Merge branch 'lammps:develop' into develop

.github/workflows/coverity.yml

@@ -67,7 +67,6 @@ jobs:
         -D PKG_MANIFOLD=on \
         -D PKG_MDI=on \
         -D PKG_MGPT=on \
-        -D PKG_ML-PACE=on \
         -D PKG_ML-RANN=on \
         -D PKG_MOLFILE=on \
         -D PKG_NETCDF=on \

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

@@ -0,0 +1,53 @@
+# GitHub action to build LAMMPS-GUI as a flatpak bundle
+name: "Build LAMMPS-GUI as flatpak bundle"
+
+on:
+  push:
+    branches:
+      - develop
+
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{github.event_name == 'pull_request'}}
+
+jobs:
+  build:
+    name: LAMMPS-GUI flatpak build
+    if: ${{ github.repository == 'lammps/lammps' }}
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 2
+
+    - name: Install extra packages
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y ccache \
+                                libeigen3-dev \
+                                libcurl4-openssl-dev \
+                                mold \
+                                ninja-build \
+                                python3-dev \
+                                flatpak \
+                                flatpak-builder
+
+    - name: Set up access to flatpak repo
+      run: flatpak --user remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
+
+    - name: Build flatpak
+      run: |
+        mkdir flatpack-state
+        sed -i -e 's/branch:.*/branch: develop/' tools/lammps-gui/org.lammps.lammps-gui.yml
+        flatpak-builder --force-clean --verbose --repo=flatpak-repo \
+                               --install-deps-from=flathub --state-dir=flatpak-state \
+                               --user --ccache --default-branch=${{ github.ref_name }} \
+                               flatpak-build 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 }}
+        flatpak install -y -v --user LAMMPS-Linux-x86_64-GUI.flatpak

.github/workflows/unittest-arm64.yml

@@ -0,0 +1,81 @@
+# GitHub action to build LAMMPS on Linux with ARM64 and run standard unit tests
+name: "Unittest for Linux on ARM64"
+
+on:
+  push:
+    branches: [develop]
+
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{github.event_name == 'pull_request'}}
+
+jobs:
+  build:
+    name: Linux ARM64 Unit Test
+    if: ${{ github.repository == 'lammps/lammps' }}
+    runs-on: ubuntu-22.04-arm
+    env:
+      CCACHE_DIR: ${{ github.workspace }}/.ccache
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 2
+
+    - name: Install extra packages
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y ccache \
+                                libeigen3-dev \
+                                libcurl4-openssl-dev \
+                                mold \
+                                ninja-build \
+                                python3-dev
+
+    - name: Create Build Environment
+      run: mkdir build
+
+    - name: Set up ccache
+      uses: actions/cache@v4
+      with:
+        path: ${{ env.CCACHE_DIR }}
+        key: linux-unit-ccache-${{ github.sha }}
+        restore-keys: linux-unit-ccache-
+
+    - name: Building LAMMPS via CMake
+      shell: bash
+      run: |
+        ccache -z
+        python3 -m venv linuxenv
+        source linuxenv/bin/activate
+        python3 -m pip install numpy
+        python3 -m pip install pyyaml
+        cmake -S cmake -B build \
+              -C cmake/presets/gcc.cmake \
+              -C cmake/presets/most.cmake \
+              -D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
+              -D CMAKE_C_COMPILER_LAUNCHER=ccache \
+              -D BUILD_SHARED_LIBS=on \
+              -D DOWNLOAD_POTENTIALS=off \
+              -D ENABLE_TESTING=on \
+              -D MLIAP_ENABLE_ACE=on \
+              -D MLIAP_ENABLE_PYTHON=off \
+              -D PKG_MANIFOLD=on \
+              -D PKG_ML-PACE=on \
+              -D PKG_ML-RANN=on \
+              -D PKG_RHEO=on \
+              -D PKG_PTM=on \
+              -D PKG_PYTHON=on \
+              -D PKG_QTB=on \
+              -D PKG_SMTBQ=on \
+              -G Ninja
+        cmake --build build
+        ccache -s
+
+    - name: Run Tests
+      working-directory: build
+      shell: bash
+      run: ctest -V -LE unstable

cmake/CMakeLists.txt

@@ -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)
@@ -95,24 +98,21 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
 #####################################################################
 include(CheckIncludeFileCXX)
 
-# set required compiler flags and compiler/CPU arch specific optimizations
+# set required compiler flags, apply checks, and compiler/CPU arch specific optimizations
 if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+  # Intel classic compilers version 19 are broken and fail to compile the embedded fmtlib
+  if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 20.0)
+    message(ERROR "Intel classic compiler version ${CMAKE_CXX_COMPILER_VERSION} is too old")
+  endif()
+
   if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
     if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
       set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /Qrestrict")
     endif()
-    if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
-      set(CMAKE_TUNE_DEFAULT "/QxCOMMON-AVX512")
-    else()
-      set(CMAKE_TUNE_DEFAULT "/QxHost")
-    endif()
+    set(CMAKE_TUNE_DEFAULT "/QxHost")
   else()
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
-    if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
-      set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
-    else()
-      set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=11074 -diag-disable=11076 -diag-disable=2196")
-    endif()
+    set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=11074 -diag-disable=11076 -diag-disable=2196")
   endif()
 endif()
 
@@ -144,16 +144,28 @@ 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 +359,17 @@ 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 [email protected] if you have any concerns "
+          "about this step.")
+  endif()
+endforeach()
+
 ######################################################
 # packages with special compiler needs or external libs
 ######################################################
@@ -579,6 +602,16 @@ 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)

cmake/Modules/Packages/INTEL.cmake

@@ -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 [email protected] 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})

cmake/Modules/Packages/KOKKOS.cmake

@@ -117,7 +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

doc/src/Build.rst

@@ -1,10 +1,14 @@
 Build LAMMPS
 ============
 
-LAMMPS is built as a library and an executable from source code using
-either traditional makefiles for use with GNU make (which may require
-manual editing), or using a build environment generated by CMake (Unix
-Makefiles, Ninja, Xcode, Visual Studio, KDevelop, CodeBlocks and more).
+LAMMPS is built as a library and an executable from source code using a
+build environment generated by CMake (Unix Makefiles, Ninja, Xcode,
+Visual Studio, KDevelop, CodeBlocks and more depending on the platform).
+Using CMake is the preferred way to build LAMMPS.  In addition, LAMMPS
+can be compiled using the legacy build system based on traditional
+makefiles for use with GNU make (which may require manual editing).
+Support for the legacy build system is slowly being phased out and may
+not be available for all optional features.
 
 As an alternative, you can download a package with pre-built executables
 or automated build trees, as described in the :doc:`Install <Install>`

doc/src/Build_cmake.rst

@@ -16,7 +16,7 @@ environments is on a :doc:`separate page <Howto_cmake>`.
 
 .. note::
 
-   LAMMPS currently requires that CMake version 3.16 or later is available.
+   LAMMPS currently requires that CMake version 3.20 or later is available.
 
 .. warning::
 
@@ -32,11 +32,11 @@ environments is on a :doc:`separate page <Howto_cmake>`.
 Advantages of using CMake
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 
-CMake is an alternative to compiling LAMMPS in the traditional way
-through :doc:`(manually customized) makefiles <Build_make>`.  Using
-CMake has multiple advantages that are specifically helpful for
-people with limited experience in compiling software or for people
-that want to modify or extend LAMMPS.
+CMake is the preferred way of compiling LAMMPS in contrast to the legacy
+build system based on GNU make and through :doc:`(manually customized)
+makefiles <Build_make>`.  Using CMake has multiple advantages that are
+specifically helpful for people with limited experience in compiling
+software or for people that want to modify or extend LAMMPS.
 
 - CMake can detect available hardware, tools, features, and libraries
   and adapt the LAMMPS default build configuration accordingly.
@@ -47,7 +47,7 @@ that want to modify or extend LAMMPS.
   knowledge of file formats or complex command-line syntax is required.
 - All enabled components are compiled in a single build operation.
 - Automated dependency tracking for all files and configuration options.
-- Support for true out-of-source compilation. Multiple configurations
+- Support for true out-of-source compilation.  Multiple configurations
   and settings with different choices of LAMMPS packages, settings, or
   compilers can be configured and built concurrently from the same
   source tree.

doc/src/Build_extras.rst

@@ -48,6 +48,7 @@ This is the list of packages that may require additional steps.
    * :ref:`LEPTON <lepton>`
    * :ref:`MACHDYN <machdyn>`
    * :ref:`MDI <mdi>`
+   * :ref:`MISC <misc>`
    * :ref:`ML-HDNNP <ml-hdnnp>`
    * :ref:`ML-IAP <mliap>`
    * :ref:`ML-PACE <ml-pace>`
@@ -2031,7 +2032,7 @@ TBB and MKL.
 .. _mdi:
 
 MDI package
------------------------------
+-----------
 
 .. tabs::
 
@@ -2058,6 +2059,37 @@ MDI package
 
 ----------
 
+.. _misc:
+
+MISC package
+------------
+
+The :doc:`fix imd <fix_imd>` style in this package can be run either
+synchronously (communication with IMD clients is done in the main
+process) or asynchronously (the fix spawns a separate thread that can
+communicate with IMD clients concurrently to the LAMMPS execution).
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      .. code-block:: bash
+
+         -D LAMMPS_ASYNC_IMD=value  # Run IMD server asynchronously
+                                    # value = no (default) or yes
+
+   .. tab:: Traditional make
+
+      To enable asynchronous mode the ``-DLAMMPS_ASYNC_IMD`` define
+      needs to be added to the ``LMP_INC`` variable in the
+      ``Makefile.machine`` you are using.  For example:
+
+      .. code-block:: make
+
+         LMP_INC = -DLAMMPS_ASYNC_IMD -DLAMMPS_MEMALIGN=64
+
+----------
+
 .. _molfile:
 
 MOLFILE package

doc/src/Build_make.rst

@@ -8,6 +8,10 @@ Building LAMMPS with traditional makefiles requires that you have a
 for customizing your LAMMPS build with a number of global compilation
 options and features.
 
+This build system is slowly being phased out and may not support all
+optional features and packages in LAMMPS.  It is recommended to switch
+to the :doc:`CMake based build system <Build_cmake>`.
+
 Requirements
 ^^^^^^^^^^^^
 

doc/src/Build_package.rst

@@ -49,6 +49,7 @@ packages:
    * :ref:`LEPTON <lepton>`
    * :ref:`MACHDYN <machdyn>`
    * :ref:`MDI <mdi>`
+   * :ref:`MISC <misc>`
    * :ref:`ML-HDNNP <ml-hdnnp>`
    * :ref:`ML-IAP <mliap>`
    * :ref:`ML-PACE <ml-pace>`