libMesh::FroIO Class Reference

#include <fro_io.h>

Inheritance diagram for libMesh::FroIO:

Public Member Functions

 FroIO (const MeshBase &)
 
virtual void write (const std::string &) override
 
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 std::vector< Number > &, const std::vector< std::string > &)
 
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
 

Detailed Description

This class implements writing meshes in the .fro format used by the MIT ACDL. Valid only for triangular meshes.

Author
Benjamin S. Kirk
Date
2007

Definition at line 42 of file fro_io.h.

Constructor & Destructor Documentation

◆ FroIO()

libMesh::FroIO::FroIO ( 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 64 of file fro_io.h.

64  :
65  MeshOutput<MeshBase> (mesh_in)
66 {
67 }

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 }

◆ mesh()

◆ write()

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

This method implements writing a mesh to a specified file.

Implements libMesh::MeshOutput< MeshBase >.

Definition at line 41 of file fro_io.C.

References libMesh::MeshOutput< MeshBase >::_is_parallel_format, libMesh::MeshBase::active_element_ptr_range(), bc_id, libMesh::BoundaryInfo::build_side_list(), libMesh::Elem::build_side_ptr(), libMesh::MeshBase::elem_ref(), libMesh::BoundaryInfo::get_boundary_ids(), libMesh::MeshBase::get_boundary_info(), libMesh::MeshOutput< MeshBase >::mesh(), libMesh::MeshOutput< MT >::mesh(), libMesh::BoundaryInfo::n_boundary_ids(), libMesh::MeshBase::n_elem(), libMesh::MeshBase::n_nodes(), libMesh::MeshBase::point(), side, and libMesh::TRI3.

