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Update a bunch of broken links / redirects
  • Loading branch information
paulromano committed Mar 7, 2025
commit 0809d6c9bfb06c03b93688131250ab72b49f35d2
2 changes: 1 addition & 1 deletion CONTRIBUTING.md
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Expand Up @@ -13,7 +13,7 @@ openmc@anl.gov.
## Resources

- [GitHub Repository](https://github.com/openmc-dev/openmc)
- [Documentation](http://docs.openmc.org/en/latest)
- [Documentation](https://docs.openmc.org/en/latest)
- [Discussion Forum](https://openmc.discourse.group)
- [Slack Community](https://openmc.slack.com/signup) (If you don't see your
domain listed, contact openmc@anl.gov)
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9 changes: 4 additions & 5 deletions docs/source/devguide/docker.rst
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Expand Up @@ -45,12 +45,11 @@ Now you can run the following to create a `Docker container`_ called
This command will open an interactive shell running from within the
Docker container where you have access to use OpenMC.

.. note:: The ``docker run`` command supports many
`options <https://docs.docker.com/engine/reference/commandline/run/>`_
.. note:: The ``docker run`` command supports many options_
for spawning containers -- including `mounting volumes`_ from the
host filesystem -- which many users will find useful.

.. _Docker image: https://docs.docker.com/engine/reference/commandline/images/
.. _Docker image: https://docs.docker.com/get-started/docker-concepts/the-basics/what-is-an-image/
.. _Docker container: https://www.docker.com/resources/what-container
.. _options: https://docs.docker.com/engine/reference/commandline/run/
.. _mounting volumes: https://docs.docker.com/storage/volumes/
.. _options: https://docs.docker.com/reference/cli/docker/container/run/
.. _mounting volumes: https://docs.docker.com/engine/storage/volumes/
9 changes: 5 additions & 4 deletions docs/source/devguide/styleguide.rst
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Expand Up @@ -47,7 +47,8 @@ is more difficult to comment out a large section of code that uses C-style
comments.)

Do not use C-style casting. Always use the C++-style casts ``static_cast``,
``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>`_)
``const_cast``, or ``reinterpret_cast``. (See `ES.49
<https://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines#es49-if-you-must-use-a-cast-use-a-named-cast>`_)

Source Files
------------
Expand Down Expand Up @@ -156,11 +157,11 @@ Prefer pathlib_ when working with filesystem paths over functions in the os_
module or other standard-library modules. Functions that accept arguments that
represent a filesystem path should work with both strings and Path_ objects.

.. _C++ Core Guidelines: http://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines
.. _PEP8: https://www.python.org/dev/peps/pep-0008/
.. _C++ Core Guidelines: https://isocpp.github.io/CppCoreGuidelines/CppCoreGuidelines
.. _PEP8: https://peps.python.org/pep-0008/
.. _numpydoc: https://numpydoc.readthedocs.io/en/latest/format.html
.. _numpy: https://numpy.org/
.. _scipy: https://www.scipy.org/
.. _scipy: https://scipy.org/
.. _matplotlib: https://matplotlib.org/
.. _pandas: https://pandas.pydata.org/
.. _h5py: https://www.h5py.org/
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4 changes: 2 additions & 2 deletions docs/source/devguide/user-input.rst
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Expand Up @@ -55,6 +55,6 @@ developer or send a message to the `developers mailing list`_.


