fix outdated or broken URLs and typos in URLs

doc/src/Build_extras.rst

@@ -1135,7 +1135,7 @@ VORONOI package
 -----------------------------
 
 To build with this package, you must download and build the
-`Voro++ library <https://math.lbl.gov/voro++>`_ or install a
+`Voro++ library <https://math.lbl.gov/voro++/>`_ or install a
 binary package provided by your operating system.
 
 .. tabs::

doc/src/Build_manual.rst

@@ -48,9 +48,9 @@ Build using GNU make
 
 The LAMMPS manual is written in `reStructuredText <rst_>`_ format which
 can be translated to different output format using the `Sphinx
-<https://sphinx-doc.org>`_ document generator tool.  It also
+<https://sphinx-doc.org/>`_ document generator tool.  It also
 incorporates programmer documentation extracted from the LAMMPS C++
-sources through the `Doxygen <https://doxygen.nl>`_ program.  Currently
+sources through the `Doxygen <https://doxygen.nl/>`_ program.  Currently
 the translation to HTML, PDF (via LaTeX), ePUB (for many e-book readers)
 and MOBI (for Amazon Kindle readers) are supported.  For that to work a
 Python 3 interpreter, the ``doxygen`` tools and internet access to

doc/src/Developer_comm_ops.rst

@@ -77,7 +77,7 @@ buffer, and they will be communicated together to minimize
 communication overhead.  The communication buffers are defined vectors
 containing ``double`` values.  To correctly store integers that may be
 64-bit (bigint, tagint, imageint) in the buffer, you need to use the
-`ubuf union <Communication buffer coding with ubuf>`_ construct.
+`ubuf union <Communication buffer coding with *ubuf*>`_ construct.
 
 The *Fix*, *Compute*, and *Dump* classes can also invoke the same kind
 of forward and reverse communication operations using the same *Comm*

doc/src/Errors_debug.rst

@@ -75,7 +75,7 @@ Using the GDB debugger to get a stack trace
 There are two options to use the GDB debugger for identifying the origin
 of the segmentation fault or similar crash. The GDB debugger has many
 more features and options, as can be seen for example its `online
-documentation <https://sourceware.org/gdb/current/onlinedocs/gdb/>`_.
+documentation <https://www.sourceware.org/gdb/documentation/>`_.
 
 Run LAMMPS from within the debugger
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

doc/src/Fortran.rst

@@ -2155,7 +2155,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
    The LAMMPS :doc:`dump style movie <dump_image>` supports generating movies
    from images on-the-fly via creating a pipe to the
-   `ffmpeg <https://ffmpeg.org/ffmpeg/>`_ program.
+   `ffmpeg <https://ffmpeg.org/>`_ program.
    This function checks whether this feature was
    :ref:`enabled at compile time <graphics>`.
    It does **not** check whether the ``ffmpeg`` itself is installed and usable.

doc/src/Install_git.rst

@@ -163,10 +163,10 @@ changed.  How to do this depends on the build system you are using.
 .. admonition:: Git protocols
    :class: note
 
-   The servers at github.com support the "https://" access protocol for
+   The servers at github.com support the "https" access protocol for
    anonymous, read-only access.  If you have a suitably configured
    GitHub account, you may also use SSH protocol with the URL
-   "git@github.com:lammps/lammps.git".
+   ``git@github.com:lammps/lammps.git``.
 
 The LAMMPS GitHub project is currently overseen by Axel Kohlmeyer
 (Temple U, akohlmey at gmail.com).

doc/src/Intro_citing.rst

@@ -46,7 +46,7 @@ In addition there are DOIs generated for individual stable releases:
 
 - 3 March 2020 version: `DOI:10.5281/zenodo.3726417 <https://dx.doi.org/10.5281/zenodo.3726417>`_
 - 29 October 2020 version: `DOI:10.5281/zenodo.4157471 <https://dx.doi.org/10.5281/zenodo.4157471>`_
-- 29 September 2021 version: `DOI:10.5281/zenodo.6386596 <https//dx.doi.org/10.5281/zenodo.6386596>`_
+- 29 September 2021 version: `DOI:10.5281/zenodo.6386596 <https://dx.doi.org/10.5281/zenodo.6386596>`_
 
 Home page
 ^^^^^^^^^

doc/src/Intro_nonfeatures.rst

@@ -34,7 +34,7 @@ Here are suggestions on how to perform these tasks:
   a true molecular builder that will generate complex molecular models.
   See the :doc:`Tools <Tools>` page for details on tools packaged with
   LAMMPS.  The `Pre-/post-processing page
-  <https:/www.lammps.org/prepost.html>`_ of the LAMMPS homepage
+  <https://www.lammps.org/prepost.html>`_ of the LAMMPS homepage
   describes a variety of third party tools for this task.  Furthermore,
   some internal LAMMPS commands allow reconstructing, or selectively adding
   topology information, as well as provide the option to insert molecule
@@ -66,10 +66,9 @@ Here are suggestions on how to perform these tasks:
   these various options.
 * **Visualization:** LAMMPS can produce NETPBM, JPG, or PNG format
   snapshot images on-the-fly via its :doc:`dump image <dump_image>`
-  command and pass them to an external program, `FFmpeg
-  <https://www.ffmpeg.org>`_, to generate movies from them.  For
-  high-quality, interactive visualization, there are many excellent and
-  free tools available.  See the `Visualization Tools
+  command and pass them to an external program, `FFmpeg  <https://ffmpeg.org/>`_,
+  to generate movies from them.  For high-quality, interactive visualization,
+  there are many excellent and free tools available.  See the `Visualization Tools
   <https://www.lammps.org/viz.html>`_ page of the LAMMPS website for
   visualization packages that can process LAMMPS output data.
 * **Plotting:** See the next bullet about Pizza.py as well as the

