Revert "Merging develop into vmmc"

.github/workflows/lammps-gui-flatpak.yml

@@ -42,11 +42,11 @@ jobs:
     - name: Build flatpak
       run: |
         mkdir flatpack-state
-        sed -i -e 's/branch:.*/branch: develop/' cmake/packaging/org.lammps.lammps-gui.yml
+        sed -i -e 's/branch:.*/branch: develop/' tools/lammps-gui/org.lammps.lammps-gui.yml
         flatpak-builder --force-clean --verbose --repo=flatpak-repo \
                                --install-deps-from=flathub --state-dir=flatpak-state \
                                --user --ccache --default-branch=${{ github.ref_name }} \
-                               flatpak-build cmake/packaging/org.lammps.lammps-gui.yml
+                               flatpak-build tools/lammps-gui/org.lammps.lammps-gui.yml
         flatpak build-bundle --runtime-repo=https://flathub.org/repo/flathub.flatpakrepo \
                                --verbose  flatpak-repo LAMMPS-Linux-x86_64-GUI.flatpak \
                                org.lammps.lammps-gui ${{ github.ref_name }}

SECURITY.md

@@ -50,23 +50,3 @@ and then merged to `stable` and published as "updates".  For a new
 stable release the `stable` branch is updated to the corresponding state
 of the `release` branch and a new stable tag is applied in addition to
 the release tag.
-
-# Integrity of Downloaded Archives
-
-For *all* files that can be downloaded from the "lammps.org" web server
-we provide SHA-256 checksum data in files named SHA256SUM.  These
-checksums can be used to validate the integrity of the downloaded
-archives.  Please note that we also use symbolic links to point to
-the latest or stable releases and the checksums for those files
- *will* change (and so their checksums) because the symbolic links
-will be updated for new releases.
-
-# Immutable GitHub Releases
-
-Starting with LAMMPS version 10 Sep 2025 the LAMMPS releases published
-on GitHub are configured as `immutable`.  This means that after the
-release is published the release tag cannot be changed or any of the
-uploaded assets, i.e. the source tarball, the static Linux executable
-tarball and the pre-compiled packages of LAMMPS with LAMMPS-GUI included.
-GitHub will generate a release attestation JSON file which can be
-used to verify the integrity of the files provided with the release.

cmake/CMakeLists.txt

@@ -2,7 +2,7 @@
 ########################################
 # CMake build system
 # This file is part of LAMMPS
-cmake_minimum_required(VERSION 3.20)
+cmake_minimum_required(VERSION 3.16)
 ########################################
 # initialize version variables with project command
 if(POLICY CMP0048)
@@ -140,26 +140,25 @@ if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND (LAMMPS_CXX_COMPILER_NAME STREQUAL
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Xcudafe --diag_suppress=unrecognized_pragma,--diag_suppress=128,--diag_suppress=186")
 endif()
 
-# We *require* C++17 without extensions
-# Kokkos also requires at least C++17 (currently)
+# we *require* C++11 without extensions but prefer C++17.
+# Kokkos requires at least C++17 (currently)
 if(NOT CMAKE_CXX_STANDARD)
-# uncomment in case we plan to switch to C++20 as minimum standard
-#  if(cxx_std_20 IN_LIST CMAKE_CXX_COMPILE_FEATURES)
-#    set(CMAKE_CXX_STANDARD 20)
-#  else()
+  if(cxx_std_17 IN_LIST CMAKE_CXX_COMPILE_FEATURES)
     set(CMAKE_CXX_STANDARD 17)
-#  endif()
+  else()
+    set(CMAKE_CXX_STANDARD 11)
+  endif()
 endif()
-if(CMAKE_CXX_STANDARD LESS 17)
-  message(FATAL_ERROR "C++ standard must be set to at least 17")
+if(CMAKE_CXX_STANDARD LESS 11)
+  message(FATAL_ERROR "C++ standard must be set to at least 11")
 endif()
 if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 17))
   set(CMAKE_CXX_STANDARD 17)
 endif()
-# turn off C++20 check in lmptype.h
-#if(LAMMPS_CXX17)
-#  add_compile_definitions(LAMMPS_CXX17)
-#endif()
+# turn off C++17 check in lmptype.h
+if(LAMMPS_CXX11)
+  add_compile_definitions(LAMMPS_CXX11)
+endif()
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
 # ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
@@ -179,9 +178,15 @@ endif()
 # warn about potentially problematic GCC compiler versions
 if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
   if (CMAKE_CXX_STANDARD GREATER_EQUAL 17)
-    if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 9.3)
-      message(WARNING "Using the GNU compilers version ${CMAKE_CXX_COMPILER_VERSION} with C++17 "
-              "or later is not recommended. Please use the GNU compilers version 9.3 or later")
+    if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 9.0)
+      message(WARNING "Using ${CMAKE_CXX_COMPILER_ID} compiler version ${CMAKE_CXX_COMPILER_VERSION} "
+        "with C++17 is not recommended. Please use ${CMAKE_CXX_COMPILER_ID} compiler version 9.x or later")
+    endif()
+  endif()
+  if (CMAKE_CXX_STANDARD GREATER_EQUAL 11)
+    if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5.0)
+      message(WARNING "Using ${CMAKE_CXX_COMPILER_ID} compiler version ${CMAKE_CXX_COMPILER_VERSION} "
+        "with C++11 is not recommended. Please use ${CMAKE_CXX_COMPILER_ID} compiler version 5.x or later")
     endif()
   endif()
 endif()
@@ -237,13 +242,6 @@ file(GLOB MAIN_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/main.cpp)
 list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
 add_library(lammps ${ALL_SOURCES})
 
-# add extra libraries for std::filesystem with older compilers
-if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 9.1)
-  target_link_libraries(lammps PRIVATE stdc++fs)
-elseif(CMAKE_CXX_COMPILER_ID STREQUAL "Clang" AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 9.0)
-  target_link_libraries(lammps PRIVATE c++fs)
-endif()
-
 # tell CMake to export all symbols to a .dll on Windows with MinGW cross-compilers
 if(BUILD_SHARED_LIBS AND (CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
   set_target_properties(lammps PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols")
@@ -265,6 +263,8 @@ set(STANDARD_PACKAGES
   AMOEBA
   APIP
   ASPHERE
+  ATC
+  AWPMD
   BOCS
   BODY
   BPM
@@ -325,6 +325,7 @@ set(STANDARD_PACKAGES
   PHONON
   PLUGIN
   PLUMED
+  POEMS
   PTM
   PYTHON
   QEQ
@@ -437,6 +438,7 @@ endif()
 # "hard" dependencies between packages resulting
 # in an error instead of skipping over files
 pkg_depends(ML-IAP ML-SNAP)
+pkg_depends(ATC MANYBODY)
 pkg_depends(LATBOLTZ MPI)
 pkg_depends(SCAFACOS MPI)
 pkg_depends(AMOEBA KSPACE)
@@ -514,7 +516,7 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_STANDARD GREATER_EQUA
           PROPERTIES COMPILE_OPTIONS "-std=c++14")
 endif()
 
-if(PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR PKG_RHEO OR BUILD_TOOLS)
+if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR PKG_RHEO OR BUILD_TOOLS)
   if (NOT USE_INTERNAL_LINALG)
     find_package(LAPACK)
     find_package(BLAS)
@@ -675,15 +677,17 @@ endforeach()
 ##############################################
 # add lib sources of (simple) enabled packages
 ############################################
-foreach(PKG_LIB H5MD)
+foreach(PKG_LIB POEMS ATC AWPMD H5MD)
   if(PKG_${PKG_LIB})
     string(TOLOWER "${PKG_LIB}" PKG_LIB)
     file(GLOB_RECURSE ${PKG_LIB}_SOURCES CONFIGURE_DEPENDS
       ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
     add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
     set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE})
     target_link_libraries(lammps PRIVATE ${PKG_LIB})
-    if(PKG_LIB STREQUAL "h5md")
+    if(PKG_LIB STREQUAL "awpmd")
+      target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)
+    elseif(PKG_LIB STREQUAL "h5md")
       target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include ${HDF5_INCLUDE_DIRS})
     else()
       target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB})
@@ -695,6 +699,23 @@ if(PKG_ELECTRODE OR PKG_ML-POD)
   target_link_libraries(lammps PRIVATE ${LAPACK_LIBRARIES})
 endif()
 
+if(PKG_AWPMD)
+  target_link_libraries(awpmd PRIVATE ${LAPACK_LIBRARIES})
+endif()
+
+if(PKG_ATC)
+  if(LAMMPS_SIZES STREQUAL "BIGBIG")
+    message(FATAL_ERROR "The ATC Package is not compatible with -DLAMMPS_BIGBIG")
+  endif()
+  if(BUILD_MPI)
+    target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES} MPI::MPI_CXX)
+  else()
+    target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES} mpi_stubs)
+  endif()
+  target_include_directories(atc PRIVATE ${LAMMPS_SOURCE_DIR})
+  target_compile_definitions(atc PRIVATE -DLAMMPS_${LAMMPS_SIZES})
+endif()
+
 if(PKG_H5MD)
   include(Packages/H5MD)
 endif()

cmake/Modules/LAMMPSInterfacePlugin.cmake

@@ -34,26 +34,26 @@ if(MSVC)
   add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
 endif()
 
-# We *require* C++17 without extensions
-# Kokkos also requires at least C++17 (currently)
 if(NOT CMAKE_CXX_STANDARD)
-# uncomment in case we plan to switch to C++20 as minimum standard
-#  if(cxx_std_20 IN_LIST CMAKE_CXX_COMPILE_FEATURES)
-#    set(CMAKE_CXX_STANDARD 20)
-#  else()
+  if(cxx_std_17 IN_LIST CMAKE_CXX_COMPILE_FEATURES)
     set(CMAKE_CXX_STANDARD 17)
-#  endif()
+  else()
+    set(CMAKE_CXX_STANDARD 11)
+  endif()
+endif()
+if(CMAKE_CXX_STANDARD LESS 11)
+  message(FATAL_ERROR "C++ standard must be set to at least 11")
 endif()
 if(CMAKE_CXX_STANDARD LESS 17)
-  message(FATAL_ERROR "C++ standard must be set to at least 17")
+  message(WARNING "Selecting C++17 standard is preferred over C++${CMAKE_CXX_STANDARD}")
 endif()
 if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 17))
   set(CMAKE_CXX_STANDARD 17)
 endif()
-# turn off C++20 check in lmptype.h
-#if(LAMMPS_CXX17)
-#  add_compile_definitions(LAMMPS_CXX17)
-#endif()
+# turn off C++17 check in lmptype.h
+if(LAMMPS_CXX11)
+  add_compile_definitions(LAMMPS_CXX11)
+endif()
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
 # Need -restrict with Intel compilers

cmake/Modules/OpenCLUtils.cmake

@@ -3,8 +3,6 @@ function(WriteOpenCLHeader varname outfile files)
     separate_arguments(files)
 
     foreach(filename ${files})
-        # In case ${filename} would have blanks, CMake will have replaced them with ';'. Revert:
-        string(REPLACE ";" " " filename "${filename}")
         file(READ ${filename} content)
         string(REGEX REPLACE "\\s*//[^\n]*\n" "\n" content "${content}")
         string(REGEX REPLACE "\\\\" "\\\\\\\\" content "${content}")

cmake/Modules/Packages/INTEL.cmake

@@ -13,11 +13,11 @@ string(TOUPPER ${INTEL_ARCH} INTEL_ARCH)
 
 find_package(Threads QUIET)
 if(Threads_FOUND)
-  set(INTEL_LRT_MODE "threads" CACHE STRING "Long-range threads mode (none, threads, or c++17)")
+  set(INTEL_LRT_MODE "threads" CACHE STRING "Long-range threads mode (none, threads, or c++11)")
 else()
-  set(INTEL_LRT_MODE "none" CACHE STRING "Long-range threads mode (none, threads, or c++17)")
+  set(INTEL_LRT_MODE "none" CACHE STRING "Long-range threads mode (none, threads, or c++11)")
 endif()
-set(INTEL_LRT_VALUES none threads c++17)
+set(INTEL_LRT_VALUES none threads c++11)
 set_property(CACHE INTEL_LRT_MODE PROPERTY STRINGS ${INTEL_LRT_VALUES})
 validate_option(INTEL_LRT_MODE INTEL_LRT_VALUES)
 string(TOUPPER ${INTEL_LRT_MODE} INTEL_LRT_MODE)
@@ -29,9 +29,9 @@ if(INTEL_LRT_MODE STREQUAL "THREADS")
     message(FATAL_ERROR "Must have working threads library for Long-range thread support")
   endif()
 endif()
-if(INTEL_LRT_MODE STREQUAL "C++17")
+if(INTEL_LRT_MODE STREQUAL "C++11")
   if(Threads_FOUND)
-    target_compile_definitions(lammps PRIVATE -DLMP_INTEL_USELRT -DLMP_INTEL_LRT17)
+    target_compile_definitions(lammps PRIVATE -DLMP_INTEL_USELRT -DLMP_INTEL_LRT11)
     target_link_libraries(lammps PRIVATE Threads::Threads)
   else()
     message(FATAL_ERROR "Must have working threads library for Long-range thread support")

cmake/Modules/Packages/VORONOI.cmake

@@ -34,7 +34,7 @@ if(DOWNLOAD_VORO)
   ExternalProject_Add(voro_build
     URL     ${VORO_URL}
     URL_MD5 ${VORO_MD5}
-    PATCH_COMMAND patch -b -p0 < ${LAMMPS_DIR}/cmake/patches/voro-make.patch
+    PATCH_COMMAND patch -b -p0 < ${LAMMPS_LIB_SOURCE_DIR}/voronoi/voro-make.patch
     CONFIGURE_COMMAND ""
     BUILD_COMMAND make ${VORO_BUILD_OPTIONS}
     BUILD_IN_SOURCE 1