Merge branch 'develop' of github.com:lammps/lammps into kk_update_4.4.0

cjknight · Sep 23, 2024 · 80832ce · 80832ce
2 parents 7e31a4f + b95f7c2
commit 80832ce
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diff --git a/.github/workflows/check-vla.yml b/.github/workflows/check-vla.yml
@@ -27,9 +27,9 @@ jobs:
 
     - name: Install extra packages
       run: |
+        sudo apt-get update
         sudo apt-get install -y ccache \
                                 libeigen3-dev \
-                                libgsl-dev \
                                 libcurl4-openssl-dev \
                                 mold \
                                 mpi-default-bin \

diff --git a/.github/workflows/compile-msvc.yml b/.github/workflows/compile-msvc.yml
@@ -11,6 +11,10 @@ on:
 
   workflow_dispatch:
 
+concurrency:
+  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{github.event_name == 'pull_request'}}
+
 jobs:
   build:
     name: Windows Compilation Test

diff --git a/.github/workflows/full-regression.yml b/.github/workflows/full-regression.yml
@@ -30,8 +30,9 @@ jobs:
 
     - name: Install extra packages
       run: |
+        sudo apt-get update
         sudo apt-get install -y ccache ninja-build libeigen3-dev \
-                     libgsl-dev libcurl4-openssl-dev python3-dev \
+                     libcurl4-openssl-dev python3-dev \
                      mpi-default-bin mpi-default-dev
 
     - name: Create Build Environment

diff --git a/.github/workflows/quick-regression.yml b/.github/workflows/quick-regression.yml
@@ -8,6 +8,10 @@ on:
 
   workflow_dispatch:
 
+concurrency:
+  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{github.event_name == 'pull_request'}}
+
 jobs:
   build:
     name: Build LAMMPS
@@ -30,8 +34,9 @@ jobs:
 
     - name: Install extra packages
       run: |
+        sudo apt-get update
         sudo apt-get install -y ccache ninja-build libeigen3-dev \
-                     libgsl-dev libcurl4-openssl-dev python3-dev \
+                     libcurl4-openssl-dev python3-dev \
                      mpi-default-bin mpi-default-dev
 
     - name: Create Build Environment

diff --git a/.github/workflows/style-check.yml b/.github/workflows/style-check.yml
@@ -0,0 +1,37 @@
+# GitHub action to run checks from tools/coding_standard
+name: "Check for Programming Style Conformance"
+
+on:
+  push:
+    branches:
+      - develop
+  pull_request:
+    branches:
+      - develop
+
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{github.event_name == 'pull_request'}}
+
+jobs:
+  build:
+    name: Programming Style Conformance
+    if: ${{ github.repository == 'lammps/lammps' }}
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 1
+
+    - name: Run Tests
+      working-directory: src
+      shell: bash
+      run: |
+         make check-whitespace
+         make check-permissions
+         make check-homepage
+         make check-errordocs
diff --git a/.github/workflows/unittest-linux.yml b/.github/workflows/unittest-linux.yml
@@ -11,6 +11,10 @@ on:
 
   workflow_dispatch:
 
+concurrency:
+  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{github.event_name == 'pull_request'}}
+
 jobs:
   build:
     name: Linux Unit Test
@@ -27,9 +31,9 @@ jobs:
 
     - name: Install extra packages
       run: |
+        sudo apt-get update
         sudo apt-get install -y ccache \
                                 libeigen3-dev \
-                                libgsl-dev \
                                 libcurl4-openssl-dev \
                                 mold \
                                 ninja-build \

diff --git a/.github/workflows/unittest-macos.yml b/.github/workflows/unittest-macos.yml
@@ -11,6 +11,10 @@ on:
 
   workflow_dispatch:
 
+concurrency:
+  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{github.event_name == 'pull_request'}}
+
 jobs:
   build:
     name: MacOS Unit Test

diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
@@ -497,7 +497,7 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_STANDARD GREATER_EQUA
           PROPERTIES COMPILE_OPTIONS "-std=c++14")
 endif()
 
-if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE 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)
   enable_language(C)
   if (NOT USE_INTERNAL_LINALG)
     find_package(LAPACK)
@@ -572,7 +572,7 @@ else()
 endif()
 
 foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
-        PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON RHEO EXTRA-COMMAND)
+        PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON EXTRA-COMMAND)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()

diff --git a/cmake/Modules/Documentation.cmake b/cmake/Modules/Documentation.cmake
@@ -4,6 +4,8 @@
 option(BUILD_DOC "Build LAMMPS HTML documentation" OFF)
 
 if(BUILD_DOC)
+  option(BUILD_DOC_VENV "Build LAMMPS documentation virtual environment" ON)
+  mark_as_advanced(BUILD_DOC_VENV)
   # Current Sphinx versions require at least Python 3.8
   # use default (or custom) Python executable, if version is sufficient
   if(Python_VERSION VERSION_GREATER_EQUAL 3.8)
@@ -18,14 +20,6 @@ if(BUILD_DOC)
   find_package(Doxygen 1.8.10 REQUIRED)
   file(GLOB DOC_SOURCES CONFIGURE_DEPENDS ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
 
-  add_custom_command(
-    OUTPUT docenv
-    COMMAND ${VIRTUALENV} docenv
-  )
-
-  set(DOCENV_BINARY_DIR ${CMAKE_BINARY_DIR}/docenv/bin)
-  set(DOCENV_REQUIREMENTS_FILE ${LAMMPS_DOC_DIR}/utils/requirements.txt)
-
   set(SPHINX_CONFIG_DIR ${LAMMPS_DOC_DIR}/utils/sphinx-config)
   set(SPHINX_CONFIG_FILE_TEMPLATE ${SPHINX_CONFIG_DIR}/conf.py.in)
   set(SPHINX_STATIC_DIR  ${SPHINX_CONFIG_DIR}/_static)
@@ -44,14 +38,32 @@ if(BUILD_DOC)
   # configure paths in conf.py, since relative paths change when file is copied
   configure_file(${SPHINX_CONFIG_FILE_TEMPLATE} ${DOC_BUILD_CONFIG_FILE})
 
-  add_custom_command(
-    OUTPUT ${DOC_BUILD_DIR}/requirements.txt
-    DEPENDS docenv ${DOCENV_REQUIREMENTS_FILE}
-    COMMAND ${CMAKE_COMMAND} -E copy ${DOCENV_REQUIREMENTS_FILE} ${DOC_BUILD_DIR}/requirements.txt
-    COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade pip
-    COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
-    COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
-  )
+  if(BUILD_DOC_VENV)
+    add_custom_command(
+      OUTPUT docenv
+      COMMAND ${VIRTUALENV} docenv
+    )
+
+    set(DOCENV_BINARY_DIR ${CMAKE_BINARY_DIR}/docenv/bin)
+    set(DOCENV_REQUIREMENTS_FILE ${LAMMPS_DOC_DIR}/utils/requirements.txt)
+
+    add_custom_command(
+      OUTPUT ${DOC_BUILD_DIR}/requirements.txt
+      DEPENDS docenv ${DOCENV_REQUIREMENTS_FILE}
+      COMMAND ${CMAKE_COMMAND} -E copy ${DOCENV_REQUIREMENTS_FILE} ${DOC_BUILD_DIR}/requirements.txt
+      COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade pip
+      COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
+      COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
+    )
+
+    set(DOCENV_DEPS docenv ${DOC_BUILD_DIR}/requirements.txt)
+    if(NOT TARGET Sphinx::sphinx-build)
+      add_executable(Sphinx::sphinx-build IMPORTED GLOBAL)
+      set_target_properties(Sphinx::sphinx-build PROPERTIES IMPORTED_LOCATION "${DOCENV_BINARY_DIR}/sphinx-build")
+    endif()
+  else()
+    find_package(Sphinx)
+  endif()
 
   set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.3.tar.gz" CACHE STRING "URL for MathJax tarball")
   set(MATHJAX_MD5 "b81661c6e6ba06278e6ae37b30b0c492" CACHE STRING "MD5 checksum of MathJax tarball")
@@ -97,8 +109,8 @@ if(BUILD_DOC)
   endif()
   add_custom_command(
     OUTPUT html
-    DEPENDS ${DOC_SOURCES} docenv ${DOC_BUILD_DIR}/requirements.txt ${DOXYGEN_XML_DIR}/index.xml ${BUILD_DOC_CONFIG_FILE}
-    COMMAND ${DOCENV_BINARY_DIR}/sphinx-build ${SPHINX_EXTRA_OPTS} -b html -c ${DOC_BUILD_DIR} -d ${DOC_BUILD_DIR}/doctrees ${LAMMPS_DOC_DIR}/src ${DOC_BUILD_DIR}/html
+    DEPENDS ${DOC_SOURCES} ${DOCENV_DEPS} ${DOXYGEN_XML_DIR}/index.xml ${BUILD_DOC_CONFIG_FILE}
+    COMMAND Sphinx::sphinx-build ${SPHINX_EXTRA_OPTS} -b html -c ${DOC_BUILD_DIR} -d ${DOC_BUILD_DIR}/doctrees ${LAMMPS_DOC_DIR}/src ${DOC_BUILD_DIR}/html
     COMMAND ${CMAKE_COMMAND} -E create_symlink Manual.html ${DOC_BUILD_DIR}/html/index.html
     COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src/PDF ${DOC_BUILD_DIR}/html/PDF
     COMMAND ${CMAKE_COMMAND} -E remove -f ${DOXYGEN_XML_DIR}/run.stamp

diff --git a/cmake/Modules/FindSphinx.cmake b/cmake/Modules/FindSphinx.cmake
@@ -0,0 +1,29 @@
+# Find sphinx-build
+find_program(Sphinx_EXECUTABLE NAMES sphinx-build
+	                       PATH_SUFFIXES bin
+			       DOC "Sphinx documenation build executable")
+mark_as_advanced(Sphinx_EXECUTABLE)
+
+if(Sphinx_EXECUTABLE)
+  execute_process(COMMAND ${Sphinx_EXECUTABLE} --version
+                  OUTPUT_VARIABLE sphinx_version
+                  OUTPUT_STRIP_TRAILING_WHITESPACE
+                  RESULT_VARIABLE _sphinx_version_result)
+
+  if(_sphinx_version_result)
+    message(WARNING "Unable to determine sphinx-build verison: ${_sphinx_version_result}")
+  else()
+    string(REGEX REPLACE "sphinx-build ([0-9.]+).*"
+                         "\\1"
+                         Sphinx_VERSION
+                         "${sphinx_version}")
+  endif()
+
+  if(NOT TARGET Sphinx::sphinx-build)
+    add_executable(Sphinx::sphinx-build IMPORTED GLOBAL)
+    set_target_properties(Sphinx::sphinx-build PROPERTIES IMPORTED_LOCATION "${Sphinx_EXECUTABLE}")
+  endif()
+endif()
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(Sphinx REQUIRED_VARS Sphinx_EXECUTABLE VERSION_VAR Sphinx_VERSION)
diff --git a/cmake/Modules/Packages/RHEO.cmake b/cmake/Modules/Packages/RHEO.cmake
diff --git a/cmake/presets/mingw-cross.cmake b/cmake/presets/mingw-cross.cmake
@@ -67,6 +67,7 @@ set(WIN_PACKAGES
   REACTION
   REAXFF
   REPLICA
+  RHEO
   RIGID
   SHOCK
   SMTBQ

diff --git a/cmake/presets/most.cmake b/cmake/presets/most.cmake
@@ -60,6 +60,7 @@ set(ALL_PACKAGES
   REACTION
   REAXFF
   REPLICA
+  RHEO
   RIGID
   SHOCK
   SPH

diff --git a/cmake/presets/windows.cmake b/cmake/presets/windows.cmake
@@ -60,6 +60,7 @@ set(WIN_PACKAGES
   REACTION
   REAXFF
   REPLICA
+  RHEO
   RIGID
   SHOCK
   SMTBQ

diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst
@@ -2251,28 +2251,38 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
 RHEO package
 ------------
 
-To build with this package you must have the `GNU Scientific Library
-(GSL) <https://www.gnu.org/software/gsl/>` installed in locations that
-are accessible in your environment.  The GSL library should be at least
-version 2.7.
+This package depends on the BPM package.
 
 .. tabs::
 
    .. tab:: CMake build
 
-      If CMake cannot find the GSL library or include files, you can set:
-
       .. code-block:: bash
 
-         -D GSL_ROOT_DIR=path    # path to root of GSL installation
+         -D PKG_RHEO=yes               # enable the package itself
+         -D PKG_BPM=yes                # the RHEO package requires BPM
+         -D USE_INTERNAL_LINALG=value  # prefer internal LAPACK if true
+
+      Some features in the RHEO package are dependent on code in the BPM
+      package so the latter one *must* be enabled as well.
+
+      The RHEO package also requires LAPACK (and BLAS) and CMake
+      can identify their locations and pass that info to the RHEO
+      build script.  But on some systems this may cause problems when
+      linking or the dependency is not desired.  By using the setting
+      ``-D USE_INTERNAL_LINALG=yes`` when running the CMake
+      configuration, you will select compiling and linking the bundled
+      linear algebra library and work around the limitations.
 
    .. tab:: Traditional make
 
-      LAMMPS will try to auto-detect the GSL compiler and linker flags
-      from the corresponding ``pkg-config`` file (``gsl.pc``), otherwise
-      you can edit the file ``lib/rheo/Makefile.lammps``
-      to specify the paths and library names where indicated by comments.
-      This must be done **before** the package is installed.
+      The RHEO package requires LAPACK (and BLAS) which can be either
+      a system provided library or the bundled "linalg" library. This
+      is a subset of LAPACK translated to C++.  For that, one of the
+      provided ``Makefile.lammps.<config>`` files needs to be copied
+      to ``Makefile.lammps`` and edited as needed.  The default file
+      uses the bundled "linalg" library, which can be built by
+      ``make lib-linalg args='-m serial'`` in the ``src`` folder.
 
 ----------
 

diff --git a/doc/src/Build_settings.rst b/doc/src/Build_settings.rst
@@ -229,8 +229,7 @@ can be used with the Intel or GNU compiler (see the ``FFT_LIB`` setting
 above).
 
 The NVIDIA Performance Libraries (NVPL) FFT library is optimized for NVIDIA
-Grace Armv9.0 architecture. You can download it from
-`https://docs.nvidia.com/nvpl/`_.
+Grace Armv9.0 architecture. You can download it from https://docs.nvidia.com/nvpl/
 
 The cuFFT and hipFFT FFT libraries are packaged with NVIDIA's CUDA and
 AMD's HIP installations, respectively. These FFT libraries require the

diff --git a/doc/src/Intro_authors.rst b/doc/src/Intro_authors.rst
@@ -56,7 +56,7 @@ lammps.org".  General questions about LAMMPS should be posted in the
      - SNL
      - jmgoff at sandia.gov
      - machine learned potentials, QEq solvers, Python
-   * - Megan McCarthy
+   * - Meg McCarthy
      - SNL
      - megmcca at sandia.gov
      - alloys, micro-structure, machine learned potentials
@@ -67,7 +67,7 @@ lammps.org".  General questions about LAMMPS should be posted in the
    * - `Trung Nguyen <tn_>`_
      - U Chicago
      - ndactrung at gmail.com
-     - soft matter, GPU package
+     - soft matter, GPU package, DIELECTRIC package, regression testing
 
 .. _rb:  https://rbberger.github.io/
 .. _gc:  https://enthalpiste.fr/
-Original file line number
+Diff line change
@@ Expand Up / @@ -67,6 +67,7 @@ set(WIN_PACKAGES @@
       REACTION
       REAXFF
       REPLICA
+      RHEO
       RIGID
       SHOCK
       SMTBQ
@@ Expand Down @@