Merge pull request #81 from fusion-energy/develop

moving to openmc develop branch
fusion-energy · Mar 28, 2022 · 66837e1 · 66837e1
2 parents ab971e8 + e697ffd
commit 66837e1
Show file tree

Hide file tree

Showing 9 changed files with 358 additions and 957 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -224,9 +224,9 @@ RUN wget https://github.com/mit-crpg/WMP_Library/releases/download/v1.1/WMP_Libr
 
 # installs OpenMc from source
 RUN cd /opt && \
-    # switch back to tagged version when 0.13.1 is released
+    # switch back to tagged version when 0.13.1 is released as develop depletion is used
     # git clone --single-branch --branch v0.13.0 --depth 1 https://github.com/openmc-dev/openmc.git && \
-    git clone --single-branch --branch changing_get_atoms_arg_to_mat_object_try2 --depth 1 https://github.com/shimwell/openmc.git && \
+    git clone --single-branch --branch develop --depth 1 https://github.com/openmc-dev/openmc.git && \
     cd openmc && \
     mkdir build && \
     cd build && \
@@ -259,9 +259,7 @@ RUN pip install neutronics_material_maker[density] \
                 openmc_source_plotter \
                 openmc_mesh_tally_to_vtk
 
-# installing a development version of the paramak that allows exporting to h5m files
-RUN conda install -c fusion-energy -c cadquery -c conda-forge paramak_develop
-
+RUN conda install -c fusion-energy -c cadquery -c conda-forge paramak
 
 # an older version of openmc is need to provide an older executable
 # this particular exectuable allows an inital_source.h5 to be written

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 
 [![CircleCI](https://circleci.com/gh/fusion-energy/neutronics-workshop/tree/main.svg?style=svg)](https://circleci.com/gh/fusion-energy/neutronics-workshop/tree/main)
-<!-- [![CI with install](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_tests.yml/badge.svg)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_tests.yml) -->
+[![CI with install](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_tests.yml/badge.svg)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/ci_tests.yml)
 
 [![docker-publish-release](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/docker-publish.yml/badge.svg)](https://github.com/fusion-energy/neutronics-workshop/actions/workflows/docker-publish.yml)
 

diff --git a/tasks/task_10_making_CAD_geometry/1_make_CAD_shapes_from_points.ipynb b/tasks/task_10_making_CAD_geometry/1_make_CAD_shapes_from_points.ipynb
@@ -2,6 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
+   "metadata": {},
    "source": [
     "# Part 1 - Making a parametric shape\n",
     "\n",
@@ -20,53 +21,54 @@
     "    Documented: https://paramak.readthedocs.io\n",
     "    Published: https://f1000research.com/articles/10-27\n",
     "    Video presentation: https://www.youtube.com/watch?v=fXboew3U7rw"
-   ],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": 9,
-   "source": [
-    "from IPython.display import HTML\n",
-    "HTML('<iframe width=\"560\" height=\"315\" src=\"https://www.youtube.com/embed/Bn_TcJSOvaA\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen></iframe>')"
-   ],
+   "metadata": {},
    "outputs": [
     {
-     "output_type": "stream",
      "name": "stderr",
+     "output_type": "stream",
      "text": [
       "/home/jshim/miniconda3/envs/openmc-dagmc/lib/python3.8/site-packages/IPython/core/display.py:724: UserWarning: Consider using IPython.display.IFrame instead\n",
       "  warnings.warn(\"Consider using IPython.display.IFrame instead\")\n"
      ]
     },
     {
-     "output_type": "execute_result",
      "data": {
-      "text/plain": [
-       "<IPython.core.display.HTML object>"
-      ],
       "text/html": [
        "<iframe width=\"560\" height=\"315\" src=\"https://www.youtube.com/embed/Bn_TcJSOvaA\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen></iframe>"
+      ],
+      "text/plain": [
+       "<IPython.core.display.HTML object>"
       ]
      },
+     "execution_count": 9,
      "metadata": {},
-     "execution_count": 9
+     "output_type": "execute_result"
     }
    ],
-   "metadata": {}
+   "source": [
+    "from IPython.display import HTML\n",
+    "HTML('<iframe width=\"560\" height=\"315\" src=\"https://www.youtube.com/embed/Bn_TcJSOvaA\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen></iframe>')"
+   ]
   },
   {
    "cell_type": "markdown",
+   "metadata": {},
    "source": [
     "3D shapes can be made using coordinates and CAD opperations such as extrude, rotate and sweep.\n",
     "\n",
     "This first example shows 4 points connected by straight edges and rotated by 180 degrees."
-   ],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "import paramak\n",
     "my_shape = paramak.RotateStraightShape(\n",
@@ -80,20 +82,20 @@
     ")\n",
     "\n",
     "my_shape.show()"
-   ],
-   "outputs": [],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "markdown",
+   "metadata": {},
    "source": [
     "This second example shows 4 points connected by spline edges and rotated by 180 degrees."
-   ],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "my_shape = paramak.RotateSplineShape(\n",
     "    points=[\n",
@@ -106,20 +108,20 @@
     ")\n",
     "\n",
     "my_shape.show()"
-   ],
-   "outputs": [],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "markdown",
+   "metadata": {},
    "source": [
     "This second example shows 4 points connected by straight edges and extruded by by 20."
-   ],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "my_shape = paramak.ExtrudeStraightShape(\n",
     "    points=[\n",
@@ -132,20 +134,20 @@
     ")\n",
     "\n",
     "my_shape.show()"
-   ],
-   "outputs": [],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "markdown",
+   "metadata": {},
    "source": [
     "This second example shows 4 points connected by spline edges and extruded by by 20."
-   ],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "my_shape = paramak.ExtrudeSplineShape(\n",
     "    points=[\n",
@@ -158,22 +160,22 @@
     ")\n",
     "\n",
     "my_shape.show()"
-   ],
-   "outputs": [],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "markdown",
+   "metadata": {},
    "source": [
     "Boolean opperations like cut, union and intersection are also supported.\n",
     "\n",
     "The following example makes two shapes and cuts the first one away from the second."
-   ],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "small_Shape = paramak.ExtrudeStraightShape(\n",
     "    points=[\n",
@@ -197,41 +199,41 @@
     ")\n",
     "\n",
     "my_shape.show()"
-   ],
-   "outputs": [],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "markdown",
+   "metadata": {},
    "source": [
     "The 3D volumes produced can then be:\n",
     "- exported to stp files.\n",
     "- exported to stl files."
-   ],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "my_shape.export_stp('example_shape.stp')\n",
     "my_shape.export_stl('example_shape.stl')"
-   ],
-   "outputs": [],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "markdown",
+   "metadata": {},
    "source": [
     "The geometry can also be converted into a DAGMC h5m file and used in neutronics simulations.\n",
     "\n",
     "To visualize the h5m file it can be converted into a vtk file"
-   ],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "from stl_to_h5m import stl_to_h5m\n",
     "\n",
@@ -242,42 +244,40 @@
     "\n",
     "import os\n",
     "os.system('mbconvert dagmc.h5m dagmc.vtk')"
-   ],
-   "outputs": [],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "markdown",
+   "metadata": {},
    "source": [
     "The geometry produced can be downloaded and viewed in FreeCAD (stp and stl) or Paraview (stl, vtk)"
-   ],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "from IPython.display import FileLink\n",
     "display(FileLink('example_shape.stp'))\n",
     "display(FileLink('example_shape.stl'))\n",
     "display(FileLink('dagmc.vtk'))"
-   ],
-   "outputs": [],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "markdown",
+   "metadata": {},
    "source": [
     "There are additional Shape attributes that allow more complex shapes to be made. For more details take a look at the Documented: https://paramak.readthedocs.io"
-   ],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "source": [],
+   "metadata": {},
    "outputs": [],
-   "metadata": {}
+   "source": []
   }
  ],
  "metadata": {
@@ -296,9 +296,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.11"
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}
diff --git a/tasks/task_10_making_CAD_geometry/2_make_CAD_components_from_parameters.ipynb b/tasks/task_10_making_CAD_geometry/2_make_CAD_components_from_parameters.ipynb
@@ -248,7 +248,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,

diff --git a/tasks/task_10_making_CAD_geometry/3_make_CAD_reactors.ipynb b/tasks/task_10_making_CAD_geometry/3_make_CAD_reactors.ipynb
@@ -143,7 +143,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,

diff --git a/...task_11_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb b/...task_11_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb
@@ -108,8 +108,8 @@
     "materials = odw.Materials(\n",
     "    h5m_filename='dagmc.h5m',\n",
     "    correspondence_dict={\n",
-    "        'mat_blanket':'Li4SiO4',\n",
-    "        'mat_plasma': 'DT_plasma'\n",
+    "        'blanket':'Li4SiO4',\n",
+    "        'plasma': 'DT_plasma'\n",
     "    }\n",
     ")\n",
     "\n",
@@ -251,7 +251,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.7"
   }
  },
  "nbformat": 4,