libMesh::AbaqusIO Class Reference

#include <abaqus_io.h>

Inheritance diagram for libMesh::AbaqusIO:

Public Member Functions

 AbaqusIO (MeshBase &mesh)
 
virtual ~AbaqusIO ()
 
virtual void read (const std::string &name) override
 

Public Attributes

bool build_sidesets_from_nodesets
 

Protected Member Functions

MeshBasemesh ()
 
void set_n_partitions (unsigned int n_parts)
 
void skip_comment_lines (std::istream &in, const char comment_start)
 

Protected Attributes

std::vector< bool > elems_of_dimension
 

Private Types

typedef std::map< std::string, std::vector< dof_id_type > > container_t
 
typedef std::map< std::string, std::vector< std::pair< dof_id_type, unsigned > > > sideset_container_t
 

Private Member Functions

void read_nodes (std::string nset_name)
 
void read_elements (std::string upper, std::string elset_name)
 
std::string parse_label (std::string line, std::string label_name) const
 
bool detect_generated_set (std::string upper) const
 
void read_ids (std::string set_name, container_t &container)
 
void generate_ids (std::string set_name, container_t &container)
 
void assign_subdomain_ids ()
 
void read_sideset (std::string sideset_name, sideset_container_t &container)
 
void assign_boundary_node_ids ()
 
void assign_sideset_ids ()
 
void process_and_discard_comments ()
 
unsigned char max_elem_dimension_seen ()
 

Private Attributes

container_t _nodeset_ids
 
container_t _elemset_ids
 
sideset_container_t _sideset_ids
 
std::ifstream _in
 
std::set< ElemType_elem_types
 
std::map< dof_id_type, dof_id_type_abaqus_to_libmesh_elem_mapping
 
std::map< dof_id_type, dof_id_type_abaqus_to_libmesh_node_mapping
 
bool _already_seen_part
 

Detailed Description

The AbaqusIO class is a preliminary implementation for reading Abaqus mesh files in ASCII format.

Author
John W. Peterson
Date
2011

Definition at line 40 of file abaqus_io.h.

Member Typedef Documentation

◆ container_t

typedef std::map<std::string, std::vector<dof_id_type> > libMesh::AbaqusIO::container_t
private

The type of data structure used to store Node and Elemset IDs.

Definition at line 72 of file abaqus_io.h.

◆ sideset_container_t

typedef std::map<std::string, std::vector<std::pair<dof_id_type, unsigned> > > libMesh::AbaqusIO::sideset_container_t
private

Type of the data structure for storing the (elem ID, side) pairs defining sidesets. These come from the *Surface sections of the input file.

Definition at line 79 of file abaqus_io.h.

Constructor & Destructor Documentation

◆ AbaqusIO()

libMesh::AbaqusIO::AbaqusIO ( MeshBase mesh)
explicit

Constructor. Takes a writable reference to a mesh object.

Definition at line 188 of file abaqus_io.C.

188  :
189  MeshInput<MeshBase> (mesh_in),
191  _already_seen_part(false)
192 {
193 }
bool _already_seen_part
Definition: abaqus_io.h:235
bool build_sidesets_from_nodesets
Definition: abaqus_io.h:66

◆ ~AbaqusIO()

libMesh::AbaqusIO::~AbaqusIO ( )
virtual

Destructor.

Definition at line 198 of file abaqus_io.C.

199 {
200 }

Member Function Documentation

◆ assign_boundary_node_ids()

void libMesh::AbaqusIO::assign_boundary_node_ids ( )
private

This function assigns boundary IDs to node sets based on the alphabetical order in which the sets are labeled in the Abaqus file. We choose the alphabetical ordering simply because Abaqus does not provide a numerical one within the file.

Definition at line 948 of file abaqus_io.C.

References _abaqus_to_libmesh_node_mapping, _nodeset_ids, libMesh::BoundaryInfo::add_node(), libMesh::MeshBase::get_boundary_info(), libMesh::MeshInput< MT >::mesh(), libMesh::MeshBase::node_ptr(), and libMesh::BoundaryInfo::nodeset_name().

Referenced by read().

949 {
950  // Get a reference to the mesh we are reading
951  MeshBase & the_mesh = MeshInput<MeshBase>::mesh();
952 
953  // Iterate over the container of nodesets
954  container_t::iterator it = _nodeset_ids.begin();
955  for (unsigned short current_id=0; it != _nodeset_ids.end(); ++it, ++current_id)
956  {
957  // Associate current_id with the name we determined earlier
958  the_mesh.get_boundary_info().nodeset_name(current_id) = it->first;
959 
960  // Get a reference to the current vector of nodeset ID values
961  std::vector<dof_id_type> & nodeset_ids = it->second;
962 
963  for (const auto & id : nodeset_ids)
964  {
965  // Map the Abaqus global node ID to the libmesh node ID
966  dof_id_type libmesh_global_node_id = _abaqus_to_libmesh_node_mapping[id];
967 
968  // Get node pointer from the mesh
969  Node * node = the_mesh.node_ptr(libmesh_global_node_id);
970 
971  if (node == nullptr)
972  libmesh_error_msg("Error! Mesh::node_ptr() returned nullptr!");
973 
974  // Add this node with the current_id (which is determined by the
975  // alphabetical ordering of the map) to the BoundaryInfo object
976  the_mesh.get_boundary_info().add_node(node, current_id);
977  }
978  }
979 }
A geometric point in (x,y,z) space associated with a DOF.
Definition: node.h:52
std::string & nodeset_name(boundary_id_type id)
const BoundaryInfo & get_boundary_info() const
Definition: mesh_base.h:131
Base class for Mesh.
Definition: mesh_base.h:77
void add_node(const Node *node, const boundary_id_type id)
container_t _nodeset_ids
Definition: abaqus_io.h:197
std::map< dof_id_type, dof_id_type > _abaqus_to_libmesh_node_mapping
Definition: abaqus_io.h:227
virtual const Node * node_ptr(const dof_id_type i) const =0
uint8_t dof_id_type
Definition: id_types.h:64

◆ assign_sideset_ids()

void libMesh::AbaqusIO::assign_sideset_ids ( )
private

Called at the end of the read() function, assigns any sideset IDs found when reading the file to the BoundaryInfo object.

Definition at line 984 of file abaqus_io.C.

References _abaqus_to_libmesh_elem_mapping, _elemset_ids, _sideset_ids, libMesh::MeshBase::active_element_ptr_range(), libMesh::BoundaryInfo::add_side(), libMesh::as_range(), libMesh::Elem::dim(), libMesh::MeshBase::elem_ref(), libMesh::Utility::enum_to_string(), libMesh::MeshBase::get_boundary_info(), libMesh::Elem::key(), max_elem_dimension_seen(), libMesh::MeshInput< MT >::mesh(), side, libMesh::BoundaryInfo::sideset_name(), and libMesh::Elem::type().

Referenced by read().

