diff --git a/.circleci/config.yml b/.circleci/config.yml index 054aeb46..d088a560 100644 --- a/.circleci/config.yml +++ b/.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 diff --git a/.github/workflows/ci_tests.yml b/.github/workflows/ci_tests.yml index 0c41d62a..dd69b5c9 100644 --- a/.github/workflows/ci_tests.yml +++ b/.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 + diff --git a/.gitignore b/.gitignore index 8e76279a..87f40abe 100644 --- a/.gitignore +++ b/.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 \ No newline at end of file diff --git a/Dockerfile b/Dockerfile index f7a48f01..cc59f3ea 100644 --- a/Dockerfile +++ b/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) diff --git a/README.md b/README.md index d6190f4b..17c1f45e 100644 --- a/README.md +++ b/README.md @@ -19,7 +19,6 @@ some motivation for learning neutronics.

- :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 | | diff --git a/install_scripts/build_embree.sh b/install_scripts/build_embree.sh deleted file mode 100755 index 0753924c..00000000 --- a/install_scripts/build_embree.sh +++ /dev/null @@ -1,108 +0,0 @@ -#!/bin/bash -set -eu - -function build_embree() { - if [ -d $PWD/embree ] ; then - echo "Embree installed" - return - fi - - # make embree - git clone https://github.com/embree/embree - cd embree - echo "EMBREE being installed in "$EMBREE_DIR - mkdir bld - cd bld - cmake .. -DCMAKE_INSTALL_PREFIX=.. -DEMBREE_ISPC_SUPPORT=OFF - make -j4 - make install - cd .. - cd .. -} - -function build_double() { - if [ -d $PWD/double-down ] ; then - echo "double down already installed" - return - fi - echo $EMBREE_DIR - # make double down - git clone https://github.com/pshriwise/double-down - cd double-down - export DD_DIR=$PWD - mkdir bld - cd bld - cmake .. -DCMAKE_INSTALL_PREFIX=.. -DMOAB_DIR=$MOAB_DIR -DEMBREE_DIR=$EMBREE_DIR -DEMBREE_ROOT=$EMBREE_DIR - make -j4 - make install - cd .. - cd .. -} - -function build_dagmc() { - if [ -d $PWD/dagmc ] ; then - echo "dagmc already built" - return - fi - # make dagmc - git clone https://github.com/svalinn/dagmc - cd dagmc - mkdir bld - cd bld - cmake .. -DMOAB_DIR=$MOAB_DIR -DBUILD_STATIC_LIBS=OFF -DDOUBLE_DOWN=ON -DDOUBLE_DOWN_DIR=$DD_DIR -DCMAKE_INSTALL_PREFIX=.. - make -j4 - make install - cd .. - cd .. -} - -function build_openmc() { - if [ -d $PWD/openmc ] ; then - echo "openmc already built" - return - fi - # make dagmc - git clone https://github.com/openmc-dev/openmc - cd openmc - mkdir bld - cd bld - cmake .. -Ddagmc=ON -DDAGMC_DIR=$DAGMC_DIR -DCMAKE_INSTALL_PREFIX=$OPENMC_INSTALL_DIR - make -j4 - make install - cd .. - cd .. -} - -# need to know where MOAB is -if [ -z $MOAB_DIR ] ; then - echo "Must set MOAB_DIR outside the script" - echo "i.e. export MOAB_DIR=/path/to/moab" - exit 1 -fi - -# need to know where to install openmc is -if [ -z $OPENMC_INSTALL_DIR ] ; then - echo "Must set OPENMC_INSTALL_DIR outside the script" - echo "i.e. export MOAB_DIR=/path/to/moab" - echo " or OPENMC_DIR=/path/to/thing/" - exit 1 -fi - -export DAGMC_DIR=$PWD/dagmc/lib/cmake -export EMBREE_DIR=$PWD/embree/lib/cmake/embree-3.12.1 -export DD_DIR=$PWD/double-down/lib/cmake - -sudo apt-get install cmake-curses-gui -sudo apt-get install libtbb-dev -sudo apt-get install libglfw3-dev -sudo apt-get install libeigen3-dev - -build_embree -build_double -build_dagmc -build_openmc - -# all done -echo "all done" - - diff --git a/install_scripts/install_miniconda_cadquery_openmc_dagmc_trelis_plugin.sh b/install_scripts/install_miniconda_cadquery_openmc_dagmc_trelis_plugin.sh deleted file mode 100644 index b33667dc..00000000 --- a/install_scripts/install_miniconda_cadquery_openmc_dagmc_trelis_plugin.sh +++ /dev/null @@ -1,190 +0,0 @@ - -sudo apt-get --yes update && sudo apt-get --yes upgrade -sudo apt-get update - -sudo apt-get install --yes wget - -# Miniconda - -# wget https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.3-Linux-x86_64.sh -# bash Miniconda3-py37_4.8.3-Linux-x86_64.sh -# conda init -# conda create -y --name cq -# conda activate cq -# conda clean --all -# conda install -c conda-forge -c python python=3.7.8 -# conda clean --all -# conda install -c conda-forge -c cadquery cadquery=2 - - -sudo apt-get --yes update && sudo apt-get --yes upgrade -sudo apt-get update - - -sudo apt-get --yes install gfortran -sudo apt-get --yes install g++ -sudo apt-get --yes install cmake -sudo apt-get --yes install libhdf5-dev - -sudo apt-get install -y python3 -sudo apt-get install -y python3-pip -sudo apt-get install -y python3-dev -sudo apt-get install -y python3-tk - -sudo apt-get install --yes imagemagick -sudo apt-get install --yes hdf5-tools -sudo apt-get install --yes paraview -sudo apt-get install --yes eog -sudo apt-get install --yes libsilo-dev -sudo apt-get install --yes git - -sudo apt-get --yes install dpkg -sudo apt-get --yes install libxkbfile1 -sudo apt-get --yes install -f -sudo apt-get --yes install libblas-dev -sudo apt-get --yes install liblapack-dev - -sudo apt-get install libeigen3-dev - -sudo apt-get --yes install libnetcdf-dev -sudo apt-get --yes install libnetcdf13 - -sudo apt remove -y cmake -pip3 install cmake -# need cmake version 3.18.2 - -pip3 install numpy pandas six h5py Matplotlib uncertainties lxml scipy cython vtk pytest -pip3 install codecov pytest-cov pylint plotly tqdm pyside2 ghalton==0.6.1 - -pip3 install neutronics_material_maker - -cd ~ -git clone https://github.com/njoy/NJOY2016 -cd NJOY2016 -mkdir build -cd build -cmake -Dstatic=on .. && make 2>/dev/null -sudo make install - -MOAB_INSTALL_DIR=$HOME/MOAB -DAGMC_INSTALL_DIR=$HOME/DAGMC -set -ex - -echo 'export MOAB_INSTALL_DIR=$HOME/MOAB' >> ~/.bashrc -echo 'export DAGMC_INSTALL_DIR=$HOME/DAGMC' >> ~/.bashrc -echo 'export LD_LIBRARY_PATH=$MOAB_INSTALL_DIR/lib:$LD_LIBRARY_PATH' >> ~/.bashrc -echo 'export LD_LIBRARY_PATH=$DAGMC_INSTALL_DIR/lib:$LD_LIBRARY_PATH' >> ~/.bashrc - -pip3 install cython - -cd ~ -mkdir MOAB -cd MOAB -git clone -b Version5.1.0 https://bitbucket.org/fathomteam/moab/ -mkdir build -cd build -# this installs without netcdf but with pymoab -#cmake ../moab -DENABLE_HDF5=ON -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=$MOAB_INSTALL_DIR -DENABLE_PYMOAB=ON -# this installs with netcdf but without pymoab -cmake ../moab -DENABLE_HDF5=ON -DENABLE_MPI=off -DENABLE_NETCDF=ON -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=$MOAB_INSTALL_DIR -make -j2 -make -j install -# this 2nd build is required which is a shame -# this is to be used if you want pymoab -# cmake ../moab -DBUILD_SHARED_LIBS=OFF -# otherwise if you want netcdf -cmake ../moab -DBUILD_SHARED_LIBS=OFF -make -j install - -LD_LIBRARY_PATH=$MOAB_INSTALL_DIR/lib:$LD_LIBRARY_PATH -echo 'export PATH=$PATH:~/MOAB/bin' >> ~/.bashrc - -cd ~ -mkdir DAGMC -cd DAGMC -git clone -b develop https://github.com/svalinn/dagmc -mkdir build -cd build -cmake ../dagmc -DBUILD_TALLY=ON -DCMAKE_INSTALL_PREFIX=$DAGMC_INSTALL_DIR -DMOAB_DIR=$MOAB_INSTALL_DIR -make -j install -LD_LIBRARY_PATH=$DAGMC_INSTALL_DIR/lib:$LD_LIBRARY_PATH -echo 'export PATH=$PATH:~/DAGMC/bin' >> ~/.bashrc - -# OpenMC Install, this must be installed to /opt/openmc, `parametric_plasma_source` python module has this path hard-coded -cd /opt -sudo git clone --recurse-submodules https://github.com/openmc-dev/openmc.git -cd /opt/openmc -sudo chmod 777 -R openmc -sudo git checkout develop -sudo mkdir build -sudo chmod 777 build -cd build -cmake -Ddagmc=ON -DDAGMC_ROOT=$DAGMC_INSTALL_DIR .. -# cmake -Ddagmc=ON -Ddebug=on -DDAGMC_ROOT=$DAGMC_INSTALL_DIR .. -sudo make -j2 -sudo make -j install -cd /opt -sudo chmod 777 -R openmc -cd /opt/openmc/ -pip install -e . - -cd ~ -git clone https://github.com/openmc-dev/data.git -cd data -python3 convert_fendl.py -python3 convert_tendl.py -python3 convert_nndc71.py - -OPENMC_CROSS_SECTIONS_NNDC=~/data/nndc-b7.1-hdf5/cross_sections.xml -echo 'export OPENMC_CROSS_SECTIONS_NNDC=~/data/nndc-b7.1-hdf5/cross_sections.xml' >> ~/.bashrc -OPENMC_CROSS_SECTIONS_TENDL=~/data/tendl-2017-hdf5/cross_sections.xml -echo 'export OPENMC_CROSS_SECTIONS_TENDL=~/data/tendl-2019-hdf5/cross_sections.xml' >> ~/.bashrc -OPENMC_CROSS_SECTIONS_FENDL=~/data/fendl-3.1d-hdf5/cross_sections.xml -echo 'export OPENMC_CROSS_SECTIONS_FENDL=~/data/fendl-3.1d-hdf5/cross_sections.xml' >> ~/.bashrc - - -# OPENMC_CROSS_SECTION library - -# Single cross-section library - -# change filepaths to desired library cross_sections.xml file -OPENMC_CROSS_SECTIONS=~/data/nndc-b7.1-hdf5/cross_sections.xml -echo 'export OPENMC_CROSS_SECTIONS=~/data/nndc-b7.1-hdf5/cross_sections.xml' >> ~/.bashrc - -# Combined cross-section library - -# cd ~/data -# python3 combine_libraries.py -l fendl-3.1d-hdf5/cross_sections.xml nndc-b7.1-hdf5/cross_sections.xml tendl-2019-hdf5/cross_sections.xml -o combined_cross_sections.xml -# OPENMC_CROSS_SECTIONS=~/data/combined_cross_sections.xml -# echo 'export OPENMC_CROSS_SECTIONS=~/data/combined_cross_sections.xml' >> ~/.bashrc - - -# Trelis - -# Download Trelis-16.5.4-Lin64.deb -# Add Trelis-16.5.4-Lin64.deb to /opt folder - -# cd /opt -# sudo dpkg -i Trelis-16.5.4-Lin64.deb - - -# Trelis-DAGMC Plugin - -cd ~ -sudo apt-get install openfortivpn -sudo apt install curl - -# Download svalinn-plugin-16.5-u18.04.tgz from https://uwmadison.app.box.com/v/dagmc-trelis -# Add svalinn-plugin-16.5-u18.04.tgz to /opt/Trelis-16.5/bin/plugins - -cd /opt/Trelis-16.5/bin/plugins -sudo tar xzf svalinn-plugin-16.5-u18.04.tgz - -cd /opt/Trelis-16.5/bin -sudo bash plugins/svalinn/install.sh - -PATH=$PATH:/opt/Trelis-16.5/bin -echo 'export PATH=$PATH:/opt/Trelis-16.5/bin' >> ~/.bashrc - -LD_LIBRARY_PATH=/opt/Trelis-16.5/bin/plugins/svalinn:$LD_LIBRARY_PATH -echo 'export LD_LIBRARY_PATH=/opt/Trelis-16.5/bin/plugins/svalinn:$LD_LIBRARY_PATH' >> ~/.bashrc \ No newline at end of file diff --git a/install_scripts/install_openmc_embree_double_down.sh b/install_scripts/install_openmc_embree_double_down.sh deleted file mode 100644 index b2150bf2..00000000 --- a/install_scripts/install_openmc_embree_double_down.sh +++ /dev/null @@ -1,177 +0,0 @@ - -sudo apt-get --yes update && sudo apt-get --yes upgrade -sudo apt-get update - -# Install dependencies from Debian package manager -sudo apt-get install --yes wget \ - git \ - gfortran \ - g++ \ - cmake \ - mpich \ - libmpich-dev \ - libhdf5-serial-dev \ - libhdf5-mpich-dev \ - imagemagick \ - autoremove \ - clean - -# Miniconda -wget https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.3-Linux-x86_64.sh -bash Miniconda3-py37_4.8.3-Linux-x86_64.sh -conda init -conda create -y --name cq -conda activate cq -conda clean --all -conda install -c conda-forge -c cadquery cadquery=master -conda install gxx_linux-64 - -# required pacakges identified from openmc travis.yml -sudo apt-get --yes install mpich \ - libmpich-dev \ - libhdf5-serial-dev \ - libhdf5-mpich-dev \ - libblas-dev \ - liblapack-dev \ - imagemagick - -# needed to allow NETCDF on MOAB which helps with tet meshes in OpenMC -sudo apt-get --yes install libnetcdf-dev - -# eigen3 needed for DAGMC -sudo apt-get --yes install libeigen3-dev - -# dependancies used in the workshop -sudo apt-get -y install git -sudo apt-get --yes install hdf5-tools - -# new version needed for openmc compile -pip install cmake - - -# Python libraries used in the workshop -pip install plotly tqdm ghalton==0.6.1 noisyopt scikit-optimize \ - inference-tools adaptive vtk itkwidgets nest_asyncio \ - neutronics_material_maker parametric-plasma-source pytest \ - pytest-cov - -# needed for moab -pip install cython - -# needed for openmc -pip install --upgrade numpy - - -# install addition packages required for DAGMC -sudo apt-get --yes install libeigen3-dev \ - libblas-dev \ - liblapack-dev \ - libnetcdf-dev \ - libtbb-dev \ - libglfw3-dev - -# needed for CadQuery functionality -sudo apt-get install -y libgl1-mesa-glx libgl1-mesa-dev libglu1-mesa-dev \ - freeglut3-dev libosmesa6 libosmesa6-dev \ - libgles2-mesa-dev - - -export compile_cores=2 - -# Clone and install Embree -git clone --single-branch --branch master https://github.com/embree/embree -cd embree -mkdir build -cd build -cmake .. -DCMAKE_INSTALL_PREFIX=.. \ - -DEMBREE_ISPC_SUPPORT=OFF -make -j"$compile_cores" -make -j"$compile_cores" install - - -cd ~ -mkdir MOAB -cd MOAB -git clone --single-branch --branch develop https://bitbucket.org/fathomteam/moab/ -mkdir build -cd build -# this installs without netcdf but with pymoab -#cmake ../moab -DENABLE_HDF5=ON -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=$MOAB_INSTALL_DIR -DENABLE_PYMOAB=ON -cmake ../moab -DENABLE_HDF5=ON \ - -DENABLE_NETCDF=ON \ - -DBUILD_SHARED_LIBS=OFF \ - -DENABLE_FORTRAN=OFF \ - -DCMAKE_INSTALL_PREFIX=$HOME/MOAB -make -j"$compile_cores" -make -j"$compile_cores" install -# this 2nd build is required and includes pymoab -cmake ../moab -DBUILD_SHARED_LIBS=ON \ - -DENABLE_HDF5=ON \ - -DENABLE_PYMOAB=ON \ - -DENABLE_BLASLAPACK=OFF \ - -DENABLE_FORTRAN=OFF \ - -DCMAKE_INSTALL_PREFIX=$HOME/MOAB -make -j"$compile_cores" -make -j"$compile_cores" install -cd pymoab -bash install.sh -python setup.py install - -# Clone and install Double-Down -cd ~ -git clone https://github.com/pshriwise/double-down -cd double-down -mkdir build -cd build -cmake .. -DCMAKE_INSTALL_PREFIX=.. \ - -DMOAB_DIR=$HOME/MOAB \ - -DEMBREE_DIR=$HOME/embree/lib/cmake/embree-3.12.1 -make -j"$compile_cores" -make -j"$compile_cores" install - -# DAGMC install -cd ~ -mkdir DAGMC -cd DAGMC -git clone --single-branch --branch develop https://github.com/svalinn/dagmc -mkdir build -cd build -cmake ../dagmc -DBUILD_TALLY=ON \ - -DCMAKE_INSTALL_PREFIX=$HOME/DAGMC \ - -DMOAB_DIR=$HOME/MOAB # this might need changing to /home/username/MOAB -make -j"$compile_cores" install - -export DAGMC_INSTALL_DIR=$HOME/DAGMC -export LD_LIBRARY_PATH=$DAGMC_INSTALL_DIR/lib:$LD_LIBRARY_PATH -export LD_LIBRARY_PATH=/opt/Trelis-16.5/bin/plugins/svalinn:$LD_LIBRARY_PATH - -# installs OpenMc from source -cd /opt -git clone --single-branch --branch develop https://github.com/openmc-dev/openmc.git -sudo chmod -R 777 openmc -cd openmc -mkdir build -cd build -cmake -Ddagmc=ON \ - -DDAGMC_DIR=$HOME/DAGMC/build \ - -DHDF5_PREFER_PARALLEL=OFF .. -make -j"$compile_cores" -sudo make -j"$compile_cores" install -cd /opt/openmc/ -pip install . - -# Clone and install NJOY2016 -cd ~ -git clone https://github.com/njoy/NJOY2016 --branch master --single-branch -cd NJOY2016 -mkdir build -cd build -cmake -Dstatic=on .. -make 2>/dev/null -sudo make install - -# clone and download nuclear data -git clone --single-branch --branch master https://github.com/openmc-dev/data.git -python3 data/convert_nndc71.py -python3 data/convert_tendl.py -python3 data/data/combine_libraries.py -l data/nndc-b7.1-hdf5/cross_sections.xml data/tendl-2019-hdf5/cross_sections.xml -o data/cross_sections.xml diff --git a/install_scripts/install_openmc_ubuntu_18.04.sh b/install_scripts/install_openmc_ubuntu_18.04.sh deleted file mode 100644 index 0c79f548..00000000 --- a/install_scripts/install_openmc_ubuntu_18.04.sh +++ /dev/null @@ -1,194 +0,0 @@ - -sudo apt-get --yes update && sudo apt-get --yes upgrade -sudo apt-get update - -sudo apt-get --yes install gfortran -sudo apt-get --yes install g++ -sudo apt-get --yes install cmake -sudo apt-get --yes install libhdf5-dev - -sudo apt-get install -y python3 -sudo apt-get install -y python3-pip -sudo apt-get install -y python3-dev -sudo apt-get install -y python3-tk - -sudo apt-get install --yes imagemagick -sudo apt-get install --yes hdf5-tools -sudo apt-get install --yes paraview -sudo apt-get install --yes eog -sudo apt-get install --yes wget -sudo apt-get install --yes libsilo-dev -sudo apt-get install --yes git - -sudo apt-get --yes install dpkg -sudo apt-get --yes install libxkbfile1 -sudo apt-get --yes install -f -sudo apt-get --yes install libblas-dev -sudo apt-get --yes install liblapack-dev - -# needed to allow NETCDF on MOAB which helps with tet meshes in OpenMC -sudo apt-get --yes install libnetcdf-dev -sudo apt-get --yes install libnetcdf13 - -# needed for newest version of openmc with dagmc -sudo apt remove -y cmake -pip3 install cmake==3.12.0 - -pip3 install numpy --user -pip3 install pandas --user -pip3 install six --user -pip3 install h5py --user -pip3 install Matplotlib --user -pip3 install uncertainties --user -pip3 install lxml --user -pip3 install scipy --user -pip3 install cython --user -pip3 install vtk --user -pip3 install pytest --user -pip3 install codecov --user -pip3 install pytest-cov --user -pip3 install pylint --user -pip3 install plotly --user -pip3 install tqdm --user -pip3 install pyside2 --user # required by openmc plotter -pip3 install ghalton==0.6.1 - -# needed for workshop tasks -pip3 install neutronics_material_maker --user - -# Clone and install NJOY2016 -cd ~ -git clone https://github.com/njoy/NJOY2016 #/opt/NJOY2016 -cd NJOY2016 -mkdir build -cd build -cmake -Dstatic=on .. && make 2>/dev/null -sudo make install - - -sudo rm /usr/bin/python -sudo ln -s /usr/bin/python3 /usr/bin/python - -# MOAB Variables -MOAB_INSTALL_DIR=$HOME/MOAB - -# DAGMC Variables -DAGMC_INSTALL_DIR=$HOME/DAGMC -set -ex - -echo 'export MOAB_INSTALL_DIR=$HOME/MOAB' >> ~/.bashrc -echo 'export DAGMC_INSTALL_DIR=$HOME/DAGMC' >> ~/.bashrc -echo 'export LD_LIBRARY_PATH=$MOAB_INSTALL_DIR/lib:$LD_LIBRARY_PATH' >> ~/.bashrc -echo 'export LD_LIBRARY_PATH=$DAGMC_INSTALL_DIR/lib:$LD_LIBRARY_PATH' >> ~/.bashrc -# echo '$PATH:/openmc/build/bin/' >> ~/.bashrc - -pip install cython - -# MOAB Install -cd ~ -mkdir MOAB -cd MOAB -git clone -b Version5.1.0 https://bitbucket.org/fathomteam/moab/ -mkdir build -cd build -# this installs without netcdf but with pymoab -#cmake ../moab -DENABLE_HDF5=ON -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=$MOAB_INSTALL_DIR -DENABLE_PYMOAB=ON -# this installs with netcdf but without pymoab -cmake ../moab -DENABLE_HDF5=ON -DENABLE_MPI=off -DENABLE_NETCDF=ON -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=$MOAB_INSTALL_DIR -make -j -make -j install -# this 2nd build is required which is a shame -# this is to be used if you want pymoab -# cmake ../moab -DBUILD_SHARED_LIBS=OFF -# otherwise if you want netcdf -cmake ../moab -DBUILD_SHARED_LIBS=OFF -make -j install - -# if you installed pymoab run these two commands as well -# cd pymoab -# python3 setup.py install --user - -#needs setting in bashrc -LD_LIBRARY_PATH=$MOAB_INSTALL_DIR/lib:$LD_LIBRARY_PATH -echo 'export PATH=$PATH:~/MOAB/bin' >> ~/.bashrc - - -# DAGMC Install -cd ~ -mkdir DAGMC -cd DAGMC -git clone -b develop https://github.com/svalinn/dagmc -mkdir build -cd build -# cmake ../dagmc -DBUILD_TALLY=ON -DCMAKE_INSTALL_PREFIX=$DAGMC_INSTALL_DIR -DMOAB_DIR=$MOAB_INSTALL_DIR -DBUILD_SHARED_LIBS=OFF -DBUILD_STATIC_EXE=ON -# cmake ../dagmc -DBUILD_TALLY=ON -DCMAKE_INSTALL_PREFIX=$DAGMC_INSTALL_DIR -DMOAB_DIR=$MOAB_INSTALL_DIR -DBUILD_STATIC_LIBS=OFF -cmake ../dagmc -DBUILD_TALLY=ON -DCMAKE_INSTALL_PREFIX=$DAGMC_INSTALL_DIR -DMOAB_DIR=$MOAB_INSTALL_DIR -make -j install -# rm -rf $HOME/DAGMC/dagmc -#needs setting in bashrc -LD_LIBRARY_PATH=$DAGMC_INSTALL_DIR/lib:$LD_LIBRARY_PATH -echo 'export PATH=$PATH:~/DAGMC/bin' >> ~/.bashrc - - -# OpenMC Install -cd /opt -sudo git clone https://github.com/mit-crpg/openmc.git --recursive -cd /opt/openmc -sudo git checkout develop -sudo mkdir build -sudo chmod 777 build -cd build -cmake -Doptimize=on -Ddagmc=ON -DDAGMC_ROOT=$DAGMC_INSTALL_DIR .. -# cmake -Ddagmc=ON -Ddebug=on -DDAGMC_ROOT=$DAGMC_INSTALL_DIR .. -sudo make -sudo make install -cd /opt/openmc/ -sudo python3 setup.py develop --user - - -# Nuclear data install -cd ~ -git clone https://github.com/openmc-dev/data.git -cd data -python3 convert_fendl.py -python3 convert_tendl.py -python3 convert_nndc71.py - - -OPENMC_CROSS_SECTIONS_NNDC=~/data/nndc-b7.1-hdf5/cross_sections.xml -echo 'export OPENMC_CROSS_SECTIONS_NNDC=~/data/nndc-b7.1-hdf5/cross_sections.xml' >> ~/.bashrc -OPENMC_CROSS_SECTIONS_TENDL=~/data/tendl-2017-hdf5/cross_sections.xml -echo 'export OPENMC_CROSS_SECTIONS_TENDL=~/data/tendl-2019-hdf5/cross_sections.xml' >> ~/.bashrc -OPENMC_CROSS_SECTIONS_FENDL=~/data/fendl-3.1d-hdf5/cross_sections.xml -echo 'export OPENMC_CROSS_SECTIONS_FENDL=~/data/fendl-3.1d-hdf5/cross_sections.xml' >> ~/.bashrc - -OPENMC_CROSS_SECTIONS=~/data/tendl-2017-hdf5/cross_sections.xml -echo 'export OPENMC_CROSS_SECTIONS=~/data/tendl-2019-hdf5/cross_sections.xml' >> ~/.bashrc - - - -RUN git clone https://github.com/openmc-dev/plotter.git -echo 'export PATH=$PATH:/plotter/' >> ~/.bashrc - - - - -# dependancies for the occ_faceter -sudo apt-get --yes update && apt-get --yes upgrade -sudo apt-get --yes install libcgal-dev -sudo apt-get --yes install software-properties-common -sudo add-apt-repository -y ppa:freecad-maintainers/freecad-stable -sudo apt-get --yes install libocc*dev -sudo apt-get --yes install occ* -sudo apt-get --yes install libtbb-dev - -# install the occ_faceter, this currently uses a branch that could be merged -cd ~ -git clone https://github.com/makeclean/occ_faceter.git -cd occ_faceter -mkdir build && cd build -cmake .. -DCMAKE_INSTALL_PREFIX=.. -make -make install -sudo cp /occ_faceter/bin/steps2h5m /bin -sudo cp /occ_faceter/bin/occ_faceter /bin diff --git a/install_scripts/install_openmc_ubuntu_20.04.sh b/install_scripts/install_openmc_ubuntu_20.04.sh new file mode 100644 index 00000000..7a51e14a --- /dev/null +++ b/install_scripts/install_openmc_ubuntu_20.04.sh @@ -0,0 +1,118 @@ + +# install openmc with dagmc embree and double down into a new conda enviroment +# packages are compiled in this install script using all available CPU cores. +# to reduce the core usage to 2 replace -j commands with -j2 + + +sudo apt-get --yes update +apt-get --yes upgrade + + +# install dependancies +sudo apt-get install libeigen3-dev +sudo apt-get install git +sudo apt-get install wget +sudo apt-get install gfortran +sudo apt-get install g++ +sudo apt-get install mpich +sudo apt-get install libmpich-dev +sudo apt-get install libhdf5-serial-dev +sudo apt-get install libhdf5-mpich-dev +sudo apt-get install hdf5-tools +sudo apt-get install imagemagick +sudo apt-get install cmake +sudo apt-get install libeigen3-dev +sudo apt-get install libnetcdf-dev +sudo apt-get install libtbb-dev +sudo apt-get install libgles2-mesa-dev + +# install conda, creates new python enviroment and activates it +cd ~ +wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh +bash Miniconda3-latest-Linux-x86_64.sh +conda create --name openmc-dagmc python=3.8 +conda activate openmc-dagmc + +# install python dependancies +conda install numpy +conda install cython + +# installs embree +cd ~ +git clone --shallow-submodules --single-branch --branch v3.12.2 --depth 1 https://github.com/embree/embree.git +cd embree +mkdir build +cd build +cmake .. -DCMAKE_INSTALL_PREFIX=.. -DEMBREE_ISPC_SUPPORT=OFF +make -j +make -j install + +# install moab +cd ~ +mkdir MOAB +cd MOAB +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 -DENABLE_NETCDF=ON -DENABLE_FORTRAN=OFF -DENABLE_BLASLAPACK=OFF -DBUILD_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX=/MOAB +make -j +sudo make -j install +cmake ../moab -DENABLE_HDF5=ON -DENABLE_PYMOAB=ON -DENABLE_FORTRAN=OFF -DBUILD_SHARED_LIBS=ON -DENABLE_BLASLAPACK=OFF -DCMAKE_INSTALL_PREFIX=/MOAB +sudo make -j install +cd pymoab +sudo bash install.sh +sudo python setup.py install + + +# add to new dirs to the path +echo 'export PATH="$HOME/MOAB/bin:$PATH"' >> ~/.bashrc +echo 'export LD_LIBRARY_PATH="$HOME/MOAB/lib:$LD_LIBRARY_PATH"' >> ~/.bashrc +source ~/.bashrc + +# install Double-Down +cd ~ +git clone --shallow-submodules --single-branch --branch v1.0.0 --depth 1 https://github.com/pshriwise/double-down.git +cd double-down +mkdir build +cd build +cmake .. -DMOAB_DIR=$HOME/MOAB -DCMAKE_INSTALL_PREFIX=.. -DEMBREE_DIR=$HOME/embree +make -j +make -j install + + +# DAGMC version develop install from source +cd ~ +mkdir DAGMC +cd DAGMC +# git clone --single-branch --branch 3.2.1-rc1 --depth 1 https://github.com/svalinn/DAGMC.git +git clone --single-branch --branch v3.2.1 --depth 1 https://github.com/svalinn/DAGMC.git +mkdir build +cd build +cmake ../DAGMC -DBUILD_TALLY=ON -DMOAB_DIR=$HOME/MOAB -DDOUBLE_DOWN=ON -DBUILD_STATIC_EXE=OFF -DBUILD_STATIC_LIBS=OFF -DCMAKE_INSTALL_PREFIX=$HOME/DAGMC/ -DDOUBLE_DOWN_DIR=$HOME/double-down +make -j install + +# add to new dirs to the path +echo 'export PATH="$HOME/DAGMC/bin:$PATH"' >> ~/.bashrc +echo 'export LD_LIBRARY_PATH="$HOME/DAGMC/lib:$LD_LIBRARY_PATH"' >> ~/.bashrc +source ~/.bashrc + +# installs OpenMC +cd ~ +git clone --single-branch --branch v0.13.0 --depth 1 https://github.com/openmc-dev/openmc.git +cd openmc +mkdir build +cd build +cmake -Doptimize=on -Ddagmc=ON -DDAGMC_ROOT=$HOME/DAGMC -DHDF5_PREFER_PARALLEL=off .. +make -j +make -j install +cd .. +pip install . + +# install WMP nuclear data +RUN wget https://github.com/mit-crpg/WMP_Library/releases/download/v1.1/WMP_Library_v1.1.tar.gz +tar -xf WMP_Library_v1.1.tar.gz -C + +# installs TENDL and ENDF nuclear data. Performed after openmc install as +# openmc is needed to write the cross_Sections.xml file +pip install openmc_data_downloader +openmc_data_downloader -d nuclear_data -l ENDFB-7.1-NNDC TENDL-2019 -p neutron photon -e all -i H3 --no-overwrite diff --git a/tasks/README.md b/tasks/README.md index 211bd514..0014e5a8 100644 --- a/tasks/README.md +++ b/tasks/README.md @@ -13,5 +13,7 @@ | [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/main/tasks/task_13_variance_reduction) | Variance reduction with weight windows | | +| [Task 14 - Activation and transmutation](https://github.com/fusion-energy/neutronics-workshop/tree/main/tasks/task_15_activation_transmutation) | Actionation of material, evolution of materials, tallies as a function of time, burn up, transmutation and isotope creation | | +| [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 | | diff --git a/tasks/task_04_make_sources/1_point_source_plots.ipynb b/tasks/task_04_make_sources/1_point_source_plots.ipynb index c9486ea9..78145915 100644 --- a/tasks/task_04_make_sources/1_point_source_plots.ipynb +++ b/tasks/task_04_make_sources/1_point_source_plots.ipynb @@ -13,33 +13,9 @@ }, { "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/home/jshimwell/miniconda3/envs/openmc-dagmc/lib/python3.8/site-packages/IPython/core/display.py:724: UserWarning:\n", - "\n", - "Consider using IPython.display.IFrame instead\n", - "\n" - ] - }, - { - "data": { - "text/html": [ - "" - ], - "text/plain": [ - "" - ] - }, - "execution_count": 8, - "metadata": {}, - "output_type": "execute_result" - } - ], + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "from IPython.display import HTML\n", "HTML('')" @@ -68,16 +44,16 @@ "outputs": [], "source": [ "# initialises a new source object\n", - "source = openmc.Source()\n", + "my_source = openmc.Source()\n", "\n", "# sets the location of the source to x=0 y=0 z=0\n", - "source.space = openmc.stats.Point((0, 0, 0))\n", + "my_source.space = openmc.stats.Point((0, 0, 0))\n", "\n", "# sets the direction to isotropic\n", - "source.angle = openmc.stats.Isotropic()\n", + "my_source.angle = openmc.stats.Isotropic()\n", "\n", "# sets the energy distribution to 100% 14MeV neutrons\n", - "source.energy = openmc.stats.Discrete([14e6], [1])" + "my_source.energy = openmc.stats.Discrete([14e6], [1])" ] }, { @@ -95,8 +71,10 @@ "source": [ "import openmc_source_plotter as osp\n", "\n", - "osp.create_initial_particles(source, openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc')\n", - "osp.plot_energy_from_initial_source()" + "osp.plot_source_energy(\n", + " source=my_source,\n", + " openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc'\n", + ")" ] }, { @@ -112,16 +90,18 @@ "metadata": {}, "outputs": [], "source": [ - "source = openmc.Source()\n", - "source.space = openmc.stats.Point((0, 0, 0))\n", - "source.angle = openmc.stats.Isotropic()\n", + "my_source_2 = openmc.Source()\n", + "my_source_2.space = openmc.stats.Point((0, 0, 0))\n", + "my_source_2.angle = openmc.stats.Isotropic()\n", "\n", "# Documentation on the Watt distribution is here\n", "# https://docs.openmc.org/en/stable/pythonapi/generated/openmc.data.WattEnergy.html\n", - "source.energy = openmc.stats.Watt(a=988000.0, b=2.249e-06)\n", + "my_source_2.energy = openmc.stats.Watt(a=988000.0, b=2.249e-06)\n", "\n", - "osp.create_initial_particles(source, openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc')\n", - "osp.plot_energy_from_initial_source()" + "osp.plot_source_energy(\n", + " source=my_source_2,\n", + " openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc'\n", + ")" ] }, { @@ -137,16 +117,18 @@ "metadata": {}, "outputs": [], "source": [ - "source = openmc.Source()\n", - "source.space = openmc.stats.Point((0, 0, 0))\n", - "source.angle = openmc.stats.Isotropic()\n", + "my_source_3 = openmc.Source()\n", + "my_source_3.space = openmc.stats.Point((0, 0, 0))\n", + "my_source_3.angle = openmc.stats.Isotropic()\n", "\n", "# Documentation on the Muir distribution is here\n", "# https://docs.openmc.org/en/stable/pythonapi/generated/openmc.stats.Muir.html\n", - "source.energy = openmc.stats.Muir(e0=14080000.0, m_rat=5.0, kt=20000.0)\n", + "my_source_3.energy = openmc.stats.Muir(e0=14080000.0, m_rat=5.0, kt=20000.0)\n", "\n", - "osp.create_initial_particles(source, openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc')\n", - "osp.plot_energy_from_initial_source()" + "osp.plot_source_energy(\n", + " source=my_source_3,\n", + " openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc'\n", + ")" ] }, { @@ -163,13 +145,15 @@ "outputs": [], "source": [ "# Creates an isotropic point source with monoenergetic 14MeV neutrons\n", - "source = openmc.Source()\n", - "source.space = openmc.stats.Point((0, 0, 0))\n", - "source.angle = openmc.stats.Isotropic()\n", - "source.energy = openmc.stats.Discrete([14e6], [1])\n", + "my_source_4 = openmc.Source()\n", + "my_source_4.space = openmc.stats.Point((0, 0, 0))\n", + "my_source_4.angle = openmc.stats.Isotropic()\n", + "my_source_4.energy = openmc.stats.Discrete([14e6], [1])\n", "\n", - "osp.create_initial_particles(source, openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc')\n", - "osp.plot_position_from_initial_source()" + "osp.plot_source_position(\n", + " source=my_source_4,\n", + " openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc'\n", + ")" ] }, { @@ -186,13 +170,15 @@ "outputs": [], "source": [ "# Creates an isotropic point source with monoenergetic 14MeV neutrons\n", - "source = openmc.Source()\n", - "source.space = openmc.stats.Point((0, 0, 0))\n", - "source.angle = openmc.stats.Isotropic()\n", - "source.energy = openmc.stats.Discrete([14e6], [1])\n", + "my_source_5 = openmc.Source()\n", + "my_source_5.space = openmc.stats.Point((0, 0, 0))\n", + "my_source_5.angle = openmc.stats.Isotropic()\n", + "my_source_5.energy = openmc.stats.Discrete([14e6], [1])\n", "\n", - "osp.create_initial_particles(source, openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc')\n", - "osp.plot_direction_from_initial_source()" + "osp.plot_source_direction(\n", + " source=my_source_5,\n", + " openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc'\n", + ")" ] }, { @@ -229,7 +215,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.12" + "version": "3.9.5" } }, "nbformat": 4, diff --git a/tasks/task_04_make_sources/2_ring_source.ipynb b/tasks/task_04_make_sources/2_ring_source.ipynb index 8fcfe1fe..9143423a 100644 --- a/tasks/task_04_make_sources/2_ring_source.ipynb +++ b/tasks/task_04_make_sources/2_ring_source.ipynb @@ -44,7 +44,7 @@ "import openmc\n", "\n", "# initialises a new source object\n", - "source = openmc.Source()\n", + "my_source = openmc.Source()\n", "\n", "# the distribution of radius is just a single value\n", "radius = openmc.stats.Discrete([10], [1])\n", @@ -56,13 +56,13 @@ "angle = openmc.stats.Uniform(a=0., b=2* 3.14159265359)\n", "\n", "# this makes the ring source using the three distributions and a radius\n", - "source.space = openmc.stats.CylindricalIndependent(r=radius, phi=angle, z=z_values, origin=(0.0, 0.0, 0.0))\n", + "my_source.space = openmc.stats.CylindricalIndependent(r=radius, phi=angle, z=z_values, origin=(0.0, 0.0, 0.0))\n", "\n", "# sets the direction to isotropic\n", - "source.angle = openmc.stats.Isotropic()\n", + "my_source.angle = openmc.stats.Isotropic()\n", "\n", "# sets the energy distribution to a Muir distribution neutrons\n", - "source.energy = openmc.stats.Muir(e0=14080000.0, m_rat=5.0, kt=20000.0)" + "my_source.energy = openmc.stats.Muir(e0=14080000.0, m_rat=5.0, kt=20000.0)" ] }, { @@ -80,8 +80,10 @@ "source": [ "import openmc_source_plotter as osp\n", "\n", - "osp.create_initial_particles(source, openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc')\n", - "osp.plot_position_from_initial_source()" + "osp.plot_source_position(\n", + " source=my_source,\n", + " openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc'\n", + ")" ] }, { @@ -116,7 +118,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.12" + "version": "3.9.5" } }, "nbformat": 4, diff --git a/tasks/task_04_make_sources/3_plasma_source_plots.ipynb b/tasks/task_04_make_sources/3_plasma_source_plots.ipynb index 859510b7..143da136 100644 --- a/tasks/task_04_make_sources/3_plasma_source_plots.ipynb +++ b/tasks/task_04_make_sources/3_plasma_source_plots.ipynb @@ -74,8 +74,10 @@ "source": [ "import openmc_source_plotter as osp\n", "\n", - "osp.create_initial_particles(my_source, openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc')\n", - "osp.plot_energy_from_initial_source()" + "osp.plot_source_energy(\n", + " source=my_source,\n", + " openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc'\n", + ")" ] }, { @@ -91,7 +93,10 @@ "metadata": {}, "outputs": [], "source": [ - "osp.plot_position_from_initial_source()" + "osp.plot_source_position(\n", + " source=my_source,\n", + " openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc'\n", + ")" ] }, { @@ -107,7 +112,10 @@ "metadata": {}, "outputs": [], "source": [ - "osp.plot_direction_from_initial_source()" + "osp.plot_source_direction(\n", + " source=my_source,\n", + " openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc'\n", + ")" ] }, { @@ -136,7 +144,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.5" + "version": "3.8.11" } }, "nbformat": 4, diff --git a/tasks/task_04_make_sources/4_neutron_tracks.ipynb b/tasks/task_04_make_sources/4_neutron_tracks.ipynb index affe6ab8..0314035d 100644 --- a/tasks/task_04_make_sources/4_neutron_tracks.ipynb +++ b/tasks/task_04_make_sources/4_neutron_tracks.ipynb @@ -204,7 +204,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.12" + "version": "3.9.5" } }, "nbformat": 4, diff --git a/tasks/task_04_make_sources/5_gamma_source_example.ipynb b/tasks/task_04_make_sources/5_gamma_source_example.ipynb index bce6e156..eb830d43 100644 --- a/tasks/task_04_make_sources/5_gamma_source_example.ipynb +++ b/tasks/task_04_make_sources/5_gamma_source_example.ipynb @@ -15,7 +15,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -54,18 +54,18 @@ "outputs": [], "source": [ "# initialises a new source object\n", - "source = openmc.Source()\n", + "my_source = openmc.Source()\n", "\n", "# sets the location of the source to x=0 y=0 z=0\n", - "source.space = openmc.stats.Point((0, 0, 0))\n", + "my_source.space = openmc.stats.Point((0, 0, 0))\n", "\n", "# sets the direction to isotropic\n", - "source.angle = openmc.stats.Isotropic()\n", + "my_source.angle = openmc.stats.Isotropic()\n", "\n", "# sets the energy distribution to 50% 1.1MeV photons and 50% 1.3MeV photons\n", - "source.energy = openmc.stats.Discrete([1.1732e6,1.3325e6], [0.5, 0.5])\n", + "my_source.energy = openmc.stats.Discrete([1.1732e6,1.3325e6], [0.5, 0.5])\n", "\n", - "source.particle = 'photon'" + "my_source.particle = 'photon'" ] }, { @@ -84,11 +84,17 @@ "outputs": [], "source": [ "import openmc_source_plotter as osp\n", + "import numpy as np\n", "\n", "# number_of_particles can be increased to sample more particles\n", - "osp.create_initial_particles(source, number_of_particles=1000, openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc')\n", - "# this time we are setting the number of energy bins for the plot\n", - "osp.plot_energy_from_initial_source(energy_bins=np.linspace(0, 2e6, 50))" + "osp.plot_source_energy(\n", + " source=my_source,\n", + " number_of_particles=1000,\n", + " openmc_exec='/opt/conda/envs/openmc_version_0_11_0/bin/openmc',\n", + " energy_bins=np.linspace(0, 2e6, 50)\n", + ")\n", + "\n", + "# this time we are setting the number of energy bins for the plot\n" ] }, { @@ -125,7 +131,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.12" + "version": "3.8.11" } }, "nbformat": 4, diff --git a/tasks/task_05_CSG_cell_tally_TBR/1_example_tritium_production.ipynb b/tasks/task_05_CSG_cell_tally_TBR/1_example_tritium_production.ipynb index c17c79d1..2c4973a7 100644 --- a/tasks/task_05_CSG_cell_tally_TBR/1_example_tritium_production.ipynb +++ b/tasks/task_05_CSG_cell_tally_TBR/1_example_tritium_production.ipynb @@ -207,7 +207,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.12" + "version": "3.8.11" } }, "nbformat": 4, diff --git a/tasks/task_11_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb b/tasks/task_11_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb index 21577890..b6f0955b 100644 --- a/tasks/task_11_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb +++ b/tasks/task_11_CAD_cell_tally_heat/1_simulate_CAD_neutronics_geometry_with_cell_tally_heat.ipynb @@ -29,7 +29,8 @@ " major_radius=450.,\n", " triangularity=0.55,\n", " elongation=2.,\n", - " rotation_angle=270\n", + " rotation_angle=180,\n", + " name='plasma'\n", ")\n", "\n", "blanket = paramak.BlanketFP(\n", @@ -38,11 +39,11 @@ " stop_angle=90,\n", " start_angle=-90,\n", " offset_from_plasma=40,\n", - " rotation_angle=270,\n", + " rotation_angle=180,\n", + " name='blanket'\n", ")\n", - "!rm blanket.stl\n", + "\n", "my_reactor = paramak.Reactor([plasma, blanket])\n", - "my_reactor.export_stl(['plasma.stl', 'blanket.stl'])\n", "my_reactor.show()" ] }, @@ -50,15 +51,11 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "This section forms the neutronics model by combining the 3D model, the plasma source and some assigned materials. Additionally, the tallies to record the heating are specified. There are a few different methods of converting a CAD model into a neutronics model. Each method has pros and cons.\n", - "\n", - "The rector can also be converted from stl or stp to h5m format which is the 3D geometry format used by DAGMC to represent neutronics geometry.\n", + "This next code block exports the 3D reactor geometry as a DAGMC compatibile h5m file which can be used as a neutronics geometry. DAGMC is a neutronics code that allows particle transport on CAD geometry with various neutronics transport codes (including OpenMC).\n", "\n", - "stl-to-h5m can convert stl files to a h5m geometry\n", - "https://github.com/fusion-energy/stl_to_h5m\n", + "More details on DAGMC here https://svalinn.github.io/DAGMC/\n", "\n", - "cad-to-h5m can convert stp files to h5m geometry\n", - "https://github.com/fusion-energy/cad_to_h5m" + "This export will take a reasonable amount of time compared to other cells" ] }, { @@ -67,14 +64,8 @@ "metadata": {}, "outputs": [], "source": [ - "from stl_to_h5m import stl_to_h5m\n", "!rm dagmc.h5m\n", - "stl_to_h5m(\n", - " files_with_tags=[\n", - " ('blanket.stl', 'blanket'),\n", - " ],\n", - " h5m_filename='dagmc.h5m',\n", - ")" + "my_reactor.export_dagmc_h5m(filename='dagmc.h5m', min_mesh_size=10, max_mesh_size=20)" ] }, { @@ -99,7 +90,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "The following code makes use of the previously created neutronics geometry (h5m file) and assigns actual materials to the material tags. Sets simulation intensity and specifies the neutronics results to record (know as tallies)." + "This section forms the neutronics model by combining the DAGMC model with a plasma source and some assigned materials. Additionally, the tallies to record the heating are specified. The code block also sets simulation intensity and specifies the neutronics results to record (know as tallies)." ] }, { @@ -111,15 +102,15 @@ "# this links the material tags in the dagmc h5m file with materials.\n", "# these materials are input as strings so they will be looked up in the\n", "# neutronics material maker package\n", - "material_tag_to_material_dict = {\n", - " 'blanket':'Li4SiO4',\n", - "}\n", "\n", - "geometry = odw.Geometry(h5m_filename='dagmc.h5m')\n", + "geometry = odw.Geometry(h5m_filename='dagmc.h5m', reflective_angles=(0, 180))\n", "\n", "materials = odw.Materials(\n", " h5m_filename='dagmc.h5m',\n", - " correspondence_dict=material_tag_to_material_dict\n", + " correspondence_dict={\n", + " 'mat_blanket':'Li4SiO4',\n", + " 'mat_plasma': 'DT_plasma'\n", + " }\n", ")\n", "\n", "tally1 = odw.CellTally(\n", @@ -135,9 +126,9 @@ "settings.batches = 1\n", "settings.particles = 100\n", "\n", - "# assigns a ring source of DT energy neutrons to the source using the\n", - "# openmc_plasma_source package\n", - "settings.source = ops.FusionRingSource(fuel=\"DT\", radius=350)\n", + "# assigns a ring source of DT energy neutrons to the source using the openmc_plasma_source package.\n", + "# This source has a 14MeV neutron energy, with a radius of 350cm and is half a ring (0 to 180 degrees)\n", + "settings.source = ops.FusionRingSource(fuel=\"DT\", radius=350, angles=(0, 3.14))\n", "\n", "my_model = openmc.Model(\n", " materials=materials, geometry=geometry, settings=settings, tallies=tallies\n", @@ -267,7 +258,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.9.5" + "version": "3.8.12" } }, "nbformat": 4, diff --git a/tasks/task_12_CAD_mesh_fast_flux/1_making_shapes_for_a_3d_mesh_tally_vtk.ipynb b/tasks/task_12_CAD_mesh_fast_flux/1_making_shapes_for_a_3d_mesh_tally_vtk.ipynb index 6e13bc76..4342186e 100644 --- a/tasks/task_12_CAD_mesh_fast_flux/1_making_shapes_for_a_3d_mesh_tally_vtk.ipynb +++ b/tasks/task_12_CAD_mesh_fast_flux/1_making_shapes_for_a_3d_mesh_tally_vtk.ipynb @@ -64,7 +64,7 @@ " (500, 300),\n", " (600, 20)\n", " ],\n", - " name='plasma',\n", + " name='blanket',\n", " rotation_angle=40,\n", " azimuth_placement_angle=[0, 45, 90, 135, 180, 225, 270, 315],\n", ")" @@ -85,8 +85,6 @@ "source": [ "my_reactor = paramak.Reactor([blanket, center_column])\n", "\n", - "my_reactor.export_stl()\n", - "\n", "my_reactor.show()" ] }, @@ -94,15 +92,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "This section forms the neutronics model by combining the 3D model, the plasma source and some assigned materials. Additionally, the tallies to record the heating are specified. There are a few different methods of converting a CAD model into a neutronics model. Each method has pros and cons.\n", - "\n", - "The rector can also be converted from stl or stp to h5m format which is the 3D geometry format used by DAGMC to represent neutronics geometry.\n", - "\n", - "stl-to-h5m can convert stl files to a h5m geometry\n", - "https://github.com/fusion-energy/stl_to_h5m\n", - "\n", - "cad-to-h5m can convert stp files to h5m geometry\n", - "https://github.com/fusion-energy/cad_to_h5m" + "This section forms the neutronics model by combining the 3D model, the plasma source and some assigned materials. Additionally, the tallies to record the heating are specified." ] }, { @@ -111,15 +101,7 @@ "metadata": {}, "outputs": [], "source": [ - "from stl_to_h5m import stl_to_h5m\n", - "\n", - "stl_to_h5m(\n", - " files_with_tags=[\n", - " ('plasma.stl', 'mat_plasma'),\n", - " ('center_column.stl', 'mat_center_column')\n", - " ],\n", - " h5m_filename='dagmc.h5m',\n", - ")" + "my_reactor.export_dagmc_h5m()" ] }, { @@ -146,7 +128,7 @@ "# these materials are input as strings so they will be looked up in the\n", "# neutronics material maker package\n", "material_tag_to_material_dict = {\n", - " 'mat_plasma': nmm.Material.from_library(name='DT_plasma'),\n", + " 'mat_blanket': nmm.Material.from_library(name='DT_plasma'),\n", " 'mat_center_column': nmm.Material.from_library(name='Li4SiO4'),\n", "}\n", "\n", diff --git a/tasks/task_12_CAD_mesh_fast_flux/2_making_components_for_a_2d_mesh_tally_vtk.ipynb b/tasks/task_12_CAD_mesh_fast_flux/2_making_components_for_a_2d_mesh_tally_vtk.ipynb index ae1225a0..4e64b5f9 100644 --- a/tasks/task_12_CAD_mesh_fast_flux/2_making_components_for_a_2d_mesh_tally_vtk.ipynb +++ b/tasks/task_12_CAD_mesh_fast_flux/2_making_components_for_a_2d_mesh_tally_vtk.ipynb @@ -22,7 +22,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -46,7 +46,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "metadata": {}, "outputs": [], "source": [ @@ -68,7 +68,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "metadata": {}, "outputs": [], "source": [ @@ -92,9 +92,226 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 4, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Overwriting auto display for cadquery Workplane and Shape\n" + ] + }, + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "ecdb600c1f354e3ba931520b5c5e7764", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "HBox(children=(VBox(children=(HBox(children=(Checkbox(value=False, description='Axes', indent=False, _dom_clas…" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "my_reactor = paramak.Reactor([blanket, pf_coil,center_column])\n", "\n", @@ -110,20 +327,42 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 5, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[32;1m\n", + "*******************************************************************\n", + "****** Statistics on Transfer (Write) ******\u001b[0m\n", + "\u001b[32;1m\n", + "*******************************************************************\n", + "****** Transfer Mode = 0 I.E. As Is ******\u001b[0m\n", + "\u001b[32;1m****** Transferring Shape, ShapeType = 0 ******\u001b[0m\n", + "\u001b[32;1m** WorkSession : Sending all data\u001b[0m\n", + "\u001b[32;1m Step File Name : my_reactor.stp(3447 ents) Write Done\u001b[0m\n" + ] + }, + { + "data": { + "text/html": [ + "my_reactor.stp
" + ], + "text/plain": [ + "/home/jshim/neutronics-workshop/tasks/task_12_CAD_mesh_fast_flux/my_reactor.stp" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ - "my_reactor.export_stp()\n", - "my_reactor.export_stl()\n", + "my_reactor.export_stp('my_reactor.stp')\n", "\n", "from IPython.display import FileLink\n", - "display(FileLink('blanket.stp'))\n", - "display(FileLink('pf_coil.stp'))\n", - "display(FileLink('center_column.stp'))\n", - "display(FileLink('blanket.stl'))\n", - "display(FileLink('pf_coil.stl'))\n", - "display(FileLink('center_column.stl'))" + "display(FileLink('my_reactor.stp'))" ] }, { @@ -135,20 +374,217 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 6, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Info : Meshing 1D...\n", + "Info : [ 0%] Meshing curve 1 (Circle)\n", + "Info : [ 10%] Meshing curve 2 (Circle)\n", + "Info : [ 10%] Meshing 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(Plane, MeshAdapt)\n", + "Info : [ 90%] Meshing surface 50 (Plane, MeshAdapt)\n", + "Info : [ 90%] Meshing surface 51 (Sphere, MeshAdapt)\n", + "Info : [100%] Meshing surface 52 (Plane, MeshAdapt)\n", + "Info : [100%] Meshing surface 53 (Surface of Revolution, MeshAdapt)\n", + "Info : [100%] Meshing surface 54 (Plane, MeshAdapt)\n", + "Info : [100%] Meshing surface 55 (Plane, MeshAdapt)\n", + "Info : [100%] Meshing surface 56 (Plane, MeshAdapt)\n", + "Info : Done meshing 2D (Wall 14.475s, CPU 14.4766s)\n", + "Info : 24024 nodes 50983 elements\n", + "Info : Writing '/tmp/volume_1ya905d6y.stl'...\n", + "Info : Done writing '/tmp/volume_1ya905d6y.stl'\n", + "Info : Writing '/tmp/volume_21713jqj7.stl'...\n", + "Info : Done writing '/tmp/volume_21713jqj7.stl'\n", + "Info : Writing '/tmp/volume_3fm04kflt.stl'...\n", + "Info : Done writing '/tmp/volume_3fm04kflt.stl'\n", + "Info : Writing '/tmp/volume_4ozp3ns7u.stl'...\n", + "Info : Done writing '/tmp/volume_4ozp3ns7u.stl'\n", + "Info : Writing '/tmp/volume_5vc_dm549.stl'...\n", + "Info : Done writing '/tmp/volume_5vc_dm549.stl'\n", + "Info : Writing '/tmp/volume_6xl62nv5j.stl'...\n", + "Info : Done writing '/tmp/volume_6xl62nv5j.stl'\n", + "Info : Writing '/tmp/volume_7p3fuo6bj.stl'...\n", + "Info : Done writing '/tmp/volume_7p3fuo6bj.stl'\n", + "Info : Writing '/tmp/volume_8fiwr678_.stl'...\n", + "Info : Done writing '/tmp/volume_8fiwr678_.stl'\n", + "Info : Writing '/tmp/volume_9i4o02pff.stl'...\n", + "Info : Done writing '/tmp/volume_9i4o02pff.stl'\n", + "Info : Writing '/tmp/volume_10qy8o513g.stl'...\n", + "Info : Done writing '/tmp/volume_10qy8o513g.stl'\n", + "file /tmp/volume_1ya905d6y.stl is watertight True\n", + "file /tmp/volume_21713jqj7.stl is watertight True\n", + "file /tmp/volume_3fm04kflt.stl is watertight True\n", + "file /tmp/volume_4ozp3ns7u.stl is watertight True\n", + "file /tmp/volume_5vc_dm549.stl is watertight True\n", + "file /tmp/volume_6xl62nv5j.stl is watertight True\n", + "file /tmp/volume_7p3fuo6bj.stl is watertight True\n", + "file /tmp/volume_8fiwr678_.stl is watertight True\n", + "file /tmp/volume_9i4o02pff.stl is watertight True\n", + "file /tmp/volume_10qy8o513g.stl is watertight True\n" + ] + } + ], "source": [ - "from stl_to_h5m import stl_to_h5m\n", - "\n", - "stl_to_h5m(\n", - " files_with_tags=[\n", - " ('pf_coil.stl', 'mat_pf_coil'),\n", - " ('blanket.stl', 'mat_blanket'),\n", - " ('center_column.stl', 'mat_center_column')\n", - " ],\n", - " h5m_filename='dagmc.h5m',\n", - ")\n", + "my_reactor.export_dagmc_h5m('dagmc.h5m')\n", "\n", "import openmc_dagmc_wrapper as odw\n", "geometry = odw.Geometry(h5m_filename='dagmc.h5m')" @@ -167,9 +603,20 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 7, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "/home/jshim/openmc-1/openmc/mixin.py:67: IDWarning: Another Surface instance already exists with id=9999.\n", + " warn(msg, IDWarning)\n", + "/home/jshim/openmc-1/openmc/mixin.py:67: IDWarning: Another Cell instance already exists with id=9999.\n", + " warn(msg, IDWarning)\n" + ] + } + ], "source": [ "# makes use of the previously created neutronics geometry (h5m file) and assigns\n", "# actual materials to the material tags. \n", @@ -203,7 +650,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 11, "metadata": {}, "outputs": [], "source": [ @@ -231,7 +678,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 12, "metadata": {}, "outputs": [], "source": [ @@ -240,11 +687,11 @@ "# finds bounding box size from the geometry size\n", "corners = DagmcBoundingBox('dagmc.h5m').corners()\n", "\n", - "tally1 = odw.MeshTally2D(\n", - " mesh_resolution=(100, 100),\n", + "tally1 = odw.MeshTally3D(\n", + " mesh_resolution=(100, 100, 100),\n", " bounding_box= corners,\n", " tally_type=\"(n,Xa)\",\n", - " plane='xz'\n", + " # plane='xz'\n", ")\n", "\n", "tallies = openmc.Tallies([tally1])" @@ -259,15 +706,118 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 17, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " %%%%%%%%%%%%%%%\n", + " %%%%%%%%%%%%%%%%%%%%%%%%\n", + " %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n", + " %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n", + " %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n", + " %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n", + " %%%%%%%%%%%%%%%%%%%%%%%%\n", + " %%%%%%%%%%%%%%%%%%%%%%%%\n", + " ############### %%%%%%%%%%%%%%%%%%%%%%%%\n", + " ################## %%%%%%%%%%%%%%%%%%%%%%%\n", + " ################### %%%%%%%%%%%%%%%%%%%%%%%\n", + " #################### %%%%%%%%%%%%%%%%%%%%%%\n", + " ##################### %%%%%%%%%%%%%%%%%%%%%\n", + " ###################### %%%%%%%%%%%%%%%%%%%%\n", + " ####################### %%%%%%%%%%%%%%%%%%\n", + " ####################### %%%%%%%%%%%%%%%%%\n", + " ###################### %%%%%%%%%%%%%%%%%\n", + " #################### %%%%%%%%%%%%%%%%%\n", + " ################# %%%%%%%%%%%%%%%%%\n", + " ############### %%%%%%%%%%%%%%%%\n", + " ############ %%%%%%%%%%%%%%%\n", + " ######## %%%%%%%%%%%%%%\n", + " %%%%%%%%%%%\n", + "\n", + " | The OpenMC Monte Carlo Code\n", + " Copyright | 2011-2021 MIT and OpenMC contributors\n", + " License | https://docs.openmc.org/en/latest/license.html\n", + " Version | 0.13.0-dev\n", + " Git SHA1 | 209fdd86ed14a16d4b73e9c44de8a9710a898e64\n", + " Date/Time | 2022-01-26 23:10:24\n", + " MPI Processes | 1\n", + " OpenMP Threads | 8\n", + "\n", + " Reading settings XML file...\n", + " Reading cross sections XML file...\n", + " Reading materials XML file...\n", + " Reading geometry XML file...\n", + "Using the DOUBLE-DOWN interface to Embree.\n", + "Loading file dagmc.h5m\n", + "Initializing the GeomQueryTool...\n", + "Using faceting tolerance: 0\n", + "Building acceleration data structures...\n", + "Implicit Complement assumed to be Vacuum\n", + " Reading Cu65 from\n", + " /home/jshim/nuc_data/cross_section_data/ENDFB-7.1-NNDC_Cu65.h5\n", + " Reading Cu63 from\n", + " /home/jshim/nuc_data/cross_section_data/ENDFB-7.1-NNDC_Cu63.h5\n", + " Reading Li6 from /home/jshim/nuc_data/cross_section_data/ENDFB-7.1-NNDC_Li6.h5\n", + " Reading Li7 from /home/jshim/nuc_data/cross_section_data/ENDFB-7.1-NNDC_Li7.h5\n", + " Reading Si28 from\n", + " /home/jshim/nuc_data/cross_section_data/ENDFB-7.1-NNDC_Si28.h5\n", + " Reading Si29 from\n", + " /home/jshim/nuc_data/cross_section_data/ENDFB-7.1-NNDC_Si29.h5\n", + " Reading Si30 from\n", + " /home/jshim/nuc_data/cross_section_data/ENDFB-7.1-NNDC_Si30.h5\n", + " Reading O16 from /home/jshim/nuc_data/cross_section_data/ENDFB-7.1-NNDC_O16.h5\n", + " Reading O18 from /home/jshim/nuc_data/cross_section_data/TENDL-2019_O18.h5\n", + " Reading O17 from /home/jshim/nuc_data/cross_section_data/ENDFB-7.1-NNDC_O17.h5\n", + " Minimum neutron data temperature: 294.0 K\n", + " Maximum neutron data temperature: 294.0 K\n", + " Reading tallies XML file...\n", + " Preparing distributed cell instances...\n", + " Writing summary.h5 file...\n", + " Maximum neutron transport energy: 20000000.0 eV for Li6\n", + "\n", + " ===============> FIXED SOURCE TRANSPORT SIMULATION <===============\n", + "\n", + " Simulating batch 1\n", + " Simulating batch 2\n", + " Simulating batch 3\n", + " Simulating batch 4\n", + " Simulating batch 5\n", + " Simulating batch 6\n", + " Simulating batch 7\n", + " Simulating batch 8\n", + " Simulating batch 9\n", + " Simulating batch 10\n", + " Creating state point statepoint.10.h5...\n", + "\n", + " =======================> TIMING STATISTICS <=======================\n", + "\n", + " Total time for initialization = 9.6893e-01 seconds\n", + " Reading cross sections = 8.6679e-01 seconds\n", + " Total time in simulation = 7.1340e-01 seconds\n", + " Time in transport only = 6.7301e-01 seconds\n", + " Time in active batches = 7.1340e-01 seconds\n", + " Time accumulating tallies = 1.8198e-02 seconds\n", + " Time writing statepoints = 2.0861e-02 seconds\n", + " Total time for finalization = 9.6260e-01 seconds\n", + " Total time elapsed = 2.6586e+00 seconds\n", + " Calculation Rate (active) = 28034.7 particles/second\n", + "\n", + " ============================> RESULTS <============================\n", + "\n", + " Leakage Fraction = 0.51210 +/- 0.00313\n", + "\n" + ] + } + ], "source": [ "import openmc_plasma_source as ops\n", "\n", "settings = odw.FusionSettings()\n", - "settings.batches = 4\n", - "settings.particles = 1000\n", + "settings.batches = 10\n", + "settings.particles = 2000\n", "\n", "# assigns a ring source of DT energy neutrons to the source using the\n", "# openmc_plasma_source package, more details here\n", @@ -298,9 +848,36 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 18, "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "{1: Tally\n", + "\tID =\t1\n", + "\tName =\t(n,Xa)_on_3D_mesh\n", + "\tFilters =\tMeshFilter\n", + "\tNuclides =\ttotal\n", + "\tScores =\t['(n,Xa)']\n", + "\tEstimator =\ttracklength}\n", + "tally.size 1000000\n", + "tally [0. 0. 0. ... 0. 0. 0.]\n", + "Writing n_Xa_on_3D_mesh.vtk\n" + ] + }, + { + "data": { + "text/plain": [ + "'n_Xa_on_3D_mesh.vtk'" + ] + }, + "execution_count": 18, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "from openmc_mesh_tally_to_vtk import write_mesh_tally_to_vtk\n", "# importing a package for converting regular mesh tallies to vtk files\n", @@ -308,29 +885,49 @@ "\n", "\n", "# assumes you have a statepoint file from the OpenMC simulation\n", - "statepoint = openmc.StatePoint('statepoint.4.h5')\n", + "statepoint = openmc.StatePoint(statepoint_file)\n", "\n", "# this shows the tallies present in the statepoint file\n", "print(statepoint.tallies)\n", "\n", "# loads up a tally from the statepoint using it's name\n", - "my_tally = statepoint.get_tally(name='(n,Xa)_on_2D_mesh_xz')\n", + "my_tally = statepoint.get_tally(name='(n,Xa)_on_3D_mesh')\n", "\n", "# converts the tally result into a VTK file\n", "write_mesh_tally_to_vtk(\n", " tally=my_tally,\n", - " filename = \"(n,Xa)_on_2D_mesh_xz.vtk\",\n", + " filename = \"n_Xa_on_3D_mesh.vtk\",\n", ")" ] }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The code block below provides a download link for a VTK which can be opened with Paraview\n" + ] + }, { "cell_type": "code", - "execution_count": null, + "execution_count": 19, "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "n_Xa_on_3D_mesh.vtk
" + ], + "text/plain": [ + "/home/jshim/neutronics-workshop/tasks/task_12_CAD_mesh_fast_flux/n_Xa_on_3D_mesh.vtk" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ "from IPython.display import FileLink\n", - "display(FileLink('n,Xa)_on_2D_mesh_xz.vtk'))\n" + "display(FileLink('n_Xa_on_3D_mesh.vtk'))" ] }, { diff --git a/tasks/task_12_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb b/tasks/task_12_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb index 74a5564e..717ef647 100644 --- a/tasks/task_12_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb +++ b/tasks/task_12_CAD_mesh_fast_flux/3_making_reactor_for_a_2d_mesh_tally_and_matplotlib_png.ipynb @@ -63,7 +63,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "The next section defines the materials. This can be done using openmc.Materials or in this case strings that look up materials from the neutronics material maker." + "Exports the 3D geometry to a DAGMC neutronics geometry. The plasma is not included as not many neutron interactions occur in the low density plasma" ] }, { @@ -72,13 +72,7 @@ "metadata": {}, "outputs": [], "source": [ - "my_reactor.export_stp()\n", - "\n", - "from IPython.display import FileLink\n", - "display(FileLink('blanket.stp'))\n", - "display(FileLink('pf_coil.stp'))\n", - "display(FileLink('center_column.stp'))\n", - "display(FileLink('Graveyard.stp'))" + "my_reactor.export_dagmc_h5m('dagmc_3.h5m', exclude='plasma')" ] }, { @@ -100,7 +94,50 @@ "\n", "mat2 = Material.from_library(name='copper')\n", "\n", - "mat3 = Material.from_library(name='WC')" + "mat3 = Material.from_library(name='WC')\n", + "\n", + "mat4 = Material.from_library(name='eurofer')" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "This next section combines the geometry with the materials and specifies a few mesh tallies" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "# makes use of the previously created neutronics geometry (h5m file) and assigns\n", + "# actual materials to the material tags. \n", + "\n", + "import openmc_dagmc_wrapper as odw\n", + "import neutronics_material_maker as nmm\n", + "\n", + "# this links the material tags in the dagmc h5m file with materials.\n", + "# these materials are input as strings so they will be looked up in the\n", + "# neutronics material maker package\n", + "material_tag_to_material_dict = {\n", + " 'mat_blanket': mat1,\n", + " 'mat_blanket_rear_wall':mat4,\n", + " 'mat_center_column_shield':mat3,\n", + " 'mat_divertor_lower':mat4,\n", + " 'mat_divertor_upper':mat4,\n", + " 'mat_firstwall':mat4,\n", + " 'mat_inboard_tf_coils':mat2,\n", + " 'mat_plasma':mat2 # todo remove\n", + "}\n", + "\n", + "geometry = odw.Geometry(h5m_filename='dagmc_3.h5m')\n", + "\n", + "materials = odw.Materials(\n", + " h5m_filename='dagmc_3.h5m',\n", + " correspondence_dict=material_tag_to_material_dict\n", + ")" ] }, { @@ -116,6 +153,7 @@ "metadata": {}, "outputs": [], "source": [ + "\n", "import openmc\n", "\n", "# initialises a new source object\n", @@ -135,7 +173,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "This next section combines the geometry with the materials and specifies a few mesh tallies" + "Makes a 3D mesh tally" ] }, { @@ -143,8 +181,27 @@ "execution_count": null, "metadata": {}, "outputs": [], + "source": [] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "starts the simulation" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "markdown", + "metadata": {}, "source": [ - "#todo add mesh tallies, settings and run simulation" + "extracts the 3d mesh tally result and plots it as a vtk" ] }, { @@ -213,7 +270,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.11" + "version": "3.8.12" } }, "nbformat": 4, diff --git a/tasks/task_13_variance_reduction/1_minimal_weight_window_mesh_tally_example.py b/tasks/task_13_variance_reduction/1_minimal_weight_window_mesh_tally_example.py new file mode 100644 index 00000000..a55ad5d4 --- /dev/null +++ b/tasks/task_13_variance_reduction/1_minimal_weight_window_mesh_tally_example.py @@ -0,0 +1,86 @@ +import openmc +import os +import matplotlib.pyplot as plt + +# MATERIALS + +# creates a single material +mats = openmc.Materials() + +shielding_material = openmc.Material(name="breeder") +shielding_material.add_nuclide('Fe56', 1, percent_type='ao') +shielding_material.set_density('g/cm3', 7) + +mats = [shielding_material] + + +# GEOMETRY + +# surfaces +sph1 = openmc.Sphere(r=250, boundary_type='vacuum') + +# cells +shield_cell = openmc.Cell(region=-sph1) +shield_cell.fill = shielding_material + +universe = openmc.Universe(cells=[shield_cell]) + +geom = openmc.Geometry(universe) + +# creates a 14MeV neutron point source +source = openmc.Source() +source.space = openmc.stats.Point((0, 0, 0)) +source.angle = openmc.stats.Isotropic() +source.energy = openmc.stats.Discrete([14e6], [1]) +source.particles = 'neutron' + +# SETTINGS + +# Instantiate a Settings object +sett = openmc.Settings() +sett.batches = 100 +sett.inactive = 0 +sett.particles = 500 +sett.source = source +sett.run_mode = 'fixed source' + + +# Create mesh which will be used for the tally +my_tally_mesh = openmc.RegularMesh() +my_tally_mesh.dimension = [25, 1, 25] # only 1 cell in the Y dimension +my_tally_mesh.lower_left = [-120, -1, -120] # physical limits (corners) of the mesh +my_tally_mesh.upper_right = [120, 1, 120] + +# Create mesh filter for tally +mesh_filter = openmc.MeshFilter(my_tally_mesh) +mesh_tally = openmc.Tally(name='flux_on_mesh') +mesh_tally.filters = [mesh_filter] +mesh_tally.scores = ['flux'] +#creates an empty tally object +tallies = openmc.Tallies() +tallies.append(mesh_tally) + +# combines the geometry, materials, settings and tallies to create a neutronics model +model = openmc.model.Model(geom, mats, sett, tallies) + +# runs the simulation with weight windows +output_no_ww_filename = model.run() + +# open the results file +results_no_ww = openmc.StatePoint(output_no_ww_filename) + +# access the flux tally +my_tally_no_ww = results_no_ww.get_tally(scores=['flux']) +my_slice_no_ww = my_tally_no_ww.get_slice(scores=['flux']) +my_slice_no_ww.mean.shape = (25, 25) +fig = plt.subplot() + +# when plotting the 2d data, added the extent is required. +# otherwise the plot uses the index of the 2d data arrays +# as the x y axis +fig.imshow(my_slice_no_ww.mean, extent=[-120,120,-120,120])#, vmin=1e-5, vmax=10) +plt.savefig('no_ww.png') +plt.show() + + + diff --git a/tasks/task_13_variance_reduction/2_no_weight_window_mesh_tally_example.py b/tasks/task_13_variance_reduction/2_no_weight_window_mesh_tally_example.py new file mode 100644 index 00000000..b681ded8 --- /dev/null +++ b/tasks/task_13_variance_reduction/2_no_weight_window_mesh_tally_example.py @@ -0,0 +1,120 @@ +import openmc +import os +import matplotlib.pyplot as plt + +# MATERIALS + +# creates a single material +mats = openmc.Materials() + +shielding_material = openmc.Material(name="breeder") +shielding_material.add_nuclide('Fe56', 1, percent_type='ao') +shielding_material.set_density('g/cm3', 7) + +mats = [shielding_material] + + +# GEOMETRY + +# surfaces +sph1 = openmc.Sphere(r=250, boundary_type='vacuum') + +# cells +shield_cell = openmc.Cell(region=-sph1) +shield_cell.fill = shielding_material + +universe = openmc.Universe(cells=[shield_cell]) + +geom = openmc.Geometry(universe) + +# creates a 14MeV neutron point source +source = openmc.Source() +source.space = openmc.stats.Point((0, 0, 0)) +source.angle = openmc.stats.Isotropic() +source.energy = openmc.stats.Discrete([14e6], [1]) +source.particles = 'neutron' + +# SETTINGS + +# Create mesh which will be used for the tally +my_tally_mesh = openmc.RegularMesh() +my_tally_mesh.dimension = [25, 1, 25] # only 1 cell in the Y dimension +my_tally_mesh.lower_left = [-120, -1, -120] # physical limits (corners) of the mesh +my_tally_mesh.upper_right = [120, 1, 120] + +# Create mesh filter for tally +mesh_filter = openmc.MeshFilter(my_tally_mesh) +mesh_tally = openmc.Tally(name='flux_on_mesh') +mesh_tally.filters = [mesh_filter] +mesh_tally.scores = ['flux'] +#creates an empty tally object +tallies = openmc.Tallies() +tallies.append(mesh_tally) + + +# Create mesh which will be used for tally and weight window +my_ww_mesh = openmc.RegularMesh() +my_ww_mesh.dimension = [25, 25, 25] +my_ww_mesh.lower_left = [-120, -120, -120] # physical limits (corners) of the mesh +my_ww_mesh.upper_right = [120, 120, 120] + +# imports values for weight windows +from weight_window_values import upper_ww_bounds, lower_ww_bounds + +# docs for ww are here +# https://docs.openmc.org/en/latest/_modules/openmc/weight_windows.html?highlight=weight%20windows +ww = openmc.WeightWindows( + mesh=my_ww_mesh, + upper_ww_bounds=upper_ww_bounds, + lower_ww_bounds=lower_ww_bounds, + particle_type='neutron', + energy_bins=(0.0, 100_000_000.), # applies this weight window to neutrons of within a large energy range (basically all neutrons in the simulation) + survival_ratio=5 +) + + +# Instantiate a Settings object +sett = openmc.Settings() +# as each particle history is now longer due to the splitting that occurs with +# weight windows. Running the same number of batches would therefore take more +# time. To make a fair comparison the batch has been reduce to 20 as this takes +# a similar amount of time as 100 without weight windows + +sett.batches = 20 +sett.inactive = 0 +sett.particles = 500 +sett.source = source +sett.run_mode = 'fixed source' +# sets the weight windows define to be used in the simulation +sett.weight_windows = ww + +# # deletes old files +# try: +# os.remove('summary.h5') +# except OSError: +# pass + + + +# combines the geometry, materials, settings and tallies to create a neutronics model +model = openmc.model.Model(geom, mats, sett, tallies) + +# runs the simulation with weight windows +output_ww_filename = model.run() + + +# open the results file +results_ww = openmc.StatePoint(output_ww_filename) + +# access the flux tally +my_tally_ww = results_ww.get_tally(scores=['flux']) +my_slice_ww = my_tally_ww.get_slice(scores=['flux']) +my_slice_ww.mean.shape = (25, 25) +fig = plt.subplot() + +# when plotting the 2d data, added the extent is required. +# otherwise the plot uses the index of the 2d data arrays +# as the x y axis +fig.imshow(my_slice_ww.mean, extent=[-120,120,-120,120])#, vmin=1e-5, vmax=10) +plt.savefig('ww.png') +plt.show() \ No newline at end of file diff --git a/tasks/task_13_variance_reduction/3_minimal_weight_window__spectra_tally_example.py b/tasks/task_13_variance_reduction/3_minimal_weight_window__spectra_tally_example.py new file mode 100644 index 00000000..e8c72a7a --- /dev/null +++ b/tasks/task_13_variance_reduction/3_minimal_weight_window__spectra_tally_example.py @@ -0,0 +1,150 @@ +import openmc +import os +from spectrum_plotter import plot_spectrum_from_tally + + +# MATERIALS + +# creates a single material +mats = openmc.Materials() + +shielding_material = openmc.Material(name="breeder") +shielding_material.add_nuclide('Fe56', 1, percent_type='ao') +shielding_material.set_density('g/cm3', 7) + +mats = [shielding_material] + + +# GEOMETRY + +# surfaces +sph1 = openmc.Sphere(r=250, boundary_type='vacuum') + +# cells +shield_cell = openmc.Cell(region=-sph1) +shield_cell.fill = shielding_material + +universe = openmc.Universe(cells=[shield_cell]) + +geom = openmc.Geometry(universe) + + +# creates a 14MeV neutron point source +source = openmc.Source() +source.space = openmc.stats.Point((0, 0, 0)) +source.angle = openmc.stats.Isotropic() +source.energy = openmc.stats.Discrete([14e6], [1]) +source.particles = 'neutron' + +# SETTINGS + +# Instantiate a Settings object +sett = openmc.Settings() +sett.batches = 100 +sett.inactive = 0 +sett.particles = 500 +sett.source = source +sett.run_mode = 'fixed source' + + +#creates an empty tally object +tallies = openmc.Tallies() + + +# setup the filters for the surface tally +# detects neutrons (not photons) +neutron_particle_filter = openmc.ParticleFilter(['neutron']) +# detects when particles across the surface +front_surface_filter = openmc.SurfaceFilter(sph1) +energy_bins = openmc.mgxs.GROUP_STRUCTURES['CCFE-709'] +energy_filter = openmc.EnergyFilter(energy_bins) + +front_surface_spectra_tally = openmc.Tally(name='front_surface_spectra_tally') +front_surface_spectra_tally.scores = ['current'] +front_surface_spectra_tally.filters = [front_surface_filter, neutron_particle_filter, energy_filter] +tallies.append(front_surface_spectra_tally) + + +# combines the geometry, materials, settings and tallies to create a neutronics model +model = openmc.model.Model(geom, mats, sett, tallies) + +# deletes old files +try: + os.remove('summary.h5') + os.remove('statepoint.*.h5') +except OSError: + pass + + +# runs the simulation without weight windows +output_filename = model.run() + +# open the results file +results = openmc.StatePoint(output_filename) +my_analogy_tally = results.get_tally(name="front_surface_spectra_tally") + + + +# Create mesh which will be used for the weight windows +my_ww_mesh = openmc.RegularMesh() + +my_ww_mesh.dimension = [25, 25, 25] +my_ww_mesh.lower_left = [-120, -120, -120] # physical limits (corners) of the mesh +my_ww_mesh.upper_right = [120, 120, 120] + +# imports values for weight windows +from weight_window_values import upper_ww_bounds, lower_ww_bounds + + +# docs for ww are here +# https://docs.openmc.org/en/latest/_modules/openmc/weight_windows.html?highlight=weight%20windows +ww = openmc.WeightWindows( + mesh=my_ww_mesh, + upper_ww_bounds=upper_ww_bounds, + lower_ww_bounds=lower_ww_bounds, + particle_type='neutron', + energy_bins=(0.0, 100_000_000.), # applies this weight window to neutrons of within a large energy range (basically all neutrons in the simulation) + survival_ratio=5 +) +# sets the weight windows define to be used in the simulation +sett.weight_windows = ww + +# deletes old files +try: + os.remove('summary.h5') +except OSError: + pass + +# as each particle history is now longer due to the splitting that occurs with +# weight windows. Running the same number of batches would therefore take more +# time. To make a fair comparison the batch has been reduce to 20 as this takes +# a similar amount of time as 100 without weight windows +sett.batches=20 + +# combines the geometry, materials, settings and tallies to create a neutronics model +model = openmc.model.Model(geom, mats, sett, tallies) + +# runs the simulation with weight windows +output_ww_filename = model.run() + +# open the results file +ww_results = openmc.StatePoint(output_ww_filename) +my_weight_window_tally = ww_results.get_tally(name="front_surface_spectra_tally") + + +# this function plots the neutron spectrum and requires spectrum_plotter to be installed +# pip install spectrum_plotter +test_plot = plot_spectrum_from_tally( + spectrum={"analogy": my_analogy_tally, 'my_weight_window_tally': my_weight_window_tally}, + x_label="Energy [MeV]", + y_label="Current [n/source_particle]", + x_scale="log", + y_scale="log", + title="example plot 1", + required_units="neutron / source_particle", + plotting_package="plotly", + filename="example_spectra_from_tally_matplotlib.html", +) + +# loads up the plot in a webbrowser +test_plot.show() diff --git a/tasks/task_13_variance_reduction/weight_window_values.py b/tasks/task_13_variance_reduction/weight_window_values.py new file mode 100644 index 00000000..e749b1d4 --- /dev/null +++ b/tasks/task_13_variance_reduction/weight_window_values.py @@ -0,0 +1,4 @@ + +lower_ww_bounds = [-1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, -1.0, 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a/tasks/task_13_variance_reduction/xml_examples/orig/with_ww/make_vtk.py b/tasks/task_13_variance_reduction/xml_examples/orig/with_ww/make_vtk.py new file mode 100644 index 00000000..9789a23a --- /dev/null +++ b/tasks/task_13_variance_reduction/xml_examples/orig/with_ww/make_vtk.py @@ -0,0 +1,16 @@ +from openmc_mesh_tally_to_vtk import write_mesh_tally_to_vtk +import openmc + +# assumes you have a statepoint file from the OpenMC simulation +statepoint = openmc.StatePoint('statepoint.2.h5') + +print(statepoint.tallies) + +# assumes the statepoint file has a RegularMesh tally with a certain name +my_tally = statepoint.get_tally(id=10) + +# converts the tally result into a VTK file +write_mesh_tally_to_vtk( + tally=my_tally, + filename = "vtk_file_from_openmc_mesh.vtk", +) \ No newline at end of file diff --git a/tasks/task_13_variance_reduction/xml_examples/orig/without_ww/make_vtk.py b/tasks/task_13_variance_reduction/xml_examples/orig/without_ww/make_vtk.py new file mode 100644 index 00000000..9789a23a --- /dev/null +++ b/tasks/task_13_variance_reduction/xml_examples/orig/without_ww/make_vtk.py @@ -0,0 +1,16 @@ +from openmc_mesh_tally_to_vtk import write_mesh_tally_to_vtk +import openmc + +# assumes you have a statepoint file from the OpenMC simulation +statepoint = openmc.StatePoint('statepoint.2.h5') + +print(statepoint.tallies) + +# assumes the statepoint file has a RegularMesh tally with a certain name +my_tally = statepoint.get_tally(id=10) + +# converts the tally result into a VTK file +write_mesh_tally_to_vtk( + tally=my_tally, + filename = "vtk_file_from_openmc_mesh.vtk", +) \ No newline at end of file diff --git a/tasks/task_14_activation_transmutation/1_example_transmutation_isotope_build_up.py b/tasks/task_14_activation_transmutation/1_example_transmutation_isotope_build_up.py new file mode 100644 index 00000000..383c7bba --- /dev/null +++ b/tasks/task_14_activation_transmutation/1_example_transmutation_isotope_build_up.py @@ -0,0 +1,96 @@ +import openmc +import openmc.deplete +import matplotlib.pyplot as plt +import math + +iron_sphere_radius = 250 + +# MATERIALS + +mats = openmc.Materials() + +# makes a simple material from Iron +shielding_material = openmc.Material(name="shielding_material") +shielding_material.add_nuclide('Co59', 1, percent_type='ao') +shielding_material.set_density('g/cm3', 7.7) +shielding_material.volume = (4/3) * math.pi * iron_sphere_radius**3 +shielding_material.depletable = True + +materials = openmc.Materials([shielding_material]) +materials.export_to_xml() + + +# GEOMETRY + +# surfaces +sph1 = openmc.Sphere(r=iron_sphere_radius, boundary_type='vacuum') + +# cells +shield_cell = openmc.Cell(region=-sph1) +shield_cell.fill = shielding_material +shield_cell.volume = (4/3) * math.pi * sph1.r**3 + +universe = openmc.Universe(cells=[shield_cell]) + +geometry = openmc.Geometry(universe) + + + +# creates a 14MeV neutron point source +source = openmc.Source() +source.space = openmc.stats.Point((0, 0, 0)) +source.angle = openmc.stats.Isotropic() +source.energy = openmc.stats.Discrete([14e6], [1]) +source.particles = 'neutron' + +# SETTINGS + +# Instantiate a Settings object +settings = openmc.Settings() +settings.batches = 5 +settings.inactive = 0 +settings.particles = 500 +settings.source = source +settings.run_mode = 'fixed source' + + +tallies = openmc.Tallies() + + +# run python generate_endf71_chain.py from the openmc-dev/data repo +chain_filename = '/home/jshim/data-shimwell/depletion/chain_endfb71.xml' +chain = openmc.deplete.Chain.from_xml(chain_filename) + +geometry.export_to_xml() +settings.export_to_xml() +# tallies.export_to_xml() # running in depletion mode doesn't write out the tallies file +materials.export_to_xml() +model = openmc.model.Model(geometry, materials, settings, tallies) + +operator = openmc.deplete.Operator(model, chain_filename) + + +time_steps = [365*24*60*60] * 5 +source_rates = [1e9]*5 # 1GW + +integrator = openmc.deplete.PredictorIntegrator( + operator=operator, timesteps=time_steps,source_rates=source_rates +) + +integrator.integrate() + +results = openmc.deplete.ResultsList.from_hdf5("depletion_results.h5") + +times, number_of_co60_atoms = results.get_atoms('1', 'Co60') + + +import matplotlib.pyplot as plt + +fig, ax = plt.subplots() +ax.plot(times, number_of_co60_atoms) + +ax.set(xlabel='time (s)', ylabel='Number of atoms', + title='Build up of atoms saturates when decay is equal to activation this occurs at circa 5 half lives') +ax.grid() +plt.savefig('atoms.png') +plt.show() \ No newline at end of file diff --git a/tasks/task_14_activation_transmutation/2_example_tally_change_with_burnup.py b/tasks/task_14_activation_transmutation/2_example_tally_change_with_burnup.py new file mode 100644 index 00000000..6d89931e --- /dev/null +++ b/tasks/task_14_activation_transmutation/2_example_tally_change_with_burnup.py @@ -0,0 +1,91 @@ +import openmc +import openmc.deplete +import matplotlib.pyplot as plt +import math + +lithium_orthosilicate_radius = 250 + +# MATERIALS + +mats = openmc.Materials() + +# makes a simple material from Iron +shielding_material = openmc.Material(name="shielding_material") +shielding_material.add_elements_from_formula('Li4SiO4') +shielding_material.set_density('g/cm3', 2.5) +shielding_material.volume = (4/3) * math.pi * lithium_orthosilicate_radius**3 +shielding_material.depletable = True + +materials = openmc.Materials([shielding_material]) +materials.export_to_xml() + + +# GEOMETRY + +# surfaces +sph1 = openmc.Sphere(r=lithium_orthosilicate_radius, boundary_type='vacuum') + +# cells +shield_cell = openmc.Cell(region=-sph1) +shield_cell.fill = shielding_material +shield_cell.volume = (4/3) * math.pi * sph1.r**3 + +universe = openmc.Universe(cells=[shield_cell]) + +geometry = openmc.Geometry(universe) + + + +# creates a 14MeV neutron point source +source = openmc.Source() +source.space = openmc.stats.Point((0, 0, 0)) +source.angle = openmc.stats.Isotropic() +source.energy = openmc.stats.Discrete([14e6], [1]) +source.particles = 'neutron' + +# SETTINGS + +# Instantiate a Settings object +settings = openmc.Settings() +settings.batches = 2 +settings.inactive = 0 +settings.particles = 500 +settings.source = source +settings.run_mode = 'fixed source' + + +tallies = openmc.Tallies() + +# added a cell tally for tritium production +cell_filter = openmc.CellFilter(shield_cell) +tbr_tally = openmc.Tally(name='TBR') +tbr_tally.filters = [cell_filter] +tbr_tally.scores = ['(n,Xt)'] # Where X is a wildcard character, this catches any tritium production +tallies.append(tbr_tally) + + +# run python generate_endf71_chain.py from the openmc-dev/data repo +chain_filename = '/home/jshim/data-shimwell/depletion/chain_endfb71.xml' +chain = openmc.deplete.Chain.from_xml(chain_filename) + +geometry.export_to_xml() +settings.export_to_xml() +tallies.export_to_xml() # running in depletion mode doesn't write out the tallies file +materials.export_to_xml() +model = openmc.model.Model(geometry, materials, settings, tallies) + +operator = openmc.deplete.Operator(model, chain_filename) + + +time_steps = [365*24*60*60] * 5 # 5 steps of 5 years in seconds +source_rates = [1e9]*5 # 1GW + + +integrator = openmc.deplete.PredictorIntegrator(operator, time_steps, source_rates) + +integrator.integrate() + +for counter in [0,1,2,3,4,5]: + sp = openmc.StatePoint(f'openmc_simulation_n{counter}.h5') + tbr_tally = sp.get_tally(name='TBR') + print(tbr_tally.mean, tbr_tally.std_dev) diff --git a/tasks/task_13_parameter_study_sampling/1_techniques_for_sampling_design_space.ipynb b/tasks/task_15_parameter_study_sampling/1_techniques_for_sampling_design_space.ipynb similarity index 100% rename from tasks/task_13_parameter_study_sampling/1_techniques_for_sampling_design_space.ipynb rename to tasks/task_15_parameter_study_sampling/1_techniques_for_sampling_design_space.ipynb diff --git a/tasks/task_13_parameter_study_sampling/README.md b/tasks/task_15_parameter_study_sampling/README.md similarity index 100% rename from tasks/task_13_parameter_study_sampling/README.md rename to tasks/task_15_parameter_study_sampling/README.md diff --git a/tasks/task_13_parameter_study_sampling/openmc_model.py b/tasks/task_15_parameter_study_sampling/openmc_model.py similarity index 100% rename from tasks/task_13_parameter_study_sampling/openmc_model.py rename to tasks/task_15_parameter_study_sampling/openmc_model.py diff --git a/tasks/task_13_parameter_study_sampling/plotting_tools.py b/tasks/task_15_parameter_study_sampling/plotting_tools.py similarity index 100% rename from tasks/task_13_parameter_study_sampling/plotting_tools.py rename to tasks/task_15_parameter_study_sampling/plotting_tools.py diff --git a/tasks/task_13_parameter_study_sampling/run_all.sh b/tasks/task_15_parameter_study_sampling/run_all.sh similarity index 100% rename from tasks/task_13_parameter_study_sampling/run_all.sh rename to tasks/task_15_parameter_study_sampling/run_all.sh diff --git a/tasks/task_14_parameter_study_optimisation/README.md b/tasks/task_16_parameter_study_optimisation/README.md similarity index 100% rename from tasks/task_14_parameter_study_optimisation/README.md rename to tasks/task_16_parameter_study_optimisation/README.md diff --git a/tasks/task_14_parameter_study_optimisation/openmc_model.py b/tasks/task_16_parameter_study_optimisation/openmc_model.py similarity index 100% rename from tasks/task_14_parameter_study_optimisation/openmc_model.py rename to tasks/task_16_parameter_study_optimisation/openmc_model.py diff --git a/tasks/task_14_parameter_study_optimisation/parameter_study_optimisation.ipynb b/tasks/task_16_parameter_study_optimisation/parameter_study_optimisation.ipynb similarity index 100% rename from tasks/task_14_parameter_study_optimisation/parameter_study_optimisation.ipynb rename to tasks/task_16_parameter_study_optimisation/parameter_study_optimisation.ipynb diff --git a/tasks/task_14_parameter_study_optimisation/run_all.sh b/tasks/task_16_parameter_study_optimisation/run_all.sh similarity index 100% rename from tasks/task_14_parameter_study_optimisation/run_all.sh rename to tasks/task_16_parameter_study_optimisation/run_all.sh diff --git a/tests/test_all_tasks.py b/tests/test_all_tasks.py deleted file mode 100644 index a1631c5f..00000000 --- a/tests/test_all_tasks.py +++ /dev/null @@ -1,136 +0,0 @@ - -""" -tests the create_isotope_plot from plotting_utils in the same way the examples -use the function. -""" - -import os -import sys -import unittest -from pathlib import Path - -import nbformat -from nbconvert.preprocessors import ExecutePreprocessor -from nbconvert.preprocessors.execute import CellExecutionError - - -def _notebook_run(path): - """ - Execute a notebook via nbconvert and collect output. - :returns (parsed nb object, execution errors) - """ - kernel_name = 'python%d' % sys.version_info[0] - this_file_directory = os.path.dirname(__file__) - errors = [] - - with open(path) as f: - nb = nbformat.read(f, as_version=4) - nb.metadata.get('kernelspec', {})['name'] = kernel_name - ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True - - try: - ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) - - except CellExecutionError as e: - if "SKIP" in e.traceback: - print(str(e.traceback).split("\n")[-2]) - else: - raise e - - return nb, errors - - -class test_tasks(unittest.TestCase): - - def test_task_1(self): - for notebook in Path().rglob("tasks/tasks/task_01_*/*.ipynb"): - print(notebook) - nb, errors = _notebook_run(notebook) - assert errors == [] - - def test_task_2(self): - for notebook in Path().rglob("tasks/task_02_*/*.ipynb"): - print(notebook) - nb, errors = _notebook_run(notebook) - assert errors == [] - - def test_task_3(self): - for notebook in Path().rglob("tasks/task_03_*/*.ipynb"): - print(notebook) - nb, errors = _notebook_run(notebook) - assert errors == [] - - def test_task_4(self): - for notebook in Path().rglob("tasks/task_04_*/1_.ipynb"): - nb, errors = _notebook_run(notebook) - assert errors == [] - for notebook in Path().rglob("tasks/task_04_*/4_.ipynb"): - nb, errors = _notebook_run(notebook) - assert errors == [] -# failing tasks -# 2_ring_source.ipynb -> no ring source in openmc 0.11 -# 3_plasma_source_plots.ipynb -> no ring source in openmc 0.11 -# 5_gamma_source_example.ipynb -> gamma outside of nuclear data energy range - - def test_task_5(self): - for notebook in Path().rglob("tasks/task_05_*/*.ipynb"): - print(notebook) - nb, errors = _notebook_run(notebook) - assert errors == [] - - def test_task_6(self): - for notebook in Path().rglob("tasks/task_06_*/*.ipynb"): - print(notebook) - nb, errors = _notebook_run(notebook) - assert errors == [] - - def test_task_7(self): - for notebook in Path().rglob("tasks/task_07_*/*.ipynb"): - print(notebook) - nb, errors = _notebook_run(notebook) - assert errors == [] - -# ModuleNotFoundError: No module named 'statepoint_to_vtk' -# def test_task_8(self): -# for notebook in Path().rglob("tasks/task_08_*/*.ipynb"): -# print(notebook) -# nb, errors = _notebook_run(notebook) -# assert errors == [] - - def test_task_9(self): - for notebook in Path().rglob("tasks/task_09_*/*.ipynb"): - print(notebook) - nb, errors = _notebook_run(notebook) - assert errors == [] - - def test_task_10(self): - for notebook in Path().rglob("tasks/task_10_*/*.ipynb"): - print(notebook) - nb, errors = _notebook_run(notebook) - assert errors == [] - - def test_task_11(self): - for notebook in Path().rglob("tasks/task_11_*/*.ipynb"): - print(notebook) - nb, errors = _notebook_run(notebook) - assert errors == [] - - def test_task_12(self): - for notebook in Path().rglob("tasks/task_12_*/*.ipynb"): - print(notebook) - nb, errors = _notebook_run(notebook) - assert errors == [] - -# No module named 'openmc_model' - # def test_task_13(self): - # for notebook in Path().rglob("tasks/task_13_*/*.ipynb"): - # print(notebook) - # nb, errors = _notebook_run(notebook) - # assert errors == [] - -# No module named 'openmc_model' - # def test_task_14(self): - # for notebook in Path().rglob("tasks/task_14_*/*.ipynb"): - # print(notebook) - # nb, errors = _notebook_run(notebook) - # assert errors == [] diff --git a/tests/test_task_1.py b/tests/test_task_1.py new file mode 100644 index 00000000..96426195 --- /dev/null +++ b/tests/test_task_1.py @@ -0,0 +1,49 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + + def test_task_1(self): + for notebook in Path().rglob("tasks/tasks/task_01_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] diff --git a/tests/test_task_10.py b/tests/test_task_10.py new file mode 100644 index 00000000..6ae16201 --- /dev/null +++ b/tests/test_task_10.py @@ -0,0 +1,49 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + + def test_task_10(self): + for notebook in Path().rglob("tasks/task_10_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] diff --git a/tests/test_task_11.py b/tests/test_task_11.py new file mode 100644 index 00000000..1373d2e0 --- /dev/null +++ b/tests/test_task_11.py @@ -0,0 +1,49 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=900) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + + def test_task_11(self): + for notebook in Path().rglob("tasks/task_11_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] diff --git a/tests/test_task_12.py b/tests/test_task_12.py new file mode 100644 index 00000000..c4a3f238 --- /dev/null +++ b/tests/test_task_12.py @@ -0,0 +1,49 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=900) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + + def test_task_12(self): + for notebook in Path().rglob("tasks/task_12_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] diff --git a/tests/test_task_13.py b/tests/test_task_13.py new file mode 100644 index 00000000..d85331c2 --- /dev/null +++ b/tests/test_task_13.py @@ -0,0 +1,50 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + +# No module named 'openmc_model' + def test_task_13(self): + for notebook in Path().rglob("tasks/task_13_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] diff --git a/tests/test_task_14.py b/tests/test_task_14.py new file mode 100644 index 00000000..a66355d2 --- /dev/null +++ b/tests/test_task_14.py @@ -0,0 +1,50 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + +# No module named 'openmc_model' + def test_task_14(self): + for notebook in Path().rglob("tasks/task_14_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] diff --git a/tests/test_task_2.py b/tests/test_task_2.py new file mode 100644 index 00000000..deb003dc --- /dev/null +++ b/tests/test_task_2.py @@ -0,0 +1,49 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + + def test_task_2(self): + for notebook in Path().rglob("tasks/task_02_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] diff --git a/tests/test_task_3.py b/tests/test_task_3.py new file mode 100644 index 00000000..8762c9bd --- /dev/null +++ b/tests/test_task_3.py @@ -0,0 +1,49 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + + def test_task_3(self): + for notebook in Path().rglob("tasks/task_03_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] diff --git a/tests/test_task_4.py b/tests/test_task_4.py new file mode 100644 index 00000000..b2eeb8f5 --- /dev/null +++ b/tests/test_task_4.py @@ -0,0 +1,55 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + + def test_task_4(self): + for notebook in Path().rglob("tasks/task_04_*/1_.ipynb"): + nb, errors = _notebook_run(notebook) + assert errors == [] + for notebook in Path().rglob("tasks/task_04_*/4_.ipynb"): + nb, errors = _notebook_run(notebook) + assert errors == [] +# failing tasks +# 2_ring_source.ipynb -> no ring source in openmc 0.11 +# 3_plasma_source_plots.ipynb -> no ring source in openmc 0.11 +# 5_gamma_source_example.ipynb -> gamma outside of nuclear data energy range diff --git a/tests/test_task_5.py b/tests/test_task_5.py new file mode 100644 index 00000000..21e3f94e --- /dev/null +++ b/tests/test_task_5.py @@ -0,0 +1,49 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + + def test_task_5(self): + for notebook in Path().rglob("tasks/task_05_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] diff --git a/tests/test_task_6.py b/tests/test_task_6.py new file mode 100644 index 00000000..9ca20f7b --- /dev/null +++ b/tests/test_task_6.py @@ -0,0 +1,49 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + + def test_task_6(self): + for notebook in Path().rglob("tasks/task_06_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] diff --git a/tests/test_task_7.py b/tests/test_task_7.py new file mode 100644 index 00000000..15123efd --- /dev/null +++ b/tests/test_task_7.py @@ -0,0 +1,49 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + + def test_task_7(self): + for notebook in Path().rglob("tasks/task_07_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] diff --git a/tests/test_task_8.py b/tests/test_task_8.py new file mode 100644 index 00000000..37735342 --- /dev/null +++ b/tests/test_task_8.py @@ -0,0 +1,50 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + +# ModuleNotFoundError: No module named 'statepoint_to_vtk' + def test_task_8(self): + for notebook in Path().rglob("tasks/task_08_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == [] diff --git a/tests/test_task_9.py b/tests/test_task_9.py new file mode 100644 index 00000000..28cc1057 --- /dev/null +++ b/tests/test_task_9.py @@ -0,0 +1,49 @@ + +""" +tests the create_isotope_plot from plotting_utils in the same way the examples +use the function. +""" + +import os +import sys +import unittest +from pathlib import Path + +import nbformat +from nbconvert.preprocessors import ExecutePreprocessor +from nbconvert.preprocessors.execute import CellExecutionError + + +def _notebook_run(path): + """ + Execute a notebook via nbconvert and collect output. + :returns (parsed nb object, execution errors) + """ + kernel_name = 'python%d' % sys.version_info[0] + this_file_directory = os.path.dirname(__file__) + errors = [] + + with open(path) as f: + nb = nbformat.read(f, as_version=4) + nb.metadata.get('kernelspec', {})['name'] = kernel_name + ep = ExecutePreprocessor(kernel_name=kernel_name, timeout=300) #, allow_errors=True + + try: + ep.preprocess(nb, {'metadata': {'path': this_file_directory}}) + + except CellExecutionError as e: + if "SKIP" in e.traceback: + print(str(e.traceback).split("\n")[-2]) + else: + raise e + + return nb, errors + + +class test_tasks(unittest.TestCase): + + def test_task_9(self): + for notebook in Path().rglob("tasks/task_09_*/*.ipynb"): + print(notebook) + nb, errors = _notebook_run(notebook) + assert errors == []