convert URLs to https where possible, check URLs for bit rot and update or remove

doc/src/Bibliography.rst

@@ -368,7 +368,7 @@ Bibliography
    Frenkel and Smit, Understanding Molecular Simulation, Academic Press, London, 2002.
 
 **(GLE4MD)**
-   `http://gle4md.org/ <http://gle4md.org/>`_
+   `https://gle4md.org/ <https://gle4md.org/>`_
 
 **(Gao)**
    Gao and Weber, Nuclear Instruments and Methods in Physics Research B 191 (2012) 504.
@@ -461,7 +461,7 @@ Bibliography
    Hunt, Mol Simul, 42, 347 (2016).
 
 **(IPI)**
-   `http://epfl-cosmo.github.io/gle4md/index.html?page=ipi <http://epfl-cosmo.github.io/gle4md/index.html?page=ipi>`_
+   `https://ipi-code.org/ <https://ipi-code.org/>`
 
 **(IPI-CPC)**
    Ceriotti, More and Manolopoulos, Comp Phys Comm, 185, 1019-1026 (2014).
@@ -875,7 +875,7 @@ Bibliography
    G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
 
 **(Paquay)**
-   Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_.
+   Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.
 
 **(Park)**
    Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)

doc/src/Build_development.rst

@@ -140,7 +140,7 @@ of the LAMMPS project on GitHub.
 The unit testing facility is integrated into the CMake build process
 of the LAMMPS source code distribution itself.  It can be enabled by
 setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
-It requires the `YAML <http://pyyaml.org/>`_ library and development
+It requires the `YAML <https://pyyaml.org/>`_ library and development
 headers (if those are not found locally a recent version will be
 downloaded and compiled along with LAMMPS and the test program) to
 compile and will download and compile a specific recent version of the

doc/src/Build_extras.rst

@@ -314,7 +314,7 @@ detailed information is available at:
 
 In addition to installing the KIM API, it is also necessary to install the
 library of KIM models (interatomic potentials).
-See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_ to
+See `Obtaining KIM Models <https://openkim.org/doc/usage/obtaining-models>`_ to
 learn how to install a pre-build binary of the OpenKIM Repository of Models.
 See the list of all KIM models here: https://openkim.org/browse/models
 
@@ -432,7 +432,7 @@ Enabling the extra unit tests have some requirements,
   ``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``,
   ``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``, and
   ``LennardJones612_UniversalShifted__MO_959249795837_003`` KIM models.
-  See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_
+  See `Obtaining KIM Models <https://openkim.org/doc/usage/obtaining-models>`_
   to learn how to install a pre-built binary of the OpenKIM Repository of
   Models or see
   `Installing KIM Models <https://openkim.org/doc/usage/obtaining-models/#installing_models>`_
@@ -1053,7 +1053,7 @@ VORONOI package
 -----------------------------
 
 To build with this package, you must download and build the
-`Voro++ library <http://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

@@ -176,7 +176,7 @@ math expressions transparently into embedded images.
 For converting the generated ePUB file to a MOBI format file (for e-book
 readers, like Kindle, that cannot read ePUB), you also need to have the
 ``ebook-convert`` tool from the "calibre" software
-installed. `http://calibre-ebook.com/ <http://calibre-ebook.com/>`_
+installed. `https://calibre-ebook.com/ <https://calibre-ebook.com/>`_
 Typing ``make mobi`` will first create the ePUB file and then convert
 it.  On the Kindle readers in particular, you also have support for PDF
 files, so you could download and view the PDF version as an alternative.

doc/src/Build_settings.rst

@@ -111,26 +111,25 @@ LAMMPS can use them if they are available on your system.
       files in its default search path.  You must specify ``FFT_LIB``
       with the appropriate FFT libraries to include in the link.
 
-The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS
+The `KISS FFT library <https://github.com/mborgerding/kissfft>`_ is
-distribution.  It is portable across all platforms.  Depending on the size
+included in the LAMMPS distribution.  It is portable across all
-of the FFTs and the number of processors used, the other libraries listed
+platforms.  Depending on the size of the FFTs and the number of
-here can be faster.
+processors used, the other libraries listed here can be faster.
 
 However, note that long-range Coulombics are only a portion of the
-per-timestep CPU cost, FFTs are only a portion of long-range
+per-timestep CPU cost, FFTs are only a portion of long-range Coulombics,
-Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
+and 1d FFTs are only a portion of the FFT cost (parallel communication
-communication can be costly).  A breakdown of these timings is printed
+can be costly).  A breakdown of these timings is printed to the screen
-to the screen at the end of a run when using the
+at the end of a run when using the :doc:`kspace_style pppm
-:doc:`kspace_style pppm <kspace_style>` command. The
+<kspace_style>` command. The :doc:`Screen and logfile output
-:doc:`Screen and logfile output <Run_output>`
+<Run_output>` page gives more details.  A more detailed (and time
-page gives more details.  A more detailed (and time consuming)
+consuming) report of the FFT performance is generated with the
-report of the FFT performance is generated with the
 :doc:`kspace_modify fftbench yes <kspace_modify>` command.
 
 FFTW is a fast, portable FFT library that should also work on any
-platform and can be faster than the KISS FFT library.  You can
+platform and can be faster than the KISS FFT library.  You can download
-download it from `www.fftw.org <http://www.fftw.org>`_.  LAMMPS requires
+it from `www.fftw.org <https://www.fftw.org>`_.  LAMMPS requires version
-version 3.X; the legacy version 2.1.X is no longer supported.
+3.X; the legacy version 2.1.X is no longer supported.
 
 Building FFTW for your box should be as simple as ``./configure; make;
 make install``.  The install command typically requires root privileges

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 <http://sourceware.org/gdb/current/onlinedocs/gdb/>`_.
+documentation <https://sourceware.org/gdb/current/onlinedocs/gdb/>`_.
 
