_HAVE_VTK is defined.

Author

Wout Ruijter

John W. Peterson

Date

2007

Definition at line 59 of file vtk_io.h.

Constructor & Destructor Documentation

VTKIO() [1/2]

libMesh::VTKIO::VTKIO ( MeshBase &  mesh )

explicit

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

Definition at line 75 of file vtk_io.C.

                             :
  MeshInput<MeshBase> (mesh, /*is_parallel_format=*/true),
  MeshOutput<MeshBase>(mesh, /*is_parallel_format=*/true)
#ifdef LIBMESH_HAVE_VTK
  ,_compress(false)
#endif
{
}



// Constructor for writing
VTKIO::VTKIO (const MeshBase & mesh) :
  MeshOutput<MeshBase>(mesh, /*is_parallel_format=*/true)
#ifdef LIBMESH_HAVE_VTK
  ,_compress(false)
#endif
{
}



// Output the mesh without solutions to a .pvtu file
void VTKIO::write (const std::string & name)
{
  std::vector<Number> soln;
  std::vector<std::string> names;
  this->write_nodal_data(name, soln, names);
}

VTKIO() [2/2]

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

explicit

Constructor. Takes a read-only reference to a mesh object. This is the constructor required to write a 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>::digits10 + 2, which should be enough to write out to ASCII and get the exact same Real back when reading in.

Definition at line 244 of file mesh_output.h.

Referenced by libMesh::TecplotIO::write_ascii(), libMesh::GMVIO::write_ascii_new_impl(), and libMesh::GMVIO::write_ascii_old_impl().

{
  return _ascii_precision;
}

build_element_maps()

VTKIO::ElementMaps libMesh::VTKIO::build_element_maps ( )

staticprivate

Static function used to construct the _element_maps struct.

Definition at line 115 of file vtk_io.C.

References libMesh::VTKIO::ElementMaps::associate(), libMesh::EDGE2, libMesh::EDGE3, libMesh::HEX20, libMesh::HEX27, libMesh::HEX8, libMesh::PRISM15, libMesh::PRISM18, libMesh::PRISM6, libMesh::PYRAMID5, libMesh::QUAD4, libMesh::QUAD8, libMesh::QUAD9, libMesh::TET10, libMesh::TET4, libMesh::TRI3, libMesh::TRI3SUBDIVISION, libMesh::TRI6, and libMesh::VTKIO::ElementMaps::writing_map.

{
  // Object to be filled up
  ElementMaps em;

  em.associate(EDGE2, VTK_LINE);
  em.associate(EDGE3, VTK_QUADRATIC_EDGE);
  em.associate(TRI3, VTK_TRIANGLE);
  em.associate(TRI6, VTK_QUADRATIC_TRIANGLE);
  em.associate(QUAD4, VTK_QUAD);
  em.associate(QUAD8, VTK_QUADRATIC_QUAD);
  em.associate(TET4, VTK_TETRA);
  em.associate(TET10, VTK_QUADRATIC_TETRA);
  em.associate(HEX8, VTK_HEXAHEDRON);
  em.associate(HEX20, VTK_QUADRATIC_HEXAHEDRON);
  em.associate(HEX27, VTK_TRIQUADRATIC_HEXAHEDRON);
  em.associate(PRISM6, VTK_WEDGE);
  em.associate(PRISM15, VTK_QUADRATIC_WEDGE);
  em.associate(PRISM18, VTK_BIQUADRATIC_QUADRATIC_WEDGE);
  em.associate(PYRAMID5, VTK_PYRAMID);

  // VTK_BIQUADRATIC_QUAD has been around since VTK 5.0
#if VTK_MAJOR_VERSION > 5 || (VTK_MAJOR_VERSION == 5 && VTK_MINOR_VERSION > 0)
  em.associate(QUAD9, VTK_BIQUADRATIC_QUAD);
#endif

  // TRI3SUBDIVISION is for writing only
  em.writing_map[TRI3SUBDIVISION] = VTK_TRIANGLE;

  return em;
}

cells_to_vtk()

void libMesh::VTKIO::cells_to_vtk ( )

private

write the cells from the mesh into a vtkUnstructuredGrid

Definition at line 407 of file vtk_io.C.

References _element_maps, _local_node_map, _vtk_grid, libMesh::MeshBase::active_local_element_ptr_range(), libMesh::VTKIO::ElementMaps::find(), libMesh::MeshInput< MeshBase >::mesh(), libMesh::MeshOutput< MT >::mesh(), libMesh::MeshBase::n_active_local_elem(), libMesh::MeshBase::point(), and libMesh::VTK.

