Refactor ExodusII

include/mesh/exodusII_io_helper.h

@@ -306,6 +306,18 @@ class ExodusII_IO_Helper : public ParallelObject
                                  int time_step,
                                  std::map<dof_id_type, Real> & elem_var_value_map);
 
+  /**
+   * Reads element "extra integer" values, using the variable names
+   * specified in \p extra_integer_var_names, and converting the
+   * stored values to integer format.  The returned value is a vector
+   * (indexed in the same way as extra_integer_vars) of maps from
+   * element id to extra integer value.
+   *
+   * Currently values from the last time step are used.
+   */
+  std::vector<std::map<dof_id_type, dof_id_type>> read_extra_integers(
+    const std::vector<std::string> & extra_integer_var_names);
+
   /**
    * Helper function that takes a (1-based) Exodus node/elem id and
    * determines the corresponding libMesh Node/Elem id. Takes into account
@@ -942,36 +954,22 @@ class ExodusII_IO_Helper : public ParallelObject
    * each processor.  This plus a node id gives a valid nodal solution
    * vector index.
    */
-  dof_id_type node_id_to_vec_id(dof_id_type n) const
-  {
-    if (_added_side_node_offsets.empty())
-      return n;
-
-    // Find the processor id that has node_id in the parallel vec
-    const auto lb = std::upper_bound(_true_node_offsets.begin(),
-                                     _true_node_offsets.end(), n);
-    libmesh_assert(lb != _true_node_offsets.end());
-    const processor_id_type p = lb - _true_node_offsets.begin();
-
-    return n + (p ? _added_side_node_offsets[p-1] : 0);
-  }
+  dof_id_type node_id_to_vec_id(dof_id_type n) const;
 
   /*
    * Returns the sum of both added node "offsets" on processors 0
    * through p-1 and real nodes added on processors 0 to p.
    * This is the starting index for added nodes' data.
    */
-  dof_id_type added_node_offset_on(processor_id_type p) const
-  {
-    libmesh_assert (p < _true_node_offsets.size());
-    const dof_id_type added_node_offsets =
-      (_added_side_node_offsets.empty() || !p) ? 0 :
-      _added_side_node_offsets[p-1];
-    return _true_node_offsets[p] + added_node_offsets;
-  }
-
+  dof_id_type added_node_offset_on(processor_id_type p) const;
 
 protected:
+  /**
+   * Calculate _added_side_node_offsets needed to add "fake" side
+   * elements to the given mesh
+   */
+  void calculate_added_side_node_offsets(const MeshBase & mesh);
+
   /**
    * When appending: during initialization, check that variable names
    * in the file match those you attempt to initialize with.
@@ -1104,13 +1102,28 @@ class ExodusII_IO_Helper : public ParallelObject
                                    int & count,
                                    std::vector<std::string> & result);
 
-private:
-
   /**
    * Set to true iff we want to write separate "side" elements too.
    */
   bool _add_sides = false;
 
+  /**
+   * Map of subdomains to element numbers.
+   */
+  std::map<subdomain_id_type, std::vector<dof_id_type>> _subdomain_map;
+
+  /**
+   * One beyond the last "real" subdomain id, in cases where we have
+   * "fake" subdomain ids for added sides
+   */
+  subdomain_id_type _subdomain_id_end;
+
+  /**
+   * Method for constructing _subdomain_map
+   */
+  void build_subdomain_map(const MeshBase & mesh, bool local);
+
+private:
   /**
    * write_var_names() dispatches to this function.
    */

include/mesh/nemesis_io_helper.h

@@ -435,11 +435,6 @@ class Nemesis_IO_Helper : public ExodusII_IO_Helper
    */
   std::set<int> nodes_attached_to_local_elems;
 
-  /**
-   * Map of subdomains to element numbers.
-   */
-  std::map<subdomain_id_type, std::vector<dof_id_type>> subdomain_map;
-
   /**
    * This is the block connectivity, i.e. for each subdomain (block) there
    * is an element connectivity list. This map associates the block ID to that vector.

src/mesh/exodusII_io.C

@@ -406,13 +406,11 @@ void ExodusII_IO::read (const std::string & fname)
   // have already been attached to spline control nodes.
   mesh.reserve_elem(exio_helper->w.size() + exio_helper->num_elem);
 
-  // Read variables for extra integer IDs
-  std::vector<std::map<dof_id_type, Real>> elem_ids(extra_ids.size());
-  // We use the last time step to load the IDs
   exio_helper->read_num_time_steps();
-  unsigned int last_step = exio_helper->num_time_steps;
-  for (auto i : index_range(extra_ids))
-    exio_helper->read_elemental_var_values(_extra_integer_vars[i], last_step, elem_ids[i]);
+
+  // Read variables for extra integer IDs
+  auto extra_integer_values =
+    exio_helper->read_extra_integers(_extra_integer_vars);
 
   // Read in the element connectivity for each block.
   int nelem_last_block = 0;
@@ -504,44 +502,7 @@ void ExodusII_IO::read (const std::string & fname)
 
           // Assign extra integer IDs
           for (auto & id : extra_ids)
-          {
-            const Real v = elem_ids[id][elem->id()];
-
-            if (v == Real(-1))
-              {
-                elem->set_extra_integer(id, DofObject::invalid_id);
-                continue;
-              }
-
-            // Ignore FE_INVALID here even if we've enabled FPEs; a
-            // thrown exception is preferred over an FPE signal.
-            FPEDisabler disable_fpes;
-            const long long iv = std::llround(v);
-
-            // Check if the real number is outside of the range we can
-            // convert exactly
-
-            long long max_representation = 1;
-            max_representation = (max_representation << std::min(std::numeric_limits<Real>::digits,
-                                                                 std::numeric_limits<double>::digits));
-            libmesh_error_msg_if(iv > max_representation,
-                                 "Error! An element integer value higher than "
-                                 << max_representation
-                                 << " was found! Exodus uses real numbers for storing element "
-                                 " integers, which can only represent integers from 0 to "
-                                 << max_representation
-                                 << ".");
-
-            libmesh_error_msg_if(iv < 0,
-                                 "Error! An element integer value less than -1"
-                                 << " was found! Exodus uses real numbers for storing element "
-                                 " integers, which can only represent integers from 0 to "
-                                 << max_representation
-                                 << ".");
-
-
-            elem->set_extra_integer(id, cast_int<dof_id_type>(iv));
-          }
+             elem->set_extra_integer(id, extra_integer_values[id][elem->id()]);
 
           // Set all the nodes for this element
           //