 Run LAMMPS from within the debugger
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

doc/src/Howto_amoeba.rst

@@ -281,7 +281,7 @@ Here is more information about the extended XYZ format defined and
 used by Tinker, and links to programs that convert standard PDB files
 to the extended XYZ format:
 
-* `http://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html <http://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html>`_
+* `https://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html <https://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html>`_
 * `https://github.com/emleddin/pdbxyz-xyzpdb <https://github.com/emleddin/pdbxyz-xyzpdb>`_
 * `https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f <https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f>`_
 

doc/src/Howto_bioFF.rst

@@ -3,24 +3,20 @@ CHARMM, AMBER, COMPASS, and DREIDING force fields
 
 A force field has 2 parts: the formulas that define it and the
 coefficients used for a particular system.  Here we only discuss
-formulas implemented in LAMMPS that correspond to formulas commonly
+formulas implemented in LAMMPS that correspond to formulas commonly used
-used in the CHARMM, AMBER, COMPASS, and DREIDING force fields.  Setting
+in the CHARMM, AMBER, COMPASS, and DREIDING force fields.  Setting
 coefficients is done either from special sections in an input data file
 via the :doc:`read_data <read_data>` command or in the input script with
-commands like :doc:`pair_coeff <pair_coeff>` or
+commands like :doc:`pair_coeff <pair_coeff>` or :doc:`bond_coeff
-:doc:`bond_coeff <bond_coeff>` and so on.  See the :doc:`Tools <Tools>` doc
+<bond_coeff>` and so on.  See the :doc:`Tools <Tools>` doc page for
-page for additional tools that can use CHARMM, AMBER, or Materials
+additional tools that can use CHARMM, AMBER, or Materials Studio
-Studio generated files to assign force field coefficients and convert
+generated files to assign force field coefficients and convert their
-their output into LAMMPS input.
+output into LAMMPS input.
 
-See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM force
+See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM
-field.  See :ref:`(Cornell) <howto-Cornell>` for a description of the AMBER
+force field.  See :ref:`(Cornell) <howto-Cornell>` for a description of
-force field.  See :ref:`(Sun) <howto-Sun>` for a description of the COMPASS
+the AMBER force field.  See :ref:`(Sun) <howto-Sun>` for a description
-force field.
+of the COMPASS force field.
-
-.. _charmm: http://www.scripps.edu/brooks
-
-.. _amber: http://amber.scripps.edu
 
 The interaction styles listed below compute force field formulas that
 are consistent with common options in CHARMM or AMBER.  See each
@@ -41,9 +37,10 @@ command's documentation for the formula it computes.
 
 .. note::
 
-   For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released
+   For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released in
-   in March 2017.  We recommend they be used instead of the older *charmm*
+   March 2017.  We recommend they be used instead of the older *charmm*
-   styles.  See discussion of the differences on the :doc:`pair charmm <pair_charmm>` and :doc:`dihedral charmm <dihedral_charmm>` doc
+   styles.  See discussion of the differences on the :doc:`pair charmm
+   <pair_charmm>` and :doc:`dihedral charmm <dihedral_charmm>` doc
    pages.
 
 COMPASS is a general force field for atomistic simulation of common

doc/src/Howto_github.rst

@@ -10,7 +10,7 @@ changes or additions you have made to LAMMPS into the official LAMMPS
 distribution.  It uses the process of updating this very tutorial as an
 example to describe the individual steps and options.  You need to be
 familiar with git and you may want to have a look at the `git book
-<http://git-scm.com/book/>`_ to familiarize yourself with some of the
+<https://git-scm.com/book/>`_ to familiarize yourself with some of the
 more advanced git features used below.
 
 As of fall 2016, submitting contributions to LAMMPS via pull requests

doc/src/Howto_manifold.rst

@@ -47,4 +47,4 @@ to the relevant fixes.
 .. _Paquay1:
 
 **(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016).
-preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_.
+preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.

doc/src/Howto_spc.rst

@@ -38,7 +38,7 @@ the partial charge assignments change:
 See the :ref:`(Berendsen) <howto-Berendsen>` reference for more details on both
 the SPC and SPC/E models.
 
-Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
+Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
 
 ----------
 

doc/src/Howto_tip3p.rst

@@ -49,7 +49,7 @@ details:
 | :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
 |
 
-Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
+Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
 
 ----------
 

doc/src/Howto_tip4p.rst

@@ -97,7 +97,7 @@ This leads to slightly larger cost for the long-range calculation, so
 you can test the trade-off for your model.  The OM distance and the LJ
 and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>` command.
 
-Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
+Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
 
 ----------
 

doc/src/Howto_viz.rst

@@ -17,9 +17,10 @@ formats.  See the :doc:`Tools <Tools>` page for details.
 
 A Python-based toolkit distributed by our group can read native LAMMPS
 dump files, including custom dump files with additional columns of
-user-specified atom information, and convert them to various formats
+user-specified atom information, and convert them to various formats or
-or pipe them into visualization software directly.  See the `Pizza.py WWW site <pizza_>`_ for details.  Specifically, Pizza.py can convert
+pipe them into visualization software directly.  See the `Pizza.py WWW
-LAMMPS dump files into PDB, XYZ, `EnSight <ensight_>`_, and VTK formats.
+site <pizza_>`_ for details.  Specifically, Pizza.py can convert LAMMPS
+dump files into PDB, XYZ, `EnSight <ensight_>`_, and VTK formats.
 Pizza.py can pipe LAMMPS dump files directly into the Raster3d and
 RasMol visualization programs.  Pizza.py has tools that do interactive
 3d OpenGL visualization and one that creates SVG images of dump file

doc/src/Install_windows.rst

@@ -6,7 +6,7 @@ Windows system can be downloaded from this site:
 
 .. parsed-literal::
 
-  `http://packages.lammps.org/windows.html <http://packages.lammps.org/windows.html>`_
+  `https://packages.lammps.org/windows.html <https://packages.lammps.org/windows.html>`_
 
 Note that each installer package has a date in its name, which
 corresponds to the LAMMPS version of the same date.  Installers for

doc/src/Intro_citing.rst

@@ -27,7 +27,7 @@ namely https://www.lammps.org.
 The original publication describing the parallel algorithms used in the
 initial versions of LAMMPS is:
 
-  `S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995). <http://www.sandia.gov/~sjplimp/papers/jcompphys95.pdf>`_
+  `S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995). <https://doi.org/10.1006/jcph.1995.1039>`_
 
 
 DOI for the LAMMPS source code

doc/src/Intro_features.rst

@@ -95,7 +95,7 @@ commands)
 * metal-organic framework potentials (QuickFF, MO-FF)
 * implicit solvent potentials: hydrodynamic lubrication, Debye
 * force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options
-* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via     :doc:`kim command <kim_commands>`
+* access to the `OpenKIM Repository <https://openkim.org>`_ of potentials via the :doc:`kim command <kim_commands>`
 * hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
 * overlaid potentials: superposition of multiple pair potentials (including many-body) with optional scale factor
 
@@ -205,7 +205,7 @@ Pre- and post-processing
 
 .. _pizza: https://lammps.github.io/pizza
 
-.. _python: http://www.python.org
+.. _python: https://www.python.org
 
 .. _special:
 

doc/src/Intro_nonfeatures.rst

@@ -33,7 +33,7 @@ Here are suggestions on how to perform these tasks:
   linear bead-spring polymer chains.  The moltemplate program is 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 <http:/www.lammps.org/prepost.html>`_ of the LAMMPS website
+  LAMMPS.  The `Pre/post processing page <https:/www.lammps.org/prepost.html>`_ of the LAMMPS website
   describes a variety of third party tools for this task.  Furthermore,
   some LAMMPS internal commands allow to reconstruct, or selectively add
   topology information, as well as provide the option to insert molecule

doc/src/Intro_opensource.rst

@@ -23,9 +23,9 @@ applies to LAMMPS is in the LICENSE file included in the LAMMPS distribution.
 
 .. _lgpl: https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html
 
-.. _gnuorg: http://www.gnu.org
+.. _gnuorg: https://www.gnu.org
 
-.. _opensource: http://www.opensource.org
+.. _opensource: https://www.opensource.org
 
 Here is a more specific summary of what the GPL means for LAMMPS users:
 

doc/src/Packages_details.rst

@@ -1071,7 +1071,7 @@ H5MD is a format for molecular simulations, built on top of HDF5.
 This package implements a :doc:`dump h5md <dump_h5md>` command to output
 LAMMPS snapshots in this format.
 
-.. _HDF5: http://www.hdfgroup.org/HDF5
+.. _HDF5: https://www.hdfgroup.org/solutions/hdf5
 
 To use this package you must have the HDF5 library available on your
 system.
@@ -1954,7 +1954,7 @@ support for new file formats can be added to LAMMPS (or VMD or other
 programs that use them) without having to re-compile the application
 itself.  More information about the VMD molfile plugins can be found
 at
-`http://www.ks.uiuc.edu/Research/vmd/plugins/molfile <http://www.ks.uiuc.edu/Research/vmd/plugins/molfile>`_.
+`https://www.ks.uiuc.edu/Research/vmd/plugins/molfile <https://www.ks.uiuc.edu/Research/vmd/plugins/molfile>`_.
 
 **Author:** Axel Kohlmeyer (Temple U).
 
@@ -2045,7 +2045,7 @@ NETCDF package
 Dump styles for writing NetCDF formatted dump files.  NetCDF is a
 portable, binary, self-describing file format developed on top of
 HDF5. The file contents follow the AMBER NetCDF trajectory conventions
-(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions.
+(https://ambermd.org/netcdf/nctraj.xhtml), but include extensions.
 
 To use this package you must have the NetCDF library available on your
 system.
@@ -2056,7 +2056,7 @@ tools:
 * `Ovito <ovito_>`_ (Ovito supports the AMBER convention and the extensions mentioned above)
 * `VMD <vmd-home_>`_
 
-.. _ovito: http://www.ovito.org
+.. _ovito: https://www.ovito.org
 
 .. _vmd-home: https://www.ks.uiuc.edu/Research/vmd/
 
@@ -2417,7 +2417,7 @@ A :doc:`fix qmmm <fix_qmmm>` command which allows LAMMPS to be used as
 the MM code in a QM/MM simulation.  This is currently only available
 in combination with the `Quantum ESPRESSO <espresso_>`_ package.
 
-.. _espresso: http://www.quantum-espresso.org
+.. _espresso: https://www.quantum-espresso.org
 
 To use this package you must have Quantum ESPRESSO (QE) available on
 your system and include its coupling library in the compilation and
@@ -2829,7 +2829,7 @@ collection of atoms by wrapping the `Voro++ library <voro-home_>`_.  This
 can be used to calculate the local volume or each atoms or its near
 neighbors.
 
-.. _voro-home: http://math.lbl.gov/voro++
+.. _voro-home: https://math.lbl.gov/voro++
 
 To use this package you must have the Voro++ library available on your
 system.
@@ -2863,9 +2863,9 @@ A :doc:`dump vtk <dump_vtk>` command which outputs snapshot info in the
 `VTK format <vtk_>`_, enabling visualization by `Paraview <paraview_>`_ or
 other visualization packages.
 
-.. _vtk: http://www.vtk.org
+.. _vtk: https://www.vtk.org
 
-.. _paraview: http://www.paraview.org
+.. _paraview: https://www.paraview.org
 
 To use this package you must have VTK library available on your
 system.
@@ -2902,7 +2902,7 @@ which discuss the `QuickFF <quickff_>`_ methodology.
 
 .. _vanduyfhuys2015: https://doi.org/10.1002/jcc.23877
 .. _vanduyfhuys2018: https://doi.org/10.1002/jcc.25173
-.. _quickff: http://molmod.github.io/QuickFF
+.. _quickff: https://molmod.github.io/QuickFF
 .. _yaff: https://github.com/molmod/yaff
 
 **Author:** Steven Vandenbrande.

doc/src/Python_examples.rst

@@ -43,26 +43,18 @@ Note that for AtomEye, you need version 3, and there is a line in the
 scripts that specifies the path and name of the executable.  See the
 AtomEye web pages for more details:
 
-* `http://li.mit.edu/Archive/Graphics/A/ <atomeye_>`_
+* `http://li.mit.edu/Archive/Graphics/A/ <http://li.mit.edu/Archive/Graphics/A/>`_
-* `http://li.mit.edu/Archive/Graphics/A3/A3.html <atomeye3_>`_
+* `http://li.mit.edu/Archive/Graphics/A3/A3.html <http://li.mit.edu/Archive/Graphics/A3/A3.html>`_
 
-.. _atomeye: http://li.mit.edu/Archive/Graphics/A/
+The latter link is to AtomEye 3 which has the scripting capability
-
+needed by these Python scripts.
-.. _atomeye3: http://li.mit.edu/Archive/Graphics/A3/A3.html
-
-The latter link is to AtomEye 3 which has the scripting
-capability needed by these Python scripts.
 
 Note that for PyMol, you need to have built and installed the
 open-source version of PyMol in your Python, so that you can import it
 from a Python script.  See the PyMol web pages for more details:
 
- * `https://www.pymol.org <pymolhome_>`_
+ * `https://www.pymol.org <https://www.pymol.org>`_
- * `https://github.com/schrodinger/pymol-open-source <pymolopen_>`_
+ * `https://github.com/schrodinger/pymol-open-source <https://github.com/schrodinger/pymol-open-source>`_
-
-.. _pymolhome: https://www.pymol.org
-
-.. _pymolopen: https://github.com/schrodinger/pymol-open-source
 
 The latter link is to the open-source version.
 

doc/src/Python_head.rst

@@ -18,17 +18,17 @@ together.
    Python_error
    Python_trouble
 
-If you are not familiar with `Python <http://www.python.org>`_, it is a
+If you are not familiar with `Python <https://www.python.org>`_, it is a
 powerful scripting and programming language which can do almost
 everything that compiled languages like C, C++, or Fortran can do in
 fewer lines of code. It also comes with a large collection of add-on
 modules for many purposes (either bundled or easily installed from
 Python code repositories).  The major drawback is slower execution speed
 of the script code compared to compiled programming languages.  But when
-the script code is interfaced to optimized compiled code, performance can
+the script code is interfaced to optimized compiled code, performance
-be on par with a standalone executable, for as long as the scripting is
+can be on par with a standalone executable, for as long as the scripting
-restricted to high-level operations.  Thus Python is also convenient to
+is restricted to high-level operations.  Thus Python is also convenient
-use as a "glue" language to "drive" a program through its library
+to use as a "glue" language to "drive" a program through its library
 interface, or to hook multiple pieces of software together, such as a
 simulation code and a visualization tool, or to run a coupled
 multi-scale or multi-physics model.

doc/src/Run_windows.rst

@@ -25,8 +25,8 @@ in parallel, follow these steps.
 
 Download and install a compatible MPI library binary package:
 
-* for 32-bit Windows: `mpich2-1.4.1p1-win-ia32.msi <http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi>`_
+* for 32-bit Windows: `mpich2-1.4.1p1-win-ia32.msi <https://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi>`_
-* for 64-bit Windows: `mpich2-1.4.1p1-win-x86-64.msi <http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi>`_
+* for 64-bit Windows: `mpich2-1.4.1p1-win-x86-64.msi <https://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi>`_
 
 The LAMMPS Windows installer packages will automatically adjust your
 path for the default location of this MPI package. After the

doc/src/Speed_gpu.rst

@@ -39,7 +39,7 @@ toolkit software on your system (this is only tested on Linux
 and unsupported on Windows):
 
 * Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/\*/information
-* Go to http://www.nvidia.com/object/cuda_get.html
+* Go to https://developer.nvidia.com/cuda-downloads
 * Install a driver and toolkit appropriate for your system (SDK is not necessary)
 * Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to
   list supported devices and properties

doc/src/Speed_intel.rst

@@ -537,5 +537,5 @@ References
 """"""""""
 
 * Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS", in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann.
-* Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. `Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. <http://dl.acm.org/citation.cfm?id=3014915>`_ 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95).
+* Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. `Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. <https://dl.acm.org/citation.cfm?id=3014915>`_ 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95).
 * Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101.

doc/src/Speed_omp.rst

@@ -97,7 +97,7 @@ sub-section.
 
 A description of the multi-threading strategy used in the OPENMP
 package and some performance examples are
-`presented here <http://sites.google.com/site/akohlmey/software/lammps-icms/lammps-icms-tms2011-talk.pdf?attredirects=0&d=1>`_.
+`presented here <https://drive.google.com/file/d/1d1gLK6Ru6aPYB50Ld2tO10Li8zgPVNB8/view?usp=sharing>`_.
 
 Guidelines for best performance
 """""""""""""""""""""""""""""""

doc/src/Tools.rst

@@ -512,8 +512,8 @@ with an ``.inputrc`` file in the home directory.  For application
 specific customization, the LAMMPS shell uses the name "lammps-shell".
 For more information about using and customizing an application using
 readline, please see the available documentation at:
-`http://www.gnu.org/s/readline/#Documentation
+https://www.gnu.org/software/readline/
-<http://www.gnu.org/s/readline/#Documentation>`_
+
 
 Additional commands
 ^^^^^^^^^^^^^^^^^^^
@@ -715,7 +715,7 @@ See the README.pdf file for more information.
 These scripts were written by Arun Subramaniyan at Purdue Univ
 (asubrama at purdue.edu).
 
-.. _matlabhome: http://www.mathworks.com
+.. _matlabhome: https://www.mathworks.com
 
 ----------
 
@@ -1046,7 +1046,7 @@ the binary file.  This usually is a so-called little endian hardware
 SWIG interface
 --------------
 
-The `SWIG tool <http://swig.org>`_ offers a mostly automated way to
+The `SWIG tool <https://swig.org>`_ offers a mostly automated way to
 incorporate compiled code modules into scripting languages.  It
 processes the function prototypes in C and generates wrappers for a wide
 variety of scripting languages from it.  Thus it can also be applied to
@@ -1126,7 +1126,7 @@ data passed or returned as pointers are included in the ``lammps.i``
 file.  So most of the functionality of the library interface should be
 accessible.  What works and what does not depends a bit on the
 individual language for which the wrappers are built and how well SWIG
-supports those.  The `SWIG documentation <http://swig.org/doc.html>`_
+supports those.  The `SWIG documentation <https://swig.org/doc.html>`_
 has very detailed instructions and recommendations.
 
 Usage examples

doc/src/compute_damage_atom.rst

@@ -24,14 +24,18 @@ Description
 """""""""""
 
 Define a computation that calculates the per-atom damage for each atom
-in a group.  This is a quantity relevant for :doc:`Peridynamics models <pair_peri>`.  See `this document <PDF/PDLammps_overview.pdf>`_
+in a group.  This is a quantity relevant for :doc:`Peridynamics models
-for an overview of LAMMPS commands for Peridynamics modeling.
+<pair_peri>`.  See `this document <PDF/PDLammps_overview.pdf>`_ for an
+overview of LAMMPS commands for Peridynamics modeling.
 
