libMesh::GnuPlotIO Class Reference

This class implements writing meshes using GNUplot, designed for use only with 1D meshes. More...

#include <gnuplot_io.h>

Inheritance diagram for libMesh::GnuPlotIO:

Public Types
enum	PlottingProperties { GRID_ON = 1 , PNG_OUTPUT = 2 }
	Define enumerations to set plotting properties on construction. More...

Public Member Functions
	GnuPlotIO (const MeshBase &, const std::string &=std::string("FE 1D Solution"), int properties=0)
	Constructor.
virtual void	write (const std::string &) override
	Write the mesh to the specified file.
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.
void	set_title (std::string title)
	Set title of plot.
void	use_grid (bool grid)
	Turn grid on or off.
void	set_png_output (bool png_output)
	Write output to a .png file using gnuplot.
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.
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.
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.
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.
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.
unsigned int &	ascii_precision ()
	Return/set the precision to use when writing ASCII files.

Public Attributes
std::string	axes_limits
	GNUplot automatically adjusts the x and y-axes of 2D plots to "zoom in" on the data.

Protected Member Functions
const MeshBase &	mesh () const
virtual bool	get_add_sides ()

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

Private Member Functions
void	write_solution (const std::string &, const std::vector< Number > *=nullptr, const std::vector< std::string > *=nullptr)
	This method implements writing a mesh with nodal data to a specified file where the nodal data and variable names are optionally provided.

Private Attributes
std::string	_title
bool	_grid
bool	_png_output
const MeshBase *const	_obj
	A pointer to a constant object.
unsigned int	_ascii_precision
	Precision to use when writing ASCII files.

Detailed Description

This class implements writing meshes using GNUplot, designed for use only with 1D meshes.

Author

David Knezevic

Date

2005

Definition at line 43 of file gnuplot_io.h.

Member Enumeration Documentation

PlottingProperties

enum libMesh::GnuPlotIO::PlottingProperties

Define enumerations to set plotting properties on construction.

Enumerator
GRID_ON
PNG_OUTPUT

Definition at line 50 of file gnuplot_io.h.

                          { GRID_ON    = 1,
                            PNG_OUTPUT = 2};

Constructor & Destructor Documentation

GnuPlotIO()

libMesh::GnuPlotIO::GnuPlotIO ( const MeshBase &  mesh_in, const std::string &  title = std::string("FE 1D Solution"), int  properties = 0  )

explicit

Constructor.

Takes a reference to a constant mesh object. To set the properties, we input a bitwise OR of the GnuPlotIO::PlottingProperties enumerations, e.g. GnuPlotIO::GRID_ON | GnuPlotIO::PNG_OUTPUT

Definition at line 32 of file gnuplot_io.C.

  :
  MeshOutput<MeshBase> (mesh_in),
  _title(title)
{
  _grid       = (mesh_properties & GRID_ON);
  _png_output = (mesh_properties & PNG_OUTPUT);
}

References _grid, _png_output, GRID_ON, and PNG_OUTPUT.

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 160 of file mesh_output.h.

{
  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; }

mesh()

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

inlineprotectedinherited

Returns

The object as a read-only reference.

Definition at line 168 of file mesh_output.h.

{
  libmesh_assert(_obj);
  return *_obj;
}

set_png_output()

void libMesh::GnuPlotIO::set_png_output ( bool  png_output )

inline

Write output to a .png file using gnuplot.

Definition at line 97 of file gnuplot_io.h.

{ _png_output = png_output; }

References _png_output.

set_title()

void libMesh::GnuPlotIO::set_title ( std::string  title )

inline

Set title of plot.

Definition at line 86 of file gnuplot_io.h.

{ _title = std::move(title); }

References _title.

use_grid()

void libMesh::GnuPlotIO::use_grid ( bool  grid )

inline

Turn grid on or off.

Definition at line 91 of file gnuplot_io.h.

{ _grid = grid; }

References _grid.

write()

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

overridevirtual

Write the mesh to the specified file.

Implements libMesh::MeshOutput< MeshBase >.

Definition at line 43 of file gnuplot_io.C.

{
  this->write_solution(fname);
}

References write_solution().

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 101 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()

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, and libMesh::ExodusII_IO.

Definition at line 92 of file mesh_output.C.

{
  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]

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 149 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() [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 136 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]

void libMesh::GnuPlotIO::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.

Reimplemented from libMesh::MeshOutput< MeshBase >.

Definition at line 48 of file gnuplot_io.C.

{
  LOG_SCOPE("write_nodal_data()", "GnuPlotIO");
  this->write_solution(fname, &soln, &names);
}

References write_solution().

write_nodal_data_discontinuous()

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

inlinevirtualinherited

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

Reimplemented in libMesh::ExodusII_IO.

Definition at line 118 of file mesh_output.h.

  { libmesh_not_implemented(); }

write_solution()

void libMesh::GnuPlotIO::write_solution ( const std::string &  fname, const std::vector< Number > *  soln = nullptr, const std::vector< std::string > *  names = nullptr  )

private

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

This will write an ASCII file.

Definition at line 59 of file gnuplot_io.C.

