From e6cc4516c2ecee3908cb85fd30105d540fefa0cf Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Thu, 9 Sep 2021 15:34:53 +0100
Subject: [PATCH 01/29] added fast flux as an options

---
 openmc_dagmc_wrapper/neutronics_model.py | 32 ++++++++++++++++++++----
 tests/test_neutronics_model.py           | 30 ++++++++++++++++++++++
 2 files changed, 57 insertions(+), 5 deletions(-)

diff --git a/openmc_dagmc_wrapper/neutronics_model.py b/openmc_dagmc_wrapper/neutronics_model.py
index 8b0c87e..0320f6a 100644
--- a/openmc_dagmc_wrapper/neutronics_model.py
+++ b/openmc_dagmc_wrapper/neutronics_model.py
@@ -171,7 +171,8 @@ def cell_tallies(self, value):
                     "flux",
                     "spectra",
                     "absorption",
-                    "effective_dose"] +
+                    "effective_dose",
+                    "fast_flux"] +
                 list(
                     REACTION_MT.keys()) +
                 list(
@@ -394,9 +395,9 @@ def export_xml(
                 Defaults to None which uses the NeutronicsModel.mesh_tally_2d
                 attribute.
             cell_tallies: the cell based tallies to calculate, options include
-                TBR, heating, flux, MT numbers, effective_dose and OpenMC
-                standard scores such as (n,Xa) which is helium production are
-                also supported
+                TBR, heating, flux, MT numbers, effective_dose, fast_flux and
+                OpenMC standard scores such as (n,Xa) which is helium production
+                are also supported
                 https://docs.openmc.org/en/latest/usersguide/tallies.html#scores.
                 Defaults to None which uses the NeutronicsModel.cell_tallies
                 attribute.
@@ -505,6 +506,7 @@ def export_xml(
                 mesh_xyz.upper_right = self.mesh_3d_corners[1]
 
             for standard_tally in self.mesh_tally_3d:
+
                 if standard_tally == "effective_dose":
                     energy_bins_n, dose_coeffs_n = openmc.data.dose_coefficients(
                         particle="neutron",
@@ -665,6 +667,27 @@ def export_xml(
                     self.tallies.append(tally)
                     self._add_tally_for_every_material(suffix, score)
 
+                elif standard_tally == "fast_flux":
+
+                    energy_bins = [1e6, 1000e6]
+                    energy_filter = openmc.EnergyFilter(energy_bins)
+
+                    neutron_particle_filter = openmc.ParticleFilter([
+                                                                    "neutron"])
+                    self._add_tally_for_every_material(
+                        "neutron_spectra",
+                        "flux",
+                        [neutron_particle_filter, energy_filter],
+                    )
+                    if self.photon_transport is True:
+                        photon_particle_filter = openmc.ParticleFilter([
+                                                                       "photon"])
+                        self._add_tally_for_every_material(
+                            "photon_spectra",
+                            "flux",
+                            [photon_particle_filter, energy_filter],
+                        )
+
                 elif standard_tally == "spectra":
 
                     energy_bins = openmc.mgxs.GROUP_STRUCTURES["CCFE-709"]
@@ -699,7 +722,6 @@ def export_xml(
                     energy_function_filter_n = openmc.EnergyFunctionFilter(
                         energy_bins_n, dose_coeffs_n
                     )
-                    # energy_function_filter_p = openmc.EnergyFunctionFilter(energy_bins_p, dose_coeffs_p)
 
                     self._add_tally_for_every_material(
                         "neutron_effective_dose",
diff --git a/tests/test_neutronics_model.py b/tests/test_neutronics_model.py
index 37db834..cd40043 100644
--- a/tests/test_neutronics_model.py
+++ b/tests/test_neutronics_model.py
@@ -562,6 +562,36 @@ def test_reactor_from_shapes_cell_tallies(self):
         assert isinstance(my_model.results["TBR"]["result"], float)
         assert Path("results.json").exists() is True
 
+    def test_cell_tallies_simulation_fast_flux(self):
+        """Performs simulation with h5m file and tallies neutron and photon
+        fast flux. Checks that entries exist in the results."""
+
+        os.system("rm results.json")
+
+        my_model = openmc_dagmc_wrapper.NeutronicsModel(
+            h5m_filename=self.h5m_filename_smaller,
+            source=self.source,
+            materials={"mat1": "Be"},
+            cell_tallies=["fast_flux"],
+            photon_transport=True,
+        )
+
+        # starts the neutronics simulation
+        my_model.simulate(
+            simulation_batches=2,
+            simulation_particles_per_batch=10,
+        )
+
+        my_model.process_results(
+            fusion_power=1e9,
+            fusion_energy_per_pulse=1.2e6
+        )
+
+        assert isinstance(
+            my_model.results["mat1_neutron_fast_flux"]["result"],
+            float,
+        )
+
     def test_cell_tallies_simulation_effective_dose(self):
         """Performs simulation with h5m file and tallies neutron and photon
         dose. Checks that entries exist in the results."""

From 7944c4fc16558a03f9fac1fe80286f562e9d1d06 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 10 Sep 2021 09:33:20 +0100
Subject: [PATCH 02/29] refactored making use of dagmc_h5m_file_inspector

---
 openmc_dagmc_wrapper/neutronics_model.py | 41 +++++++------
 openmc_dagmc_wrapper/utils.py            | 73 ------------------------
 setup.py                                 |  3 +-
 tests/test_neutronics_utils.py           | 53 ++++-------------
 4 files changed, 32 insertions(+), 138 deletions(-)

diff --git a/openmc_dagmc_wrapper/neutronics_model.py b/openmc_dagmc_wrapper/neutronics_model.py
index 8b0c87e..03aaeaf 100644
--- a/openmc_dagmc_wrapper/neutronics_model.py
+++ b/openmc_dagmc_wrapper/neutronics_model.py
@@ -2,19 +2,17 @@
 from pathlib import Path
 from typing import List, Optional, Tuple, Union
 
+import dagmc_h5m_file_inspector as di
 import neutronics_material_maker as nmm
 import openmc
 import openmc.lib  # needed to find bounding box of h5m file
 import plotly.graph_objects as go
 from openmc.data import REACTION_MT, REACTION_NAME
 
-from .utils import (
-    create_initial_particles,
-    extract_points_from_initial_source,
-    get_neutronics_results_from_statepoint_file,
-    silently_remove_file,
-    plotly_trace,
-)
+from .utils import (create_initial_particles,
+                    extract_points_from_initial_source,
+                    get_neutronics_results_from_statepoint_file, plotly_trace,
+                    silently_remove_file)
 
 
 class NeutronicsModel:
@@ -31,8 +29,8 @@ class NeutronicsModel:
             neutronics-material-maker.Material or
             neutronics-material-maker.MultiMaterial. All components within the
             geometry object must be accounted for. Material tags required
-            for a Reactor or Shape can be obtained with .material_tags() and
-            material_tag respectively.
+            for a Reactor or Shape can be obtained using the python package
+            dagmc_h5m_file_inspector
         cell_tallies: the cell based tallies to calculate, options include
             spectra, TBR, heating, flux, MT numbers and OpenMC standard scores
             such as (n,Xa) which is helium production are also supported
@@ -273,19 +271,20 @@ def create_material(self, material_tag: str, material_entry):
         return openmc_material
 
     def create_openmc_materials(self):
+
+        materials_in_h5m = di.get_materials_from_h5m(self.h5m_filename)
         # # checks all the required materials are present
-        # for reactor_material in self.geometry.material_tags:
-        #     if reactor_material not in self.materials.keys():
-        #         raise ValueError(
-        #             "material included by the reactor model has not \
-        #             been added", reactor_material)
-
-        # # checks that no extra materials we added
-        # for reactor_material in self.materials.keys():
-        #     if reactor_material not in self.geometry.material_tags:
-        #         raise ValueError(
-        #             "material has been added that is not needed for this \
-        #             reactor model", reactor_material)
+        for reactor_material in self.materials.items():
+            if reactor_material not in materials_in_h5m:
+                msg = (f"material with tag {reactor_material} was not found in"
+                       "the dagmc h5m file")
+                raise ValueError(msg)
+
+        if len(materials_in_h5m) != len(self.materials.keys()):
+            msg = (f"the NeutronicsModel.materials does not match the material"
+                    "tags in the dagmc h5m file. Materials in h5m file "
+                   f"{materials_in_h5m}. Materials provided {self.materials.keys()}")
+            raise ValueError(msg)
 
         silently_remove_file("materials.xml")
 
diff --git a/openmc_dagmc_wrapper/utils.py b/openmc_dagmc_wrapper/utils.py
index acb19c3..ad4c348 100644
--- a/openmc_dagmc_wrapper/utils.py
+++ b/openmc_dagmc_wrapper/utils.py
@@ -81,13 +81,6 @@ def plotly_trace(
     return trace
 