985 {
986  // Get a reference to the mesh we are reading
987  MeshBase & the_mesh = MeshInput<MeshBase>::mesh();
988 
989  // initialize the eletypes map (eletypes is a file-global variable)
990  init_eletypes();
991 
992  // Iterate over the container of sidesets
993  {
994  sideset_container_t::iterator it = _sideset_ids.begin();
995  for (unsigned short current_id=0; it != _sideset_ids.end(); ++it, ++current_id)
996  {
997  // Associate current_id with the name we determined earlier
998  the_mesh.get_boundary_info().sideset_name(current_id) = it->first;
999 
1000  // Get a reference to the current vector of nodeset ID values
1001  std::vector<std::pair<dof_id_type,unsigned>> & sideset_ids = it->second;
1002 
1003  for (const auto & id : sideset_ids)
1004  {
1005  // sideset_ids is a vector of pairs (elem id, side id). Pull them out
1006  // now to make the code below more readable.
1007  dof_id_type abaqus_elem_id = id.first;
1008  unsigned abaqus_side_number = id.second;
1009 
1010  // Map the Abaqus element ID to LibMesh numbering
1011  dof_id_type libmesh_elem_id = _abaqus_to_libmesh_elem_mapping[ abaqus_elem_id ];
1012 
1013  // Get a reference to that element
1014  Elem & elem = the_mesh.elem_ref(libmesh_elem_id);
1015 
1016  // Grab a reference to the element definition for this element type
1017  const ElementDefinition & eledef = eletypes[elem.type()];
1018 
1019  // If the element definition was not found, the call above would have
1020  // created one with an uninitialized struct. Check for that here...
1021  if (eledef.abaqus_zero_based_side_id_to_libmesh_side_id.size() == 0)
1022  libmesh_error_msg("No Abaqus->LibMesh mapping information for ElemType " \
1023  << Utility::enum_to_string(elem.type()) \
1024  << "!");
1025 
1026  // Add this node with the current_id (which is determined by the
1027  // alphabetical ordering of the map). Side numbers in Abaqus are 1-based,
1028  // so we subtract 1 here before passing the abaqus side number to the
1029  // mapping array
1030  the_mesh.get_boundary_info().add_side
1031  (&elem,
1032  eledef.abaqus_zero_based_side_id_to_libmesh_side_id[abaqus_side_number-1],
1033  current_id);
1034  }
1035  }
1036  }
1037 
1038 
1039  // Some elsets (if they contain lower-dimensional elements) also
1040  // define sidesets. So loop over them and build a searchable data
1041  // structure we can use to assign sidesets.
1042  {
1043  unsigned char max_dim = this->max_elem_dimension_seen();
1044 
1045  // multimap from lower-dimensional-element-hash-key to
1046  // pair(lower-dimensional-element, boundary_id). The
1047  // lower-dimensional element is used to verify the results of the
1048  // hash table search. The boundary_id will be used to set a
1049  // boundary ID on a higher-dimensional element. We use a multimap
1050  // because the lower-dimensional elements can belong to more than
1051  // 1 sideset, and multiple lower-dimensional elements can hash to
1052  // the same value, but this is very rare.
1053  std::unordered_multimap<dof_id_type, std::pair<Elem *, boundary_id_type>> provide_bcs;
1054 
1055  // The elemset_id counter assigns a logical numbering to the
1056  // _elemset_ids keys. We are going to use these ids as boundary
1057  // ids, so elemset_id is of type boundary_id_type.
1058  container_t::iterator it = _elemset_ids.begin();
1059  for (boundary_id_type elemset_id=0; it != _elemset_ids.end(); ++it, ++elemset_id)
1060  {
1061  // Grab a reference to the vector of IDs
1062  std::vector<dof_id_type> & id_vector = it->second;
1063 
1064  // Loop over this vector
1065  for (const auto & id : id_vector)
1066  {
1067  // Map the id_vector[i]'th element ID (Abaqus numbering) to LibMesh numbering
1068  dof_id_type libmesh_elem_id = _abaqus_to_libmesh_elem_mapping[id];
1069 
1070  // Get a reference to that element
1071  Elem & elem = the_mesh.elem_ref(libmesh_elem_id);
1072 
1073  // If the element dimension is equal to the maximum
1074  // dimension seen, we can break out of this for loop --
1075  // this elset does not contain sideset information.
1076  if (elem.dim() == max_dim)
1077  break;
1078 
1079  // We can only handle elements that are *exactly*
1080  // one dimension lower than the max element
1081  // dimension. Not sure if "edge" BCs in 3D
1082  // actually make sense/are required...
1083  if (elem.dim()+1 != max_dim)
1084  libmesh_error_msg("ERROR: Expected boundary element of dimension " << max_dim-1 << " but got " << elem.dim());
1085 
1086  // Insert the current (key, pair(elem,id)) into the multimap.
1087  provide_bcs.insert(std::make_pair(elem.key(),
1088  std::make_pair(&elem,
1089  elemset_id)));
1090 
1091  // Associate the name of this sideset with the ID we've
1092  // chosen. It's not necessary to do this for every
1093  // element in the set, but it's convenient to do it here
1094  // since we have all the necessary information...
1095  the_mesh.get_boundary_info().sideset_name(elemset_id) = it->first;
1096  }
1097  }
1098 
1099  // Loop over elements and try to assign boundary information
1100  for (auto & elem : the_mesh.active_element_ptr_range())
1101  if (elem->dim() == max_dim)
1102  for (auto sn : elem->side_index_range())
1103  {
1104  // This is a max-dimension element that may require BCs.
1105  // For each of its sides, including internal sides, we'll
1106  // see if a lower-dimensional element provides boundary
1107  // information for it. Note that we have not yet called
1108  // find_neighbors(), so we can't use elem->neighbor(sn) in
1109  // this algorithm...
1110  auto bounds = provide_bcs.equal_range (elem->key(sn));
1111 
1112  // Add boundary information for each side in the range.
1113  for (const auto & pr : as_range(bounds))
1114  {
1115  // We'll need to compare the lower dimensional element against the current side.
1116  std::unique_ptr<Elem> side (elem->build_side_ptr(sn));
1117 
1118  // Extract the relevant data. We don't need the key for anything.
1119  Elem * lower_dim_elem = pr.second.first;
1120  boundary_id_type bid = pr.second.second;
1121 
1122  // This was a hash, so it might not be perfect. Let's verify...
1123  if (*lower_dim_elem == *side)
1124  the_mesh.get_boundary_info().add_side(elem, sn, bid);
1125  }
1126  }
1127  }
1128 }
IntRange< unsigned short > side_index_range() const
Definition: elem.h:2166
sideset_container_t _sideset_ids
Definition: abaqus_io.h:199
unsigned short int side
Definition: xdr_io.C:50
The base class for all geometric element types.
Definition: elem.h:100
virtual SimpleRange< element_iterator > active_element_ptr_range()=0
const BoundaryInfo & get_boundary_info() const
Definition: mesh_base.h:131
Base class for Mesh.
Definition: mesh_base.h:77
std::map< dof_id_type, dof_id_type > _abaqus_to_libmesh_elem_mapping
Definition: abaqus_io.h:217
virtual std::unique_ptr< Elem > build_side_ptr(const unsigned int i, bool proxy=true)=0
int8_t boundary_id_type
Definition: id_types.h:51
virtual dof_id_type key(const unsigned int s) const =0
SimpleRange< I > as_range(const std::pair< I, I > &p)
Definition: simple_range.h:57
std::string & sideset_name(boundary_id_type id)
std::string enum_to_string(const T e)
virtual unsigned short dim() const =0
unsigned char max_elem_dimension_seen()
Definition: abaqus_io.C:1175
void add_side(const dof_id_type elem, const unsigned short int side, const boundary_id_type id)
virtual const Elem & elem_ref(const dof_id_type i) const
Definition: mesh_base.h:504
container_t _elemset_ids
Definition: abaqus_io.h:198
virtual ElemType type() const =0
uint8_t dof_id_type
Definition: id_types.h:64

◆ assign_subdomain_ids()

void libMesh::AbaqusIO::assign_subdomain_ids ( )
private

This function is called after all the elements have been read and assigns element subdomain IDs.

The IDs are simply chosen in the order in which the elset labels are stored in the map (roughly alphabetically). To make this easy on people who are planning to use Exodus output, we'll assign different geometric elements to different (but related) subdomains, i.e. assuming there are E elemsets:

Elemset 0, Geometric Type 0: ID 0 Elemset 0, Geometric Type 1: ID 0+E ...

