Rigid shear

.github/CODEOWNERS

@@ -73,8 +73,8 @@ src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
 src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps
 src/EXTRA-DUMP/dump_extxyz.*          @fxcoudert
 src/EXTRA-FIX/fix_deform_pressure.* @jtclemm
-src/EXTRA-PAIR/pair_dispersion_d3.* @soniasolomoni @arthurfl
-src/EXTRA-PAIR/d3_parameters.h      @soniasolomoni @arthurfl
+src/EXTRA-PAIR/pair_dispersion_d3.* @soniasalomoni @arthurfl
+src/EXTRA-PAIR/d3_parameters.h      @soniasalomoni @arthurfl
 src/MISC/*_tracker.*                @jtclemm
 src/MC/fix_gcmc.*                   @athomps
 src/MC/fix_sgcmc.*                  @athomps

cmake/Modules/Documentation.cmake

@@ -73,7 +73,7 @@ if(BUILD_DOC)
   # download mathjax distribution and unpack to folder "mathjax"
   if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/mathjax/es5)
     if(EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz)
-      file(MD5 ${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz)
+      file(MD5 ${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz DL_MD5)
     endif()
     if(NOT "${DL_MD5}" STREQUAL "${MATHJAX_MD5}")
       file(DOWNLOAD ${MATHJAX_URL} "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz" STATUS DL_STATUS SHOW_PROGRESS)

cmake/Modules/Packages/COLVARS.cmake

@@ -27,6 +27,7 @@ if(BUILD_OMP)
 endif()
 
 if(BUILD_MPI)
+  target_compile_definitions(colvars PUBLIC -DCOLVARS_MPI)
   target_link_libraries(colvars PUBLIC MPI::MPI_CXX)
 endif()
 

cmake/Modules/Packages/PLUMED.cmake

@@ -32,9 +32,9 @@ endif()
 
 # Note: must also adjust check for supported API versions in
 # fix_plumed.cpp when version changes from v2.n.x to v2.n+1.y
-set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.9.3/plumed-src-2.9.3.tgz"
+set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.9.4/plumed-src-2.9.4.tgz"
   CACHE STRING "URL for PLUMED tarball")
-set(PLUMED_MD5 "ee1249805fe94bccee17d10610d3f6f1" CACHE STRING "MD5 checksum of PLUMED tarball")
+set(PLUMED_MD5 "e540bf5132e3270e843398a6080d00c7" CACHE STRING "MD5 checksum of PLUMED tarball")
 
 mark_as_advanced(PLUMED_URL)
 mark_as_advanced(PLUMED_MD5)

cmake/packaging/build_linux_tgz.sh

@@ -5,7 +5,7 @@ DESTDIR=${PWD}/../LAMMPS_GUI
 VERSION="$1"
 
 echo "Delete old files, if they exist"
-rm -rf ${DESTDIR} ../LAMMPS_GUI-Linux-amd64*.tar.gz
+rm -rf ${DESTDIR} ../LAMMPS-GUI-Linux-amd64*.tar.gz
 
 echo "Create staging area for deployment and populate"
 DESTDIR=${DESTDIR} cmake --install .  --prefix "/"
@@ -25,18 +25,18 @@ rm -f ${DESTDIR}/lib/libgcc_s*
 rm -f ${DESTDIR}/lib/libstdc++*
 
 # get qt dir
-QTDIR=$(ldd ${DESTDIR}/bin/lammps-gui | grep libQt5Core | sed -e 's/^.*=> *//' -e 's/libQt5Core.so.*$/qt5/')
+QTDIR=$(ldd ${DESTDIR}/bin/lammps-gui | grep libQt.Core | sed -e 's/^.*=> *//' -e 's/libQt\(.\)Core.so.*$/qt\1/')
 cat > ${DESTDIR}/bin/qt.conf <<EOF
 [Paths]
-Plugins = ../qt5plugins
+Plugins = ../qtplugins
 EOF
 
 # platform plugin
-mkdir -p ${DESTDIR}/qt5plugins/platforms
-cp ${QTDIR}/plugins/platforms/libqxcb.so ${DESTDIR}/qt5plugins/platforms
+mkdir -p ${DESTDIR}/qtplugins/platforms
+cp ${QTDIR}/plugins/platforms/libqxcb.so ${DESTDIR}/qtplugins/platforms
 
 # get platform plugin dependencies
-QTDEPS=$(LD_LIBRARY_PATH=${DESTDIR}/lib ldd ${QTDIR}/plugins/platforms/libqxcb.so | grep -v ${DESTDIR} | grep libQt5 | sed -e 's/^.*=> *//' -e 's/\(libQt5.*.so.*\) .*$/\1/')
+QTDEPS=$(LD_LIBRARY_PATH=${DESTDIR}/lib ldd ${QTDIR}/plugins/platforms/libqxcb.so | grep -v ${DESTDIR} | grep libQt[56] | sed -e 's/^.*=> *//' -e 's/\(libQt[56].*.so.*\) .*$/\1/')
 for dep in ${QTDEPS}
 do \
     cp ${dep} ${DESTDIR}/lib
@@ -45,13 +45,13 @@ done
 echo "Add additional plugins for Qt"
 for dir in styles imageformats
 do \
-    cp -r  ${QTDIR}/plugins/${dir} ${DESTDIR}/qt5plugins/
+    cp -r  ${QTDIR}/plugins/${dir} ${DESTDIR}/qtplugins/
 done
 
 # get imageplugin dependencies
-for s in ${DESTDIR}/qt5plugins/imageformats/*.so
+for s in ${DESTDIR}/qtplugins/imageformats/*.so
 do \
-    QTDEPS=$(LD_LIBRARY_PATH=${DESTDIR}/lib ldd $s | grep -v ${DESTDIR} | grep -E '(libQt5|jpeg)' | sed -e 's/^.*=> *//' -e 's/\(lib.*.so.*\) .*$/\1/')
+    QTDEPS=$(LD_LIBRARY_PATH=${DESTDIR}/lib ldd $s | grep -v ${DESTDIR} | grep -E '(libQt.|jpeg)' | sed -e 's/^.*=> *//' -e 's/\(lib.*.so.*\) .*$/\1/')
     for dep in ${QTDEPS}
     do \
         cp ${dep} ${DESTDIR}/lib
@@ -72,7 +72,7 @@ do \
 done
 
 pushd ..
-tar -czvvf LAMMPS_GUI-Linux-amd64-${VERSION}.tar.gz LAMMPS_GUI
+tar -czvvf LAMMPS-GUI-Linux-amd64-${VERSION}.tar.gz LAMMPS_GUI
 popd
 
 echo "Cleanup dir"

doc/Makefile

@@ -66,11 +66,13 @@ help:
 	@echo "  mobi          convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
 	@echo "                      (requires ebook-convert tool from calibre)"
 	@echo "  fasthtml      approximate HTML page creation in fasthtml dir (for development)"
+	@echo "  upgrade       upgrade sphinx, extensions, and dependencies to latest supported versions"
 	@echo "  clean         remove all intermediate files"
 	@echo "  clean-all     reset the entire build environment"
 	@echo "  anchor_check  scan for duplicate anchor labels"
 	@echo "  style_check   check for complete and consistent style lists"
 	@echo "  package_check check for complete and consistent package lists"
+	@echo "  char_check    check for non-ASCII characters"
 	@echo "  role_check    check for misformatted role keywords"
 	@echo "  spelling      spell-check the manual"
 

doc/src/Bibliography.rst

@@ -380,7 +380,7 @@ Bibliography
    Eike and Maginn, Journal of Chemical Physics, 124, 164503 (2006).
 
 **(Elliott)**
-   Elliott, Tadmor and Bernstein, `https://openkim.org/kim-api <https://openkim.org/kim-api>`_ (2011) doi: `https://doi.org/10.25950/FF8F563A <https://doi.org/10.25950/FF8F563A>`_
+   Elliott, Tadmor and Bernstein, `https://openkim.org/kim-api/ <https://openkim.org/kim-api/>`_ (2011) doi: `https://doi.org/10.25950/FF8F563A <https://doi.org/10.25950/FF8F563A>`_
 
 **(Ellis)**
    Ellis, Fiedler, Popoola, Modine, Stephens, Thompson, Cangi, Rajamanickam,  Phys Rev B, 104, 035120, (2021)
@@ -1098,9 +1098,6 @@ Bibliography
 **(Parrinello)**
    Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
 
-**(PASS)**
-   PASS webpage: https://www.sdu.dk/en/DPASS
-
 **(Paula Leite2016)**
    Paula Leite , Freitas, Azevedo, and de Koning, J Chem Phys, 126, 044509 (2016).
 
@@ -1213,7 +1210,7 @@ Bibliography
    S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
 
 **(Roberts)**
-   R. Roberts (2019) "Evenly Distributing Points in a Triangle." Extreme Learning.  `<http://extremelearning.com.au/evenly-distributing-points-in-a-triangle/>`_
+   R. Roberts (2019) "Evenly Distributing Points in a Triangle." Extreme Learning.  `<https://extremelearning.com.au/evenly-distributing-points-in-a-triangle/>`_
 
 **(Rohart)**
    Rohart and Thiaville, Physical Review B, 88(18), 184422. (2013).

doc/src/Build_cmake.rst

@@ -217,6 +217,5 @@ Most Linux distributions offer pre-compiled cmake packages through their
 package management system. If you do not have CMake or a recent enough
 version (Note: for CentOS 7.x you need to enable the EPEL repository),
 you can download the latest version from `https://cmake.org/download/
-<https://cmake.org/download/>`_.  Instructions on how to install it on
-various platforms can be found `on this page
-<https://cmake.org/install/>`_.
+<https://cmake.org/download/>`_.  Links to more details on CMake can
+be found `on this page <https://cmake.org/resources/>`_.

doc/src/Build_extras.rst

@@ -1752,7 +1752,7 @@ within CMake will download the non-commercial use version.
 PLUMED package
 -------------------------------------
 
-.. _plumedinstall: https://plumed.github.io/doc-master/user-doc/html/_installation.html
+.. _plumedinstall: https://www.plumed.org/doc-v2.9/user-doc/html/_installation.html
 
 Before building LAMMPS with this package, you must first build PLUMED.
 PLUMED can be built as part of the LAMMPS build or installed separately
@@ -2379,7 +2379,7 @@ SCAFACOS package
 -----------------------------------------
 
 To build with this package, you must download and build the
-`ScaFaCoS Coulomb solver library <http://www.scafacos.de>`_
+`ScaFaCoS Coulomb solver library <http://www.scafacos.de/>`_
 
 .. tabs::
 

doc/src/Build_manual.rst

@@ -82,14 +82,18 @@ folder.  The following ``make`` commands are available:
 
    make fasthtml      # generate approximate HTML in fasthtml dir using pandoc
 
+   make upgrade       # upgrade sphinx, extensions, and dependencies to latest supported versions
    make clean         # remove intermediate RST files created by HTML build
    make clean-all     # remove entire build folder and any cached data
    make upgrade       # upgrade the python packages in the virtual environment
 
    make anchor_check  # check for duplicate anchor labels
    make style_check   # check for complete and consistent style lists
    make package_check # check for complete and consistent package lists
-   make link_check    # check for broken or outdated URLs
+   make char_check    # check for non-ASCII characters
+   make role_check    # check for misformatted role keywords
+
+   make link_check    # check for broken external URLs
    make spelling      # spell-check the manual
 
 ----------
@@ -303,7 +307,7 @@ be multiple tests run automatically:
 
 In addition, there is the option to run a spellcheck on the entire
 manual with ``make spelling``.  This requires `a library called enchant
-<https://github.com/AbiWord/enchant>`_.  To avoid printing out *false
+<https://github.com/rrthomas/enchant>`_.  To avoid printing out *false
 positives* (e.g. keywords, names, abbreviations) those can be added to
 the file ``lammps/doc/utils/sphinx-config/false_positives.txt``.
 

doc/src/Build_settings.rst

@@ -286,7 +286,7 @@ find a heFFTe installation with the correct back end (e.g., FFTW or
 MKL), it will attempt to download and build the library automatically.
 In this case, LAMMPS CMake will also accept all heFFTe specific
 variables listed in the `heFFTe documentation
-<https://mkstoyanov.bitbucket.io/heffte/md_doxygen_installation.html>`_
+<https://icl-utk-edu.github.io/heffte/md_doxygen_installation.html>`_
 and those variables will be passed into the heFFTe build.
 
 ----------

doc/src/Developer_code_design.rst

@@ -397,8 +397,11 @@ value, for example "{:{}d}" will consume two integer arguments, the
 first will be the value shown and the second the minimum width.
 
 For more details and examples, please consult the `{fmt} syntax
-documentation <https://fmt.dev/latest/syntax.html>`_ website.
-
+documentation <https://fmt.dev/latest/syntax/>`_ website.  Since we
+plan to eventually transition from {fmt} to using ``std::format()``
+of the C++ standard library, it is advisable to avoid using any
+extensions beyond what the `C++20 standard offers
+<https://en.cppreference.com/w/cpp/utility/format/format.html>`_.
 
 Memory management
 ^^^^^^^^^^^^^^^^^

doc/src/Developer_notes.rst

@@ -292,16 +292,21 @@ processing similar to the "format()" functionality in Python.
 
 .. note::
 
-   For commands like :doc:`fix ave/time <fix_ave_time>` that accept
-   wildcard arguments, the :cpp:func:`utils::expand_args` function
-   may be passed as an optional argument where the function will provide
-   a map to the original arguments from the expanded argument indices.
+   Commands that accept wildcard arguments, for example
+   :doc:`fix ave/time <fix_ave_time>`, use
+   :cpp:func:`utils::expand_args() <LAMMPS_NS::utils::expand_args>`
+   to convert the wildcards into a list of explicit arguments.
+   This function accepts a pointer address as an optional argument,
+   which will be set to a map to the original arguments from the
+   expanded argument indices.  Please see the corresponding source
+   code for details on how to apply this map in error messages.
 
 For complex errors, that can have multiple causes and which cannot be
 explained in a single line, you can append to the error message, the
-string created by :cpp:func:`utils::errorurl`, which then provides a
-URL pointing to a paragraph of the :doc:`Errors_details` that
-corresponds to the number provided. Example:
+string created by :cpp:func:`utils::errorurl()
+<LAMMPS_NS::utils::errorurl>`, which then provides a URL pointing to a
+paragraph of the :doc:`Errors_details` that corresponds to the number
+provided. Example:
 
 .. code-block:: c++
 

doc/src/Developer_updating.rst

@@ -164,7 +164,7 @@ New:
 .. seealso::
 
    :cpp:func:`utils::count_words() <LAMMPS_NS::utils::count_words>`,
-   :cpp:func:`utils::trim_comments() <LAMMPS_NS::utils::trim_comments>`
+   :cpp:func:`utils::trim_comment() <LAMMPS_NS::utils::trim_comment>`
 
 
 Use utils::numeric() functions instead of force->numeric()
@@ -663,7 +663,8 @@ Use utils::logmesg() instead of error->warning()
 .. versionchanged:: 22Jul2025
 
 The ``Error::message()`` method has been removed since its functionality
-has been superseded by the :cpp:func:`utils::logmesg` function.
+has been superseded by the :cpp:func:`utils::logmesg()
+<LAMMPS_NS::utils::logmesg>` function.
 
 Old:
 

doc/src/Developer_write_command.rst

@@ -38,7 +38,7 @@ Interfacing the *libcurl* library
 """""""""""""""""""""""""""""""""
 
 Rather than implementing the various protocols for downloading files, we
-rely on an external library: `libcurl library <https:://curl.se/libcurl/>`_.
+rely on an external library: `libcurl library <https://curl.se/libcurl/>`_.
 This requires that the library and its headers are installed.  For the
 traditional GNU make build system, this simply requires edits to the machine
 makefile to add compilation flags like for other libraries.  For the CMake

doc/src/Howto_amoeba.rst

@@ -281,7 +281,8 @@ 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:
 
-* `https://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html <https://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html>`_
+* `https://dasher.wustl.edu/tinker/distribution/doc/sphinx/tinker/_build/html/text/file-types.html <https://dasher.wustl.edu/tinker/distribution/doc/sphinx/tinker/_build/html/text/file-types.html>`_
+* `https://openbabel.org/docs/FileFormats/Tinker_XYZ_format.html <https://openbabel.org/docs/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_bpm.rst

@@ -85,50 +85,56 @@ files to render bond data.
 
 ----------
 
-As bonds can be broken between neighbor list builds, the
-:doc:`special_bonds <special_bonds>` command works differently for BPM
-bond styles. There are two possible settings which determine how pair
-interactions work between bonded particles.  First, one can overlay
-pair forces with bond forces such that all bonded particles also
-feel pair interactions. This can be accomplished by setting the *overlay/pair*
-keyword present in all bpm bond styles to *yes* and requires using the
-following special bond settings
+As bonds can potentially be broken between neighbor list builds, BPM bond
+styles may place restrictions on the :doc:`special_bonds <special_bonds>` command. There are three possible scenarios which determine how pair
+interactions between bonded particles and special bond weights work.
+
+The first option is the simplest. If bonds cannot break, then one can use any
+special bond settings to control pair forces. Namely, this is accomplished by
+setting the *break* keyword to *no*. Note that a zero coul weight for 1-2 bonds
+can be used to exclude bonded atoms from the neighbor list builds
+
+   .. code-block:: LAMMPS
+
+      special_bonds lj 0 1 1 coul 0 1 1
+
+This can be useful for post-processing, or to determine pair interaction
+properties between distinct bonded particles.
+
+If bonds can break, the second scenario is if pair forces are overlaid
+on top of bond forces such that atoms can simultaneously exchange both types
+of forces. This is accomplished by setting the *overlay/pair* keyword present
+in all bpm bond styles to *yes*. This case requires the following special
+bond settings
 
    .. code-block:: LAMMPS
 
       special_bonds lj/coul 1 1 1
 
-Alternatively, one can turn off all pair interactions between bonded
-particles. Unlike :doc:`bond quartic <bond_quartic>`, this is not done
-by subtracting pair forces during the bond computation, but rather by
-dynamically updating the special bond list. This is the default behavior
-of BPM bond styles and is done by updating the 1-2 special bond list as
-bonds break.  To do this, LAMMPS requires :doc:`newton <newton>` bond off
-such that all processors containing an atom know when a bond breaks.
+Note that this scenario does not update special bond lists when bonds break,
+hence why fractional weights are not allowed. Whether or not two particles
+are bonded has no bearing on pair forces.
+
+In the third scenario, bonds can break but pair forces are disabled between
+bonded particles. This is the default behavior of BPM bond styles. Unlike
+:doc:`bond quartic <bond_quartic>`, pair forces are not removed by subtracting
+pair forces during the bond computation, but rather by dynamically updating the
+1-2 special bond list. To do this, LAMMPS requires :doc:`newton <newton>` bond
+off such that all processors containing an atom know when a bond breaks.
 Additionally, one must use the following special bond settings
 
    .. code-block:: LAMMPS
 
       special_bonds lj 0 1 1 coul 1 1 1
 
 These settings accomplish two goals. First, they turn off 1-3 and 1-4
-special bond lists, which are not currently supported for BPMs. As
-BPMs often have dense bond networks, generating 1-3 and 1-4 special
-bond lists is expensive.  By setting the lj weight for 1-2 bonds to
-zero, this turns off pairwise interactions.  Even though there are no
-charges in BPM models, setting a nonzero coul weight for 1-2 bonds
+special bond lists, which are not currently supported for breakable BPMs.
+As BPMs often have dense bond networks, generating/updating 1-3 and 1-4
+special bond lists can be expensive. By setting the lj weight for 1-2
+bonds to zero, this turns off pairwise interactions.  Even though there
+are no charges in BPM models, setting a nonzero coul weight for 1-2 bonds
 ensures all bonded neighbors are still included in the neighbor list
-in case bonds break between neighbor list builds. If bond breakage is
-disabled during a simulation run by setting the *break* keyword to *no*,
-a zero coul weight for 1-2 bonds can be used to exclude bonded atoms
-from the neighbor list builds
-
-   .. code-block:: LAMMPS
-
-      special_bonds lj 0 1 1 coul 0 1 1
-
-This can be useful for post-processing, or to determine pair interaction
-properties between distinct bonded particles.
+in case bonds break between neighbor list builds.
 
 To monitor the fracture of bonds in the system, all BPM bond styles
 have the ability to record instances of bond breakage to output using

doc/src/Howto_couple.rst

@@ -18,7 +18,7 @@ the context of your application.
    make library calls to the other code, which has been linked to LAMMPS
    as a library.  This is the way the :ref:`VORONOI <PKG-VORONOI>`
    package, which computes Voronoi tesselations using the `Voro++
-   library <http://math.lbl.gov/voro++>`_, is interfaced to LAMMPS.  See
+   library <https://math.lbl.gov/voro++/>`_, is interfaced to LAMMPS.  See
    the :doc:`compute voronoi <compute_voronoi_atom>` command for more
    details.  Also see the :doc:`Modify <Modify>` pages for information
    on how to add a new fix or compute to LAMMPS.