libMesh
Public Member Functions | Protected Member Functions | Protected Attributes | Private Member Functions | Private Attributes | List of all members
libMesh::MEDITIO Class Reference

This class implements writing meshes in the mesh format used by the MEdit visualization tool developed in the Gamma Project at INRIA Roquencourt. More...

#include <medit_io.h>

Inheritance diagram for libMesh::MEDITIO:
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Public Member Functions

 MEDITIO (const MeshBase &)
 Constructor. More...
 
 MEDITIO (const MeshBase &, unsigned int c)
 Constructor. More...
 
virtual void write (const std::string &) libmesh_override
 This method implements writing a mesh to a specified ".mesh" file. More...
 
virtual void write_nodal_data (const std::string &, const std::vector< Number > &, const std::vector< std::string > &) libmesh_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 & binary ()
 Flag indicating whether or not to write a binary file. More...
 
virtual void write_equation_systems (const std::string &, const EquationSystems &, const std::set< std::string > *system_names=libmesh_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_nodal_data (const std::string &, const NumericVector< Number > &, const std::vector< std::string > &)
 This method should be overridden by "parallel" output formats for writing nodal data. More...
 
unsigned intascii_precision ()
 Return/set the precision to use when writing ASCII files. More...
 

Protected Member Functions

const MeshBasemesh () const
 

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 Member Functions

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

Private Attributes

bool _binary
 Flag to write binary data. More...
 
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)
explicit

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
bool _binary
Flag to write binary data.
Definition: medit_io.h:103
libMesh::MEDITIO::MEDITIO ( const MeshBase mesh_in,
unsigned int  c 
)

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
bool _binary
Flag to write binary data.
Definition: medit_io.h:103

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 ( )

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 }
bool _binary
Flag to write binary data.
Definition: medit_io.h:103
const MeshBase & libMesh::MeshOutput< MeshBase >::mesh ( ) const
protectedinherited
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)
This method implements writing a mesh with nodal data to a specified file where the nodal data and va...
Definition: medit_io.C:59
const MeshBase & mesh() const
bool & binary()
Flag indicating whether or not to write a binary file.
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_element_ptr_range(), 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  for (const auto & elem : the_mesh.active_element_ptr_range())
108  {
109  if (elem->type() == TRI3) n_tri3++;
110  if (elem->type() == QUAD4) n_quad4++;
111  if (elem->type() == QUAD9) n_quad4+=4; // (QUAD9 is written as 4 QUAD4.)
112  if (elem->type() == TET4) n_tet4++;
113  }
114 
115  // First: write out TRI3 elements:
116  out_stream << "Triangles\n";
117  out_stream << n_tri3 << "\n";
118 
119  for (const auto & elem : the_mesh.active_element_ptr_range())
120  if (elem->type() == TRI3)
121  out_stream << elem->node_id(0)+1 << " "
122  << elem->node_id(1)+1 << " "
123  << elem->node_id(2)+1 << " 0\n";
124 
125  // Second: write out QUAD4 elements:
126  out_stream << "Quadrilaterals\n";
127  out_stream << n_quad4 << "\n";
128 
129  for (const auto & elem : the_mesh.active_element_ptr_range())
130  {
131  if (elem->type() == QUAD4)
132  {
133  out_stream << elem->node_id(0)+1 << " "
134  << elem->node_id(1)+1 << " "
135  << elem->node_id(2)+1 << " "
136  << elem->node_id(3)+1 <<" 0\n";
137  } // if
138  else if (elem->type() == QUAD9)
139  {
140  out_stream << elem->node_id(0)+1 << " "
141  << elem->node_id(4)+1 << " "
142  << elem->node_id(8)+1 << " "
143  << elem->node_id(7)+1 <<" 0\n";
144  out_stream << elem->node_id(7)+1 << " "
145  << elem->node_id(8)+1 << " "
146  << elem->node_id(6)+1 << " "
147  << elem->node_id(3)+1 <<" 0\n";
148  out_stream << elem->node_id(4)+1 << " "
149  << elem->node_id(1)+1 << " "
150  << elem->node_id(5)+1 << " "
151  << elem->node_id(8)+1 <<" 0\n";
152  out_stream << elem->node_id(8)+1 << " "
153  << elem->node_id(5)+1 << " "
154  << elem->node_id(2)+1 << " "
155  << elem->node_id(6)+1 <<" 0\n";
156  }
157  }
158 
159  // Third: write out TET4 elements:
160  out_stream << "Tetrahedra\n";
161  out_stream << n_tet4 << "\n";
162 
163  for (const auto & elem : the_mesh.active_element_ptr_range())
164  if (elem->type() == TET4)
165  {
166  out_stream << elem->node_id(0)+1 << " "
167  << elem->node_id(1)+1 << " "
168  << elem->node_id(2)+1 << " "
169  << elem->node_id(3)+1 <<" 0\n";
170  }
171  }
172  // end of the out file
173  out_stream << '\n' << "# end of file\n";
174 
175  // optionally write the data
176  if ((solution_names != libmesh_nullptr) &&
177  (vec != libmesh_nullptr))
178  {
179  // Open the ".bb" file stream
180  std::size_t idx = fname.find_last_of(".");
181  std::string bbname = fname.substr(0,idx) + ".bb";
182 
183  std::ofstream bbout (bbname.c_str());
184 
185  // Make sure it opened correctly
186  if (!bbout.good())
187  libmesh_file_error(bbname.c_str());
188 
189  // Header: 3: 3D mesh, 1: scalar output, 2: node-indexed
190  const std::size_t n_vars = solution_names->size();
191  bbout << "3 1 " << the_mesh.n_nodes() << " 2\n";
192  for (dof_id_type n=0; n<the_mesh.n_nodes(); n++)
193  bbout << std::setprecision(10) << (*vec)[n*n_vars + scalar_idx] << " ";
194  bbout << "\n";
195  } // endif
196 }
unsigned int scalar_idx
Definition: medit_io.h:105
const class libmesh_nullptr_t libmesh_nullptr
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)
A useful inline function which replaces the macros used previously.
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)
This method implements writing a mesh with nodal data to a specified file where the nodal data and va...
Definition: medit_io.C:59
const MeshBase & mesh() const
bool & binary()
Flag indicating whether or not to write a binary file.
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: