Merge pull request #210 from fusion-energy/develop

updates from develop
fusion-energy · May 31, 2023 · 7dbaa10 · 7dbaa10
2 parents 78a85c6 + 6358094
commit 7dbaa10
Show file tree

Hide file tree

Showing 5 changed files with 228 additions and 55 deletions.
diff --git a/tasks/task_01_cross_sections/4_Doppler_broadening.ipynb b/tasks/task_01_cross_sections/4_Doppler_broadening.ipynb
@@ -50,7 +50,7 @@
     "\n",
     "mt_number = REACTION_MT[\"(n,total)\"]  # looks up the MT number for the total reaction\n",
     "\n",
-    "h5_file = f\"/home/jshimwell/WMP_Library/WMP_Library/074186.h5\"  # 074186 is W186\n",
+    "h5_file = f\"WMP_Library/074186.h5\"  # 074186 is W186\n",
     "\n",
     "isotope_multipole = openmc.data.WindowedMultipole.from_hdf5(h5_file)  # loads up the WMP cross section file\n",
     "\n",
@@ -93,7 +93,7 @@
     "\n",
     "mt_number = REACTION_MT[\"(n,total)\"]  # looks up the MT number for the total reaction\n",
     "\n",
-    "h5_file = f\"/home/jshimwell/WMP_Library/WMP_Library/026056.h5\"  # 026056 is Fe56\n",
+    "h5_file = f\"WMP_Library/026056.h5\"  # 026056 is Fe56\n",
     "\n",
     "isotope_multipole = openmc.data.WindowedMultipole.from_hdf5(h5_file)  # loads up the WMP cross section file\n",
     "\n",

diff --git a/tasks/task_08_CSG_mesh_tally/1_example_2d_mesh_tallies.ipynb b/tasks/task_08_CSG_mesh_tally/1_example_2d_mesh_tallies.ipynb
@@ -2,6 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
+   "metadata": {},
    "source": [
     "# Part 1 - 2D mesh tallies\n",
     "\n",
@@ -14,31 +15,32 @@
     "This can form a 2D slice of the neutron interactions throughout the model.\n",
     "\n",
     "This notebook allows users to create a simple geometry from a few different materials and plot the results of a 2D regular mesh tally applied to the geometry."
-   ],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "from IPython.display import IFrame\n",
     "IFrame(src=\"https://www.youtube.com/embed/KYIsDjip1nQ\", width=560, height=340)"
-   ],
-   "outputs": [],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "markdown",
+   "metadata": {},
    "source": [
     "This code block defines the model geometry, materials, neutron source and regular mesh tally. Run the cell to see the model geometry.\n",
     "\n",
     "Observe how a 2D mesh is achieved by creating a 3D mesh with a thickness of one mesh cell in one dimension."
-   ],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "import openmc\n",
     "import matplotlib.pyplot as plt\n",
@@ -112,20 +114,20 @@
     "\n",
     "# combines the geometry, materials, settings and tallies to create a neutronics model\n",
     "model = openmc.model.Model(my_geometry, my_materials, my_settings, my_tallies)\n"
-   ],
-   "outputs": [],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "markdown",
+   "metadata": {},
    "source": [
     "The next code block performs the simulation which tallies neutron flux on the mesh, and loads the results for inspection."
-   ],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# deletes old files\n",
     "!rm summary.h5\n",
@@ -136,20 +138,20 @@
     "\n",
     "# open the results file\n",
     "results = openmc.StatePoint(output_filename)"
-   ],
-   "outputs": [],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "markdown",
+   "metadata": {},
    "source": [
     "This code block filters the results to show the neutron flux recorded by the mesh tally."
-   ],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# access the flux tally\n",
     "my_tally = results.get_tally(scores=['flux'])\n",
@@ -161,24 +163,24 @@
     "# when plotting the 2d data, added the extent is required.\n",
     "# otherwise the plot uses the index of the 2d data arrays\n",
     "# as the x y axis\n",
-    "plt.show(fig.imshow(my_slice.mean, extent=[-200,200,-200,200]))\n",
+    "plt.show(fig.imshow(my_slice.mean, extent=mesh.bounding_box.extent['xz']))\n",
     "\n",
     "# notice that neutrons are produced and emitted isotropically from a point source.\n",
     "# There is a slight increase in flux within the neutron multiplier."
-   ],
-   "outputs": [],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "markdown",
+   "metadata": {},
    "source": [
     "This code block filters the results to show the neutron absorption recorded by the mesh tally."
-   ],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# access the absorption tally\n",
     "my_tally = results.get_tally(scores=['absorption'])\n",
@@ -190,23 +192,23 @@
     "# when plotting the 2d data, added the extent is required.\n",
     "# otherwise the plot uses the index of the 2d data arrays\n",
     "# as the x y axis\n",
-    "plt.show(fig.imshow(my_slice.mean, extent=[-200,200,-200,200]))\n",
+    "plt.show(fig.imshow(my_slice.mean, extent=mesh.bounding_box.extent['xz']))\n",
     "\n",
     "# notice that neutrons are being absorpted on the left hand side of the model"
-   ],
-   "outputs": [],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "markdown",
+   "metadata": {},
    "source": [
     "This code block filters the results to show the neutron multiplication recorded by the mesh tally."
-   ],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# access the neutron multiplication tally\n",
     "my_tally = results.get_tally(scores=['(n,2n)'])\n",
@@ -218,16 +220,16 @@
     "# when plotting the 2d data, added the extent is required.\n",
     "# otherwise the plot uses the index of the 2d data arrays\n",
     "# as the x y axis\n",
-    "plt.show(fig.imshow(my_slice.mean, extent=[-200,200,-200,200]))\n",
+    "plt.show(fig.imshow(my_slice.mean, extent=mesh.bounding_box.extent['xz']))\n",
     "\n",
     "# notice that neutrons are being muliplied on the right hand side of the model"
-   ],
-   "outputs": [],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "# Bonus information\n",
     "# The 2D mesh tally is currently recording all interactions in the 3rd dimention (z).\n",
@@ -240,18 +242,16 @@
     "mesh.dimension = [100, 1, 100] # only one entry in the Y direction\n",
     "mesh.lower_left = [-200, -0.5, -200] # Y thickness is now smaller\n",
     "mesh.upper_right = [200, 0.5, 200] # Y thickness is now smaller"
-   ],
-   "outputs": [],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "markdown",
+   "metadata": {},
    "source": [
     "**Learning Outcomes for Part 1:**\n",
     "\n",
     "- Mesh tallies can be used to visualise neutron interactions spatially throughout geometry."
-   ],
-   "metadata": {}
+   ]
   }
  ],
  "metadata": {
@@ -273,9 +273,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.13"
+   "version": "3.10.10"
   }
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}
diff --git a/tasks/task_09_CSG_dose_tallies/5_mesh_dose_from_neutrons.py b/tasks/task_09_CSG_dose_tallies/5_mesh_dose_from_neutrons.py
@@ -108,10 +108,9 @@
 
 data_slice = data_slice * neutrons_per_second * pico_to_milli
 
-
 plot_1 = plt.imshow(
     data_slice,
-    extent=mesh.get_mpl_plot_extent(view_direction="x"),
+    extent=mesh.bounding_box.extent['xy'],
     interpolation=None,
     norm=LogNorm(
         vmin=1e-12,  # trims out the lower section of the colors
@@ -134,7 +133,7 @@
     linestyles="solid",
     levels=levels,
     linewidths=2.0,
-    extent=my_geometry.get_mpl_plot_extent(view_direction="x"),
+    extent=my_geometry.bounding_box.extent['xy'],
 )
 xlabel, ylabel = my_geometry.get_axis_labels(view_direction="x")
 plt.xlabel(xlabel)