 The "damage" of a Peridynamics particles is based on the bond breakage
 between the particle and its neighbors.  If all the bonds are broken
 the particle is considered to be fully damaged.
 
-See the `PDLAMMPS user guide <http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf>`_ for a formal
+.. TODO the link below is broken
+
+See the `PDLAMMPS user guide
+<http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf>`_ for a formal
 definition of "damage" and more details about Peridynamics as it is
 implemented in LAMMPS.
 
@@ -53,8 +57,9 @@ The per-atom vector values are unitless numbers (damage) :math:`\ge 0.0`.
 Restrictions
 """"""""""""
 
-This compute is part of the PERI package.  It is only enabled if
+This compute is part of the PERI package.  It is only enabled if LAMMPS
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
 
 Related commands
 """"""""""""""""

doc/src/compute_dilatation_atom.rst

@@ -24,12 +24,15 @@ Description
 """""""""""
 
 Define a computation that calculates the per-atom dilatation for each
-atom in a group.  This is a quantity relevant for :doc:`Peridynamics models <pair_peri>`.  See `this document <PDF/PDLammps_overview.pdf>`_
+atom in a group.  This is a quantity relevant for :doc:`Peridynamics
+models <pair_peri>`.  See `this document <PDF/PDLammps_overview.pdf>`_
 for an overview of LAMMPS commands for Peridynamics modeling.
 
 For small deformation, dilatation of is the measure of the volumetric
 strain.
 
+.. TODO the link below is broken
+
 The dilatation :math:`\theta` for each peridynamic particle :math:`i` is
 calculated as a sum over its neighbors with unbroken bonds, where the
 contribution of the :math:`ij` pair is a function of the change in bond length
@@ -38,7 +41,8 @@ fraction of the particles and an influence function.  See the
 `PDLAMMPS user guide <http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf>`_ for
 a formal definition of dilatation.
 
-This command can only be used with a subset of the Peridynamic :doc:`pair styles <pair_peri>`: peri/lps, peri/ves and peri/eps.
+This command can only be used with a subset of the Peridynamic
+:doc:`pair styles <pair_peri>`: peri/lps, peri/ves and peri/eps.
 
 The dilatation value will be 0.0 for atoms not in the specified
 compute group.
@@ -56,9 +60,9 @@ The per-atom vector values are unitless numbers :math:`(\theta \ge 0.0)`.
 Restrictions
 """"""""""""
 
-This compute is part of the PERI package.  It is only enabled if
+This compute is part of the PERI package.  It is only enabled if LAMMPS
-LAMMPS was built with that package.  See the
+was built with that package.  See the :doc:`Build package
-:doc:`Build package <Build_package>` page for more info.
+<Build_package>` page for more info.
 
 Related commands
 """"""""""""""""

doc/src/compute_voronoi_atom.rst

@@ -154,25 +154,25 @@ which must be installed on your system when building LAMMPS for use
 with this compute.  See instructions on obtaining and installing the
 Voro++ software in the src/VORONOI/README file.
 
-.. _voronoi: http://math.lbl.gov/voro++/
+.. _voronoi: https://math.lbl.gov/voro++/
 
 .. note::
 
-   The calculation of Voronoi volumes is performed by each
+   The calculation of Voronoi volumes is performed by each processor for
-   processor for the atoms it owns, and includes the effect of ghost
+   the atoms it owns, and includes the effect of ghost atoms stored by
-   atoms stored by the processor.  This assumes that the Voronoi cells of
+   the processor.  This assumes that the Voronoi cells of owned atoms
-   owned atoms are not affected by atoms beyond the ghost atom cut-off
+   are not affected by atoms beyond the ghost atom cut-off distance.
-   distance.  This is usually a good assumption for liquid and solid
+   This is usually a good assumption for liquid and solid systems, but
-   systems, but may lead to underestimation of Voronoi volumes in low
+   may lead to underestimation of Voronoi volumes in low density
-   density systems.  By default, the set of ghost atoms stored by each
+   systems.  By default, the set of ghost atoms stored by each processor
-   processor is determined by the cutoff used for
+   is determined by the cutoff used for :doc:`pair_style <pair_style>`
-   :doc:`pair_style <pair_style>` interactions.  The cutoff can be set
+   interactions.  The cutoff can be set explicitly via the
-   explicitly via the :doc:`comm_modify cutoff <comm_modify>` command.  The
+   :doc:`comm_modify cutoff <comm_modify>` command.  The Voronoi cells
-   Voronoi cells for atoms adjacent to empty regions will extend into
+   for atoms adjacent to empty regions will extend into those regions up
-   those regions up to the communication cutoff in :math:`x`, :math:`y`, or
+   to the communication cutoff in :math:`x`, :math:`y`, or :math:`z`.
-   :math:`z`.  In that situation, an exterior face is created at the cutoff
+   In that situation, an exterior face is created at the cutoff distance
-   distance normal to the :math:`x`, :math:`y`, or :math:`z` direction.
+   normal to the :math:`x`, :math:`y`, or :math:`z` direction.  For
-   For triclinic systems, the exterior face is parallel to the corresponding
+   triclinic systems, the exterior face is parallel to the corresponding
    reciprocal lattice vector.
 
 .. note::

doc/src/dump.rst

@@ -480,7 +480,7 @@ style.
 ----------
 
 Note that *atom*, *custom*, *dcd*, *xtc*, and *xyz* style dump files
-can be read directly by `VMD <http://www.ks.uiuc.edu/Research/vmd>`_, a
+can be read directly by `VMD <https://www.ks.uiuc.edu/Research/vmd>`_, a
 popular molecular viewing program.
 
 ----------

doc/src/dump_h5md.rst

@@ -64,7 +64,7 @@ stored within the same file by defining several dumps.  A dump that
 refers (via *file_from*) to an already open dump ID and that concerns
 another particle group must specify *create_group yes*.
 
-.. _h5md: http://nongnu.org/h5md/
+.. _h5md: https://nongnu.org/h5md/
 
 Each data element is written every N\*N_element steps. For *image*, no
 sub-interval is needed as it must be present at the same interval as
@@ -113,7 +113,7 @@ the `HDF5 <HDF5-ws_>`_ library installed (C bindings are sufficient) on
 your system.  The library ch5md is compiled with the h5cc wrapper
 provided by the HDF5 library.
 
