libMesh::GmshIO Class Reference

Reading and writing meshes in the Gmsh format. More...

#include <gmsh_io.h>

Inheritance diagram for libMesh::GmshIO:

Classes
struct	ElementDefinition
	Defines mapping from libMesh element types to Gmsh element types or vice-versa. More...
struct	ElementMaps
	struct which holds a map from Gmsh to libMesh element numberings and vice-versa. More...

Public Member Functions
	GmshIO (MeshBase &mesh)
	Constructor. More...
	GmshIO (const MeshBase &mesh)
	Constructor. More...
virtual void	read (const std::string &name) override
	Reads in a mesh in the Gmsh *.msh format from the ASCII file given by name. More...
virtual void	write (const std::string &name) override
	This method implements writing a mesh to a specified file in the Gmsh *.msh format. More...
virtual void	write_nodal_data (const std::string &, const std::vector< Number > &, const std::vector< std::string > &) 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...
bool &	write_lower_dimensional_elements ()
	Access to the flag which controls whether boundary elements are written to the Mesh 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 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
MeshBase &	mesh ()
void	set_n_partitions (unsigned int n_parts)
	Sets the number of partitions in the mesh. More...
void	skip_comment_lines (std::istream &in, const char comment_start)
	Reads input from in, skipping all the lines that start with the character comment_start. More...
const MeshBase &	mesh () const

Protected Attributes
std::vector< bool >	elems_of_dimension
	A vector of bools describing what dimension elements have been encountered when reading a mesh. More...
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	read_mesh (std::istream &in)
	Implementation of the read() function. More...
void	write_mesh (std::ostream &out)
	This method implements writing a mesh to a specified file. More...
void	write_post (const std::string &, const std::vector< Number > *=nullptr, const std::vector< std::string > *=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...

Static Private Member Functions
static ElementMaps	build_element_maps ()
	A static function used to construct the _element_maps struct, statically. More...

Private Attributes
bool	_binary
	Flag to write binary data. More...
bool	_write_lower_dimensional_elements
	If true, lower-dimensional elements based on the boundary conditions get written to the output file. More...
MeshBase *	_obj
	A pointer to a non-const object object. More...
const bool	_is_parallel_format
	Flag specifying whether this format is parallel-capable. More...
unsigned int	_ascii_precision
	Precision to use when writing ASCII files. More...

Static Private Attributes
static ElementMaps	_element_maps = GmshIO::build_element_maps()
	A static ElementMaps object that is built statically and used by all instances of this class. More...

Detailed Description

Reading and writing meshes in the Gmsh format.

For a full description of the Gmsh format and to obtain the GMSH software see the Gmsh home page

Author

John W. Peterson

Date

2004, 2014

Author

Martin Luthi

Date

2005

Definition at line 51 of file gmsh_io.h.

Constructor & Destructor Documentation

GmshIO() [1/2]

libMesh::GmshIO::GmshIO ( MeshBase &  mesh )

explicit

Constructor.

Takes a non-const Mesh reference which it will fill up with elements via the read() command.

Definition at line 123 of file gmsh_io.C.

                               :
  MeshInput<MeshBase>  (mesh),
  MeshOutput<MeshBase> (mesh),
  _binary (false),
  _write_lower_dimensional_elements(true)
{
}

GmshIO() [2/2]

libMesh::GmshIO::GmshIO ( const MeshBase &  mesh )

explicit

Constructor.

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

Definition at line 114 of file gmsh_io.C.

                                     :
  MeshOutput<MeshBase>(mesh),
  _binary(false),
  _write_lower_dimensional_elements(true)
{
}

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.

{
  return _ascii_precision;
}

binary()

bool & libMesh::GmshIO::binary

(

)

Flag indicating whether or not to write a binary file.

While binary files may end up being smaller than equivalent ASCII files, they will almost certainly take longer to write. The reason for this is that the ostream::write() function which is used to write "binary" data to streams, only takes a pointer to char as its first argument. This means if you want to write anything other than a buffer of chars, you first have to use a strange memcpy hack to get the data into the desired format. See the templated to_binary_stream() function below.

Definition at line 133 of file gmsh_io.C.

{
  return _binary;
}

References _binary.

Referenced by write_post().

build_element_maps()

GmshIO::ElementMaps libMesh::GmshIO::build_element_maps ( )

staticprivate

A static function used to construct the _element_maps struct, statically.

Definition at line 45 of file gmsh_io.C.

{
  // Object to be filled up
  ElementMaps em;
 
  // POINT (import only)
  em.in.insert(std::make_pair(15, ElementDefinition(NODEELEM, 15, 0, 1)));
 
  // Add elements with trivial node mappings
  em.add_def(ElementDefinition(EDGE2, 1, 1, 2));
  em.add_def(ElementDefinition(EDGE3, 8, 1, 3));
  em.add_def(ElementDefinition(TRI3, 2, 2, 3));
  em.add_def(ElementDefinition(TRI6, 9, 2, 6));
  em.add_def(ElementDefinition(QUAD4, 3, 2, 4));
  em.add_def(ElementDefinition(QUAD8, 16, 2, 8));
  em.add_def(ElementDefinition(QUAD9, 10, 2, 9));
  em.add_def(ElementDefinition(HEX8, 5, 3, 8));
  em.add_def(ElementDefinition(TET4, 4, 3, 4));
  em.add_def(ElementDefinition(PRISM6, 6, 3, 6));
  em.add_def(ElementDefinition(PYRAMID5, 7, 3, 5));
 
  // Add elements with non-trivial node mappings
 
  // HEX20
  {
    ElementDefinition eledef(HEX20, 17, 3, 20);
    const unsigned int nodes[] = {0,1,2,3,4,5,6,7,8,11,12,9,13,10,14,15,16,19,17,18};
    std::vector<unsigned int>(nodes, nodes+eledef.nnodes).swap(eledef.nodes); // swap trick
    em.add_def(eledef);
  }
 
  // HEX27
  {
    ElementDefinition eledef(HEX27, 12, 3, 27);
    const unsigned int nodes[] = {0,1,2,3,4,5,6,7,8,11,12,9,13,10,14,
                                  15,16,19,17,18,20,21,24,22,23,25,26};
    std::vector<unsigned int>(nodes, nodes+eledef.nnodes).swap(eledef.nodes); // swap trick
    em.add_def(eledef);
  }
 
  // TET10
  {
    ElementDefinition eledef(TET10, 11, 3, 10);
    const unsigned int nodes[] = {0,1,2,3,4,5,6,7,9,8};
    std::vector<unsigned int>(nodes, nodes+eledef.nnodes).swap(eledef.nodes); // swap trick
    em.add_def(eledef);
  }
 
  // PRISM15
  {
    ElementDefinition eledef(PRISM15, 18, 3, 15);
    const unsigned int nodes[] = {0,1,2,3,4,5,6,8,9,7,10,11,12,14,13};
    std::vector<unsigned int>(nodes, nodes+eledef.nnodes).swap(eledef.nodes); // swap trick
    em.add_def(eledef);
  }
 
  // PRISM18
  {
    ElementDefinition eledef(PRISM18, 13, 3, 18);
    const unsigned int nodes[] = {0,1,2,3,4,5,6,8,9,7,10,11,12,14,13,15,17,16};
    std::vector<unsigned int>(nodes, nodes+eledef.nnodes).swap(eledef.nodes); // swap trick
    em.add_def(eledef);
  }
 
  return em;
}

References libMesh::GmshIO::ElementMaps::add_def(), libMesh::EDGE2, libMesh::EDGE3, libMesh::HEX20, libMesh::HEX27, libMesh::HEX8, libMesh::GmshIO::ElementMaps::in, libMesh::GmshIO::ElementDefinition::nnodes, libMesh::NODEELEM, libMesh::GmshIO::ElementDefinition::nodes, libMesh::PRISM15, libMesh::PRISM18, libMesh::PRISM6, libMesh::PYRAMID5, libMesh::QUAD4, libMesh::QUAD8, libMesh::QUAD9, libMesh::TET10, libMesh::TET4, libMesh::TRI3, and libMesh::TRI6.

mesh() [1/2]

MeshBase & libMesh::MeshInput< MeshBase >::mesh ( )

inlineprotectedinherited

Returns

The object as a writable reference.

