Merge pull request #34 from fusion-energy/develop

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fusion-energy · Aug 17, 2021 · b9b6892 · b9b6892
2 parents c2b82fa + bdba16d
commit b9b6892
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Showing 27 changed files with 604 additions and 809 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -18,17 +18,17 @@ jobs:
       - run:
           name: run test_NeutronicModel
           command: 
-            pytest tests/test_NeutronicModel.py -v --cov=paramak_neutronics --cov-append --cov-report term --cov-report xml
+            pytest tests/test_neutronic_model.py -v --cov=paramak_neutronics --cov-append --cov-report term --cov-report xml
 
       - run:
-          name: run test_Reactor_neutronics
+          name: run test_shape_neutronics
           command: 
-            pytest tests/test_Reactor_neutronics.py -v --cov=paramak_neutronics --cov-append --cov-report term --cov-report xml
+            pytest tests/test_shape_neutronics.py -v --cov=paramak_neutronics --cov-append --cov-report term --cov-report xml
 
       - run:
-          name: run test_Shape_neutronics
+          name: run test_reactor_neutronics
           command: 
-            pytest tests/test_Shape_neutronics.py -v --cov=paramak_neutronics --cov-append --cov-report term --cov-report xml
+            pytest tests/test_reactor_neutronics.py -v --cov=paramak_neutronics --cov-append --cov-report term --cov-report xml
 
       - run:
           name: run test_neutronics_utils

diff --git a/Dockerfile b/Dockerfile
@@ -29,6 +29,7 @@ ENV LANG=C.UTF-8 LC_ALL=C.UTF-8 \
     CC=/usr/bin/mpicc CXX=/usr/bin/mpicxx \
     DEBIAN_FRONTEND=noninteractive
 
+RUN apt-get --allow-releaseinfo-change update
 RUN apt-get update -y && \
     apt-get upgrade -y
 
@@ -126,7 +127,8 @@ RUN git clone --shallow-submodules --single-branch --branch main --depth 1 https
 RUN mkdir DAGMC && \
     cd DAGMC && \
     # git clone --single-branch --branch 3.2.0 --depth 1 https://github.com/svalinn/DAGMC.git && \
-    git clone --shallow-submodules --single-branch --branch develop --depth 1 https://github.com/svalinn/DAGMC.git && \
+    # git clone --shallow-submodules --single-branch --branch develop --depth 1 https://github.com/svalinn/DAGMC.git && \
+    git clone --shallow-submodules --single-branch --branch dd_bbox --depth 1 https://github.com/pshriwise/DAGMC.git && \
     mkdir build && \
     cd build && \
     cmake ../DAGMC -DBUILD_TALLY=ON \
@@ -165,15 +167,14 @@ ENV OPENMC_CROSS_SECTIONS=/nuclear_data/cross_sections.xml
 ENV PATH="/MOAB/build/bin:${PATH}"
 ENV PATH="/DAGMC/bin:${PATH}"
 
-RUN pip install paramak
 
 FROM dependencies as final
 
 COPY run_tests.sh run_tests.sh
 COPY paramak_neutronics paramak_neutronics/
 COPY setup.py setup.py
-COPY examples examples/
-COPY tests tests/
 COPY README.md README.md
+COPY tests tests/
+COPY examples examples/
 
 RUN python setup.py install
diff --git a/examples/ball_reactor.ipynb b/examples/ball_reactor.ipynb
@@ -2,14 +2,16 @@
  "cells": [
   {
    "cell_type": "markdown",
+   "metadata": {},
    "source": [
     "This example makes a reactor geometry and a neutronics model. A homogenised material made of enriched lithium lead and eurofer is being used as the blanket material for this simulation in order to demonstrate the use of more complex materials."
-   ],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "import neutronics_material_maker as nmm\n",
     "import openmc\n",
@@ -61,7 +63,7 @@
     "\n",
     "# makes the neutronics material\n",
     "neutronics_model = paramak_neutronics.NeutronicsModel(\n",
-    "    geometry=my_reactor,\n",
+    "    h5m_filename=my_reactor.export_h5m(),\n",
     "    source=source,\n",
     "    materials={\n",
     "        'inboard_tf_coils_mat': 'copper',\n",
@@ -80,28 +82,20 @@
     "\n",
     "# prints the results to screen\n",
     "print('TBR', neutronics_model.results['TBR'])"
-   ],
-   "outputs": [],
-   "metadata": {}
+   ]
   }
  ],
  "metadata": {
+  "interpreter": {
+   "hash": "71893251c0b0cd78b546a9c905312457257aecf63dc5b51c6968316964f80317"
+  },
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
+   "display_name": "Python 3.8.10 64-bit ('cq': conda)",
    "name": "python3"
   },
   "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
    "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": ""
   }
  },
  "nbformat": 4,

diff --git a/examples/ball_reactor_minimal.ipynb b/examples/ball_reactor_minimal.ipynb
@@ -2,14 +2,16 @@
  "cells": [
   {
    "cell_type": "markdown",
+   "metadata": {},
    "source": [
     "This is a minimal example that obtains the TBR (Tritium Breeding Ratio) for a parametric ball reactor"
-   ],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": [
     "import openmc\n",
     "import paramak\n",
@@ -49,7 +51,7 @@
     "\n",
     "# makes the neutronics model from the geometry and material allocations\n",
     "neutronics_model = paramak_neutronics.NeutronicsModel(\n",
-    "    geometry=my_reactor,\n",
+    "    h5m_filename=my_reactor.export_h5m(),\n",
     "    source=source,\n",
     "    materials={\n",
     "        'inboard_tf_coils_mat': 'eurofer',\n",
@@ -66,35 +68,27 @@
     "# simulate the neutronics model\n",
     "neutronics_model.simulate()\n",
     "print(neutronics_model.results)\n"
-   ],
-   "outputs": [],
-   "metadata": {}
+   ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "source": [],
+   "metadata": {},
    "outputs": [],
-   "metadata": {}
+   "source": []
   }
  ],
  "metadata": {
+  "interpreter": {
+   "hash": "71893251c0b0cd78b546a9c905312457257aecf63dc5b51c6968316964f80317"
+  },
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
+   "display_name": "Python 3.8.10 64-bit ('cq': conda)",
    "name": "python3"
   },
   "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
    "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": ""
   }
  },
  "nbformat": 4,

diff --git a/examples/ball_reactor_source_plot.ipynb b/examples/ball_reactor_source_plot.ipynb
@@ -82,7 +82,7 @@
     "\n",
     "# makes the neutronics material\n",
     "neutronics_model = paramak_neutronics.NeutronicsModel(\n",
-    "    geometry=my_reactor,\n",
+    "    h5m_filename=my_reactor.export_h5m(),\n",
     "    source=source,\n",
     "    materials={\n",
     "        'inboard_tf_coils_mat': 'copper',\n",
@@ -132,24 +132,18 @@
   }
  ],
  "metadata": {
+  "interpreter": {
+   "hash": "71893251c0b0cd78b546a9c905312457257aecf63dc5b51c6968316964f80317"
+  },
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
+   "display_name": "Python 3.8.10 64-bit ('cq': conda)",
    "name": "python3"
   },
   "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
    "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": ""
   }
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}
diff --git a/examples/center_column_study_reactor.ipynb b/examples/center_column_study_reactor.ipynb
@@ -58,7 +58,7 @@
     "    # makes the neutronics model and assigns basic materials to each\n",
     "    # component\n",
     "    neutronics_model = paramak_neutronics.NeutronicsModel(\n",
-    "        geometry=my_reactor,\n",
+    "        h5m_filename=my_reactor.export_h5m(),\n",
     "        source=source,\n",
     "        materials={\n",
     "            'DT_plasma': 'DT_plasma',\n",
@@ -91,24 +91,18 @@
   }
  ],
  "metadata": {
+  "interpreter": {
+   "hash": "71893251c0b0cd78b546a9c905312457257aecf63dc5b51c6968316964f80317"
+  },
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
+   "display_name": "Python 3.8.10 64-bit ('cq': conda)",
    "name": "python3"
   },
   "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
    "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": ""
   }
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}
diff --git a/examples/center_column_study_reactor_minimal.ipynb b/examples/center_column_study_reactor_minimal.ipynb
@@ -46,7 +46,7 @@
     "\n",
     "# creates a neutronics model from the geometry and assigned materials\n",
     "neutronics_model = paramak_neutronics.NeutronicsModel(\n",
-    "    geometry=my_reactor,\n",
+    "    h5m_filename=my_reactor.export_h5m(),\n",
     "    source=source,\n",
     "    materials={\n",
     "        'inboard_tf_coils_mat': 'eurofer',\n",
@@ -75,24 +75,18 @@
   }
  ],
  "metadata": {
+  "interpreter": {
+   "hash": "71893251c0b0cd78b546a9c905312457257aecf63dc5b51c6968316964f80317"
+  },
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
+   "display_name": "Python 3.8.10 64-bit ('cq': conda)",
    "name": "python3"
   },
   "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
    "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": ""
   }
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}
diff --git a/examples/component_based_mesh_simulation.py b/examples/component_based_mesh_simulation.py
@@ -29,7 +29,7 @@ def main():
 
     # converts the geometry into a neutronics geometry
     my_model = paramak.NeutronicsModel(
-        geometry=my_shape,
+        h5m_filename=my_shape.export_h5m(),
         source=source,
         materials={'center_column_shield_mat': 'WB'},  # WB is tungsten boride
         cell_tallies=['heating', 'TBR'],

diff --git a/examples/component_based_parameter_study.ipynb b/examples/component_based_parameter_study.ipynb
@@ -43,7 +43,7 @@
     "\n",
     "    # converts the geometry into a neutronics geometry\n",
     "    my_model = paramak_neutronics.NeutronicsModel(\n",
-    "        geometry=my_shape,\n",
+    "        h5m_filename=my_shape.export_h5m(),\n",
     "        source=source,\n",
     "        materials={\n",
     "            'center_column_shield_mat': 'WB'},\n",
@@ -87,24 +87,18 @@
   }
  ],
  "metadata": {
+  "interpreter": {
+   "hash": "71893251c0b0cd78b546a9c905312457257aecf63dc5b51c6968316964f80317"
+  },
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
+   "display_name": "Python 3.8.10 64-bit ('cq': conda)",
    "name": "python3"
   },
   "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
    "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": ""
   }
  },
  "nbformat": 4,
  "nbformat_minor": 4
-}
+}