-.. _HDF5-ws: http://www.hdfgroup.org/HDF5/
+.. _HDF5-ws: https://www.hdfgroup.org/solutions/hdf5/
 
 ----------
 
@@ -129,4 +129,4 @@ Related commands
 **(de Buyl)** de Buyl, Colberg and Hofling, H5MD: A structured,
 efficient, and portable file format for molecular data,
 Comp. Phys. Comm. 185(6), 1546-1553 (2014) -
-`[arXiv:1308.6382] <http://arxiv.org/abs/1308.6382/>`_.
+`[arXiv:1308.6382] <https://arxiv.org/abs/1308.6382/>`_.

doc/src/dump_image.rst

@@ -212,7 +212,7 @@ is used.
 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
-<http://ffmpeg.org/ffmpeg.html>`_.  Typical examples are: .avi, .mpg,
+<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.
@@ -642,7 +642,7 @@ 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 <http://www.ffmpeg.org/>`_
+  information see the `FFmpeg homepage <https://www.ffmpeg.org/>`_
 
 ----------
 

doc/src/dump_modify.rst

@@ -881,7 +881,7 @@ levels that sacrifice compression for performance. 0 is the default,
 positive levels are 1 to 22, with 22 being the most expensive
 compression. Zstd promises higher compression/decompression speeds for
 similar compression ratios. For more details see
-`http://facebook.github.io/zstd/`.
+`https://facebook.github.io/zstd/`.
 
 In addition, Zstd compressed files can include a checksum of the
 entire contents. The Zstd enabled dump styles enable this feature by

doc/src/dump_molfile.rst

@@ -34,7 +34,7 @@ Dump a snapshot of atom coordinates and selected additional quantities
 to one or more files every N timesteps in one of several formats.
 Only information for atoms in the specified group is dumped.  This
 specific dump style uses molfile plugins that are bundled with the
-`VMD <http://www.ks.uiuc.edu/Research/vmd>`_ molecular visualization and
+`VMD <https://www.ks.uiuc.edu/Research/vmd>`_ molecular visualization and
 analysis program.
 
 Unless the filename contains a \* character, the output will be written

doc/src/dump_netcdf.rst

@@ -48,21 +48,17 @@ rank.
 
 NetCDF files can be directly visualized via the following tools:
 
-Ovito (http://www.ovito.org/). Ovito supports the AMBER convention and
+* Ovito (https://www.ovito.org/). Ovito supports the AMBER convention and
   all extensions of this dump style.
-
+* VMD (https://www.ks.uiuc.edu/Research/vmd/).
-* VMD (http://www.ks.uiuc.edu/Research/vmd/).
-* AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye
-  contains a NetCDF reader that is not present in the standard
-  distribution of AtomEye.
 
 In addition to per-atom data, :doc:`thermo <thermo>` data can be included in the
 dump file. The data included in the dump file is identical to the data specified
 by :doc:`thermo_style <thermo_style>`.
 
-.. _netcdf-home: http://www.unidata.ucar.edu/software/netcdf/
+.. _netcdf-home: https://www.unidata.ucar.edu/software/netcdf/
 
-.. _pnetcdf-home: http://trac.mcs.anl.gov/projects/parallel-netcdf/
+.. _pnetcdf-home: https://trac.mcs.anl.gov/projects/parallel-netcdf/
 
 ----------
 

doc/src/dump_vtk.rst

@@ -29,8 +29,9 @@ Description
 """""""""""
 
 Dump a snapshot of atom quantities to one or more files every :math:`N`
-timesteps in a format readable by the `VTK visualization toolkit <http://www.vtk.org>`_ or other visualization tools that use it,
+timesteps in a format readable by the `VTK visualization toolkit
-such as `ParaView <http://www.paraview.org>`_.  The time steps on which dump
+<https://www.vtk.org>`_ or other visualization tools that use it, such
+as `ParaView <https://www.paraview.org>`_.  The time steps on which dump
 output is written can also be controlled by a variable; see the
 :doc:`dump_modify every <dump_modify>` command for details.
 
@@ -38,8 +39,8 @@ This dump style is similar to :doc:`dump_style custom <dump>` but uses
 the VTK library to write data to VTK simple legacy or XML format,
 depending on the filename extension specified for the dump file.  This
 can be either *\*.vtk* for the legacy format or *\*.vtp* and *\*.vtu*,
-respectively, for XML format; see the
+respectively, for XML format; see the `VTK homepage
-`VTK homepage <http://www.vtk.org/VTK/img/file-formats.pdf>`_ for a detailed
+<https://www.vtk.org/VTK/img/file-formats.pdf>`_ for a detailed
 description of these formats.  Since this naming convention conflicts
 with the way binary output is usually specified (see below), the
 :doc:`dump_modify binary <dump_modify>` command allows setting of a
@@ -61,14 +62,15 @@ determine the kind of output.
 
 .. warning::
 
-   Unless the :doc:`dump_modify sort <dump_modify>` option
+   Unless the :doc:`dump_modify sort <dump_modify>` option is invoked,
-   is invoked, the lines of atom information written to dump files will
+   the lines of atom information written to dump files will be in an
-   be in an indeterminate order for each snapshot.  This is even true
+   indeterminate order for each snapshot.  This is even true when
-   when running on a single processor, if the :doc:`atom_modify sort <atom_modify>` option is on, which it is by default.  In this
+   running on a single processor, if the :doc:`atom_modify sort
-   case atoms are re-ordered periodically during a simulation, due to
+   <atom_modify>` option is on, which it is by default.  In this case
-   spatial sorting.  It is also true when running in parallel, because
+   atoms are re-ordered periodically during a simulation, due to spatial
-   data for a single snapshot is collected from multiple processors, each
+   sorting.  It is also true when running in parallel, because data for
-   of which owns a subset of the atoms.
+   a single snapshot is collected from multiple processors, each of
+   which owns a subset of the atoms.
 
 For the *vtk* style, sorting is off by default. See the
 :doc:`dump_modify <dump_modify>` page for details.

doc/src/fix_external.rst

@@ -78,7 +78,7 @@ example of how this is done.  This sample application performs
 classical MD using quantum forces computed by a density functional
 code `Quest <quest_>`_.
 