Definition at line 169 of file mesh_input.h.

{
  if (_obj == nullptr)
    libmesh_error_msg("ERROR: _obj should not be nullptr!");
  return *_obj;
}

mesh() [2/2]

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.

{
  libmesh_assert(_obj);
  return *_obj;
}

read()

void libMesh::GmshIO::read ( const std::string &  name )

overridevirtual

Reads in a mesh in the Gmsh *.msh format from the ASCII file given by name.

Note

The user is responsible for calling Mesh::prepare_for_use() after reading the mesh and before using it.

The physical group names defined in the Gmsh-file are stored, depending on the element dimension, as either subdomain name or as side name. The IDs of the former can be retrieved by using the MeshBase::get_id_by_name method; the IDs of the latter can be retrieved by using the MeshBase::get_boundary_info and the BoundaryInfo::get_id_by_name methods.

Implements libMesh::MeshInput< MeshBase >.

Definition at line 147 of file gmsh_io.C.

{
  std::ifstream in (name.c_str());
  this->read_mesh (in);
}

References libMesh::Quality::name(), and read_mesh().

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

read_mesh()

void libMesh::GmshIO::read_mesh ( std::istream &  in )

private

Implementation of the read() function.

This function is called by the public interface function and implements reading the file.

Definition at line 155 of file gmsh_io.C.

{
  // This is a serial-only process for now;
  // the Mesh should be read on processor 0 and
  // broadcast later
  libmesh_assert_equal_to (MeshOutput<MeshBase>::mesh().processor_id(), 0);
 
  libmesh_assert(in.good());
 
  // clear any data in the mesh
  MeshBase & mesh = MeshInput<MeshBase>::mesh();
  mesh.clear();
 
  // some variables
  int format=0, size=0;
  Real version = 1.0;
 
  // Keep track of lower-dimensional blocks which are not BCs, but
  // actually blocks of lower-dimensional elements.
  std::set<subdomain_id_type> lower_dimensional_blocks;
 
  // Mapping from physical id -> (physical dim, physical name) pairs.
  // These can refer to either "sidesets" or "subdomains"; we need to
  // wait until the Mesh has been read to know which is which.  Note
  // that we are using 'int' as the key here rather than
  // subdomain_id_type or boundary_id_type, since at this point, it
  // could be either.
  typedef std::pair<unsigned, std::string> GmshPhysical;
  std::map<int, GmshPhysical> gmsh_physicals;
 
  // map to hold the node numbers for translation
  // note the the nodes can be non-consecutive
  std::map<unsigned int, unsigned int> nodetrans;
 
  // Map from entity tag to physical id. The key is a pair with the first
  // item being the dimension of the entity and the second item being
  // the entity tag/id
  std::map<std::pair<unsigned, int>, int> entity_to_physical_id;
 
  // For reading the file line by line
  std::string s;
 
  while (true)
    {
      // Try to read something.  This may set EOF!
      std::getline(in, s);
 
      if (in)
        {
          // Process s...
 
          if (s.find("$MeshFormat") == static_cast<std::string::size_type>(0))
            {
              in >> version >> format >> size;
              if (version < 2.0)
                {
                  // Some notes on gmsh mesh versions:
                  //
                  // Mesh version 2.0 goes back as far as I know.  It's not explicitly
                  // mentioned here: http://www.geuz.org/gmsh/doc/VERSIONS.txt
                  //
                  // As of gmsh-2.4.0:
                  // bumped mesh version format to 2.1 (small change in the $PhysicalNames
                  // section, where the group dimension is now required);
                  // [Since we don't even parse the PhysicalNames section at the time
                  //  of this writing, I don't think this change affects us.]
                  //
                  // Mesh version 2.2 tested by Manav Bhatia; no other
                  // libMesh code changes were required for support
                  //
                  // Mesh version 4.0 is a near complete rewrite of the previous mesh version
                  //
                  libmesh_error_msg("Error: Unknown msh file version " << version);
                }
 
              if (format)
                libmesh_error_msg("Error: Unknown data format for mesh in Gmsh reader.");
            }
 
          // Read and process the "PhysicalNames" section.
          else if (s.find("$PhysicalNames") == static_cast<std::string::size_type>(0))
            {
              // The lines in the PhysicalNames section should look like the following:
              // 2 1 "frac" lower_dimensional_block
              // 2 3 "top"
              // 2 4 "bottom"
              // 3 2 "volume"
 
              // Read in the number of physical groups to expect in the file.
              unsigned int num_physical_groups = 0;
              in >> num_physical_groups;
 
              // Read rest of line including newline character.
              std::getline(in, s);
 
              for (unsigned int i=0; i<num_physical_groups; ++i)
                {
                  // Read an entire line of the PhysicalNames section.
                  std::getline(in, s);
 
                  // Use an istringstream to extract the physical
                  // dimension, physical id, and physical name from
                  // this line.
                  std::istringstream s_stream(s);
                  unsigned phys_dim;
                  int phys_id;
                  std::string phys_name;
                  s_stream >> phys_dim >> phys_id >> phys_name;
 
                  // Not sure if this is true for all Gmsh files, but
                  // my test file has quotes around the phys_name
                  // string.  So let's erase any quotes now...
                  phys_name.erase(std::remove(phys_name.begin(), phys_name.end(), '"'), phys_name.end());
 
                  // Record this ID for later assignment of subdomain/sideset names.
                  gmsh_physicals[phys_id] = std::make_pair(phys_dim, phys_name);
 
                  // If 's' also contains the libmesh-specific string
                  // "lower_dimensional_block", add this block ID to
                  // the list of blocks which are not boundary
                  // conditions.
                  if (s.find("lower_dimensional_block") != std::string::npos)
                    {
                      lower_dimensional_blocks.insert(cast_int<subdomain_id_type>(phys_id));
 
