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 &) override
 
virtual void write_nodal_data (const std::string &, const std::vector< Number > &, const std::vector< std::string > &) override
 
bool & binary ()
 
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

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 > *=nullptr, const std::vector< std::string > *=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

◆ MEDITIO() [1/2]

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

◆ MEDITIO() [2/2]

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

◆ 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().

245 {
246  return _ascii_precision;
247 }

◆ binary()

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 }

◆ mesh()

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

◆ write()

void libMesh::MEDITIO::write ( const std::string &  fname)
overridevirtual

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(), 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 }
const MeshBase & mesh() const
Definition: mesh_output.h:234
bool & binary()
Definition: medit_io.h:130
void write_ascii(const std::string &, const std::vector< Number > *=nullptr, const std::vector< std::string > *=nullptr)
Definition: medit_io.C:59

◆ write_ascii()

void libMesh::MEDITIO::write_ascii ( const std::string &  fname,
const std::vector< Number > *  vec = nullptr,
const std::vector< std::string > *  solution_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 medit_io.C.

References libMesh::MeshBase::active_element_ptr_range(), libMesh::MeshTools::Generation::Private::idx(), 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 != nullptr) &&
177  (vec != 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 }
const MeshBase & mesh() const
Definition: mesh_output.h:234
unsigned int scalar_idx
Definition: medit_io.h:105
const unsigned int n_vars
Definition: tecplot_io.C:69
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

◆ 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().

95 {
96  LOG_SCOPE("write_discontinuous_equation_systems()", "MeshOutput");
97 
98  // We may need to gather and/or renumber a DistributedMesh to output
99  // it, making that const qualifier in our constructor a dirty lie
100  MT & my_mesh = const_cast<MT &>(*_obj);
101 
102  // If we're asked to write data that's associated with a different
103  // mesh, output files full of garbage are the result.
104  libmesh_assert_equal_to(&es.get_mesh(), _obj);
105 
106  // A non-renumbered mesh may not have a contiguous numbering, and
107  // that needs to be fixed before we can build a solution vector.
108  if (my_mesh.max_elem_id() != my_mesh.n_elem() ||
109  my_mesh.max_node_id() != my_mesh.n_nodes())
110  {
111  // If we were allowed to renumber then we should have already
112  // been properly renumbered...
113  libmesh_assert(!my_mesh.allow_renumbering());
114 
115  libmesh_do_once(libMesh::out <<
116  "Warning: This MeshOutput subclass only supports meshes which are contiguously renumbered!"
117  << std::endl;);
118 
119  my_mesh.allow_renumbering(true);
120 
121  my_mesh.renumber_nodes_and_elements();
122 
123  // Not sure what good going back to false will do here, the
124  // renumbering horses have already left the barn...
125  my_mesh.allow_renumbering(false);
126  }
127 
128  MeshSerializer serialize(const_cast<MT &>(*_obj), !_is_parallel_format, _serial_only_needed_on_proc_0);
129 
130  // Build the list of variable names that will be written.
131  std::vector<std::string> names;
132  es.build_variable_names (names, nullptr, system_names);
133 
134  if (!_is_parallel_format)
135  {
136  // Build the nodal solution values & get the variable
137  // names from the EquationSystems object
138  std::vector<Number> soln;
139  es.build_discontinuous_solution_vector (soln, system_names);
140 
141  this->write_nodal_data_discontinuous (fname, soln, names);
142  }
143  else // _is_parallel_format
144  {
145  libmesh_not_implemented();
146  }
147 }
virtual void write_nodal_data_discontinuous(const std::string &, const std::vector< Number > &, const std::vector< std::string > &)
Definition: mesh_output.h:114
const MeshBase *const _obj
Definition: mesh_output.h:177
OStreamProxy out(std::cout)

◆ 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().

34 {
35  LOG_SCOPE("write_equation_systems()", "MeshOutput");
36 
37  // We may need to gather and/or renumber a DistributedMesh to output
38  // it, making that const qualifier in our constructor a dirty lie
39  MT & my_mesh = const_cast<MT &>(*_obj);
40 
41  // If we're asked to write data that's associated with a different
42  // mesh, output files full of garbage are the result.
43  libmesh_assert_equal_to(&es.get_mesh(), _obj);
44 
45  // A non-renumbered mesh may not have a contiguous numbering, and
46  // that needs to be fixed before we can build a solution vector.
47  if (my_mesh.max_elem_id() != my_mesh.n_elem() ||
48  my_mesh.max_node_id() != my_mesh.n_nodes())
49  {
50  // If we were allowed to renumber then we should have already
51  // been properly renumbered...
52  libmesh_assert(!my_mesh.allow_renumbering());
53 
54  libmesh_do_once(libMesh::out <<
55  "Warning: This MeshOutput subclass only supports meshes which are contiguously renumbered!"
56  << std::endl;);
57 
58  my_mesh.allow_renumbering(true);
59 
60  my_mesh.renumber_nodes_and_elements();
61 
62  // Not sure what good going back to false will do here, the
63  // renumbering horses have already left the barn...
64  my_mesh.allow_renumbering(false);
65  }
66 
67  MeshSerializer serialize(const_cast<MT &>(*_obj), !_is_parallel_format, _serial_only_needed_on_proc_0);
68 
69  // Build the list of variable names that will be written.
70  std::vector<std::string> names;
71  es.build_variable_names (names, nullptr, system_names);
72 
74  {
75  // Build the nodal solution values & get the variable
76  // names from the EquationSystems object
77  std::vector<Number> soln;
78  es.build_solution_vector (soln, system_names);
79 
80  this->write_nodal_data (fname, soln, names);
81  }
82  else // _is_parallel_format
83  {
84  std::unique_ptr<NumericVector<Number>> parallel_soln =
85  es.build_parallel_solution_vector(system_names);
86 
87  this->write_nodal_data (fname, *parallel_soln, names);
88  }
89 }
virtual void write_nodal_data(const std::string &, const std::vector< Number > &, const std::vector< std::string > &)
Definition: mesh_output.h:105
const MeshBase *const _obj
Definition: mesh_output.h:177
OStreamProxy out(std::cout)

◆ write_nodal_data() [1/2]

void libMesh::MEDITIO::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 46 of file medit_io.C.

References binary(), libMesh::MeshOutput< MeshBase >::mesh(), 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 }
const MeshBase & mesh() const
Definition: mesh_output.h:234
bool & binary()
Definition: medit_io.h:130
void write_ascii(const std::string &, const std::vector< Number > *=nullptr, const std::vector< std::string > *=nullptr)
Definition: medit_io.C:59

◆ 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().

153 {
154  // This is the fallback implementation for parallel I/O formats that
155  // do not yet implement proper writing in parallel, and instead rely
156  // on the full solution vector being available on all processors.
157  std::vector<Number> soln;
158  parallel_soln.localize(soln);
159  this->write_nodal_data(fname, soln, names);
160 }
virtual void write_nodal_data(const std::string &, const std::vector< Number > &, const std::vector< std::string > &)
Definition: mesh_output.h:105
virtual void localize(std::vector< T > &v_local) const =0

◆ 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.

117  { libmesh_not_implemented(); }

Member Data Documentation

◆ _binary

bool libMesh::MEDITIO::_binary
private

Flag to write binary data.

Definition at line 103 of file medit_io.h.

Referenced by binary().

◆ _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().

◆ _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.

◆ scalar_idx

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: