Exemplo n.º 1
0
// ========================================================================
void process_elementblocks(Ioss::Region &region, stk::mesh::BulkData &bulk)
{
    const Ioss::ElementBlockContainer& elem_blocks = region.get_element_blocks();

    for(Ioss::ElementBlockContainer::const_iterator it = elem_blocks.begin();
            it != elem_blocks.end(); ++it) {
        Ioss::ElementBlock *entity = *it;

        if (stk::io::include_entity(entity)) {
            const std::string &name = entity->name();
            const stk::mesh::MetaData& meta = stk::mesh::MetaData::get(bulk);
            stk::mesh::Part* const part = meta.get_part(name);
            STKIORequire(part != NULL);

            const stk::topology topo = part->topology();
            if (topo == stk::topology::INVALID_TOPOLOGY) {
                std::ostringstream msg ;
                msg << " INTERNAL_ERROR: Part " << part->name() << " returned INVALID from get_topology()";
                throw std::runtime_error( msg.str() );
            }

            std::vector<int> elem_ids ;
            std::vector<int> connectivity ;

            entity->get_field_data("ids", elem_ids);
            entity->get_field_data("connectivity", connectivity);

            size_t element_count = elem_ids.size();
            int nodes_per_elem = topo.num_nodes();

            stk::mesh::EntityIdVector connectivity2(nodes_per_elem);

            std::vector<int>::const_iterator connBegin = connectivity.begin();
            std::vector<stk::mesh::Entity> elements(element_count);
            for(size_t i=0; i<element_count; ++i, connBegin += nodes_per_elem) {
                std::copy(connBegin, connBegin + nodes_per_elem, connectivity2.begin());
                elements[i] = stk::mesh::declare_element(bulk, *part, elem_ids[i], connectivity2);
            }

            // For this example, we are just taking all attribute fields
            // found on the io database and populating fields on the
            // corresponding mesh part.  In practice, would probably be
            // selective about which attributes to use...
            Ioss::NameList names;
            entity->field_describe(Ioss::Field::ATTRIBUTE, &names);
            for (Ioss::NameList::const_iterator I = names.begin(); I != names.end(); ++I) {
                if (*I == "attribute" && names.size() > 1)
                    continue;
                stk::mesh::FieldBase *field = meta.get_field<stk::mesh::FieldBase>(stk::topology::ELEMENT_RANK, *I);
                stk::io::field_data_from_ioss(bulk, field, elements, entity, *I);

            }
        }
    }
}
Exemplo n.º 2
0
// ========================================================================
void process_elementblocks(Ioss::Region &region, stk::mesh::MetaData &meta)
{
    const stk::mesh::EntityRank element_rank = stk::topology::ELEMENT_RANK;

    const Ioss::ElementBlockContainer& elem_blocks = region.get_element_blocks();
    stk::io::default_part_processing(elem_blocks, meta, element_rank);

    // Parts were created above, now handle element block specific
    // information (topology, attributes, ...);
    for(Ioss::ElementBlockContainer::const_iterator it = elem_blocks.begin();
            it != elem_blocks.end(); ++it) {
        Ioss::ElementBlock *entity = *it;

        if (stk::io::include_entity(entity)) {
            stk::mesh::Part* const part = meta.get_part(entity->name());
            STKIORequire(part != NULL);

            const stk::mesh::EntityRank part_rank = part->primary_entity_rank();

            // Element Block attributes (if any)...
            /** \todo IMPLEMENT truly handle attribute fields... For this
             * case we are just defining a field for each attribute field
             * that is present in the mesh...
             */
            stk::io::define_io_fields(entity, Ioss::Field::ATTRIBUTE,
                                      *part,
                                      part_rank);

            /** \todo IMPLEMENT truly handle fields... For this case we
             * are just defining a field for each transient field that is
             * present in the mesh...
             */
            stk::io::define_io_fields(entity, Ioss::Field::TRANSIENT,
                                      *part,
                                      part_rank);
        }
    }
}
Exemplo n.º 3
0
void
Albany::IossSTKMeshStruct::setFieldAndBulkData(
                                               const Teuchos::RCP<const Epetra_Comm>& comm,
                                               const Teuchos::RCP<Teuchos::ParameterList>& params,
                                               const unsigned int neq_,
                                               const AbstractFieldContainer::FieldContainerRequirements& req,
                                               const Teuchos::RCP<Albany::StateInfoStruct>& sis,
                                               const unsigned int worksetSize)
{
  this->SetupFieldData(comm, neq_, req, sis, worksetSize);

  *out << "IOSS-STK: number of node sets = " << nsPartVec.size() << std::endl;
  *out << "IOSS-STK: number of side sets = " << ssPartVec.size() << std::endl;

  metaData->commit();