                      // The user has explicitly told us that this
                      // block is a subdomain, so set that association
                      // in the Mesh.
                      mesh.subdomain_name(cast_int<subdomain_id_type>(phys_id)) = phys_name;
                    }
                }
            }
 
          else if (s.find("$Entities") == static_cast<std::string::size_type>(0))
          {
            if (version >= 4.0)
            {
              std::size_t num_point_entities, num_curve_entities, num_surface_entities, num_volume_entities;
              in >> num_point_entities >> num_curve_entities >> num_surface_entities >> num_volume_entities;
 
              for (std::size_t n = 0; n < num_point_entities; ++n)
              {
                int point_tag, physical_tag;
                Real x, y, z;
                std::size_t num_physical_tags;
                in >> point_tag >> x >> y >> z >> num_physical_tags;
                if (num_physical_tags > 1)
                  libmesh_error_msg("Sorry, you cannot currently specify multiple subdomain or " <<
                                    "boundary ids for a given geometric entity");
                else if (num_physical_tags)
                {
                  in >> physical_tag;
                  entity_to_physical_id[std::make_pair(0, point_tag)] = physical_tag;
                }
              }
              for (std::size_t n = 0; n < num_curve_entities; ++n)
              {
                int curve_tag, physical_tag;
                Real minx, miny, minz, maxx, maxy, maxz;
                std::size_t num_physical_tags;
                in >> curve_tag >> minx >> miny >> minz >> maxx >> maxy >> maxz >> num_physical_tags;
                if (num_physical_tags > 1)
                  libmesh_error_msg("I don't believe that we can specify multiple subdomain or " <<
                                    "boundary ids for a given geometric entity");
                else if (num_physical_tags)
                {
                  in >> physical_tag;
                  entity_to_physical_id[std::make_pair(1, curve_tag)] = physical_tag;
                }
 
                // Read to end of line; this captures bounding information that we don't care about
                std::getline(in, s);
              }
              for (std::size_t n = 0; n < num_surface_entities; ++n)
              {
                int surface_tag, physical_tag;
                Real minx, miny, minz, maxx, maxy, maxz;
                std::size_t num_physical_tags;
                in >> surface_tag >> minx >> miny >> minz >> maxx >> maxy >> maxz >> num_physical_tags;
                if (num_physical_tags > 1)
                  libmesh_error_msg("I don't believe that we can specify multiple subdomain or " <<
                                    "boundary ids for a given geometric entity");
                else if (num_physical_tags)
                {
                  in >> physical_tag;
                  entity_to_physical_id[std::make_pair(2, surface_tag)] = physical_tag;
                }
 
                // Read to end of line; this captures bounding information that we don't care about
                std::getline(in, s);
              }
              for (std::size_t n = 0; n < num_volume_entities; ++n)
              {
                int volume_tag, physical_tag;
                Real minx, miny, minz, maxx, maxy, maxz;
                std::size_t num_physical_tags;
                in >> volume_tag >> minx >> miny >> minz >> maxx >> maxy >> maxz >> num_physical_tags;
                if (num_physical_tags > 1)
                  libmesh_error_msg("I don't believe that we can specify multiple subdomain or " <<
                                    "boundary ids for a given geometric entity");
                else if (num_physical_tags)
                {
                  in >> physical_tag;
                  entity_to_physical_id[std::make_pair(3, volume_tag)] = physical_tag;
                }
 
                // Read to end of line; this captures bounding information that we don't care about
                std::getline(in, s);
              }
              // Read the $EndEntities
              std::getline(in, s);
            } // end if (version >= 4.0)
 
            else
              libmesh_error_msg("The Entities block was introduced in mesh version 4.0");
          } // end if $Entities
 
          // read the node block
          else if (s.find("$NOD") == static_cast<std::string::size_type>(0) ||
                   s.find("$NOE") == static_cast<std::string::size_type>(0) ||
                   s.find("$Nodes") == static_cast<std::string::size_type>(0))
          {
            if (version < 4.0)
            {
              unsigned int num_nodes = 0;
              in >> num_nodes;
              mesh.reserve_nodes (num_nodes);
 
              // read in the nodal coordinates and form points.
              Real x, y, z;
              unsigned int id;
 
              // add the nodal coordinates to the mesh
              for (unsigned int i=0; i<num_nodes; ++i)
              {
                in >> id >> x >> y >> z;
                mesh.add_point (Point(x, y, z), i);
                nodetrans[id] = i;
              }
            }
            else
            {
              // Read numEntityBlocks line
              std::size_t num_entities = 0, num_nodes = 0, min_node_tag, max_node_tag;
              in >> num_entities >> num_nodes >> min_node_tag >> max_node_tag;
 
              mesh.reserve_nodes(num_nodes);
 
              std::size_t node_counter = 0;
 
              // Now loop over entities
              for (std::size_t i = 0; i < num_entities; ++i)
              {
                int entity_dim, entity_tag, parametric;
                std::size_t num_nodes_in_block = 0;
                in >> entity_dim >> entity_tag >> parametric >> num_nodes_in_block;
                if (parametric)
                  libmesh_error_msg("We don't currently support reading parametric gmsh entities");
 
                // Read the node tags/ids
                std::size_t gmsh_id;
                for (std::size_t n = 0; n < num_nodes_in_block; ++n)
                {
 
                  in >> gmsh_id;
                  nodetrans[gmsh_id] = node_counter++;
                }
 
                // Read the node coordinates and add the nodes to the mesh
                Real x, y, z;
                for (std::size_t libmesh_id = node_counter - num_nodes_in_block;
                     libmesh_id < node_counter;
                     ++libmesh_id)
                {
                  in >> x >> y >> z;
                  mesh.add_point(Point(x, y, z), libmesh_id);
                }
              }
            }
            // read the $ENDNOD delimiter
            std::getline(in, s);
          }
 
          // Read the element block
          else if (s.find("$ELM") == static_cast<std::string::size_type>(0) ||
                   s.find("$Elements") == static_cast<std::string::size_type>(0))
          {
            // Keep track of element dimensions seen
            std::vector<unsigned> elem_dimensions_seen(3);
 
            if (version < 4.0)
            {
              // For reading the number of elements and the node ids from the stream
              unsigned int
                num_elem = 0,
                node_id = 0;
 
              // read how many elements are there, and reserve space in the mesh
              in >> num_elem;
              mesh.reserve_elem (num_elem);
 
              // As of version 2.2, the format for each element line is:
              // elm-number elm-type number-of-tags < tag > ... node-number-list
              // From the Gmsh docs:
              // * the first tag is the number of the
              //   physical entity to which the element belongs
              // * the second is the number of the elementary geometrical
              //   entity to which the element belongs
              // * the third is the number of mesh partitions to which the element
              //   belongs
              // * The rest of the tags are the partition ids (negative
              //   partition ids indicate ghost cells). A zero tag is
              //   equivalent to no tag. Gmsh and most codes using the
              //   MSH 2 format require at least the first two tags
              //   (physical and elementary tags).
 