Referenced by write_nodal_data().

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

  vtkSmartPointer<vtkCellArray> cells = vtkSmartPointer<vtkCellArray>::New();
  vtkSmartPointer<vtkIdList> pts = vtkSmartPointer<vtkIdList>::New();

  std::vector<int> types(mesh.n_active_local_elem());

  vtkSmartPointer<vtkIntArray> elem_id = vtkSmartPointer<vtkIntArray>::New();
  elem_id->SetName("libmesh_elem_id");
  elem_id->SetNumberOfComponents(1);

  vtkSmartPointer<vtkIntArray> subdomain_id = vtkSmartPointer<vtkIntArray>::New();
  subdomain_id->SetName("subdomain_id");
  subdomain_id->SetNumberOfComponents(1);

  vtkSmartPointer<vtkIntArray> elem_proc_id = vtkSmartPointer<vtkIntArray>::New();
  elem_proc_id->SetName("processor_id");
  elem_proc_id->SetNumberOfComponents(1);

  unsigned active_element_counter = 0;
  for (const auto & elem : mesh.active_local_element_ptr_range())
    {
      pts->SetNumberOfIds(elem->n_nodes());

      // get the connectivity for this element
      std::vector<dof_id_type> conn;
      elem->connectivity(0, VTK, conn);

      for (unsigned int i=0,
           n_conn = cast_int<unsigned int>(conn.size());
           i != n_conn; ++i)
        {
          // If the node ID is not found in the _local_node_map, we'll
          // add it to the _vtk_grid.  NOTE[JWP]: none of the examples
          // I have actually enters this section of code...
          if (_local_node_map.find(conn[i]) == _local_node_map.end())
            {
              dof_id_type global_node_id = elem->node_id(i);

              const Point & the_node = mesh.point(global_node_id);

              // InsertNextPoint accepts either a double or float array of length 3.
              double pt[3] = {0., 0., 0.};
              for (unsigned int d=0; d<LIBMESH_DIM; ++d)
                pt[d] = the_node(d);

              // Insert the point into the _vtk_grid
              vtkIdType local = _vtk_grid->GetPoints()->InsertNextPoint(pt);

              // Update the _local_node_map with the ID returned by VTK
              _local_node_map[global_node_id] =
                cast_int<dof_id_type>(local);
            }

          // Otherwise, the node ID was found in the _local_node_map, so
          // insert it into the vtkIdList.
          pts->InsertId(i, _local_node_map[conn[i]]);
        }

      vtkIdType vtkcellid = cells->InsertNextCell(pts);
      types[active_element_counter] = cast_int<int>(_element_maps.find(elem->type()));

      elem_id->InsertTuple1(vtkcellid, elem->id());
      subdomain_id->InsertTuple1(vtkcellid, elem->subdomain_id());
      elem_proc_id->InsertTuple1(vtkcellid, elem->processor_id());
      ++active_element_counter;
    } // end loop over active elements

  _vtk_grid->SetCells(types.data(), cells);
  _vtk_grid->GetCellData()->AddArray(elem_id);
  _vtk_grid->GetCellData()->AddArray(subdomain_id);
  _vtk_grid->GetCellData()->AddArray(elem_proc_id);
}

get_vtk_grid()

vtkUnstructuredGrid * libMesh::VTKIO::get_vtk_grid

(

)

Get a pointer to the VTK unstructured grid data structure.

Definition at line 350 of file vtk_io.C.

References _vtk_grid.

{
  return _vtk_grid;
}

mesh() [1/2]

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

inlineprotectedinherited

Returns

The object as a writable reference.

Definition at line 169 of file mesh_input.h.

Referenced by libMesh::GMVIO::_read_one_cell(), cells_to_vtk(), libMesh::TetGenIO::element_in(), libMesh::UNVIO::elements_in(), libMesh::UNVIO::elements_out(), libMesh::UNVIO::groups_in(), libMesh::TetGenIO::node_in(), libMesh::UNVIO::nodes_in(), libMesh::UNVIO::nodes_out(), nodes_to_vtk(), libMesh::Nemesis_IO::prepare_to_write_nodal_data(), libMesh::Nemesis_IO::read(), libMesh::ExodusII_IO::read(), libMesh::GMVIO::read(), libMesh::XdrIO::read(), libMesh::CheckpointIO::read(), read(), libMesh::CheckpointIO::read_bcs(), libMesh::CheckpointIO::read_connectivity(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::UCDIO::read_implementation(), libMesh::UNVIO::read_implementation(), libMesh::GmshIO::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::OFFIO::read_stream(), libMesh::MatlabIO::read_stream(), libMesh::CheckpointIO::read_subdomain_names(), libMesh::TetGenIO::write(), libMesh::Nemesis_IO::write(), libMesh::ExodusII_IO::write(), libMesh::XdrIO::write(), libMesh::CheckpointIO::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::UCDIO::write_header(), libMesh::UCDIO::write_implementation(), libMesh::UCDIO::write_interior_elems(), libMesh::GmshIO::write_mesh(), write_nodal_data(), libMesh::UCDIO::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::UCDIO::write_soln(), and libMesh::CheckpointIO::write_subdomain_names().