  // Restart index to read solution from exodus file.
  int index = params->get("Restart Index",-1); // Default to no restart
  double res_time = params->get<double>("Restart Time",-1.0); // Default to no restart
  Ioss::Region *region = mesh_data->m_input_region;

  /*
   * The following code block reads a single mesh on PE 0, then distributes the mesh across
   * the other processors. stk_rebalance is used, which requires Zoltan
   *
   * This code is only compiled if ALBANY_MPI and ALBANY_ZOLTAN are true
   */

#ifdef ALBANY_ZOLTAN // rebalance needs Zoltan

  if(useSerialMesh){

    bulkData->modification_begin();

    if(comm->MyPID() == 0){ // read in the mesh on PE 0

      stk::io::process_mesh_bulk_data(region, *bulkData);

      // Read solution from exodus file.
      if (index >= 0) { // User has specified a time step to restart at
        *out << "Restart Index set, reading solution index : " << index << std::endl;
        stk::io::input_mesh_fields(region, *bulkData, index);
        m_restartDataTime = region->get_state_time(index);
        m_hasRestartSolution = true;
      }
      else if (res_time >= 0) { // User has specified a time to restart at
        *out << "Restart solution time set, reading solution time : " << res_time << std::endl;
        stk::io::input_mesh_fields(region, *bulkData, res_time);
        m_restartDataTime = res_time;
        m_hasRestartSolution = true;
      }
      else {

        *out << "Neither restart index or time are set. Not reading solution data from exodus file"<< std::endl;

      }
    }

    bulkData->modification_end();

  } // End UseSerialMesh - reading mesh on PE 0

  else 
#endif

    /*
     * The following code block reads a single mesh when Albany is compiled serially, or a
     * Nemspread fileset if ALBANY_MPI is true.
     *
     */

  { // running in Serial or Parallel read from Nemspread files

    stk::io::populate_bulk_data(*bulkData, *mesh_data);

    if (!usePamgen)  {

      // Read solution from exodus file.
      if (index >= 0) { // User has specified a time step to restart at
        *out << "Restart Index set, reading solution index : " << index << std::endl;
        stk::io::process_input_request(*mesh_data, *bulkData, index);
        m_restartDataTime = region->get_state_time(index);
        m_hasRestartSolution = true;
      }
      else if (res_time >= 0) { // User has specified a time to restart at
        *out << "Restart solution time set, reading solution time : " << res_time << std::endl;
        stk::io::process_input_request(*mesh_data, *bulkData, res_time);
        m_restartDataTime = res_time;
        m_hasRestartSolution = true;
      }
      else {
        *out << "Restart Index not set. Not reading solution from exodus (" 
             << index << ")"<< std::endl;

      }
    }

    bulkData->modification_end();

  } // End Parallel Read - or running in serial

  if(m_hasRestartSolution){

    Teuchos::Array<std::string> default_field;
    default_field.push_back("solution");
    Teuchos::Array<std::string> restart_fields =
      params->get<Teuchos::Array<std::string> >("Restart Fields", default_field);

    // Get the fields to be used for restart

    // See what state data was initialized from the stk::io request
    // This should be propagated into stk::io
    const Ioss::ElementBlockContainer& elem_blocks = region->get_element_blocks();

    /*
    // Uncomment to print what fields are in the exodus file
    Ioss::NameList exo_fld_names;
    elem_blocks[0]->field_describe(&exo_fld_names);
    for(std::size_t i = 0; i < exo_fld_names.size(); i++){
    *out << "Found field \"" << exo_fld_names[i] << "\" in exodus file" << std::endl;
    }
    */

    for (std::size_t i=0; i<sis->size(); i++) {
      Albany::StateStruct& st = *((*sis)[i]);

      if(elem_blocks[0]->field_exists(st.name))

        for(std::size_t j = 0; j < restart_fields.size(); j++)

          if(boost::iequals(st.name, restart_fields[j])){

            *out << "Restarting from field \"" << st.name << "\" found in exodus file." << std::endl;
            st.restartDataAvailable = true;
            break;

          }
    }
  }

//  coordinates_field = metaData->get_field<VectorFieldType>(std::string("coordinates"));
//#ifdef ALBANY_FELIX
//  surfaceHeight_field = metaData->get_field<ScalarFieldType>(std::string("surface height"));
//#endif

  // Refine the mesh before starting the simulation if indicated
  uniformRefineMesh(comm);

  // Rebalance the mesh before starting the simulation if indicated
  rebalanceInitialMesh(comm);

  // Build additional mesh connectivity needed for mesh fracture (if indicated)
  computeAddlConnectivity();

}