              // read the elements
              for (unsigned int iel=0; iel<num_elem; ++iel)
              {
                unsigned int
                  id, type,
                  physical=1, elementary=1,
                  nnodes=0, ntags;
 
                // Note: tag has to be an int because it could be negative,
                // see above.
                int tag;
 
                if (version <= 1.0)
                  in >> id >> type >> physical >> elementary >> nnodes;
 
                else
                {
                  in >> id >> type >> ntags;
 
                  if (ntags > 2)
                    libmesh_do_once(libMesh::err << "Warning, ntags=" << ntags << ", but we currently only support reading 2 flags." << std::endl;);
 
                  for (unsigned int j = 0; j < ntags; j++)
                  {
                    in >> tag;
                    if (j == 0)
                      physical = tag;
                    else if (j == 1)
                      elementary = tag;
                  }
                }
 
                // Get a reference to the ElementDefinition, throw an error if not found.
                const GmshIO::ElementDefinition & eletype =
                  libmesh_map_find(_element_maps.in, type);
 
                // If we read nnodes, make sure it matches the number in eletype.nnodes
                if (nnodes != 0 && nnodes != eletype.nnodes)
                  libmesh_error_msg("nnodes = " << nnodes << " and eletype.nnodes = " << eletype.nnodes << " do not match.");
 
                // Assign the value from the eletype object.
                nnodes = eletype.nnodes;
 
                // Don't add 0-dimensional "point" elements to the
                // Mesh.  They should *always* be treated as boundary
                // "nodeset" data.
                if (eletype.dim > 0)
                {
                  // Record this element dimension as being "seen".
                  // We will treat all elements with dimension <
                  // max(dimension) as specifying boundary conditions,
                  // but we won't know what max_elem_dimension_seen is
                  // until we read the entire file.
                  elem_dimensions_seen[eletype.dim-1] = 1;
 
                  // Add the element to the mesh
                  {
                    Elem * elem = Elem::build(eletype.type).release();
                    elem->set_id(iel);
                    elem = mesh.add_elem(elem);
 
                    // Make sure that the libmesh element we added has nnodes nodes.
                    if (elem->n_nodes() != nnodes)
                      libmesh_error_msg("Number of nodes for element " \
                                        << id \
                                        << " of type " << eletype.type \
                                        << " (Gmsh type " << type \
                                        << ") does not match Libmesh definition. " \
                                        << "I expected " << elem->n_nodes() \
                                        << " nodes, but got " << nnodes);
 
                    // Add node pointers to the elements.
                    // If there is a node translation table, use it.
                    if (eletype.nodes.size() > 0)
                      for (unsigned int i=0; i<nnodes; i++)
                      {
                        in >> node_id;
                        elem->set_node(eletype.nodes[i]) = mesh.node_ptr(nodetrans[node_id]);
                      }
                    else
                    {
                      for (unsigned int i=0; i<nnodes; i++)
                      {
                        in >> node_id;
                        elem->set_node(i) = mesh.node_ptr(nodetrans[node_id]);
                      }
                    }
 
                    // Finally, set the subdomain ID to physical.  If this is a lower-dimension element, this ID will
                    // eventually go into the Mesh's BoundaryInfo object.
                    elem->subdomain_id() = static_cast<subdomain_id_type>(physical);
                  }
                }
 
                // Handle 0-dimensional elements (points) by adding
                // them to the BoundaryInfo object with
                // boundary_id == physical.
                else
                {
                  // This seems like it should always be the same
                  // number as the 'id' we already read in on this
                  // line.  At least it was in the example gmsh
                  // file I had...
                  in >> node_id;
                  mesh.get_boundary_info().add_node
                    (nodetrans[node_id],
                     static_cast<boundary_id_type>(physical));
                }
              } // element loop
            } // end if (version < 4.0)
 
            else
            {
              std::size_t num_entity_blocks = 0, num_elem = 0, min_element_tag, max_element_tag;
 
              // Read entity information
              in >> num_entity_blocks >> num_elem >> min_element_tag >> max_element_tag;
 
              mesh.reserve_elem(num_elem);
 
              std::size_t iel = 0;
 
              // Loop over entity blocks
              for (std::size_t i = 0; i < num_entity_blocks; ++i)
              {
                int entity_dim, entity_tag;
                unsigned int element_type;
                std::size_t num_elems_in_block = 0;
                in >> entity_dim >> entity_tag >> element_type >> num_elems_in_block;
 
                // Get a reference to the ElementDefinition
                const GmshIO::ElementDefinition & eletype =
                  libmesh_map_find(_element_maps.in, element_type);
 
                // Don't add 0-dimensional "point" elements to the
                // Mesh.  They should *always* be treated as boundary
                // "nodeset" data.
                if (eletype.dim > 0)
                {
                  // Record this element dimension as being "seen".
                  // We will treat all elements with dimension <
                  // max(dimension) as specifying boundary conditions,
                  // but we won't know what max_elem_dimension_seen is
                  // until we read the entire file.
                  elem_dimensions_seen[eletype.dim-1] = 1;
 
                  // Loop over elements with dim > 0
                  for (std::size_t n = 0; n < num_elems_in_block; ++n)
                  {
                    Elem * elem = Elem::build(eletype.type).release();
                    elem->set_id(iel++);
                    elem = mesh.add_elem(elem);
 
                    std::size_t gmsh_element_id;
                    in >> gmsh_element_id;
 
                    // Get the remainer of the line that includes the nodes ids
                    std::getline(in, s);
                    std::istringstream is(s);
                    std::size_t local_node_counter = 0, gmsh_node_id;
                    while (is >> gmsh_node_id)
                    {
                      // Add node pointers to the elements.
                      // If there is a node translation table, use it.
                      if (eletype.nodes.size() > 0)
                          elem->set_node(eletype.nodes[local_node_counter++]) =
                            mesh.node_ptr(nodetrans[gmsh_node_id]);
                      else
                          elem->set_node(local_node_counter++) = mesh.node_ptr(nodetrans[gmsh_node_id]);
                    }
 
                    // Make sure that the libmesh element we added has nnodes nodes.
                    if (elem->n_nodes() != local_node_counter)
                      libmesh_error_msg("Number of nodes for element " \
                                        << gmsh_element_id \
                                        << " of type " << eletype.type \
                                        << " (Gmsh type " << element_type \
                                        << ") does not match Libmesh definition. " \
                                        << "I expected " << elem->n_nodes() \
                                        << " nodes, but got " << local_node_counter);
 
 
                    // Finally, set the subdomain ID to physical.  If this is a lower-dimension element, this ID will
                    // eventually go into the Mesh's BoundaryInfo object.
                    elem->subdomain_id() = static_cast<subdomain_id_type>(
                      entity_to_physical_id[std::make_pair(entity_dim, entity_tag)]);
 
                  } // end for (loop over elements in entity block)
                } // end if (eletype.dim > 0)
 
                else
                {
                  for (std::size_t n = 0; n < num_elems_in_block; ++n)
                  {
                    std::size_t gmsh_element_id, gmsh_node_id;
                    in >> gmsh_element_id;
                    in >> gmsh_node_id;
                    mesh.get_boundary_info().add_node(
                      nodetrans[gmsh_node_id],
                      static_cast<boundary_id_type>(entity_to_physical_id[
                                                      std::make_pair(entity_dim, entity_tag)]));
                  } // end for (loop over elements in entity block)
                } // end if (eletype.dim == 0)
              } // end for (loop over entity blocks)
            } // end if (version >= 4.0)
 
            // read the $ENDELM delimiter
            std::getline(in, s);
 
            // Record the max and min element dimension seen while reading the file.
            unsigned char
              max_elem_dimension_seen=1,
              min_elem_dimension_seen=3;
 
            for (auto i : index_range(elem_dimensions_seen))
              if (elem_dimensions_seen[i])
              {
                // Debugging
                // libMesh::out << "Seen elements of dimension " << i+1 << std::endl;
                max_elem_dimension_seen =
                  std::max(max_elem_dimension_seen, cast_int<unsigned char>(i+1));
                min_elem_dimension_seen =
                  std::min(min_elem_dimension_seen, cast_int<unsigned char>(i+1));
              }
 