{
  // Even when writing on a serialized DistributedMesh, we expect
  // non-proc-0 help with calls like n_active_elem
  // libmesh_assert_equal_to (this->mesh().processor_id(), 0);
 
  const MeshBase & the_mesh = MeshOutput<MeshBase>::mesh();
 
  dof_id_type n_active_elem = the_mesh.n_active_elem();
 
  if (this->mesh().processor_id() == 0)
    {
      std::stringstream data_stream_name;
      data_stream_name << fname << "_data";
      const std::string data_file_name = data_stream_name.str();
 
      // This class is designed only for use with 1D meshes
      libmesh_assert_equal_to (the_mesh.mesh_dimension(), 1);
 
      // Make sure we have a solution to plot
      libmesh_assert ((names != nullptr) && (soln != nullptr));
 
      // Create an output stream for script file
      std::ofstream out_stream(fname.c_str());
 
      // Make sure it opened correctly
      if (!out_stream.good())
        libmesh_file_error(fname.c_str());
 
      // The number of variables in the equation system
      const unsigned int n_vars =
        cast_int<unsigned int>(names->size());
 
      // Write header to stream
      out_stream << "# This file was generated by gnuplot_io.C\n"
                 << "# Stores 1D solution data in GNUplot format\n"
                 << "# Execute this by loading gnuplot and typing "
                 << "\"call '" << fname << "'\"\n"
                 << "reset\n"
                 << "set title \"" << _title << "\"\n"
                 << "set xlabel \"x\"\n"
                 << "set xtics nomirror\n";
 
      // Loop over the elements to find the minimum and maximum x values,
      // and also to find the element boundaries to write out as xtics
      // if requested.
      Real x_min=0., x_max=0.;
 
      // construct string for xtic positions at element edges
      std::stringstream xtics_stream;
 
      unsigned int count = 0;
 
      for (const auto & el : the_mesh.active_element_ptr_range())
        {
          // if el is the left edge of the mesh, print its left node position
          if (el->neighbor_ptr(0) == nullptr)
            {
              x_min = (el->point(0))(0);
              xtics_stream << "\"\" " << x_min << ", \\\n";
            }
          if (el->neighbor_ptr(1) == nullptr)
            {
              x_max = (el->point(1))(0);
            }
          xtics_stream << "\"\" " << (el->point(1))(0);
 
          if (count+1 != n_active_elem)
            {
              xtics_stream << ", \\\n";
            }
          count++;
        }
 
      out_stream << "set xrange [" << x_min << ":" << x_max << "]\n";
 
      if (_grid)
        out_stream << "set x2tics (" << xtics_stream.str() << ")\nset grid noxtics noytics x2tics\n";
 
      if (_png_output)
        {
          out_stream << "set terminal png\n";
          out_stream << "set output \"" << fname << ".png\"\n";
        }
 
      out_stream << "plot "
                 << axes_limits
                 << " \"" << data_file_name << "\" using 1:2 title \"" << (*names)[0]
                 << "\" with lines";
      if (n_vars > 1)
        {
          for (unsigned int i=1; i<n_vars; i++)
            {
              out_stream << ", \\\n\"" << data_file_name << "\" using 1:" << i+2
                         << " title \"" << (*names)[i] << "\" with lines";
            }
        }
 
      out_stream.close();
 
 
      // Create an output stream for data file
      std::ofstream data(data_file_name.c_str());
 
      libmesh_error_msg_if(!data.good(), "ERROR: opening output data file " << data_file_name);
 
      // get ordered nodal data using a map
      std::map<Real, std::vector<Number>> node_map;
 
      for (const auto & elem : the_mesh.active_element_ptr_range())
        for (const auto & node : elem->node_ref_range())
          {
            dof_id_type global_id = node.id();
 
            std::vector<Number> values;
            for (unsigned int c=0; c<n_vars; c++)
              values.push_back((*soln)[global_id*n_vars + c]);
 
            node_map[the_mesh.point(global_id)(0)] = values;
          }
 
      for (const auto & pr : node_map)
        {
          const std::vector<Number> & values = pr.second;
 
          data << pr.first << "\t";
 
          for (const auto & val : values)
            data << val << "\t";
 
          data << "\n";
        }
 
      data.close();
    }
}

References _grid, _png_output, _title, axes_limits, libMesh::libmesh_assert(), libMesh::MeshOutput< MeshBase >::mesh(), libMesh::MeshOutput< MT >::mesh(), libMesh::MeshBase::mesh_dimension(), libMesh::MeshBase::n_active_elem(), n_vars, libMesh::MeshBase::point(), and libMesh::Real.

Referenced by write(), and write_nodal_data().

Member Data Documentation

_ascii_precision

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

privateinherited

Precision to use when writing ASCII files.

Definition at line 207 of file mesh_output.h.

_grid

bool libMesh::GnuPlotIO::_grid

private

Definition at line 121 of file gnuplot_io.h.

Referenced by GnuPlotIO(), use_grid(), and write_solution().

_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.

_obj

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

privateinherited

A pointer to a constant object.

This allows us to write the object to file.

Definition at line 202 of file mesh_output.h.

_png_output

bool libMesh::GnuPlotIO::_png_output

private

Definition at line 122 of file gnuplot_io.h.

Referenced by GnuPlotIO(), set_png_output(), and write_solution().

_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.

_title

std::string libMesh::GnuPlotIO::_title

private

Definition at line 119 of file gnuplot_io.h.

Referenced by set_title(), and write_solution().

axes_limits

std::string libMesh::GnuPlotIO::axes_limits

GNUplot automatically adjusts the x and y-axes of 2D plots to "zoom in" on the data.

You can set this string to force GNUplot to maintain a fixed set of axes. Example: axes_limits = "[0:1] [0:1]" would force x and y to be plotted on the range 0<=x<=1 and 0<=y<=1 regardless of where the data lie.

Definition at line 107 of file gnuplot_io.h.

Referenced by write_solution().

---

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

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