Moving to jupyter labs

Dockerfile

@@ -58,10 +58,9 @@ RUN apt-get --yes install libeigen3-dev \
 
 
 # installing cadquery and jupyter
-RUN conda install jupyter -y && \
-    conda install -c conda-forge -c python python=3.7.8 && \
-    conda install -c conda-forge -c cadquery cadquery=2
-# cadquery master dose not appear to show the .solid in the notebook
+RUN conda install -c conda-forge -c python python=3.8 && \
+    conda install -c conda-forge -c cadquery cadquery=2.1 && \
+    pip install jupyter-cadquery==2.0.0-rc1
 
 
 # Python libraries used in the workshop
@@ -250,8 +249,9 @@ COPY tasks tasks/
 
 WORKDIR /tasks
 
-#this sets the port, gcr looks for this varible
+#this sets the port, gcr looks for this ENV varible
 ENV PORT 8888
+EXPOSE 8888
 
 # could switch to --ip='*'
-CMD ["jupyter", "notebook", "--notebook-dir=/tasks", "--port=8888", "--no-browser", "--ip=0.0.0.0", "--allow-root"]
+CMD ["jupyter", "lab", "--notebook-dir=/tasks", "--port=8888", "--no-browser", "--ip=0.0.0.0", "--allow-root"]

tasks/task_01_cross_sections/1_isotope_xs_plot.ipynb

@@ -13,7 +13,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [
     {
@@ -216,5 +216,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

tasks/task_08_CSG_mesh_tally/2_example_3d_mesh_tallies.ipynb

@@ -89,15 +89,39 @@
     "sett.batches = batches\n",
     "sett.inactive = 0\n",
     "sett.particles = 5000\n",
-    "sett.run_mode = 'fixed source'\n",
+    "sett.run_mode = 'fixed source'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from parametric_plasma_source import PlasmaSource, SOURCE_SAMPLING_PATH\n",
     "\n",
-    "# Create a DT point source\n",
-    "source = openmc.Source()\n",
-    "source.angle = openmc.stats.Isotropic()\n",
-    "source.energy = openmc.stats.Discrete([14e6], [1])\n",
-    "source.space = openmc.stats.Point((150, 150, 0))\n",
+    "my_plasma = PlasmaSource(\n",
+    "    ion_density_origin=1.09e20,\n",
+    "    ion_density_peaking_factor=1,\n",
+    "    ion_density_pedestal=1.09e20,\n",
+    "    ion_density_separatrix=3e19,\n",
+    "    ion_temperature_origin=45.9,\n",
+    "    ion_temperature_peaking_factor=8.06,\n",
+    "    ion_temperature_pedestal=6.09,\n",
+    "    ion_temperature_separatrix=0.1,\n",
+    "    elongation=2,\n",
+    "    triangularity=0.55,\n",
+    "    major_radius=4.5,  # note the source takes m arguments\n",
+    "    minor_radius=1.,\n",
+    "    pedestal_radius=0.8 * 100,\n",
+    "    plasma_id=1,\n",
+    "    shafranov_shift=0.44789,\n",
+    "    ion_temperature_beta=6\n",
+    ")\n",
     "\n",
-    "sett.source = source"
+    "source = openmc.Source()\n",
+    "source.library = SOURCE_SAMPLING_PATH\n",
+    "source.parameters = str(my_plasma)"
    ]
   },
   {
@@ -138,16 +162,22 @@
     "# Create mesh filter for tally\n",
     "mesh_filter = openmc.MeshFilter(mesh)\n",
     "\n",
-    "# Create flux mesh tally to score flux\n",
+    "# Create tritium production mesh tally to score flux\n",
     "mesh_tally = openmc.Tally(tally_id=1, name='tbr_on_mesh')  # note the tally_id is specified\n",
     "mesh_tally.filters = [mesh_filter]\n",
     "mesh_tally.scores = ['(n,Xt)']\n",
     "tallies.append(mesh_tally)\n",
     "\n",
-    "# Create flux mesh tally to score flux\n",
+    "# Create heat mesh tally to score flux\n",
     "mesh_tally = openmc.Tally(tally_id=2, name='heating_on_mesh')  # note the tally_id is specified\n",
     "mesh_tally.filters = [mesh_filter]\n",
     "mesh_tally.scores = ['heating']\n",
+    "tallies.append(mesh_tally)\n",
+    "\n",
+    "# Create flux mesh tally to score flux\n",
+    "mesh_tally = openmc.Tally(tally_id=3,name='flux_on_mesh')  # note the tally_id is specified\n",
+    "mesh_tally.filters = [mesh_filter]\n",
+    "mesh_tally.scores = ['flux']\n",
     "tallies.append(mesh_tally)"
    ]
   },
@@ -185,7 +215,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from statepoint_to_vtk import initiate_mesh\n",
+    "from statepoint_to_vtk import *\n",
     "\n",
     "initiate_mesh(\n",
     "    statepoint_filename=sp_filename,\n",
@@ -201,6 +231,14 @@
     "    output_filename='heating_tally_on_mesh.vtk',\n",
     "    mesh_id=1,  # note the mesh_id from earlier is used\n",
     "    tally_id=2 # note the tally_id from earlier is used\n",
+    ")\n",
+    "\n",
+    "initiate_mesh(\n",
+    "    statepoint_filename=sp_filename,\n",
+    "    tally_name='flux_on_mesh',\n",
+    "    output_filename='flux_tally_on_mesh.vtk',\n",
+    "    mesh_id=1,  # note the mesh_id from earlier is used\n",
+    "    tally_id=3 # note the tally_id from earlier is used\n",
     ")"
    ]
   },

tasks/task_10_making_CAD_geometry/1_make_CAD_shapes_from_points.ipynb

@@ -25,23 +25,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "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": 2,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
+   "outputs": [],
    "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>')"
@@ -63,6 +49,8 @@
    "outputs": [],
    "source": [
     "import paramak\n",
+    "from jupyter_cadquery.cadquery import show\n",
+    "\n",
     "my_shape = paramak.RotateStraightShape(\n",
     "    points=[\n",
     "        (50,50),\n",
@@ -73,7 +61,7 @@
     "    rotation_angle=180\n",
     ")\n",
     "\n",
-    "my_shape.solid"
+    "show(my_shape.solid)"
    ]
   },
   {
@@ -99,7 +87,7 @@
     "    rotation_angle=180\n",
     ")\n",
     "\n",
-    "my_shape.solid"
+    "show(my_shape.solid)"
    ]
   },
   {
@@ -125,7 +113,7 @@
     "    distance=20\n",
     ")\n",
     "\n",
-    "my_shape.solid"
+    "show(my_shape.solid)"
    ]
   },
   {
@@ -151,7 +139,7 @@
     "    distance=20\n",
     ")\n",
     "\n",
-    "my_shape.solid"
+    "show(my_shape.solid)"
    ]
   },
   {
@@ -190,7 +178,7 @@
     "    cut=small_Shape\n",
     ")\n",
     "\n",
-    "my_shape.solid"
+    "show(my_shape.solid)"
    ]
   },
   {

tasks/task_10_making_CAD_geometry/2_make_CAD_components_from_parameters.ipynb

@@ -47,6 +47,7 @@
    "outputs": [],
    "source": [
     "import paramak\n",
+    "from jupyter_cadquery.cadquery import show\n",
     "\n",
     "pf_1 = paramak.PoloidalFieldCoil(\n",
     "    height=50,\n",
@@ -55,7 +56,7 @@
     "    rotation_angle=180\n",
     ")\n",
     "\n",
-    "pf_1.solid"
+    "show(pf_1.solid)"
    ]
   },
   {
@@ -93,7 +94,7 @@
     "    rotation_angle=180\n",
     ")\n",
     "\n",
-    "tf.solid"
+    "show(tf.solid)"
    ]
   },
   {
@@ -130,7 +131,7 @@
     "    rotation_angle=180\n",
     ")\n",
     "\n",
-    "plasma.solid"
+    "show(plasma.solid)"
    ]
   },
   {
@@ -168,7 +169,7 @@
     "    rotation_angle=180\n",
     ")\n",
     "\n",
-    "blanket.solid"
+    "show(blanket.solid)"
    ]
   },
   {
@@ -191,7 +192,7 @@
     "my_reactor.export_stp()\n",
     "my_reactor.export_stl()\n",
     "\n",
-    "my_reactor.solid"
+    "show(my_reactor.solid)"
    ]
   },
   {

tasks/task_10_making_CAD_geometry/3_make_CAD_reactors.ipynb

@@ -46,6 +46,7 @@
    "outputs": [],
    "source": [
     "import paramak\n",
+    "from jupyter_cadquery.cadquery import show\n",
     "\n",
     "my_reactor = paramak.BallReactor(\n",
     "    inner_bore_radial_thickness=10,\n",
@@ -70,7 +71,7 @@
     "    outboard_tf_coil_poloidal_thickness=50\n",
     ")\n",
     "\n",
-    "my_reactor.solid"
+    "show(my_reactor.solid)"
    ]
   },
   {

tasks/task_11_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb

@@ -23,6 +23,7 @@
    "outputs": [],
    "source": [
     "import paramak\n",
+    "from jupyter_cadquery.cadquery import show\n",
     "\n",
     "pf_1 = paramak.PoloidalFieldCoil(\n",
     "    height=50,\n",
@@ -44,7 +45,6 @@
     "    with_inner_leg=True\n",
     ")\n",
     "\n",
-    "\n",
     "plasma = paramak.Plasma(\n",
     "    minor_radius=150.,\n",
     "    major_radius=450.,\n",
@@ -69,7 +69,7 @@
     "# so it has been removed to speed up the example\n",
     "\n",
     "my_reactor.rotation_angle=360  # this is a small \"feature\" which we will fix soon\n",
-    "my_reactor.solid"
+    "show(my_reactor.solid)"
    ]
   },
   {
@@ -185,7 +185,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.8.3"
   }
  },
  "nbformat": 4,

tasks/task_12_CAD_mesh_fast_flux/1_making_shapes_into_a_neutronics_model.ipynb

@@ -27,6 +27,7 @@
    "outputs": [],
    "source": [
     "import paramak\n",
+    "from jupyter_cadquery.cadquery import show\n",
     "\n",
     "pf_coil = paramak.RotateStraightShape(\n",
     "    points=[\n",
@@ -39,7 +40,7 @@
     "    material_tag = 'pf_coil_material'\n",
     ")\n",
     "\n",
-    "pf_coil.solid"
+    "show(pf_coil.solid)"
    ]
   },
   {
@@ -67,7 +68,7 @@
     "    material_tag = 'center_column_material'\n",
     ")\n",
     "\n",
-    "center_column.solid"
+    "show(center_column.solid)"
    ]
   },
   {
@@ -100,7 +101,7 @@
     "    material_tag = 'blanket_material'\n",
     ")\n",
     "\n",
-    "blanket.solid"
+    "show(blanket.solid)"
    ]
   },
   {