-.. _quest: http://dft.sandia.gov/Quest
+.. _quest: https://dft.sandia.gov/Quest
 
 ----------
 

doc/src/fix_gle.rst

@@ -159,7 +159,7 @@ Related commands
 
 .. _GLE4MD:
 
-**(GLE4MD)** `http://gle4md.org/ <http://gle4md.org/>`_
+**(GLE4MD)** `https://gle4md.org/ <https://gle4md.org/>`_
 
 .. _Ceriotti2:
 

doc/src/fix_imd.rst

@@ -51,16 +51,11 @@ from the main execution thread and potentially lower the inferred
 latencies for slow communication links. This feature has only been
 tested under linux.
 
-There are example scripts for using this package with LAMMPS in
+The source code for this fix includes code developed by the Theoretical
-examples/PACKAGES/imd. Additional examples and a driver for use with the
+and Computational Biophysics Group in the Beckman Institute for Advanced
-Novint Falcon game controller as haptic device can be found at:
+Science and Technology at the University of Illinois at
-http://sites.google.com/site/akohlmey/software/vrpn-icms.
+Urbana-Champaign.  We thank them for providing a software interface that
-
+allows codes like LAMMPS to hook to `VMD <VMD_>`_.
-The source code for this fix includes code developed by the
-Theoretical and Computational Biophysics Group in the Beckman
-Institute for Advanced Science and Technology at the University of
-Illinois at Urbana-Champaign.  We thank them for providing a software
-interface that allows codes like LAMMPS to hook to `VMD <VMD_>`_.
 
 Upon initialization of the fix, it will open a communication port on
 the node with MPI task 0 and wait for an incoming connection.  As soon
@@ -117,40 +112,40 @@ VMD are the following:
 In the Mouse menu of the VMD Main window, select "Mouse -> Force ->
 Atom".  You may alternately select "Residue", or "Fragment" to apply
 forces to whole residues or fragments. Your mouse can now be used to
-apply forces to your simulation. Click on an atom, residue, or
+apply forces to your simulation. Click on an atom, residue, or fragment
-fragment and drag to apply a force. Click quickly without moving the
+and drag to apply a force. Click quickly without moving the mouse to
-mouse to turn the force off. You can also use a variety of 3D position
+turn the force off. You can also use a variety of 3D position trackers
-trackers to apply forces to your simulation. Game controllers or haptic
+to apply forces to your simulation. Game controllers or haptic devices
-devices with force-feedback such as the Novint Falcon or Sensable
+with force-feedback such as the Novint Falcon or Sensable PHANTOM allow
-PHANTOM allow you to feel the resistance due to inertia or interactions
+you to feel the resistance due to inertia or interactions with neighbors
-with neighbors that the atoms experience you are trying to move, as if
+that the atoms experience you are trying to move, as if they were real
-they were real objects. See the `VMD IMD Homepage <imdvmd_>`_ and the
+objects. See the `VMD IMD Homepage <imdvmd_>`_ for more details.
-`VRPN-ICMS Homepage <vrpnicms_>`_ for more details.
 
 If IMD control messages are received, a line of text describing the
 message and its effect will be printed to the LAMMPS output screen, if
 screen output is active.
 
-.. _VMD: http://www.ks.uiuc.edu/Research/vmd
+.. _VMD: https://www.ks.uiuc.edu/Research/vmd
 
-.. _imdvmd: http://www.ks.uiuc.edu/Research/vmd/imd/
+.. _imdvmd: https://www.ks.uiuc.edu/Research/vmd/imd/
-
-.. _vrpnicms: http://sites.google.com/site/akohlmey/software/vrpn-icms
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
+No information about this fix is written to :doc:`binary restart files
-are relevant to this fix.  No global scalar or vector or per-atom
+<restart>`.  None of the :doc:`fix_modify <fix_modify>` options are
-quantities are stored by this fix for access by various :doc:`output commands <Howto_output>`.  No parameter of this fix can be used
+relevant to this fix.  No global scalar or vector or per-atom quantities
-with the *start/stop* keywords of the :doc:`run <run>` command.  This
+are stored by this fix for access by various :doc:`output commands
-fix is not invoked during :doc:`energy minimization <minimize>`.
+<Howto_output>`.  No parameter of this fix can be used with the
+*start/stop* keywords of the :doc:`run <run>` command.  This fix is not
+invoked during :doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""
 
-This fix is part of the MISC package.  It is only enabled if
+This fix is part of the MISC package.  It is only enabled if LAMMPS was
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+built with that package.  See the :doc:`Build package <Build_package>`
+page for more info.
 
 When used in combination with VMD, a topology or coordinate file has
 to be loaded, which matches (in number and ordering of atoms) the

doc/src/fix_ipi.rst

@@ -111,4 +111,4 @@ Related commands
 .. _ipihome:
 
 **(IPI)**
-`http://epfl-cosmo.github.io/gle4md/index.html?page=ipi <http://epfl-cosmo.github.io/gle4md/index.html?page=ipi>`_
+`https://ipi-code.org <https://ipi-code.org>`_

doc/src/fix_nve_manifold_rattle.rst

@@ -108,4 +108,4 @@ every = 0, tchain = 3
 .. _Paquay2:
 
 **(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016).
-preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_.
+preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.

doc/src/fix_nvt_manifold_rattle.rst

@@ -82,4 +82,4 @@ Related commands
 .. _Paquay3:
 
 **(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016).
-preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_.
+preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.

doc/src/fix_phonon.rst

@@ -134,7 +134,7 @@ for other systems, *nasr* = 10 is typically sufficient.
 The *map_file* contains the mapping information between the lattice
 indices and the atom IDs, which tells the code which atom sits at
 which lattice point; the lattice indices start from 0. An auxiliary
-code, `latgen <http://code.google.com/p/latgen>`_, can be employed to
+code, `latgen <https://code.google.com/p/latgen>`_, can be employed to
 generate the compatible map file for various crystals.
 
 In case one simulates a non-periodic system, where the whole simulation

doc/src/fix_qmmm.rst

@@ -31,7 +31,7 @@ wave DFT package.  Electrostatic coupling is in preparation and the
 interface has been written in a manner that coupling to other QM codes
 should be possible without changes to LAMMPS itself.
 