.. _property attribute: https://docs.python.org/3.6/library/functions.html#property
.. _XML Schema Part 2: http://www.w3.org/TR/xmlschema-2/
.. _boolean: http://www.w3.org/TR/xmlschema-2/#boolean
.. _XML Schema Part 2: https://www.w3.org/TR/xmlschema-2/
.. _boolean: https://www.w3.org/TR/xmlschema-2/#boolean
.. _developers mailing list: https://groups.google.com/forum/?fromgroups=#!forum/openmc-dev
2 changes: 1 addition & 1 deletion docs/source/devguide/workflow.rst
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Expand Up @@ -129,7 +129,7 @@ can interfere with virtual environments.
.. _git: https://git-scm.com/
.. _GitHub: https://github.com/
.. _git flow: https://nvie.com/git-model
.. _valgrind: https://www.valgrind.org/
.. _valgrind: https://valgrind.org/
.. _style guide: https://docs.openmc.org/en/latest/devguide/styleguide.html
.. _pull request: https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/about-pull-requests
.. _openmc-dev/openmc: https://github.com/openmc-dev/openmc
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4 changes: 2 additions & 2 deletions docs/source/methods/cross_sections.rst
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Expand Up @@ -295,8 +295,8 @@ or even isotropic scattering.
.. _Josey: https://doi.org/10.1016/j.jcp.2015.08.013
.. _WMP Library: https://github.com/mit-crpg/WMP_Library
.. _MCNP: https://mcnp.lanl.gov
.. _Serpent: https://serpent.vtt.fi/serpent/
.. _NJOY: https://www.njoy21.io/NJOY21/
.. _Serpent: https://serpent.vtt.fi
.. _NJOY: https://www.njoy21.io/
.. _ENDF/B data: https://www.nndc.bnl.gov/endf-b8.0/
.. _Leppanen: https://doi.org/10.1016/j.anucene.2009.03.019
.. _algorithms: http://ab-initio.mit.edu/faddeeva/
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2 changes: 1 addition & 1 deletion docs/source/methods/depletion.rst
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Expand Up @@ -114,7 +114,7 @@ The predictor method only requires one evaluation and its error converges as
twice as expensive as the predictor method, but achieves an error of
:math:`\mathcal{O}(h^2)`. An exhaustive description of time integration methods
and their merits can be found in the `thesis of Colin Josey
<http://dspace.mit.edu/handle/1721.1/7582>`_.
<https://dspace.mit.edu/handle/1721.1/7582>`_.

OpenMC does not rely on a single time integration method but rather has several
classes that implement different algorithms. For example, the
Expand Down
2 changes: 1 addition & 1 deletion docs/source/methods/geometry.rst
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Expand Up @@ -1066,5 +1066,5 @@ surface is known as in :ref:`reflection`.
.. _constructive solid geometry: https://en.wikipedia.org/wiki/Constructive_solid_geometry
.. _surfaces: https://en.wikipedia.org/wiki/Surface
.. _MCNP: https://mcnp.lanl.gov
.. _Serpent: https://serpent.vtt.fi/serpent/
.. _Serpent: https://serpent.vtt.fi
.. _Monte Carlo Performance benchmark: https://github.com/mit-crpg/benchmarks/tree/master/mc-performance/openmc
12 changes: 5 additions & 7 deletions docs/source/methods/neutron_physics.rst
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Expand Up @@ -1743,26 +1743,24 @@ types.

.. _Watt fission spectrum: https://doi.org/10.1103/PhysRev.87.1037

.. _Foderaro: http://hdl.handle.net/1721.1/1716
.. _Foderaro: https://dspace.mit.edu/handle/1721.1/1716

.. _OECD: https://www.oecd-nea.org/tools/abstract/detail/NEA-1792

.. _NJOY: https://www.njoy21.io/NJOY2016/

.. _PREPRO: https://www-nds.iaea.org/ndspub/endf/prepro/
.. _PREPRO: https://www-nds.iaea.org/public/endf/prepro/

.. _ENDF-6 Format: https://www.oecd-nea.org/dbdata/data/manual-endf/endf102.pdf

.. _Monte Carlo Sampler: https://permalink.lanl.gov/object/tr?what=info:lanl-repo/lareport/LA-09721-MS
.. _Monte Carlo Sampler: https://mcnp.lanl.gov/pdf_files/TechReport_1983_LANL_LA-9721-MS_EverettCashwell.pdf

.. _LA-UR-14-27694: https://permalink.lanl.gov/object/tr?what=info:lanl-repo/lareport/LA-UR-14-27694
.. _LA-UR-14-27694: https://www.osti.gov/biblio/1159204

.. _MC21: https://www.osti.gov/biblio/903083

.. _Romano: https://doi.org/10.1016/j.cpc.2014.11.001

.. _Sutton and Brown: https://www.osti.gov/biblio/307911

.. _lectures: https://laws.lanl.gov/vhosts/mcnp.lanl.gov/pdf_files/la-ur-05-4983.pdf

.. _MCNP Manual: https://laws.lanl.gov/vhosts/mcnp.lanl.gov/pdf_files/la-ur-03-1987.pdf
.. _lectures: https://mcnp.lanl.gov/pdf_files/TechReport_2005_LANL_LA-UR-05-4983_Brown.pdf
6 changes: 3 additions & 3 deletions docs/source/methods/parallelization.rst
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Expand Up @@ -609,17 +609,17 @@ is actually independent of the number of nodes:

.. _first paper: https://doi.org/10.2307/2280232

.. _work of Forrest Brown: http://hdl.handle.net/2027.42/24996
.. _work of Forrest Brown: https://deepblue.lib.umich.edu/handle/2027.42/24996

.. _Brissenden and Garlick: https://doi.org/10.1016/0306-4549(86)90095-2

.. _MPICH: http://www.mpich.org
.. _MPICH: https://www.mpich.org

.. _binomial tree: https://www.mcs.anl.gov/~thakur/papers/ijhpca-coll.pdf

.. _Geary: https://doi.org/10.2307/2342070

.. _Barnett: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.51.7772
.. _Barnett: https://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.51.7772

.. _single-instruction multiple-data: https://en.wikipedia.org/wiki/SIMD

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2 changes: 1 addition & 1 deletion docs/source/methods/photon_physics.rst
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Expand Up @@ -1059,7 +1059,7 @@ emitted photon.

.. _anomalous scattering: http://pd.chem.ucl.ac.uk/pdnn/diff1/anomscat.htm

.. _Kahn's rejection method: https://mcnp.lanl.gov/pdf_files/TechReport_1956_RC_AECU-3259RM-1237-AEC_Kahn.pdf
.. _Kahn's rejection method: https://doi.org/10.2172/4353680

.. _Klein-Nishina: https://en.wikipedia.org/wiki/Klein%E2%80%93Nishina_formula

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2 changes: 1 addition & 1 deletion docs/source/methods/tallies.rst
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Expand Up @@ -522,4 +522,4 @@ improve the estimate of the percentile.

.. _unpublished rational approximation: https://stackedboxes.org/2017/05/01/acklams-normal-quantile-function/

.. _MC21: http://www.osti.gov/bridge/servlets/purl/903083-HT5p1o/903083.pdf
.. _MC21: https://www.osti.gov/servlets/purl/903083
10 changes: 6 additions & 4 deletions docs/source/publications.rst
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Expand Up @@ -138,8 +138,8 @@ Geometry and Visualization
*Trans. Am. Nucl. Soc.*, **114**, 391-394 (2016).

- Derek M. Lax, "`Memory efficient indexing algorithm for physical properties in
OpenMC <http://hdl.handle.net/1721.1/97862>`_," S. M. Thesis, Massachusetts
Institute of Technology (2015).
OpenMC <https://dspace.mit.edu/handle/1721.1/97862>`_," S. M. Thesis,
Massachusetts Institute of Technology (2015).

- Derek Lax, William Boyd, Nicholas Horelik, Benoit Forget, and Kord Smith, "A
memory efficient algorithm for classifying unique regions in constructive
Expand Down Expand Up @@ -399,7 +399,8 @@ Doppler Broadening
- Jonathan A. Walsh, Benoit Forget, Kord S. Smith, Brian C. Kiedrowski, and
Forrest B. Brown, "`Direct, on-the-fly calculation of unresolved resonance
region cross sections in Monte Carlo simulations
<http://hdl.handle.net/1721.1/108644>`_," *Proc. Joint Int. Conf. M&C+SNA+MC*,
<https://dspace.mit.edu/handle/1721.1/108644>`_," *Proc. Joint Int. Conf.
M&C+SNA+MC*,
Nashville, Tennessee, Apr. 19--23 (2015).

- Colin Josey, Benoit Forget, and Kord Smith, "`Windowed multipole sensitivity
Expand Down Expand Up @@ -596,7 +597,8 @@ Depletion

- Matthew S. Ellis, Colin Josey, Benoit Forget, and Kord Smith, "`Spatially
Continuous Depletion Algorithm for Monte Carlo Simulations
<http://hdl.handle.net/1721.1/107880>`_," *Trans. Am. Nucl. Soc.*, **115**,
<https://dspace.mit.edu/handle/1721.1/107880>`_," *Trans. Am. Nucl. Soc.*,
**115**,
1221-1224 (2016).

- Anas Gul, K. S. Chaudri, R. Khan, and M. Azeen, "`Development and verification
Expand Down
2 changes: 1 addition & 1 deletion docs/source/pythonapi/deplete.rst
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Expand Up @@ -26,7 +26,7 @@ provided to obtain reaction rates from cross-section data. Several classes are
provided that implement different time-integration algorithms for depletion
calculations, which are described in detail in Colin Josey's thesis,
`Development and analysis of high order neutron transport-depletion coupling
algorithms <http://hdl.handle.net/1721.1/113721>`_.
algorithms <https://dspace.mit.edu/handle/1721.1/113721>`_.

.. autosummary::
:toctree: generated
Expand Down
16 changes: 8 additions & 8 deletions docs/source/quickinstall.rst
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Expand Up @@ -12,17 +12,17 @@ OpenMC, see :ref:`usersguide_install` in the User's Manual.
Installing on Linux/Mac with Mamba and conda-forge
--------------------------------------------------

`Conda <https://conda.io/en/latest/>`_ is an open source package management
`Conda <https://docs.conda.io/en/latest/>`_ is an open source package management
system and environments management system for installing multiple versions of
software packages and their dependencies and switching easily between them.
`Mamba <https://mamba.readthedocs.io/en/latest/>`_ is a cross-platform package
manager and is compatible with `conda` packages.
OpenMC can be installed in a `conda` environment with `mamba`.
First, `conda` should be installed with one of the following installers:
`Miniconda <https://docs.conda.io/en/latest/miniconda.html>`_,
`Anaconda <https://www.anaconda.com/>`_, or `Miniforge <https://github.com/conda-forge/miniforge>`_.
Once you have `conda` installed on your system, OpenMC can be installed via the
`conda-forge` channel with `mamba`.
manager and is compatible with `conda` packages. OpenMC can be installed in a
`conda` environment with `mamba`. First, `conda` should be installed with one of
the following installers: `Miniconda
<https://docs.conda.io/en/latest/miniconda.html>`_, `Anaconda
<https://www.anaconda.com/>`_, or `Miniforge
<https://github.com/conda-forge/miniforge>`_. Once you have `conda` installed on
your system, OpenMC can be installed via the `conda-forge` channel with `mamba`.

First, add the `conda-forge` channel with:

Expand Down
2 changes: 1 addition & 1 deletion docs/source/usersguide/basics.rst
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Expand Up @@ -53,7 +53,7 @@ eXtensible Markup Language (XML)
Unlike many other Monte Carlo codes which use an arbitrary-format ASCII file
with "cards" to specify a particular geometry, materials, and associated run
settings, the input files for OpenMC are structured in a set of `XML
<http://www.w3.org/XML/>`_ files. XML, which stands for eXtensible Markup
<https://www.w3.org/XML/>`_ files. XML, which stands for eXtensible Markup
Language, is a simple format that allows data to be exchanged efficiently
between different programs and interfaces.

Expand Down
12 changes: 6 additions & 6 deletions docs/source/usersguide/beginners.rst
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Expand Up @@ -109,8 +109,8 @@ familiar with. Whether you plan on working in Linux, macOS, or Windows, you
should be comfortable working in a command line environment. There are many
resources online for learning command line environments. If you are using Linux
or Mac OS X (also Unix-derived), `this tutorial
<http://www.ee.surrey.ac.uk/Teaching/Unix/>`_ will help you get acquainted with
commonly-used commands.
<https://info-ee.surrey.ac.uk/Teaching/Unix/>`_ will help you get acquainted
with commonly-used commands.

To reap the full benefits of OpenMC, you should also have basic proficiency in
the use of `Python <https://www.python.org/>`_, as OpenMC includes a rich Python
Expand All @@ -127,8 +127,8 @@ are hosted at `GitHub`_. In order to receive updates to the code directly,
submit `bug reports`_, and perform other development tasks, you may want to sign
up for a free account on GitHub. Once you have an account, you can follow `these
instructions
<https://docs.github.com/en/github/getting-started-with-github/set-up-git>`_ on
how to set up your computer for using GitHub.
<https://docs.github.com/en/get-started/getting-started-with-git/set-up-git>`_
on how to set up your computer for using GitHub.