Elemset 0, Geometric Type N: ID 0+N*E

Elemset 1, Geometric Type 0: ID 1 Elemset 1, Geometric Type 1: ID 1+E ... Elemset 1, Geometric Type N: ID 1+N*E etc.

Definition at line 879 of file abaqus_io.C.

References _abaqus_to_libmesh_elem_mapping, _elem_types, _elemset_ids, libMesh::Elem::dim(), libMesh::MeshBase::elem_ref(), libMesh::Utility::enum_to_string(), max_elem_dimension_seen(), libMesh::MeshInput< MT >::mesh(), libMesh::Elem::subdomain_id(), libMesh::MeshBase::subdomain_name(), and libMesh::Elem::type().

Referenced by read().

880 {
881  // Get a reference to the mesh we are reading
882  MeshBase & the_mesh = MeshInput<MeshBase>::mesh();
883 
884  // The number of elemsets we've found while reading
885  std::size_t n_elemsets = _elemset_ids.size();
886 
887  // Fill in a temporary map with (ElemType, index) pairs based on the _elem_types set. This
888  // will allow us to easily look up this index in the loop below.
889  std::map<ElemType, unsigned> elem_types_map;
890  {
891  unsigned ctr=0;
892  for (const auto & type : _elem_types)
893  elem_types_map[type] = ctr++;
894  }
895 
896  // Loop over each Elemset and assign subdomain IDs to Mesh elements
897  {
898  // The maximum element dimension seen while reading the Mesh
899  unsigned char max_dim = this->max_elem_dimension_seen();
900 
901  // The elemset_id counter assigns a logical numbering to the _elemset_ids keys
902  container_t::iterator it = _elemset_ids.begin();
903  for (unsigned elemset_id=0; it != _elemset_ids.end(); ++it, ++elemset_id)
904  {
905  // Grab a reference to the vector of IDs
906  std::vector<dof_id_type> & id_vector = it->second;
907 
908  // Loop over this vector
909  for (const auto & id : id_vector)
910  {
911  // Map the id'th element ID (Abaqus numbering) to LibMesh numbering
912  dof_id_type libmesh_elem_id = _abaqus_to_libmesh_elem_mapping[id];
913 
914  // Get reference to that element
915  Elem & elem = the_mesh.elem_ref(libmesh_elem_id);
916 
917  // We won't assign subdomain ids to lower-dimensional
918  // elements, as they are assumed to represent boundary
919  // conditions. Since lower-dimensional elements can
920  // appear in multiple sidesets, it doesn't make sense to
921  // assign them a single subdomain id... only the last one
922  // assigned would actually "stick".
923  if (elem.dim() < max_dim)
924  break;
925 
926  // Compute the proper subdomain ID, based on the formula in the
927  // documentation for this function.
928  subdomain_id_type computed_id = cast_int<subdomain_id_type>
929  (elemset_id + (elem_types_map[elem.type()] * n_elemsets));
930 
931  // Assign this ID to the element in question
932  elem.subdomain_id() = computed_id;
933 
934  // We will also assign a unique name to the computed_id,
935  // which is created by appending the geometric element
936  // name to the elset name provided by the user in the
937  // Abaqus file.
938  std::string computed_name = it->first + "_" + Utility::enum_to_string(elem.type());
939  the_mesh.subdomain_name(computed_id) = computed_name;
940  }
941  }
942  }
943 }
The base class for all geometric element types.
Definition: elem.h:100
Base class for Mesh.
Definition: mesh_base.h:77
std::map< dof_id_type, dof_id_type > _abaqus_to_libmesh_elem_mapping
Definition: abaqus_io.h:217
std::string & subdomain_name(subdomain_id_type id)
Definition: mesh_base.C:538
std::string enum_to_string(const T e)
std::set< ElemType > _elem_types
Definition: abaqus_io.h:210
subdomain_id_type subdomain_id() const
Definition: elem.h:2034
virtual unsigned short dim() const =0
unsigned char max_elem_dimension_seen()
Definition: abaqus_io.C:1175
virtual const Elem & elem_ref(const dof_id_type i) const
Definition: mesh_base.h:504
container_t _elemset_ids
Definition: abaqus_io.h:198
virtual ElemType type() const =0
uint8_t dof_id_type
Definition: id_types.h:64

◆ detect_generated_set()

bool libMesh::AbaqusIO::detect_generated_set ( std::string  upper) const
private
Returns
true if the input string is a generated elset or nset, false otherwise.

The input string is assumed to already be in all upper case. Generated nsets are assumed to have the following format: *Nset, nset=Set-1, generate

Definition at line 747 of file abaqus_io.C.

Referenced by read().

748 {
749  // Avoid issues with weird line endings, spaces before commas, etc.
750  upper.erase(std::remove_if(upper.begin(), upper.end(), isspace), upper.end());
751 
752  // Check each comma-separated value in "upper" to see if it is the generate flag.
753  std::string cell;
754  std::stringstream line_stream(upper);
755  while (std::getline(line_stream, cell, ','))
756  if (cell == "GENERATE")
757  return true;
758 
759  return false;
760 }

◆ generate_ids()

void libMesh::AbaqusIO::generate_ids ( std::string  set_name,
container_t container 
)
private

This function handles "generated" nset and elset sections. These are denoted by having the comma-separated "GENERATE" keyword in their definition, e.g. *Nset, nset=Set-1, generate

Definition at line 809 of file abaqus_io.C.

References _in, and end.

Referenced by read().

810 {
811  // Grab a reference to a vector that will hold all the IDs
812  std::vector<dof_id_type> & id_storage = container[set_name];
813 
814  // Read until the start of another section is detected, or EOF is
815  // encountered. "generate" sections seem to only have one line,
816  // although I suppose it's possible they could have more.
817  while (_in.peek() != '*' && _in.peek() != EOF)
818  {
819  // Read entire comma-separated line into a string
820  std::string csv_line;
821  std::getline(_in, csv_line);
822 
823  // Remove all whitespaces from csv_line.
824  csv_line.erase(std::remove_if(csv_line.begin(), csv_line.end(), isspace), csv_line.end());
825 
826  // Create a new stringstream object from the string, and stream
827  // in the comma-separated values.
828  char c;
829  dof_id_type start, end, stride;
830  std::stringstream line_stream(csv_line);
831  line_stream >> start >> c >> end >> c >> stride;
832 
833  // Generate entries in the id_storage. Note: each element can
834  // only belong to a single Elset (since this corresponds to the
835  // subdomain_id) so if an element appears in multiple Elsets,
836  // the "last" one (alphabetically, based on set name) in the
837  // _elemset_ids map will "win".
838  for (dof_id_type current = start; current <= end; current += stride)
839  id_storage.push_back(current);
840  }
841 }
IterBase * end
std::ifstream _in
Definition: abaqus_io.h:204
uint8_t dof_id_type
Definition: id_types.h:64

◆ max_elem_dimension_seen()

unsigned char libMesh::AbaqusIO::max_elem_dimension_seen ( )
private
Returns
The maximum geometric element dimension encountered while reading the Mesh.

Only valid after the elements have been read in and the elems_of_dimension array has been populated.

Definition at line 1175 of file abaqus_io.C.

References libMesh::MeshInput< MeshBase >::elems_of_dimension.

Referenced by assign_sideset_ids(), assign_subdomain_ids(), and read().

1176 {
1177  unsigned char max_dim = 0;
1178 
1179  unsigned char elem_dimensions_size = cast_int<unsigned char>
1180  (elems_of_dimension.size());
1181  // The elems_of_dimension array is 1-based in the UNV reader
1182  for (unsigned char i=1; i<elem_dimensions_size; ++i)
1183  if (elems_of_dimension[i])
1184  max_dim = i;
1185 
1186  return max_dim;
1187 }
std::vector< bool > elems_of_dimension
Definition: mesh_input.h:97

◆ mesh()

MeshBase & libMesh::MeshInput< MeshBase >::mesh ( )
inlineprotectedinherited
Returns
The object as a writable reference.

Definition at line 169 of file mesh_input.h.

Referenced by libMesh::GMVIO::_read_one_cell(), libMesh::VTKIO::cells_to_vtk(), libMesh::TetGenIO::element_in(), libMesh::UNVIO::elements_in(), libMesh::UNVIO::elements_out(), libMesh::UNVIO::groups_in(), libMesh::TetGenIO::node_in(), libMesh::UNVIO::nodes_in(), libMesh::UNVIO::nodes_out(), libMesh::VTKIO::nodes_to_vtk(), libMesh::Nemesis_IO::prepare_to_write_nodal_data(), libMesh::Nemesis_IO::read(), libMesh::ExodusII_IO::read(), libMesh::GMVIO::read(), libMesh::XdrIO::read(), libMesh::CheckpointIO::read(), libMesh::VTKIO::read(), libMesh::CheckpointIO::read_bcs(), libMesh::CheckpointIO::read_connectivity(), libMesh::CheckpointIO::read_header(), libMesh::XdrIO::read_header(), libMesh::UCDIO::read_implementation(), libMesh::UNVIO::read_implementation(), libMesh::GmshIO::read_mesh(), libMesh::CheckpointIO::read_nodes(), libMesh::CheckpointIO::read_nodesets(), libMesh::CheckpointIO::read_remote_elem(), libMesh::XdrIO::read_serialized_bcs_helper(), libMesh::XdrIO::read_serialized_connectivity(), libMesh::XdrIO::read_serialized_nodes(), libMesh::XdrIO::read_serialized_nodesets(), libMesh::XdrIO::read_serialized_subdomain_names(), libMesh::OFFIO::read_stream(), libMesh::MatlabIO::read_stream(), libMesh::CheckpointIO::read_subdomain_names(), libMesh::TetGenIO::write(), libMesh::Nemesis_IO::write(), libMesh::ExodusII_IO::write(), libMesh::XdrIO::write(), libMesh::CheckpointIO::write(), libMesh::GMVIO::write_ascii_new_impl(), libMesh::GMVIO::write_ascii_old_impl(), libMesh::GMVIO::write_binary(), libMesh::GMVIO::write_discontinuous_gmv(), libMesh::Nemesis_IO::write_element_data(), libMesh::ExodusII_IO::write_element_data(), libMesh::UCDIO::write_header(), libMesh::UCDIO::write_implementation(), libMesh::UCDIO::write_interior_elems(), libMesh::GmshIO::write_mesh(), libMesh::VTKIO::write_nodal_data(), libMesh::UCDIO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data(), libMesh::ExodusII_IO::write_nodal_data_common(), libMesh::ExodusII_IO::write_nodal_data_discontinuous(), libMesh::UCDIO::write_nodes(), libMesh::CheckpointIO::write_nodesets(), libMesh::XdrIO::write_parallel(), libMesh::GmshIO::write_post(), libMesh::XdrIO::write_serialized_bcs_helper(), libMesh::XdrIO::write_serialized_connectivity(), libMesh::XdrIO::write_serialized_nodes(), libMesh::XdrIO::write_serialized_nodesets(), libMesh::XdrIO::write_serialized_subdomain_names(), libMesh::UCDIO::write_soln(), and libMesh::CheckpointIO::write_subdomain_names().

170 {
171  if (_obj == nullptr)
172  libmesh_error_msg("ERROR: _obj should not be nullptr!");
173  return *_obj;
174 }

◆ parse_label()

std::string libMesh::AbaqusIO::parse_label ( std::string  line,
std::string  label_name 
) const
private

This function parses a label of the form foo=bar from a comma-delimited line of the form ..., foo=bar, ... The input to the function in this case would be foo, the output would be bar

Definition at line 702 of file abaqus_io.C.

References end.

Referenced by read().

703 {
704  // Handle files which have weird line endings from e.g. windows.
705  // You can check what kind of line endings you have with 'cat -vet'.
706  // For example, some files may have two kinds of line endings like:
707  //
708  // 4997,^I496,^I532,^I487,^I948^M$
709  //
710  // and we don't want to deal with this when extracting a label, so
711  // just remove all the space characters, which should include all
712  // kinds of remaining newlines. (I don't think Abaqus allows
713  // whitespace in label names.)
714  line.erase(std::remove_if(line.begin(), line.end(), isspace), line.end());
715 
716  // Do all string comparisons in upper-case
717  std::string
718  upper_line(line),
719  upper_label_name(label_name);
720  std::transform(upper_line.begin(), upper_line.end(), upper_line.begin(), ::toupper);
721  std::transform(upper_label_name.begin(), upper_label_name.end(), upper_label_name.begin(), ::toupper);
722 
723  // Get index of start of "label="
724  size_t label_index = upper_line.find(upper_label_name + "=");
725 
726  if (label_index != std::string::npos)
727  {
728  // Location of the first comma following "label="
729  size_t comma_index = upper_line.find(",", label_index);
730 
731  // Construct iterators from which to build the sub-string.
732  // Note: The +1 while initializing beg is to skip past the "=" which follows the label name
733  std::string::iterator
734  beg = line.begin() + label_name.size() + 1 + label_index,
735  end = (comma_index == std::string::npos) ? line.end() : line.begin() + comma_index;
736 
737  return std::string(beg, end);
738  }
739 
740  // The label index was not found, return the empty string
741  return std::string("");
742 }
IterBase * end

◆ process_and_discard_comments()

void libMesh::AbaqusIO::process_and_discard_comments ( )
private

Any of the various sections can start with some number of lines of comments, which start with "**". This function discards any lines of comments that it finds from the stream, leaving trailing data intact.

Definition at line 1132 of file abaqus_io.C.

References _in.

Referenced by read().

1133 {
1134  std::string dummy;
1135  while (true)
1136  {
1137  // We assume we are at the beginning of a line that may be
1138  // comments or may be data. We need to only discard the line if
1139  // it begins with **, but we must avoid calling std::getline()
1140  // since there's no way to put that back.
1141  if (_in.peek() == '*')
1142  {
1143  // The first character was a star, so actually read it from the stream.
1144  _in.get();
1145 
1146  // Peek at the next character...
1147  if (_in.peek() == '*')
1148  {
1149  // OK, second character was star also, by definition this
1150  // line must be a comment! Read the rest of the line and discard!
1151  std::getline(_in, dummy);
1152  }
1153  else
1154  {
1155  // The second character was _not_ a star, so put back the first star
1156  // we pulled out so that the line can be parsed correctly by somebody
1157  // else!
1158  _in.unget();
1159 
1160  // Finally, break out of the while loop, we are done parsing comments
1161  break;
1162  }
1163  }
1164  else
1165  {
1166  // First character was not *, so this line must be data! Break out of the
1167  // while loop!
1168  break;
1169  }
1170  }
1171 }
std::ifstream _in
Definition: abaqus_io.h:204

◆ read()

void libMesh::AbaqusIO::read ( const std::string &  name)
overridevirtual

This method implements reading a mesh from a specified file.

Implements libMesh::MeshInput< MeshBase >.

Definition at line 205 of file abaqus_io.C.

