diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml index c33628ac04..58b001be24 100644 --- a/.github/workflows/codeql-analysis.yml +++ b/.github/workflows/codeql-analysis.yml @@ -25,7 +25,7 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 2 diff --git a/.github/workflows/compile-msvc.yml b/.github/workflows/compile-msvc.yml index 5ae0654ee0..5c6ceeefb4 100644 --- a/.github/workflows/compile-msvc.yml +++ b/.github/workflows/compile-msvc.yml @@ -19,7 +19,7 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 2 diff --git a/.github/workflows/coverity.yml b/.github/workflows/coverity.yml index 7bda3a071f..b1c23e1f6a 100644 --- a/.github/workflows/coverity.yml +++ b/.github/workflows/coverity.yml @@ -16,7 +16,7 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 2 diff --git a/.github/workflows/unittest-macos.yml b/.github/workflows/unittest-macos.yml index ea979ca94f..6970faceaa 100644 --- a/.github/workflows/unittest-macos.yml +++ b/.github/workflows/unittest-macos.yml @@ -21,7 +21,7 @@ jobs: steps: - name: Checkout repository - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 2 diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index ec28fdb06b..b075fc8f8d 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -145,6 +145,7 @@ if(MSVC) add_compile_options(/Zc:__cplusplus) add_compile_options(/wd4244) add_compile_options(/wd4267) + add_compile_options(/wd4250) add_compile_options(/EHsc) endif() add_compile_definitions(_CRT_SECURE_NO_WARNINGS) @@ -268,7 +269,6 @@ set(STANDARD_PACKAGES MOFFF MOLECULE MOLFILE - MPIIO NETCDF ORIENT PERI @@ -377,7 +377,6 @@ endif() # "hard" dependencies between packages resulting # in an error instead of skipping over files pkg_depends(ML-IAP ML-SNAP) -pkg_depends(MPIIO MPI) pkg_depends(ATC MANYBODY) pkg_depends(LATBOLTZ MPI) pkg_depends(SCAFACOS MPI) @@ -388,6 +387,7 @@ pkg_depends(CG-DNA MOLECULE) pkg_depends(CG-DNA ASPHERE) pkg_depends(ELECTRODE KSPACE) pkg_depends(EXTRA-MOLECULE MOLECULE) +pkg_depends(MESONT MOLECULE) # detect if we may enable OpenMP support by default set(BUILD_OMP_DEFAULT OFF) @@ -579,13 +579,6 @@ foreach(PKG ${STANDARD_PACKAGES}) RegisterPackages(${${PKG}_SOURCES_DIR}) endforeach() -# packages that need defines set -foreach(PKG MPIIO) - if(PKG_${PKG}) - target_compile_definitions(lammps PRIVATE -DLMP_${PKG}) - endif() -endforeach() - # dedicated check for entire contents of accelerator packages foreach(PKG ${SUFFIX_PACKAGES}) set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG}) diff --git a/cmake/Modules/FindClangFormat.cmake b/cmake/Modules/FindClangFormat.cmake index 80c3b0d0ae..3f0257f34f 100644 --- a/cmake/Modules/FindClangFormat.cmake +++ b/cmake/Modules/FindClangFormat.cmake @@ -1,5 +1,7 @@ # Find clang-format find_program(ClangFormat_EXECUTABLE NAMES clang-format + clang-format-17.0 + clang-format-16.0 clang-format-15.0 clang-format-14.0 clang-format-13.0 @@ -19,7 +21,7 @@ if(ClangFormat_EXECUTABLE) OUTPUT_VARIABLE clang_format_version ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE) - if(clang_format_version MATCHES "^(Ubuntu |)clang-format version .*") + if(clang_format_version MATCHES "^(Ubuntu |Debian |)clang-format version .*") # Arch Linux output: # clang-format version 10.0.0 # @@ -32,9 +34,15 @@ if(ClangFormat_EXECUTABLE) # Ubuntu 22.04 LTS output: # Ubuntu clang-format version 14.0.0-1ubuntu1 # + # Debian 11 output: + # Debian clang-format version 11.0.1-2 + # + # Debian 12 output: + # Debian clang-format version 14.0.6 + # # Fedora 36 output: # clang-format version 14.0.5 (Fedora 14.0.5-1.fc36) - string(REGEX REPLACE "^(Ubuntu |)clang-format version ([0-9.]+).*" + string(REGEX REPLACE "^(Ubuntu |Debian |)clang-format version ([0-9.]+).*" "\\2" ClangFormat_VERSION "${clang_format_version}") diff --git a/cmake/Modules/LAMMPSInterfacePlugin.cmake b/cmake/Modules/LAMMPSInterfacePlugin.cmake index 7d4c06184e..151e0a04f7 100644 --- a/cmake/Modules/LAMMPSInterfacePlugin.cmake +++ b/cmake/Modules/LAMMPSInterfacePlugin.cmake @@ -28,6 +28,7 @@ if(MSVC) add_compile_options(/Zc:__cplusplus) add_compile_options(/wd4244) add_compile_options(/wd4267) + add_compile_options(/wd4250) add_compile_options(/EHsc) endif() add_compile_definitions(_CRT_SECURE_NO_WARNINGS) diff --git a/cmake/Modules/Packages/ML-PACE.cmake b/cmake/Modules/Packages/ML-PACE.cmake index 6cdb751617..ce8f02f5f4 100644 --- a/cmake/Modules/Packages/ML-PACE.cmake +++ b/cmake/Modules/Packages/ML-PACE.cmake @@ -1,6 +1,6 @@ -set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.01.3.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources") +set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.10.04.tar.gz" CACHE STRING "URL for PACE evaluator library sources") -set(PACELIB_MD5 "4f0b3b5b14456fe9a73b447de3765caa" CACHE STRING "MD5 checksum of PACE evaluator library tarball") +set(PACELIB_MD5 "70ff79f4e59af175e55d24f3243ad1ff" CACHE STRING "MD5 checksum of PACE evaluator library tarball") mark_as_advanced(PACELIB_URL) mark_as_advanced(PACELIB_MD5) GetFallbackURL(PACELIB_URL PACELIB_FALLBACK) diff --git a/cmake/packaging/LAMMPS_DMG_Background.png b/cmake/packaging/LAMMPS_DMG_Background.png index 5ceb55c5e7..978b7d1987 100644 Binary files a/cmake/packaging/LAMMPS_DMG_Background.png and b/cmake/packaging/LAMMPS_DMG_Background.png differ diff --git a/cmake/packaging/MacOSXBundleInfo.plist.in b/cmake/packaging/MacOSXBundleInfo.plist.in index 33ce5a602b..bc08591e97 100644 --- a/cmake/packaging/MacOSXBundleInfo.plist.in +++ b/cmake/packaging/MacOSXBundleInfo.plist.in @@ -17,7 +17,7 @@ CFBundleLongVersionString ${MACOSX_BUNDLE_LONG_VERSION_STRING} CFBundleName - LAMMPS + LAMMPS_GUI CFBundlePackageType APPL CFBundleShortVersionString diff --git a/cmake/packaging/README.macos b/cmake/packaging/README.macos index 0325045983..d7583e7034 100644 --- a/cmake/packaging/README.macos +++ b/cmake/packaging/README.macos @@ -9,7 +9,7 @@ of the available packages. The following individual commands are included: binary2txt lammps-gui lmp msi2lmp phana stl_bin2txt -After copying the lammps-gui folder into your Applications folder, please follow +After copying the LAMMPS_GUI folder into your Applications folder, please follow these steps: 1. Open the Terminal app @@ -23,7 +23,7 @@ these steps: 3. Add the following lines to the end of the file, save it, and close the editor - LAMMPS_INSTALL_DIR=/Applications/LAMMPS.app/Contents + LAMMPS_INSTALL_DIR=/Applications/LAMMPS_GUI.app/Contents LAMMPS_POTENTIALS=${LAMMPS_INSTALL_DIR}/share/lammps/potentials LAMMPS_BENCH_DIR=${LAMMPS_INSTALL_DIR}/share/lammps/bench MSI2LMP_LIBRARY=${LAMMPS_INSTALL_DIR}/share/lammps/frc_files @@ -38,9 +38,9 @@ these steps: the changes from .zprofile automatically. Note: the above assumes you use the default shell (zsh) that comes with - MacOS. If you customized MacOS to use a different shell, you'll need to modify - that shell's init file (.cshrc, .bashrc, etc.) instead with appropiate commands - to modify the same environment variables. + MacOS. If you customized MacOS to use a different shell, you'll need to + modify that shell's init file (.cshrc, .bashrc, etc.) instead with + appropiate commands to modify the same environment variables. 5. Try running LAMMPS (which might fail, see step 7) @@ -50,10 +50,10 @@ these steps: lammps-gui ${LAMMPS_BENCH_DIR}/in.rhodo - Depending on the size and resolution of your screen, the fonts may - be too small to read. This can be adjusted by setting the environment - variable QT_FONT_DPI. The default value would be 72, so to increase - the fonts by a third one can add to the .zprofile file the line + Depending on the size and resolution of your screen, the fonts may be too + small to read. This can be adjusted by setting the environment variable + QT_FONT_DPI. The default value would be 72, so to increase the fonts by a + third, one can add to the .zprofile file the line export QT_FONT_DPI=96 @@ -61,9 +61,9 @@ these steps: 7. Give permission to execute the commands (lmp, lammps-gui, msi2lmp, binary2txt, phana, stl_bin2txt) - MacOS will likely block the initial run of the executables, since they - were downloaded from the internet and are missing a known signature from an - identified developer. Go to "Settings" and search for "Security settings". It - should display a message that an executable like "lmp" was blocked. Press + MacOS will likely block the initial run of the executables, since they were + downloaded from the internet and are missing a known signature from an + identified developer. Go to "Settings" and search for "Security settings". + It should display a message that an executable like "lmp" was blocked. Press "Open anyway", which might prompt you for your admin credentials. Afterwards "lmp" and the other executables should work as expected. diff --git a/cmake/packaging/build_linux_tgz.sh b/cmake/packaging/build_linux_tgz.sh index e0222858ce..48e3017f61 100755 --- a/cmake/packaging/build_linux_tgz.sh +++ b/cmake/packaging/build_linux_tgz.sh @@ -4,7 +4,7 @@ APP_NAME=lammps-gui DESTDIR=${PWD}/../LAMMPS_GUI echo "Delete old files, if they exist" -rm -rf ${DESTDIR} ../LAMMPS-Linux-amd64.tar.gz +rm -rf ${DESTDIR} ../LAMMPS_GUI-Linux-amd64.tar.gz echo "Create staging area for deployment and populate" DESTDIR=${DESTDIR} cmake --install . --prefix "/" @@ -69,7 +69,7 @@ do \ done pushd .. -tar -czvvf LAMMPS-Linux-amd64.tar.gz LAMMPS_GUI +tar -czvvf LAMMPS_GUI-Linux-amd64.tar.gz LAMMPS_GUI popd echo "Cleanup dir" diff --git a/cmake/packaging/build_macos_dmg.sh b/cmake/packaging/build_macos_dmg.sh index 5204e519c2..4da3e40eaf 100755 --- a/cmake/packaging/build_macos_dmg.sh +++ b/cmake/packaging/build_macos_dmg.sh @@ -3,7 +3,7 @@ APP_NAME=lammps-gui echo "Delete old files, if they exist" -rm -f ${APP_NAME}.dmg ${APP_NAME}-rw.dmg LAMMPS-macOS-multiarch.dmg +rm -f ${APP_NAME}.dmg ${APP_NAME}-rw.dmg LAMMPS_GUI-macOS-multiarch.dmg echo "Create initial dmg file with macdeployqt" macdeployqt lammps-gui.app -dmg @@ -22,8 +22,8 @@ ln -s /Applications . mv ${APP_NAME}.app/Contents/Resources/README.txt . mkdir .background mv ${APP_NAME}.app/Contents/Resources/LAMMPS_DMG_Background.png .background/background.png -mv ${APP_NAME}.app LAMMPS.app -cd LAMMPS.app/Contents +mv ${APP_NAME}.app LAMMPS_GUI.app +cd LAMMPS_GUI.app/Contents echo "Attach icons to LAMMPS console and GUI executables" echo "read 'icns' (-16455) \"Resources/lammps.icns\";" > icon.rsrc @@ -75,7 +75,7 @@ echo ' set statusbar visible to false set toolbar visible to false set the bounds to { 100, 40, 868, 640 } - set position of item "'LAMMPS'.app" to { 190, 216 } + set position of item "'LAMMPS_GUI'.app" to { 190, 216 } set position of item "Applications" to { 576, 216 } set position of item "README.txt" to { 190, 400 } end tell @@ -96,12 +96,12 @@ sync echo "Unmount modified disk image and convert to compressed read-only image" hdiutil detach "${DEVICE}" -hdiutil convert "${APP_NAME}-rw.dmg" -format UDZO -o "LAMMPS-macOS-multiarch.dmg" +hdiutil convert "${APP_NAME}-rw.dmg" -format UDZO -o "LAMMPS_GUI-macOS-multiarch.dmg" echo "Attach icon to .dmg file" echo "read 'icns' (-16455) \"lammps-gui.app/Contents/Resources/lammps.icns\";" > icon.rsrc -Rez -a icon.rsrc -o LAMMPS-macOS-multiarch.dmg -SetFile -a C LAMMPS-macOS-multiarch.dmg +Rez -a icon.rsrc -o LAMMPS_GUI-macOS-multiarch.dmg +SetFile -a C LAMMPS_GUI-macOS-multiarch.dmg rm icon.rsrc echo "Delete temporary disk images" diff --git a/cmake/packaging/build_windows_vs.cmake b/cmake/packaging/build_windows_vs.cmake index f051ff351f..283425ff65 100644 --- a/cmake/packaging/build_windows_vs.cmake +++ b/cmake/packaging/build_windows_vs.cmake @@ -1,7 +1,7 @@ # CMake script to be run post installation to build zipped package # clean up old zipfile and deployment tree -file(REMOVE LAMMPS-Win10-amd64.zip) +file(REMOVE LAMMPS_GUI-Win10-amd64.zip) file(REMOVE_RECURSE LAMMPS_GUI) file(RENAME ${INSTNAME} LAMMPS_GUI) @@ -21,8 +21,15 @@ file(WRITE qtdeploy.bat "@ECHO OFF\r\nset VSCMD_DEBUG=0\r\nCALL ${VC_INIT} x64\r execute_process(COMMAND cmd.exe /c qtdeploy.bat COMMAND_ECHO STDERR) file(REMOVE qtdeploy.bat) +# download and uncompress static FFMpeg and gzip binaries +file(DOWNLOAD "https://download.lammps.org/thirdparty/ffmpeg-gzip.zip" ffmpeg-gzip.zip) +file(WRITE unpackzip.ps1 "Expand-Archive -Path ffmpeg-gzip.zip -DestinationPath LAMMPS_GUI") +execute_process(COMMAND powershell -ExecutionPolicy Bypass -File unpackzip.ps1) +file(REMOVE unpackzip.ps1) +file(REMOVE ffmpeg-gzip.zip) + # create zip archive -file(WRITE makearchive.ps1 "Compress-Archive -Path LAMMPS_GUI -CompressionLevel Optimal -DestinationPath LAMMPS-Win10-amd64.zip") +file(WRITE makearchive.ps1 "Compress-Archive -Path LAMMPS_GUI -CompressionLevel Optimal -DestinationPath LAMMPS_GUI-Win10-amd64.zip") execute_process(COMMAND powershell -ExecutionPolicy Bypass -File makearchive.ps1) file(REMOVE makearchive.ps1) file(REMOVE_RECURSE LAMMPS_GUI) diff --git a/cmake/packaging/linux_wrapper.sh b/cmake/packaging/linux_wrapper.sh index b3aee1cb4f..a679030188 100755 --- a/cmake/packaging/linux_wrapper.sh +++ b/cmake/packaging/linux_wrapper.sh @@ -1,6 +1,9 @@ #!/bin/sh # wrapper for bundled executables +# reset locale to avoid problems with decimal numbers +export LC_ALL=C + BASEDIR=$(dirname "$0") EXENAME=$(basename "$0") diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index a920460b7b..e078879f70 100644 --- a/cmake/presets/all_off.cmake +++ b/cmake/presets/all_off.cmake @@ -63,7 +63,6 @@ set(ALL_PACKAGES MOFFF MOLECULE MOLFILE - MPIIO NETCDF OPENMP OPT diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index 99563bc82e..3f44a863f7 100644 --- a/cmake/presets/all_on.cmake +++ b/cmake/presets/all_on.cmake @@ -65,7 +65,6 @@ set(ALL_PACKAGES MOFFF MOLECULE MOLFILE - MPIIO NETCDF OPENMP OPT diff --git a/cmake/presets/macos-multiarch.cmake b/cmake/presets/macos-multiarch.cmake index 58ef013f68..8ceaec11f8 100644 --- a/cmake/presets/macos-multiarch.cmake +++ b/cmake/presets/macos-multiarch.cmake @@ -10,5 +10,3 @@ set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE) set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE) set(BUILD_MPI FALSE CACHE BOOL "" FORCE) -set(BUILD_SHARED_LIBS FALSE CACHE BOOL "" FORCE) -set(LAMMPS_EXCEPTIONS TRUE CACHE BOOL "" FORCE) diff --git a/cmake/presets/mingw-cross.cmake b/cmake/presets/mingw-cross.cmake index 85f61be95b..f3565668b2 100644 --- a/cmake/presets/mingw-cross.cmake +++ b/cmake/presets/mingw-cross.cmake @@ -83,7 +83,6 @@ endforeach() # these two packages require a full MPI implementation if(BUILD_MPI) - set(PKG_MPIIO ON CACHE BOOL "" FORCE) set(PKG_LATBOLTZ ON CACHE BOOL "" FORCE) endif() diff --git a/cmake/presets/nolib.cmake b/cmake/presets/nolib.cmake index 5899f4bcb2..4a4a557505 100644 --- a/cmake/presets/nolib.cmake +++ b/cmake/presets/nolib.cmake @@ -19,7 +19,6 @@ set(PACKAGES_WITH_LIB ML-PACE ML-QUIP MOLFILE - MPIIO NETCDF PLUMED PYTHON diff --git a/doc/src/Build_basics.rst b/doc/src/Build_basics.rst index 0a0d4919a0..233b825d01 100644 --- a/doc/src/Build_basics.rst +++ b/doc/src/Build_basics.rst @@ -90,7 +90,7 @@ standard. A more detailed discussion of that is below. directory, or ``make`` from the ``src/STUBS`` dir. If the build fails, you may need to edit the ``STUBS/Makefile`` for your platform. The stubs library does not provide MPI/IO functions - required by some LAMMPS packages, e.g. ``MPIIO`` or ``LATBOLTZ``, + required by some LAMMPS packages, e.g. ``LATBOLTZ``, and thus is not compatible with those packages. .. note:: @@ -128,14 +128,13 @@ and adds vectorization support when compiled with compatible compilers, in particular the Intel compilers on top of OpenMP. Also, the ``KOKKOS`` package can be compiled to include OpenMP threading. -In addition, there are a few commands in LAMMPS that have native -OpenMP support included as well. These are commands in the ``MPIIO``, -``ML-SNAP``, ``DIFFRACTION``, and ``DPD-REACT`` packages. -Furthermore, some packages support OpenMP threading indirectly through -the libraries they interface to: e.g. ``KSPACE``, and ``COLVARS``. -See the :doc:`Packages details ` page for more info -on these packages, and the pages for their respective commands for -OpenMP threading info. +In addition, there are a few commands in LAMMPS that have native OpenMP +support included as well. These are commands in the ``ML-SNAP``, +``DIFFRACTION``, and ``DPD-REACT`` packages. Furthermore, some packages +support OpenMP threading indirectly through the libraries they interface +to: e.g. ``KSPACE``, and ``COLVARS``. See the :doc:`Packages details +` page for more info on these packages, and the pages +for their respective commands for OpenMP threading info. For CMake, if you use ``BUILD_OMP=yes``, you can use these packages and turn on their native OpenMP support and turn on their native OpenMP @@ -489,8 +488,9 @@ using CMake or Make. .. code-block:: bash - -D BUILD_TOOLS=value # yes or no (default) - -D BUILD_LAMMPS_SHELL=value # yes or no (default) + -D BUILD_TOOLS=value # yes or no (default). Build binary2txt, chain.x, micelle2d.x, msi2lmp, phana, stl_bin2txt + -D BUILD_LAMMPS_SHELL=value # yes or no (default). Build lammps-shell + -D BUILD_LAMMPS_GUI=value # yes or no (default). Build lammps-gui The generated binaries will also become part of the LAMMPS installation (see below). @@ -504,7 +504,6 @@ using CMake or Make. make binary2txt # build only binary2txt tool make chain # build only chain tool make micelle2d # build only micelle2d tool - make thermo_extract # build only thermo_extract tool cd lammps/tools/lammps-shell make # build LAMMPS shell diff --git a/doc/src/Build_cmake.rst b/doc/src/Build_cmake.rst index 6c46f6d672..e622f9f208 100644 --- a/doc/src/Build_cmake.rst +++ b/doc/src/Build_cmake.rst @@ -177,13 +177,13 @@ configuration is selected with the *-C* flag: ctest -C Debug -The CMake scripts in LAMMPS have basic support for being compiled using a -multi-config build system, but not all of it has been ported. This is in -particular applicable to compiling packages that require additional libraries -that would be downloaded and compiled by CMake. The "windows" preset file -tries to keep track of which packages can be compiled natively with the -MSVC compilers out-of-the box. Not all of those external libraries are -portable to Windows, either. +The CMake scripts in LAMMPS have basic support for being compiled using +a multi-config build system, but not all of it has been ported. This is +in particular applicable to compiling packages that require additional +libraries that would be downloaded and compiled by CMake. The +``windows.cmake`` preset file tries to keep track of which packages can +be compiled natively with the MSVC compilers out-of-the box. Not all of +the external libraries are portable to Windows, either. Installing CMake diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 6e2069c0ec..393d7e1c20 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -722,9 +722,10 @@ This list was last updated for version 4.0.1 of the Kokkos library. ``cmake/presets`` folder, ``kokkos-serial.cmake``, ``kokkos-openmp.cmake``, ``kokkos-cuda.cmake``, ``kokkos-hip.cmake``, and ``kokkos-sycl.cmake``. They will enable - the KOKKOS package and enable some hardware choice. So to compile - with CUDA device parallelization (for GPUs with CC 5.0 and up) - with some common packages enabled, you can do the following: + the KOKKOS package and enable some hardware choices. For GPU + support those preset files must be customized to match the + hardware used. So to compile with CUDA device parallelization with + some common packages enabled, you can do the following: .. code-block:: bash @@ -886,6 +887,50 @@ included in the LAMMPS source distribution in the ``lib/lepton`` folder. ---------- +.. _machdyn: + +MACHDYN package +------------------------------- + +To build with this package, you must download the Eigen3 library. +Eigen3 is a template library, so you do not need to build it. + +.. tabs:: + + .. tab:: CMake build + + .. code-block:: bash + + -D DOWNLOAD_EIGEN3 # download Eigen3, value = no (default) or yes + -D EIGEN3_INCLUDE_DIR=path # path to Eigen library (only needed if a custom location) + + If ``DOWNLOAD_EIGEN3`` is set, the Eigen3 library will be + downloaded and inside the CMake build directory. If the Eigen3 + library is already on your system (in a location where CMake + cannot find it), set ``EIGEN3_INCLUDE_DIR`` to the directory the + ``Eigen3`` include file is in. + + .. tab:: Traditional make + + You can download the Eigen3 library manually if you prefer; follow + the instructions in ``lib/machdyn/README``. You can also do it in one + step from the ``lammps/src`` dir, using a command like these, + which simply invokes the ``lib/machdyn/Install.py`` script with the + specified args: + + .. code-block:: bash + + make lib-machdyn # print help message + make lib-machdyn args="-b" # download to lib/machdyn/eigen3 + make lib-machdyn args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3 + + Note that a symbolic (soft) link named ``includelink`` is created + in ``lib/machdyn`` to point to the Eigen dir. When LAMMPS builds it + will use this link. You should not need to edit the + ``lib/machdyn/Makefile.lammps`` file. + +---------- + .. _mliap: ML-IAP package @@ -1431,6 +1476,55 @@ ML-POD package ---------- +.. _ml-quip: + +ML-QUIP package +--------------------------------- + +To build with this package, you must download and build the QUIP +library. It can be obtained from GitHub. For support of GAP +potentials, additional files with specific licensing conditions need +to be downloaded and configured. The automatic download will from +within CMake will download the non-commercial use version. + +.. tabs:: + + .. tab:: CMake build + + .. code-block:: bash + + -D DOWNLOAD_QUIP=value # download QUIP library for build, value = no (default) or yes + -D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location) + -D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK + # value = no (default) or yes + + CMake will try to download and build the QUIP library from GitHub, + if it is not found on the local machine. This requires to have git + installed. It will use the same compilers and flags as used for + compiling LAMMPS. Currently this is only supported for the GNU + and the Intel compilers. Set the ``QUIP_LIBRARY`` variable if you + want to use a previously compiled and installed QUIP library and + CMake cannot find it. + + The QUIP library requires LAPACK (and BLAS) and CMake can identify + their locations and pass that info to the QUIP build script. But + on some systems this triggers a (current) limitation of CMake and + the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in + those cases to use the bundled linear algebra library and work around + the limitation. + + .. tab:: Traditional make + + The download/build procedure for the QUIP library, described in + ``lib/quip/README`` file requires setting two environment + variables, ``QUIP_ROOT`` and ``QUIP_ARCH``. These are accessed by + the ``lib/quip/Makefile.lammps`` file which is used when you + compile and link LAMMPS with this package. You should only need + to edit ``Makefile.lammps`` if the LAMMPS build can not use its + settings to successfully build on your system. + +---------- + .. _plumed: PLUMED package @@ -1952,55 +2046,6 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to ---------- -.. _ml-quip: - -ML-QUIP package ---------------------------------- - -To build with this package, you must download and build the QUIP -library. It can be obtained from GitHub. For support of GAP -potentials, additional files with specific licensing conditions need -to be downloaded and configured. The automatic download will from -within CMake will download the non-commercial use version. - -.. tabs:: - - .. tab:: CMake build - - .. code-block:: bash - - -D DOWNLOAD_QUIP=value # download QUIP library for build, value = no (default) or yes - -D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location) - -D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK - # value = no (default) or yes - - CMake will try to download and build the QUIP library from GitHub, - if it is not found on the local machine. This requires to have git - installed. It will use the same compilers and flags as used for - compiling LAMMPS. Currently this is only supported for the GNU - and the Intel compilers. Set the ``QUIP_LIBRARY`` variable if you - want to use a previously compiled and installed QUIP library and - CMake cannot find it. - - The QUIP library requires LAPACK (and BLAS) and CMake can identify - their locations and pass that info to the QUIP build script. But - on some systems this triggers a (current) limitation of CMake and - the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in - those cases to use the bundled linear algebra library and work around - the limitation. - - .. tab:: Traditional make - - The download/build procedure for the QUIP library, described in - ``lib/quip/README`` file requires setting two environment - variables, ``QUIP_ROOT`` and ``QUIP_ARCH``. These are accessed by - the ``lib/quip/Makefile.lammps`` file which is used when you - compile and link LAMMPS with this package. You should only need - to edit ``Makefile.lammps`` if the LAMMPS build can not use its - settings to successfully build on your system. - ----------- - .. _scafacos: SCAFACOS package @@ -2048,50 +2093,6 @@ To build with this package, you must download and build the ---------- -.. _machdyn: - -MACHDYN package -------------------------------- - -To build with this package, you must download the Eigen3 library. -Eigen3 is a template library, so you do not need to build it. - -.. tabs:: - - .. tab:: CMake build - - .. code-block:: bash - - -D DOWNLOAD_EIGEN3 # download Eigen3, value = no (default) or yes - -D EIGEN3_INCLUDE_DIR=path # path to Eigen library (only needed if a custom location) - - If ``DOWNLOAD_EIGEN3`` is set, the Eigen3 library will be - downloaded and inside the CMake build directory. If the Eigen3 - library is already on your system (in a location where CMake - cannot find it), set ``EIGEN3_INCLUDE_DIR`` to the directory the - ``Eigen3`` include file is in. - - .. tab:: Traditional make - - You can download the Eigen3 library manually if you prefer; follow - the instructions in ``lib/smd/README``. You can also do it in one - step from the ``lammps/src`` dir, using a command like these, - which simply invokes the ``lib/smd/Install.py`` script with the - specified args: - - .. code-block:: bash - - make lib-smd # print help message - make lib-smd args="-b" # download to lib/smd/eigen3 - make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3 - - Note that a symbolic (soft) link named ``includelink`` is created - in ``lib/smd`` to point to the Eigen dir. When LAMMPS builds it - will use this link. You should not need to edit the - ``lib/smd/Makefile.lammps`` file. - ----------- - .. _vtk: VTK package diff --git a/doc/src/Build_package.rst b/doc/src/Build_package.rst index bc6445f813..63ccac534d 100644 --- a/doc/src/Build_package.rst +++ b/doc/src/Build_package.rst @@ -182,6 +182,7 @@ make a copy of one of them and modify it to suit your needs. cmake -C ../cmake/presets/all_on.cmake [OPTIONS] ../cmake # enable all packages cmake -C ../cmake/presets/all_off.cmake [OPTIONS] ../cmake # disable all packages mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake # compile with MinGW cross-compilers + cmake -C ../cmake/presets/macos-multiarch.cmake [OPTIONS] ../cmake # compile serial multi-arch binaries on macOS Presets that have names starting with "windows" are specifically for compiling LAMMPS :doc:`natively on Windows ` and diff --git a/doc/src/Commands_compute.rst b/doc/src/Commands_compute.rst index 9066531459..dbd6b58ce7 100644 --- a/doc/src/Commands_compute.rst +++ b/doc/src/Commands_compute.rst @@ -91,6 +91,7 @@ KOKKOS, o = OPENMP, t = OPT. * :doc:`ke/atom/eff ` * :doc:`ke/eff ` * :doc:`ke/rigid ` + * :doc:`composition/atom (k) ` * :doc:`mliap ` * :doc:`momentum ` * :doc:`msd ` diff --git a/doc/src/Commands_dump.rst b/doc/src/Commands_dump.rst index 870cb168ef..d7c8e73b58 100644 --- a/doc/src/Commands_dump.rst +++ b/doc/src/Commands_dump.rst @@ -23,17 +23,14 @@ An alphabetic list of all LAMMPS :doc:`dump ` commands. * :doc:`atom ` * :doc:`atom/adios ` * :doc:`atom/gz ` - * :doc:`atom/mpiio ` * :doc:`atom/zstd ` * :doc:`cfg ` * :doc:`cfg/gz ` - * :doc:`cfg/mpiio ` * :doc:`cfg/uef ` * :doc:`cfg/zstd ` * :doc:`custom ` * :doc:`custom/adios ` * :doc:`custom/gz ` - * :doc:`custom/mpiio ` * :doc:`custom/zstd ` * :doc:`dcd ` * :doc:`grid ` @@ -51,7 +48,6 @@ An alphabetic list of all LAMMPS :doc:`dump ` commands. * :doc:`xtc ` * :doc:`xyz ` * :doc:`xyz/gz ` - * :doc:`xyz/mpiio ` * :doc:`xyz/zstd ` * :doc:`yaml ` diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst index 5aabb7967c..7301d1345e 100644 --- a/doc/src/Commands_fix.rst +++ b/doc/src/Commands_fix.rst @@ -69,7 +69,7 @@ OPT. * :doc:`drude/transform/inverse ` * :doc:`dt/reset (k) ` * :doc:`edpd/source ` - * :doc:`efield ` + * :doc:`efield (k) ` * :doc:`efield/tip4p ` * :doc:`ehex ` * :doc:`electrode/conp (i) ` @@ -181,6 +181,7 @@ OPT. * :doc:`pour ` * :doc:`precession/spin ` * :doc:`press/berendsen ` + * :doc:`press/langevin ` * :doc:`print ` * :doc:`propel/self ` * :doc:`property/atom (k) ` @@ -232,7 +233,7 @@ OPT. * :doc:`spring ` * :doc:`spring/chunk ` * :doc:`spring/rg ` - * :doc:`spring/self ` + * :doc:`spring/self (k) ` * :doc:`srd ` * :doc:`store/force ` * :doc:`store/state ` diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index c45a1d778c..923c040aaf 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -265,7 +265,7 @@ OPT. * :doc:`smd/tri_surface ` * :doc:`smd/ulsph ` * :doc:`smtbq ` - * :doc:`snap (k) ` + * :doc:`snap (ik) ` * :doc:`soft (go) ` * :doc:`sph/heatconduction ` * :doc:`sph/idealgas ` @@ -305,5 +305,5 @@ OPT. * :doc:`wf/cut ` * :doc:`ylz ` * :doc:`yukawa (gko) ` - * :doc:`yukawa/colloid (go) ` + * :doc:`yukawa/colloid (gko) ` * :doc:`zbl (gko) ` diff --git a/doc/src/Commands_removed.rst b/doc/src/Commands_removed.rst index f33d8f4988..84cc534304 100644 --- a/doc/src/Commands_removed.rst +++ b/doc/src/Commands_removed.rst @@ -85,6 +85,25 @@ The same functionality is available through :doc:`bond style mesocnt ` and :doc:`angle style mesocnt `. +MPIIO package +------------- + +.. deprecated:: TBD + +The MPIIO package has been removed from LAMMPS since it was unmaintained +for many years and thus not updated to incorporate required changes that +had been applied to the corresponding non-MPIIO commands. As a +consequence the MPIIO commands had become unreliable and sometimes +crashing LAMMPS or corrupting data. Similar functionality is available +through the :ref:`ADIOS package ` and the :ref:`NETCDF +package `. Also, the :doc:`dump_modify nfile or dump_modify +fileper ` keywords may be used for an efficient way of +writing out dump files when running on large numbers of processors. +Similarly, the "nfile" and "fileper" keywords exist for restarts: +see :doc:`restart `, :doc:`read_restart `, +:doc:`write_restart `. + + MSCG package ------------ diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index 293cf6ab53..bfdba4f6a1 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -7148,9 +7148,6 @@ keyword to allow for additional bonds to be formed *Read_dump xyz fields do not have consistent scaling/wrapping* Self-explanatory. -*Reading from MPI-IO filename when MPIIO package is not installed* - Self-explanatory. - *Reax_defs.h setting for NATDEF is too small* Edit the setting in the ReaxFF library and re-compile the library and re-build LAMMPS. @@ -8489,9 +8486,6 @@ keyword to allow for additional bonds to be formed The write_restart command cannot be used before a read_data, read_restart, or create_box command. -*Writing to MPI-IO filename when MPIIO package is not installed* - Self-explanatory. - *Zero length rotation vector with displace_atoms* Self-explanatory. diff --git a/doc/src/Howto.rst b/doc/src/Howto.rst index 4752cf6aea..b1f5da8abc 100644 --- a/doc/src/Howto.rst +++ b/doc/src/Howto.rst @@ -100,6 +100,7 @@ Tutorials howto Howto_cmake Howto_github + Howto_lammps_gui Howto_pylammps Howto_wsl diff --git a/doc/src/Howto_cmake.rst b/doc/src/Howto_cmake.rst index 8f9bcc0a38..42324cf2f1 100644 --- a/doc/src/Howto_cmake.rst +++ b/doc/src/Howto_cmake.rst @@ -1,10 +1,10 @@ -Using CMake with LAMMPS tutorial -================================ +Using CMake with LAMMPS +======================= The support for building LAMMPS with CMake is a recent addition to LAMMPS thanks to the efforts of Christoph Junghans (LANL) and Richard Berger (LANL). One of the key strengths of CMake is that it is not -tied to a specific platform or build system and thus it generates the +tied to a specific platform or build system. Instead it generates the files necessary to build and develop for different build systems and on different platforms. Note, that this applies to the build system itself not the LAMMPS code. In other words, without additional porting effort, @@ -32,7 +32,8 @@ program ``cmake`` (or ``cmake3``), a text mode interactive user interface (TUI) program ``ccmake`` (or ``ccmake3``), or a graphical user interface (GUI) program ``cmake-gui``. All of them are portable software available on all supported platforms and can be used -interchangeably. The minimum required CMake version is 3.16. +interchangeably. As of LAMMPS version 2 August 2023, the minimum +required CMake version is 3.16. All details about features and settings for CMake are in the `CMake online documentation `_. We focus diff --git a/doc/src/Howto_lammps_gui.rst b/doc/src/Howto_lammps_gui.rst new file mode 100644 index 0000000000..165ed84d95 --- /dev/null +++ b/doc/src/Howto_lammps_gui.rst @@ -0,0 +1,700 @@ +Using the LAMMPS GUI +==================== + +This document describes **LAMMPS GUI version 1.5**. + +----- + +LAMMPS GUI is a graphical text editor customized for editing LAMMPS +input files that is linked to the :ref:`LAMMPS library ` +and thus can run LAMMPS directly using the contents of the editor's text +buffer as input. It can retrieve and display information from LAMMPS +while it is running, display visualizations created with the :doc:`dump +image command `, and is adapted specifically for editing +LAMMPS input files through text completion and reformatting, and linking +to the online LAMMPS documentation for known LAMMPS commands and styles. + +.. note:: + + Pre-compiled, ready-to-use LAMMPS GUI executables for Linux (Ubuntu + 20.04LTS or later and compatible), macOS (version 11 aka Big Sur or + later), and Windows (version 10 or later) :ref:`are available + ` for download. They may be linked to a + development version of LAMMPS in case they need features not yet + available in a released version. Serial LAMMPS executables of the + same LAMMPS version are included as well. The source code for the + LAMMPS GUI is included in the LAMMPS source code and can be found in + the ``tools/lammps-gui`` folder. It can be compiled alongside LAMMPS + when :doc:`compiling with CMake `. + +LAMMPS GUI tries to provide an experience similar to what people +traditionally would do to run LAMMPS using a command line window: + +- editing inputs with a text editor +- run LAMMPS on the input with selected command line flags +- and then use or extract data from the created files and visualize it + +That procedure is quite effective for people proficient in using the +command line, as that allows them to use tools for the individual steps +which they are most comfortable with. It is often required when running +LAMMPS on high-performance computing facilities. + +The main benefit of using the LAMMPS GUI application instead is that +many basic tasks can be done directly from the GUI without switching to +a text console window or using external programs, let alone writing +scripts to extract data from the generated output. It also integrates +well with graphical desktop environments. + +LAMMPS GUI thus makes it easier for beginners to get started running +simple LAMMPS simulations. It is very suitable for tutorials on LAMMPS +since you only need to learn how to use a single program for most tasks +and thus time can be saved and people can focus on learning LAMMPS. It +is also designed to keep the barrier low when you decide to switch to a +full featured, standalone programming editor and more sophisticated +visualization and analysis tools and run LAMMPS from a command line. + +The following text provides a detailed tour of the features and +functionality of the LAMMPS GUI. + +Suggestions for new features and reports of bugs are always welcome. +You can use the :doc:`the same channels as for LAMMPS itself +` for that purpose. + +----- + +Main window +----------- + +When LAMMPS GUI starts, it will show a main window with either an +empty buffer or the contents of a loaded file. In the latter case it +may look like the following: + +.. image:: JPG/lammps-gui-main.png + :align: center + :scale: 50% + +There is the typical menu bar at the top, then the main editor buffer, +and a status bar at the bottom. The input file contents are shown +with line numbers on the left and the input is colored according to +the LAMMPS input file syntax. The status bar shows the status of +LAMMPS execution on the left (e.g. "Ready." when idle) and the current +working directory on the right. The name of the current file in the +buffer is shown in the window title; the word `*modified*` is added if +the buffer edits have not yet saved to a file. The size of the main +window will be stored when exiting and restored when starting again. + +Opening Files +^^^^^^^^^^^^^ + +The LAMMPS GUI application will try to open the first command line +argument as a LAMMPS input script, further arguments are ignored. +When no argument is given, LAMMPS GUI will start with an empty buffer. +Files can also be opened via the ``File`` menu or by drag-and-drop of +a file from a graphical file manager into the editor window. Only one +file can be open at a time, so opening a new file with a filled buffer +will close the buffer. If the buffer has unsaved modifications, you +will be asked to either cancel the operation, discard the changes, or +save them. + +Running LAMMPS +^^^^^^^^^^^^^^ + +From within the LAMMPS GUI main window LAMMPS can be started either from +the ``Run`` menu using the ``Run LAMMPS from Editor Buffer`` entry, by +the keyboard shortcut `Ctrl-Enter` (`Command-Enter` on macOS), or by +clicking on the green "Run" button in the status bar. All of these +operations will cause LAMMPS to process the entire input script, which +may contain multiple :doc:`run ` or :doc:`minimize ` +commands. + +LAMMPS runs in a separate thread, so the GUI stays responsive and is +able to interact with the running calculation and access data it +produces. It is important to note that running LAMMPS this way is +using the contents of the input buffer for the run (via the +:cpp:func:`lammps_commands_string()` function of the LAMMPS C-library +interface), and **not** the original file it was read from. Thus, if +there are unsaved changes in the buffer, they *will* be used. As an +alternative, it is also possible to run LAMMPS by reading the contents +of a file from the ``Run LAMMPS from File`` menu entry or with +`Ctrl-Shift-Enter`. This option may be required in some rare cases +where the input uses some functionality that is not compatible with +running LAMMPS from a string buffer. For consistency, any unsaved +changes in the buffer must be either saved to the file or undone +before LAMMPS can be run from a file. + +.. image:: JPG/lammps-gui-running.png + :align: center + :scale: 75% + +While LAMMPS is running, the contents of the status bar change. On +the left side there is a text indicating that LAMMPS is running, which +will also show the number of active threads, if thread-parallel +acceleration was selected in the ``Preferences`` dialog. On the right +side, a progress bar is shown that displays the estimated progress for +the current :doc:`run command `. + +Also, the line number of the currently executed command will be +highlighted in green. + +.. image:: JPG/lammps-gui-run-highlight.png + :align: center + :scale: 75% + +If an error occurs (in the example below the command :doc:`label +