From 33375dfa30f80de5fe69dcfb47425d21642e479a Mon Sep 17 00:00:00 2001
From: Sterling Harper <smharper@mit.edu>
Date: Wed, 30 Dec 2015 15:57:44 -0500
Subject: [PATCH] Small fixes for #538

---
 openmc/filter.py   |  2 +-
 openmc/geometry.py |  5 +++--
 openmc/universe.py | 22 +++++++++++-----------
 src/initialize.F90 | 14 +++++++-------
 4 files changed, 22 insertions(+), 21 deletions(-)

diff --git a/openmc/filter.py b/openmc/filter.py
index ea92f5257..d61fb648f 100644
--- a/openmc/filter.py
+++ b/openmc/filter.py
@@ -609,7 +609,7 @@ class Filter(object):
                     # If this region is in Cell corresponding to the
                     # distribcell filter bin, store it in dictionary
                     if cell_id == self.bins[0]:
-                        offset = openmc_geometry.get_offset(path)
+                        offset = openmc_geometry.get_cell_instance(path)
                         offsets_to_coords[offset] = coords
 
                 # Each distribcell offset is a DataFrame bin
diff --git a/openmc/geometry.py b/openmc/geometry.py
index 16f6a45e5..baadfce3c 100644
--- a/openmc/geometry.py
+++ b/openmc/geometry.py
@@ -42,7 +42,7 @@ class Geometry(object):
 
         self._root_universe = root_universe
 
-    def get_offset(self, path):
+    def get_cell_instance(self, path):
         """Returns the corresponding location in the results array for a given path and
         filter number. This is primarily intended to post-processing result when
         a distribcell filter is used.
@@ -77,7 +77,8 @@ class Geometry(object):
 
         # Begin recursive call to compute offset starting with the base Universe
         else:
-            offset = self._root_universe.get_offset(path, distribcell_ind)
+            offset = self._root_universe.get_cell_instance(path,
+                                                           distribcell_ind)
             self._offsets[(path, distribcell_ind)] = offset
 
         # Return the final offset
diff --git a/openmc/universe.py b/openmc/universe.py
index b346ffd00..e7b2151a3 100644
--- a/openmc/universe.py
+++ b/openmc/universe.py
@@ -285,7 +285,7 @@ class Cell(object):
             else:
                 self.region = Intersection(self.region, region)
 
-    def get_offset(self, path, distribcell_ind):
+    def get_cell_instance(self, path, distribcell_ind):
         # Get the current element and remove it from the list
         cell_id = path[0]
         path = path[1:]
@@ -296,12 +296,12 @@ class Cell(object):
 
         # If the Cell is filled by a Universe
         elif self._type == 'fill':
-            offset = self._offsets[distribcell_ind-1]
-            offset += self._fill.get_offset(path, distribcell_ind)
+            offset = self.offsets[distribcell_ind-1]
+            offset += self.fill.get_cell_instance(path, distribcell_ind)
 
         # If the Cell is filled by a Lattice
         else:
-            offset = self._fill.get_offset(path, distribcell_ind)
+            offset = self.fill.get_cell_instance(path, distribcell_ind)
 
         return offset
 
@@ -605,7 +605,7 @@ class Universe(object):
 
         self._cells.clear()
 
-    def get_offset(self, path, distribcell_ind):
+    def get_cell_instance(self, path, distribcell_ind):
         # Get the current element and remove it from the list
         path = path[1:]
 
@@ -613,7 +613,7 @@ class Universe(object):
         cell_id = path[0]
 
         # Make a recursive call to the Cell within this Universe
-        offset = self._cells[cell_id].get_offset(path, distribcell_ind)
+        offset = self.cells[cell_id].get_cell_instance(path, distribcell_ind)
 
         # Return the offset computed at all nested Universe levels
         return offset
@@ -1073,7 +1073,7 @@ class RectLattice(Lattice):
             cv.check_greater_than('lattice pitch', dim, 0.0)
         self._pitch = pitch
 
-    def get_offset(self, path, distribcell_ind):
+    def get_cell_instance(self, path, distribcell_ind):
         # Get the current element and remove it from the list
         i = path[0]
         path = path[1:]
@@ -1081,14 +1081,14 @@ class RectLattice(Lattice):
         # For 2D Lattices
         if len(self._dimension) == 2:
             offset = self._offsets[i[1]-1, i[2]-1, 0, distribcell_ind-1]
-            offset += self._universes[i[1]][i[2]].get_offset(path,
-                                                             distribcell_ind)
+            offset += self._universes[i[1]][i[2]].get_cell_instance(path,
+                                                                distribcell_ind)
 
         # For 3D Lattices
         else:
             offset = self._offsets[i[1]-1, i[2]-1, i[3]-1, distribcell_ind-1]
-            offset += self._universes[i[1]-1][i[2]-1][i[3]-1].get_offset(path,
-                                                                 distribcell_ind)
+            offset += self._universes[i[1]-1][i[2]-1][i[3]-1].get_cell_instance(
+                                                          path, distribcell_ind)
 
         return offset
 
diff --git a/src/initialize.F90 b/src/initialize.F90
index acfe92b92..1134040e9 100644
--- a/src/initialize.F90
+++ b/src/initialize.F90
@@ -1086,16 +1086,16 @@ contains
     found(:,:) = .false.
     k = 1
 
+    ! Search through universes for distributed cells and assign each one a
+    ! unique distribcell array index.
     do i = 1, n_universes
       univ => universes(i)
-
       do j = 1, univ % n_cells
-        if (.not. cell_list % contains(univ % cells(j))) cycle
-
-        cells(univ % cells(j)) % distribcell_ind = k
-
-        univ_list(k) = univ % id
-        k = k + 1
+        if (cell_list % contains(univ % cells(j))) then
+          cells(univ % cells(j)) % distribcell_ind = k
+          univ_list(k) = univ % id
+          k = k + 1
+        end if
       end do
     end do