Merge pull request #4044 from lammps/maintenance

Third Set of Collected Bug Fixes and Maintenance Updates for 2 August 2023 Stable release

cmake/CMakeLists.txt

@@ -126,6 +126,19 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "
   set(CMAKE_TUNE_DEFAULT "-Minform=severe")
 endif()
 
+# this hack is required to compile fmt lib with CrayClang version 15.0.2
+# CrayClang is only directly recognized by version 3.28 and later
+if(CMAKE_VERSION VERSION_LESS 3.28)
+  get_filename_component(_exe "${CMAKE_CXX_COMPILER}" NAME)
+  if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (_exe STREQUAL "crayCC"))
+    set(CMAKE_TUNE_DEFAULT "-DFMT_STATIC_THOUSANDS_SEPARATOR")
+  endif()
+else()
+  if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")
+    set(CMAKE_TUNE_DEFAULT "-DFMT_STATIC_THOUSANDS_SEPARATOR")
+  endif()
+endif()
+
 # silence nvcc warnings
 if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))
   set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT} -Xcudafe --diag_suppress=unrecognized_pragma")
@@ -212,6 +225,10 @@ endif()
 add_executable(lmp ${MAIN_SOURCES})
 target_link_libraries(lmp PRIVATE lammps)
 set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})
+# re-export all symbols for plugins
+if(PKG_PLUGIN AND (NOT ((CMAKE_SYSTEM_NAME STREQUAL "Windows"))))
+  set_target_properties(lmp PROPERTIES ENABLE_EXPORTS TRUE)
+endif()
 install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
 
 option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
@@ -426,6 +443,7 @@ if(BUILD_OMP)
       (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM") OR (CMAKE_CXX_COMPILER_ID STREQUAL "XLClang") OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
+      ((CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
     # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
     # Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.

cmake/Modules/ExternalCMakeProject.cmake

@@ -43,5 +43,5 @@ function(ExternalCMakeProject target url hash basedir cmakedir cmakefile)
       "${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}/CMakeLists.txt")
   endif()
   add_subdirectory("${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}"
-    "${CMAKE_BINARY_DIR}/_deps/${target}-build")
+    "${CMAKE_BINARY_DIR}/_deps/${target}-build" EXCLUDE_FROM_ALL)
 endfunction(ExternalCMakeProject)

cmake/Modules/Packages/KOKKOS.cmake

@@ -132,8 +132,12 @@ if(PKG_KSPACE)
                                  ${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
   if(Kokkos_ENABLE_CUDA)
     if(NOT (FFT STREQUAL "KISS"))
+      find_library(CUFFT_LIBRARY cufft)
+      if (CUFFT_LIBRARY STREQUAL "CUFFT_LIBRARY-NOTFOUND")
+        message(FATAL_ERROR "Required cuFFT library not found. Check your environment or set CUFFT_LIBRARY to its location")
+      endif()
       target_compile_definitions(lammps PRIVATE -DFFT_CUFFT)
-      target_link_libraries(lammps PRIVATE cufft)
+      target_link_libraries(lammps PRIVATE ${CUFFT_LIBRARY})
     endif()
   elseif(Kokkos_ENABLE_HIP)
     if(NOT (FFT STREQUAL "KISS"))

cmake/Modules/Packages/MDI.cmake

@@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
 
 if(DOWNLOAD_MDI)
   message(STATUS "MDI download requested - we will build our own")
-  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.16.tar.gz" CACHE STRING "URL for MDI tarball")
-  set(MDI_MD5 "407db44e2d79447ab5c1233af1965f65" CACHE STRING "MD5 checksum for MDI tarball")
+  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.26.tar.gz" CACHE STRING "URL for MDI tarball")
+  set(MDI_MD5 "3124bb85259471e2a53a891f04bf697a" CACHE STRING "MD5 checksum for MDI tarball")
   mark_as_advanced(MDI_URL)
   mark_as_advanced(MDI_MD5)
   GetFallbackURL(MDI_URL MDI_FALLBACK)

cmake/Modules/Packages/ML-QUIP.cmake

@@ -18,7 +18,7 @@ if(DOWNLOAD_QUIP)
     set(temp "${temp}F77FLAGS += -fpp -fixed -fPIC\n")
     set(temp "${temp}F95_PRE_FILENAME_FLAG = -Tf\n")
   elseif(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
-    set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${CMAKE_Fortran_FLAGS_${BTYPE}}\n")
+    set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${CMAKE_Fortran_FLAGS_${BTYPE}} -fmax-stack-var-size=6553600\n")
     set(temp "${temp}DEFINES += -DGETARG_F2003 -DGETENV_F2003 -DGFORTRAN -DFORTRAN_UNDERSCORE\n")
     set(temp "${temp}F95FLAGS += -x f95-cpp-input -ffree-line-length-none -ffree-form -fno-second-underscore -fPIC\n")
     set(temp "${temp}F77FLAGS += -x f77-cpp-input -fno-second-underscore -fPIC\n")
@@ -41,6 +41,11 @@ if(DOWNLOAD_QUIP)
   set(temp "${temp}HAVE_TURBOGAP=0\nHAVE_QR=1\nHAVE_THIRDPARTY=0\nHAVE_FX=0\nHAVE_SCME=0\nHAVE_MTP=0\n")
   set(temp "${temp}HAVE_MBD=0\nHAVE_TTM_NF=0\nHAVE_CH4=0\nHAVE_NETCDF4=0\nHAVE_MDCORE=0\nHAVE_ASAP=0\n")
   set(temp "${temp}HAVE_CGAL=0\nHAVE_METIS=0\nHAVE_LMTO_TBE=0\nHAVE_SCALAPACK=0\n")
+  # for gfortran, the -std= flag, if present, *must* be -std=gnu or else the compilation will fail.
+  if(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
+    string(REGEX REPLACE -std=f[0-9]+ -std=gnu newtemp "${temp}")
+    set(temp "${newtemp}")
+  endif()
   file(WRITE ${CMAKE_BINARY_DIR}/quip.config "${temp}")
 