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

42 {
43  // We may need to gather a DistributedMesh to output it, making that
44  // const qualifier in our constructor a dirty lie
45  MeshSerializer serialize(const_cast<MeshBase &>(this->mesh()), !_is_parallel_format);
46 
47  if (this->mesh().processor_id() == 0)
48  {
49  // Open the output file stream
50  std::ofstream out_stream (fname.c_str());
51  libmesh_assert (out_stream.good());
52 
53  // Make sure it opened correctly
54  if (!out_stream.good())
55  libmesh_file_error(fname.c_str());
56 
57  // Get a reference to the mesh
58  const MeshBase & the_mesh = MeshOutput<MeshBase>::mesh();
59 
60  // Write the header
61  out_stream << the_mesh.n_elem() << " "
62  << the_mesh.n_nodes() << " "
63  << "0 0 "
64  << the_mesh.get_boundary_info().n_boundary_ids() << " 1\n";
65 
66  // Write the nodes -- 1-based!
67  for (unsigned int n=0; n<the_mesh.n_nodes(); n++)
68  out_stream << n+1 << " \t"
69  << std::scientific
70  << std::setprecision(12)
71  << the_mesh.point(n)(0) << " \t"
72  << the_mesh.point(n)(1) << " \t"
73  << 0. << '\n';
74 
75  // Write the elements -- 1-based!
76  unsigned int e = 0;
77  for (const auto & elem : the_mesh.active_element_ptr_range())
78  {
79  // .fro likes TRI3's
80  if (elem->type() != TRI3)
81  libmesh_error_msg("ERROR: .fro format only valid for triangles!\n" \
82  << " writing of " << fname << " aborted.");
83 
84  out_stream << ++e << " \t";
85 
86  for (unsigned int n=0; n<elem->n_nodes(); n++)
87  out_stream << elem->node_id(n)+1 << " \t";
88 
89  // // LHS -> RHS Mapping, for inverted triangles
90  // out_stream << elem->node_id(0)+1 << " \t";
91  // out_stream << elem->node_id(2)+1 << " \t";
92  // out_stream << elem->node_id(1)+1 << " \t";
93 
94  out_stream << "1\n";
95  }
96 
97  // Write BCs.
98  {
99  const std::set<boundary_id_type> & bc_ids =
100  the_mesh.get_boundary_info().get_boundary_ids();
101 
102  // Build a list of (elem, side, bc) tuples.
103  auto bc_triples = the_mesh.get_boundary_info().build_side_list();
104 
105  // Map the boundary ids into [1,n_bc_ids],
106  // treat them one at a time.
108  for (const auto & id : bc_ids)
109  {
110  std::deque<dof_id_type> node_list;
111 
112  std::map<dof_id_type, dof_id_type>
113  forward_edges, backward_edges;
114 
115  // Get all sides on this element with the relevant BC id.
116  for (const auto & t : bc_triples)
117  if (std::get<2>(t) == id)
118  {
119  // need to build up node_list as a sorted array of edge nodes...
120  // for the following:
121  // a---b---c---d---e
122  // node_list [ a b c d e];
123  //
124  // the issue is just how to get this out of the elem/side based data structure.
125  // the approach is to build up 'chain links' like this:
126  // a---b b---c c---d d---e
127  // and piece them together.
128  //
129  // so, for an arbitrary edge n0---n1, we build the
130  // "forward_edges" map n0-->n1
131  // "backward_edges" map n1-->n0
132  // and then start with one chain link, and add on...
133  //
134  std::unique_ptr<const Elem> side =
135  the_mesh.elem_ref(std::get<0>(t)).build_side_ptr(std::get<1>(t));
136 
137  const dof_id_type
138  n0 = side->node_id(0),
139  n1 = side->node_id(1);
140 
141  // insert into forward-edge set
142  forward_edges.insert (std::make_pair(n0, n1));
143 
144  // insert into backward-edge set
145  backward_edges.insert (std::make_pair(n1, n0));
146 
147  // go ahead and add one edge to the list -- this will give us the beginning of a
148  // chain to work from!
149  if (node_list.empty())
150  {
151  node_list.push_front(n0);
152  node_list.push_back (n1);
153  }
154  }
155 
156  // we now have the node_list with one edge, the forward_edges, and the backward_edges
157  // the node_list will be filled when (node_list.size() == (n_edges+1))
158  // until that is the case simply add on to the beginning and end of the node_list,
159  // building up a chain of ordered nodes...
160  const std::size_t n_edges = forward_edges.size();
161 
162  while (node_list.size() != (n_edges+1))
163  {
164  const dof_id_type
165  front_node = node_list.front(),
166  back_node = node_list.back();
167 
168  // look for front_pair in the backward_edges list
169  {
170  auto pos = backward_edges.find(front_node);
171 
172  if (pos != backward_edges.end())
173  {
174  node_list.push_front(pos->second);
175 
176  backward_edges.erase(pos);
177  }
178  }
179 
180  // look for back_pair in the forward_edges list
181  {
182  auto pos = forward_edges.find(back_node);
183 
184  if (pos != forward_edges.end())
185  {
186  node_list.push_back(pos->second);
187 
188  forward_edges.erase(pos);
189  }
190  }
191  }
192 
193  out_stream << ++bc_id << " " << node_list.size() << '\n';
194 
195  for (const auto & node_id : node_list)
196  out_stream << node_id + 1 << " \t0\n";
197  }
198  }
199  }
200 }
const MeshBase & mesh() const
Definition: mesh_output.h:234
unsigned short int side
Definition: xdr_io.C:50
boundary_id_type bc_id
Definition: xdr_io.C:51
int8_t boundary_id_type
Definition: id_types.h:51
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]

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

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

Reimplemented in libMesh::ExodusII_IO, libMesh::Nemesis_IO, libMesh::UCDIO, libMesh::NameBasedIO, libMesh::GmshIO, libMesh::GMVIO, libMesh::VTKIO, libMesh::MEDITIO, libMesh::GnuPlotIO, and libMesh::TecplotIO.

Definition at line 105 of file mesh_output.h.

108  { libmesh_not_implemented(); }

◆ 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

◆ _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 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.


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