ohenrich · ohenrich · Apr 3, 2025 · Mar 13, 2025 · Mar 13, 2025 · Mar 13, 2025
diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
@@ -71,7 +71,10 @@ src/EXTRA-COMMAND/group_ndx.*       @akohlmey
 src/EXTRA-COMMAND/ndx_group.*       @akohlmey
 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/MISC/*_tracker.*                @jtclemm
 src/MC/fix_gcmc.*                   @athomps
 src/MC/fix_sgcmc.*                  @athomps

diff --git a/.github/release_steps.md b/.github/release_steps.md
@@ -216,7 +216,7 @@ and using the CMake settings:
 
 ``` sh
 -D CMAKE_OSX_ARCHITECTURES=arm64;x86_64
--D CMAKE_OSX_DEPLOYMENT_TARGER=11.0
+-D CMAKE_OSX_DEPLOYMENT_TARGET=11.0
 ```
 
 This will add the compiler flags `-arch arm64 -arch x86_64
@@ -324,6 +324,47 @@ At this point it should be possible to do a fast-forward merge of
 
 ### Push branches and tags
 
+## LAMMPS Stable Update Release
 
+After making a stable release, bugfixes from the 'develop' branch
+are selectively backported to the 'maintenance' branch.  This is
+done with "git cherry-pick \<commit hash\>' wherever possible.
+The LAMMPS\_UPDATE define in "src/version.h" is set to "Maintenance".
 
-## LAMMPS Stable Update Release
+### Prerequesites
+
+When a sufficient number of bugfixes has accumulated or an urgent
+or important bugfix needs to be distributed a new stable update
+release is made.  To make this publicly visible a pull request
+is submitted that will merge 'maintenance' into 'stable'.  Before
+merging, set LAMMPS\_UPDATE in "src/version.h" to "Update #" with
+"#" indicating the update count (1, 2, and so on).
+Also draft suitable release notes under https://github.com/lammps/lammps/releases
+
+### Fast-forward merge of 'maintenance' into 'stable', apply tag, and publish
+
+Do a fast-forward merge of 'maintenance' to 'stable' and then
+apply the stable\_DMmmYYYY\_update# tag and push branch and tag
+to GitHub. The corresponding pull request will be automatically
+closed.   Example:
+
+```
+git checkout maintenance
+git pull
+git checkout stable
+git pull
+git merge --ff-only maintenance
+git tag -s -m 'Update 2 for Stable LAMMPS version 29 August 2024' stable_29Aug2024_update2
+git push git@github.com:lammps/lammps.git --tags maintenance stable
+```
+
+Associate draft release notes with new tag and publish as "latest release".
+
+On https://ci.lammps.org/ go to "dev", "stable" and manually execute
+the "update\_release" task. This will update https://docs.lammps.org/stable
+and prepare a stable tarball.
+
+### Build and upload binary packages and source tarball to GitHub
+
+The build procedure is the same as for the feature releases, only
+that packages are built from the 'stable' branch.
diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
@@ -431,8 +431,8 @@ else()
   target_link_libraries(lammps PUBLIC mpi_stubs)
 endif()
 
-set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
-set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
+set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
+set(LAMMPS_SIZES_VALUES smallbig bigbig)
 set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
 validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
 string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)

diff --git a/cmake/Modules/LAMMPSInterfacePlugin.cmake b/cmake/Modules/LAMMPSInterfacePlugin.cmake
@@ -260,8 +260,8 @@ endif()
 
