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Merge remote-tracking branch 'upstream/develop' into skbuild-minimal
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‎CONTRIBUTING.md

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@@ -13,7 +13,7 @@ [email protected].
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## Resources
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- [GitHub Repository](https://github.com/openmc-dev/openmc)
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- [Documentation](http://docs.openmc.org/en/latest)
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- [Documentation](https://docs.openmc.org/en/latest)
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- [Discussion Forum](https://openmc.discourse.group)
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- [Slack Community](https://openmc.slack.com/signup) (If you don't see your
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domain listed, contact [email protected])

‎cmake/Modules/GetVersionFromGit.cmake

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@@ -37,11 +37,17 @@ if(EXISTS "${CMAKE_SOURCE_DIR}/.git" AND GIT_FOUND)
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WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
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OUTPUT_VARIABLE VERSION_STRING
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OUTPUT_STRIP_TRAILING_WHITESPACE
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ERROR_QUIET
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)
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# If no tags are found, instruct user to fetch them
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# If no tags are found, set version to 0 and show a warning
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if(VERSION_STRING STREQUAL "")
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message(FATAL_ERROR "No git tags found. Run 'git fetch --tags' and try again.")
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set(VERSION_STRING "0.0.0")
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message(WARNING
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"No git tags found. Version set to 0.0.0.\n"
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"Run 'git fetch --tags' to ensure proper versioning.\n"
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"For more information, see OpenMC developer documentation."
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)
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endif()
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# Extract the commit hash

‎docs/source/devguide/docker.rst

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@@ -45,12 +45,11 @@ Now you can run the following to create a `Docker container`_ called
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This command will open an interactive shell running from within the
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Docker container where you have access to use OpenMC.
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.. note:: The ``docker run`` command supports many
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`options <https://docs.docker.com/engine/reference/commandline/run/>`_
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.. note:: The ``docker run`` command supports many options_
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for spawning containers -- including `mounting volumes`_ from the
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host filesystem -- which many users will find useful.
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.. _Docker image: https://docs.docker.com/engine/reference/commandline/images/
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.. _Docker image: https://docs.docker.com/get-started/docker-concepts/the-basics/what-is-an-image/
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.. _Docker container: https://www.docker.com/resources/what-container
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.. _options: https://docs.docker.com/engine/reference/commandline/run/
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.. _mounting volumes: https://docs.docker.com/storage/volumes/
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.. _options: https://docs.docker.com/reference/cli/docker/container/run/
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.. _mounting volumes: https://docs.docker.com/engine/storage/volumes/

‎docs/source/devguide/styleguide.rst

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@@ -47,7 +47,8 @@ is more difficult to comment out a large section of code that uses C-style
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comments.)
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Do not use C-style casting. Always use the C++-style casts ``static_cast``,
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``const_cast``, or ``reinterpret_cast``. (See `ES.49 <http://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines#es49-if-you-must-use-a-cast-use-a-named-cast>`_)
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``const_cast``, or ``reinterpret_cast``. (See `ES.49
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<https://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines#es49-if-you-must-use-a-cast-use-a-named-cast>`_)
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Source Files
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------------
@@ -156,11 +157,11 @@ Prefer pathlib_ when working with filesystem paths over functions in the os_
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module or other standard-library modules. Functions that accept arguments that
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represent a filesystem path should work with both strings and Path_ objects.
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.. _C++ Core Guidelines: http://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines
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.. _PEP8: https://www.python.org/dev/peps/pep-0008/
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.. _C++ Core Guidelines: https://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines
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.. _PEP8: https://peps.python.org/pep-0008/
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.. _numpydoc: https://numpydoc.readthedocs.io/en/latest/format.html
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.. _numpy: https://numpy.org/
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.. _scipy: https://www.scipy.org/
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.. _scipy: https://scipy.org/
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.. _matplotlib: https://matplotlib.org/
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.. _pandas: https://pandas.pydata.org/
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.. _h5py: https://www.h5py.org/

‎docs/source/devguide/user-input.rst

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@@ -55,6 +55,6 @@ developer or send a message to the `developers mailing list`_.
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.. _property attribute: https://docs.python.org/3.6/library/functions.html#property
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.. _XML Schema Part 2: http://www.w3.org/TR/xmlschema-2/
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.. _boolean: http://www.w3.org/TR/xmlschema-2/#boolean
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.. _XML Schema Part 2: https://www.w3.org/TR/xmlschema-2/
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.. _boolean: https://www.w3.org/TR/xmlschema-2/#boolean
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.. _developers mailing list: https://groups.google.com/forum/?fromgroups=#!forum/openmc-dev

‎docs/source/devguide/workflow.rst

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@@ -91,6 +91,30 @@ features and bug fixes. The general steps for contributing are as follows:
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6. After the pull request has been thoroughly vetted, it is merged back into the
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*develop* branch of openmc-dev/openmc.
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Setting Up Upstream Tracking (Required for Versioning)
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------------------------------------------------------
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By default, your fork **does not** include tags from the upstream OpenMC repository.
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OpenMC relies on `git describe --tags` for versioning in source builds, and missing tags can lead
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to incorrect version detection (i.e., ``0.0.0``). To ensure proper versioning, follow these steps:
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1. **Add the Upstream Repository**
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This allows you to fetch updates from the main OpenMC repository.
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.. code-block:: sh
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git remote add upstream https://github.com/openmc-dev/openmc.git
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2. **Fetch and Push Tags**
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Retrieve tags from the upstream repository and update your fork:
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.. code-block:: sh
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git fetch --tags upstream
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git push --tags origin
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This ensures that both your **local** and **remote** fork have the correct versioning information.
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Private Development
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-------------------
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.. _git: https://git-scm.com/
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.. _GitHub: https://github.com/
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.. _git flow: https://nvie.com/git-model
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.. _valgrind: https://www.valgrind.org/
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.. _valgrind: https://valgrind.org/
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.. _style guide: https://docs.openmc.org/en/latest/devguide/styleguide.html
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.. _pull request: https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/about-pull-requests
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.. _openmc-dev/openmc: https://github.com/openmc-dev/openmc

‎docs/source/methods/cross_sections.rst

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@@ -295,8 +295,8 @@ or even isotropic scattering.
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.. _Josey: https://doi.org/10.1016/j.jcp.2015.08.013
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.. _WMP Library: https://github.com/mit-crpg/WMP_Library
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.. _MCNP: https://mcnp.lanl.gov
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.. _Serpent: https://serpent.vtt.fi/serpent/
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.. _NJOY: https://www.njoy21.io/NJOY21/
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.. _Serpent: https://serpent.vtt.fi
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.. _NJOY: https://www.njoy21.io/
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.. _ENDF/B data: https://www.nndc.bnl.gov/endf-b8.0/
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.. _Leppanen: https://doi.org/10.1016/j.anucene.2009.03.019
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.. _algorithms: http://ab-initio.mit.edu/faddeeva/

‎docs/source/methods/depletion.rst

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twice as expensive as the predictor method, but achieves an error of
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:math:`\mathcal{O}(h^2)`. An exhaustive description of time integration methods
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and their merits can be found in the `thesis of Colin Josey
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<http://dspace.mit.edu/handle/1721.1/7582>`_.
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<https://dspace.mit.edu/handle/1721.1/7582>`_.
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OpenMC does not rely on a single time integration method but rather has several
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‎docs/source/methods/geometry.rst

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.. _constructive solid geometry: https://en.wikipedia.org/wiki/Constructive_solid_geometry
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.. _surfaces: https://en.wikipedia.org/wiki/Surface
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.. _MCNP: https://mcnp.lanl.gov
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.. _Serpent: https://serpent.vtt.fi/serpent/
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.. _Serpent: https://serpent.vtt.fi
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.. _Monte Carlo Performance benchmark: https://github.com/mit-crpg/benchmarks/tree/master/mc-performance/openmc

‎docs/source/methods/neutron_physics.rst

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.. _Watt fission spectrum: https://doi.org/10.1103/PhysRev.87.1037
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.. _Foderaro: http://hdl.handle.net/1721.1/1716
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.. _Foderaro: https://dspace.mit.edu/handle/1721.1/1716
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.. _OECD: https://www.oecd-nea.org/tools/abstract/detail/NEA-1792
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.. _NJOY: https://www.njoy21.io/NJOY2016/
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.. _PREPRO: https://www-nds.iaea.org/ndspub/endf/prepro/
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.. _PREPRO: https://www-nds.iaea.org/public/endf/prepro/
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.. _ENDF-6 Format: https://www.oecd-nea.org/dbdata/data/manual-endf/endf102.pdf
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.. _Monte Carlo Sampler: https://permalink.lanl.gov/object/tr?what=info:lanl-repo/lareport/LA-09721-MS
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.. _Monte Carlo Sampler: https://mcnp.lanl.gov/pdf_files/TechReport_1983_LANL_LA-9721-MS_EverettCashwell.pdf
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.. _LA-UR-14-27694: https://permalink.lanl.gov/object/tr?what=info:lanl-repo/lareport/LA-UR-14-27694
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.. _LA-UR-14-27694: https://www.osti.gov/biblio/1159204
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.. _MC21: https://www.osti.gov/biblio/903083
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.. _Romano: https://doi.org/10.1016/j.cpc.2014.11.001
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.. _Sutton and Brown: https://www.osti.gov/biblio/307911
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.. _lectures: https://laws.lanl.gov/vhosts/mcnp.lanl.gov/pdf_files/la-ur-05-4983.pdf
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.. _MCNP Manual: https://laws.lanl.gov/vhosts/mcnp.lanl.gov/pdf_files/la-ur-03-1987.pdf
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.. _lectures: https://mcnp.lanl.gov/pdf_files/TechReport_2005_LANL_LA-UR-05-4983_Brown.pdf

‎docs/source/methods/parallelization.rst

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.. _first paper: https://doi.org/10.2307/2280232
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.. _work of Forrest Brown: http://hdl.handle.net/2027.42/24996
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.. _work of Forrest Brown: https://deepblue.lib.umich.edu/handle/2027.42/24996
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.. _Brissenden and Garlick: https://doi.org/10.1016/0306-4549(86)90095-2
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.. _MPICH: http://www.mpich.org
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.. _MPICH: https://www.mpich.org
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.. _binomial tree: https://www.mcs.anl.gov/~thakur/papers/ijhpca-coll.pdf
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.. _Geary: https://doi.org/10.2307/2342070
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.. _Barnett: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.51.7772
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.. _Barnett: https://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.51.7772
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‎docs/source/methods/photon_physics.rst

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.. _anomalous scattering: http://pd.chem.ucl.ac.uk/pdnn/diff1/anomscat.htm
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.. _Kahn's rejection method: https://mcnp.lanl.gov/pdf_files/TechReport_1956_RC_AECU-3259RM-1237-AEC_Kahn.pdf
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.. _Kahn's rejection method: https://doi.org/10.2172/4353680
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.. _Klein-Nishina: https://en.wikipedia.org/wiki/Klein%E2%80%93Nishina_formula
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‎docs/source/methods/tallies.rst

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.. _unpublished rational approximation: https://stackedboxes.org/2017/05/01/acklams-normal-quantile-function/
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.. _MC21: http://www.osti.gov/bridge/servlets/purl/903083-HT5p1o/903083.pdf
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.. _MC21: https://www.osti.gov/servlets/purl/903083