-.. _espresso: http://www.quantum-espresso.org
+.. _espresso: https://www.quantum-espresso.org
 
 The interface code for this is in the lib/qmmm directory of the LAMMPS
 distribution and is being made available at this early stage of

doc/src/kspace_style.rst

@@ -314,9 +314,10 @@ pressure simulation with MSM will cause the code to run slower.
 
 ----------
 
-The *scafacos* style is a wrapper on the `ScaFaCoS Coulomb solver library <http://www.scafacos.de>`_ which provides a variety of solver
+The *scafacos* style is a wrapper on the `ScaFaCoS Coulomb solver
-methods which can be used with LAMMPS.  The paper by :ref:`(Sutman) <Sutmann2014>`
+library <http://www.scafacos.de>`_ which provides a variety of solver
-gives an overview of ScaFaCoS.
+methods which can be used with LAMMPS.  The paper by :ref:`(Sutman)
+<Sutmann2014>` gives an overview of ScaFaCoS.
 
 ScaFaCoS was developed by a consortium of German research facilities
 with a BMBF (German Ministry of Science and Education) funded project

doc/src/pair_adp.rst

@@ -54,7 +54,7 @@ command to specify them.
 
 **ADP potentials are available from:**
 
-* The NIST WWW site at http://www.ctcms.nist.gov/potentials.
+* The NIST WWW site at https://www.ctcms.nist.gov/potentials.
   Note that ADP potentials obtained from NIST must be converted
   into the extended DYNAMO *setfl* format discussed below.
 * The OpenKIM Project at

doc/src/pair_charmm.rst

@@ -110,7 +110,7 @@ These pair styles compute Lennard Jones (LJ) and Coulombic
 interactions with additional switching or shifting functions that ramp
 the energy and/or force smoothly to zero between an inner and outer
 cutoff.  They are implementations of the widely used CHARMM force
-field used in the `CHARMM <http://www.scripps.edu/brooks>`_ MD code (and
+field used in the `CHARMM <https://www.charmm.org>`_ MD code (and
 others).  See :ref:`(MacKerell) <pair-MacKerell>` for a description of the
 CHARMM force field.
 

doc/src/pair_eam.rst

@@ -122,15 +122,11 @@ are parameterized in terms of LAMMPS :doc:`metal units <units>`.
    EAM potential files list atomic masses; thus you do not need to use
    the :doc:`mass <mass>` command to specify them.
 
-There are several WWW sites that distribute and document EAM
+There are web sites that distribute and document EAM potentials stored
-potentials stored in DYNAMO or other formats:
+in DYNAMO or other formats:
 
-.. parsed-literal::
+* https://www.ctcms.nist.gov/potentials
-
+* https://openkim.org
-   http://www.ctcms.nist.gov/potentials
-   http://cst-www.nrl.navy.mil/ccm6/ap
-   http://enpub.fulton.asu.edu/cms/potentials/main/main.htm
-   https://openkim.org
 
 These potentials should be usable with LAMMPS, though the alternate
 formats would need to be converted to the DYNAMO format used by LAMMPS

doc/src/pair_gromacs.rst

@@ -53,7 +53,7 @@ Description
 The *lj/gromacs* styles compute shifted LJ and Coulombic interactions
 with an additional switching function S(r) that ramps the energy and force
 smoothly to zero between an inner and outer cutoff.  It is a commonly
-used potential in the `GROMACS <http://www.gromacs.org>`_ MD code and for
+used potential in the `GROMACS <https://www.gromacs.org>`_ MD code and for
 the coarse-grained models of :ref:`(Marrink) <Marrink>`.
 
 .. math::

doc/src/pair_meam.rst

@@ -426,6 +426,8 @@ none
 **(Gullet)** Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003).
 This report may be accessed on-line via `this link <sandreport_>`_.
 
+.. TODO the following URL is not accessible
+
 .. _sandreport: http://infoserve.sandia.gov/sand_doc/2003/038782.pdf
 
 .. _Lee:

doc/src/pair_peri.rst

@@ -66,10 +66,14 @@ peridynamic viscoelastic solid (VES) model.
 Style *peri/eps* implements the Peridynamic state-based elastic-plastic
 solid (EPS) model.
 
-The canonical papers on Peridynamics are :ref:`(Silling 2000) <Silling2000>`
+.. TODO the following URL is not valid
-and :ref:`(Silling 2007) <Silling2007>`.  The implementation of Peridynamics
+
-in LAMMPS is described in :ref:`(Parks) <Parks>`.  Also see the `PDLAMMPS user guide <http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf>`_ for
+The canonical papers on Peridynamics are :ref:`(Silling 2000)
-more details about its implementation.
+<Silling2000>` and :ref:`(Silling 2007) <Silling2007>`.  The
+implementation of Peridynamics in LAMMPS is described in :ref:`(Parks)
+<Parks>`.  Also see the `PDLAMMPS user guide
+<http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf>`_ for more details
+about its implementation.
 
 The peridynamic VES and EPS models in PDLAMMPS were implemented by
 R. Rahman and J. T. Foster at University of Texas at San Antonio.  The

doc/src/pair_quip.rst

@@ -49,11 +49,12 @@ A QUIP potential is fully specified by the filename which contains the
 parameters of the potential in XML format, the initialization string,
 and the map of atomic numbers.
 
-GAP potentials can be obtained from the Data repository section of
+GAP potentials can be obtained from the `GAP models and databases page
-`http://www.libatoms.org <http://www.libatoms.org>`_, where the
+on the libAtoms homepage `https://libatoms.github.io
-appropriate initialization strings are also advised. The list of
+<https://libatoms.github.io/GAP/data.html>`_, where the appropriate
-atomic numbers must be matched to the LAMMPS atom types specified in
+initialization strings are also advised. The list of atomic numbers must
-the LAMMPS data file or elsewhere.
+be matched to the LAMMPS atom types specified in the LAMMPS data file or
+elsewhere.
 
 Two examples input scripts are provided in the examples/PACKAGES/quip
 directory.

doc/src/read_dump.rst

@@ -397,4 +397,4 @@ Default
 The option defaults are box = yes, timestep = yes, replace = yes, purge = no,
 trim = no, add = no, scaled = no, wrapped = yes, and format = native.
 
-.. _vmd: http://www.ks.uiuc.edu/Research/vmd
+.. _vmd: https://www.ks.uiuc.edu/Research/vmd