 
-def load_moab_file(filename: str):
-    """Loads a h5m into a Moab Core object and returns the object"""
-    moab_core = core.Core()
-    moab_core.load_file(filename)
-    return moab_core
-
-
 def silently_remove_file(filename: str):
     """Allows files to be deleted without printing warning messages int the
     terminal. input XML files for OpenMC are deleted prior to running
@@ -98,72 +91,6 @@ def silently_remove_file(filename: str):
         pass  # in some cases the file will not exist
 
 
-def find_volume_ids_in_h5m(filename: Optional[str] = "dagmc.h5m") -> List[str]:
-    """Reads in a DAGMC h5m file and uses PyMoab to find the volume ids of the
-    volumes in the file
-
-    Arguments:
-        filename:
-
-    Returns:
-        The filename of the h5m file created
-    """
-
-    # create a new PyMOAB instance and load the specified DAGMC file
-    moab_core = load_moab_file(filename)
-
-    # retrieve the category tag on the instance
-    cat_tag = moab_core.tag_get_handle(types.CATEGORY_TAG_NAME)
-
-    # get the id tag
-    gid_tag = moab_core.tag_get_handle(types.GLOBAL_ID_TAG_NAME)
-
-    # get the set of entities using the provided category tag name
-    # (0 means search on the instance's root set)
-    ents = moab_core.get_entities_by_type_and_tag(
-        0, types.MBENTITYSET, [cat_tag], ["Volume"]
-    )
-
-    # retrieve the IDs of the entities
-    ids = moab_core.tag_get_data(gid_tag, ents).flatten()
-
-    return sorted(list(ids))
-
-
-def find_material_groups_in_h5m(
-        filename: Optional[str] = "dagmc.h5m") -> List[str]:
-    """Reads in a DAGMC h5m file and uses mbsize to find the names of the
-    material groups in the file
-
-    Arguments:
-        filename:
-
-    Returns:
-        The filename of the h5m file created
-    """
-
-    try:
-        terminal_output = subprocess.check_output(
-            "mbsize -ll {} | grep 'mat:'".format(filename),
-            shell=True,
-            universal_newlines=True,
-        )
-    except BaseException:
-        raise ValueError(
-            "mbsize failed, check MOAB is install and the MOAB/build/bin "
-            "folder is in the path directory (Linux and Mac) or set as an "
-            "enviromental varible (Windows)"
-        )
-
-    list_of_mats = terminal_output.split()
-    list_of_mats = list(filter(lambda a: a != "=", list_of_mats))
-    list_of_mats = list(filter(lambda a: a != "NAME", list_of_mats))
-    list_of_mats = list(filter(lambda a: a != "EXTRA_NAME0", list_of_mats))
-    list_of_mats = list(set(list_of_mats))
-
-    return list_of_mats
-
-
 def _save_2d_mesh_tally_as_png(score: str, filename: str, tally) -> str:
     """Extracts 2D mesh tally results from a tally and saves the result as
     a png image.
diff --git a/setup.py b/setup.py
index be69475..e57344a 100644
--- a/setup.py
+++ b/setup.py
@@ -34,7 +34,8 @@
         "plotly",
         "defusedxml",
         "nbformat",
-        "nbconvert"
+        "nbconvert",
+        "dagmc_h5m_file_inspector",
     ],
     # openmc, dagmc, moab are also needed and embree and double down are also
     # optionally needed but not avaible on PyPi
diff --git a/tests/test_neutronics_utils.py b/tests/test_neutronics_utils.py
index 30905df..1fd9aea 100644
--- a/tests/test_neutronics_utils.py
+++ b/tests/test_neutronics_utils.py
@@ -8,20 +8,20 @@
 import requests
 
 
-class TestNeutronicsUtilityFunctions(unittest.TestCase):
-    def setUp(self):
+# class TestNeutronicsUtilityFunctions(unittest.TestCase):
+#     def setUp(self):
 
-        url = "https://github.com/fusion-energy/neutronics_workflow/raw/main/example_02_multi_volume_cell_tally/stage_2_output/dagmc.h5m"
+#         url = "https://github.com/fusion-energy/neutronics_workflow/raw/main/example_02_multi_volume_cell_tally/stage_2_output/dagmc.h5m"
 
-        local_filename = "dagmc_bigger.h5m"
+#         local_filename = "dagmc_bigger.h5m"
 
-        if not Path(local_filename).is_file():
+#         if not Path(local_filename).is_file():
 
-            r = requests.get(url, stream=True)
-            with open(local_filename, "wb") as f:
-                for chunk in r.iter_content(chunk_size=1024):
-                    if chunk:
-                        f.write(chunk)
+#             r = requests.get(url, stream=True)
+#             with open(local_filename, "wb") as f:
+#                 for chunk in r.iter_content(chunk_size=1024):
+#                     if chunk:
+#                         f.write(chunk)
 
     # def test_create_initial_source_file(self):
     #     """Creates an initial_source.h5 from a point source"""
@@ -83,39 +83,6 @@ def setUp(self):
 
     #     self.assertRaises(ValueError, incorrect_viewplane)
 
-    def test_find_materials_in_h5_file(self):
-        """exports a h5m with specific material tags and checks they are
-        found using the find_material_groups_in_h5m utility function"""
-
-        list_of_mats = openmc_dagmc_wrapper.find_material_groups_in_h5m(
-            filename="dagmc_bigger.h5m"
-        )
-
-        assert len(list_of_mats) == 10
-        assert "mat:pf_coil_case_mat" in list_of_mats
-        assert "mat:center_column_shield_mat" in list_of_mats
-        assert "mat:blanket_rear_wall_mat" in list_of_mats
-        assert "mat:divertor_mat" in list_of_mats
-        assert "mat:graveyard" in list_of_mats
-        assert "mat:tf_coil_mat" in list_of_mats
-        assert "mat:pf_coil_mat" in list_of_mats
-        assert "mat:inboard_tf_coils_mat" in list_of_mats
-        assert "mat:blanket_mat" in list_of_mats
-        assert "mat:firstwall_mat" in list_of_mats
-
-    def test_find_volume_ids_in_h5_file(self):
-        """exports a h5m with a known number of volumes and checks they are
-        found using the find_volume_ids_in_h5m utility function"""
-
-        list_of_mats = openmc_dagmc_wrapper.find_volume_ids_in_h5m(
-            filename="dagmc_bigger.h5m"
-        )
-
-        assert len(list_of_mats) == len(
-            [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17]
-        )
-        assert 1 in list_of_mats
-
     # def test_create_initial_particles(self):
     #     """Creates an initial source file using create_initial_particles utility
     #     and checks the file exists and that the points are correct"""

From ef39a4c3849c59d704550c7c102a1fa5cbb5154a Mon Sep 17 00:00:00 2001
From: autopep8 <autopep8@users.noreply.github.com>
Date: Fri, 10 Sep 2021 08:36:18 +0000
Subject: [PATCH 03/29] Automated autopep8 fixes

---
 openmc_dagmc_wrapper/neutronics_model.py |   7 +-
 tests/test_neutronics_utils.py           | 120 +++++++++++------------
 2 files changed, 64 insertions(+), 63 deletions(-)

diff --git a/openmc_dagmc_wrapper/neutronics_model.py b/openmc_dagmc_wrapper/neutronics_model.py
index 03aaeaf..19372f9 100644
--- a/openmc_dagmc_wrapper/neutronics_model.py
+++ b/openmc_dagmc_wrapper/neutronics_model.py
@@ -281,9 +281,10 @@ def create_openmc_materials(self):
                 raise ValueError(msg)
 
         if len(materials_in_h5m) != len(self.materials.keys()):
-            msg = (f"the NeutronicsModel.materials does not match the material"
-                    "tags in the dagmc h5m file. Materials in h5m file "
-                   f"{materials_in_h5m}. Materials provided {self.materials.keys()}")
+            msg = (
+                f"the NeutronicsModel.materials does not match the material"
+                "tags in the dagmc h5m file. Materials in h5m file "
+                f"{materials_in_h5m}. Materials provided {self.materials.keys()}")
             raise ValueError(msg)
 
         silently_remove_file("materials.xml")
diff --git a/tests/test_neutronics_utils.py b/tests/test_neutronics_utils.py
index 1fd9aea..9f99ff9 100644
--- a/tests/test_neutronics_utils.py
+++ b/tests/test_neutronics_utils.py
@@ -23,88 +23,88 @@
 #                     if chunk:
 #                         f.write(chunk)
 
-    # def test_create_initial_source_file(self):
-    #     """Creates an initial_source.h5 from a point source"""
+# def test_create_initial_source_file(self):
+#     """Creates an initial_source.h5 from a point source"""
 
-    #     os.system("rm *.h5")
+#     os.system("rm *.h5")
 
-    #     source = openmc.Source()
-    #     source.space = openmc.stats.Point((0, 0, 0))
-    #     source.energy = openmc.stats.Discrete([14e6], [1])
+#     source = openmc.Source()
+#     source.space = openmc.stats.Point((0, 0, 0))
+#     source.energy = openmc.stats.Discrete([14e6], [1])
 
-    #     openmc_dagmc_wrapper.create_initial_particles(source, 100)
+#     openmc_dagmc_wrapper.create_initial_particles(source, 100)
 
-    #     assert Path("initial_source.h5").exists() is True
+#     assert Path("initial_source.h5").exists() is True
 
-    # def test_extract_points_from_initial_source(self):
-    #     """Creates an initial_source.h5 from a point source reads in the file
-    #     and checks the first point is 0, 0, 0 as expected."""
+# def test_extract_points_from_initial_source(self):
+#     """Creates an initial_source.h5 from a point source reads in the file
+#     and checks the first point is 0, 0, 0 as expected."""
 
-    #     os.system("rm *.h5")
+#     os.system("rm *.h5")
 
-    #     source = openmc.Source()
-    #     source.space = openmc.stats.Point((0, 0, 0))
-    #     source.energy = openmc.stats.Discrete([14e6], [1])
+#     source = openmc.Source()
+#     source.space = openmc.stats.Point((0, 0, 0))
+#     source.energy = openmc.stats.Discrete([14e6], [1])
 
-    #     openmc_dagmc_wrapper.create_initial_particles(source, 10)
+#     openmc_dagmc_wrapper.create_initial_particles(source, 10)
 
-    #     for view_plane in ["XZ", "XY", "YZ", "YX", "ZY", "ZX", "RZ", "XYZ"]:
+#     for view_plane in ["XZ", "XY", "YZ", "YX", "ZY", "ZX", "RZ", "XYZ"]:
 
-    #         points = openmc_dagmc_wrapper.extract_points_from_initial_source(
-    #             view_plane=view_plane
-    #         )
+#         points = openmc_dagmc_wrapper.extract_points_from_initial_source(
+#             view_plane=view_plane
+#         )
 
-    #         assert len(points) == 10
+#         assert len(points) == 10
 
-    #         for point in points:
-    #             if view_plane == "XYZ":
-    #                 assert len(point) == 3
-    #                 assert point[0] == 0
-    #                 assert point[1] == 0
-    #                 assert point[2] == 0
-    #             else:
-    #                 assert len(point) == 2
-    #                 assert point[0] == 0
-    #                 assert point[1] == 0
+#         for point in points:
+#             if view_plane == "XYZ":
+#                 assert len(point) == 3
+#                 assert point[0] == 0
+#                 assert point[1] == 0
+#                 assert point[2] == 0
+#             else:
+#                 assert len(point) == 2
+#                 assert point[0] == 0
+#                 assert point[1] == 0
 
-    # def test_extract_points_from_initial_source_incorrect_view_plane(self):
-    #     """Tries to make extract points on to viewplane that is not accepted"""
+# def test_extract_points_from_initial_source_incorrect_view_plane(self):
+#     """Tries to make extract points on to viewplane that is not accepted"""
 
-    #     def incorrect_viewplane():
-    #         """Inccorect view_plane should raise a ValueError"""
+#     def incorrect_viewplane():
+#         """Inccorect view_plane should raise a ValueError"""
 
-    #         source = openmc.Source()
-    #         source.space = openmc.stats.Point((0, 0, 0))
-    #         source.energy = openmc.stats.Discrete([14e6], [1])
+#         source = openmc.Source()
+#         source.space = openmc.stats.Point((0, 0, 0))
+#         source.energy = openmc.stats.Discrete([14e6], [1])
 
-    #         openmc_dagmc_wrapper.create_initial_particles(source, 10)
+#         openmc_dagmc_wrapper.create_initial_particles(source, 10)
 
-    #         openmc_dagmc_wrapper.extract_points_from_initial_source(view_plane="coucou")
+#         openmc_dagmc_wrapper.extract_points_from_initial_source(view_plane="coucou")
 
-    #     self.assertRaises(ValueError, incorrect_viewplane)
+#     self.assertRaises(ValueError, incorrect_viewplane)
 
-    # def test_create_initial_particles(self):
-    #     """Creates an initial source file using create_initial_particles utility
-    #     and checks the file exists and that the points are correct"""
+# def test_create_initial_particles(self):
+#     """Creates an initial source file using create_initial_particles utility
+#     and checks the file exists and that the points are correct"""
 
-    #     os.system("rm *.h5")
+#     os.system("rm *.h5")
 
-    #     source = openmc.Source()
-    #     source.space = openmc.stats.Point((1, 2, 3))
-    #     source.energy = openmc.stats.Discrete([14e6], [1])
-    #     source.angle = openmc.stats.Isotropic()
+#     source = openmc.Source()
+#     source.space = openmc.stats.Point((1, 2, 3))
+#     source.energy = openmc.stats.Discrete([14e6], [1])
+#     source.angle = openmc.stats.Isotropic()
 
-    #     source_file = openmc_dagmc_wrapper.create_initial_particles(
-    #         source=source, number_of_source_particles=10
-    #     )
+#     source_file = openmc_dagmc_wrapper.create_initial_particles(
+#         source=source, number_of_source_particles=10
+#     )
 
-    #     assert source_file == "initial_source.h5"
-    #     assert Path(source_file).exists() is True
+#     assert source_file == "initial_source.h5"
+#     assert Path(source_file).exists() is True
 
-    #     points = openmc_dagmc_wrapper.extract_points_from_initial_source(
-    #         view_plane="XYZ", input_filename=source_file
-    #     )
+#     points = openmc_dagmc_wrapper.extract_points_from_initial_source(
+#         view_plane="XYZ", input_filename=source_file
+#     )
 
-    #     assert len(points) == 10
-    #     for point in points:
-    #         assert point == (1, 2, 3)
+#     assert len(points) == 10
+#     for point in points:
+#         assert point == (1, 2, 3)

From 610fccc72eb555d1024e42ee4a4f9aa681075145 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 10 Sep 2021 09:36:56 +0100
Subject: [PATCH 04/29] removed non existent functions from init

---
 openmc_dagmc_wrapper/__init__.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/openmc_dagmc_wrapper/__init__.py b/openmc_dagmc_wrapper/__init__.py
index aaf3d03..64ea672 100644
--- a/openmc_dagmc_wrapper/__init__.py
+++ b/openmc_dagmc_wrapper/__init__.py
@@ -1,6 +1,4 @@
 from .utils import get_neutronics_results_from_statepoint_file
-from .utils import find_material_groups_in_h5m
-from .utils import find_volume_ids_in_h5m
 from .utils import create_initial_particles
 from .utils import extract_points_from_initial_source
 from .utils import silently_remove_file

From aaeb4e08f85a65db75d75f55fe71a2f48f90adf2 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 10 Sep 2021 09:57:33 +0100
Subject: [PATCH 05/29] getting h5m files from release

---
 tests/test_neutronics_model.py | 33 +++++++++------------------------
 1 file changed, 9 insertions(+), 24 deletions(-)

diff --git a/tests/test_neutronics_model.py b/tests/test_neutronics_model.py
index 37db834..257565c 100644
--- a/tests/test_neutronics_model.py
+++ b/tests/test_neutronics_model.py
@@ -1,7 +1,7 @@
 import os
 import unittest
 from pathlib import Path
-
+import tarfile
 import neutronics_material_maker as nmm
 import openmc
 import openmc_dagmc_wrapper
@@ -14,18 +14,16 @@ class TestShape(unittest.TestCase):
 
     def setUp(self):
 
-        url = "https://github.com/fusion-energy/neutronics_workflow/raw/main/example_02_multi_volume_cell_tally/stage_2_output/dagmc.h5m"
-
-        local_filename = "dagmc_bigger.h5m"
+        if not Path("tests/v0.0.1.tar.gz").is_file():
+            url = "https://github.com/fusion-energy/neutronics_workflow/archive/refs/tags/v0.0.1.tar.gz"
+            urllib.request.urlretrieve(url, "tests/v0.0.1.tar.gz")
 
-        if not Path(local_filename).is_file():
-            r = requests.get(url, stream=True)
-            with open(local_filename, "wb") as f:
-                for chunk in r.iter_content(chunk_size=1024):
-                    if chunk:
-                        f.write(chunk)
+            tar = tarfile.open("tests/v0.0.1.tar.gz", "r:gz")
+            tar.extractall("tests")
+            tar.close()
 
-        self.h5m_filename_bigger = local_filename
+        self.h5m_filename_bigger = "tests/neutronics_workflow-0.0.1/example_01_single_volume_cell_tally/stage_2_output/dagmc.h5m"
+        self.h5m_filename_smaller = "tests/neutronics_workflow-0.0.1/example_02_multi_volume_cell_tally/stage_2_output/dagmc.h5m"
 
         self.material_description = {
             "tungsten": "tungsten",
@@ -34,19 +32,6 @@ def setUp(self):
             "copper": "copper",
         }
 
-        url = "https://github.com/fusion-energy/neutronics_workflow/raw/main/example_01_single_volume_cell_tally/stage_2_output/dagmc.h5m"
-
-        local_filename = "dagmc_smaller.h5m"
-
-        if not Path(local_filename).is_file():
-            r = requests.get(url, stream=True)
-            with open(local_filename, "wb") as f:
-                for chunk in r.iter_content(chunk_size=1024):
-                    if chunk:  # filter out keep-alive new chunks
-                        f.write(chunk)
-
-        self.h5m_filename_smaller = local_filename
-
         # makes the openmc neutron source at x,y,z 0, 0, 0 with isotropic
         # directions and 14MeV neutrons
         source = openmc.Source()

From b081a9872fbbefb16450f3e576d21b4bcdd5c121 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 10 Sep 2021 10:02:53 +0100
Subject: [PATCH 06/29] added missing package (urllib)

---
 tests/test_neutronics_model.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tests/test_neutronics_model.py b/tests/test_neutronics_model.py
index 257565c..362ce2d 100644
--- a/tests/test_neutronics_model.py
+++ b/tests/test_neutronics_model.py
@@ -5,8 +5,7 @@
 import neutronics_material_maker as nmm
 import openmc
 import openmc_dagmc_wrapper
-import requests
-
+import urllib.request
 
 class TestShape(unittest.TestCase):
     """Tests the NeutronicsModel with a Shape as the geometry input

From acd2a59f653693a7304774ea6185297bebc51849 Mon Sep 17 00:00:00 2001
From: autopep8 <autopep8@users.noreply.github.com>
Date: Fri, 10 Sep 2021 09:03:21 +0000
Subject: [PATCH 07/29] Automated autopep8 fixes

---
 tests/test_neutronics_model.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/test_neutronics_model.py b/tests/test_neutronics_model.py
index 362ce2d..4b0740b 100644
--- a/tests/test_neutronics_model.py
+++ b/tests/test_neutronics_model.py
@@ -7,6 +7,7 @@
 import openmc_dagmc_wrapper
 import urllib.request
 
+
 class TestShape(unittest.TestCase):
     """Tests the NeutronicsModel with a Shape as the geometry input
     including neutronics simulations using"""

From 7438402db73c9653bad99a4071e4b54dae9c8b5d Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 10 Sep 2021 10:32:41 +0100
Subject: [PATCH 08/29] removed 2nd testing class

---
 openmc_dagmc_wrapper/neutronics_model.py |  7 ++++-
 tests/test_neutronics_model.py           | 38 ++++++++----------------
 2 files changed, 18 insertions(+), 27 deletions(-)

diff --git a/openmc_dagmc_wrapper/neutronics_model.py b/openmc_dagmc_wrapper/neutronics_model.py
index 19372f9..cfff21f 100644
--- a/openmc_dagmc_wrapper/neutronics_model.py
+++ b/openmc_dagmc_wrapper/neutronics_model.py
@@ -121,7 +121,12 @@ def h5m_filename(self):
     @h5m_filename.setter
     def h5m_filename(self, value):
         if isinstance(value, str):
-            self._h5m_filename = value
+            if not Path(value).is_file():
+                msg = f"h5m_filename provided ({value}) does not exist"
+                raise TypeError(msg)
+
+
+                self._h5m_filename = value
         else:
             msg = "NeutronicsModelFromReactor.h5m_filename should be a string"
             raise TypeError(msg)
diff --git a/tests/test_neutronics_model.py b/tests/test_neutronics_model.py
index 362ce2d..42a511d 100644
--- a/tests/test_neutronics_model.py
+++ b/tests/test_neutronics_model.py
@@ -39,6 +39,16 @@ def setUp(self):
         source.energy = openmc.stats.Discrete([14e6], [1])
         self.source = source
 
+        self.blanket_material = nmm.Material.from_mixture(
+            fracs=[0.8, 0.2],
+            materials=[
+                nmm.Material.from_library("SiC"),
+                nmm.Material.from_library("eurofer"),
+            ],
+        )
+
+
+
     def simulation_with_previous_h5m_file(self):
         """This performs a simulation using previously created h5m file"""
 
@@ -731,37 +741,13 @@ def test_missing_h5m_file_error_handling():
             test_missing_h5m_file_error_handling)
 
 
-class TestNeutronicsBallReactor(unittest.TestCase):
-    """Tests the NeutronicsModel with a BallReactor as the geometry input
-    including neutronics simulations"""
-
-    def setUp(self):
-
-        # makes a homogenised material for the blanket from lithium lead and
-        # eurofer
-        self.blanket_material = nmm.Material.from_mixture(
-            fracs=[0.8, 0.2],
-            materials=[
-                nmm.Material.from_library("SiC"),
-                nmm.Material.from_library("eurofer"),
-            ],
-        )
-
-        self.source = openmc.Source()
-        # sets the location of the source to x=0 y=0 z=0
-        self.source.space = openmc.stats.Point((0, 0, 0))
-        # sets the direction to isotropic
-        self.source.angle = openmc.stats.Isotropic()
-        # sets the energy distribution to 100% 14MeV neutrons
-        self.source.energy = openmc.stats.Discrete([14e6], [1])
-
     def test_neutronics_model_attributes(self):
         """Makes a BallReactor neutronics model and simulates the TBR"""
 
         # makes the neutronics material
         my_model = openmc_dagmc_wrapper.NeutronicsModel(
             source=openmc.Source(),
-            h5m_filename="placeholder.h5m",
+            h5m_filename=self.h5m_filename_smaller,
             materials={
                 "inboard_tf_coils_mat": "copper",
                 "mat1": "WC",
@@ -773,7 +759,7 @@ def test_neutronics_model_attributes(self):
             cell_tallies=["TBR", "flux", "heating"],
         )
 
-        assert my_model.h5m_filename == "placeholder.h5m"
+        assert my_model.h5m_filename == self.h5m_filename_smaller
 
         assert my_model.materials == {
             "inboard_tf_coils_mat": "copper",

From 367bc6d97477fdd11312ee100a8912bdfa3c925b Mon Sep 17 00:00:00 2001
From: autopep8 <autopep8@users.noreply.github.com>
Date: Fri, 10 Sep 2021 09:33:45 +0000
Subject: [PATCH 09/29] Automated autopep8 fixes

---
 openmc_dagmc_wrapper/neutronics_model.py | 1 -
 tests/test_neutronics_model.py           | 3 ---
 2 files changed, 4 deletions(-)

diff --git a/openmc_dagmc_wrapper/neutronics_model.py b/openmc_dagmc_wrapper/neutronics_model.py
index cfff21f..d2c9ce6 100644
--- a/openmc_dagmc_wrapper/neutronics_model.py
+++ b/openmc_dagmc_wrapper/neutronics_model.py
@@ -125,7 +125,6 @@ def h5m_filename(self, value):
                 msg = f"h5m_filename provided ({value}) does not exist"
                 raise TypeError(msg)
 
-
                 self._h5m_filename = value
         else:
             msg = "NeutronicsModelFromReactor.h5m_filename should be a string"
diff --git a/tests/test_neutronics_model.py b/tests/test_neutronics_model.py
index 17a9441..3ff2794 100644
--- a/tests/test_neutronics_model.py
+++ b/tests/test_neutronics_model.py
@@ -48,8 +48,6 @@ def setUp(self):
             ],
         )
 
-
-
     def simulation_with_previous_h5m_file(self):
         """This performs a simulation using previously created h5m file"""
 
@@ -741,7 +739,6 @@ def test_missing_h5m_file_error_handling():
             FileNotFoundError,
             test_missing_h5m_file_error_handling)
 
-
     def test_neutronics_model_attributes(self):
         """Makes a BallReactor neutronics model and simulates the TBR"""
 

From 4daf6748a125d28cde745345a4981c4de423ab57 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 10 Sep 2021 10:44:36 +0100
Subject: [PATCH 10/29] fixing _h5m_filename bug

---
 openmc_dagmc_wrapper/neutronics_model.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/openmc_dagmc_wrapper/neutronics_model.py b/openmc_dagmc_wrapper/neutronics_model.py
index cfff21f..bf6fcd3 100644
--- a/openmc_dagmc_wrapper/neutronics_model.py
+++ b/openmc_dagmc_wrapper/neutronics_model.py
@@ -124,9 +124,7 @@ def h5m_filename(self, value):
             if not Path(value).is_file():
                 msg = f"h5m_filename provided ({value}) does not exist"
                 raise TypeError(msg)
-
-
-                self._h5m_filename = value
+            self._h5m_filename = value
         else:
             msg = "NeutronicsModelFromReactor.h5m_filename should be a string"
             raise TypeError(msg)

From 41f1cbe2b0b05e1fb658c894e84a1457bf9f0dca Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 10 Sep 2021 11:43:07 +0100
Subject: [PATCH 11/29] removed test for from dir

---
 tests/test_neutronics_model.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/tests/test_neutronics_model.py b/tests/test_neutronics_model.py
index 3ff2794..a92b668 100644
--- a/tests/test_neutronics_model.py
+++ b/tests/test_neutronics_model.py
@@ -7,7 +7,6 @@
 import openmc_dagmc_wrapper
 import urllib.request
 
-
 class TestShape(unittest.TestCase):
     """Tests the NeutronicsModel with a Shape as the geometry input
     including neutronics simulations using"""
@@ -22,8 +21,8 @@ def setUp(self):
             tar.extractall("tests")
             tar.close()
 
-        self.h5m_filename_bigger = "tests/neutronics_workflow-0.0.1/example_01_single_volume_cell_tally/stage_2_output/dagmc.h5m"
-        self.h5m_filename_smaller = "tests/neutronics_workflow-0.0.1/example_02_multi_volume_cell_tally/stage_2_output/dagmc.h5m"
+        self.h5m_filename_bigger = "neutronics_workflow-0.0.1/example_01_single_volume_cell_tally/stage_2_output/dagmc.h5m"
+        self.h5m_filename_smaller = "neutronics_workflow-0.0.1/example_02_multi_volume_cell_tally/stage_2_output/dagmc.h5m"
 
         self.material_description = {
             "tungsten": "tungsten",
@@ -48,6 +47,7 @@ def setUp(self):
             ],
         )
 
+
     def simulation_with_previous_h5m_file(self):
         """This performs a simulation using previously created h5m file"""
 
@@ -739,6 +739,7 @@ def test_missing_h5m_file_error_handling():
             FileNotFoundError,
             test_missing_h5m_file_error_handling)
 
+
     def test_neutronics_model_attributes(self):
         """Makes a BallReactor neutronics model and simulates the TBR"""
 

From a6dd5e15085dbcf48e095acd55393b09f9f18bd7 Mon Sep 17 00:00:00 2001
From: autopep8 <autopep8@users.noreply.github.com>
Date: Fri, 10 Sep 2021 10:43:36 +0000
Subject: [PATCH 12/29] Automated autopep8 fixes

---
 tests/test_neutronics_model.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tests/test_neutronics_model.py b/tests/test_neutronics_model.py
index a92b668..ce3b005 100644
--- a/tests/test_neutronics_model.py
+++ b/tests/test_neutronics_model.py
@@ -7,6 +7,7 @@
 import openmc_dagmc_wrapper
 import urllib.request
 
+
 class TestShape(unittest.TestCase):
     """Tests the NeutronicsModel with a Shape as the geometry input
     including neutronics simulations using"""
@@ -47,7 +48,6 @@ def setUp(self):
             ],
         )
 
-
     def simulation_with_previous_h5m_file(self):
         """This performs a simulation using previously created h5m file"""
 
@@ -739,7 +739,6 @@ def test_missing_h5m_file_error_handling():
             FileNotFoundError,
             test_missing_h5m_file_error_handling)
 
-
     def test_neutronics_model_attributes(self):
         """Makes a BallReactor neutronics model and simulates the TBR"""
 

From d776b86e7445d1d0330b624bc18a8140c2ca894d Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 10 Sep 2021 11:46:07 +0100
Subject: [PATCH 13/29] added tests folder back to dir

---
 tests/test_neutronics_model.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_neutronics_model.py b/tests/test_neutronics_model.py
index a92b668..eb2d326 100644
--- a/tests/test_neutronics_model.py
+++ b/tests/test_neutronics_model.py
@@ -21,8 +21,8 @@ def setUp(self):
             tar.extractall("tests")
             tar.close()
 
-        self.h5m_filename_bigger = "neutronics_workflow-0.0.1/example_01_single_volume_cell_tally/stage_2_output/dagmc.h5m"
-        self.h5m_filename_smaller = "neutronics_workflow-0.0.1/example_02_multi_volume_cell_tally/stage_2_output/dagmc.h5m"
+        self.h5m_filename_bigger = "tests/neutronics_workflow-0.0.1/example_01_single_volume_cell_tally/stage_2_output/dagmc.h5m"
+        self.h5m_filename_smaller = "tests/neutronics_workflow-0.0.1/example_02_multi_volume_cell_tally/stage_2_output/dagmc.h5m"
 
         self.material_description = {
             "tungsten": "tungsten",

From d46bb2e94597c250f290494d73b26bdb5d073046 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 10 Sep 2021 12:34:58 +0100
Subject: [PATCH 14/29] allowing tet mesh file to be none

---
 openmc_dagmc_wrapper/neutronics_model.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/openmc_dagmc_wrapper/neutronics_model.py b/openmc_dagmc_wrapper/neutronics_model.py
index bf6fcd3..77297eb 100644
--- a/openmc_dagmc_wrapper/neutronics_model.py
+++ b/openmc_dagmc_wrapper/neutronics_model.py
@@ -123,7 +123,7 @@ def h5m_filename(self, value):
         if isinstance(value, str):
             if not Path(value).is_file():
                 msg = f"h5m_filename provided ({value}) does not exist"
-                raise TypeError(msg)
+                raise FileNotFoundError(msg)
             self._h5m_filename = value
         else:
             msg = "NeutronicsModelFromReactor.h5m_filename should be a string"
@@ -135,7 +135,12 @@ def tet_mesh_filename(self):
 
     @tet_mesh_filename.setter
     def tet_mesh_filename(self, value):
-        if isinstance(value, (str, type(None))):
+        if isinstance(value, str):
+            if not Path(value).is_file():
+                msg = f"tet_mesh_filename provided ({value}) does not exist"
+                raise FileNotFoundError(msg)
+            self._tet_mesh_filename = value
+        if isinstance(value, type(None)):
             self._tet_mesh_filename = value
         else:
             msg = "NeutronicsModelFromReactor.tet_mesh_filename should be a string"

From f60c51e4a365caca54ae3ee8f0dcf9c50f24fa55 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 10 Sep 2021 12:39:51 +0100
Subject: [PATCH 15/29] changed bash to pytest cmd

---
 .github/workflows/ci_with_install.yml | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
index 9addc87..4dbb71c 100644
--- a/.github/workflows/ci_with_install.yml
+++ b/.github/workflows/ci_with_install.yml
@@ -24,5 +24,12 @@ jobs:
           python setup.py install
       - name: run tests
         run: |
-          bash run_tests.sh
+          apt-get install tree
+          tree tests
+          pytest tests/notebook_testing.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
+          pytest tests/test_neutronics_model.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
+          pytest tests/test_reactor_neutronics.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xmlpytest tests/test_shape_neutronics.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
+          pytest tests/test_example_neutronics_simulations.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
+          pytest tests/test_neutronics_utils.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
+          tree tests
           curl -s https://codecov.io/bash

From 3490cdf7874b76f0de691bf18ba0f9ae40dcf117 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 10 Sep 2021 12:43:26 +0100
Subject: [PATCH 16/29] corrected long line typo

---
 .github/workflows/ci_with_install.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
index 4dbb71c..04fdede 100644
--- a/.github/workflows/ci_with_install.yml
+++ b/.github/workflows/ci_with_install.yml
@@ -28,7 +28,8 @@ jobs:
           tree tests
           pytest tests/notebook_testing.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
           pytest tests/test_neutronics_model.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
-          pytest tests/test_reactor_neutronics.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xmlpytest tests/test_shape_neutronics.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
+          pytest tests/test_reactor_neutronics.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
+          pytest tests/test_shape_neutronics.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
           pytest tests/test_example_neutronics_simulations.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
           pytest tests/test_neutronics_utils.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
           tree tests

From 69004eaa49671658b22c25e80fd006f59a5a67ff Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 10 Sep 2021 12:57:04 +0100
Subject: [PATCH 17/29] changed order of pytests

---
 .github/workflows/ci_with_install.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
index 04fdede..f222d8c 100644
--- a/.github/workflows/ci_with_install.yml
+++ b/.github/workflows/ci_with_install.yml
@@ -26,11 +26,12 @@ jobs:
         run: |
           apt-get install tree
           tree tests
-          pytest tests/notebook_testing.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
           pytest tests/test_neutronics_model.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
+          tree tests
           pytest tests/test_reactor_neutronics.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
           pytest tests/test_shape_neutronics.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
           pytest tests/test_example_neutronics_simulations.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
           pytest tests/test_neutronics_utils.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
+          pytest tests/notebook_testing.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
           tree tests
           curl -s https://codecov.io/bash

From cb07887af566a0e4c42aa76ac37f9d81f7dbc339 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 10 Sep 2021 13:09:08 +0100
Subject: [PATCH 18/29] wget to download h5m test files

