[pull] develop from lammps:develop

.github/copilot-instructions.md

@@ -245,6 +245,10 @@ lammps/
 5. **Documentation:** All new commands or features must be documented. Put `.. versionadded:: TBD` or
    `.. versionchanged:: TBD` in front of paragraphs documenting the new or changed functionality.
    The `TBD` will be manually replaced with the release version string during the release preparation.
+   This does not apply when the change is only adding an accelerated version of an existing style.
+   Instead the corresponding code letter should be added to the respective Commands_\*.rst file.
+   Also the documentation should pass running "make check" in the doc folder without any
+   output indicating non-ASCII characters, missing entries, or duplicate anchors.
 
 ### Testing
 

cmake/CMakeLists.txt

@@ -867,6 +867,14 @@ else()
     ${CMAKE_COMMAND} -E echo "Must build LAMMPS as a shared library to use the Python module")
 endif()
 
+###############################################################################
+# Create tarball for download with html and PDF version of manual included
+###############################################################################
+add_custom_target(tarball
+  COMMAND ${LAMMPS_DIR}/cmake/packaging/build_tarball.sh ${LAMMPS_DIR}/doc
+)
+
+
 include(Testing)
 include(CodeCoverage)
 include(CodingStandard)

cmake/packaging/build_tarball.sh

@@ -0,0 +1,24 @@
+#!/bin/bash
+set -euo pipefail
+
+APP_NAME=lammps
+DOCDIR="$1"
+DESTDIR="${PWD}"
+
+echo "Delete tar files, if they exist"
+rm -rvf "${PWD}"/lammps-src-*.tar.gz
+pushd "${DOCDIR}/.."
+VERSION=$(grep LAMMPS_VERSION src/version.h | sed 's/^.*LAMMPS_VERSION //' | tr -d \" | tr -d \ )
+TARNAME=lammps-src-${VERSION}.tar
+TARPATH="${DESTDIR}/${TARNAME}"
+git archive --output="${TARPATH}" --prefix=lammps-${VERSION}/ HEAD
+
+cd "${DOCDIR}"
+make clean-all
+make html pdf
+rm html/index.html
+cp html/Manual.html html/index.html
+tar -rf "${TARPATH}" --owner=root --group=root --transform "s,^,lammps-${VERSION}/doc/," html Manual.pdf
+popd
+gzip -9v "${TARNAME}"
+exit 0

cmake/packaging/org.lammps.lammps-gui.yml

@@ -61,6 +61,7 @@ modules:
       - -D PKG_EXTRA-MOLECULE=yes
       - -D PKG_EXTRA-PAIR=yes
       - -D PKG_FEP=yes
+      - -D PKG_GRAPHICS=yes
       - -D PKG_GRANULAR=yes
       - -D PKG_GPU=yes
       - -D GPU_API=opencl

doc/Makefile

@@ -52,7 +52,7 @@ 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 link_check role_check xmlgen fasthtml fasthtml-init
+.PHONY: help clean-all clean clean-spelling epub mobi html pdf spelling anchor_check style_check char_check link_check role_check xmlgen fasthtml fasthtml-init check
 
 FASTHTMLFILES = $(patsubst $(RSTDIR)/%.rst,fasthtml/%.html,$(wildcard $(RSTDIR)/*rst))
 # ------------------------------------------
@@ -69,6 +69,7 @@ help:
 	@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 "  check         run 'anchor_check', 'style_check', 'package_check', 'char_check', and 'role_check'"
 	@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"
@@ -236,6 +237,8 @@ pdf: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@rm -rf latex/PDF/.[sg]*
 	@echo "Build finished. Manual.pdf is in this directory."
 
+check : anchor_check style_check package_check char_check role_check
+
 anchor_check : $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \

doc/src/Build_manual.rst

@@ -87,6 +87,7 @@ folder.  The following ``make`` commands are available:
    make clean-all     # remove entire build folder and any cached data
    make upgrade       # upgrade the python packages in the virtual environment
 
+   make check         # run all checks listed in this block
    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

doc/src/Intro_features.rst

@@ -29,7 +29,7 @@ General features
 * spatial decomposition of simulation domain for MPI parallelism
 * particle decomposition inside spatial decomposition for OpenMP and GPU parallelism
 * GPLv2 licensed open-source distribution
-* highly portable C++-11 (optional packages may require C++17)
+* highly portable C++-17 (optional packages may require C++20)
 * modular code with most functionality in optional packages
 * only depends on MPI library for basic parallel functionality, MPI stub for serial compilation
 * other libraries are optional and only required for specific packages

doc/src/Packages_details.rst

@@ -1306,12 +1306,12 @@ Also see the :ref:`GPU <PKG-GPU>`, :ref:`OPT <PKG-OPT>`, :ref:`INTEL
 <PKG-INTEL>`, and :ref:`OPENMP <PKG-OPENMP>` packages, which have styles
 optimized for CPUs, KNLs, and GPUs.
 
-You must have a C++17 compatible compiler to use this package.
-KOKKOS makes extensive use of advanced C++ features, which can
-expose compiler bugs, especially when compiling for maximum
-performance at high optimization levels. Please see the file
-``lib/kokkos/README`` for a list of compilers and their respective
-platforms, that are known to work.
+You must have a C++20 compatible compiler to use this package.  KOKKOS
+makes extensive use of advanced C++ features, which can expose compiler
+bugs, especially when compiling for maximum performance at high
+optimization levels.  Please see the file ``lib/kokkos/README`` for a
+list of compilers and their respective platforms, that are known to
+work.
 
 **Authors:** The KOKKOS package was created primarily by Christian Trott
 and Stan Moore (Sandia), with contributions from other folks as well.

doc/src/Speed_kokkos.rst

@@ -41,39 +41,42 @@ center GPUs) are under development.  You choose the mode at build time
 to produce an executable compatible with a specific hardware.
 
 The following compatibility notes have been last updated for LAMMPS
-version 23 November 2023 and Kokkos version 4.2.
+version 11 February 2026 and its bundled Kokkos library version 5.0.2.
 
-.. admonition:: C++17 support
+.. admonition:: C++20 support
    :class: note
 
-   Kokkos requires using a compiler that supports the c++17 standard. For
-   some compilers, it may be necessary to add a flag to enable c++17 support.
-   For example, the GNU compiler uses the ``-std=c++17`` flag. For a list of
-   compilers that have been tested with the Kokkos library, see the
-   `requirements document of the Kokkos Wiki
+   Kokkos requires using a compiler that supports the C++20
+   standard. For some compilers, it may be necessary to add a flag to
+   enable C++20 support.  For example, the GNU compiler uses the
+   ``-std=c++20`` flag.  For a list of compilers that have been tested
+   with the Kokkos library, see the `requirements document of the Kokkos
+   Wiki
    <https://kokkos.org/kokkos-core-wiki/get-started/requirements.html>`_.
 
 .. admonition:: NVIDIA CUDA support
    :class: note
 
    To build with Kokkos support for NVIDIA GPUs, the NVIDIA CUDA toolkit
-   software version 11.0 or later must be installed on your system. See
+   software version 12.2 or later must be installed on your system. See
    the discussion for the :doc:`GPU package <Speed_gpu>` for details of
    how to check and do this.
 
 .. admonition:: AMD ROCm (HIP) support
    :class: note
 
    To build with Kokkos support for AMD GPUs, the AMD ROCm toolkit
-   software version 5.2.0 or later must be installed on your system.
+   software version 6.2.0 or later must be installed on your system.
 
 .. admonition:: Intel Data Center GPU support
    :class: note
 
    Support for Kokkos with Intel Data Center GPU accelerators (formerly
    known under the code name "Ponte Vecchio") in LAMMPS is still a work
-   in progress.  Only a subset of the functionality works correctly.
-   Please contact the LAMMPS developers if you run into problems.
+   in progress.  Minimum required version is the Intel LLVM (not
+   classic) compiler version 2024.1.  The LAMMPS developers do not
+   regularly test the status of this, so please contact the LAMMPS
+   developers if you run into problems.
 
 .. admonition:: CUDA and MPI library compatibility
    :class: note

src/EXTRA-COMPUTE/compute_hbond_local.cpp

@@ -216,8 +216,8 @@ int ComputeHBondLocal::compute_image(int *&objs, double **&parms)
     numobjs = 0;
     for (int i = 0; i < ncount; ++i) {
       int idonor = atom->map((tagint) alocal[i][DONOR]);
-      int iacceptor = domain->closest_image(idonor, (tagint) atom->map(alocal[i][ACCEPTOR]));
-      int ihydrogen = domain->closest_image(idonor, (tagint) atom->map(alocal[i][HYDROGEN]));
+      int iacceptor = domain->closest_image(idonor, atom->map((tagint) alocal[i][ACCEPTOR]));
+      int ihydrogen = domain->closest_image(idonor, atom->map((tagint) alocal[i][HYDROGEN]));
       if ((idonor < 0) || (iacceptor < 0) || (ihydrogen < 0)) continue;    // paranoia
 
       imgobjs[numobjs] = Graphics::ARROW;

src/comm.cpp

@@ -36,6 +36,8 @@
 #include "update.h"
 
 #include <cstring>
+#include <limits>
+
 #ifdef _OPENMP
 #include <omp.h>
 #endif
@@ -45,6 +47,10 @@ using namespace LAMMPS_NS;
 enum{ONELEVEL,TWOLEVEL,NUMA,CUSTOM};
 enum{CART,CARTREORDER,XYZ};
 
+namespace {
+  constexpr double EPSILON = std::numeric_limits<double>::epsilon();
+}
+
 /* ---------------------------------------------------------------------- */
 
 Comm::Comm(LAMMPS *lmp) : Pointers(lmp)
@@ -684,7 +690,7 @@ double Comm::get_comm_cutoff()
   if (!force->pair && (cutghostuser == 0.0)) {
     maxcommcutoff = MAX(maxcommcutoff,maxbondcutoff);
   } else {
-    if ((me == 0) && (maxbondcutoff > maxcommcutoff))
+    if ((me == 0) && ((maxbondcutoff - EPSILON) > maxcommcutoff))
       error->warning(FLERR,"Communication cutoff {} is shorter than a bond "
                      "length based estimate of {}. This may lead to errors.",
                      maxcommcutoff,maxbondcutoff);
@@ -693,7 +699,7 @@ double Comm::get_comm_cutoff()
   // print warning if neighborlist cutoff overrides user cutoff
 
   if ((me == 0) && (update->setupflag == 1)) {
-    if ((cutghostuser > 0.0) && (maxcommcutoff > cutghostuser))
+    if ((cutghostuser > 0.0) && ((maxcommcutoff - EPSILON) > cutghostuser))
       error->warning(FLERR,"Communication cutoff adjusted to {}",maxcommcutoff);
   }
 

src/version.h

@@ -1 +1,2 @@
 #define LAMMPS_VERSION "11 Feb 2026"
+#define LAMMPS_UPDATE "Development"