‎docs/source/publications.rst

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*Trans. Am. Nucl. Soc.*, **114**, 391-394 (2016).
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- Derek M. Lax, "`Memory efficient indexing algorithm for physical properties in
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OpenMC <http://hdl.handle.net/1721.1/97862>`_," S. M. Thesis, Massachusetts
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Institute of Technology (2015).
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OpenMC <https://dspace.mit.edu/handle/1721.1/97862>`_," S. M. Thesis,
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Massachusetts Institute of Technology (2015).
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- Derek Lax, William Boyd, Nicholas Horelik, Benoit Forget, and Kord Smith, "A
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memory efficient algorithm for classifying unique regions in constructive
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- Jonathan A. Walsh, Benoit Forget, Kord S. Smith, Brian C. Kiedrowski, and
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Forrest B. Brown, "`Direct, on-the-fly calculation of unresolved resonance
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region cross sections in Monte Carlo simulations
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<http://hdl.handle.net/1721.1/108644>`_," *Proc. Joint Int. Conf. M&C+SNA+MC*,
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<https://dspace.mit.edu/handle/1721.1/108644>`_," *Proc. Joint Int. Conf.
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M&C+SNA+MC*,
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Nashville, Tennessee, Apr. 19--23 (2015).
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- Colin Josey, Benoit Forget, and Kord Smith, "`Windowed multipole sensitivity
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- Matthew S. Ellis, Colin Josey, Benoit Forget, and Kord Smith, "`Spatially
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Continuous Depletion Algorithm for Monte Carlo Simulations
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<http://hdl.handle.net/1721.1/107880>`_," *Trans. Am. Nucl. Soc.*, **115**,
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<https://dspace.mit.edu/handle/1721.1/107880>`_," *Trans. Am. Nucl. Soc.*,
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**115**,
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1221-1224 (2016).
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- Anas Gul, K. S. Chaudri, R. Khan, and M. Azeen, "`Development and verification

‎docs/source/pythonapi/deplete.rst

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provided that implement different time-integration algorithms for depletion
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calculations, which are described in detail in Colin Josey's thesis,
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`Development and analysis of high order neutron transport-depletion coupling
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algorithms <http://hdl.handle.net/1721.1/113721>`_.
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algorithms <https://dspace.mit.edu/handle/1721.1/113721>`_.
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.. autosummary::
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:toctree: generated

‎docs/source/quickinstall.rst

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your computer. For more detailed instructions on configuring and installing
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OpenMC, see :ref:`usersguide_install` in the User's Manual.
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--------------------------------------------------
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Installing on Linux/Mac with Mamba and conda-forge
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--------------------------------------------------
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----------------------------------
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Installing on Linux/Mac with Conda
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----------------------------------
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`Conda <https://conda.io/en/latest/>`_ is an open source package management
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`Conda <https://docs.conda.io/en/latest/>`_ is an open source package management
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system and environments management system for installing multiple versions of
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software packages and their dependencies and switching easily between them.
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`Mamba <https://mamba.readthedocs.io/en/latest/>`_ is a cross-platform package
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manager and is compatible with `conda` packages.
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OpenMC can be installed in a `conda` environment with `mamba`.
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First, `conda` should be installed with one of the following installers:
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`Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_,
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`Anaconda <https://www.anaconda.com/>`_, or `Miniforge <https://github.com/conda-forge/miniforge>`_.
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Once you have `conda` installed on your system, OpenMC can be installed via the
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`conda-forge` channel with `mamba`.
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OpenMC can be installed in a `conda` environment. First, `conda` should be
19+
`installed <https://www.anaconda.com/docs/getting-started/getting-started>`_
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with either Anaconda Distribution or Miniconda. Once you have `conda` installed
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on your system, OpenMC can be installed via the `conda-forge` channel.
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First, add the `conda-forge` channel with:
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.. code-block:: sh
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conda config --add channels conda-forge
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conda config --set channel_priority strict
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Then create and activate a new conda enviroment called `openmc-env` in
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which to install OpenMC.
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Then create and activate a new conda enviroment called `openmc-env` (or whatever
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you wish) with OpenMC installed.
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.. code-block:: sh
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conda create -n openmc-env
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conda create --name openmc-env openmc
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conda activate openmc-env
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Then install `mamba`, which will be used to install OpenMC.
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.. code-block:: sh
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conda install mamba
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To list the versions of OpenMC that are available on the `conda-forge` channel,
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in your terminal window or an Anaconda Prompt run:
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.. code-block:: sh
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mamba search openmc
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OpenMC can then be installed with:
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.. code-block:: sh
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mamba install openmc
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You are now in a conda environment called `openmc-env` that has OpenMC installed.
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You are now in a conda environment called `openmc-env` that has OpenMC
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installed.
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-------------------------------------------
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Installing on Linux/Mac/Windows with Docker

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