paulromano · Mar 7, 2025 · Feb 21, 2025 · Feb 21, 2025 · Feb 24, 2025 · Mar 7, 2025
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -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)

diff --git a/docs/source/devguide/docker.rst b/docs/source/devguide/docker.rst
@@ -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/
diff --git a/docs/source/devguide/styleguide.rst b/docs/source/devguide/styleguide.rst
@@ -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
 ------------
@@ -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/

diff --git a/docs/source/devguide/user-input.rst b/docs/source/devguide/user-input.rst
@@ -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
diff --git a/docs/source/devguide/workflow.rst b/docs/source/devguide/workflow.rst
@@ -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

diff --git a/docs/source/methods/cross_sections.rst b/docs/source/methods/cross_sections.rst
@@ -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/

diff --git a/docs/source/methods/depletion.rst b/docs/source/methods/depletion.rst
@@ -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

diff --git a/docs/source/methods/geometry.rst b/docs/source/methods/geometry.rst
@@ -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
diff --git a/docs/source/methods/neutron_physics.rst b/docs/source/methods/neutron_physics.rst
@@ -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
diff --git a/docs/source/methods/parallelization.rst b/docs/source/methods/parallelization.rst
@@ -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
 

diff --git a/docs/source/methods/photon_physics.rst b/docs/source/methods/photon_physics.rst
@@ -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
 

diff --git a/docs/source/methods/tallies.rst b/docs/source/methods/tallies.rst
@@ -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
diff --git a/docs/source/publications.rst b/docs/source/publications.rst
@@ -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
@@ -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
@@ -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

diff --git a/docs/source/pythonapi/deplete.rst b/docs/source/pythonapi/deplete.rst
@@ -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

diff --git a/docs/source/quickinstall.rst b/docs/source/quickinstall.rst
@@ -8,56 +8,35 @@ This quick install guide outlines the basic steps needed to install OpenMC on
 your computer. For more detailed instructions on configuring and installing
 OpenMC, see :ref:`usersguide_install` in the User's Manual.
 
---------------------------------------------------
-Installing on Linux/Mac with Mamba and conda-forge
---------------------------------------------------
+----------------------------------
+Installing on Linux/Mac with Conda
+----------------------------------
 
-`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`.
+OpenMC can be installed in a `conda` environment. First, `conda` should be
+`installed <https://www.anaconda.com/docs/getting-started/getting-started>`_
+with either Anaconda Distribution or Miniconda. Once you have `conda` installed
+on your system, OpenMC can be installed via the `conda-forge` channel.
 
 First, add the `conda-forge` channel with:
 
 .. code-block:: sh
 
     conda config --add channels conda-forge
+    conda config --set channel_priority strict
 
-Then create and activate a new conda enviroment called `openmc-env` in
-which to install OpenMC.
+Then create and activate a new conda enviroment called `openmc-env` (or whatever
+you wish) with OpenMC installed.
 
 .. code-block:: sh
 
-    conda create -n openmc-env
+    conda create --name openmc-env openmc
     conda activate openmc-env
 
-Then install `mamba`, which will be used to install OpenMC.
-
-.. code-block:: sh
-
-    conda install mamba
-
-To list the versions of OpenMC that are available on the `conda-forge` channel,
-in your terminal window or an Anaconda Prompt run:
-
-.. code-block:: sh
-
-    mamba search openmc
-
-OpenMC can then be installed with:
-
-.. code-block:: sh
-
-    mamba install openmc
-
-You are now in a conda environment called `openmc-env` that has OpenMC installed.
+You are now in a conda environment called `openmc-env` that has OpenMC
+installed.
 
 -------------------------------------------
 Installing on Linux/Mac/Windows with Docker
Original file line number	Diff line number	Diff line change
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