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

This class implements writing meshes in the .fro format used by the MIT ACDL. More...

#include <fro_io.h>

Inheritance diagram for libMesh::FroIO:
[legend]

Public Member Functions

 FroIO (const MeshBase &)
 Constructor. More...
 
virtual void write (const std::string &) override
 This method implements writing a mesh to a specified file. More...
 
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. More...
 
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. More...
 
virtual void write_nodal_data (const std::string &, const std::vector< Number > &, const std::vector< std::string > &)
 This method implements writing a mesh with nodal data to a specified file where the nodal data and variable names are provided. More...
 
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. More...
 
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. More...
 
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. More...
 
unsigned int & ascii_precision ()
 Return/set the precision to use when writing ASCII files. More...
 

Protected Member Functions

const MeshBase & mesh () 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 Attributes

const MeshBase *const _obj
 A pointer to a constant object. More...
 
unsigned int _ascii_precision
 Precision to use when writing ASCII files. More...
 

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>::max_digits10, which should be enough to write out to ASCII and get the exact same Real back when reading in.

Definition at line 257 of file mesh_output.h.

258 {
259  return _ascii_precision;
260 }

◆ mesh()

const MeshBase & libMesh::MeshOutput< MeshBase >::mesh ( ) const
inlineprotectedinherited
Returns
The object as a read-only reference.

Definition at line 247 of file mesh_output.h.

248 {
249  libmesh_assert(_obj);
250  return *_obj;
251 }

◆ 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.

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 (auto n : IntRange<unsigned int>(0, the_mesh.n_nodes()))
68  out_stream << n+1 << " \t"
69  << std::scientific
70  << std::setprecision(this->ascii_precision())
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 (const Node & node : elem->node_ref_range())
87  out_stream << node.id()+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.
107  boundary_id_type bc_id=0;
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 }

References libMesh::MeshOutput< MeshBase >::_is_parallel_format, libMesh::MeshBase::active_element_ptr_range(), libMesh::MeshOutput< MeshBase >::ascii_precision(), 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::libmesh_assert(), libMesh::MeshOutput< MeshBase >::mesh(), libMesh::MeshOutput< MT >::mesh(), libMesh::BoundaryInfo::n_boundary_ids(), libMesh::MeshBase::n_elem(), libMesh::MeshBase::n_nodes(), libMesh::MeshBase::point(), and libMesh::TRI3.

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

◆ 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 87 of file mesh_output.C.

90 {
91  LOG_SCOPE("write_discontinuous_equation_systems()", "MeshOutput");
92 
93  // We may need to gather and/or renumber a DistributedMesh to output
94  // it, making that const qualifier in our constructor a dirty lie
95  MT & my_mesh = const_cast<MT &>(*_obj);
96 
97  // If we're asked to write data that's associated with a different
98  // mesh, output files full of garbage are the result.
99  libmesh_assert_equal_to(&es.get_mesh(), _obj);
100 
101  // A non-renumbered mesh may not have a contiguous numbering, and
102  // that needs to be fixed before we can build a solution vector.
103  if (my_mesh.max_elem_id() != my_mesh.n_elem() ||
104  my_mesh.max_node_id() != my_mesh.n_nodes())
105  {
106  // If we were allowed to renumber then we should have already
107  // been properly renumbered...
108  libmesh_assert(!my_mesh.allow_renumbering());
109 
110  libmesh_do_once(libMesh::out <<
111  "Warning: This MeshOutput subclass only supports meshes which are contiguously renumbered!"
112  << std::endl;);
113 
114  my_mesh.allow_renumbering(true);
115 
116  my_mesh.renumber_nodes_and_elements();
117 
118  // Not sure what good going back to false will do here, the
119  // renumbering horses have already left the barn...
120  my_mesh.allow_renumbering(false);
121  }
122 
123  MeshSerializer serialize(const_cast<MT &>(*_obj), !_is_parallel_format, _serial_only_needed_on_proc_0);
124 
125  // Build the list of variable names that will be written.
126  std::vector<std::string> names;
127  es.build_variable_names (names, nullptr, system_names);
128 
129  if (!_is_parallel_format)
130  {
131  // Build the nodal solution values & get the variable
132  // names from the EquationSystems object
133  std::vector<Number> soln;
134  es.build_discontinuous_solution_vector (soln, system_names);
135 
136  this->write_nodal_data_discontinuous (fname, soln, names);
137  }
138  else // _is_parallel_format
139  {
140  libmesh_not_implemented();
141  }
142 }

◆ 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.