{
  if (_obj == nullptr)
    libmesh_error_msg("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 234 of file mesh_output.h.

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;
}

nodes_to_vtk()

void libMesh::VTKIO::nodes_to_vtk ( )

private

write the nodes from the mesh into a vtkUnstructuredGrid

Definition at line 364 of file vtk_io.C.

References _local_node_map, _vtk_grid, libMesh::DofObject::id(), libMesh::MeshBase::local_node_ptr_range(), libMesh::MeshInput< MeshBase >::mesh(), libMesh::MeshOutput< MT >::mesh(), and libMesh::MeshBase::n_local_nodes().

Referenced by write_nodal_data().

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

  // containers for points and coordinates of points
  vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();
  vtkSmartPointer<vtkDoubleArray> pcoords = vtkSmartPointer<vtkDoubleArray>::New();
  // if this grid is to be used in VTK then the dimension of the points should be 3
  pcoords->SetNumberOfComponents(LIBMESH_DIM);
  pcoords->Allocate(3*mesh.n_local_nodes());
  points->SetNumberOfPoints(mesh.n_local_nodes()); // it seems that it needs this to prevent a segfault

  unsigned int local_node_counter = 0;

  for (const auto & node_ptr : mesh.local_node_ptr_range())
    {
      const Node & node = *node_ptr;

      double pnt[3] = {0, 0, 0};
      for (unsigned int i=0; i<LIBMESH_DIM; ++i)
        pnt[i] = node(i);

      // Fill mapping between global and local node numbers
      _local_node_map[node.id()] = local_node_counter;

      // add point
#if VTK_VERSION_LESS_THAN(7,1,0)
      pcoords->InsertNextTupleValue(pnt);
#else
      pcoords->InsertNextTuple(pnt);
#endif
      ++local_node_counter;
    }

  // add coordinates to points
  points->SetData(pcoords);

  // add points to grid
  _vtk_grid->SetPoints(points);
}

read()

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

overridevirtual

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

As with other Mesh IO classes, this interface is still still "available" when !LIBMESH_HAVE_VTK, however, it will throw a runtime error.

FIXME: This is known to write nonsense on AMR meshes and it strips the imaginary parts of complex Numbers

This function is not currently used by anything, so it is commented out, and may eventually be removed entirely.

Implements libMesh::MeshInput< MeshBase >.

Definition at line 149 of file vtk_io.C.

References _element_maps, _vtk_grid, libMesh::MeshBase::add_elem(), libMesh::MeshBase::add_point(), libMesh::Elem::build(), libMesh::MeshBase::clear(), libMesh::Elem::connectivity(), libMesh::Elem::dim(), libMesh::MeshInput< MeshBase >::elems_of_dimension, libMesh::VTKIO::ElementMaps::find(), libMesh::MeshInput< MeshBase >::mesh(), libMesh::MeshInput< MT >::mesh(), libMesh::MeshBase::mesh_dimension(), libMesh::Elem::n_nodes(), libMesh::Quality::name(), libMesh::MeshBase::node_ptr(), libMesh::DofObject::set_id(), libMesh::MeshBase::set_mesh_dimension(), libMesh::Elem::set_node(), and libMesh::VTK.

Referenced by libMesh::NameBasedIO::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);

  // Keep track of what kinds of elements this file contains
  elems_of_dimension.clear();
  elems_of_dimension.resize(4, false);

  // Use a typedef, because these names are just crazy
  typedef vtkSmartPointer<vtkXMLUnstructuredGridReader> MyReader;
  MyReader reader = MyReader::New();

  // Pass the filename along to the reader
  reader->SetFileName(name.c_str());

  // Force reading
  reader->Update();

  // read in the grid
  _vtk_grid = reader->GetOutput();

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

  // Clear out any pre-existing data from the Mesh
  mesh.clear();

  // Get the number of points from the _vtk_grid object
  const unsigned int vtk_num_points = static_cast<unsigned int>(_vtk_grid->GetNumberOfPoints());

