Merge pull request #91 from fusion-energy/develop

Fixing tests and making use of dagmc-bounding-box package
fusion-energy · Nov 25, 2021 · c6d9a99 · c6d9a99
2 parents 48a74ba + aeb5f1d
commit c6d9a99
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Showing 29 changed files with 488 additions and 441 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -15,6 +15,11 @@ jobs:
           command: |
             python setup.py install
 
+      - run:
+          name: install packages required for testing
+          command: |
+            pip install -r requirements-test.txt
+
       - run:
           name: run test_neutronics_utils
           command: 

diff --git a/.github/workflows/ci_with_install.yml b/.github/workflows/ci_with_install.yml
@@ -23,6 +23,10 @@ jobs:
         run: |
           python setup.py install
 
+      - name: install packages required for testing
+        run: |
+          pip install -r requirements-test.txt
+
       - name: run tests
         run: |
           pytest tests/test_neutronics_utils.py -v --cov=openmc_dagmc_wrapper --cov-append --cov-report term --cov-report xml

diff --git a/Dockerfile b/Dockerfile
@@ -109,7 +109,7 @@ RUN pip install --upgrade numpy cython && \
 
 
 # Clone and install Double-Down
-RUN git clone --shallow-submodules --single-branch --branch main --depth 1 https://github.com/pshriwise/double-down.git && \
+RUN 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 && \
@@ -125,7 +125,11 @@ RUN mkdir DAGMC && \
     cd DAGMC && \
     # change to version 3.2.1 when released
     # git clone --single-branch --branch 3.2.1 --depth 1 https://github.com/svalinn/DAGMC.git && \
-    git clone --shallow-submodules --single-branch --branch develop --depth 1 https://github.com/svalinn/DAGMC.git && \
+    git clone --single-branch --branch develop 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 .. && \
     mkdir build && \
     cd build && \
     cmake ../DAGMC -DBUILD_TALLY=ON \
@@ -140,7 +144,11 @@ RUN mkdir DAGMC && \
 
 # Clone and install OpenMC with DAGMC
 # TODO clone a specific release when the next release containing (PR 1825) is avaialble.
-RUN git clone --shallow-submodules --recurse-submodules --single-branch --branch develop --depth 1 https://github.com/openmc-dev/openmc.git  /opt/openmc && \
+RUN cd /opt && \
+    git clone --single-branch --branch develop 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 && \
     cd /opt/openmc && \
     mkdir build && \
     cd build && \

diff --git a/README.md b/README.md
@@ -20,33 +20,26 @@
 
 # OpenMC DAGMC Wrapper
 
-The openmc-dagmc-wrapper python package allows convenient access to a series of standard neutronics simulations and post using OpenMC and DAGMC.
-
-The intended use case is to take DAGMC compatible h5m files generated by 
-[cad_to_h5m](https://github.com/fusion-energy/cad_to_h5m) with CAD file inputs
-from the [Paramak](https://github.com/fusion-energy/paramak) as demonstrated in
-the [neutronics_workflow](https://github.com/fusion-energy/neutronics_workflow). However the package can also be used with h5m files generated in other ways.
-
-Standard simulations tallies are facilitated:
-- Volume / cell tallies
-- Regular 2D mesh tallies
-- Regular 3D mesh tallies
-- Unstructured mesh tally (on road map)
-
-Neutronics responses can be obtained:
-- Tritium Breeding Ratio (TBR)
-- Heating (photon and neutron)
-- Effective dose (photon and neutron)
-- Any supported reaction from the [standard OpenMC reactions](https://docs.openmc.org/en/latest/usersguide/tallies.html#scores)
-
-A standard collection of materials are available by making use of the
-[neutronics_material_maker](https://github.com/fusion-energy/neutronics_material_maker) package.
-
-OpenMC sources definitions are used for the particle sources. 
-
-Post processing of the OpenMC output files are also carried out to automatically
-provide: JSON text files, PNG images, VTK files for convenient access to the
-results.
+
+The openmc-dagmc-wrapper python package extends OpenMC base classes and adds
+convenience features aimed as easing the use of OpenMC with DAGMC for
+fixed-source simulations.
+
+The openmc-dagmc-wrapper is built around the assumption that a DAGMC geometry
+in the form of a h5m is used as the simulation geometry. This allows several
+aspects of openmc simulations to be simplified and automated.
+
+Additional convenience is available when making tallies as standard tally types
+are added which automated the application of openmc.Filters and openmc.scores
+for standard tallies such as neutron spectra, effective dose, heating, TBR and
+others. 
+
+Further simplifications are access by using additional packages from the
+[fusion-neutronics-workflow](https://github.com/fusion-energy/fusion_neutronics_workflow)
+
+If you are looking for an easy neutronics interface for performing simulations
+of fusion reactors this package was built for you.
+
 
 :point_right: [Documentation](https://openmc-dagmc-wrapper.readthedocs.io)
 

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -35,7 +35,7 @@
 
 # If your documentation needs a minimal Sphinx version, state it here.
 #
-needs_sphinx = '3.5.4'
+needs_sphinx = "3.5.4"
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
@@ -136,11 +136,13 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc,
-     "OpenMC-DAGMC-Wrapper.tex",
-     "OpenMC-DAGMC-Wrapper Documentation",
-     "OpenMC-DAGMC-Wrapper contributors",
-     "manual"),
+    (
+        master_doc,
+        "OpenMC-DAGMC-Wrapper.tex",
+        "OpenMC-DAGMC-Wrapper Documentation",
+        "OpenMC-DAGMC-Wrapper contributors",
+        "manual",
+    ),
 ]
 
 
@@ -149,11 +151,14 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc,
-     "OpenMC-DAGMC-Wrapper",
-     "OpenMC-DAGMC-Wrapper Documentation",
-     [author],
-     1)]
+    (
+        master_doc,
+        "OpenMC-DAGMC-Wrapper",
+        "OpenMC-DAGMC-Wrapper Documentation",
+        [author],
+        1,
+    )
+]
 
 
 # -- Options for Texinfo output ----------------------------------------------
@@ -194,4 +199,4 @@
 
 # -- Extension configuration -------------------------------------------------
 
-html_favicon = 'favicon.ico'
+html_favicon = "favicon.ico"
diff --git a/docs/source/example_neutronics_simulations.rst b/docs/source/example_neutronics_simulations.rst
diff --git a/docs/source/fusion_settings.rst b/docs/source/fusion_settings.rst
@@ -0,0 +1,7 @@
+
+FusionSettings()
+----------------
+
+.. automodule:: openmc_dagmc_wrapper.FusionSettings
+   :members:
+   :show-inheritance:
diff --git a/docs/source/geometry.rst b/docs/source/geometry.rst
@@ -0,0 +1,7 @@
+
+Geometry()
+----------
+
+.. automodule:: openmc_dagmc_wrapper.Geometry
+   :members:
+   :show-inheritance:
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -1,60 +1,32 @@
 openmc-dagmc-wrapper
 ====================
 
-The openmc-dagmc-wrapper python package allows convenient access to a series of
-standard neutronics simulations and post using OpenMC and DAGMC.
+The openmc-dagmc-wrapper python package extends OpenMC base classes and adds
+convenience features aimed as easing the use of OpenMC with DAGMC for
+fixed-source simulations.
 
-.. toctree::
-   :maxdepth: 1
-
-   install
-   example_neutronics_simulations
-   neutronics_model
-   tests
-
-History
--------
-
-The package was originally conceived by Jonathan Shimwell to help automate
-neutronics simulations of fusion reactors in a reproducible manner.
-
-The source code is distributed with a permissive open-source
-license (MIT) and is available from the GitHub repository 
-`https://github.com/fusion-energy/openmc-dagmc-wrapper <https://github.com/fusion-energy/openmc-dagmc-wrapper>`_
+The openmc-dagmc-wrapper is built around the assumption that a DAGMC geometry
+in the form of a h5m is used as the simulation geometry. This allows several
+aspects of openmc simulations to be simplified and automated.
 
+Additional convenience is available when making tallies as standard tally types
+are added which automated the application of openmc.Filters and openmc.scores
+for standard tallies such as neutron spectra, effective dose, heating, TBR and
+others. 
 
-Features
---------
+Further simplifications are access by using additional packages from the
+`fusion-neutronics-workflow <https://github.com/fusion-energy/fusion_neutronics_workflow>`_
 
-In general the openmc-dagmc-wrapper takes a DAGMC geometry in the form of a h5m
-file and helps adding tallies, materials and a source term to be easily added to 
-create a complete neutronics model. The package will also post processes the
-results of the neutronics simulation to allow easy access to the outputs.
-The simulated results are extracted from the statepoint.h5 file that
-OpenMC produces and converted to vtk, png and JSON files depending on the tally.
+If you are looking for an easy neutronics interface for performing simulations
+of fusion reactors this package was built for you.
 
-To create a model it is also necessary to define the source and the materials
-used. 
-
-The Paramak accepts native OpenMC materials and also Neutronics Material Maker
-materials. Further details on the Neutronics Material Maker is avaialbe via online
-`documentation <https://neutronics-material-maker.readthedocs.io/en/latest/>`_ 
-and the `source code repository <https://github.com/fusion-energy/neutronics_material_maker>`_
-.
-
-The `OpenMC workshop <https://github.com/fusion-energy/neutronics_workshop>`_ 
-also has some tasks that make use of this package. The workshop also
-demonstrates methods of creating the CAD geometry and h5m files from CAD
-geometry.
-
-The `OpenMC workflow <https://github.com/fusion-energy/neutronics_workflow>`_ 
-demonstrates the use of this package along side others in a complete neutronics
-tool chain.
-
-`CAD-to-h5m <https://github.com/fusion-energy/cad_to_h5m>`_ makes use of the
-`Cubit API <https://coreform.com/products/coreform-cubit/>`_ to convert CAD
-files (stp or sat format) into `DAGMC <https://svalinn.github.io/DAGMC/>`_ 
-compatible h5m files for use in DAGMC enabled neutronics codes.
+.. toctree::
+   :maxdepth: 2
 
-For magnetic confinement fusion simulations you might want to use the parametric-plasma-source
-`Git repository <https://github.com/open-radiation-sources/parametric-plasma-source>`_ 
+   install
+   geometry
+   materials
+   fusion_settings
+   tally
+   tests
+   license
diff --git a/docs/source/install.rst b/docs/source/install.rst
@@ -2,13 +2,29 @@
 Installation
 ============
 
-
-Install
--------
-
 To use the OpenMC-DAGMC-Wrapper package you will need the Python, MOAB, DAGMC
 and OpenMC installed.
 
+
+To complete the software stack OpenMC, DAGMC and MOAB will also need installing.
+We don't have simple instructions for these packages yet but one option is to
+duplicate the stages in the `Dockerfile https://github.com/fusion-energy/neutronics_workflow/blob/main/Dockerfile>`_
+or to make use of the `install scripts <https://github.com/fusion-energy/neutronics_workflow/blob/main/install_scripts/`_
+
+
+Pip install
+-----------
+
+Then install the OpenMC-DAGMC-Wrapper package using Pip.
+
+.. code-block:: python
+
+   pip install openmc-dagmc-wrapper
+
+
+Conda install
+-------------
+
 The recommended method is to install Python 3 using Anaconda or Miniconda
 
 * `Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_ (preferable to avoid hdf5 conflicts)
@@ -38,12 +54,6 @@ Then install the OpenMC-DAGMC-Wrapper package using Pip.
    pip install openmc-dagmc-wrapper
 
 
-To complete the software stack OpenMC, DAGMC and MOAB will also need installing.
-We don't have simple instructions for these packages yet but one option is to
-duplicate the stages in the `Dockerfile https://github.com/fusion-energy/neutronics_workflow/blob/main/Dockerfile>`_
-or to make use of the `install scripts <https://github.com/fusion-energy/neutronics_workflow/blob/main/install_scripts/`_
-
-
 Docker Image Installation
 -------------------------
 

diff --git a/docs/source/license.rst b/docs/source/license.rst
@@ -0,0 +1,7 @@
+
+License
+-------
+
+The source code is distributed with a permissive open-source license (MIT) and
+is available from the GitHub repository 
+`https://github.com/fusion-energy/openmc-dagmc-wrapper <https://github.com/fusion-energy/openmc-dagmc-wrapper>`_
diff --git a/docs/source/materials.rst b/docs/source/materials.rst
@@ -0,0 +1,10 @@
+
+A standard collection of materials are available by making use of the
+[neutronics_material_maker](https://github.com/fusion-energy/neutronics_material_maker) package.
+
+Materials()
+-----------
+
+.. automodule:: openmc_dagmc_wrapper.Materials
+   :members:
+   :show-inheritance:
diff --git a/docs/source/neutronics_model.rst b/docs/source/neutronics_model.rst