From 1dca4d842bfff20f6ea3cb8a9a5faab2734f8792 Mon Sep 17 00:00:00 2001
From: Sterling Harper <sterlingmharper@gmail.com>
Date: Wed, 5 Aug 2015 19:10:03 -0600
Subject: [PATCH] Fix hex lattices in HDF5 summary

---
 openmc/summary.py    | 72 ++++++++++++++++++++++++++++++++++++++------
 src/hdf5_summary.F90 |  8 ++---
 2 files changed, 67 insertions(+), 13 deletions(-)

diff --git a/openmc/summary.py b/openmc/summary.py
index c0673ef23..2165d114a 100644
--- a/openmc/summary.py
+++ b/openmc/summary.py
@@ -411,16 +411,70 @@ class Summary(object):
                 if outer != -22:
                     lattice.outer = self.universes[outer]
 
-                # Build array of Universe pointers for the Lattice
-                universes = \
-                    np.ndarray(tuple(universe_ids.shape), dtype=openmc.Universe)
+                # Build array of Universe pointers for the Lattice.  Note that
+                # we need to convert between the HDF5's square array of
+                # (x, alpha, z) to the PythonAPI's format of a ragged nested
+                # nested list of (z, ring, theta).
+                universes = []
+                for z in range(lattice.num_axial):
+                    # Add a list for this axial level.
+                    universes.append([])
+                    x = lattice.num_rings - 1
+                    a = 2*lattice.num_rings - 2
+                    for r in range(lattice.num_rings - 1, 0, -1):
+                        # Add a list for this ring.
+                        universes[-1].append([])
 
-                for i in range(universe_ids.shape[0]):
-                    for j in range(universe_ids.shape[1]):
-                        for k in range(universe_ids.shape[2]):
-                            if universe_ids[i, j, k] != -1:
-                                universes[i, j, k] = self.get_universe_by_id(
-                                    universe_ids[i, j, k])
+                        # Climb down the top-right.
+                        for i in range(r):
+                            universes[-1][-1].append(universe_ids[z, a, x])
+                            x += 1
+                            a -= 1
+
+                        # Climb down the right.
+                        for i in range(r):
+                            universes[-1][-1].append(universe_ids[z, a, x])
+                            a -= 1
+
+                        # Climb down the bottom-right.
+                        for i in range(r):
+                            universes[-1][-1].append(universe_ids[z, a, x])
+                            x -= 1
+
+                        # Climb up the bottom-left.
+                        for i in range(r):
+                            universes[-1][-1].append(universe_ids[z, a, x])
+                            x -= 1
+                            a += 1
+
+                        # Climb up the left.
+                        for i in range(r):
+                            universes[-1][-1].append(universe_ids[z, a, x])
+                            a += 1
+
+                        # Climb up the top-left.
+                        for i in range(r):
+                            universes[-1][-1].append(universe_ids[z, a, x])
+                            x += 1
+
+                        # Move down to the next ring.
+                        a -= 1
+
+                        # Convert the ids into Universe objects.
+                        universes[-1][-1] = [self.get_universe_by_id(u_id)
+                                             for u_id in universes[-1][-1]]
+
+                    # Handle the degenerate center ring separately.
+                    u_id = universe_ids[z, a, x]
+                    universes[-1].append([self.get_universe_by_id(u_id)])
+
+                # Add the universes to the lattice.
+                if len(pitch) == 2:
+                    # Lattice is 3D
+                    lattice.universes = universes
+                else:
+                    # Lattice is 2D; extract the only axial level
+                    lattice.universes = universes[0]
 
                 if offset_size > 0:
                     lattice.offsets = offsets
diff --git a/src/hdf5_summary.F90 b/src/hdf5_summary.F90
index 161246f1c..15caf2edf 100644
--- a/src/hdf5_summary.F90
+++ b/src/hdf5_summary.F90
@@ -394,7 +394,7 @@ contains
         ! Write number of lattice cells.
         call su % write_data(lat % n_rings, "n_rings", &
              group="geometry/lattices/lattice " // trim(to_str(lat % id)))
-        call su % write_data(lat % n_rings, "n_axial", &
+        call su % write_data(lat % n_axial, "n_axial", &
              group="geometry/lattices/lattice " // trim(to_str(lat % id)))
 
         ! Write lattice center, pitch and outer universe.
@@ -407,10 +407,10 @@ contains
         end if
  
         if (lat % is_3d) then
-          call su % write_data(lat % pitch, "pitch", length=3, &
+          call su % write_data(lat % pitch, "pitch", length=2, &
                group="geometry/lattices/lattice " // trim(to_str(lat % id)))
         else
-          call su % write_data(lat % pitch, "pitch", length=2, &
+          call su % write_data(lat % pitch, "pitch", length=1, &
                group="geometry/lattices/lattice " // trim(to_str(lat % id)))
         end if
 
@@ -447,7 +447,7 @@ contains
           end do
         end do
         call su % write_data(lattice_universes, "universes", &
-             &length=(/lat % n_axial, 2*lat % n_rings-1, 2*lat % n_rings-1/), &
+             &length=(/2*lat % n_rings-1, 2*lat % n_rings-1, lat % n_axial/), &
              &group="geometry/lattices/lattice " // trim(to_str(lat % id)))
         deallocate(lattice_universes)
       end select