Merge branch 'develop' of github.com:lammps/lammps into develop

.github/workflows/codeql-analysis.yml

@@ -30,12 +30,12 @@ jobs:
         fetch-depth: 2
 
     - name: Setup Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
 
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         config-file: ./.github/codeql/${{ matrix.language }}.yml
@@ -55,4 +55,4 @@ jobs:
         cmake --build . --parallel 2
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3

.github/workflows/compile-msvc.yml

@@ -24,7 +24,7 @@ jobs:
         fetch-depth: 2
 
     - name: Select Python version
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.11'
 

cmake/CMakeLists.txt

@@ -971,33 +971,53 @@ if(PKG_KOKKOS)
   endif()
 endif()
 if(PKG_KSPACE)
-  message(STATUS "<<< FFT settings >>>
--- Primary FFT lib:  ${FFT}")
-  if(FFT_SINGLE)
-    message(STATUS "Using single precision FFTs")
-  else()
-    message(STATUS "Using double precision FFTs")
-  endif()
-  if(FFT_FFTW_THREADS OR FFT_MKL_THREADS)
-    message(STATUS "Using threaded FFTs")
+  if (LMP_HEFFTE)
+    message(STATUS "<<< FFT settings >>>
+-- Primary FFT lib:  heFFTe")
+    if (HEFFTE_BACKEND)
+      message(STATUS "heFFTe backend:  ${HEFFTE_BACKEND}")
+    else()
+      message(STATUS "heFFTe backend:  stock (builtin FFT implementation, tested for corrected but not optimized for production)")
+    endif()
+    if(FFT_SINGLE)
+      message(STATUS "Using single precision FFTs")
+    else()
+      message(STATUS "Using double precision FFTs")
+    endif()
   else()
-    message(STATUS "Using non-threaded FFTs")
-  endif()
-  if(PKG_KOKKOS)
-    if(Kokkos_ENABLE_CUDA)
-      if(FFT STREQUAL "KISS")
-        message(STATUS "Kokkos FFT: KISS")
-      else()
-        message(STATUS "Kokkos FFT: cuFFT")
-      endif()
-    elseif(Kokkos_ENABLE_HIP)
-      if(FFT STREQUAL "KISS")
-        message(STATUS "Kokkos FFT: KISS")
+    message(STATUS "<<< FFT settings >>>
+-- Primary FFT lib:  ${FFT}")
+    if(FFT_SINGLE)
+      message(STATUS "Using single precision FFTs")
+    else()
+      message(STATUS "Using double precision FFTs")
+    endif()
+    if(FFT_FFTW_THREADS OR FFT_MKL_THREADS)
+      message(STATUS "Using threaded FFTs")
+    else()
+      message(STATUS "Using non-threaded FFTs")
+    endif()
+    if (FFT_HEFFTE)
+      message(STATUS "Using distributed algorithms from heFTTe")
+    else()
+      message(STATUS "Using builtin distributed algorithms")
+    endif()
+    if(PKG_KOKKOS)
+      if(Kokkos_ENABLE_CUDA)
+        if(FFT STREQUAL "KISS")
+          message(STATUS "Kokkos FFT: KISS")
+        else()
+          message(STATUS "Kokkos FFT: cuFFT")
+        endif()
+      elseif(Kokkos_ENABLE_HIP)
+        if(FFT STREQUAL "KISS")
+          message(STATUS "Kokkos FFT: KISS")
+        else()
+          message(STATUS "Kokkos FFT: hipFFT")
+        endif()
       else()
-        message(STATUS "Kokkos FFT: hipFFT")
+        message(STATUS "Kokkos FFT: ${FFT}")
       endif()
-    else()
-      message(STATUS "Kokkos FFT: ${FFT}")
     endif()
   endif()
 endif()

cmake/Modules/Packages/GPU.cmake

@@ -151,10 +151,10 @@ if(GPU_API STREQUAL "CUDA")
   endif()
 
   cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
-          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
+          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -allow-unsupported-compiler -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
 
   cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
-          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
+          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -allow-unsupported-compiler -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
 
   foreach(CU_OBJ ${GPU_GEN_OBJS})
     get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)

cmake/Modules/Packages/KSPACE.cmake

@@ -46,6 +46,42 @@ else()
   target_compile_definitions(lammps PRIVATE -DFFT_KISS)
 endif()
 
+option(FFT_USE_HEFFTE  "Use heFFTe as the distributed FFT engine, overrides the FFT option."  OFF)
+if(FFT_USE_HEFFTE)
+  # if FFT_HEFFTE is enabled, switch the builtin FFT engine with Heffte
+  set(FFT_HEFFTE_BACKEND_VALUES FFTW MKL)
+  set(FFT_HEFFTE_BACKEND "" CACHE STRING "Select heFFTe backend, e.g., FFTW or MKL")
+  set_property(CACHE FFT_HEFFTE_BACKEND PROPERTY STRINGS ${FFT_HEFFTE_BACKEND_VALUES})
+
+  if(FFT_HEFFTE_BACKEND STREQUAL "FFTW") # respect the backend choice, FFTW or MKL
+    set(HEFFTE_COMPONENTS "FFTW")
+    set(Heffte_ENABLE_FFTW "ON" CACHE BOOL "Enables FFTW backend for heFFTe")
+  elseif(FFT_HEFFTE_BACKEND STREQUAL "MKL")
+    set(HEFFTE_COMPONENTS "MKL")
+    set(Heffte_ENABLE_MKL "ON" CACHE BOOL "Enables MKL backend for heFFTe")
+  else()
+    message(WARNING "FFT_HEFFTE_BACKEND not selected, defaulting to the builtin 'stock' backend, which is intended for testing and is not optimized for production runs")
+  endif()
+
+  find_package(Heffte 2.4.0 QUIET COMPONENTS ${HEFFTE_COMPONENTS})
+  if (NOT Heffte_FOUND) # download and build
+    include(FetchContent)
+    FetchContent_Declare(HEFFTE_PROJECT # using v2.4.0
+      URL  "https://github.com/icl-utk-edu/heffte/archive/refs/tags/v2.4.0.tar.gz"
+      URL_HASH SHA256=02310fb4f9688df02f7181667e61c3adb7e38baf79611d80919d47452ff7881d
+      )
+    FetchContent_Populate(HEFFTE_PROJECT)
+    add_subdirectory(${heffte_project_SOURCE_DIR} ${heffte_project_BINARY_DIR})
+    set_target_properties(lmp PROPERTIES INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+    set_target_properties(lammps PROPERTIES INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+    add_library(Heffte::Heffte INTERFACE IMPORTED GLOBAL)
+    target_link_libraries(Heffte::Heffte INTERFACE Heffte)
+  endif()
+
+  target_compile_definitions(lammps PRIVATE -DFFT_HEFFTE "-DFFT_HEFFTE_${FFT_HEFFTE_BACKEND}")
+  target_link_libraries(lammps PRIVATE Heffte::Heffte)
+endif()
+
 set(FFT_PACK "array" CACHE STRING "Optimization for FFT")
 set(FFT_PACK_VALUES array pointer memcpy)
 set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES})

cmake/Modules/Packages/ML-PACE.cmake

@@ -1,33 +1,40 @@
-set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.10.04.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.11.25.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
 
-set(PACELIB_MD5 "70ff79f4e59af175e55d24f3243ad1ff" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+set(PACELIB_MD5 "b45de9a633f42ed65422567e3ce56f9f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
 mark_as_advanced(PACELIB_URL)
 mark_as_advanced(PACELIB_MD5)
 GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)
 
-# download library sources to build folder
-if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
-  file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
-endif()
-if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
-  message(STATUS "Downloading ${PACELIB_URL}")
-  file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz STATUS DL_STATUS SHOW_PROGRESS)
-  file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
-  if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}"))
-    message(WARNING "Download from primary URL ${PACELIB_URL} failed\nTrying fallback URL ${PACELIB_FALLBACK}")
-    file(DOWNLOAD ${PACELIB_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5} SHOW_PROGRESS)
-  endif()
+# LOCAL_ML-PACE points to top-level dir with local lammps-user-pace repo,
+# to make it easier to check local build without going through the public github releases
+if(LOCAL_ML-PACE)
+ set(lib-pace "${LOCAL_ML-PACE}")
 else()
-  message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
-endif()
+  # download library sources to build folder
+  if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
+    file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
+  endif()
+  if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
+    message(STATUS "Downloading ${PACELIB_URL}")
+    file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz STATUS DL_STATUS SHOW_PROGRESS)
+    file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
+    if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}"))
+      message(WARNING "Download from primary URL ${PACELIB_URL} failed\nTrying fallback URL ${PACELIB_FALLBACK}")
+      file(DOWNLOAD ${PACELIB_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5} SHOW_PROGRESS)
+    endif()
+  else()
+    message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
+  endif()
+
 
-# uncompress downloaded sources
-execute_process(
-  COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
-  COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
-  WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
-)
-get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
+  # uncompress downloaded sources
+  execute_process(
+    COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
+    COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
+    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+  )
+  get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
+endif()
 
 add_subdirectory(${lib-pace} build-pace)
 set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})

cmake/presets/gpu-cuda.cmake

@@ -0,0 +1,11 @@
+# preset that enables GPU and selects CUDA API
+
+set(PKG_GPU ON CACHE BOOL "Build GPU package" FORCE)
+set(GPU_API "cuda" CACHE STRING "APU used by GPU package" FORCE)
+set(GPU_PREC "mixed" CACHE STRING "" FORCE)
+
+set(CUDA_NVCC_FLAGS "-allow-unsupported-compiler" CACHE STRING "" FORCE)
+set(CUDA_NVCC_FLAGS_DEBUG "-allow-unsupported-compiler" CACHE STRING "" FORCE)
+set(CUDA_NVCC_FLAGS_MINSIZEREL "-allow-unsupported-compiler" CACHE STRING "" FORCE)
+set(CUDA_NVCC_FLAGS_RELWITHDEBINFO "-allow-unsupported-compiler" CACHE STRING "" FORCE)
+set(CUDA_NVCC_FLAGS_RELEASE "-allow-unsupported-compiler" CACHE STRING "" FORCE)

cmake/presets/oneapi.cmake

@@ -18,11 +18,11 @@ set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 
 unset(HAVE_OMP_H_INCLUDE CACHE)
 set(OpenMP_C "icx" CACHE STRING "" FORCE)
-set(OpenMP_C_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
 set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
 set(OpenMP_CXX "icpx" CACHE STRING "" FORCE)
-set(OpenMP_CXX_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
 set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
-set(OpenMP_Fortran_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
+set(OpenMP_Fortran_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
 set(OpenMP_omp_LIBRARY "libiomp5.so" CACHE PATH "" FORCE)
 

doc/github-development-workflow.md

@@ -36,10 +36,10 @@ requests.
 MUST be submitted as a pull request to GitHub.  All changes to the
 "develop" branch must be made exclusively through merging pull requests.
 The "release" and "stable" branches, respectively, are only to be
-updated upon feature or stable releases based on the associated
-tags.  Updates to the stable release in between stable releases
+updated upon "feature releases" or "stable releases" based on the
+associated tags.  Updates to the stable release in between stable releases
 (for example, back-ported bug fixes) are first merged into the "maintenance"
-branch and then into the "stable" branch as update releases.
+branch and then into the "stable" branch as "stable update releases".
 
 Pull requests may also be submitted to (long-running) feature branches
 created by LAMMPS developers inside the LAMMPS project, if needed. Those
@@ -131,7 +131,7 @@ testing -- that the code in the branch "develop" does not get easily
 broken.  These tests are run after every update to a pull request.  More
 extensive and time-consuming tests (including regression testing) are
 performed after code is merged to the "develop" branch.  There are feature
-releases of LAMMPS made about every 4-6 weeks at a point, when the LAMMPS
+releases of LAMMPS made about every 4-8 weeks at a point, when the LAMMPS
 developers feel, that a sufficient number of changes have been included
 and all post-merge testing has been successful.  These feature releases are
 marked with a `patch_<version date>` tag and the "release" branch

doc/graphviz/Makefile

@@ -16,8 +16,11 @@ clean:
 	rm -f $(IMGSVG) $(IMGPDF) $(IMGPNG) *~
 
 ifeq ($(HAS_DOT),YES)
-$(IMGDIR)/%.png: %.dot
+$(IMGDIR)/lammps-classes.png : lammps-classes.dot
 	dot -Tpng -Kneato -o $@ $<
+
+$(IMGDIR)/%.png: %.dot
+	dot -Tpng -Kdot -o $@ $<
 endif
 
 ifeq ($(HAS_DOT),NO)

doc/graphviz/lammps-releases.dot

@@ -0,0 +1,34 @@
+// LAMMPS branches and releases
+digraph releases {
+    rankdir="LR";
+    github [shape="box" label="Pull Requests\non GitHub" height=0.75];
+    github -> develop [label="Merge commits"];
+    {
+        rank = "same";
+        work [shape="none" label="Development branches:"]
+        develop [label="'develop' branch" height=0.75];
+        maintenance [label="'maintenance' branch" height=0.75];
+    };
+    {
+        rank = "same";
+        upload [shape="none" label="Release branches:"]
+        release [label="'release' branch" height=0.75];
+        stable [label="'stable' branch" height=0.75];
+    };
+    develop -> release [label="Feature release\n(every 4-8 weeks)"];
+    release -> stable [label="Stable release\n(once per year)"];
+    stable -> maintenance [label="Reset on stable release" style="setlinewidth(2)"];
+    develop -> maintenance [label="Backports of bugfixes" style="dashed"];
+    maintenance -> stable [label="Updates to stable release"];
+    {
+        rank = "same";
+        tag [shape="none" label="Applied tags:"];
+        patchtag [shape="box" label="patch_<date>"];
+        stabletag [shape="box" label="stable_<date>"];
+        updatetag [shape="box" label="stable_<date>_update<num>"];
+    };
+    release -> patchtag [label="feature release" style="dotted"];
+    stable -> stabletag [label="stable release" style="dotted"];
+    stable -> updatetag [label="update release" style="dotted"];
+}
+

doc/src/Bibliography.rst

@@ -562,6 +562,9 @@ Bibliography
 **(Kumar)**
    Kumar and Skinner, J. Phys. Chem. B, 112, 8311 (2008)
 
+**(Lafourcade)**
+  Lafourcade, Maillet, Denoual, Duval, Allera, Goryaeva, and Marinica, `Comp. Mat. Science, 230, 112534 (2023) <https://doi.org/10.1016/j.commatsci.2023.112534>`_
+
 **(Lamoureux and Roux)**
    G.\  Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
 

doc/src/Build_development.rst

@@ -255,16 +255,18 @@ A test run is then a a collection multiple individual test runs each
 with many comparisons to reference results based on template input
 files, individual command settings, relative error margins, and
 reference data stored in a YAML format file with ``.yaml``
-suffix. Currently the programs ``test_pair_style``, ``test_bond_style``, and
-``test_angle_style`` are implemented.  They will compare forces, energies and
-(global) stress for all atoms after a ``run 0`` calculation and after a
-few steps of MD with :doc:`fix nve <fix_nve>`, each in multiple variants
-with different settings and also for multiple accelerated styles. If a
-prerequisite style or package is missing, the individual tests are
-skipped.  All tests will be executed on a single MPI process, so using
-the CMake option ``-D BUILD_MPI=off`` can significantly speed up testing,
-since this will skip the MPI initialization for each test run.
-Below is an example command and output:
+suffix. Currently the programs ``test_pair_style``, ``test_bond_style``,
+``test_angle_style``, ``test_dihedral_style``, and
+``test_improper_style`` are implemented.  They will compare forces,
+energies and (global) stress for all atoms after a ``run 0`` calculation
+and after a few steps of MD with :doc:`fix nve <fix_nve>`, each in
+multiple variants with different settings and also for multiple
+accelerated styles. If a prerequisite style or package is missing, the
+individual tests are skipped.  All force style tests will be executed on
+a single MPI process, so using the CMake option ``-D BUILD_MPI=off`` can
+significantly speed up testing, since this will skip the MPI
+initialization for each test run.  Below is an example command and
+output:
 
 .. code-block:: console
 
@@ -416,15 +418,16 @@ When compiling LAMMPS with enabled tests, most test executables will
 need to be linked against the LAMMPS library.  Since this can be a very
 large library with many C++ objects when many packages are enabled, link
 times can become very long on machines that use the GNU BFD linker (e.g.
-Linux systems).  Alternatives like the ``lld`` linker of the LLVM project
-or the ``gold`` linker available with GNU binutils can speed up this step
-substantially. CMake will by default test if any of the two can be
-enabled and use it when ``ENABLE_TESTING`` is active.  It can also be
-selected manually through the ``CMAKE_CUSTOM_LINKER`` CMake variable.
-Allowed values are ``lld``, ``gold``, ``bfd``, or ``default``.  The
-``default`` option will use the system default linker otherwise, the
-linker is chosen explicitly.  This option is only available for the
-GNU or Clang C++ compiler.
+Linux systems).  Alternatives like the ``mold`` linker, the ``lld``
+linker of the LLVM project, or the ``gold`` linker available with GNU
+binutils can speed up this step substantially (in this order).  CMake
+will by default test if any of the three can be enabled and use it when
+``ENABLE_TESTING`` is active.  It can also be selected manually through
+the ``CMAKE_CUSTOM_LINKER`` CMake variable.  Allowed values are
+``mold``, ``lld``, ``gold``, ``bfd``, or ``default``.  The ``default``
+option will use the system default linker otherwise, the linker is
+chosen explicitly.  This option is only available for the GNU or Clang
+C++ compilers.
 
 Tests for other components and utility functions
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -518,6 +521,8 @@ The following options are available.
    make fix-errordocs       # remove error docs in header files
    make check-permissions   # search for files with permissions issues
    make fix-permissions     # correct permissions issues in files
+   make check-docs          # search for several issues in the manual
+   make check-version       # list files with pending release version tags
    make check               # run all check targets from above
 
 These should help to make source and documentation files conforming