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  if (!_is_parallel_format)
68  {
69  MeshSerializer serialize(const_cast<MT &>(*_obj), !_is_parallel_format, _serial_only_needed_on_proc_0);
70 
71  // Build the list of variable names that will be written.
72  std::vector<std::string> names;
73  es.build_variable_names (names, nullptr, system_names);
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  this->write_nodal_data (fname, es, system_names);
84 }

◆ 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 158 of file mesh_output.C.

161 {
162  std::vector<std::string> names;
163  es.build_variable_names (names, nullptr, system_names);
164 
165  std::unique_ptr<NumericVector<Number>> parallel_soln =
166  es.build_parallel_solution_vector(system_names);
167 
168  this->write_nodal_data (fname, *parallel_soln, names);
169 }

◆ 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 145 of file mesh_output.C.

148 {
149  // This is the fallback implementation for parallel I/O formats that
150  // do not yet implement proper writing in parallel, and instead rely
151  // on the full solution vector being available on all processors.
152  std::vector<Number> soln;
153  parallel_soln.localize(soln);
154  this->write_nodal_data(fname, soln, names);
155 }

◆ write_nodal_data() [3/3]

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::Nemesis_IO, libMesh::UCDIO, libMesh::ExodusII_IO, libMesh::GmshIO, libMesh::NameBasedIO, 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_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

◆ _ascii_precision

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

Precision to use when writing ASCII files.

Definition at line 195 of file mesh_output.h.

◆ _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 172 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 190 of file mesh_output.h.

◆ _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 181 of file mesh_output.h.

The documentation for this class was generated from the following files:
libMesh::dof_id_type
uint8_t dof_id_type
Definition: id_types.h:67
libMesh::MeshOutput< MeshBase >::_serial_only_needed_on_proc_0
const bool _serial_only_needed_on_proc_0
Flag specifying whether this format can be written by only serializing the mesh to processor zero.
Definition: mesh_output.h:181
libMesh::boundary_id_type
int8_t boundary_id_type
Definition: id_types.h:51
libMesh::MeshOutput< MeshBase >::ascii_precision
unsigned int & ascii_precision()
Return/set the precision to use when writing ASCII files.
Definition: mesh_output.h:257
libMesh::libmesh_assert
libmesh_assert(ctx)
libMesh::NumericVector::localize
virtual void localize(std::vector< T > &v_local) const =0
Creates a copy of the global vector in the local vector v_local.
libMesh::MeshOutput< MeshBase >::_is_parallel_format
const bool _is_parallel_format
Flag specifying whether this format is parallel-capable.
Definition: mesh_output.h:172
libMesh::TRI3
Definition: enum_elem_type.h:39
libMesh::MeshOutput< MeshBase >::write_nodal_data
virtual void write_nodal_data(const std::string &, const std::vector< Number > &, const std::vector< std::string > &)
This method implements writing a mesh with nodal data to a specified file where the nodal data and va...
Definition: mesh_output.h:105
libMesh::MeshOutput< MeshBase >::mesh
const MeshBase & mesh() const
Definition: mesh_output.h:247
libMesh::MeshOutput< MeshBase >::write_nodal_data_discontinuous
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 dat...
Definition: mesh_output.h:114
libMesh::MeshOutput< MeshBase >::_obj
const MeshBase *const _obj
A pointer to a constant object.
Definition: mesh_output.h:190
libMesh::out
OStreamProxy out
libMesh::MeshOutput< MeshBase >::_ascii_precision
unsigned int _ascii_precision
Precision to use when writing ASCII files.
Definition: mesh_output.h:195
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