Merge pull request #515 from wbinventor/mgxs-ipython-notebooks

MGXS IPython Notebook Tutorial Suite

.gitignore

@@ -71,4 +71,6 @@ docs/source/pythonapi/examples/*.xml
 docs/source/pythonapi/examples/*.png
 docs/source/pythonapi/examples/*.xls
 docs/source/pythonapi/examples/mgxs
-docs/source/pythonapi/examples/tracks
+docs/source/pythonapi/examples/tracks
+docs/source/pythonapi/examples/fission-rates
+docs/source/pythonapi/examples/plots

docs/source/pythonapi/examples/mgxs-part-i.rst

@@ -0,0 +1,13 @@
+.. _notebook_mgxs_part_i:
+
+=========================
+MGXS Part I: Introduction
+=========================
+
+.. only:: html
+
+    .. notebook:: mgxs-part-i.ipynb
+
+.. only:: latex
+
+    IPython notebooks must be viewed in the online HTML documentation.

docs/source/pythonapi/examples/mgxs-part-ii.rst

@@ -0,0 +1,13 @@
+.. _notebook_mgxs_part_ii:
+
+===============================
+MGXS Part II: Advanced Features
+===============================
+
+.. only:: html
+
+    .. notebook:: mgxs-part-ii.ipynb
+
+.. only:: latex
+
+    IPython notebooks must be viewed in the online HTML documentation.

docs/source/pythonapi/examples/mgxs-part-iii.rst

@@ -0,0 +1,13 @@
+.. _notebook_mgxs_part_iii:
+
+========================
+MGXS Part III: Libraries
+========================
+
+.. only:: html
+
+    .. notebook:: mgxs-part-iii.ipynb
+
+.. only:: latex
+
+    IPython notebooks must be viewed in the online HTML documentation.

docs/source/pythonapi/examples/multi-group-cross-sections.rst

@@ -1,11 +0,0 @@
-====================================
-Multi-Group Cross Section Generation
-====================================
-
-.. only:: html
-
-    .. notebook:: multi-group-cross-sections.ipynb
-
-.. only:: latex
-
-    IPython notebooks must be viewed in the online HTML documentation.

docs/source/pythonapi/examples/pandas-dataframes.ipynb

@@ -126,7 +126,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Now let's move on to the geometry. This problem will be a square array of fuel pins, which we can use OpenMC's lattice/universe feature for. The basic universe will have three regions for the fuel, the clad, and the surrounding coolant. The first step is to create the bounding surfaces for fuel and clad, as well as the outer bounding surfaces of the problem."
+    "Now let's move on to the geometry. This problem will be a square array of fuel pins for which we can use OpenMC's lattice/universe feature. The basic universe will have three regions for the fuel, the clad, and the surrounding coolant. The first step is to create the bounding surfaces for fuel and clad, as well as the outer bounding surfaces of the problem."
    ]
   },
   {
@@ -155,7 +155,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "With the surfaces defined, we can now create cells that are defined by intersections of half-spaces created by the surfaces."
+    "With the surfaces defined, we can now construct a fuel pin cell from cells that are defined by intersections of half-spaces created by the surfaces."
    ]
   },
   {
@@ -192,7 +192,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Using the pin cell universe, we can construct a 17x17 rectangular lattice with a 1.26cm pitch."
+    "Using the pin cell universe, we can construct a 17x17 rectangular lattice with a 1.26 cm pitch."
    ]
   },
   {
@@ -242,7 +242,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We now must create a geometry that is assigned a root universe, put the geometry into a geometry file, and export it to XML."
+    "We now must create a geometry that is assigned a root universe, put the geometry into a `GeometryFile` object, and export it to XML."
    ]
   },
   {

docs/source/pythonapi/index.rst

@@ -74,7 +74,9 @@ on a given module or class.
     examples/post-processing
     examples/pandas-dataframes
     examples/tally-arithmetic
-    examples/multi-group-cross-sections
+    examples/mgxs-part-i
+    examples/mgxs-part-ii
+    examples/mgxs-part-iii
 
 .. _Jupyter: https://jupyter.org/
 .. _NumPy: http://www.numpy.org/

openmc/mgxs/mgxs.py

@@ -1225,28 +1225,29 @@ class MGXS(object):
             df = df.drop('score', axis=1)
 
         # Override energy groups bounds with indices
-        groups = np.arange(self.num_groups, 0, -1, dtype=np.int)
-        groups = np.repeat(groups, self.num_nuclides)
+        all_groups = np.arange(self.num_groups, 0, -1, dtype=np.int)
+        all_groups = np.repeat(all_groups, self.num_nuclides)
         if 'energy [MeV]' in df and 'energyout [MeV]' in df:
             df.rename(columns={'energy [MeV]': 'group in'}, inplace=True)
-            in_groups = np.tile(groups, self.num_subdomains)
+            in_groups = np.tile(all_groups, self.num_subdomains)
             in_groups = np.repeat(in_groups, self.num_groups)
             df['group in'] = in_groups
 
             df.rename(columns={'energyout [MeV]': 'group out'}, inplace=True)
-            out_groups = np.tile(groups, self.num_subdomains * self.num_groups)
+            out_groups = \
+                np.tile(all_groups, self.num_subdomains * self.num_groups)
             df['group out'] = out_groups
             columns = ['group in', 'group out']
 
         elif 'energyout [MeV]' in df:
             df.rename(columns={'energyout [MeV]': 'group out'}, inplace=True)
-            in_groups = np.tile(groups, self.num_subdomains)
+            in_groups = np.tile(all_groups, self.num_subdomains)
             df['group out'] = in_groups
             columns = ['group out']
 
         elif 'energy [MeV]' in df:
             df.rename(columns={'energy [MeV]': 'group in'}, inplace=True)
-            in_groups = np.tile(groups, self.num_subdomains)
+            in_groups = np.tile(all_groups, self.num_subdomains)
             df['group in'] = in_groups
             columns = ['group in']
 

openmc/opencg_compatible.py

@@ -882,7 +882,7 @@ def get_opencg_lattice(openmc_lattice):
     outer = openmc_lattice.outer
 
     if len(pitch) == 2:
-        new_pitch = np.ones(3, dtype=np.float64)
+        new_pitch = np.ones(3, dtype=np.float64) * np.inf
         new_pitch[:2] = pitch
         pitch = new_pitch