Merge pull request #54 from fusion-energy/develop

normalising spectra

.gitignore

@@ -141,3 +141,4 @@ dmypy.json
 *.stp
 *.trelis
 *.out
+*.tar.gz

Dockerfile

@@ -164,6 +164,8 @@ ENV OPENMC_CROSS_SECTIONS=/nuclear_data/cross_sections.xml
 ENV PATH="/MOAB/build/bin:${PATH}"
 ENV PATH="/DAGMC/bin:${PATH}"
 
+COPY requirements-test.txt requirements-test.txt
+RUN pip install -r requirements-test.txt
 
 FROM dependencies as final
 

README.md

@@ -36,16 +36,17 @@ Standard simulations tallies are facilitated:
 Neutronics responses can be obtained:
 - Tritium Breeding Ratio (TBR)
 - Heating (photon and neutron)
-- Dose (on road map)
-- Any supported reaction from the standard OpenMC reactions
+- Effective dose (photon and neutron)
+- Any supported reaction from the [standard OpenMC reactions](https://docs.openmc.org/en/latest/usersguide/tallies.html#scores)
 
 A standard collection of materials are available by making use of the
 [neutronics_material_maker](https://github.com/fusion-energy/neutronics_material_maker) package.
 
 OpenMC sources definitions are used for the particle sources. 
 
-Post processing of results are also carried out to automatically provide images,
-JSON output files and VTK files for convenient access to the results.
+Post processing of the OpenMC output files are also carried out to automatically
+provide: JSON text files, PNG images, VTK files for convenient access to the
+results.
 
 :point_right: [Documentation](https://openmc-dagmc-wrapper.readthedocs.io)
 

examples/ball_reactor.ipynb

@@ -15,7 +15,7 @@
    "source": [
     "import neutronics_material_maker as nmm\n",
     "import openmc\n",
-    "import openmc_dagmc_wrapper\n",
+    "import openmc_dagmc_wrapper as odw\n",
     "\n",
     "# makes a homogenised material for the blanket from lithium lead and\n",
     "# eurofer\n",
@@ -31,15 +31,15 @@
     "\n",
     "source = openmc.Source()\n",
     "# sets the location of the source to x=0 y=0 z=0\n",
-    "source.space = openmc.stats.Point((my_reactor.major_radius, 0, 0))\n",
+    "source.space = openmc.stats.Point((450, 0, 0))\n",
     "# sets the direction to isotropic\n",
     "source.angle = openmc.stats.Isotropic()\n",
     "# sets the energy distribution to 100% 14MeV neutrons\n",
     "source.energy = openmc.stats.Discrete([14e6], [1])\n",
     "\n",
     "# makes the neutronics material\n",
-    "neutronics_model = paramak_neutronics.NeutronicsModel(\n",
-    "    h5m_filename=my_reactor.export_h5m(),\n",
+    "neutronics_model = odw.NeutronicsModel(\n",
+    "    h5m_filename='dagmc.h5m,\n",
     "    source=source,\n",
     "    materials={\n",
     "        'inboard_tf_coils_mat': 'copper',\n",
@@ -52,17 +52,24 @@
     ")\n",
     "\n",
     "# starts the neutronics simulation\n",
-    "neutronics_model.simulate(\n",
+    "h5m_filename = neutronics_model.simulate(\n",
     "    simulation_batches=2,\n",
     "    simulation_particles_per_batch=10,  # this will need increasing to obtain accurate results\n",
     ")\n",
     "\n",
     "# extracts and processes the results from the statepoint file\n",
-    "neutronics_model.process_results()\n",
+    "odw.process_results(statepoint_filename=h5m_filename)\n",
     "\n",
     "# prints the results to screen\n",
     "print('TBR', neutronics_model.results['TBR'])"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -84,7 +91,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.8.11"
   }
  },
  "nbformat": 4,

examples/ball_reactor_minimal.ipynb

@@ -9,23 +9,37 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "FileNotFoundError",
+     "evalue": "h5m_filename provided (dagmc.h5m) does not exist",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mFileNotFoundError\u001b[0m                         Traceback (most recent call last)",
+      "\u001b[0;32m/tmp/ipykernel_11288/4029085043.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m     11\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     12\u001b[0m \u001b[0;31m# makes the neutronics model from the geometry and material allocations\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 13\u001b[0;31m neutronics_model = odw.NeutronicsModel(\n\u001b[0m\u001b[1;32m     14\u001b[0m     \u001b[0mh5m_filename\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m\"dagmc.h5m\"\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     15\u001b[0m     \u001b[0msource\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0msource\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/openmc-dagmc-wrapper/openmc_dagmc_wrapper/neutronics_model.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, h5m_filename, source, materials, cell_tallies, tet_mesh_filename, mesh_tally_2d, mesh_tally_3d, mesh_tally_tet, mesh_2d_resolution, mesh_3d_resolution, mesh_2d_corners, mesh_3d_corners, photon_transport, bounding_box)\u001b[0m\n\u001b[1;32m     91\u001b[0m     ):\n\u001b[1;32m     92\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmaterials\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mmaterials\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 93\u001b[0;31m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mh5m_filename\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mh5m_filename\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     94\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtet_mesh_filename\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mtet_mesh_filename\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     95\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msource\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msource\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/openmc-dagmc-wrapper/openmc_dagmc_wrapper/neutronics_model.py\u001b[0m in \u001b[0;36mh5m_filename\u001b[0;34m(self, value)\u001b[0m\n\u001b[1;32m    123\u001b[0m             \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mPath\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mvalue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mis_file\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    124\u001b[0m                 \u001b[0mmsg\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34mf\"h5m_filename provided ({value}) does not exist\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 125\u001b[0;31m                 \u001b[0;32mraise\u001b[0m \u001b[0mFileNotFoundError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    126\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_h5m_filename\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mvalue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    127\u001b[0m         \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;31mFileNotFoundError\u001b[0m: h5m_filename provided (dagmc.h5m) does not exist"
+     ]
+    }
+   ],
    "source": [
     "import openmc\n",
-    "import openmc_dagmc_wrapper\n",
+    "import openmc_dagmc_wrapper as odw\n",
     "\n",
     "source = openmc.Source()\n",
     "# sets the location of the source to x=0 y=0 z=0\n",
-    "source.space = openmc.stats.Point((my_reactor.major_radius, 0, 0))\n",
+    "source.space = openmc.stats.Point((450, 0, 0))\n",
     "# sets the direction to isotropic\n",
     "source.angle = openmc.stats.Isotropic()\n",
     "# sets the energy distribution to 100% 14MeV neutrons\n",
     "source.energy = openmc.stats.Discrete([14e6], [1])\n",
     "\n",
     "# makes the neutronics model from the geometry and material allocations\n",
-    "neutronics_model = openmc_dagmc_wrapper.NeutronicsModel(\n",
+    "neutronics_model = odw.NeutronicsModel(\n",
     "    h5m_filename=\"dagmc.h5m\",\n",
     "    source=source,\n",
     "    materials={\n",
@@ -39,14 +53,14 @@
     ")\n",
     "\n",
     "# simulate the neutronics model\n",
-    "neutronics_model.simulate(\n",
+    "h5m_filename = neutronics_model.simulate(\n",
     "    simulation_batches=2,\n",
     "    simulation_particles_per_batch=10,  # this will need increasing to obtain accurate results\n",
     "\n",
     ")\n",
     "\n",
     "# extracts and processes the results from the statepoint file\n",
-    "neutronics_model.process_results()\n",
+    "odw.process_results(statepoint_filename=h5m_filename)\n",
     "\n",
     "print(neutronics_model.results)\n"
    ]
@@ -78,7 +92,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.8.11"
   }
  },
  "nbformat": 4,

examples/ball_reactor_source_plot.ipynb

@@ -43,10 +43,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import paramak_neutronics\n",
+    "import openmc_dagmc_wrapper as odw\n",
     "\n",
     "# makes the neutronics material\n",
-    "neutronics_model = paramak_neutronics.NeutronicsModel(\n",
+    "neutronics_model = odw.NeutronicsModel(\n",
     "    h5m_filename=\"dagmc.h5m\",\n",
     "    source=source,\n",
     "    materials={\n",
@@ -115,7 +115,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.8.11"
   }
  },
  "nbformat": 4,

examples/center_column_study_reactor.ipynb

@@ -14,7 +14,7 @@
     "\n",
     "import matplotlib.pyplot as plt\n",
     "import openmc\n",
-    "import openmc_dagmc_wrapper\n",
+    "import openmc_dagmc_wrapper as odw\n",
     "\n",
     "\n",
     "source = openmc.Source()\n",
@@ -27,7 +27,7 @@
     "\n",
     "# makes the neutronics model and assigns basic materials to each\n",
     "# component\n",
-    "neutronics_model = openmc_dagmc_wrapper.NeutronicsModel(\n",
+    "neutronics_model = odw.NeutronicsModel(\n",
     "    h5m_filename=my_reactor.export_h5m(),\n",
     "    source=source,\n",
     "    materials={\n",
@@ -41,16 +41,16 @@
     ")\n",
     "\n",
     "# starts the neutronics simulation\n",
-    "neutronics_model.simulate(\n",
+    "h5m_filename = neutronics_model.simulate(\n",
     "    simulation_batches=2,\n",
     "    simulation_particles_per_batch=10,  # this would need increasing to get a accurate result\n",
     ")\n",
     "\n",
     "# extracts and processes the results from the statepoint file\n",
-    "neutronics_model.process_results()\n",
+    "results = neutronics_model.process_results(statepoint_filename=h5m_filename)\n",
     "\n",
     "# converts the results to mega watts\n",
-    "total_heat_in_MW = neutronics_model.results['firstwall_mat_heating']['Watts']['result'] / 1e6\n",
+    "total_heat_in_MW = results['firstwall_mat_heating']['Watts']['result'] / 1e6\n",
     "\n"
    ]
   }
@@ -74,7 +74,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.8.11"
   }
  },
  "nbformat": 4,

examples/center_column_study_reactor_minimal.ipynb

@@ -10,18 +10,18 @@
     "parametric reactor.\"\"\"\n",
     "\n",
     "import openmc\n",
-    "import openmc_dagmc_wrapper\n",
+    "import openmc_dagmc_wrapper as odw\n",
     "\n",
     "source = openmc.Source()\n",
     "# sets the location of the source to x=0 y=0 z=0\n",
-    "source.space = openmc.stats.Point((my_reactor.major_radius, 0, 0))\n",
+    "source.space = openmc.stats.Point((450, 0, 0))\n",
     "# sets the direction to isotropic\n",
     "source.angle = openmc.stats.Isotropic()\n",
     "# sets the energy distribution to 100% 14MeV neutrons\n",
     "source.energy = openmc.stats.Discrete([14e6], [1])\n",
     "\n",
     "# creates a neutronics model from the geometry and assigned materials\n",
-    "neutronics_model = paramak_neutronics.NeutronicsModel(\n",
+    "neutronics_model = odw.NeutronicsModel(\n",
     "    h5m_filename=my_reactor.export_h5m(),\n",
     "    source=source,\n",
     "    materials={\n",
@@ -34,16 +34,16 @@
     ")\n",
     "\n",
     "# starts the neutronics simulation\n",
-    "neutronics_model.simulate(\n",
+    "h5m_filename = neutronics_model.simulate(\n",
     "    simulation_batches=2,\n",
     "    simulation_particles_per_batch=10, # this will need increasing to obtain accurate results\n",
     ")\n",
     "\n",
     "# extracts and processes the results from the statepoint file\n",
-    "neutronics_model.process_results()\n",
+    "results = odw.process_results(statepoint_filename=h5m_filename)\n",
     "\n",
     "# prints the results\n",
-    "print(neutronics_model.results)\n"
+    "print(results)\n"
    ]
   },
   {
@@ -73,7 +73,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.8.11"
   }
  },
  "nbformat": 4,

examples/component_based_parameter_study.ipynb

@@ -16,7 +16,7 @@
    "outputs": [],
    "source": [
     "import openmc\n",
-    "import openmc_dagmc_wrapper\n",
+    "import openmc_dagmc_wrapper as odw\n",
     "\n",
     "# makes the openmc neutron source at x,y,z 0, 0, 0 with isotropic\n",
     "# diections\n",
@@ -25,7 +25,7 @@
     "source.angle = openmc.stats.Isotropic()\n",
     "\n",
     "# converts the geometry into a neutronics geometry\n",
-    "my_model = paramak_neutronics.NeutronicsModel(\n",
+    "my_model = odw.NeutronicsModel(\n",
     "    h5m_filename=\"dagmc.h5m\",\n",
     "    source=source,\n",
     "    materials={\n",
@@ -35,16 +35,16 @@
     ")\n",
     "\n",
     "# performs an openmc simulation on the model\n",
-    "my_model.simulate(\n",
+    "h5m_filename = my_model.simulate(\n",
     "    simulation_batches=10,  # should be increased for more accurate result\n",
     "    simulation_particles_per_batch=10,  # settings are low to reduce time required\n",
     ")\n",
     "\n",
     "# extracts and processes the results from the statepoint file\n",
-    "my_model.process_results()\n",
+    "results = my_model.process_results(statepoint_filename=h5m_filename)\n",
     "\n",
     "# extracts the heat from the results dictionary\n",
-    "heat = my_model.results['center_column_shield_mat_heating']['Watts']['result']\n",
+    "heat = results['center_column_shield_mat_heating']['Watts']['result']\n",
     "\n",
     "print(heat)"
    ]
@@ -76,7 +76,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.8.11"
   }
  },
  "nbformat": 4,

examples/openmc_logo_example.ipynb

@@ -17,7 +17,7 @@
    "outputs": [],
    "source": [
     "import openmc\n",
-    "import openmc_dagmc_wrapper"
+    "import openmc_dagmc_wrapper as odw"
    ]
   },
   {
@@ -45,7 +45,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "my_model = paramak_neutronics.NeutronicsModel(\n",
+    "my_model = odw.NeutronicsModel(\n",
     "    h5m_filename=\"dagmc.h5m\",\n",
     "    source=source,\n",
     "    materials = {'red_part_material':'P91', 'grey_part_material':'Li4SiO4'},\n",
@@ -54,14 +54,14 @@
     "    cell_tallies=['(n,Xt)','heating', 'spectra'],\n",
     ")\n",
     "\n",
-    "my_model.simulate(\n",
+    "h5m_filename = my_model.simulate(\n",
     "    simulation_batches=2,  # this should be increased to get a better mesh tally result\n",
     "    simulation_particles_per_batch=10,  # this should be increased to get a better mesh tally result\n",
     ")\n",
     "\n",
     "\n",
     "# extracts and processes the results from the statepoint file\n",
-    "my_model.process_results()"
+    "results = my_model.process_results(statepoint_filename=h5m_filename)"
    ]
   },
   {
@@ -77,7 +77,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "my_model.results"
+    "print(results)"
    ]
   }
  ],
@@ -97,7 +97,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.8.11"
   }
  },
  "nbformat": 4,