  // always numbered nicely so we can loop like this
  for (unsigned int i=0; i<vtk_num_points; ++i)
    {
      // add to the id map
      // and add the actual point
      double pnt[3];
      _vtk_grid->GetPoint(static_cast<vtkIdType>(i), pnt);
      Point xyz(pnt[0], pnt[1], pnt[2]);
      mesh.add_point(xyz, i);
    }

  // Get the number of cells from the _vtk_grid object
  const unsigned int vtk_num_cells = static_cast<unsigned int>(_vtk_grid->GetNumberOfCells());

  vtkSmartPointer<vtkGenericCell> cell = vtkSmartPointer<vtkGenericCell>::New();
  for (unsigned int i=0; i<vtk_num_cells; ++i)
    {
      _vtk_grid->GetCell(i, cell);

      // Get the libMesh element type corresponding to this VTK element type.
      ElemType libmesh_elem_type = _element_maps.find(cell->GetCellType());
      Elem * elem = Elem::build(libmesh_elem_type).release();

      // get the straightforward numbering from the VTK cells
      for (unsigned int j=0; j<elem->n_nodes(); ++j)
        elem->set_node(j) =
          mesh.node_ptr(cast_int<dof_id_type>(cell->GetPointId(j)));

      // then get the connectivity
      std::vector<dof_id_type> conn;
      elem->connectivity(0, VTK, conn);

      // then reshuffle the nodes according to the connectivity, this
      // two-time-assign would evade the definition of the vtk_mapping
      for (unsigned int j=0,
           n_conn = cast_int<unsigned int>(conn.size());
           j != n_conn; ++j)
        elem->set_node(j) = mesh.node_ptr(conn[j]);

      elem->set_id(i);

      elems_of_dimension[elem->dim()] = true;

      mesh.add_elem(elem);
    } // end loop over VTK cells

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

set_compression()

void libMesh::VTKIO::set_compression

(

bool

b

)

Setter for compression flag

Definition at line 357 of file vtk_io.C.

References _compress.

{
  this->_compress = b;
}

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 91 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 179 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()

virtual void libMesh::VTKIO::write ( const std::string &  )

overridevirtual

Output the mesh without solutions to a .pvtu file.

As with other Mesh IO classes, this interface is still still "available" when !LIBMESH_HAVE_VTK, however, it will throw a runtime error.

Implements libMesh::MeshOutput< MeshBase >.

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

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 92 of file mesh_output.C.

References libMesh::EquationSystems::build_discontinuous_solution_vector(), libMesh::EquationSystems::build_variable_names(), libMesh::EquationSystems::get_mesh(), 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);

      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_parallel_solution_vector(), libMesh::EquationSystems::build_solution_vector(), libMesh::EquationSystems::build_variable_names(), libMesh::EquationSystems::get_mesh(), 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-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_solution_vector (soln, system_names);

      this->write_nodal_data (fname, soln, names);
    }
  else // _is_parallel_format
    {
      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() [1/2]

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

overridevirtual

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

As with other Mesh IO classes, this interface is still still "available" when !LIBMESH_HAVE_VTK, however, it will throw a runtime error.

Reimplemented from libMesh::MeshOutput< MeshBase >.

Definition at line 245 of file vtk_io.C.

References _compress, _local_node_map, _vtk_grid, cells_to_vtk(), data, libMesh::err, libMesh::MeshInput< MeshBase >::mesh(), libMesh::MeshOutput< MT >::mesh(), libMesh::MeshBase::n_nodes(), and nodes_to_vtk().

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

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

  // Warn that the .pvtu file extension should be used.  Paraview
  // recognizes this, and it works in both serial and parallel.  Only
  // warn about this once.
  if (fname.substr(fname.rfind("."), fname.size()) != ".pvtu")
    libmesh_do_once(libMesh::err << "The .pvtu extension should be used when writing VTK files in libMesh.");

  // If there are variable names being written, the solution vector
  // should not be empty, it should have been broadcast to all
  // processors by the MeshOutput base class, since VTK is a parallel
  // format.  Verify this before going further.
  if (!names.empty() && soln.empty())
    libmesh_error_msg("Empty soln vector in VTKIO::write_nodal_data().");

  // we only use Unstructured grids
  _vtk_grid = vtkSmartPointer<vtkUnstructuredGrid>::New();
  vtkSmartPointer<vtkXMLPUnstructuredGridWriter> writer = vtkSmartPointer<vtkXMLPUnstructuredGridWriter>::New();

  // add nodes to the grid and update _local_node_map
  _local_node_map.clear();
  this->nodes_to_vtk();

