libMesh::MEDITIO Class Reference

#include <medit_io.h>

Inheritance diagram for libMesh::MEDITIO:

Public Member Functions

 MEDITIO (const MeshBase &)
 
 MEDITIO (const MeshBase &, unsigned int c)
 
virtual void write (const std::string &) libmesh_override
 
virtual void write_nodal_data (const std::string &, const std::vector< Number > &, const std::vector< std::string > &) libmesh_override
 
bool & binary ()
 
virtual void write_equation_systems (const std::string &, const EquationSystems &, const std::set< std::string > *system_names=libmesh_nullptr)
 
virtual void write_nodal_data (const std::string &, const NumericVector< Number > &, const std::vector< std::string > &)
 
unsigned int & ascii_precision ()
 

Protected Member Functions

const MeshBasemesh () const
 

Protected Attributes

const bool _is_parallel_format
 
const bool _serial_only_needed_on_proc_0
 

Private Member Functions

void write_ascii (const std::string &, const std::vector< Number > *=libmesh_nullptr, const std::vector< std::string > *=libmesh_nullptr)
 

Private Attributes

bool _binary
 
unsigned int scalar_idx
 

Detailed Description

This class implements writing meshes in the mesh format used by the MEdit visualization tool developed in the Gamma Project at INRIA Roquencourt. For a full description of the mesh format and to obtain the MEdit software see the MEdit home page.

Author
Florian Prill
Date
2004

Definition at line 47 of file medit_io.h.

Constructor & Destructor Documentation

libMesh::MEDITIO::MEDITIO ( const MeshBase mesh_in)
inlineexplicit

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

Definition at line 113 of file medit_io.h.

113  :
114  MeshOutput<MeshBase> (mesh_in),
115  _binary (false),
116  scalar_idx (0)
117 {
118 }
unsigned int scalar_idx
Definition: medit_io.h:105
libMesh::MEDITIO::MEDITIO ( const MeshBase mesh_in,
unsigned int  c 
)
inline

Constructor. Takes a reference to a constant mesh object. and the desired scalar index for mesh colouring. MEdit seems to understand only one scalar value.

Definition at line 121 of file medit_io.h.

121  :
122  MeshOutput<MeshBase> (mesh_in),
123  _binary (false),
124  scalar_idx (c)
125 {
126 }
unsigned int scalar_idx
Definition: medit_io.h:105

Member Function Documentation

unsigned int& libMesh::MeshOutput< MeshBase >::ascii_precision ( )
inherited

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.

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

bool & libMesh::MEDITIO::binary ( )
inline

Flag indicating whether or not to write a binary file

Definition at line 130 of file medit_io.h.

References _binary.

Referenced by write(), and write_nodal_data().

131 {
132  return _binary;
133 }
void libMesh::MEDITIO::write ( const std::string &  fname)
virtual

This method implements writing a mesh to a specified ".mesh" file.

Implements libMesh::MeshOutput< MeshBase >.

Definition at line 37 of file medit_io.C.

References binary(), libMesh::MeshOutput< MeshBase >::mesh(), libMesh::processor_id(), and write_ascii().

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

38 {
39  if (this->mesh().processor_id() == 0)
40  if (!this->binary())
41  this->write_ascii (fname);
42 }
void write_ascii(const std::string &, const std::vector< Number > *=libmesh_nullptr, const std::vector< std::string > *=libmesh_nullptr)
Definition: medit_io.C:59
const MeshBase & mesh() const
bool & binary()
Definition: medit_io.h:130
processor_id_type processor_id()
Definition: libmesh_base.h:96
void libMesh::MEDITIO::write_ascii ( const std::string &  fname,
const std::vector< Number > *  vec = libmesh_nullptr,
const std::vector< std::string > *  solution_names = libmesh_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 medit_io.C.

References libMesh::MeshBase::active_elements_begin(), libMesh::MeshBase::active_elements_end(), end, libMesh::MeshTools::Generation::Private::idx(), libmesh_nullptr, libMesh::MeshOutput< MT >::mesh(), libMesh::MeshBase::n_nodes(), n_vars, libMesh::MeshBase::point(), libMesh::QUAD4, libMesh::QUAD9, scalar_idx, libMesh::TET4, and libMesh::TRI3.