If you are new to nuclear engineering, you may want to review the NRC's `Reactor
Concepts Manual`_. This manual describes the basics of nuclear power for
Expand All @@ -149,9 +149,9 @@ and `Volume II`_. You may also find it helpful to review the following terms:
.. _neutron transport: https://en.wikipedia.org/wiki/Neutron_transport
.. _discretization: https://en.wikipedia.org/wiki/Discretization
.. _constructive solid geometry: https://en.wikipedia.org/wiki/Constructive_solid_geometry
.. _git: http://git-scm.com/
.. _git: https://git-scm.com/
.. _git tutorials: https://git-scm.com/doc
.. _Reactor Concepts Manual: http://www.tayloredge.com/periodic/trivia/ReactorConcepts.pdf
.. _Reactor Concepts Manual: https://www.tayloredge.com/periodic/trivia/ReactorConcepts.pdf
.. _Volume I: https://www.standards.doe.gov/standards-documents/1000/1019-bhdbk-1993-v1
.. _Volume II: https://www.standards.doe.gov/standards-documents/1000/1019-bhdbk-1993-v2
.. _OpenMC source code: https://github.com/openmc-dev/openmc
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18 changes: 9 additions & 9 deletions docs/source/usersguide/data.rst
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Expand Up @@ -12,9 +12,9 @@ responsible for specifying one or more of the following:
file (commonly named ``cross_sections.xml``) contains a listing of other data
files, in particular neutron cross sections, photon cross sections, and
windowed multipole data. Each of those files, in turn, uses a `HDF5
<https://support.hdfgroup.org/documentation/index.html>`_ format (see :ref:`io_nuclear_data`). In
order to run transport simulations with continuous-energy cross sections, you
need to specify this file.
<https://www.hdfgroup.org/solutions/hdf5/>`_ format (see
:ref:`io_nuclear_data`). In order to run transport simulations with
continuous-energy cross sections, you need to specify this file.

- **Depletion chain (XML)** -- A :ref:`depletion chain XML <io_depletion_chain>`
file contains decay data, fission product yields, and information on what
Expand Down Expand Up @@ -69,7 +69,7 @@ If you want to persistently set the environment variables used to initialized
the configuration, export them from your shell profile (``.profile`` or
``.bashrc`` in bash_).

.. _bash: http://www.linuxfromscratch.org/blfs/view/6.3/postlfs/profile.html
.. _bash: https://www.linuxfromscratch.org/blfs/view/6.3/postlfs/profile.html

--------------------------------
Continuous-Energy Cross Sections
Expand Down Expand Up @@ -290,16 +290,16 @@ calculation to be performed. Therefore, at this point in time, OpenMC is not
distributed with any pre-existing multigroup cross section libraries. However,
if a multigroup library file is downloaded or generated, the path to the file
needs to be specified as described in :ref:`usersguide_data_runtime`. For an
example of how to create a multigroup library, see the `example notebook
<https://nbviewer.org/github/openmc-dev/openmc-notebooks/blob/main/mgxs-part-i.ipynb>`_.
example of how to create a multigroup library, see this `MG mode notebook
<https://nbviewer.org/github/openmc-dev/openmc-notebooks/blob/main/mg-mode-part-i.ipynb>`_.

.. _NJOY: http://www.njoy21.io/
.. _NJOY: https://www.njoy21.io/
.. _NNDC: https://www.nndc.bnl.gov/endf
.. _MCNP: https://mcnp.lanl.gov
.. _Serpent: https://serpent.vtt.fi/serpent/
.. _Serpent: https://serpent.vtt.fi
.. _ENDF/B: https://www.nndc.bnl.gov/endf-b7.1/acefiles.html
.. _JEFF: https://www.oecd-nea.org/dbdata/jeff/jeff33/
.. _TENDL: https://tendl.web.psi.ch/tendl_2017/tendl2017.html
.. _TENDL: https://tendl.web.psi.ch/tendl_2023/tendl2023.html
.. _Seltzer and Berger: https://doi.org/10.1016/0092-640X(86)90014-8
.. _NIST ESTAR database: https://physics.nist.gov/PhysRefData/Star/Text/ESTAR.html
.. _Biggs et al.: https://doi.org/10.1016/0092-640X(75)90030-3
16 changes: 8 additions & 8 deletions docs/source/usersguide/decay_sources.rst
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Expand Up @@ -47,14 +47,14 @@ Direct 1-Step (D1S) Calculations
================================