 ################
 # integer size selection
-set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
-set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
+set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
+set(LAMMPS_SIZES_VALUES smallbig bigbig)
 set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
 validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
 string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)

diff --git a/cmake/Modules/Packages/KOKKOS.cmake b/cmake/Modules/Packages/KOKKOS.cmake
@@ -57,8 +57,8 @@ if(DOWNLOAD_KOKKOS)
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
   include(ExternalProject)
-  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.5.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "4d832aa0284169d9e3fbae3165286bc6" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.6.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_MD5 "61b2b69ae50d83eedcc7d47a3fa3d6cb" CACHE STRING "MD5 checksum of KOKKOS tarball")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
   GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@@ -83,7 +83,7 @@ if(DOWNLOAD_KOKKOS)
   add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
   add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 4.5.01 REQUIRED CONFIG)
+  find_package(Kokkos 4.6.00 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
 else()
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)

diff --git a/cmake/presets/kokkos-cuda.cmake b/cmake/presets/kokkos-cuda.cmake
@@ -1,6 +1,5 @@
 # preset that enables KOKKOS and selects CUDA compilation with OpenMP
-# enabled as well. This preselects CC 5.0 as default GPU arch, since
-# that is compatible with all higher CC, but not the default CC 3.5
+# enabled as well. The GPU architecture *must* match your hardware
 set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_CUDA   ON CACHE BOOL "" FORCE)

diff --git a/doc/Makefile b/doc/Makefile
@@ -17,9 +17,11 @@ MATHJAXTAG     = 3.2.2
 
 PYTHON         = $(word 3,$(shell type python3))
 DOXYGEN        = $(word 3,$(shell type doxygen))
+PANDOC         = $(word 3,$(shell type pandoc))
 HAS_PYTHON3    = NO
 HAS_DOXYGEN    = NO
 HAS_PDFLATEX   = NO
+HAS_PANDOC     = NO
 
 ifeq ($(shell type python3 >/dev/null 2>&1; echo $$?), 0)
 HAS_PYTHON3    = YES
@@ -31,10 +33,14 @@ endif
 
 ifeq ($(shell type pdflatex >/dev/null 2>&1; echo $$?), 0)
 ifeq ($(shell type latexmk >/dev/null 2>&1; echo $$?), 0)
-HAS_PDFLATEX = YES
+HAS_PDFLATEX   = YES
 endif
 endif
 
+ifeq ($(shell type pandoc >/dev/null 2>&1; echo $$?), 0)
+HAS_PANDOC     = YES
+endif
+
 # override settings for PIP commands
 # PIP_OPTIONS = --cert /etc/pki/ca-trust/extracted/openssl/ca-bundle.trust.crt --proxy http://proxy.mydomain.org
 
@@ -45,8 +51,9 @@ SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocess
 # we only want to use explicitly listed files.
 DOXYFILES      = $(shell sed -n -e 's/\#.*$$//' -e '/^ *INPUT \+=/,/^[A-Z_]\+ \+=/p' doxygen/Doxyfile.in | sed -e 's/@LAMMPS_SOURCE_DIR@/..\/src/g' -e 's/\\//g' -e 's/ \+/ /' -e 's/[A-Z_]\+ \+= *\(YES\|NO\|\)//') 
 
-.PHONY: help clean-all clean clean-spelling epub mobi html pdf spelling anchor_check style_check char_check role_check xmlgen fasthtml
+.PHONY: help clean-all clean clean-spelling epub mobi html pdf spelling anchor_check style_check char_check role_check xmlgen fasthtml fasthtml-init 
 
+FASTHTMLFILES = $(patsubst $(RSTDIR)/%.rst,fasthtml/%.html,$(wildcard $(RSTDIR)/*rst))
 # ------------------------------------------
 
 help:
@@ -105,6 +112,8 @@ html: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJ
 		env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst ;\
 		$(PYTHON) $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
+		env LC_ALL=C grep -n -E '^ *\.\. [a-z0-9]+:(\s+.*|)$$' \
+                         $(RSTDIR)/*.rst ../src/*.{cpp,h} ../src/*/*.{cpp,h} ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
@@ -116,25 +125,23 @@ html: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJ
 	@rm -rf html/PDF/.[sg]*
 	@echo "Build finished. The HTML pages are in doc/html."
 
-fasthtml: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
-	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
-	@$(MAKE) $(MFLAGS) -C graphviz all
-	@mkdir -p fasthtml
-	@(\
-		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
-		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
-		touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
-		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
-		deactivate ;\
-	)
-	@rm -rf fasthtml/_sources
-	@rm -rf fasthtml/PDF
-	@rm -rf fasthtml/USER
-	@rm -rf fasthtml/JPG
-	@cp -r src/PDF fasthtml/PDF
-	@rm -rf fasthtml/PDF/.[sg]*
+fasthtml: fasthtml-init $(FASTHTMLFILES)
 	@echo "Fast HTML build finished. The HTML pages are in doc/fasthtml."
 
+fasthtml-init:
+	@mkdir -p fasthtml/JPG
+	@cp src/JPG/*.* fasthtml/JPG
+	@cp $(RSTDIR)/accel_styles.rst $(RSTDIR)/lepton_expression.rst fasthtml/
+	@cp $(BUILDDIR)/utils/pandoc.css fasthtml/
+
+fasthtml/%.html: $(RSTDIR)/%.rst
+	@if [ "$(HAS_PANDOC)" == "NO" ] ; then echo "Make 'fasthtml' requires the 'pandoc' software" 1>&2; exit 1; fi
+	@mkdir -p fasthtml
+	@echo converting $< to $@
+	@sed -e 's/\\AA/\\mathring{\\mathrm{A}}/g' $< > fasthtml/$*.temp.rst
+	@pandoc -s --mathml --css="pandoc.css" --template=$(BUILDDIR)/utils/pandoc.html --metadata title="$@" -o $@ fasthtml/$*.temp.rst
+	@rm -f fasthtml/$*.temp.rst
+
 spelling: xmlgen globbed-tocs $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives.txt
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@(\
@@ -188,6 +195,8 @@ pdf: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 		env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst ;\
 		$(PYTHON) utils/check-styles.py -s ../src -d src ;\
+		env LC_ALL=C grep -n -E '^ *\.\. [a-z0-9]+:(\s+.*|)$$' \
+                         $(RSTDIR)/*.rst ../src/*.{cpp,h} ../src/*/*.{cpp,h} ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
@@ -237,6 +246,8 @@ role_check :
 	@( env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst && exit 1 || : )
 	@( env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst && exit 1 || : )
 	@( env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst && exit 1 || : )
+	@( env LC_ALL=C grep -n -E '^ *\.\. [a-z0-9]+:(\s+.*|)$$' \
+                        $(RSTDIR)/*.rst ../src/*.{cpp,h} ../src/*/*.{cpp,h} && exit 1 || : )
 
 link_check : $(VENV) html
 	@(\

diff --git a/doc/lammps.1 b/doc/lammps.1
@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "4 February 2025" "2025-02-04"
+.TH LAMMPS "1" "2 April 2025" "2025-04-02"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 4 February 2025
+\- Molecular Dynamics Simulator.  Version 2 April 2025
 
 .SH SYNOPSIS
 .B lmp

diff --git a/doc/src/Build_cmake.rst b/doc/src/Build_cmake.rst
@@ -119,6 +119,13 @@ configured) and additional files like LAMMPS API headers, manpages,
 potential and force field files.  The location of the installation tree
 defaults to ``${HOME}/.local``.
 
+.. note::
+
+   If you have set `-D CMAKE_INSTALL_PREFIX` to install LAMMPS into a
+   system location on a Linux machine , you may also have to run (as
+   root) the `ldconfig` program to update the cache file for fast lookup
+   of system shared libraries.
+
 .. _cmake_options:
 
 Configuration and build options

diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst
@@ -255,11 +255,10 @@ Traditional make
 
 Before building LAMMPS, you must build the GPU library in ``lib/gpu``\ .
 You can do this manually if you prefer; follow the instructions in
-``lib/gpu/README``.  Note that the GPU library uses MPI calls, so you must
-use the same MPI library (or the STUBS library) settings as the main
-LAMMPS code.  This also applies to the ``-DLAMMPS_BIGBIG``\ ,
-``-DLAMMPS_SMALLBIG``\ , or ``-DLAMMPS_SMALLSMALL`` settings in whichever
-Makefile you use.
+``lib/gpu/README``.  Note that the GPU library uses MPI calls, so you
+must use the same MPI library (or the STUBS library) settings as the
+main LAMMPS code.  This also applies to the ``-DLAMMPS_BIGBIG`` or
+``-DLAMMPS_SMALLBIG`` settings in whichever Makefile you use.
 
