Merge pull request #76 from fusion-energy/develop

using open source workflow for dagmc

.circleci/config.yml

@@ -21,12 +21,44 @@ jobs:
       - checkout
 
       - run:
-          name: run tests
-          no_output_timeout: 30m
-          command: |
-            cd ..
-            pytest repo/tests -v --cov=tasks/ --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
-      - store_test_results:
-          path: test-reports
-      - store_artifacts:
-          path: test-reports
+          name: test task 1
+          command: pytest tests/test_task_1.py -v
+      - run:
+          name: test task 2
+          command: pytest tests/test_task_2.py -v
+      - run:
+          name: test task 3
+          command: pytest tests/test_task_3.py -v
+      - run:
+          name: test task 4
+          command: pytest tests/test_task_4.py -v
+      - run:
+          name: test task 5
+          command: pytest tests/test_task_5.py -v
+      - run:
+          name: test task 6
+          command: pytest tests/test_task_6.py -v
+      - run:
+          name: test task 7
+          command: pytest tests/test_task_7.py -v
+      - run:
+          name: test task 8
+          command: pytest tests/test_task_8.py -v
+      - run:
+          name: test task 9
+          command: pytest tests/test_task_9.py -v
+      - run:
+          name: test task 10
+          command: pytest tests/test_task_10.py -v
+      - run:
+          name: test task 11
+          command: pytest tests/test_task_11.py -v
+      - run:
+          name: test task 12
+          command: pytest tests/test_task_12.py -v
+      - run:
+          name: test task 13
+          command: pytest tests/test_task_13.py -v
+      - run:
+          name: test task 14
+          command: pytest tests/test_task_14.py -v

.github/workflows/ci_tests.yml

@@ -23,6 +23,59 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v2
 
-      - name: run tests
+      - name: test task 1
         run: |
-          pytest tests -v --cov=tasks/ --cov-report term --cov-report xml --junitxml=test-reports/junit.xml
+          pytest tests/test_task_1.py -v
+
+      - name: test task 2
+        run: |
+          pytest tests/test_task_2.py -v
+
+      - name: test task 3
+        run: |
+          pytest tests/test_task_3.py -v
+
+      - name: test task 4
+        run: |
+          pytest tests/test_task_4.py -v
+
+      - name: test task 5
+        run: |
+          pytest tests/test_task_5.py -v
+
+      - name: test task 6
+        run: |
+          pytest tests/test_task_6.py -v
+
+      - name: test task 7
+        run: |
+          pytest tests/test_task_7.py -v
+
+      - name: test task 8
+        run: |
+          pytest tests/test_task_8.py -v
+
+      - name: test task 9
+        run: |
+          pytest tests/test_task_9.py -v
+
+      - name: test task 10
+        run: |
+          pytest tests/test_task_10.py -v
+
+      - name: test task 11
+        run: |
+          pytest tests/test_task_11.py -v
+
+      - name: test task 12
+        run: |
+          pytest tests/test_task_12.py -v
+
+      - name: test task 13
+        run: |
+          pytest tests/test_task_13.py -v
+
+      - name: test task 14
+        run: |
+          pytest tests/test_task_14.py -v
+

.gitignore

@@ -1,20 +1,21 @@
-
+# openmc files
 *.xml
-
 tallies.out
-
 *.h5
 
+# DAGMC files
 *.h5m
 
+# Cubit files
 *.trelis
-
 *.jou
-
+*.log
 *.cub
 
+# Python library files
 *.so
 
+# Paraview files
 *.vtk
 *.vtp
 *.pvtp
@@ -26,8 +27,9 @@ __pycache__/
 
 .ipynb_checkpoints/
 
+# CAD files
+*.brep
 *.stl
 *.stp
 *.svg
-*.log
 *.png

Dockerfile

@@ -29,6 +29,8 @@
 
 # for local testing I tend to use this build command
 # docker build -t neutronics-workshop --build-arg compile_cores=14 --build-arg build_double_down=ON .
+# and then run with this command
+# docker run -p 8888:8888 neutronics-workshop
 
 # This can't be done currently as the base images uses conda installs for moab / dagmc which don't compile with OpenMC
 FROM ghcr.io/openmc-data-storage/miniconda3_4.9.2_endfb-7.1_nndc_tendl_2019:latest as dependencies
@@ -58,8 +60,6 @@ RUN apt-get --yes install libeigen3-dev \
                           hdf5-tools \
                           imagemagick \
                           cmake \
-                          # libeigen3-dev required for DAGMC
-                          libeigen3-dev \
                           # libnetcdf-dev is needed to allow NETCDF on MOAB which helps with tet meshes in OpenMC
                           libnetcdf-dev \
                           # libtbb-dev required for DAGMC
@@ -87,9 +87,14 @@ RUN apt-get --yes install libeigen3-dev \
 # installing cadquery and jupyter
 RUN conda install jupyter -y && \
     conda install -c conda-forge -c python python=3.8 && \
-    conda install -c conda-forge -c cadquery cadquery=2.1
+    # conda install -c conda-forge -c cadquery cadquery=2.2
+    # commented out until next CQ release
+    conda install -c conda-forge -c cadquery cadquery=master
 # cadquery master dose not appear to show the .solid in the notebook
 
+# Installing Gmsh
+RUN conda install -c conda-forge gmsh
+RUN apt-get install libxft2 
 
 # Python libraries used in the workshop
 RUN pip install cmake\
@@ -148,7 +153,7 @@ RUN if [ "$build_double_down" = "ON" ] ; \
 # Clone and install MOAB
 RUN mkdir MOAB && \
     cd MOAB && \
-    git clone  --single-branch --branch 5.3.0 --depth 1 https://bitbucket.org/fathomteam/moab.git && \
+    git clone  --single-branch --branch 5.3.1 --depth 1 https://bitbucket.org/fathomteam/moab.git && \
     mkdir build && \
     cd build && \
     cmake ../moab -DENABLE_HDF5=ON \
@@ -184,8 +189,8 @@ RUN if [ "$build_double_down" = "ON" ] ; \
         mkdir build ; \
         cd build ; \
         cmake .. -DMOAB_DIR=/MOAB \
-                -DCMAKE_INSTALL_PREFIX=.. \
-                -DEMBREE_DIR=/embree ; \
+                 -DCMAKE_INSTALL_PREFIX=.. \
+                 -DEMBREE_DIR=/embree ; \
         make -j"$compile_cores" ; \
         make -j"$compile_cores" install ; \
         rm -rf /double-down/build /double-down/double-down ; \
@@ -195,12 +200,7 @@ RUN if [ "$build_double_down" = "ON" ] ; \
 # DAGMC version develop install from source
 RUN mkdir DAGMC && \
     cd DAGMC && \
-    git clone --single-branch --branch develop https://github.com/svalinn/DAGMC.git && \
-    # git clone --single-branch --branch develop --depth 1 https://github.com/svalinn/DAGMC.git && \
-    cd DAGMC && \
-    # this commit is from this PR https://github.com/svalinn/DAGMC/pull/786
-    git checkout fbd0cdbad100a0fd8d80de42321e69d09fdd67f4 && \
-    cd .. && \
+    git clone --single-branch --branch v3.2.1 --depth 1 https://github.com/svalinn/DAGMC.git && \
     mkdir build && \
     cd build && \
     cmake ../DAGMC -DBUILD_TALLY=ON \
@@ -224,18 +224,14 @@ RUN wget https://github.com/mit-crpg/WMP_Library/releases/download/v1.1/WMP_Libr
 
 # installs OpenMc from source
 RUN cd /opt && \
-    # git clone --single-branch --branch model_lib_fix --depth 1 https://github.com/fusion-energy/openmc.git && \
-    git clone --single-branch --branch develop https://github.com/openmc-dev/openmc.git && \
-    # git clone --single-branch --branch v0.12.1 --depth 1 https://github.com/openmc-dev/openmc.git && \
+    git clone --single-branch --branch v0.13.0 --depth 1 https://github.com/openmc-dev/openmc.git && \
     cd openmc && \
-    # this commit is from this PR https://github.com/openmc-dev/openmc/pull/1900
-    git checkout 0157dc219ff8dca814859b3140c6cef1e78cdee1 && \
     mkdir build && \
     cd build && \
     cmake -Doptimize=on \
           -Ddagmc=ON \
           -DDAGMC_ROOT=/DAGMC \
-          -DHDF5_PREFER_PARALLEL=off ..  && \
+          -DHDF5_PREFER_PARALLEL=off .. && \
     make -j"$compile_cores" && \
     make -j"$compile_cores" install && \
     cd /opt/openmc/ && \
@@ -251,20 +247,20 @@ ENV OPENMC_CROSS_SECTIONS=/nuclear_data/cross_sections.xml
 
 
 # python packages from the neutronics workflow
-RUN pip install neutronics_material_maker \
+RUN pip install neutronics_material_maker[density] \
                 openmc-plasma-source \
                 remove_dagmc_tags \
-                paramak \
-                cad_to_h5m \
-                stl_to_h5m \
                 openmc-dagmc-wrapper \
                 openmc-tally-unit-converter \
                 regular_mesh_plotter \
                 spectrum_plotter \
                 openmc_source_plotter \
-                dagmc_bounding_box \
                 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
+
+
 # an older version of openmc is need to provide an older executable
 # this particular exectuable allows an inital_source.h5 to be written
 # a specific openmc executable can be called using model.run(openmc_exec=path)

README.md

@@ -19,7 +19,6 @@ some motivation for learning neutronics.
 
 <p align="center"><a href="https://youtu.be/HH-poTG-FxM" target="_blank"><img src="https://user-images.githubusercontent.com/8583900/144746742-3e31e0ee-6380-4db7-b8ea-0b1c302d497b.png" height="400" /></a></p>
 
-
 :point_right: [Try the workshop in your browser](https://neutronics-workshop-4zf6u4tg6a-lz.a.run.app/)
 
 # History
@@ -38,8 +37,6 @@ also welcome as pull requests to the develop branch.
 The resource has proven most useful as it is one of the few open source and
 accessible fusion neutronics training resources.
 
-
-
 ## Installation
 
 There are video tutorials for this section which accompany the step by step
@@ -54,7 +51,6 @@ instructions below.
 [Windows](https://hub.docker.com/editions/community/docker-ce-desktop-windows),
 including the part where you enable docker use as a non-root user. 
 
-
 2. Pull the docker image from the store by typing the following command in a
 terminal window, or Windows users might prefer PowerShell.
 
@@ -128,5 +124,7 @@ map which is great for working through the workshop with colleagues.
 | [Task 10 - Making CAD geometry](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_10_making_CAD_geometry) | Parametric CAD geometry, Paramak, Geometry visualisation | [link](https://www.youtube.com/watch?v=Bn_TcJSOvaA) |
 | [Task 11 - CAD Cell tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_11_CAD_cell_tally_heat) | CAD-based neutronics, Cell tallies, DAGMC, Heating |  |
 | [Task 12 - CAD Mesh tallies](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_12_CAD_mesh_fast_flux) | CAD-based neutronics, Mesh tallies, Paramak, DAGMC, Fast flux |  |
-| [Task 13 - Techniques for sampling parameter space](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_13_parameter_study_sampling) | Sampling, Interpolation, Multi-dimensional parameter studies |  |
-| [Task 14 - Parameter study optimisation](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_14_parameter_study_optimisation) | Data science machine learning approaches |  |
+| [Task 13 - Variance_reduction](https://github.com/fusion-energy/neutronics-workshop/tree/develop/tasks/task_13_variance_reduction) | Variance reduction, weight windows |  |
+| [Task 14 - Activation transmutation](https://github.com/fusion-energy/neutronics-workshop/tree/develop/tasks/task_14_activation_transmutation) | Isotope build up and tally variation as a function of time |  |
+| [Task 15 - Techniques for sampling parameter space](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_15_parameter_study_sampling) | Sampling, Interpolation, Multi-dimensional parameter studies |  |
+| [Task 16 - Parameter study optimisation](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_16_parameter_study_optimisation) | Data science machine learning approaches |  |