Fix broken links, use https over http, replace redirects

docs/source/usersguide/beginners.rst

@@ -113,7 +113,7 @@ or Mac OS X (also Unix-derived), `this tutorial
 commonly-used commands.
 
 To reap the full benefits of OpenMC, you should also have basic proficiency in
-the use of `Python <http://www.python.org/>`_, as OpenMC includes a rich Python
+the use of `Python <https://www.python.org/>`_, as OpenMC includes a rich Python
 API that offers many usability improvements over dealing with raw XML input
 files.
 
@@ -126,8 +126,9 @@ at the git documentation website. The `OpenMC source code`_ and documentation
 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://help.github.com/articles/set-up-git/>`_ on how to set up
-your computer for using GitHub.
+instructions
+<https://docs.github.com/en/github/getting-started-with-github/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
@@ -149,7 +150,7 @@ and `Volume II`_. You may also find it helpful to review the following terms:
 .. _discretization: https://en.wikipedia.org/wiki/Discretization
 .. _constructive solid geometry: https://en.wikipedia.org/wiki/Constructive_solid_geometry
 .. _git: http://git-scm.com/
-.. _git tutorials: http://git-scm.com/documentation
+.. _git tutorials: https://git-scm.com/doc
 .. _Reactor Concepts Manual: http://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

docs/source/usersguide/cross_sections.rst

@@ -260,7 +260,7 @@ For an example of how to create a multi-group library, see the `example notebook
 .. _MCNP: https://mcnp.lanl.gov
 .. _Serpent: http://montecarlo.vtt.fi
 .. _ENDF/B: https://www.nndc.bnl.gov/endf/b7.1/acefiles.html
-.. _JEFF: http://www.oecd-nea.org/dbdata/jeff/jeff33/
+.. _JEFF: https://www.oecd-nea.org/dbdata/jeff/jeff33/
 .. _TENDL: https://tendl.web.psi.ch/tendl_2017/tendl2017.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

docs/source/usersguide/geometry.rst

@@ -261,7 +261,7 @@ lowest-level cell at that location::
 
 As you are building a geometry, it is also possible to display a plot of single
 universe using the :meth:`Universe.plot` method. This method requires that you
-have `matplotlib <http://matplotlib.org/>`_ installed.
+have `matplotlib <https://matplotlib.org/>`_ installed.
 
 .. _usersguide_lattices:
 

docs/source/usersguide/install.rst

@@ -71,7 +71,7 @@ Now OpenMC should be recognized within the repository and can be installed:
 Binary packages from this PPA may exist for earlier versions of Ubuntu, but they
 are no longer supported.
 
-.. _Personal Package Archive: https://launchpad.net/~paulromano/+archive/staging
+.. _Personal Package Archive: https://launchpad.net/~paulromano/+archive/ubuntu/staging
 .. _APT package manager: https://help.ubuntu.com/community/AptGet/Howto
 
 .. _install-spack:
@@ -242,9 +242,9 @@ Prerequisites
 
 
 .. _gcc: https://gcc.gnu.org/
-.. _CMake: http://www.cmake.org
-.. _OpenMPI: http://www.open-mpi.org
-.. _MPICH: http://www.mpich.org
+.. _CMake: https://cmake.org
+.. _OpenMPI: https://www.open-mpi.org
+.. _MPICH: https://www.mpich.org
 .. _HDF5: https://www.hdfgroup.org/solutions/hdf5/
 .. _DAGMC: https://svalinn.github.io/DAGMC/index.html
 
@@ -256,10 +256,10 @@ directly from GitHub or, if you have the git_ version control software installed
 on your computer, you can use git to obtain the source code. The latter method
 has the benefit that it is easy to receive updates directly from the GitHub
 repository. GitHub has a good set of `instructions
-<http://help.github.com/set-up-git-redirect>`_ for how to set up git to work
-with GitHub since this involves setting up ssh_ keys. With git installed and
-setup, the following command will download the full source code from the GitHub
-repository::
+<https://docs.github.com/en/github/getting-started-with-github/set-up-git>`_ for
+how to set up git to work with GitHub since this involves setting up ssh_ keys.
+With git installed and setup, the following command will download the full
+source code from the GitHub repository::
 
     git clone --recurse-submodules https://github.com/openmc-dev/openmc.git
 
@@ -408,8 +408,8 @@ Compiling on Windows 10
 
 Recent versions of Windows 10 include a subsystem for Linux that allows one to
 run Bash within Ubuntu running in Windows. First, follow the installation guide
-`here <https://msdn.microsoft.com/en-us/commandline/wsl/install_guide>`_ to get
-Bash on Ubuntu on Windows setup. Once you are within bash, obtain the necessary
+`here <https://docs.microsoft.com/en-us/windows/wsl/install-win10>`_ to get Bash
+on Ubuntu on Windows setup. Once you are within bash, obtain the necessary
 :ref:`prerequisites <prerequisites>` via ``apt``. Finally, follow the
 :ref:`instructions for compiling on linux <compile_linux>`.
 
@@ -494,7 +494,7 @@ distributions.
 .. admonition:: Required
    :class: error
 
-   `NumPy <http://www.numpy.org/>`_
+   `NumPy <https://numpy.org/>`_
       NumPy is used extensively within the Python API for its powerful
       N-dimensional array.
 
@@ -502,7 +502,7 @@ distributions.
       SciPy's special functions, sparse matrices, and spatial data structures
       are used for several optional features in the API.
 
-   `pandas <http://pandas.pydata.org/>`_
+   `pandas <https://pandas.pydata.org/>`_
       Pandas is used to generate tally DataFrames as demonstrated in
       an `example notebook <../examples/pandas-dataframes.ipynb>`_.
 
@@ -511,14 +511,14 @@ distributions.
       various HDF5 files, h5py is needed to provide access to data within these
       files from Python.
 
-   `Matplotlib <http://matplotlib.org/>`_
+   `Matplotlib <https://matplotlib.org/>`_
       Matplotlib is used to providing plotting functionality in the API like the
       :meth:`Universe.plot` method and the :func:`openmc.plot_xs` function.
 
    `uncertainties <https://pythonhosted.org/uncertainties/>`_
       Uncertainties are used for decay data in the :mod:`openmc.data` module.
 
-   `lxml <http://lxml.de/>`_
+   `lxml <https://lxml.de/>`_
       lxml is used for the :ref:`scripts_validate` script and various other
       parts of the Python API.
 
@@ -530,11 +530,11 @@ distributions.
       parallel runs. This package is needed if you plan on running depletion
       simulations in parallel using MPI.
 
-   `Cython <http://cython.org/>`_
+   `Cython <https://cython.org/>`_
       Cython is used for resonance reconstruction for ENDF data converted to
       :class:`openmc.data.IncidentNeutron`.
 
-   `vtk <http://www.vtk.org/>`_
+   `vtk <https://vtk.org/>`_
       The Python VTK bindings are needed to convert voxel and track files to VTK
       format.
 
@@ -588,7 +588,7 @@ schemas.xml file in your own OpenMC source directory.
 
 .. _GNU Emacs: http://www.gnu.org/software/emacs/
 .. _validation: https://en.wikipedia.org/wiki/XML_validation
-.. _RELAX NG: http://relaxng.org/
+.. _RELAX NG: https://relaxng.org/
 .. _ctest: https://cmake.org/cmake/help/latest/manual/ctest.1.html
 .. _Conda: https://conda.io/en/latest/
 .. _pip: https://pip.pypa.io/en/stable/

docs/source/usersguide/materials.rst

@@ -45,7 +45,7 @@ This method can also accept case-insensitive element names such as
 ::
 
   mat.add_element('aluminium', 1.0)
-   
+
 Internally, OpenMC stores data on the atomic masses and natural abundances of
 all known isotopes and then uses this data to determine what isotopes should be
 added to the material. When the material is later exported to XML for use by the
@@ -105,7 +105,7 @@ you would need to add hydrogen and oxygen to a material and then assign the
 Naming Conventions
 ------------------
 
-OpenMC uses the GND_ naming convention for nuclides, metastable states, and
+OpenMC uses the GNDS_ naming convention for nuclides, metastable states, and
 compounds:
 
 :Nuclides: ``SymA`` where "A" is the mass number (e.g., ``Fe56``)
@@ -122,7 +122,7 @@ compounds:
                ENDF/B-VII.1! If you are adding an element via
                :meth:`Material.add_element`, just use ``Sym``.
 
-.. _GND: https://www.oecd-nea.org/science/wpec/sg38/Meetings/2016_May/tlh4gnd-main.pdf
+.. _GNDS: https://www.oecd-nea.org/jcms/pl_39689/specifications-for-the-generalised-nuclear-database-structure-gnds
 
 -----------
 Temperature
@@ -160,26 +160,26 @@ Material Mixtures
 -----------------
 
 In OpenMC it is possible to mix any number of materials to create a new material
-with the correct nuclide composition and density. The 
+with the correct nuclide composition and density. The
 :meth:`Material.mix_materials` method takes a list of materials and
-a list of their mixing fractions. Mixing fractions can be provided as atomic 
+a list of their mixing fractions. Mixing fractions can be provided as atomic
 fractions, weight fractions, or volume fractions. The fraction type
-can be specified by passing 'ao', 'wo', or 'vo' as the third argument, respectively. 
-For example, assuming the required materials have already been defined, a MOX 
+can be specified by passing 'ao', 'wo', or 'vo' as the third argument, respectively.
+For example, assuming the required materials have already been defined, a MOX
 material with 3% plutonium oxide by weight could be created using the following:
 
 ::
 
    mox = openmc.Material.mix_materials([uo2, puo2], [0.97, 0.03], 'wo')
 
-It should be noted that, if mixing fractions are specifed as atomic or weight 
+It should be noted that, if mixing fractions are specifed as atomic or weight
 fractions, the supplied fractions should sum to one. If the fractions are specified
-as volume fractions, and the sum of the fractions is less than one, then the remaining 
-fraction is set as void material. 
+as volume fractions, and the sum of the fractions is less than one, then the remaining
+fraction is set as void material.
 