  // add cells to the grid
  this->cells_to_vtk();

  // add nodal solutions to the grid, if solutions are given
  if (names.size() > 0)
    {
      std::size_t num_vars = names.size();
      dof_id_type num_nodes = mesh.n_nodes();

      for (std::size_t variable=0; variable<num_vars; ++variable)
        {
          vtkSmartPointer<vtkDoubleArray> data = vtkSmartPointer<vtkDoubleArray>::New();
          data->SetName(names[variable].c_str());

          // number of local and ghost nodes
          data->SetNumberOfValues(_local_node_map.size());

          // loop over all nodes and get the solution for the current
          // variable, if the node is in the current partition
          for (dof_id_type k=0; k<num_nodes; ++k)
            {
              std::map<dof_id_type, dof_id_type>::iterator local_node_it = _local_node_map.find(k);
              if (local_node_it == _local_node_map.end())
                continue; // not a local node

#ifdef LIBMESH_USE_COMPLEX_NUMBERS
              libmesh_do_once (libMesh::err << "Only writing the real part for complex numbers!\n"
                               << "if you need this support contact " << LIBMESH_PACKAGE_BUGREPORT
                               << std::endl);
              data->SetValue(local_node_it->second, soln[k*num_vars + variable].real());
#else
              data->SetValue(local_node_it->second, soln[k*num_vars + variable]);
#endif
            }
          _vtk_grid->GetPointData()->AddArray(data);
        }
    }

  // Tell the writer how many partitions exist and on which processor
  // we are currently
  writer->SetNumberOfPieces(MeshOutput<MeshBase>::mesh().n_processors());
  writer->SetStartPiece(MeshOutput<MeshBase>::mesh().processor_id());
  writer->SetEndPiece(MeshOutput<MeshBase>::mesh().processor_id());

  // partitions overlap by one node
  // FIXME: According to this document
  // http://paraview.org/Wiki/images/5/51/SC07_tut107_ParaView_Handouts.pdf
  // the ghosts are cells rather than nodes.
  writer->SetGhostLevel(1);

  // VTK 6 replaces SetInput() with SetInputData(). See
  // http://www.vtk.org/Wiki/VTK/VTK_6_Migration/Replacement_of_SetInput
  // for the full explanation.
#if VTK_VERSION_LESS_THAN(6,0,0)
  writer->SetInput(_vtk_grid);
#else
  writer->SetInputData(_vtk_grid);
#endif

  writer->SetFileName(fname.c_str());
  writer->SetDataModeToAscii();

  // compress the output, if desired (switches also to binary)
  if (this->_compress)
    {
#if !VTK_VERSION_LESS_THAN(5,6,0)
      writer->SetCompressorTypeToZLib();
#else
      libmesh_do_once(libMesh::err << "Compression not implemented with old VTK libs!" << std::endl;);
#endif
    }

  writer->Write();

}

write_nodal_data() [2/2]

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 should 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 150 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_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 114 of file mesh_output.h.

  { libmesh_not_implemented(); }

Member Data Documentation

_compress

bool libMesh::VTKIO::_compress

private

Flag to indicate whether the output should be compressed

Definition at line 156 of file vtk_io.h.

Referenced by set_compression(), and write_nodal_data().

_element_maps

VTKIO::ElementMaps libMesh::VTKIO::_element_maps = VTKIO::build_element_maps()

staticprivate

ElementMaps object that is built statically and used by all instances of this class.

Definition at line 207 of file vtk_io.h.

Referenced by cells_to_vtk(), and read().

_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 159 of file mesh_output.h.

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

_local_node_map

std::map<dof_id_type, dof_id_type> libMesh::VTKIO::_local_node_map

private

maps global node id to node id of partition

Definition at line 161 of file vtk_io.h.

Referenced by cells_to_vtk(), nodes_to_vtk(), and write_nodal_data().

_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 168 of file mesh_output.h.

_vtk_grid

vtkSmartPointer<vtkUnstructuredGrid> libMesh::VTKIO::_vtk_grid

private

Write the system vectors to vtk

This function is not currently used by anything, so it is commented out, and may eventually be removed entirely. pointer to the VTK grid. the vtkSmartPointer will automatically initialize the value to null and keep track of reference counting.

Definition at line 151 of file vtk_io.h.

Referenced by cells_to_vtk(), get_vtk_grid(), nodes_to_vtk(), read(), and write_nodal_data().

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 97 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::Nemesis_IO::read(), libMesh::ExodusII_IO::read(), libMesh::GMVIO::read(), 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:

• vtk_io.h
• vtk_io.C