   message(STATUS "QUIP download via git requested - we will build our own")
@@ -56,7 +61,7 @@ if(DOWNLOAD_QUIP)
     GIT_SUBMODULES "src/fox;src/GAP"
     PATCH_COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_BINARY_DIR}/quip.config <SOURCE_DIR>/arch/Makefile.lammps
     CONFIGURE_COMMAND env QUIP_ARCH=lammps make config
-    BUILD_COMMAND env QUIP_ARCH=lammps make libquip
+    BUILD_COMMAND env QUIP_ARCH=lammps make -j1 libquip
     INSTALL_COMMAND ""
     BUILD_IN_SOURCE YES
     BUILD_BYPRODUCTS <SOURCE_DIR>/build/lammps/${CMAKE_STATIC_LIBRARY_PREFIX}quip${CMAKE_STATIC_LIBRARY_SUFFIX}

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/src/fix_charge_regulation.rst

@@ -253,11 +253,11 @@ built with that package.  See the :doc:`Build package <Build_package>`
 page for more info.
 
 The :doc:`atom_style <atom_style>`, used must contain the charge
-property, for example, the style could be *charge* or *full*. Only
-usable for 3D simulations. Atoms specified as free ions cannot be part
-of rigid bodies or molecules and cannot have bonding interactions. The
-scheme is limited to integer charges, any atoms with non-integer charges
-will not be considered by the fix.
+property and have per atom type masses, for example, the style could be
+*charge* or *full*. Only usable for 3D simulations.  Atoms specified as
+free ions cannot be part of rigid bodies or molecules and cannot have
+bonding interactions.  The scheme is limited to integer charges, any
+atoms with non-integer charges will not be considered by the fix.
 
 All interaction potentials used must be continuous, otherwise the MD
 integration and the particle exchange MC moves do not correspond to the

doc/src/fix_gcmc.rst

@@ -440,8 +440,11 @@ This fix is part of the MC package.  It is only enabled if LAMMPS was
 built with that package.  See the :doc:`Build package <Build_package>`
 doc page for more info.
 
+This fix style requires an :doc:`atom style <atom_style>` with per atom
+type masses.
+
 Do not set "neigh_modify once yes" or else this fix will never be
-called.  Reneighboring is required.
+called.  Reneighboring is **required**.
 
 Only usable for 3D simulations.
 

doc/src/fix_qeq.rst

@@ -232,8 +232,6 @@ These fixes are part of the QEQ package.  They are only enabled if
 LAMMPS was built with that package.  See the :doc:`Build package
 <Build_package>` page for more info.
 
-These qeq fixes are not compatible with the GPU and USER-INTEL packages.
-
 These qeq fixes will ignore electric field contributions from
 :doc:`fix efield <fix_efield>`.
 

doc/src/fix_sgcmc.rst

@@ -155,6 +155,9 @@ This fix is part of the MC package. It is only enabled if LAMMPS was
 built with that package.  See the :doc:`Build package <Build_package>`
 page for more info.
 
+This fix style requires an :doc:`atom style <atom_style>` with per atom
+type masses.
+
 At present the fix provides optimized subroutines for EAM type
 potentials (see above) that calculate potential energy changes due to
 *local* atom type swaps very efficiently.  Other potentials are

doc/src/fix_widom.rst

@@ -195,8 +195,11 @@ doc page for more info.
 Do not set "neigh_modify once yes" or else this fix will never be
 called.  Reneighboring is **required**.
 
-Can be run in parallel, but aspects of the GCMC part will not scale well
-in parallel. Only usable for 3D simulations.
+This fix style requires an :doc:`atom style <atom_style>` with per atom
+type masses.
+
+Can be run in parallel, but some aspects of the insertion procedure
+will not scale well in parallel. Only usable for 3D simulations.
 
 
 Related commands

doc/src/pair_dsmc.rst

@@ -138,8 +138,12 @@ This pair style can only be used via the *pair* keyword of the
 Restrictions
 """"""""""""
 
-This style is part of the MC package.  It is only enabled if LAMMPS
-was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+This pair style is part of the MC package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
+
+This pair style requires an :doc:`atom style <atom_style>` with per
+atom type masses.
 
 Related commands
 """"""""""""""""