Referenced by write(), and write_nodal_data().

62 {
63  // Current lacks in implementation:
64  // (i) only 3D meshes.
65  // (ii) only QUAD4, TRI3, TET4 elements, others are omitted !
66  // (iii) no distinction between materials.
67  // (iv) no vector output, just first scalar as output
68 
69  // libmesh_assert three dimensions (should be extended later)
70  libmesh_assert_equal_to (MeshOutput<MeshBase>::mesh().mesh_dimension(), 3);
71 
72  // Open the output file stream
73  std::ofstream out_stream (fname.c_str());
74 
75  // Make sure it opened correctly
76  if (!out_stream.good())
77  libmesh_file_error(fname.c_str());
78 
79  // Get a reference to the mesh
80  const MeshBase & the_mesh = MeshOutput<MeshBase>::mesh();
81 
82  // Begin interfacing with the MEdit data file
83  {
84  // header:
85  out_stream << "MeshVersionFormatted 1\n";
86  out_stream << "Dimension 3\n";
87  out_stream << "# Mesh generated by libmesh\n\n";
88 
89  // write the nodes:
90  out_stream << "# Set of mesh vertices\n";
91  out_stream << "Vertices\n";
92  out_stream << the_mesh.n_nodes() << "\n";
93 
94  for (unsigned int v=0; v<the_mesh.n_nodes(); v++)
95  out_stream << the_mesh.point(v)(0) << " " << the_mesh.point(v)(1) << " " << the_mesh.point(v)(2) << " 0\n";
96  }
97 
98  {
99  // write the connectivity:
100  out_stream << "\n# Set of Polys\n\n";
101 
102  // count occurrences of output elements:
103  int n_tri3 = 0;
104  int n_quad4 = 0;
105  int n_tet4 = 0;
106 
107  {
108  MeshBase::const_element_iterator it = the_mesh.active_elements_begin();
109  const MeshBase::const_element_iterator end = the_mesh.active_elements_end();
110 
111  for ( ; it != end; ++it)
112  {
113  if ((*it)->type() == TRI3) n_tri3++;
114  if ((*it)->type() == QUAD4) n_quad4++;
115  if ((*it)->type() == QUAD9) n_quad4+=4; // (QUAD9 is written as 4 QUAD4.)
116  if ((*it)->type() == TET4) n_tet4++;
117  } // for
118  }
119 
120  // First: write out TRI3 elements:
121  out_stream << "Triangles\n";
122  out_stream << n_tri3 << "\n";
123 
124  {
125  MeshBase::const_element_iterator it = the_mesh.active_elements_begin();
126  const MeshBase::const_element_iterator end = the_mesh.active_elements_end();
127 
128  for ( ; it != end; ++it)
129  if ((*it)->type() == TRI3)
130  out_stream << (*it)->node_id(0)+1 << " "
131  << (*it)->node_id(1)+1 << " "
132  << (*it)->node_id(2)+1 << " 0\n";
133  }
134 
135  // Second: write out QUAD4 elements:
136  out_stream << "Quadrilaterals\n";
137  out_stream << n_quad4 << "\n";
138 
139  {
140  MeshBase::const_element_iterator it = the_mesh.active_elements_begin();
141  const MeshBase::const_element_iterator end = the_mesh.active_elements_end();
142 
143  for ( ; it != end; ++it)
144  if ((*it)->type() == QUAD4)
145  {
146  out_stream << (*it)->node_id(0)+1 << " "
147  << (*it)->node_id(1)+1 << " "
148  << (*it)->node_id(2)+1 << " "
149  << (*it)->node_id(3)+1 <<" 0\n";
150  } // if
151  else if ((*it)->type() == QUAD9)
152  {
153  out_stream << (*it)->node_id(0)+1 << " "
154  << (*it)->node_id(4)+1 << " "
155  << (*it)->node_id(8)+1 << " "
156  << (*it)->node_id(7)+1 <<" 0\n";
157  out_stream << (*it)->node_id(7)+1 << " "
158  << (*it)->node_id(8)+1 << " "
159  << (*it)->node_id(6)+1 << " "
160  << (*it)->node_id(3)+1 <<" 0\n";
161  out_stream << (*it)->node_id(4)+1 << " "
162  << (*it)->node_id(1)+1 << " "
163  << (*it)->node_id(5)+1 << " "
164  << (*it)->node_id(8)+1 <<" 0\n";
165  out_stream << (*it)->node_id(8)+1 << " "
166  << (*it)->node_id(5)+1 << " "
167  << (*it)->node_id(2)+1 << " "
168  << (*it)->node_id(6)+1 <<" 0\n";
169  } // if
170  }
171 
172 
173  // Third: write out TET4 elements:
174  out_stream << "Tetrahedra\n";
175  out_stream << n_tet4 << "\n";
176 
177  {
178  MeshBase::const_element_iterator it = the_mesh.active_elements_begin();
179  const MeshBase::const_element_iterator end = the_mesh.active_elements_end();
180 
181  for ( ; it != end; ++it)
182  if ((*it)->type() == TET4)
183  {
184  out_stream << (*it)->node_id(0)+1 << " "
185  << (*it)->node_id(1)+1 << " "
186  << (*it)->node_id(2)+1 << " "
187  << (*it)->node_id(3)+1 <<" 0\n";
188  } // if
189  }
190 
191  }
192  // end of the out file
193  out_stream << '\n' << "# end of file\n";
194 
195  // optionally write the data
196  if ((solution_names != libmesh_nullptr) &&
197  (vec != libmesh_nullptr))
198  {
199  // Open the ".bb" file stream
200  std::size_t idx = fname.find_last_of(".");
201  std::string bbname = fname.substr(0,idx) + ".bb";
202 
203  std::ofstream bbout (bbname.c_str());
204 
205  // Make sure it opened correctly
206  if (!bbout.good())
207  libmesh_file_error(bbname.c_str());
208 
209  // Header: 3: 3D mesh, 1: scalar output, 2: node-indexed
210  const std::size_t n_vars = solution_names->size();
211  bbout << "3 1 " << the_mesh.n_nodes() << " 2\n";
212  for (dof_id_type n=0; n<the_mesh.n_nodes(); n++)
213  bbout << std::setprecision(10) << (*vec)[n*n_vars + scalar_idx] << " ";
214  bbout << "\n";
215  } // endif
216 }
unsigned int scalar_idx
Definition: medit_io.h:105
const class libmesh_nullptr_t libmesh_nullptr
IterBase * end
const MeshBase & mesh() const
const unsigned int n_vars
Definition: tecplot_io.C:68
unsigned int idx(const ElemType type, const unsigned int nx, const unsigned int i, const unsigned int j)
uint8_t dof_id_type
Definition: id_types.h:64
virtual void libMesh::MeshOutput< MeshBase >::write_equation_systems ( const std::string &  ,
const EquationSystems ,
const std::set< std::string > *  system_names = libmesh_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.