 .. warning:: Materials with :math:`S(\alpha,\beta)` thermal scattering data
              cannot be used in :meth:`Material.mix_materials`. However, thermal
-             scattering data can be added to a material created by 
+             scattering data can be added to a material created by
              :meth:`Material.mix_materials`.
 
 --------------------

docs/source/usersguide/parallel.rst

@@ -8,8 +8,8 @@ If you are running a simulation on a computer with multiple cores, multiple
 sockets, or multiple nodes (i.e., a cluster), you can benefit from the fact that
 OpenMC is able to use all available hardware resources if configured
 correctly. OpenMC is capable of using both distributed-memory (`MPI
-<http://mpi-forum.org/>`_) and shared-memory (`OpenMP
-<http://www.openmp.org/>`_) parallelism. If you are on a single-socket
+<https://www.mpi-forum.org/>`_) and shared-memory (`OpenMP
+<https://www.openmp.org/>`_) parallelism. If you are on a single-socket
 workstation or a laptop, using shared-memory parallelism is likely
 sufficient. On a multi-socket node, cluster, or supercomputer, chances are you
 will need to use both distributed-memory (across nodes) and shared-memory
@@ -49,7 +49,7 @@ Distributed-Memory Parallelism (MPI)
 
 MPI defines a library specification for message-passing between processes. There
 are two major implementations of MPI, `OpenMPI <https://www.open-mpi.org/>`_ and
-`MPICH <http://www.mpich.org/>`_. Both implementations are known to work with
+`MPICH <https://www.mpich.org/>`_. Both implementations are known to work with
 OpenMC; there is no obvious reason to prefer one over the other. Building OpenMC
 with support for MPI requires that you have one of these implementations
 installed on your system. For instructions on obtaining MPI, see

docs/source/usersguide/plots.rst

@@ -97,7 +97,7 @@ derivatives: ``sudo apt install imagemagick``).  Images are then converted like:
 
     convert myplot.ppm myplot.png
 
-Alternatively, if you're working within a `Jupyter <http://jupyter.org/>`_
+Alternatively, if you're working within a `Jupyter <https://jupyter.org/>`_
 Notebook or QtConsole, you can use the :func:`openmc.plot_inline` to run OpenMC
 in plotting mode and display the resulting plot within the notebook.
 
@@ -122,7 +122,7 @@ should be three items long, e.g.::
 
 The voxel plot data is written to an :ref:`HDF5 file <io_voxel>`. The voxel file
 can subsequently be converted into a standard mesh format that can be viewed in
-`ParaView <http://www.paraview.org/>`_, `VisIt
+`ParaView <https://www.paraview.org/>`_, `VisIt
 <https://wci.llnl.gov/simulation/computer-codes/visit>`_, etc. This typically
 will compress the size of the file significantly. The provided
 :ref:`scripts_voxel` script can convert the HDF5 voxel file to VTK formats. Once

docs/source/usersguide/processing.rst

@@ -54,7 +54,7 @@ Getting Data into MATLAB
 There is currently no front-end utility to dump tally data to MATLAB files, but
 the process is straightforward. First extract the data using the Python API via
 ``openmc.statepoint`` and then use the `Scipy MATLAB IO routines
-<http://docs.scipy.org/doc/scipy/reference/tutorial/io.html>`_ to save to a MAT
+<https://docs.scipy.org/doc/scipy/reference/tutorial/io.html>`_ to save to a MAT
 file. Note that all arrays that are accessible in a statepoint are already in
 NumPy arrays that can be reshaped and dumped to MATLAB in one step.
 

docs/source/usersguide/scripts.rst

@@ -110,8 +110,8 @@ otherwise.
 
 This script generates an HDF5 file called ``compton_profiles.h5`` that contains
 Compton profile data using an existing data library from `Geant4
-<http://geant4.cern.ch/>`_. Note that OpenMC includes this data file by default
-so it should not be necessary in practice to generate it yourself.
+<https://geant4.web.cern.ch/>`_. Note that OpenMC includes this data file by
+default so it should not be necessary in practice to generate it yourself.
 
 
 .. _scripts_depletion_chain:
@@ -250,7 +250,7 @@ Message                   Description
 When OpenMC generates :ref:`voxel plots <usersguide_voxel>`, they are in an
 :ref:`HDF5 format <io_voxel>` that is not terribly useful by itself. The
 ``openmc-voxel-to-vtk`` script converts a voxel HDF5 file to a `VTK
-<http://www.vtk.org/>`_ file. To run this script, you will need to have the VTK
+<https://vtk.org/>`_ file. To run this script, you will need to have the VTK
 Python bindings installed. To convert a voxel file, simply provide the path to
 the file: