[pull] develop from lammps:develop #87

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Merged

pull merged 143 commits into comphy-lab:develop from lammps:develop

Jan 29, 2026

cmake/CMakeLists.txt

-Original file line number
+Diff line change
@@ Expand Up / @@ -306,6 +306,7 @@ set(STANDARD_PACKAGES @@
       MACHDYN
       MANIFOLD
       MANYBODY
+      MBX
       MC
       MDI
       MEAM
@@ Expand Down Expand Up / @@ -561,7 +562,7 @@ else() @@
     endif()
     foreach(PKG_WITH_INCL GRAPHICS KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
-            PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON EXTRA-COMMAND)
+            PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON EXTRA-COMMAND MBX)
       if(PKG_${PKG_WITH_INCL})
         include(Packages/${PKG_WITH_INCL})
       endif()
@@ Expand Down @@

cmake/Modules/LAMMPSInterfacePlugin.cmake

-Original file line number
+Diff line change
@@ Expand Up / @@ -65,6 +65,10 @@ set(CMAKE_POSITION_INDEPENDENT_CODE TRUE) @@
     # skip over obsolete MPI-2 C++ bindings
     set(MPI_CXX_SKIP_MPICXX TRUE)
+    # compile external libraries for linking to shared objects
+    set(CONFIGURE_REQUEST_PIC "--with-pic")
+    set(CMAKE_REQUEST_PIC "-DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE}")
     #######
     # helper functions from LAMMPSUtils.cmake
     function(validate_option name values)
@@ Expand Down @@

cmake/Modules/Packages/MBX.cmake

-Original file line number
+Diff line change
@@ -0,0 +1,107 @@
+    # MBX v1.3.0+ support for MBX package
+    # Based off of PLUMED.cmake
+    # 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()
+    if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
+      message(FATAL_ERROR "Compiling the MBX package for Windows is currently not supported")
+    endif()
+    # for supporting multiple concurrent mbx installations for debugging and testing
+    set(MBX_SUFFIX "" CACHE STRING "Suffix for MBX library")
+    mark_as_advanced(MBX_SUFFIX)
+    set(MBX_CONFIG_CC  ${CMAKE_C_COMPILER})
+    set(MBX_CONFIG_CXX  ${CMAKE_CXX_COMPILER})
+    if(BUILD_MPI)
+      set(MBX_CONFIG_FLAGS "--enable-mpi")
+      set(MBX_CONFIG_CC  ${MPI_C_COMPILER})
+      set(MBX_CONFIG_CXX  ${MPI_CXX_COMPILER})
+    else()
+      set(MBX_CONFIG_FLAGS "--disable-mpi")
+    endif()
+    if(BUILD_OMP)
+      list(APPEND MBX_CONFIG_FLAGS --enable-openmp)
+    else()
+      list(APPEND MBX_CONFIG_FLAGS --disable-openmp)
+    endif()
+    if(CONFIGURE_REQUEST_PIC)
+      list(APPEND MBX_CONFIG_FLAGS ${CONFIGURE_REQUEST_PIC})
+    endif()
+    set(MBXLIB_URL "https://github.com/paesanilab/MBX/releases/download/v1.3.3/mbx-1.3.3.tar.gz" CACHE STRING "URL for MBX tarball")
+    set(MBXLIB_MD5 "78abbf597e8077e5e0b18e86fc3248c1" CACHE STRING "MD5 checksum of MBX tarball")
+    mark_as_advanced(MBXLIB_URL)
+    mark_as_advanced(MBXLIB_MD5)
+    set(MBX_LINK_LIBS)
+    find_package(FFTW3 REQUIRED)
+    if(FFTW3_FOUND)
+      list(APPEND MBX_LINK_LIBS FFTW3::FFTW3)
+    endif()
+    find_package(PkgConfig QUIET)
+    set(DOWNLOAD_MBX_DEFAULT ON)
+    if(PKG_CONFIG_FOUND)
+      pkg_check_modules(MBX QUIET mbx)
+      if(MBX_FOUND)
+        set(DOWNLOAD_MBX_DEFAULT OFF)
+      endif()
+    endif()
+    option(DOWNLOAD_MBX "Download MBX package instead of using an already installed one" ${DOWNLOAD_MBX_DEFAULT})
+    if(DOWNLOAD_MBX)
+      message(STATUS "MBX download requested - we will build our own")
+      set(MBX_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}mbx${CMAKE_STATIC_LIBRARY_SUFFIX}")
+      message(STATUS "MBX_CONFIG_CC: ${MBX_CONFIG_CC}")
+      message(STATUS "MBX_CONFIG_CXX: ${MBX_CONFIG_CXX}")
+      message(STATUS "MBX_CONFIG_FLAGS: ${MBX_CONFIG_FLAGS}")
+      include(ExternalProject)
+      ExternalProject_Add(mbx_build
+        URL     ${MBXLIB_URL}
+        URL_HASH MD5=${MBXLIB_MD5}
+        CONFIGURE_COMMAND <SOURCE_DIR>/configure
+                          --prefix=<INSTALL_DIR>
+                          ${MBX_CONFIG_FLAGS}
+                          CXX=${MBX_CONFIG_CXX}
+                          CC=${MBX_CONFIG_CC}
+                          CPPFLAGS=-I${FFTW3_INCLUDE_DIRS}
+        BUILD_BYPRODUCTS ${MBX_BUILD_BYPRODUCTS}
+      )
+      ExternalProject_get_property(mbx_build INSTALL_DIR)
+      add_library(LAMMPS::MBX UNKNOWN IMPORTED)
+      add_dependencies(LAMMPS::MBX mbx_build)
+      set_target_properties(LAMMPS::MBX PROPERTIES
+        IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}mbx${CMAKE_STATIC_LIBRARY_SUFFIX}
+        INTERFACE_LINK_LIBRARIES "${MBX_LINK_LIBS};${CMAKE_DL_LIBS}"
+      )
+      set_target_properties(LAMMPS::MBX PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
+      file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
+      if(CMAKE_PROJECT_NAME STREQUAL "lammps")
+        target_link_libraries(lammps PRIVATE LAMMPS::MBX)
+      endif()
+    else()
+      find_package(PkgConfig REQUIRED)
+      pkg_check_modules(MBX REQUIRED mbx${MBX_SUFFIX})
+      add_library(LAMMPS::MBX INTERFACE IMPORTED)
+      file(MAKE_DIRECTORY ${MBX_INCLUDE_DIRS})
+      target_include_directories(LAMMPS::MBX INTERFACE ${MBX_INCLUDE_DIRS})
+      target_link_directories(LAMMPS::MBX INTERFACE ${MBX_LIBRARY_DIRS})
+      target_link_libraries(LAMMPS::MBX INTERFACE "${MBX_LINK_LIBS};${MBX_LIBRARIES};${CMAKE_DL_LIBS}")
+      if(CMAKE_PROJECT_NAME STREQUAL "lammps")
+        target_link_libraries(lammps PUBLIC LAMMPS::MBX)
+      endif()
+    endif()

cmake/presets/all_off.cmake

-Original file line number
+Diff line change
@@ Expand Up / @@ -48,6 +48,7 @@ set(ALL_PACKAGES @@
       MACHDYN
       MANIFOLD
       MANYBODY
+      MBX
       MC
       MDI
       MEAM
@@ Expand Down @@

cmake/presets/all_on.cmake

-Original file line number
+Diff line change
@@ Expand Up / @@ -50,6 +50,7 @@ set(ALL_PACKAGES @@
       MACHDYN
       MANIFOLD
       MANYBODY
+      MBX
       MC
       MDI
       MEAM
@@ Expand Down @@

doc/src/Build_extras.rst

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -49,6 +49,7 @@ This is the list of packages that may require additional steps.
  
       * :ref:`KOKKOS <kokkos>`

       * :ref:`LEPTON <lepton>`

       * :ref:`MACHDYN <machdyn>`

       * :ref:`MBX <mbx>`

       * :ref:`MDI <mdi>`

       * :ref:`MISC <misc>`

       * :ref:`ML-HDNNP <ml-hdnnp>`

    @@ -106,7 +107,7 @@ versions use an incompatible API and thus LAMMPS will fail to compile.
  
          .. versionchanged:: 10Sep2025

          The COMPRESS package no longer supports the the traditional make build.

          The COMPRESS package no longer supports the traditional make build.

          You need to build LAMMPS with CMake.

    ----------

    @@ -440,7 +441,7 @@ minutes to hours) to build.  Of course you only need to do that once.)
  
          .. versionchanged:: 10Sep2025

          The KIM package no longer supports the the traditional make build.

          The KIM package no longer supports the traditional make build.

          You need to build LAMMPS with CMake.

    Debugging OpenKIM web queries in LAMMPS

    @@ -915,7 +916,7 @@ included in the LAMMPS source distribution in the ``lib/lepton`` folder.
  
          .. versionchanged:: 10Sep2025

          The LEPTON package no longer supports the the traditional make build.

          The LEPTON package no longer supports the traditional make build.

          You need to build LAMMPS with CMake.

    ----------

    @@ -948,7 +949,7 @@ Eigen3 is a template library, so you do not need to build it.
  
          .. versionchanged:: 10Sep2025

          The MACHDYN package no longer supports the the traditional make build.

          The MACHDYN package no longer supports the traditional make build.

          You need to build LAMMPS with CMake.

    ----------

    @@ -1053,7 +1054,7 @@ for additional details.
  
          .. versionchanged:: 10Sep2025

          The PYTHON package no longer supports the the traditional make build.

          The PYTHON package no longer supports the traditional make build.

          You need to build LAMMPS with CMake.

    ----------

    @@ -1092,7 +1093,7 @@ binary package provided by your operating system.
  
          .. versionchanged:: 10Sep2025

          The VORONOI package no longer supports the the traditional make build.

          The VORONOI package no longer supports the traditional make build.

          You need to build LAMMPS with CMake.

    ----------

    @@ -1162,7 +1163,7 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
  
          .. versionchanged:: 10Sep2025

          The APIP package no longer supports the the traditional make

          The APIP package no longer supports the traditional make

          build.  You need to build LAMMPS with CMake.

    ----------

    @@ -1194,7 +1195,7 @@ module included in the LAMMPS source distribution.
  
          .. versionchanged:: 10Sep2025

          The COLVARS package no longer supports the the traditional make build.

          The COLVARS package no longer supports the traditional make build.

          You need to build LAMMPS with CMake.

    ----------

    @@ -1228,11 +1229,52 @@ This package depends on the KSPACE package.
  
       .. tab:: Traditional make

          The ELECTRODE package no longer supports the the traditional make

          The ELECTRODE package no longer supports the traditional make

          build.  You need to build LAMMPS with CMake.

    ----------

    .. _mbx:

    MBX package

    -----------

    .. versionadded:: TBD

    This package requires the MBX library that can be downloaded and built

    either before LAMMPS is built or as part of the LAMMPS compilation.  The

    code for the library can be found at:

    `https://github.com/paesanilab/MBX/

    <https://github.com/paesanilab/MBX/>`_

    Instead of including the MBX package directly into LAMMPS, it is also

    possible to skip this step and build the MBX package as a plugin using

    the CMake script files in the ``examples/PACKAGE/mbx/plugin`` folder and

    then load this plugin at runtime with the :doc:`plugin command

    <plugin>`.

    .. tabs::

       .. tab:: CMake build

          By default the MBX library will be downloaded from the git repository

          and built automatically when the MBX package is enabled with

          ``-D PKG_MBX=yes``.  The location for the sources may be

          customized by setting the variable ``MBXLIB_URL`` when

          configuring with CMake (e.g. to use a local archive on machines

          without internet access).  Since CMake checks the validity of the

          archive with ``md5sum`` you may also need to set ``MBXLIB_MD5``

          if you provide a different library version than what is downloaded

          automatically.

       .. tab:: Traditional make

          The MBX package does not support the traditional make

          build.  You need to build LAMMPS with CMake to use it.

    ----------

    .. _ml-pace:

    ML-PACE package

    @@ -1267,7 +1309,7 @@ folder and then load this plugin at runtime with the :doc:`plugin command <plugi
  
          .. versionchanged:: 10Sep2025

          The ML-PACE package no longer supports the the traditional make

          The ML-PACE package no longer supports the traditional make

          build.  You need to build LAMMPS with CMake.

    ----------

    @@ -1287,7 +1329,7 @@ ML-POD package
  
          .. versionchanged:: 10Sep2025

          The ML-POD package no longer supports the the traditional make

          The ML-POD package no longer supports the traditional make

          build.  You need to build LAMMPS with CMake.

    ----------

    @@ -1336,7 +1378,7 @@ within CMake will download the non-commercial use version.
  
          .. versionchanged:: 10Sep2025

          The ML-QUIP package no longer supports the the traditional make

          The ML-QUIP package no longer supports the traditional make

          build.  You need to build LAMMPS with CMake.

    ----------

    @@ -1431,7 +1473,7 @@ folder and then load this plugin at runtime with the :doc:`plugin command <plugi
  
          .. versionchanged:: 10Sep2025

          The PLUMED package no longer supports the the traditional make

          The PLUMED package no longer supports the traditional make

          build.  You need to build LAMMPS with CMake.

    ----------

    @@ -1461,7 +1503,7 @@ the HDF5 library.
  
          .. versionchanged:: 10Sep2025

          The H5MD package no longer supports the the traditional make

          The H5MD package no longer supports the traditional make

          build.  You need to build LAMMPS with CMake.

    ----------

    @@ -1516,7 +1558,7 @@ details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
  
          .. versionchanged:: 10Sep2025

          The ML-HDNNP package no longer supports the the traditional make

          The ML-HDNNP package no longer supports the traditional make

          build.  You need to build LAMMPS with CMake.

    ----------

    @@ -1609,7 +1651,7 @@ MDI package
  
          .. versionchanged:: 10Sep2025

          The MDI package no longer supports the the traditional make build.

          The MDI package no longer supports the traditional make build.

          You need to build LAMMPS with CMake.

    ----------

    @@ -1672,7 +1714,7 @@ MOLFILE package
  
          .. versionchanged:: 10Sep2025

          The MOLFILE package no longer supports the the traditional make

          The MOLFILE package no longer supports the traditional make

          build.  You need to build LAMMPS with CMake.

    ----------

    @@ -1702,7 +1744,7 @@ on your system.
  
          .. versionchanged:: 10Sep2025

          The NETCDF package no longer supports the the traditional make build.

          The NETCDF package no longer supports the traditional make build.

          You need to build LAMMPS with CMake.

    ----------

    @@ -1801,7 +1843,7 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
  
          .. versionchanged:: 10Sep2025

          The QMMM package no longer supports the the traditional make build.

          The QMMM package no longer supports the traditional make build.

          You need to build LAMMPS with CMake.

    ----------

    @@ -1838,7 +1880,7 @@ This package depends on the BPM package.
  
          .. versionchanged:: 10Sep2025

          The RHEO package no longer supports the the traditional make build.

          The RHEO package no longer supports the traditional make build.

          You need to build LAMMPS with CMake.

    ----------

    @@ -1873,7 +1915,7 @@ To build with this package, you must download and build the
  
          .. versionchanged:: 10Sep2025

          The SCAFACOS package no longer supports the the traditional make build.

          The SCAFACOS package no longer supports the traditional make build.

          You need to build LAMMPS with CMake.

    ----------

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[pull] develop from lammps:develop #87

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