Referenced by libMesh::Nemesis_IO::write_timestep(), and libMesh::ExodusII_IO::write_timestep().

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

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 46 of file medit_io.C.

References binary(), libMesh::MeshOutput< MeshBase >::mesh(), libMesh::processor_id(), and write_ascii().

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

49 {
50  LOG_SCOPE("write_nodal_data()", "MEDITIO");
51 
52  if (this->mesh().processor_id() == 0)
53  if (!this->binary())
54  this->write_ascii (fname, &soln, &names);
55 }
void write_ascii(const std::string &, const std::vector< Number > *=libmesh_nullptr, const std::vector< std::string > *=libmesh_nullptr)
Definition: medit_io.C:59
const MeshBase & mesh() const
bool & binary()
Definition: medit_io.h:130
processor_id_type processor_id()
Definition: libmesh_base.h:96
virtual void libMesh::MeshOutput< MeshBase >::write_nodal_data ( const std::string &  ,
const NumericVector< Number > &  ,
const std::vector< std::string > &   
)
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.

Member Data Documentation

bool libMesh::MEDITIO::_binary
private

Flag to write binary data.

Definition at line 103 of file medit_io.h.

Referenced by binary().

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 141 of file mesh_output.h.

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

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 150 of file mesh_output.h.

unsigned int libMesh::MEDITIO::scalar_idx
private

Definition at line 105 of file medit_io.h.

Referenced by write_ascii().


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