 You can also build the library in one step from the ``lammps/src`` dir,
 using a command like these, which simply invokes the ``lib/gpu/Install.py``
@@ -612,6 +611,9 @@ They must be specified in uppercase.
    *  - ZEN3
       - HOST
       - AMD Zen3 architecture
+   *  - ZEN4
+      - HOST
+      - AMD Zen4 architecture
    *  - RISCV_SG2042
       - HOST
       - SG2042 (RISC-V) CPUs
@@ -715,7 +717,7 @@ They must be specified in uppercase.
       - GPU
       - Intel GPU Ponte Vecchio
 
-This list was last updated for version 4.5.1 of the Kokkos library.
+This list was last updated for version 4.6.0 of the Kokkos library.
 
 .. tabs::
 

diff --git a/doc/src/Build_manual.rst b/doc/src/Build_manual.rst
@@ -78,8 +78,7 @@ folder.  The following ``make`` commands are available:
    make epub          # generate LAMMPS.epub in ePUB format using Sphinx
    make mobi          # generate LAMMPS.mobi in MOBI format using ebook-convert
 
-   make fasthtml      # generate approximate HTML in fasthtml dir using Sphinx
-                      # some Sphinx extensions do not work correctly with this
+   make fasthtml      # generate approximate HTML in fasthtml dir using pandoc
 
    make clean         # remove intermediate RST files created by HTML build
    make clean-all     # remove entire build folder and any cached data
@@ -205,12 +204,42 @@ documentation is required and either existing files in the ``src``
 folder need to be updated or new files added. These files are written in
 `reStructuredText <rst_>`_ markup for translation with the Sphinx tool.
 
+Testing your contribution
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
 Before contributing any documentation, please check that both the HTML
-and the PDF format documentation can translate without errors.  During
-testing the html translation, you may use the ``make fasthtml`` command
-which does an approximate translation (i.e. not all Sphinx features and
-extensions will work), but runs very fast because it will only translate
-files that have been changed since the last ``make fasthtml`` command.
+and the PDF format documentation can translate without errors and that
+there are no spelling issues.  This is done with ``make html``, ``make pdf``,
+and ``make spelling``, respectively.
+
+Fast and approximate translation to HTML
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Translating the full manual to HTML or PDF can take a long time.  Thus
+there is a fast and approximate way to translate the reStructuredText to
+HTML as a quick-n-dirty way of checking your manual page.
+
+This translation uses `Pandoc <https://pandoc.org>`_ instead of Sphinx
+and thus all special Sphinx features (cross-references, advanced tables,
+embedding of Python docstrings or doxygen documentation, and so on) will
+not render correctly.  Most embedded math should render correctly.  This
+is a **very fast** way to check the syntax and layout of a documentation
+file translated to HTML while writing or updating it.
+
+To translate **all** manual pages, you can type ``make fasthtml`` at the
+command line.  The translated HTML files are then in the ``fasthtml``
+folder. All subsequent ``make fasthtml`` commands will only translate
+``.rst`` files that have been changed.  The ``make fasthtml`` command
+can be parallelized with make using the `-j` flag.  You can also
+directly translate only individual pages: e.g. to translate only the
+``doc/src/pair_lj.rst`` page type ``make fasthtml/pair_lj.html``
+
+After writing the documentation is completed, you will still need
+to verify with ``make html`` and ``make pdf`` that it translates
+correctly in both formats.
+
+Tests for consistency, completeness, and other known issues
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Please also check the output to the console for any warnings or problems.  There will
 be multiple tests run automatically: