Fix broken tests on Py3.4, 3.5

openmc/deplete/atom_number.py

@@ -2,6 +2,7 @@
 
 An ndarray to store atom densities with string, integer, or slice indexing.
 """
+from collections import OrderedDict
 
 import numpy as np
 
@@ -44,8 +45,8 @@ class AtomNumber(object):
 
     """
     def __init__(self, local_mats, nuclides, volume, n_nuc_burn):
-        self.index_mat = {mat: i for i, mat in enumerate(local_mats)}
-        self.index_nuc = {nuc: i for i, nuc in enumerate(nuclides)}
+        self.index_mat = OrderedDict((mat, i) for i, mat in enumerate(local_mats))
+        self.index_nuc = OrderedDict((nuc, i) for i, nuc in enumerate(nuclides))
 
         self.volume = np.ones(len(local_mats))
         for mat, val in volume.items():

openmc/deplete/integrator/save_results.py

@@ -22,12 +22,12 @@ def save_results(op, x, op_results, t, step_ind):
 
     """
     # Get indexing terms
-    vol_list, nuc_list, burn_list, full_burn_list = op.get_results_info()
+    vol_dict, nuc_list, burn_list, full_burn_list = op.get_results_info()
 
     # Create results
     stages = len(x)
     results = Results()
-    results.allocate(vol_list, nuc_list, burn_list, full_burn_list, stages)
+    results.allocate(vol_dict, nuc_list, burn_list, full_burn_list, stages)
 
     n_mat = len(burn_list)
 

openmc/deplete/operator.py

@@ -111,9 +111,8 @@ class Operator(TransportOperator):
         self._extract_number(self.local_mats, volume, nuclides)
 
         # Create reaction rates array
-        index_rx = {rx: i for i, rx in enumerate(self.chain.reactions)}
         self.reaction_rates = ReactionRates(
-            self.local_mats, self._burnable_nucs, index_rx)
+            self.local_mats, self._burnable_nucs, self.chain.reactions)
 
     def __call__(self, vec, power, print_out=True):
         """Runs a simulation.

openmc/deplete/reaction_rates.py

@@ -2,6 +2,7 @@
 
 An ndarray to store reaction rates with string, integer, or slice indexing.
 """
+from collections import OrderedDict
 
 import numpy as np
 
@@ -19,8 +20,8 @@ class ReactionRates(np.ndarray):
         Material IDs
     nuclides : list of str
         Depletable nuclides
-    index_rx : OrderedDict of str to int
-        A dictionary mapping reaction name as string to index.
+    reactions : list of str
+        Transmutation reactions being tracked
 
     Attributes
     ----------
@@ -46,16 +47,16 @@ class ReactionRates(np.ndarray):
     # the __array_finalize__ method (discussed here:
     # https://docs.scipy.org/doc/numpy/user/basics.subclassing.html)
 
-    def __new__(cls, local_mats, nuclides, index_rx):
+    def __new__(cls, local_mats, nuclides, reactions):
         # Create appropriately-sized zeroed-out ndarray
-        shape = (len(local_mats), len(nuclides), len(index_rx))
+        shape = (len(local_mats), len(nuclides), len(reactions))
         obj = super().__new__(cls, shape)
         obj[:] = 0.0
 
         # Add mapping attributes
         obj.index_mat = {mat: i for i, mat in enumerate(local_mats)}
         obj.index_nuc = {nuc: i for i, nuc in enumerate(nuclides)}
-        obj.index_rx = index_rx
+        obj.index_rx = {rx: i for i, rx in enumerate(reactions)}
 
         return obj
 

openmc/deplete/results.py

@@ -76,16 +76,10 @@ class Results(object):
 
         """
         self.volume = copy.deepcopy(volume)
-        self.nuc_to_ind = OrderedDict()
-        self.mat_to_ind = OrderedDict()
+        self.nuc_to_ind = {nuc: i for i, nuc in enumerate(nuc_list)}
+        self.mat_to_ind = {mat: i for i, mat in enumerate(burn_list)}
         self.mat_to_hdf5_ind = {mat: i for i, mat in enumerate(full_burn_list)}
 
-        for i, mat in enumerate(burn_list):
-            self.mat_to_ind[mat] = i
-
-        for i, nuc in enumerate(nuc_list):
-            self.nuc_to_ind[nuc] = i
-
         # Create storage array
         self.data = np.zeros((stages, self.n_mat, self.n_nuc))
 
@@ -123,8 +117,8 @@ class Results(object):
         -------
         float
             The atoms for stage, mat, nuc
-        """
 
+        """
         stage, mat, nuc = pos
         if isinstance(mat, str):
             mat = self.mat_to_ind[mat]
@@ -145,8 +139,8 @@ class Results(object):
 
         val : float
             The value to set data to.
-        """
 
+        """
         stage, mat, nuc = pos
         if isinstance(mat, str):
             mat = self.mat_to_ind[mat]
@@ -162,8 +156,8 @@ class Results(object):
         ----------
         handle : h5py.File or h5py.Group
             An hdf5 file or group type to store this in.
-        """
 
+        """
         # Create and save the 5 dictionaries:
         # quantities
         #   self.mat_to_ind -> self.volume (TODO: support for changing volumes)
@@ -234,8 +228,8 @@ class Results(object):
             An hdf5 file or group type to store this in.
         index : int
             What step is this?
-        """
 
+        """
         if "/number" not in handle:
             comm.barrier()
             self.create_hdf5(handle)
@@ -299,6 +293,7 @@ class Results(object):
             An hdf5 file or group type to load from.
         index : int
             What step is this?
+
         """
         results = cls()
 
@@ -357,8 +352,8 @@ def write_results(result, filename, index):
         Target filename.
     index : int
         What step is this?
-    """
 
+    """
     if have_mpi and h5py.get_config().mpi:
         kwargs = {'driver': 'mpio', 'comm': comm}
     else:

tests/unit_tests/test_deplete_chain.py

@@ -136,11 +136,10 @@ def test_form_matrix():
 
     chain = Chain.from_xml(_test_filename)
 
-    mat_ind = {"10000": 0, "10001": 1}
-    nuc_ind = {"A": 0, "B": 1, "C": 2}
-    react_ind = {rx: i for i, rx in enumerate(chain.reactions)}
+    mats = ["10000", "10001"]
+    nuclides = ["A", "B", "C"]
 
-    react = reaction_rates.ReactionRates(mat_ind, nuc_ind, react_ind)
+    react = reaction_rates.ReactionRates(mats, nuclides, chain.reactions)
 
     react.set("10000", "C", "fission", 1.0)
     react.set("10000", "A", "(n,gamma)", 2.0)

tests/unit_tests/test_deplete_integrator.py

@@ -26,20 +26,18 @@ def test_save_results(run_in_tmpdir):
     op = MagicMock()
 
     vol_dict = {}
-    full_burn_dict = {}
+    full_burn_list = []
 
-    j = 0
     for i in range(comm.size):
         vol_dict[str(2*i)] = 1.2
         vol_dict[str(2*i + 1)] = 1.2
-        full_burn_dict[str(2*i)] = j
-        full_burn_dict[str(2*i + 1)] = j + 1
-        j += 2
+        full_burn_list.append(str(2*i))
+        full_burn_list.append(str(2*i + 1))
 
-    burn_list = [str(i) for i in range(2*comm.rank, 2*comm.rank + 2)]
+    burn_list = full_burn_list[2*comm.rank : 2*comm.rank + 2]
     nuc_list = ["na", "nb"]
 
-    op.get_results_info.return_value = vol_dict, nuc_list, burn_list, full_burn_dict
+    op.get_results_info.return_value = vol_dict, nuc_list, burn_list, full_burn_list
 
     # Construct x
     x1 = []
@@ -50,18 +48,17 @@ def test_save_results(run_in_tmpdir):
         x2.append([np.random.rand(2), np.random.rand(2)])
 
     # Construct r
-    cell_dict = {s: i for i, s in enumerate(burn_list)}
-    r1 = ReactionRates(cell_dict, {"na": 0, "nb": 1}, {"ra": 0, "rb": 1})
-    r1.rates = np.random.rand(2, 2, 2)
+    r1 = ReactionRates(burn_list, ["na", "nb"], ["ra", "rb"])
+    r1[:] = np.random.rand(2, 2, 2)
 
     rate1 = []
     rate2 = []
 
     for i in range(stages):
         rate1.append(copy.deepcopy(r1))
-        r1.rates = np.random.rand(2, 2, 2)
+        r1[:] = np.random.rand(2, 2, 2)
         rate2.append(copy.deepcopy(r1))
-        r1.rates = np.random.rand(2, 2, 2)
+        r1[:] = np.random.rand(2, 2, 2)
 
     # Create global terms
     eigvl1 = np.random.rand(stages)

tests/unit_tests/test_deplete_reaction.py

@@ -9,9 +9,9 @@ def test_get_set():
 
     local_mats = ["10000", "10001"]
     nuclides = ["U238", "U235"]
-    react_to_ind = {"fission": 0, "(n,gamma)": 1}
+    reactions = ["fission", "(n,gamma)"]
 
-    rates = ReactionRates(local_mats, nuclides, react_to_ind)
+    rates = ReactionRates(local_mats, nuclides, reactions)
     assert rates.shape == (2, 2, 2)
     assert np.all(rates == 0.0)
 
@@ -54,9 +54,9 @@ def test_properties():
     """Test number of materials property."""
     local_mats = ["10000", "10001"]
     nuclides = ["U238", "U235", "Gd157"]
-    react_to_ind = {"fission": 0, "(n,gamma)": 1, "(n,2n)": 2, "(n,3n)": 3}
+    reactions = ["fission", "(n,gamma)", "(n,2n)", "(n,3n)"]
 
-    rates = ReactionRates(local_mats, nuclides, react_to_ind)
+    rates = ReactionRates(local_mats, nuclides, reactions)
 
     assert rates.n_mat == 2
     assert rates.n_nuc == 3