References _already_seen_part, _elemset_ids, _in, _nodeset_ids, _sideset_ids, assign_boundary_node_ids(), assign_sideset_ids(), assign_subdomain_ids(), libMesh::BoundaryInfo::build_side_list_from_node_list(), build_sidesets_from_nodesets, libMesh::MeshBase::clear(), libMesh::MeshBase::delete_elem(), detect_generated_set(), libMesh::MeshBase::element_ptr_range(), libMesh::MeshInput< MeshBase >::elems_of_dimension, generate_ids(), libMesh::MeshBase::get_boundary_info(), max_elem_dimension_seen(), libMesh::MeshInput< MT >::mesh(), libMesh::BoundaryInfo::n_boundary_conds(), parse_label(), process_and_discard_comments(), read_elements(), read_ids(), read_nodes(), read_sideset(), and libMesh::MeshBase::set_mesh_dimension().

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

206 {
207  // Get a reference to the mesh we are reading
208  MeshBase & the_mesh = MeshInput<MeshBase>::mesh();
209 
210  // Clear any existing mesh data
211  the_mesh.clear();
212 
213  // Open stream for reading
214  _in.open(fname.c_str());
215  libmesh_assert(_in.good());
216 
217  // Initialize the elems_of_dimension array. We will use this in a
218  // "1-based" manner so that elems_of_dimension[d]==true means
219  // elements of dimension d have been seen.
220  elems_of_dimension.resize(4, false);
221 
222  // Read file line-by-line... this is based on a set of different
223  // test input files. I have not looked at the full input file
224  // specs for Abaqus.
225  std::string s;
226  while (true)
227  {
228  // Try to read something. This may set EOF!
229  std::getline(_in, s);
230 
231  if (_in)
232  {
233  // Process s...
234  //
235  // There are many sections in Abaqus files, we read some
236  // but others are just ignored... Some sections may occur
237  // more than once. For example for a hybrid grid, you
238  // will have multiple *Element sections...
239 
240  // Some Abaqus files use all upper-case for section names,
241  // so we will just convert s to uppercase
242  std::string upper(s);
243  std::transform(upper.begin(), upper.end(), upper.begin(), ::toupper);
244 
245  // 0.) Look for the "*Part" section
246  if (upper.find("*PART") == static_cast<std::string::size_type>(0))
247  {
248  if (_already_seen_part)
249  libmesh_error_msg("We currently don't support reading Abaqus files with multiple PART sections");
250 
251  _already_seen_part = true;
252  }
253 
254  // 1.) Look for the "*Nodes" section
255  if (upper.find("*NODE") == static_cast<std::string::size_type>(0))
256  {
257  // Some sections that begin with *NODE are actually
258  // "*NODE OUTPUT" sections which we want to skip. I
259  // have only seen this with a single space, but it would
260  // probably be more robust to remove whitespace before
261  // making this check.
262  if (upper.find("*NODE OUTPUT") == static_cast<std::string::size_type>(0))
263  continue;
264 
265  // Some *Node sections also specify an Nset name on the same line.
266  // Look for one here.
267  std::string nset_name = this->parse_label(s, "nset");
268 
269  // Process any lines of comments that may be present
271 
272  // Read a block of nodes
273  this->read_nodes(nset_name);
274  }
275 
276 
277 
278  // 2.) Look for the "*Element" section
279  else if (upper.find("*ELEMENT,") == static_cast<std::string::size_type>(0))
280  {
281  // Some sections that begin with *ELEMENT are actually
282  // "*ELEMENT OUTPUT" sections which we want to skip. I
283  // have only seen this with a single space, but it would
284  // probably be more robust to remove whitespace before
285  // making this check.
286  if (upper.find("*ELEMENT OUTPUT") == static_cast<std::string::size_type>(0))
287  continue;
288 
289  // Some *Element sections also specify an Elset name on the same line.
290  // Look for one here.
291  std::string elset_name = this->parse_label(s, "elset");
292 
293  // Process any lines of comments that may be present
295 
296  // Read a block of elements
297  this->read_elements(upper, elset_name);
298  }
299 
300 
301 
302  // 3.) Look for a Nodeset section
303  else if (upper.find("*NSET") == static_cast<std::string::size_type>(0))
304  {
305  std::string nset_name = this->parse_label(s, "nset");
306 
307  // I haven't seen an unnamed nset yet, but let's detect it
308  // just in case...
309  if (nset_name == "")
310  libmesh_error_msg("Unnamed nset encountered!");
311 
312  // Is this a "generated" nset, i.e. one which has three
313  // entries corresponding to (first, last, stride)?
314  bool is_generated = this->detect_generated_set(upper);
315 
316  // Process any lines of comments that may be present
318 
319  // Read the IDs, storing them in _nodeset_ids
320  if (is_generated)
321  this->generate_ids(nset_name, _nodeset_ids);
322  else
323  this->read_ids(nset_name, _nodeset_ids);
324  } // *Nodeset
325 
326 
327 
328  // 4.) Look for an Elset section
329  else if (upper.find("*ELSET") == static_cast<std::string::size_type>(0))
330  {
331  std::string elset_name = this->parse_label(s, "elset");
332 
333  // I haven't seen an unnamed elset yet, but let's detect it
334  // just in case...
335  if (elset_name == "")
336  libmesh_error_msg("Unnamed elset encountered!");
337 
338  // Is this a "generated" elset, i.e. one which has three
339  // entries corresponding to (first, last, stride)?
340  bool is_generated = this->detect_generated_set(upper);
341 
342  // Process any lines of comments that may be present
344 
345  // Read the IDs, storing them in _elemset_ids
346  if (is_generated)
347  this->generate_ids(elset_name, _elemset_ids);
348  else
349  this->read_ids(elset_name, _elemset_ids);
350  } // *Elset
351 
352 
353 
354  // 5.) Look for a Surface section. Need to be a little
355  // careful, since there are also "surface interaction"
356  // sections we don't want to read here.
357  else if (upper.find("*SURFACE,") == static_cast<std::string::size_type>(0))
358  {
359  // Get the name from the Name=Foo label. This will be the map key.
360  std::string sideset_name = this->parse_label(s, "name");
361 
362  // Process any lines of comments that may be present
364 
365  // Read the sideset IDs
366  this->read_sideset(sideset_name, _sideset_ids);
367  }
368 
369  continue;
370  } // if (_in)
371 
372  // If !file, check to see if EOF was set. If so, break out
373  // of while loop.
374  if (_in.eof())
375  break;
376 
377  // If !in and !in.eof(), stream is in a bad state!
378  libmesh_error_msg("Stream is bad! Perhaps the file: " << fname << " does not exist?");
379  } // while
380 
381  // Set the Mesh dimension based on the highest dimension element seen.
383 
384  // Set element IDs based on the element sets.
385  this->assign_subdomain_ids();
386 
387  // Assign nodeset values to the BoundaryInfo object
388  this->assign_boundary_node_ids();
389 
390  // Assign sideset values in the BoundaryInfo object
391  this->assign_sideset_ids();
392 
393  // If the Abaqus file contains only nodesets, we can have libmesh
394  // generate sidesets from them. This BoundaryInfo function currently
395  // *overwrites* existing sidesets in surprising ways, so we don't
396  // call it if there are already sidesets present in the original file.
399 
400  // Delete lower-dimensional elements from the Mesh. We assume these
401  // were only used for setting BCs, and aren't part of the actual
402  // Mesh.
403  {
404  unsigned char max_dim = this->max_elem_dimension_seen();
405 
406  for (auto & elem : the_mesh.element_ptr_range())
407  if (elem->dim() < max_dim)
408  the_mesh.delete_elem(elem);
409  }
410 }
void read_sideset(std::string sideset_name, sideset_container_t &container)
Definition: abaqus_io.C:846
void process_and_discard_comments()
Definition: abaqus_io.C:1132
std::size_t n_boundary_conds() const
bool _already_seen_part
Definition: abaqus_io.h:235
std::vector< bool > elems_of_dimension
Definition: mesh_input.h:97
sideset_container_t _sideset_ids
Definition: abaqus_io.h:199
void read_ids(std::string set_name, container_t &container)
Definition: abaqus_io.C:764
bool build_sidesets_from_nodesets
Definition: abaqus_io.h:66
void assign_sideset_ids()
Definition: abaqus_io.C:984
const BoundaryInfo & get_boundary_info() const
Definition: mesh_base.h:131
void read_nodes(std::string nset_name)
Definition: abaqus_io.C:418
Base class for Mesh.
Definition: mesh_base.h:77
void read_elements(std::string upper, std::string elset_name)
Definition: abaqus_io.C:497
std::string parse_label(std::string line, std::string label_name) const
Definition: abaqus_io.C:702
bool detect_generated_set(std::string upper) const
Definition: abaqus_io.C:747
virtual void delete_elem(Elem *e)=0
virtual SimpleRange< element_iterator > element_ptr_range()=0
void build_side_list_from_node_list()
void generate_ids(std::string set_name, container_t &container)
Definition: abaqus_io.C:809
void assign_subdomain_ids()
Definition: abaqus_io.C:879
void assign_boundary_node_ids()
Definition: abaqus_io.C:948
container_t _nodeset_ids
Definition: abaqus_io.h:197
void set_mesh_dimension(unsigned char d)
Definition: mesh_base.h:213
virtual void clear()
Definition: mesh_base.C:260
unsigned char max_elem_dimension_seen()
Definition: abaqus_io.C:1175
container_t _elemset_ids
Definition: abaqus_io.h:198
std::ifstream _in
Definition: abaqus_io.h:204

