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

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This commit is contained in:
Jacob Tavenner
2025-01-28 19:00:08 -07:00
parent a678a3b474 800a5f6310
commit ea6e702184
1254 changed files with 103054 additions and 30447 deletions
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45
cmake/CMakeLists.txt
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@ -3,6 +3,9 @@
# CMake build system
# This file is part of LAMMPS
cmake_minimum_required(VERSION 3.16)
if(CMAKE_VERSION VERSION_LESS 3.20)
message(WARNING "LAMMPS is planning to require at least CMake version 3.20 by Summer 2025. Please upgrade!")
endif()
########################################
# set policy to silence warnings about ignoring <PackageName>_ROOT but use it
if(POLICY CMP0074)
@ -144,16 +147,28 @@ if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL
set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT}" "-Xcudafe --diag_suppress=unrecognized_pragma,--diag_suppress=128")
endif()
# we require C++11 without extensions. Kokkos requires at least C++17 (currently)
# we *require* C++11 without extensions but prefer C++17.
# Kokkos requires at least C++17 (currently)
if(NOT CMAKE_CXX_STANDARD)
set(CMAKE_CXX_STANDARD 11)
if(cxx_std_17 IN_LIST CMAKE_CXX_COMPILE_FEATURES)
set(CMAKE_CXX_STANDARD 17)
else()
set(CMAKE_CXX_STANDARD 11)
endif()
endif()
if(CMAKE_CXX_STANDARD LESS 11)
message(FATAL_ERROR "C++ standard must be set to at least 11")
endif()
if(CMAKE_CXX_STANDARD LESS 17)
message(WARNING "Selecting C++17 standard is preferred over C++${CMAKE_CXX_STANDARD}")
endif()
if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 17))
set(CMAKE_CXX_STANDARD 17)
endif()
# turn off C++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
@ -347,6 +362,17 @@ foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
option(PKG_${PKG} "Build ${PKG} Package" OFF)
endforeach()
set(DEPRECATED_PACKAGES AWPMD ATC POEMS)
foreach(PKG ${DEPRECATED_PACKAGES})
if(PKG_${PKG})
message(WARNING
"The ${PKG} package will be removed from LAMMPS in Summer 2025 due to lack of "
"maintenance and use of code constructs that conflict with modern C++ compilers "
"and standards. Please contact developers@lammps.org if you have any concerns "
"about this step.")
endif()
endforeach()
######################################################
# packages with special compiler needs or external libs
######################################################
@ -579,6 +605,16 @@ foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE
endif()
endforeach()
# settings for misc packages and styles
if(PKG_MISC)
option(LAMMPS_ASYNC_IMD "Asynchronous IMD processing" OFF)
mark_as_advanced(LAMMPS_ASYNC_IMD)
if(LAMMPS_ASYNC_IMD)
target_compile_definitions(lammps PRIVATE -DLAMMPS_ASYNC_IMD)
message(STATUS "Using IMD in asynchronous mode")
endif()
endif()
# optionally enable building script wrappers using swig
option(WITH_SWIG "Build scripting language wrappers with SWIG" OFF)
if(WITH_SWIG)
@ -1078,12 +1114,15 @@ if(BUILD_TOOLS)
message(STATUS "<<< Building Tools >>>")
endif()
if(BUILD_LAMMPS_GUI)
message(STATUS "<<< Building LAMMPS GUI >>>")
message(STATUS "<<< Building LAMMPS-GUI >>>")
if(LAMMPS_GUI_USE_PLUGIN)
message(STATUS "Loading LAMMPS library as plugin at run time")
else()
message(STATUS "Linking LAMMPS library at compile time")
endif()
if(BUILD_WHAM)
message(STATUS "<<< Building WHAM >>>")
endif()
endif()
if(ENABLE_TESTING)
message(STATUS "<<< Building Unit Tests >>>")

4
cmake/Modules/Packages/INTEL.cmake
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@ -72,6 +72,10 @@ if(INTEL_ARCH STREQUAL "KNL")
if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
message(FATAL_ERROR "Must use Intel compiler with INTEL for KNL architecture")
endif()
message(WARNING, "Support for Intel Xeon Phi accelerators and Knight's Landing CPUs "
"will be removed from LAMMPS in Summer 2025 due to lack of available machines "
"in labs and HPC centers and removed support in recent compilers "
"Please contact developers@lammps.org if you have any concerns about this step.")
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload")
set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"")
target_compile_options(lammps PRIVATE -xMIC-AVX512 -qoffload -fno-alias -ansi-alias -restrict -qoverride-limits ${MIC_OPTIONS})

22
cmake/Modules/Packages/KOKKOS.cmake
View File

@ -7,26 +7,13 @@ endif()
########################################################################
# consistency checks and Kokkos options/settings required by LAMMPS
if(Kokkos_ENABLE_CUDA)
option(Kokkos_ENABLE_IMPL_CUDA_MALLOC_ASYNC "CUDA asynchronous malloc support" OFF)
mark_as_advanced(Kokkos_ENABLE_IMPL_CUDA_MALLOC_ASYNC)
if(Kokkos_ENABLE_IMPL_CUDA_MALLOC_ASYNC)
message(STATUS "KOKKOS: CUDA malloc async support enabled")
else()
message(STATUS "KOKKOS: CUDA malloc async support disabled")
endif()
endif()
if(Kokkos_ENABLE_HIP)
option(Kokkos_ENABLE_HIP_MULTIPLE_KERNEL_INSTANTIATIONS "Enable multiple kernel instantiations with HIP" ON)
mark_as_advanced(Kokkos_ENABLE_HIP_MULTIPLE_KERNEL_INSTANTIATIONS)
option(Kokkos_ENABLE_ROCTHRUST "Use RoCThrust library" ON)
mark_as_advanced(Kokkos_ENABLE_ROCTHRUST)
if(Kokkos_ARCH_AMD_GFX942 OR Kokkos_ARCH_AMD_GFX940)
option(Kokkos_ENABLE_IMPL_HIP_UNIFIED_MEMORY "Enable unified memory with HIP" ON)
mark_as_advanced(Kokkos_ENABLE_IMPL_HIP_UNIFIED_MEMORY)
endif()
endif()
# Adding OpenMP compiler flags without the checks done for
# BUILD_OMP can result in compile failures. Enforce consistency.
if(Kokkos_ENABLE_OPENMP)
@ -70,8 +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/4.4.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
set(KOKKOS_MD5 "de6ee80d00b6212b02bfb7f1e71a8392" CACHE STRING "MD5 checksum of KOKKOS tarball")
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")
mark_as_advanced(KOKKOS_URL)
mark_as_advanced(KOKKOS_MD5)
GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@ -96,7 +83,7 @@ if(DOWNLOAD_KOKKOS)
add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 4.4.01 REQUIRED CONFIG)
find_package(Kokkos 4.5.01 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
else()
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
@ -130,7 +117,6 @@ set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/group_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/min_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/min_linesearch_kokkos.cpp
${KOKKOS_PKG_SOURCES_DIR}/neighbor_kokkos.cpp

98
cmake/Modules/Packages/ML-PACE.cmake
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@ -1,50 +1,62 @@
# PACE library support for ML-PACE package
find_package(pace QUIET)
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
endif()
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 "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)
# 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}")
if(pace_FOUND)
find_package(pace)
target_link_libraries(lammps PRIVATE pace::pace)
else()
# 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)
# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
if(POLICY CMP0135)
cmake_policy(SET CMP0135 OLD)
endif()
else()
message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
endif()
set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.11.25.fix2.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
set(PACELIB_MD5 "a53bd87cfee8b07d9f44bc17aad69c3f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
mark_as_advanced(PACELIB_URL)
mark_as_advanced(PACELIB_MD5)
GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)
# LOCAL_ML-PACE points to top-level dir with local lammps-user-pace repo,
# to make it easier to check local build without going through the public github releases
if(LOCAL_ML-PACE)
set(lib-pace "${LOCAL_ML-PACE}")
else()
# 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)
endif()
add_subdirectory(${lib-pace} build-pace)
set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps PRIVATE 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()
# some preinstalled yaml-cpp versions don't provide a namespaced target
find_package(yaml-cpp QUIET)
if(TARGET yaml-cpp AND NOT TARGET yaml-cpp::yaml-cpp)
add_library(yaml-cpp::yaml-cpp ALIAS yaml-cpp)
endif()
add_subdirectory(${lib-pace} build-pace)
set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
if(CMAKE_PROJECT_NAME STREQUAL "lammps")
target_link_libraries(lammps PRIVATE pace)
endif()
endif()

4
cmake/Modules/Packages/PLUMED.cmake
View File

@ -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/v2.9.2/plumed-src-2.9.2.tgz"
set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.9.3/plumed-src-2.9.3.tgz"
CACHE STRING "URL for PLUMED tarball")
set(PLUMED_MD5 "04862602a372c1013bdfee2d6d03bace" CACHE STRING "MD5 checksum of PLUMED tarball")
set(PLUMED_MD5 "ee1249805fe94bccee17d10610d3f6f1" CACHE STRING "MD5 checksum of PLUMED tarball")
mark_as_advanced(PLUMED_URL)
mark_as_advanced(PLUMED_MD5)

2
cmake/Modules/Packages/VTK.cmake
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@ -1,3 +1,5 @@
# FindVTK requires that C support is enabled when looking for MPI support
enable_language(C)
find_package(VTK REQUIRED NO_MODULE)
target_compile_definitions(lammps PRIVATE -DLAMMPS_VTK)
if (VTK_MAJOR_VERSION VERSION_LESS 9.0)