Merge pull request #3 from shimwell/develop

adds CI

.github/workflows/ci_with_install.yml

@@ -0,0 +1,56 @@
+
+# This CI will launch a Docker image that contains all the dependencies required
+# within that image the pytest test suite is run 
+
+
+name: CI with install
+
+on:
+  pull_request:    
+    branches:
+    - develop
+    - main
+
+jobs:
+  testing:
+    runs-on: ubuntu-latest
+    container:
+      image: continuumio/miniconda3
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: install dependencies package
+        run: |
+          apt update -y
+          apt-get install ffmpeg libsm6 libxext6  -y
+
+      - name: create environment 1
+        run: |
+          conda env create -f environment_cad.yml
+          conda init bash
+          .source ~/.bashrc    
+          conda activate env_cad
+
+      - name: conda init
+        run: |
+          bash -i conda_init_for_ci.sh
+
+      - name: run script 1 of 3
+        run: |
+          python 1_creation_of_dagmc_geometry.py
+
+      - name: create environment 1
+        run: |
+          conda env create -f environment_neutronics.yml
+          conda init bash
+          .source ~/.bashrc   
+          conda activate env_neutronics
+
+      - name: run script 2 of 3
+        run: |
+          2_run_openmc_dagmc_simulation.py
+
+      - name: run script 3 of 3
+        run: |
+          3_extract_results.py

.gitignore

@@ -127,3 +127,12 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# output files
+*.h5m
+*.html
+*.xml
+*.h5
+*.out
+*.xml
+*.vtk

2_run_openmc_dagmc_simulation.py

@@ -1,30 +1,31 @@
 import openmc
+import openmc_data_downloader as odd
+
 
 # Names of material tags can be found with the command line tool
 # mbsize -ll dagmc.h5m | grep 'NAME = mat:'
 
-
-mat_vacuum_vessel = openmc.Material(name="mat_vacuum_vessel")
+mat_vacuum_vessel = openmc.Material(name="vacuum_vessel")
 mat_vacuum_vessel.add_element("Fe", 1, "ao")
 mat_vacuum_vessel.set_density("g/cm3", 7.7)
 
-mat_upper_blanket = openmc.Material(name="mat_upper_blanket")
+mat_upper_blanket = openmc.Material(name="upper_blanket")
 mat_upper_blanket.add_element("Li", 1, "ao")
 mat_upper_blanket.set_density("g/cm3", 0.5)
 
-mat_lower_blanket = openmc.Material(name="mat_lower_blanket")
+mat_lower_blanket = openmc.Material(name="lower_blanket")
 mat_lower_blanket.add_element("Li", 1, "ao")
 mat_lower_blanket.set_density("g/cm3", 0.5)
 
-mat_lower_vacuum_vessel = openmc.Material(name="mat_lower_vacuum_vessel")
+mat_lower_vacuum_vessel = openmc.Material(name="lower_vacuum_vessel")
 mat_lower_vacuum_vessel.add_element("Fe", 1, "ao")
 mat_lower_vacuum_vessel.set_density("g/cm3", 7.7)
 
-mat_upper_vacuum_vessel = openmc.Material(name="mat_upper_vacuum_vessel")
+mat_upper_vacuum_vessel = openmc.Material(name="upper_vacuum_vessel")
 mat_upper_vacuum_vessel.add_element("Fe", 1, "ao")
 mat_upper_vacuum_vessel.set_density("g/cm3", 7.7)
 
-mat_blanket = openmc.Material(name="mat_blanket")
+mat_blanket = openmc.Material(name="blanket")
 mat_blanket.add_element("Li", 1, "ao")
 mat_blanket.set_density("g/cm3", 0.5)
 
@@ -39,6 +40,12 @@
     ]
 )
 
+#downloads the nuclear data and sets the openmc_cross_sections environmental variable
+odd.just_in_time_library_generator(
+    libraries='ENDFB-7.1-NNDC',
+    materials=materials
+)
+
 # makes use of the dagmc geometry
 dag_univ = openmc.DAGMCUniverse("dagmc.h5m")
 
@@ -62,7 +69,7 @@
 # specifies the simulation computational intensity
 settings = openmc.Settings()
 settings.batches = 10
-settings.particles = 100000
+settings.particles = 10000
 settings.inactive = 0
 settings.run_mode = "fixed source"
 settings.source = my_source

README.md

@@ -1,23 +1,37 @@
-This example simulates a simplfied model of an inertial confinement fusion reactor.
+<!-- [![CI with install](https://github.com/shimwell/cad-to-dagmc-to-openmc-example/actions/workflows/ci_with_install.yml/badge.svg)](https://github.com/shimwell/cad-to-dagmc-to-openmc-example/actions/workflows/ci_with_install.yml) -->
+
+This example simulates a simplified model of an inertial confinement fusion reactor.
 
 - A CAD model is made and automatically converted to a DAGMC geometry that is then used in OpenMC for a neutronics simulation.
 - The neutronics simulation obtains the tritium breeding ratio and a 3D map of tritium production.
 - The simulation outputs are post processed to display the results and produce a VTK file for visualization.
 
+# Prerequisites
+
+This minimal example makes use of Conda to manage and install the packages.
+
+You will need one of these conda distributions to be installed or work within a [Docker image](https://hub.docker.com/r/continuumio/miniconda3)
+
+- [Miniconda](https://docs.conda.io/en/latest/miniconda.html)
+
+- [Anaconda](https://www.anaconda.com/)
+
+- [Miniforge](https://github.com/conda-forge/miniforge)
+
+- [Miniconda](https://docs.conda.io/en/latest/miniconda.html)
+
 # First clone the repository
 ```bash
 git clone https://github.com/shimwell/cad-to-dagmc-to-openmc-example.git
 cd cad-to-dagmc-to-openmc-example
 ```
 
-# Making the DAGMC model.
+# Making the DAGMC model
 
 Make an environment for the model preparation
 ```
-conda create --name paramak_env python=3.9
-conda activate paramak_env
-conda install -c fusion-energy -c cadquery -c conda-forge paramak
-pip install jupyter_cadquery
+conda env create -f environment_cad.yml
+conda activate env_cad
 ```
 
 Then run the script for making the DAGMC model.
@@ -29,25 +43,20 @@ Then open the ```dagmc.html``` file in an internet browser to view the CAD creat
 
 ![CAD geometry image](https://user-images.githubusercontent.com/8583900/159698975-d82544c7-635b-4117-b4bc-4d61a8cf9ecc.png)
 
-
 Optionally you can inspect the DAGMC file at this stage by converting the h5m file to a vtk file and opening this with [Paraview](https://www.paraview.org/)
 ```
 mbconvert dagmc.h5m dagmc.vtk
 paraview dagmc.vtk
 ```
 ![DAGMC model image](https://user-images.githubusercontent.com/8583900/159698979-3665e14b-ca42-4df2-8a1e-deee6597efc0.png)
 
-
-
-# Simulating the model in OpenMC.
+# Simulating the model in OpenMC
 
 First make an environment for simulation.
 
 ```
-conda create --name openmc_dagmc_env python=3.9
-conda activate openmc_dagmc_env
-conda install -c conda-forge openmc
-pip install openmc_mesh_tally_to_vtk
+conda env create -f environment_neutronics.yml
+conda activate env_neutronics
 ```
 
 Then run the simulation which will produce a statepoint.10.h5 file that contains the simulation outputs
@@ -60,7 +69,7 @@ Then run the post processing script that should output the Tritium Breeding Rati
 python 3_extract_results.py
 ```
 
-Open up the VTK file with paraview
+Open up the VTK file with Paraview and slice the data to see the high tritium breeding region
 ```bash
 paraview tritium_production_map.vtk
 ```

conda_init_for_ci.sh

@@ -0,0 +1 @@
+conda init

environment_cad.yml

@@ -0,0 +1,13 @@
+
+
+name: env_cad
+channels:
+  - fusion-energy
+  - cadquery
+  - conda-forge
+dependencies:
+  - python=3.9
+  - paramak=0.7.2
+  - pip
+  - pip:
+    - jupyter-cadquery

environment_neutronics.yml

@@ -0,0 +1,12 @@
+
+
+name: env_neutronics
+channels:
+  - conda-forge
+dependencies:
+  - python=3.9
+  - openmc=0.13.0
+  - pip
+  - pip:
+    - openmc_data_downloader
+    - openmc_mesh_tally_to_vtk