◆ read_elements()

void libMesh::AbaqusIO::read_elements ( std::string  upper,
std::string  elset_name 
)
private

This function parses a block of elements in the Abaqus file. You must pass it an upper-cased version of the string declaring this section, which is typically something like: *ELEMENT, TYPE=CPS3 so that it can determine the type of elements to read.

Definition at line 497 of file abaqus_io.C.

References _abaqus_to_libmesh_elem_mapping, _abaqus_to_libmesh_node_mapping, _elem_types, _elemset_ids, _in, libMesh::MeshBase::add_elem(), libMesh::Elem::build(), libMesh::EDGE2, libMesh::EDGE3, libMesh::MeshInput< MeshBase >::elems_of_dimension, libMesh::Utility::enum_to_string(), libMesh::HEX20, libMesh::HEX27, libMesh::HEX8, libMesh::DofObject::id(), libMesh::INVALID_ELEM, libMesh::MeshInput< MT >::mesh(), libMesh::MeshBase::node_ptr(), libMesh::PRISM15, libMesh::PRISM6, libMesh::QUAD4, libMesh::QUAD8, libMesh::Elem::set_node(), libMesh::TET10, libMesh::TET4, libMesh::TRI3, and libMesh::TRI6.

Referenced by read().

498 {
499  // Get a reference to the mesh we are reading
500  MeshBase & the_mesh = MeshInput<MeshBase>::mesh();
501 
502  // initialize the eletypes map (eletypes is a file-global variable)
503  init_eletypes();
504 
505  ElemType elem_type = INVALID_ELEM;
506  unsigned n_nodes_per_elem = 0;
507 
508  // Within s, we should have "type=XXXX"
509  if (upper.find("T3D2") != std::string::npos ||
510  upper.find("B31") != std::string::npos)
511  {
512  elem_type = EDGE2;
513  n_nodes_per_elem = 2;
514  elems_of_dimension[1] = true;
515  }
516  else if (upper.find("B32") != std::string::npos)
517  {
518  elem_type = EDGE3;
519  n_nodes_per_elem = 3;
520  elems_of_dimension[1] = true;
521  }
522  else if (upper.find("S3") != std::string::npos ||
523  upper.find("CPE3") != std::string::npos ||
524  upper.find("2D3") != std::string::npos)
525  {
526  elem_type = TRI3;
527  n_nodes_per_elem = 3;
528  elems_of_dimension[2] = true;
529  }
530  else if (upper.find("CPE4") != std::string::npos ||
531  upper.find("S4") != std::string::npos ||
532  upper.find("CPEG4") != std::string::npos ||
533  upper.find("2D4") != std::string::npos)
534  {
535  elem_type = QUAD4;
536  n_nodes_per_elem = 4;
537  elems_of_dimension[2] = true;
538  }
539  else if (upper.find("CPE6") != std::string::npos ||
540  upper.find("S6") != std::string::npos ||
541  upper.find("CPEG6") != std::string::npos ||
542  upper.find("2D6") != std::string::npos)
543  {
544  elem_type = TRI6;
545  n_nodes_per_elem = 6;
546  elems_of_dimension[2] = true;
547  }
548  else if (upper.find("CPE8") != std::string::npos ||
549  upper.find("S8") != std::string::npos ||
550  upper.find("CPEG8") != std::string::npos ||
551  upper.find("2D8") != std::string::npos)
552  {
553  elem_type = QUAD8;
554  n_nodes_per_elem = 8;
555  elems_of_dimension[2] = true;
556  }
557  else if (upper.find("3D8") != std::string::npos)
558  {
559  elem_type = HEX8;
560  n_nodes_per_elem = 8;
561  elems_of_dimension[3] = true;
562  }
563  else if (upper.find("3D4") != std::string::npos)
564  {
565  elem_type = TET4;
566  n_nodes_per_elem = 4;
567  elems_of_dimension[3] = true;
568  }
569  else if (upper.find("3D20") != std::string::npos)
570  {
571  elem_type = HEX20;
572  n_nodes_per_elem = 20;
573  elems_of_dimension[3] = true;
574  }
575  else if (upper.find("3D27") != std::string::npos)
576  {
577  elem_type = HEX27;
578  n_nodes_per_elem = 27;
579  elems_of_dimension[3] = true;
580  }
581  else if (upper.find("3D6") != std::string::npos)
582  {
583  elem_type = PRISM6;
584  n_nodes_per_elem = 6;
585  elems_of_dimension[3] = true;
586  }
587  else if (upper.find("3D15") != std::string::npos)
588  {
589  elem_type = PRISM15;
590  n_nodes_per_elem = 15;
591  elems_of_dimension[3] = true;
592  }
593  else if (upper.find("3D10") != std::string::npos)
594  {
595  elem_type = TET10;
596  n_nodes_per_elem = 10;
597  elems_of_dimension[3] = true;
598  }
599  else
600  libmesh_error_msg("Unrecognized element type: " << upper);
601 
602  // Insert the elem type we detected into the set of all elem types for this mesh
603  _elem_types.insert(elem_type);
604 
605  // Grab a reference to the element definition for this element type
606  const ElementDefinition & eledef = eletypes[elem_type];
607 
608  // If the element definition was not found, the call above would have
609  // created one with an uninitialized struct. Check for that here...
610  if (eledef.abaqus_zero_based_node_id_to_libmesh_node_id.size() == 0)
611  libmesh_error_msg("No Abaqus->LibMesh mapping information for ElemType " \
612  << Utility::enum_to_string(elem_type) \
613  << "!");
614 
615  // We will read elements until the next line begins with *, since that will be the
616  // next section.
617  while (_in.peek() != '*' && _in.peek() != EOF)
618  {
619  // Read the element ID, it is the first number on each line. It is
620  // followed by a comma, so read that also. We will need this ID later
621  // when we try to assign subdomain IDs
622  dof_id_type abaqus_elem_id = 0;
623  char c;
624  _in >> abaqus_elem_id >> c;
625 
626  // Add an element of the appropriate type to the Mesh.
627  Elem * elem = the_mesh.add_elem(Elem::build(elem_type).release());
628 
629  // Associate the ID returned from libmesh with the abaqus element ID
630  //_libmesh_to_abaqus_elem_mapping[elem->id()] = abaqus_elem_id;
631  _abaqus_to_libmesh_elem_mapping[abaqus_elem_id] = elem->id();
632 
633  // The count of the total number of IDs read for the current element.
634  unsigned id_count=0;
635 
636  // Continue reading line-by-line until we have read enough nodes for this element
637  while (id_count < n_nodes_per_elem)
638  {
639  // Read entire line (up to carriage return) of comma-separated values
640  std::string csv_line;
641  std::getline(_in, csv_line);
642 
643  // Create a stream object out of the current line
644  std::stringstream line_stream(csv_line);
645 
646  // Process the comma-separated values
647  std::string cell;
648  while (std::getline(line_stream, cell, ','))
649  {
650  // FIXME: factor out this strtol stuff into a utility function.
651  char * endptr;
652  dof_id_type abaqus_global_node_id = cast_int<dof_id_type>
653  (std::strtol(cell.c_str(), &endptr, /*base=*/10));
654 
655  if (abaqus_global_node_id!=0 || cell.c_str() != endptr)
656  {
657  // Use the global node number mapping to determine the corresponding libmesh global node id
658  dof_id_type libmesh_global_node_id = _abaqus_to_libmesh_node_mapping[abaqus_global_node_id];
659 
660  // Grab the node pointer from the mesh for this ID
661  Node * node = the_mesh.node_ptr(libmesh_global_node_id);
662 
663  // If node_ptr() returns nullptr, it may mean we have not yet read the
664  // *Nodes section, though I assumed that always came before the *Elements section...
665  if (node == nullptr)
666  libmesh_error_msg("Error! Mesh::node_ptr() returned nullptr. Either no node exists with ID " \
667  << libmesh_global_node_id \
668  << " or perhaps this input file has *Elements defined before *Nodes?");
669 
670  // Note: id_count is the zero-based abaqus (elem local) node index. We therefore map
671  // it to a libmesh elem local node index using the element definition map
672  unsigned libmesh_elem_local_node_id =
673  eledef.abaqus_zero_based_node_id_to_libmesh_node_id[id_count];
674 
675  // Set this node pointer within the element.
676  elem->set_node(libmesh_elem_local_node_id) = node;
677 
678  // Increment the count of IDs read for this element
679  id_count++;
680  } // end if strtol success
681  } // end while getline(',')
682  } // end while (id_count)
683 
684  // Ensure that we read *exactly* as many nodes as we were expecting to, no more.
685  if (id_count != n_nodes_per_elem)
686  libmesh_error_msg("Error: Needed to read " \
687  << n_nodes_per_elem \
688  << " nodes, but read " \
689  << id_count \
690  << " instead!");
691 
692  // If we are recording Elset IDs, add this element to the correct set for later processing.
693  // Make sure to add it with the Abaqus ID, not the libmesh one!
694  if (elset_name != "")
695  _elemset_ids[elset_name].push_back(abaqus_elem_id);
696  } // end while (peek)
697 }
virtual Node *& set_node(const unsigned int i)
Definition: elem.h:2024
A geometric point in (x,y,z) space associated with a DOF.
Definition: node.h:52
std::vector< bool > elems_of_dimension
Definition: mesh_input.h:97
The base class for all geometric element types.
Definition: elem.h:100
Base class for Mesh.
Definition: mesh_base.h:77
std::map< dof_id_type, dof_id_type > _abaqus_to_libmesh_elem_mapping
Definition: abaqus_io.h:217
dof_id_type id() const
Definition: dof_object.h:655
virtual Elem * add_elem(Elem *e)=0
static std::unique_ptr< Elem > build(const ElemType type, Elem *p=nullptr)
Definition: elem.C:245
std::string enum_to_string(const T e)
std::set< ElemType > _elem_types
Definition: abaqus_io.h:210
std::map< dof_id_type, dof_id_type > _abaqus_to_libmesh_node_mapping
Definition: abaqus_io.h:227
virtual const Node * node_ptr(const dof_id_type i) const =0
container_t _elemset_ids
Definition: abaqus_io.h:198
std::ifstream _in
Definition: abaqus_io.h:204
uint8_t dof_id_type
Definition: id_types.h:64

◆ read_ids()

void libMesh::AbaqusIO::read_ids ( std::string  set_name,
container_t container 
)
private

This function reads all the IDs for the current node or element set of the given name, storing them in the passed map using the name as key.

Definition at line 764 of file abaqus_io.C.

References _in.

Referenced by read().

765 {
766  // Grab a reference to a vector that will hold all the IDs
767  std::vector<dof_id_type> & id_storage = container[set_name];
768 
769  // Read until the start of another section is detected, or EOF is encountered
770  while (_in.peek() != '*' && _in.peek() != EOF)
771  {
772  // Read entire comma-separated line into a string
773  std::string csv_line;
774  std::getline(_in, csv_line);
775 
776  // On that line, use std::getline again to parse each
777  // comma-separated entry.
778  std::string cell;
779  std::stringstream line_stream(csv_line);
780  while (std::getline(line_stream, cell, ','))
781  {
782  // If no conversion can be performed by strtol, 0 is returned.
783  //
784  // If endptr is not nullptr, strtol() stores the address of the
785  // first invalid character in *endptr. If there were no
786  // digits at all, however, strtol() stores the original
787  // value of str in *endptr.
788  char * endptr;
789 
790  // FIXME - this needs to be updated for 64-bit inputs
791  dof_id_type id = cast_int<dof_id_type>
792  (std::strtol(cell.c_str(), &endptr, /*base=*/10));
793 
794  // Note that lists of comma-separated values in abaqus also
795  // *end* with a comma, so the last call to getline on a given
796  // line will get an empty string, which we must detect.
797  if (id != 0 || cell.c_str() != endptr)
798  {
799  // 'cell' is now a string with an integer id in it
800  id_storage.push_back( id );
801  }
802  }
803  }
804 }
std::ifstream _in
Definition: abaqus_io.h:204
uint8_t dof_id_type
Definition: id_types.h:64

◆ read_nodes()

void libMesh::AbaqusIO::read_nodes ( std::string  nset_name)
private

This function parses a block of nodes in the Abaqus file once such a block has been found. If the *NODE section specifies an NSET name, also pass that to this function.

Definition at line 418 of file abaqus_io.C.

References _abaqus_to_libmesh_node_mapping, _in, _nodeset_ids, libMesh::MeshBase::add_point(), libMesh::MeshInput< MT >::mesh(), libMesh::MeshBase::n_nodes(), and libMesh::Real.

Referenced by read().

419 {
420  // Get a reference to the mesh we are reading
421  MeshBase & the_mesh = MeshInput<MeshBase>::mesh();
422 
423  // In the input files I have, Abaqus neither tells what
424  // the mesh dimension is nor how many nodes it has...
425  //
426  // The node line format is:
427  // id, x, y, z
428  // and you do have to parse out the commas.
429  // The z-coordinate will only be present for 3D meshes
430 
431  // Temporary variables for parsing lines of text
432  char c;
433  std::string line;
434 
435  // Defines the sequential node numbering used by libmesh. Since
436  // there can be multiple *NODE sections in an Abaqus file, we always
437  // start our numbering with the number of nodes currently in the
438  // Mesh.
439  dof_id_type libmesh_node_id = the_mesh.n_nodes();
440 
441  // We need to duplicate some of the read_ids code if this *NODE
442  // section also defines an NSET. We'll set up the id_storage
443  // pointer and push back IDs into this vector in the loop below...
444  std::vector<dof_id_type> * id_storage = nullptr;
445  if (nset_name != "")
446  id_storage = &(_nodeset_ids[nset_name]);
447 
448  // We will read nodes until the next line begins with *, since that will be the
449  // next section.
450  // TODO: Is Abaqus guaranteed to start the line with '*' or can there be leading white space?
451  while (_in.peek() != '*' && _in.peek() != EOF)
452  {
453  // Read an entire line which corresponds to a single point's id
454  // and (x,y,z) values.
455  std::getline(_in, line);
456 
457  // Remove all whitespace characters from the line. This way we
458  // can do the remaining parsing without worrying about tabs,
459  // different numbers of spaces, etc.
460  line.erase(std::remove_if(line.begin(), line.end(), isspace), line.end());
461 
462  // Make a stream out of the modified line so we can stream values
463  // from it in the usual way.
464  std::stringstream ss(line);
465 
466  // Values to be read in from file
467  dof_id_type abaqus_node_id=0;
468  Real x=0, y=0, z=0;
469 
470  // Note: we assume *at least* 2D points here, should we worry about
471  // trying to read 1D Abaqus meshes?
472  ss >> abaqus_node_id >> c >> x >> c >> y;
473 
474  // Peek at the next character. If it is a comma, then there is another
475  // value to read!
476  if (ss.peek() == ',')
477  ss >> c >> z;
478 
479  // If this *NODE section defines an NSET, also store the abaqus ID in id_storage
480  if (id_storage)
481  id_storage->push_back(abaqus_node_id);
482 
483  // Set up the abaqus -> libmesh node mapping. This is usually just the
484  // "off-by-one" map, but it doesn't have to be.
485  _abaqus_to_libmesh_node_mapping[abaqus_node_id] = libmesh_node_id;
486 
487  // Add the point to the mesh using libmesh's numbering,
488  // and post-increment the libmesh node counter.
489  the_mesh.add_point(Point(x,y,z), libmesh_node_id++);
490  } // while
491 }
virtual Node * add_point(const Point &p, const dof_id_type id=DofObject::invalid_id, const processor_id_type proc_id=DofObject::invalid_processor_id)=0
Base class for Mesh.
Definition: mesh_base.h:77
container_t _nodeset_ids
Definition: abaqus_io.h:197
DIE A HORRIBLE DEATH HERE typedef LIBMESH_DEFAULT_SCALAR_TYPE Real
std::map< dof_id_type, dof_id_type > _abaqus_to_libmesh_node_mapping
Definition: abaqus_io.h:227
A geometric point in (x,y,z) space.
Definition: point.h:38
virtual dof_id_type n_nodes() const =0
std::ifstream _in
Definition: abaqus_io.h:204
uint8_t dof_id_type
Definition: id_types.h:64

◆ read_sideset()

void libMesh::AbaqusIO::read_sideset ( std::string  sideset_name,
sideset_container_t container 
)
private

This function reads a sideset from the input file. This is defined by a "*Surface" section in the file, and then a list of element ID and side IDs for the set.

Definition at line 846 of file abaqus_io.C.

References _in.

Referenced by read().

847 {
848  // Grab a reference to a vector that will hold all the IDs
849  std::vector<std::pair<dof_id_type, unsigned>> & id_storage = container[sideset_name];
850 
851  // Variables for storing values read in from file
852  dof_id_type elem_id=0;
853  unsigned side_id=0;
854  char c;
855  std::string dummy;
856 
857  // Read until the start of another section is detected, or EOF is encountered
858  while (_in.peek() != '*' && _in.peek() != EOF)
859  {
860  // The strings are of the form: "391, S2"
861 
862  // Read the element ID and the leading comma
863  _in >> elem_id >> c;
864 
865  // Read another character (the 'S') and finally the side ID
866  _in >> c >> side_id;
867 
868  // Store this pair of data in the vector
869  id_storage.push_back( std::make_pair(elem_id, side_id) );
870 
871  // Extract remaining characters on line including newline
872  std::getline(_in, dummy);
873  } // while
874 }
std::ifstream _in
Definition: abaqus_io.h:204
uint8_t dof_id_type
Definition: id_types.h:64

◆ 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.

References libMesh::MeshInput< MT >::mesh().

Referenced by libMesh::Nemesis_IO::read(), and libMesh::XdrIO::read_header().

91 { this->mesh().set_n_partitions() = n_parts; }
unsigned int & set_n_partitions()
Definition: mesh_base.h:1371

◆ 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.

Referenced by libMesh::TetGenIO::read(), and libMesh::UCDIO::read_implementation().

181 {
182  char c, line[256];
183 
184  while (in.get(c), c==comment_start)
185  in.getline (line, 255);
186 
187  // put back first character of
188  // first non-comment line
189  in.putback (c);
190 }

Member Data Documentation

◆ _abaqus_to_libmesh_elem_mapping

std::map<dof_id_type, dof_id_type> libMesh::AbaqusIO::_abaqus_to_libmesh_elem_mapping
private

Map from libmesh element number -> abaqus element number, and the converse.

Definition at line 217 of file abaqus_io.h.

Referenced by assign_sideset_ids(), assign_subdomain_ids(), and read_elements().

◆ _abaqus_to_libmesh_node_mapping

std::map<dof_id_type, dof_id_type> libMesh::AbaqusIO::_abaqus_to_libmesh_node_mapping
private

Map from abaqus node number -> sequential, 0-based libmesh node numbering.

Note
In every Abaqus file I've ever seen the node numbers were 1-based, sequential, and all in order, so that this map is probably overkill. Nevertheless, it is the most general solution in case we come across a weird Abaqus file some day.

Definition at line 227 of file abaqus_io.h.

Referenced by assign_boundary_node_ids(), read_elements(), and read_nodes().

◆ _already_seen_part

bool libMesh::AbaqusIO::_already_seen_part
private

This flag gets set to true after the first "*PART" section we see. If it is still true when we see a second PART section, we will print an error message... we don't currently handle input files with multiple parts.

Definition at line 235 of file abaqus_io.h.

Referenced by read().

◆ _elem_types

std::set<ElemType> libMesh::AbaqusIO::_elem_types
private

A set of the different geometric element types detected when reading the mesh.

Definition at line 210 of file abaqus_io.h.

Referenced by assign_subdomain_ids(), and read_elements().

◆ _elemset_ids

container_t libMesh::AbaqusIO::_elemset_ids
private

Definition at line 198 of file abaqus_io.h.

Referenced by assign_sideset_ids(), assign_subdomain_ids(), read(), and read_elements().

◆ _in

std::ifstream libMesh::AbaqusIO::_in
private

Stream object used to interact with the file

Definition at line 204 of file abaqus_io.h.

Referenced by generate_ids(), process_and_discard_comments(), read(), read_elements(), read_ids(), read_nodes(), and read_sideset().

◆ _nodeset_ids

container_t libMesh::AbaqusIO::_nodeset_ids
private

Abaqus writes nodesets and elemsets with labels. As we read them in, we'll use these maps to provide a natural ordering for them.

Definition at line 197 of file abaqus_io.h.

Referenced by assign_boundary_node_ids(), read(), and read_nodes().

◆ _sideset_ids

sideset_container_t libMesh::AbaqusIO::_sideset_ids
private

Definition at line 199 of file abaqus_io.h.

Referenced by assign_sideset_ids(), and read().

◆ build_sidesets_from_nodesets

bool libMesh::AbaqusIO::build_sidesets_from_nodesets

Default false. Set this flag to true if you want libmesh to automatically generate sidesets from Abaqus' nodesets. If the Abaqus file already contains some sidesets, we ignore this flag and don't generate sidesets, because the algorithm to do so currently does not take into account existing sidesets.

Definition at line 66 of file abaqus_io.h.

Referenced by read().

◆ elems_of_dimension


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