            // Debugging:
            // libMesh::out << "max_elem_dimension_seen=" << max_elem_dimension_seen << std::endl;
            // libMesh::out << "min_elem_dimension_seen=" << min_elem_dimension_seen << std::endl;
 
 
            // How many different element dimensions did we see while reading from file?
            unsigned n_dims_seen = std::accumulate(elem_dimensions_seen.begin(),
                                                   elem_dimensions_seen.end(),
                                                   static_cast<unsigned>(0),
                                                   std::plus<unsigned>());
 
 
            // Set mesh_dimension based on the largest element dimension seen.
            mesh.set_mesh_dimension(max_elem_dimension_seen);
 
            // Now that we know the maximum element dimension seen,
            // we know whether the physical names are subdomain
            // names or sideset names.
            for (const auto & pr : gmsh_physicals)
            {
              // Extract data
              int phys_id = pr.first;
              unsigned phys_dim = pr.second.first;
              const std::string & phys_name = pr.second.second;
 
              // If the physical's dimension matches the largest
              // dimension we've seen, it's a subdomain name.
              if (phys_dim == max_elem_dimension_seen)
                mesh.subdomain_name(cast_int<subdomain_id_type>(phys_id)) = phys_name;
 
              // Otherwise, if it's not a lower-dimensional
              // block, it's a sideset name.
              else if (phys_dim < max_elem_dimension_seen &&
                       !lower_dimensional_blocks.count(cast_int<boundary_id_type>(phys_id)))
                mesh.get_boundary_info().sideset_name(cast_int<boundary_id_type>(phys_id)) = phys_name;
            }
 
            if (n_dims_seen > 1)
            {
              // Store lower-dimensional elements in a map sorted
              // by Elem::key().  We use a multimap for two reasons:
              // 1.) The hash function is not guaranteed to be
              // unique, so different lower-dimensional elements
              // could theoretically hash to the same value,
              // although this is pretty unlikely.
              // 2.) The Gmsh file may contain multiple
              // lower-dimensional elements for a single side in
              // order to implement multiple boundary ids for a
              // single side.  These lower-dimensional elements
              // will all hash to the same value, and we need to
              // be able to store all of them.
              typedef std::unordered_multimap<dof_id_type, Elem *> provide_container_t;
              provide_container_t provide_bcs;
 
              // 1st loop over active elements - get info about lower-dimensional elements.
              for (auto & elem : mesh.active_element_ptr_range())
                if (elem->dim() < max_elem_dimension_seen &&
                    !lower_dimensional_blocks.count(elem->subdomain_id()))
                {
                  // To be consistent with the previous
                  // GmshIO behavior, add all the
                  // lower-dimensional elements' nodes to
                  // the Mesh's BoundaryInfo object with the
                  // lower-dimensional element's subdomain
                  // ID.
                  for (auto n : elem->node_index_range())
                    mesh.get_boundary_info().add_node(elem->node_id(n),
                                                      elem->subdomain_id());
 
                  // Store this elem in a quickly-searchable
                  // container to use it to assign boundary
                  // conditions later.
                  provide_bcs.insert(std::make_pair(elem->key(), elem));
                }
 
              // 2nd loop over active elements - use lower dimensional element data to set BCs for higher dimensional elements
              for (auto & elem : mesh.active_element_ptr_range())
                if (elem->dim() == max_elem_dimension_seen)
                {
                  // This is a max-dimension element that
                  // may require BCs.  For each of its
                  // sides, including internal sides, we'll
                  // see if one more more lower-dimensional elements
                  // provides boundary information for it.
                  // Note that we have not yet called
                  // find_neighbors(), so we can't use
                  // elem->neighbor(sn) in this algorithm...
                  for (auto sn : elem->side_index_range())
                    for (const auto & pr : as_range(provide_bcs.equal_range(elem->key(sn))))
                    {
                      // For each side side in the provide_bcs multimap...
                      // Construct the side for hash verification.
                      std::unique_ptr<Elem> side (elem->build_side_ptr(sn));
 
                      // Construct the lower-dimensional element to compare to the side.
                      Elem * lower_dim_elem = pr.second;
 
                      // This was a hash, so it might not be perfect.  Let's verify...
                      if (*lower_dim_elem == *side)
                      {
                        // Add the lower-dimensional
                        // element's subdomain_id as a
                        // boundary_id for the
                        // higher-dimensional element.
                        boundary_id_type bid = cast_int<boundary_id_type>(lower_dim_elem->subdomain_id());
                        mesh.get_boundary_info().add_side(elem, sn, bid);
                      }
                    }
                }
 
              // 3rd loop over active elements - Remove the lower-dimensional elements
              for (auto & elem : mesh.active_element_ptr_range())
                if (elem->dim() < max_elem_dimension_seen &&
                    !lower_dimensional_blocks.count(elem->subdomain_id()))
                  mesh.delete_elem(elem);
            } // end if (n_dims_seen > 1)
          } // if $ELM
 
          continue;
        } // if (in)
 
 
      // If !in, check to see if EOF was set.  If so, break out
      // of while loop.
      if (in.eof())
        break;
 
      // If !in and !in.eof(), stream is in a bad state!
      libmesh_error_msg("Stream is bad! Perhaps the file does not exist?");
 
    } // while true
}

References _element_maps, libMesh::MeshBase::active_element_ptr_range(), libMesh::MeshBase::add_elem(), libMesh::BoundaryInfo::add_node(), libMesh::MeshBase::add_point(), libMesh::BoundaryInfo::add_side(), libMesh::as_range(), libMesh::Elem::build(), libMesh::MeshBase::clear(), libMesh::MeshBase::delete_elem(), libMesh::GmshIO::ElementDefinition::dim, libMesh::err, libMesh::MeshBase::get_boundary_info(), libMesh::GmshIO::ElementMaps::in, libMesh::index_range(), libMesh::is, libMesh::libmesh_assert(), libMesh::MeshInput< MeshBase >::mesh(), libMesh::MeshInput< MT >::mesh(), libMesh::Elem::n_nodes(), libMesh::GmshIO::ElementDefinition::nnodes, libMesh::MeshBase::node_ptr(), libMesh::GmshIO::ElementDefinition::nodes, libMesh::Real, libMesh::MeshBase::reserve_elem(), libMesh::MeshBase::reserve_nodes(), libMesh::DofObject::set_id(), libMesh::MeshBase::set_mesh_dimension(), libMesh::Elem::set_node(), libMesh::BoundaryInfo::sideset_name(), libMesh::Elem::subdomain_id(), libMesh::MeshBase::subdomain_name(), and libMesh::GmshIO::ElementDefinition::type.

Referenced by read().

set_n_partitions()

void libMesh::MeshInput< MeshBase >::set_n_partitions ( unsigned int  n_parts )

inlineprotectedinherited

Sets the number of partitions in the mesh.

Typically this gets done by the partitioner, but some parallel file formats begin "pre-partitioned".

Definition at line 91 of file mesh_input.h.