---
 .github/workflows/ci_with_install.yml | 28 +++++++++++++++++----------
 tests/test_neutronics_model.py        |  7 +++++--
 2 files changed, 23 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
index f222d8c..9cbb22a 100644
--- a/.github/workflows/ci_with_install.yml
+++ b/.github/workflows/ci_with_install.yml
@@ -25,13 +25,21 @@ jobs:
       - name: run tests
         run: |
           apt-get install tree
-          tree tests
-          pytest tests/test_neutronics_model.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
-          tree tests
-          pytest tests/test_reactor_neutronics.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
-          pytest tests/test_shape_neutronics.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
-          pytest tests/test_example_neutronics_simulations.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
-          pytest tests/test_neutronics_utils.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
-          pytest tests/notebook_testing.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
-          tree tests
-          curl -s https://codecov.io/bash
+          wget https://github.com/fusion-energy/neutronics_workflow/archive/refs/tags/v0.0.1.tar.gz
+          tar -xvzf v0.0.1.tar.gz -C tests
+          tree
+          pytest tests/test_neutronics_model.py -vv
+
+      # - name: run tests
+      #   run: |
+      #     apt-get install tree
+      #     tree tests
+      #     pytest tests/test_neutronics_model.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
+      #     tree tests
+      #     pytest tests/test_reactor_neutronics.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
+      #     pytest tests/test_shape_neutronics.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
+      #     pytest tests/test_example_neutronics_simulations.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
+      #     pytest tests/test_neutronics_utils.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
+      #     pytest tests/notebook_testing.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
+      #     tree tests
+      #     curl -s https://codecov.io/bash
diff --git a/tests/test_neutronics_model.py b/tests/test_neutronics_model.py
index 3ff2794..1da1f5c 100644
--- a/tests/test_neutronics_model.py
+++ b/tests/test_neutronics_model.py
@@ -720,8 +720,11 @@ def test_missing_h5m_file_error_handling():
             """Attempts to simulate without a dagmc_smaller.h5m file which should fail
             with a FileNotFoundError"""
 
+            import shutil
+            shutil.copy(self.h5m_filename_smaller, '.')
+
             my_model = openmc_dagmc_wrapper.NeutronicsModel(
-                h5m_filename=self.h5m_filename_smaller,
+                h5m_filename='dagmc.h5m',
                 source=self.source,
                 materials={"mat1": "WC"},
             )
@@ -731,7 +734,7 @@ def test_missing_h5m_file_error_handling():
             os.system("touch materials.xml")
             os.system("touch settings.xml")
             os.system("touch tallies.xml")
-            os.system("rm dagmc_smaller.h5m")
+            os.system("rm dagmc.h5m")
 
             my_model.simulate()
 

From 85a7ca70fe4d70272b9b2d8dcd0073aac95df022 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 10 Sep 2021 15:41:37 +0100
Subject: [PATCH 19/29] renamed h5m files

---
 tests/test_neutronics_model.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_neutronics_model.py b/tests/test_neutronics_model.py
index 1da1f5c..ff036f2 100644
--- a/tests/test_neutronics_model.py
+++ b/tests/test_neutronics_model.py
@@ -22,8 +22,8 @@ def setUp(self):
             tar.extractall("tests")
             tar.close()
 
-        self.h5m_filename_bigger = "tests/neutronics_workflow-0.0.1/example_01_single_volume_cell_tally/stage_2_output/dagmc.h5m"
-        self.h5m_filename_smaller = "tests/neutronics_workflow-0.0.1/example_02_multi_volume_cell_tally/stage_2_output/dagmc.h5m"
+        self.h5m_filename_smaller = "tests/neutronics_workflow-0.0.1/example_01_single_volume_cell_tally/stage_2_output/dagmc.h5m"
+        self.h5m_filename_bigger = "tests/neutronics_workflow-0.0.1/example_02_multi_volume_cell_tally/stage_2_output/dagmc.h5m"
 
         self.material_description = {
             "tungsten": "tungsten",

From 799d30f66b918ca40707f170f748508392d5b887 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 10 Sep 2021 15:57:57 +0100
Subject: [PATCH 20/29] checking key instead of items

---
 openmc_dagmc_wrapper/neutronics_model.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/openmc_dagmc_wrapper/neutronics_model.py b/openmc_dagmc_wrapper/neutronics_model.py
index 77297eb..e570234 100644
--- a/openmc_dagmc_wrapper/neutronics_model.py
+++ b/openmc_dagmc_wrapper/neutronics_model.py
@@ -282,7 +282,7 @@ def create_openmc_materials(self):
 
         materials_in_h5m = di.get_materials_from_h5m(self.h5m_filename)
         # # checks all the required materials are present
-        for reactor_material in self.materials.items():
+        for reactor_material in self.materials.keys():
             if reactor_material not in materials_in_h5m:
                 msg = (f"material with tag {reactor_material} was not found in"
                        "the dagmc h5m file")

From 5ab7d21c70199b6e1c7bb6b5bfab650e48cbffcc Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 10 Sep 2021 16:04:56 +0100
Subject: [PATCH 21/29] added -1 to materials len if graveyard found

---
 openmc_dagmc_wrapper/neutronics_model.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/openmc_dagmc_wrapper/neutronics_model.py b/openmc_dagmc_wrapper/neutronics_model.py
index e570234..fadf034 100644
--- a/openmc_dagmc_wrapper/neutronics_model.py
+++ b/openmc_dagmc_wrapper/neutronics_model.py
@@ -288,7 +288,12 @@ def create_openmc_materials(self):
                        "the dagmc h5m file")
                 raise ValueError(msg)
 
-        if len(materials_in_h5m) != len(self.materials.keys()):
+        if 'graveyard' in materials_in_h5m:
+            required_number_of_materials = len(materials_in_h5m) -1
+        else:
+            required_number_of_materials = len(materials_in_h5m)
+
+        if required_number_of_materials != len(self.materials.keys()):
             msg = (
                 f"the NeutronicsModel.materials does not match the material"
                 "tags in the dagmc h5m file. Materials in h5m file "

From 1a1ce163f161190e50fae3840d7dba1d9b6f2384 Mon Sep 17 00:00:00 2001
From: autopep8 <autopep8@users.noreply.github.com>
Date: Fri, 10 Sep 2021 15:05:28 +0000
Subject: [PATCH 22/29] Automated autopep8 fixes

---
 openmc_dagmc_wrapper/neutronics_model.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/openmc_dagmc_wrapper/neutronics_model.py b/openmc_dagmc_wrapper/neutronics_model.py
index fadf034..bb53013 100644
--- a/openmc_dagmc_wrapper/neutronics_model.py
+++ b/openmc_dagmc_wrapper/neutronics_model.py
@@ -289,7 +289,7 @@ def create_openmc_materials(self):
                 raise ValueError(msg)
 
         if 'graveyard' in materials_in_h5m:
-            required_number_of_materials = len(materials_in_h5m) -1
+            required_number_of_materials = len(materials_in_h5m) - 1
         else:
             required_number_of_materials = len(materials_in_h5m)
 

From fd7b170163f47a7cd1289c4d7548931bbc1fc703 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 10 Sep 2021 16:08:26 +0100
Subject: [PATCH 23/29] added all the tests back

---
 .github/workflows/ci_with_install.yml | 27 ++++++++-------------------
 1 file changed, 8 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
index 9cbb22a..96117d4 100644
--- a/.github/workflows/ci_with_install.yml
+++ b/.github/workflows/ci_with_install.yml
@@ -22,24 +22,13 @@ jobs:
       - name: install package
         run: |
           python setup.py install
+
       - name: run tests
         run: |
-          apt-get install tree
-          wget https://github.com/fusion-energy/neutronics_workflow/archive/refs/tags/v0.0.1.tar.gz
-          tar -xvzf v0.0.1.tar.gz -C tests
-          tree
-          pytest tests/test_neutronics_model.py -vv
-
-      # - name: run tests
-      #   run: |
-      #     apt-get install tree
-      #     tree tests
-      #     pytest tests/test_neutronics_model.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
-      #     tree tests
-      #     pytest tests/test_reactor_neutronics.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
-      #     pytest tests/test_shape_neutronics.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
-      #     pytest tests/test_example_neutronics_simulations.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
-      #     pytest tests/test_neutronics_utils.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
-      #     pytest tests/notebook_testing.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
-      #     tree tests
-      #     curl -s https://codecov.io/bash
+          pytest tests/test_neutronics_model.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
+          pytest tests/test_reactor_neutronics.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
+          pytest tests/test_shape_neutronics.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
+          pytest tests/test_example_neutronics_simulations.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
+          pytest tests/test_neutronics_utils.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
+          pytest tests/notebook_testing.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
+          curl -s https://codecov.io/bash

From 4c4c6dc37971045a8df6b5b2285642418176b40c Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 10 Sep 2021 16:15:47 +0100
Subject: [PATCH 24/29] removed gravyard material

---
 tests/test_shape_neutronics.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/test_shape_neutronics.py b/tests/test_shape_neutronics.py
index 15c0110..1669bcc 100644
--- a/tests/test_shape_neutronics.py
+++ b/tests/test_shape_neutronics.py
@@ -30,7 +30,6 @@ def setUp(self):
             "center_column_shield_mat": "Be",
             "blanket_rear_wall_mat": "Be",
             "divertor_mat": "Be",
-            "graveyard": "Be",
             "tf_coil_mat": "Be",
             "pf_coil_mat": "Be",
             "inboard_tf_coils_mat": "Be",

From 125236e626ef67e3b0100114312e5c642ff9dfb5 Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 10 Sep 2021 16:25:19 +0100
Subject: [PATCH 25/29] removed graveyard in test materials

---
 openmc_dagmc_wrapper/neutronics_model.py | 4 ++--
 tests/test_reactor_neutronics.py         | 1 -
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/openmc_dagmc_wrapper/neutronics_model.py b/openmc_dagmc_wrapper/neutronics_model.py
index bb53013..b444ea5 100644
--- a/openmc_dagmc_wrapper/neutronics_model.py
+++ b/openmc_dagmc_wrapper/neutronics_model.py
@@ -284,7 +284,7 @@ def create_openmc_materials(self):
         # # checks all the required materials are present
         for reactor_material in self.materials.keys():
             if reactor_material not in materials_in_h5m:
-                msg = (f"material with tag {reactor_material} was not found in"
+                msg = (f"material with tag {reactor_material} was not found in "
                        "the dagmc h5m file")
                 raise ValueError(msg)
 
@@ -295,7 +295,7 @@ def create_openmc_materials(self):
 
         if required_number_of_materials != len(self.materials.keys()):
             msg = (
-                f"the NeutronicsModel.materials does not match the material"
+                f"the NeutronicsModel.materials does not match the material "
                 "tags in the dagmc h5m file. Materials in h5m file "
                 f"{materials_in_h5m}. Materials provided {self.materials.keys()}")
             raise ValueError(msg)
diff --git a/tests/test_reactor_neutronics.py b/tests/test_reactor_neutronics.py
index dddbf6c..ed67759 100644
--- a/tests/test_reactor_neutronics.py
+++ b/tests/test_reactor_neutronics.py
@@ -29,7 +29,6 @@ def setUp(self):
             "center_column_shield_mat": "Be",
             "blanket_rear_wall_mat": "Be",
             "divertor_mat": "Be",
-            "graveyard": "Be",
             "tf_coil_mat": "Be",
             "pf_coil_mat": "Be",
             "inboard_tf_coils_mat": "Be",

From 4ea5fd946c57aaca21637eb967f657a2991ac82d Mon Sep 17 00:00:00 2001
From: autopep8 <autopep8@users.noreply.github.com>
Date: Fri, 10 Sep 2021 15:25:56 +0000
Subject: [PATCH 26/29] Automated autopep8 fixes

---
 openmc_dagmc_wrapper/neutronics_model.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/openmc_dagmc_wrapper/neutronics_model.py b/openmc_dagmc_wrapper/neutronics_model.py
index b444ea5..935a27c 100644
--- a/openmc_dagmc_wrapper/neutronics_model.py
+++ b/openmc_dagmc_wrapper/neutronics_model.py
@@ -284,8 +284,9 @@ def create_openmc_materials(self):
         # # checks all the required materials are present
         for reactor_material in self.materials.keys():
             if reactor_material not in materials_in_h5m:
-                msg = (f"material with tag {reactor_material} was not found in "
-                       "the dagmc h5m file")
+                msg = (
+                    f"material with tag {reactor_material} was not found in "
+                    "the dagmc h5m file")
                 raise ValueError(msg)
 
         if 'graveyard' in materials_in_h5m:

From f1c77bcbb990b95da1e897c75b417af269ca2eea Mon Sep 17 00:00:00 2001
From: Jonathan Shimwell <mail@jshimwell.com>
Date: Fri, 10 Sep 2021 16:33:37 +0100
Subject: [PATCH 27/29] removed utils testing

---
 .circleci/config.yml                  | 18 +++++++++---------
 .github/workflows/ci_with_install.yml |  2 +-
 run_tests.sh                          |  2 +-
 tests/test_neutronics_utils.py        | 16 ++++++++--------
 4 files changed, 19 insertions(+), 19 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index b91af56..24ca930 100755
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -18,33 +18,33 @@ jobs:
       - run:
           name: run test_NeutronicModel
           command: 
-            pytest tests/test_neutronics_model.py -v --cov=openmc-dagmc_wrapper --cov-append --cov-report term --cov-report xml
+            pytest tests/test_neutronics_model.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
 
       - run:
           name: run test_shape_neutronics
           command: 
-            pytest tests/test_shape_neutronics.py -v --cov=openmc-dagmc_wrapper --cov-append --cov-report term --cov-report xml
+            pytest tests/test_shape_neutronics.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
 
       - run:
           name: run test_reactor_neutronics
           command: 
-            pytest tests/test_reactor_neutronics.py -v --cov=openmc-dagmc_wrapper --cov-append --cov-report term --cov-report xml
+            pytest tests/test_reactor_neutronics.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
 
-      - run:
-          name: run test_neutronics_utils
-          command: 
-            pytest tests/test_neutronics_utils.py -v --cov=openmc-dagmc_wrapper --cov-append --cov-report term --cov-report xml
+      # - run:
+      #     name: run test_neutronics_utils
+      #     command: 
+      #       pytest tests/test_neutronics_utils.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
 
       - run:
           name: run test_example_neutronics_simulations
           command: 
-            pytest tests/test_example_neutronics_simulations.py -v --cov=openmc-dagmc_wrapper --cov-append --cov-report term --cov-report xml
+            pytest tests/test_example_neutronics_simulations.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
 
       # TODO add example notebooks
       # - run:
       #     name: run notebook_testing
       #     command: 
-      #       pytest tests/notebook_testing.py -v --cov=openmc-dagmc_wrapper --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
+      #       pytest tests/notebook_testing.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
 
 
       - store_test_results:
diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
index 96117d4..d84bd77 100644
--- a/.github/workflows/ci_with_install.yml
+++ b/.github/workflows/ci_with_install.yml
@@ -29,6 +29,6 @@ jobs:
           pytest tests/test_reactor_neutronics.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
           pytest tests/test_shape_neutronics.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
           pytest tests/test_example_neutronics_simulations.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
-          pytest tests/test_neutronics_utils.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
+          # pytest tests/test_neutronics_utils.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
           pytest tests/notebook_testing.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
           curl -s https://codecov.io/bash
diff --git a/run_tests.sh b/run_tests.sh
index b7ffab5..3231442 100644
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -4,4 +4,4 @@ pytest tests/test_neutronics_model.py -v --cov=openmc_dagmc_wrapper --cov-append
 pytest tests/test_reactor_neutronics.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
 pytest tests/test_shape_neutronics.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
 pytest tests/test_example_neutronics_simulations.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
-pytest tests/test_neutronics_utils.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
+# pytest tests/test_neutronics_utils.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml
diff --git a/tests/test_neutronics_utils.py b/tests/test_neutronics_utils.py
index 9f99ff9..37ad17d 100644
--- a/tests/test_neutronics_utils.py
+++ b/tests/test_neutronics_utils.py
@@ -1,11 +1,11 @@
-import json
-import os
-import unittest
-from pathlib import Path
-
-import openmc
-import openmc_dagmc_wrapper
-import requests
+# import json
+# import os
+# import unittest
+# from pathlib import Path
+
+# import openmc
+# import openmc_dagmc_wrapper
+# import requests
 
 
 # class TestNeutronicsUtilityFunctions(unittest.TestCase):

From e3462ed5c2a4ac46235857c8617b42fa21823e10 Mon Sep 17 00:00:00 2001
From: Jonathan <mail@jshimwell.com>
Date: Fri, 10 Sep 2021 22:35:42 +0100
Subject: [PATCH 28/29] changed keys and local tests pass

---
 openmc_dagmc_wrapper/neutronics_model.py | 18 +++++++++++-------
 openmc_dagmc_wrapper/utils.py            | 23 ++++++++++++++++++-----
 tests/test_neutronics_model.py           | 20 +++++++++++++-------
 3 files changed, 42 insertions(+), 19 deletions(-)

diff --git a/openmc_dagmc_wrapper/neutronics_model.py b/openmc_dagmc_wrapper/neutronics_model.py
index 6c9c382..c991bdd 100644
--- a/openmc_dagmc_wrapper/neutronics_model.py
+++ b/openmc_dagmc_wrapper/neutronics_model.py
@@ -689,7 +689,7 @@ def export_xml(
                     neutron_particle_filter = openmc.ParticleFilter([
                                                                     "neutron"])
                     self._add_tally_for_every_material(
-                        "neutron_spectra",
+                        "neutron_fast_flux",
                         "flux",
                         [neutron_particle_filter, energy_filter],
                     )
@@ -697,7 +697,7 @@ def export_xml(
                         photon_particle_filter = openmc.ParticleFilter([
                                                                        "photon"])
                         self._add_tally_for_every_material(
-                            "photon_spectra",
+                            "photon_fast_flux",
                             "flux",
                             [photon_particle_filter, energy_filter],
                         )
@@ -767,6 +767,9 @@ def export_xml(
                     suffix = standard_tally
                     self._add_tally_for_every_material(suffix, score)
 
+                    # todo add photon tallys for standard tallies
+                    # if self.photon_transport:
+
         # make the model from geometry, materials, settings and tallies
         model = openmc.model.Model(geom, self.mats, settings, self.tallies)
 
@@ -849,6 +852,12 @@ def simulate(
             )
             raise TypeError(msg)
 
+        if not Path(self.h5m_filename).is_file():
+            msg = f"""{self.h5m_filename} file was not found. Please set
+                  export_h5m to True or use the export_h5m() methods to create
+                  the dagmc.h5m file"""
+            raise FileNotFoundError(msg)
+
         if export_xml is True:
             self.export_xml(
                 simulation_batches=simulation_batches,
@@ -871,11 +880,6 @@ def simulate(
                 )
                 raise FileNotFoundError(msg)
 
-        if not Path(self.h5m_filename).is_file():
-            msg = f"""{self.h5m_filename} file was not found. Please set
-                  export_h5m to True or use the export_h5m() methods to create
-                  the dagmc.h5m file"""
-            raise FileNotFoundError(msg)
 
         # Deletes summary.h5m if it already exists.
         # This avoids permission problems when trying to overwrite the file
diff --git a/openmc_dagmc_wrapper/utils.py b/openmc_dagmc_wrapper/utils.py
index ad4c348..7a94f4a 100644
--- a/openmc_dagmc_wrapper/utils.py
+++ b/openmc_dagmc_wrapper/utils.py
@@ -205,15 +205,22 @@ def get_neutronics_results_from_statepoint_file(
                     * number_of_neutrons_in_pulse,
                 }
 
-        # todo add fast flux tally
-        # energies = [0.1e6, 100e6] 0.1MeV to 100MeV
-        # energy_filter = openmc.EnergyFilter(energies)
+        elif tally.name.endswith("fast_flux"):
+
+            data_frame = tally.get_pandas_dataframe()
+            tally_result = data_frame["mean"].sum()
+            tally_std_dev = data_frame["std. dev."].sum()
+            results[tally.name]["fast flux per source particle"] = {
+                "result": tally_result,
+                "std. dev.": tally_std_dev,
+            }
+
         elif tally.name.endswith("flux"):
 
             data_frame = tally.get_pandas_dataframe()
             tally_result = data_frame["mean"].sum()
             tally_std_dev = data_frame["std. dev."].sum()
-            results[tally.name]["Flux per source particle"] = {
+            results[tally.name]["flux per source particle"] = {
                 "result": tally_result,
                 "std. dev.": tally_std_dev,
             }
@@ -222,7 +229,7 @@ def get_neutronics_results_from_statepoint_file(
             data_frame = tally.get_pandas_dataframe()
             tally_result = data_frame["mean"]
             tally_std_dev = data_frame["std. dev."]
-            results[tally.name]["Flux per source particle"] = {
+            results[tally.name]["flux per source particle"] = {
                 "energy": openmc.mgxs.GROUP_STRUCTURES["CCFE-709"].tolist(),
                 "result": tally_result.tolist(),
                 "std. dev.": tally_std_dev.tolist(),
@@ -331,6 +338,12 @@ def get_neutronics_results_from_statepoint_file(
 
     return results
 
+#to do find particles from tally
+# def find_particle_from_tally(tally):
+#     for filter in talliy.filters:
+#         if isinstance(filter, openmc.ParticleFilter):
+#             return filter.bins[0]
+#     return None
 
 def write_3d_mesh_tally_to_vtk(
     xs: np.linspace,
diff --git a/tests/test_neutronics_model.py b/tests/test_neutronics_model.py
index eaddf36..5457984 100644
--- a/tests/test_neutronics_model.py
+++ b/tests/test_neutronics_model.py
@@ -348,16 +348,16 @@ def test_neutronics_component_cell_simulation_heating(self):
 
         # extracts the heat from the results dictionary
         heat = my_model.results["mat1_heating"]["Watts"]["result"]
-        flux = my_model.results["mat1_flux"]["Flux per source particle"]["result"]
+        flux = my_model.results["mat1_flux"]["flux per source particle"]["result"]
         mat_tbr = my_model.results["mat1_TBR"]["result"]
         tbr = my_model.results["TBR"]["result"]
         spectra_neutrons = my_model.results["mat1_neutron_spectra"][
-            "Flux per source particle"
+            "flux per source particle"
         ]["result"]
         spectra_photons = my_model.results["mat1_photon_spectra"][
-            "Flux per source particle"
+            "flux per source particle"
         ]["result"]
-        energy = my_model.results["mat1_photon_spectra"]["Flux per source particle"][
+        energy = my_model.results["mat1_photon_spectra"]["flux per source particle"][
             "energy"
         ]
 
@@ -565,14 +565,14 @@ def test_cell_tallies_simulation_fast_flux(self):
             h5m_filename=self.h5m_filename_smaller,
             source=self.source,
             materials={"mat1": "Be"},
-            cell_tallies=["fast_flux"],
+            cell_tallies=["fast_flux", "flux"],
             photon_transport=True,
         )
 
         # starts the neutronics simulation
         my_model.simulate(
             simulation_batches=2,
-            simulation_particles_per_batch=10,
+            simulation_particles_per_batch=1000,
         )
 
         my_model.process_results(
@@ -581,9 +581,15 @@ def test_cell_tallies_simulation_fast_flux(self):
         )
 
         assert isinstance(
-            my_model.results["mat1_neutron_fast_flux"]["result"],
+            my_model.results["mat1_neutron_fast_flux"]["fast flux per source particle"]["result"],
             float,
         )
+        assert isinstance(
+            my_model.results["mat1_flux"]["flux per source particle"]["result"],
+            float,
+        )
+
+        assert my_model.results["mat1_flux"]["flux per source particle"]["result"] > my_model.results["mat1_neutron_fast_flux"]["fast flux per source particle"]["result"]
 
     def test_cell_tallies_simulation_effective_dose(self):
         """Performs simulation with h5m file and tallies neutron and photon

From 525d4a85ce90f70b763d85f9c174c5cad4369803 Mon Sep 17 00:00:00 2001
From: autopep8 <autopep8@users.noreply.github.com>
Date: Fri, 10 Sep 2021 21:36:08 +0000
Subject: [PATCH 29/29] Automated autopep8 fixes

---
 openmc_dagmc_wrapper/neutronics_model.py | 1 -
 openmc_dagmc_wrapper/utils.py            | 3 ++-
 tests/test_neutronics_model.py           | 3 ++-
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/openmc_dagmc_wrapper/neutronics_model.py b/openmc_dagmc_wrapper/neutronics_model.py
index c991bdd..c365f09 100644
--- a/openmc_dagmc_wrapper/neutronics_model.py
+++ b/openmc_dagmc_wrapper/neutronics_model.py
@@ -880,7 +880,6 @@ def simulate(
                 )
                 raise FileNotFoundError(msg)
 
-
         # Deletes summary.h5m if it already exists.
         # This avoids permission problems when trying to overwrite the file
         silently_remove_file("summary.h5")
diff --git a/openmc_dagmc_wrapper/utils.py b/openmc_dagmc_wrapper/utils.py
index 7a94f4a..22848b6 100644
--- a/openmc_dagmc_wrapper/utils.py
+++ b/openmc_dagmc_wrapper/utils.py
@@ -338,13 +338,14 @@ def get_neutronics_results_from_statepoint_file(
 
     return results
 
-#to do find particles from tally
+# to do find particles from tally
 # def find_particle_from_tally(tally):
 #     for filter in talliy.filters:
 #         if isinstance(filter, openmc.ParticleFilter):
 #             return filter.bins[0]
 #     return None
 
+
 def write_3d_mesh_tally_to_vtk(
     xs: np.linspace,
     ys: np.linspace,
diff --git a/tests/test_neutronics_model.py b/tests/test_neutronics_model.py
index 5457984..c2c25e2 100644
--- a/tests/test_neutronics_model.py
+++ b/tests/test_neutronics_model.py
@@ -589,7 +589,8 @@ def test_cell_tallies_simulation_fast_flux(self):
             float,
         )
 
-        assert my_model.results["mat1_flux"]["flux per source particle"]["result"] > my_model.results["mat1_neutron_fast_flux"]["fast flux per source particle"]["result"]
+        assert my_model.results["mat1_flux"]["flux per source particle"]["result"] > my_model.results[
+            "mat1_neutron_fast_flux"]["fast flux per source particle"]["result"]
 
     def test_cell_tallies_simulation_effective_dose(self):
         """Performs simulation with h5m file and tallies neutron and photon