Adjust cell universe indices from C++

src/cell.cpp

@@ -294,8 +294,8 @@ Cell::to_hdf5(hid_t cell_group) const
     write_string(cell_group, "name", name);
   }
 
-  //TODO: Lookup universe id in universe_dict
-  //write_int(cell_group, "universe", universe);
+  //TODO: Fix the off-by-one indexing.
+  write_int(cell_group, "universe", universes_c[universe-1]->id);
 
   // Write the region specification.
   if (!region.empty()) {
@@ -428,6 +428,24 @@ read_cells(pugi::xml_node *node)
   }
 }
 
+extern "C" void
+adjust_indices_c()
+{
+  // Change cell.universe values from IDs to indices.
+  for (Cell *c : cells_c) {
+    auto it = universe_dict.find(c->universe);
+    if (it != universe_dict.end()) {
+      //TODO: Remove this off-by-one indexing.
+      c->universe = it->second + 1;
+    } else {
+      std::stringstream err_msg;
+      err_msg << "Could not find universe " << c->universe
+              << " specified on cell " << c->id;
+      fatal_error(err_msg);
+    }
+  }
+}
+
 //==============================================================================
 // Fortran compatibility functions
 //==============================================================================

src/cell.h

@@ -73,7 +73,8 @@ public:
   //! Simple cells can be evaluated with short circuit evaluation, i.e., as soon
   //! as we know that one half-space is not satisfied, we can exit. This
   //! provides a performance benefit for the common case. In
-  //! contains_complex, we evaluate the RPN expression using a stack, similar to  //! how a RPN calculator would work.
+  //! contains_complex, we evaluate the RPN expression using a stack, similar to
+  //! how a RPN calculator would work.
   //! @param xyz[3] The 3D Cartesian coordinate to check.
   //! @param uvw[3] A direction used to "break ties" the coordinates are very
   //!   close to a surface.

src/input_xml.F90

@@ -49,6 +49,11 @@ module input_xml
   save
 
   interface
+    subroutine adjust_indices_c() bind(C)
+      use ISO_C_BINDING
+      implicit none
+    end subroutine adjust_indices_c
+
     subroutine read_surfaces(node_ptr) bind(C)
       use ISO_C_BINDING
       implicit none
@@ -4263,18 +4268,10 @@ contains
     integer :: id                     ! user-specified id
     class(Lattice),    pointer :: lat => null()
 
-    do i = 1, n_cells
-      ! =======================================================================
-      ! ADJUST UNIVERSE INDEX FOR EACH CELL
-      associate (c => cells(i))
+    call adjust_indices_c()
 
-      id = c % universe()
-      if (universe_dict % has(id)) then
-        call c % set_universe(universe_dict % get(id))
-      else
-        call fatal_error("Could not find universe " // trim(to_str(id)) &
-             &// " specified on cell " // trim(to_str(c % id())))
-      end if
+    do i = 1, n_cells
+      associate (c => cells(i))
 
       ! =======================================================================
       ! ADJUST MATERIAL/FILL POINTERS FOR EACH CELL

src/summary.F90

@@ -148,9 +148,6 @@ contains
 
       call c % to_hdf5(cell_group)
 
-      ! Write universe for this cell
-      call write_dataset(cell_group, "universe", universes(c%universe())%id)
-
       ! Write information on what fills this cell
       select case (c%type)
       case (FILL_MATERIAL)