{ this->mesh().set_n_partitions() = n_parts; }

skip_comment_lines()

void libMesh::MeshInput< MeshBase >::skip_comment_lines ( std::istream &  in, const char  comment_start  )

protectedinherited

Reads input from in, skipping all the lines that start with the character comment_start.

Definition at line 179 of file mesh_input.h.

{
  char c, line[256];
 
  while (in.get(c), c==comment_start)
    in.getline (line, 255);
 
  // put back first character of
  // first non-comment line
  in.putback (c);
}

write()

void libMesh::GmshIO::write ( const std::string &  name )

overridevirtual

This method implements writing a mesh to a specified file in the Gmsh *.msh format.

Implements libMesh::MeshOutput< MeshBase >.

Definition at line 831 of file gmsh_io.C.

{
  if (MeshOutput<MeshBase>::mesh().processor_id() == 0)
    {
      // Open the output file stream
      std::ofstream out_stream (name.c_str());
 
      // Make sure it opened correctly
      if (!out_stream.good())
        libmesh_file_error(name.c_str());
 
      this->write_mesh (out_stream);
    }
}

References libMesh::Quality::name(), and write_mesh().

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.

{
  LOG_SCOPE("write_discontinuous_equation_systems()", "MeshOutput");
 
  // We may need to gather and/or renumber a DistributedMesh to output
  // it, making that const qualifier in our constructor a dirty lie
  MT & my_mesh = const_cast<MT &>(*_obj);
 
  // If we're asked to write data that's associated with a different
  // mesh, output files full of garbage are the result.
  libmesh_assert_equal_to(&es.get_mesh(), _obj);
 
  // A non-renumbered mesh may not have a contiguous numbering, and
  // that needs to be fixed before we can build a solution vector.
  if (my_mesh.max_elem_id() != my_mesh.n_elem() ||
      my_mesh.max_node_id() != my_mesh.n_nodes())
    {
      // If we were allowed to renumber then we should have already
      // been properly renumbered...
      libmesh_assert(!my_mesh.allow_renumbering());
 
      libmesh_do_once(libMesh::out <<
                      "Warning:  This MeshOutput subclass only supports meshes which are contiguously renumbered!"
                      << std::endl;);
 
      my_mesh.allow_renumbering(true);
 
      my_mesh.renumber_nodes_and_elements();
 
      // Not sure what good going back to false will do here, the
      // renumbering horses have already left the barn...
      my_mesh.allow_renumbering(false);
    }
 
  MeshSerializer serialize(const_cast<MT &>(*_obj), !_is_parallel_format, _serial_only_needed_on_proc_0);
 
  // Build the list of variable names that will be written.
  std::vector<std::string> names;
  es.build_variable_names  (names, nullptr, system_names);
 
  if (!_is_parallel_format)
    {
      // Build the nodal solution values & get the variable
      // names from the EquationSystems object
      std::vector<Number> soln;
      es.build_discontinuous_solution_vector (soln, system_names);
 
      this->write_nodal_data_discontinuous (fname, soln, names);
    }
  else // _is_parallel_format
    {
      libmesh_not_implemented();
    }
}

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.

{
  LOG_SCOPE("write_equation_systems()", "MeshOutput");
 
  // We may need to gather and/or renumber a DistributedMesh to output
  // it, making that const qualifier in our constructor a dirty lie
  MT & my_mesh = const_cast<MT &>(*_obj);
 
  // If we're asked to write data that's associated with a different
  // mesh, output files full of garbage are the result.
  libmesh_assert_equal_to(&es.get_mesh(), _obj);
 
  // A non-renumbered mesh may not have a contiguous numbering, and
  // that needs to be fixed before we can build a solution vector.
  if (my_mesh.max_elem_id() != my_mesh.n_elem() ||
      my_mesh.max_node_id() != my_mesh.n_nodes())
    {
      // If we were allowed to renumber then we should have already
      // been properly renumbered...
      libmesh_assert(!my_mesh.allow_renumbering());
 
      libmesh_do_once(libMesh::out <<
                      "Warning:  This MeshOutput subclass only supports meshes which are contiguously renumbered!"
                      << std::endl;);
 
      my_mesh.allow_renumbering(true);
 
      my_mesh.renumber_nodes_and_elements();
 
      // Not sure what good going back to false will do here, the
      // renumbering horses have already left the barn...
      my_mesh.allow_renumbering(false);
    }
 
  if (!_is_parallel_format)
    {
      MeshSerializer serialize(const_cast<MT &>(*_obj), !_is_parallel_format, _serial_only_needed_on_proc_0);
 
      // Build the list of variable names that will be written.
      std::vector<std::string> names;
      es.build_variable_names  (names, nullptr, system_names);
 
      // Build the nodal solution values & get the variable
      // names from the EquationSystems object
      std::vector<Number> soln;
      es.build_solution_vector (soln, system_names);
 
      this->write_nodal_data (fname, soln, names);
    }
  else // _is_parallel_format
    this->write_nodal_data (fname, es, system_names);
}

write_lower_dimensional_elements()

bool & libMesh::GmshIO::write_lower_dimensional_elements

(

)

Access to the flag which controls whether boundary elements are written to the Mesh file.

Definition at line 140 of file gmsh_io.C.

{
  return _write_lower_dimensional_elements;
}

References _write_lower_dimensional_elements.

Referenced by write_mesh().

write_mesh()

void libMesh::GmshIO::write_mesh ( std::ostream &  out )

private

This method implements writing a mesh to a specified file.

This will write an ASCII *.msh file.

Definition at line 860 of file gmsh_io.C.

{
  // Be sure that the stream is valid.
  libmesh_assert (out_stream.good());
 
  // Get a const reference to the mesh
  const MeshBase & mesh = MeshOutput<MeshBase>::mesh();
 
  // If requested, write out lower-dimensional elements for
  // element-side-based boundary conditions.
  std::size_t n_boundary_faces = 0;
  if (this->write_lower_dimensional_elements())
    n_boundary_faces = mesh.get_boundary_info().n_boundary_conds();
 
  // Note: we are using version 2.0 of the gmsh output format.
 
  // Write the file header.
  out_stream << "$MeshFormat\n";
  out_stream << "2.0 0 " << sizeof(Real) << '\n';
  out_stream << "$EndMeshFormat\n";
 
  // write the nodes in (n x y z) format
  out_stream << "$Nodes\n";
  out_stream << mesh.n_nodes() << '\n';
 
  for (auto v : IntRange<unsigned int>(0, mesh.n_nodes()))
    out_stream << mesh.node_ref(v).id()+1 << " "
               << mesh.node_ref(v)(0) << " "
               << mesh.node_ref(v)(1) << " "
               << mesh.node_ref(v)(2) << '\n';
  out_stream << "$EndNodes\n";
 
  {
    // write the connectivity
    out_stream << "$Elements\n";
    out_stream << mesh.n_active_elem() + n_boundary_faces << '\n';
 
    // loop over the elements
    for (const auto & elem : mesh.active_element_ptr_range())
      {
        // Get a reference to the ElementDefinition object
        const ElementDefinition & eletype =
          libmesh_map_find(_element_maps.out, elem->type());
 
        // The element mapper better not require any more nodes
        // than are present in the current element!
        libmesh_assert_less_equal (eletype.nodes.size(), elem->n_nodes());
 
        // elements ids are 1 based in Gmsh
        out_stream << elem->id()+1 << " ";
        // element type
        out_stream << eletype.gmsh_type;
 
        // write the number of tags (3) and their values:
        // 1 (physical entity)
        // 2 (geometric entity)
        // 3 (partition entity)
        out_stream << " 3 "
                   << static_cast<unsigned int>(elem->subdomain_id())
                   << " 0 "
                   << elem->processor_id()+1
                   << " ";
 
        // if there is a node translation table, use it
        if (eletype.nodes.size() > 0)
          for (auto i : elem->node_index_range())
            out_stream << elem->node_id(eletype.nodes[i])+1 << " "; // gmsh is 1-based
        // otherwise keep the same node order
        else
          for (auto i : elem->node_index_range())
            out_stream << elem->node_id(i)+1 << " ";                  // gmsh is 1-based
        out_stream << "\n";
      } // element loop
  }
 
  {
    // A counter for writing surface elements to the Gmsh file
    // sequentially.  We start numbering them with a number strictly
    // larger than the largest element ID in the mesh.  Note: the
    // MeshBase docs say "greater than or equal to" the maximum
    // element id in the mesh, so technically we might need a +1 here,
    // but all of the implementations return an ID strictly greater
    // than the largest element ID in the Mesh.
    unsigned int e_id = mesh.max_elem_id();
 
    // loop over the elements, writing out boundary faces
    if (n_boundary_faces)
      {
        // Build a list of (elem, side, bc) tuples.
        auto bc_triples = mesh.get_boundary_info().build_side_list();
 
        // Loop over these lists, writing data to the file.
        for (const auto & t : bc_triples)
          {
            const Elem & elem = mesh.elem_ref(std::get<0>(t));
 
            std::unique_ptr<const Elem> side = elem.build_side_ptr(std::get<1>(t));
 
            // consult the export element table
            const GmshIO::ElementDefinition & eletype =
              libmesh_map_find(_element_maps.out, side->type());
 
            // The element mapper better not require any more nodes
            // than are present in the current element!
            libmesh_assert_less_equal (eletype.nodes.size(), side->n_nodes());
 
            // elements ids are 1-based in Gmsh
            out_stream << e_id+1 << " ";
 
            // element type
            out_stream << eletype.gmsh_type;
 
            // write the number of tags:
            // 1 (physical entity)
            // 2 (geometric entity)
            // 3 (partition entity)
            out_stream << " 3 "
                       << std::get<2>(t)
                       << " 0 "
                       << elem.processor_id()+1
                       << " ";
 
            // if there is a node translation table, use it
            if (eletype.nodes.size() > 0)
              for (auto i : side->node_index_range())
                out_stream << side->node_id(eletype.nodes[i])+1 << " "; // gmsh is 1-based
 
            // otherwise keep the same node order
            else
              for (auto i : side->node_index_range())
                out_stream << side->node_id(i)+1 << " ";                // gmsh is 1-based
 
            // Go to the next line
            out_stream << "\n";
 
            // increment this index too...
            ++e_id;
          }
      }
 
    out_stream << "$EndElements\n";
  }
}

References _element_maps, libMesh::MeshBase::active_element_ptr_range(), libMesh::BoundaryInfo::build_side_list(), libMesh::Elem::build_side_ptr(), libMesh::MeshBase::elem_ref(), libMesh::MeshBase::get_boundary_info(), libMesh::GmshIO::ElementDefinition::gmsh_type, libMesh::DofObject::id(), libMesh::libmesh_assert(), libMesh::MeshBase::max_elem_id(), libMesh::MeshInput< MeshBase >::mesh(), libMesh::MeshOutput< MT >::mesh(), libMesh::MeshBase::n_active_elem(), libMesh::BoundaryInfo::n_boundary_conds(), libMesh::MeshBase::n_nodes(), libMesh::MeshBase::node_ref(), libMesh::GmshIO::ElementDefinition::nodes, libMesh::GmshIO::ElementMaps::out, libMesh::DofObject::processor_id(), libMesh::Real, and write_lower_dimensional_elements().

Referenced by write().

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.

{
  std::vector<std::string> names;
  es.build_variable_names  (names, nullptr, system_names);
 
  std::unique_ptr<NumericVector<Number>> parallel_soln =
    es.build_parallel_solution_vector(system_names);
 
  this->write_nodal_data (fname, *parallel_soln, names);
}

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.

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

write_nodal_data() [3/3]

void libMesh::GmshIO::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 848 of file gmsh_io.C.

{
  LOG_SCOPE("write_nodal_data()", "GmshIO");
 
  if (MeshOutput<MeshBase>::mesh().processor_id() == 0)
    this->write_post  (fname, &soln, &names);
}

References write_post().

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

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.

  { libmesh_not_implemented(); }

write_post()

void libMesh::GmshIO::write_post ( const std::string &  fname, const std::vector< Number > *  v = 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 or binary *.pos file, depending on the binary flag.

Definition at line 1006 of file gmsh_io.C.

{
 
  // Should only do this on processor 0!
  libmesh_assert_equal_to (MeshOutput<MeshBase>::mesh().processor_id(), 0);
 
  // Create an output stream
  std::ofstream out_stream(fname.c_str());
 
  // Make sure it opened correctly
  if (!out_stream.good())
    libmesh_file_error(fname.c_str());
 
  // create a character buffer
  char buf[80];
 
  // Get a constant reference to the mesh.
  const MeshBase & mesh = MeshOutput<MeshBase>::mesh();
 
  //  write the data
  if ((solution_names != nullptr) && (v != nullptr))
    {
      const unsigned int n_vars =
        cast_int<unsigned int>(solution_names->size());
 
      if (!(v->size() == mesh.n_nodes()*n_vars))
        libMesh::err << "ERROR: v->size()=" << v->size()
                     << ", mesh.n_nodes()=" << mesh.n_nodes()
                     << ", n_vars=" << n_vars
                     << ", mesh.n_nodes()*n_vars=" << mesh.n_nodes()*n_vars
                     << "\n";
 
      libmesh_assert_equal_to (v->size(), mesh.n_nodes()*n_vars);
 
      // write the header
      out_stream << "$PostFormat\n";
      if (this->binary())
        out_stream << "1.2 1 " << sizeof(double) << "\n";
      else
        out_stream << "1.2 0 " << sizeof(double) << "\n";
      out_stream << "$EndPostFormat\n";
 
      // Loop over the elements to see how much of each type there are
      unsigned int n_points=0, n_lines=0, n_triangles=0, n_quadrangles=0,
        n_tetrahedra=0, n_hexahedra=0, n_prisms=0, n_pyramids=0;
      unsigned int n_scalar=0, n_vector=0, n_tensor=0;
      unsigned int nb_text2d=0, nb_text2d_chars=0, nb_text3d=0, nb_text3d_chars=0;
 
      {
        for (const auto & elem : mesh.active_element_ptr_range())
          {
            const ElemType elemtype = elem->type();
 
            switch (elemtype)
              {
              case EDGE2:
              case EDGE3:
              case EDGE4:
                {
                  n_lines += 1;
                  break;
                }
              case TRI3:
              case TRI6:
                {
                  n_triangles += 1;
                  break;
                }
              case QUAD4:
              case QUAD8:
              case QUAD9:
                {
                  n_quadrangles += 1;
                  break;
                }
              case TET4:
              case TET10:
                {
                  n_tetrahedra += 1;
                  break;
                }
              case HEX8:
              case HEX20:
              case HEX27:
                {
                  n_hexahedra += 1;
                  break;
                }
              case PRISM6:
              case PRISM15:
              case PRISM18:
                {
                  n_prisms += 1;
                  break;
                }
              case PYRAMID5:
                {
                  n_pyramids += 1;
                  break;
                }
              default:
                libmesh_error_msg("ERROR: Nonexistent element type " << elem->type());
              }
          }
      }
 
      // create a view for each variable
      for (unsigned int ivar=0; ivar < n_vars; ivar++)
        {
          std::string varname = (*solution_names)[ivar];
 
          // at the moment, we just write out scalar quantities
          // later this should be made configurable through
          // options to the writer class
          n_scalar = 1;
 
          // write the variable as a view, and the number of time steps
          out_stream << "$View\n" << varname << " " << 1 << "\n";
 
          // write how many of each geometry type are written
          out_stream << n_points * n_scalar << " "
                     << n_points * n_vector << " "
                     << n_points * n_tensor << " "
                     << n_lines * n_scalar << " "
                     << n_lines * n_vector << " "
                     << n_lines * n_tensor << " "
                     << n_triangles * n_scalar << " "
                     << n_triangles * n_vector << " "
                     << n_triangles * n_tensor << " "
                     << n_quadrangles * n_scalar << " "
                     << n_quadrangles * n_vector << " "
                     << n_quadrangles * n_tensor << " "
                     << n_tetrahedra * n_scalar << " "
                     << n_tetrahedra * n_vector << " "
                     << n_tetrahedra * n_tensor << " "
                     << n_hexahedra * n_scalar << " "
                     << n_hexahedra * n_vector << " "
                     << n_hexahedra * n_tensor << " "
                     << n_prisms * n_scalar << " "
                     << n_prisms * n_vector << " "
                     << n_prisms * n_tensor << " "
                     << n_pyramids * n_scalar << " "
                     << n_pyramids * n_vector << " "
                     << n_pyramids * n_tensor << " "
                     << nb_text2d << " "
                     << nb_text2d_chars << " "
                     << nb_text3d << " "
                     << nb_text3d_chars << "\n";
 
          // if binary, write a marker to identify the endianness of the file
          if (this->binary())
            {
              const int one = 1;
              std::memcpy(buf, &one, sizeof(int));
              out_stream.write(buf, sizeof(int));
            }
 
          // the time steps (there is just 1 at the moment)
          if (this->binary())
            {
              double one = 1;
              std::memcpy(buf, &one, sizeof(double));
              out_stream.write(buf, sizeof(double));
            }
          else
            out_stream << "1\n";
 
          // Loop over the elements and write out the data
          for (const auto & elem : mesh.active_element_ptr_range())
            {
              const unsigned int nv = elem->n_vertices();
              // this is quite crappy, but I did not invent that file format!
              for (unsigned int d=0; d<3; d++)  // loop over the dimensions
                {
                  for (unsigned int n=0; n < nv; n++)   // loop over vertices
                    {
                      const Point & vertex = elem->point(n);
                      if (this->binary())
                        {
#if defined(LIBMESH_DEFAULT_TRIPLE_PRECISION) || defined(LIBMESH_DEFAULT_QUADRUPLE_PRECISION)
                          libmesh_warning("Gmsh binary writes use only double precision!");
#endif
                          double tmp = double(vertex(d));
                          std::memcpy(buf, &tmp, sizeof(double));
                          out_stream.write(reinterpret_cast<char *>(buf), sizeof(double));
                        }
                      else
                        out_stream << vertex(d) << " ";
                    }
                  if (!this->binary())
                    out_stream << "\n";
                }
 
              // now finally write out the data
              for (unsigned int i=0; i < nv; i++)   // loop over vertices
                if (this->binary())
                  {
#ifdef LIBMESH_USE_COMPLEX_NUMBERS
                    libMesh::out << "WARNING: Gmsh::write_post does not fully support "
                                 << "complex numbers. Will only write the real part of "
                                 << "variable " << varname << std::endl;
#endif
                    double tmp = double(libmesh_real((*v)[elem->node_id(i)*n_vars + ivar]));
                    std::memcpy(buf, &tmp, sizeof(double));
                    out_stream.write(reinterpret_cast<char *>(buf), sizeof(double));
                  }
                else
                  {
#ifdef LIBMESH_USE_COMPLEX_NUMBERS
                    libMesh::out << "WARNING: Gmsh::write_post does not fully support "
                                 << "complex numbers. Will only write the real part of "
                                 << "variable " << varname << std::endl;
#endif
                    out_stream << libmesh_real((*v)[elem->node_id(i)*n_vars + ivar]) << "\n";
                  }
            }
          if (this->binary())
            out_stream << "\n";
          out_stream << "$EndView\n";
 
        } // end variable loop (writing the views)
    }
}

References libMesh::MeshBase::active_element_ptr_range(), binary(), libMesh::EDGE2, libMesh::EDGE3, libMesh::EDGE4, libMesh::err, libMesh::HEX20, libMesh::HEX27, libMesh::HEX8, libMesh::libmesh_real(), libMesh::MeshInput< MeshBase >::mesh(), libMesh::MeshOutput< MT >::mesh(), libMesh::MeshBase::n_nodes(), n_vars, libMesh::out, libMesh::PRISM15, libMesh::PRISM18, libMesh::PRISM6, libMesh::PYRAMID5, libMesh::QUAD4, libMesh::QUAD8, libMesh::QUAD9, libMesh::TET10, libMesh::TET4, libMesh::TRI3, and libMesh::TRI6.

Referenced by write_nodal_data().

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.

_binary

bool libMesh::GmshIO::_binary

private

Flag to write binary data.

Definition at line 149 of file gmsh_io.h.

Referenced by binary().

_element_maps

GmshIO::ElementMaps libMesh::GmshIO::_element_maps = GmshIO::build_element_maps()

staticprivate

A static ElementMaps object that is built statically and used by all instances of this class.

Definition at line 200 of file gmsh_io.h.

Referenced by read_mesh(), and write_mesh().

_is_parallel_format [1/2]

const bool libMesh::MeshInput< MeshBase >::_is_parallel_format

privateinherited

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 121 of file mesh_input.h.

_is_parallel_format [2/2]

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

MeshBase * libMesh::MeshInput< MeshBase >::_obj

privateinherited

A pointer to a non-const object object.

This allows us to read the object from file.

Definition at line 114 of file mesh_input.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.

_write_lower_dimensional_elements

bool libMesh::GmshIO::_write_lower_dimensional_elements

private

If true, lower-dimensional elements based on the boundary conditions get written to the output file.

Definition at line 155 of file gmsh_io.h.

Referenced by write_lower_dimensional_elements().

elems_of_dimension

std::vector<bool> libMesh::MeshInput< MeshBase >::elems_of_dimension

protectedinherited

A vector of bools describing what dimension elements have been encountered when reading a mesh.

Definition at line 97 of file mesh_input.h.

---

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

• include/mesh/gmsh_io.h
• src/mesh/gmsh_io.C