OpenMC also includes built-in capability for performing shutdown dose rate
calculations using the `direct 1-step <https://10.1016/S0920-3796(01)00188-0>`_
(D1S) method. In this method, a single coupled neutron--photon transport
calculation is used where the prompt photon production is replaced with photons
produced from the decay of radionuclides in an activated material. To obtain
properly scaled results, it is also necessary to apply time correction factors.
A normal neutron transport calculation can be extended to a D1S calculation with
a few helper functions. First, import the ``d1s`` submodule, which is part of
:mod:`openmc.deplete`::
calculations using the `direct 1-step
<https://doi.org/10.1016/S0920-3796(01)00188-0>`_ (D1S) method. In this method,
a single coupled neutron--photon transport calculation is used where the prompt
photon production is replaced with photons produced from the decay of
radionuclides in an activated material. To obtain properly scaled results, it is
also necessary to apply time correction factors. A normal neutron transport
calculation can be extended to a D1S calculation with a few helper functions.
First, import the ``d1s`` submodule, which is part of :mod:`openmc.deplete`::

from openmc.deplete import d1s

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2 changes: 1 addition & 1 deletion docs/source/usersguide/install.rst
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Expand Up @@ -557,7 +557,7 @@ distributions.
notebook
<https://nbviewer.jupyter.org/github/openmc-dev/openmc-notebooks/blob/main/pandas-dataframes.ipynb>`_.

`h5py <http://www.h5py.org/>`_
`h5py <https://www.h5py.org/>`_
h5py provides Python bindings to the HDF5 library. Since OpenMC outputs
various HDF5 files, h5py is needed to provide access to data within these
files from Python.
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2 changes: 1 addition & 1 deletion docs/source/usersguide/parallel.rst
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Expand Up @@ -101,5 +101,5 @@ performance on a machine when running in parallel:
settings = openmc.Settings()
settings.output = {'tallies': False}

.. _Haswell-EP: http://www.anandtech.com/show/8423/intel-xeon-e5-version-3-up-to-18-haswell-ep-cores-/4
.. _Haswell-EP: https://www.anandtech.com/show/8423/intel-xeon-e5-version-3-up-to-18-haswell-ep-cores-/4
.. _bound: https://github.com/pmodels/mpich/blob/main/doc/wiki/how_to/Using_the_Hydra_Process_Manager.md#process-core-binding
4 changes: 2 additions & 2 deletions include/openmc/random_dist.h
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Expand Up @@ -64,8 +64,8 @@ extern "C" double watt_spectrum(double a, double b, uint64_t* seed);
//! Samples from a normal distribution with a given mean and standard deviation
//! The PDF is defined as s(x) = (1/2*sigma*sqrt(2) * e-((mu-x)/2*sigma)^2
//! Its sampled according to
//! http://www-pdg.lbl.gov/2009/reviews/rpp2009-rev-monte-carlo-techniques.pdf
//! section 33.4.4
//! https://pdg.lbl.gov/2023/reviews/rpp2023-rev-monte-carlo-techniques.pdf
//! section 42.4.4
//!
//! \param mean mean of the Gaussian distribution
//! \param std_dev standard deviation of the Gaussian distribution
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6 changes: 3 additions & 3 deletions openmc/data/ace.py
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Expand Up @@ -9,9 +9,9 @@
ENDF data has been reconstructed and Doppler-broadened, the ACER module
generates ACE-format cross sections.

.. _MCNP: https://laws.lanl.gov/vhosts/mcnp.lanl.gov/
.. _NJOY: http://t2.lanl.gov/codes.shtml
.. _ENDF: http://www.nndc.bnl.gov/endf
.. _MCNP: https://mcnp.lanl.gov/
.. _NJOY: https://www.njoy21.io/
.. _ENDF: https://www.nndc.bnl.gov/endf-library/

"""

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