doc/src/Python_install.rst

@@ -15,9 +15,6 @@ Two components are necessary for Python to be able to invoke LAMMPS code:
   ``liblammps.dll``) from the folder where you compiled LAMMPS.
 
 .. _ctypes: https://docs.python.org/3/library/ctypes.html
-.. _python_virtualenv: https://packaging.python.org/guides/installing-using-pip-and-virtual-environments/#creating-a-virtual-environment
-.. _python_venv: https://docs.python.org/3/library/venv.html
-.. _python_pep405: https://www.python.org/dev/peps/pep-0405
 
 .. _python_install_guides:
 
@@ -232,11 +229,11 @@ folder that the dynamic loader searches or inside of the installed
       install (newer/different) versions of Python packages that would
       potentially conflict with already installed system packages.  It
       also does not requite any superuser privileges. See `PEP 405:
-      Python Virtual Environments <python_pep405>`_ for more
+      Python Virtual Environments <https://peps.python.org/pep-0405/>`_ for more
       information.
 
       To create a virtual environment in the folder ``$HOME/myenv``,
-      use the `venv <python_venv>`_ module as follows.
+      use the `venv <https://docs.python.org/3/library/venv.html>`_ module as follows.
 
       .. code-block:: bash
 
@@ -244,8 +241,9 @@ folder that the dynamic loader searches or inside of the installed
          python3 -m venv $HOME/myenv
 
       For Python versions prior 3.3 you can use `virtualenv
-      <python_virtualenv>`_ command instead of "python3 -m venv".  This
-      step has to be done only once.
+      <https://packaging.python.org/en/latest/key_projects/#virtualenv>`_
+      command instead of "python3 -m venv".  This step has to be done
+      only once.
 
       To activate the virtual environment type:
 
@@ -414,10 +412,8 @@ follows:
 
      sudo pip install mpi4py
 
-.. _mpi4py_install: https://mpi4py.readthedocs.io/en/stable/install.html
-
 For more detailed installation instructions and additional options,
-please see the `mpi4py installation <mpi4py_install>`_ page.
+please see the `mpi4py installation <https://mpi4py.readthedocs.io/en/stable/install.html>`_ page.
 
 
 To use ``mpi4py`` and LAMMPS in parallel from Python, you **must** make

doc/src/dump_image.rst

@@ -218,13 +218,13 @@ is used.
 .. _png_format: https://en.wikipedia.org/wiki/Portable_Network_Graphics
 .. _ppm_format: https://en.wikipedia.org/wiki/Netpbm
 
-Similarly, the format of the resulting movie is chosen with the
-*movie* dump style. This is handled by the underlying FFmpeg converter
-and thus details have to be looked up in the `FFmpeg documentation
-<https://ffmpeg.org/ffmpeg.html>`_.  Typical examples are: .avi, .mpg,
-.m4v, .mp4, .mkv, .flv, .mov, .gif Additional settings of the movie
-compression like *bitrate* and *framerate* can be set using the
-dump_modify command as described below.
+Similarly, the format of the resulting movie is chosen with the *movie*
+dump style. This is handled by the underlying FFmpeg converter and thus
+details have to be looked up in the `FFmpeg documentation
+<https://ffmpeg.org/>`_.  Typical examples are: .avi, .mpg, .m4v, .mp4,
+.mkv, .flv, .mov, .gif Additional settings of the movie compression like
+*bitrate* and *framerate* can be set using the dump_modify command as
+described below.
 
 To write out JPEG and PNG format files, you must build LAMMPS with
 support for the corresponding JPEG or PNG library. To convert images
@@ -651,7 +651,7 @@ MPEG or other movie file you can use:
      cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi
 
   Front ends for FFmpeg exist for multiple platforms. For more
-  information see the `FFmpeg homepage <https://www.ffmpeg.org/>`_
+  information see the `FFmpeg homepage <https://ffmpeg.org/>`_
 
 ----------
 

doc/src/group.rst

@@ -304,7 +304,7 @@ group and running further.
    not all allow for use of a dynamic group.  If you get an error
    message that this is not allowed, but feel that it should be for the
    fix or compute in question, then please post your reasoning to the
-   `LAMMPS forum at MatSci <https://matsci.org/c/lammps-development/>`_
+   `LAMMPS forum at MatSci <https://matsci.org/c/lammps-development/42>`_
    and we can look into changing it.  The same applies if you come
    across inconsistent behavior when dynamic groups are allowed.