Merge branch 'develop' into saip-TMDC-Metal

Author: akohlmey

cmake/CMakeLists.txt

@@ -779,16 +779,17 @@ if(_index GREATER -1)
   target_link_libraries(lammps PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
 endif()
 set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h command.h compute.h dihedral.h domain.h
-  error.h exceptions.h fix.h force.h group.h improper.h input.h info.h kspace.h lammps.h lattice.h
-  library.h lmppython.h lmptype.h memory.h modify.h neighbor.h neigh_list.h output.h pair.h
-  platform.h pointers.h region.h timer.h universe.h update.h utils.h variable.h)
+  error.h exceptions.h fix.h force.h group.h improper.h input.h info.h json.h json_fwd.h kspace.h
+  lammps.h lattice.h library.h lmppython.h lmptype.h memory.h modify.h neighbor.h neigh_list.h
+  output.h pair.h platform.h pointers.h region.h timer.h universe.h update.h utils.h variable.h)
 set(LAMMPS_FMT_HEADERS core.h format.h)
+set(LAMMPS_JSON_HEADERS json_fwd.hpp json.hpp)
 
 set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
 set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
 set_target_properties(lammps PROPERTIES PREFIX "lib")
-target_include_directories(lammps PUBLIC $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/lammps>)
-file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt)
+target_include_directories(lammps PUBLIC $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>)
+file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/nlohmann)
 foreach(_HEADER ${LAMMPS_CXX_HEADERS})
   add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/${_HEADER})
   add_custom_target(${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER})
@@ -805,6 +806,14 @@ foreach(_HEADER ${LAMMPS_FMT_HEADERS})
     install(FILES ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps/fmt)
   endif()
 endforeach()
+foreach(_HEADER ${LAMMPS_JSON_HEADERS})
+  add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/nlohmann/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/nlohmann/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/nlohmann/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/nlohmann/${_HEADER})
+  add_custom_target(json_${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/nlohmann/${_HEADER})
+  add_dependencies(lammps json_${_HEADER})
+  if(BUILD_SHARED_LIBS)
+    install(FILES ${LAMMPS_SOURCE_DIR}/nlohmann/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps/nlohmann)
+  endif()
+endforeach()
 target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/includes>)
 add_library(LAMMPS::lammps ALIAS lammps)
 get_target_property(LAMMPS_DEFINES lammps INTERFACE_COMPILE_DEFINITIONS)
@@ -827,7 +836,7 @@ if(BUILD_SHARED_LIBS)
   install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
   install(EXPORT LAMMPS_Targets FILE LAMMPS_Targets.cmake NAMESPACE LAMMPS:: DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
   include(CMakePackageConfigHelpers)
-  configure_file(LAMMPSConfig.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake @ONLY)
+  configure_file(LAMMPSConfig.cmake.in "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake" @ONLY)
   write_basic_package_version_file("LAMMPSConfigVersion.cmake" VERSION ${PROJECT_VERSION} COMPATIBILITY ExactVersion)
   install(FILES "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfig.cmake" "${CMAKE_CURRENT_BINARY_DIR}/LAMMPSConfigVersion.cmake" DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/LAMMPS)
 endif()

cmake/LAMMPSConfig.cmake.in

@@ -1,5 +1,22 @@
+# created by cmake version @CMAKE_VERSION@ for LAMMPS version @PROJECT_VERSION@
+
 include(CMakeFindDependencyMacro)
 if(@BUILD_MPI@)
   find_dependency(MPI REQUIRED CXX)
 endif()
+if(@BUILD_OMP@)
+  find_dependency(OpenMP REQUIRED CXX)
+endif()
 include("${CMAKE_CURRENT_LIST_DIR}/LAMMPS_Targets.cmake")
+add_library(LAMMPS::LAMMPS ALIAS LAMMPS::lammps)
+
+get_target_property(LAMMPS_CONFIG LAMMPS::lammps IMPORTED_CONFIGURATIONS)
+get_target_property(LAMMPS_LIBRARY LAMMPS::lammps IMPORTED_LOCATION_${LAMMPS_CONFIG})
+get_target_property(LAMMPS_INCLUDE_DIR LAMMPS::lammps INTERFACE_INCLUDE_DIRECTORIES)
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(LAMMPS
+  REQUIRED_VARS LAMMPS_LIBRARY LAMMPS_INCLUDE_DIR
+  VERSION_VAR PACKAGE_VERSION
+  HANDLE_VERSION_RANGE
+)

doc/src/Build_cmake.rst

@@ -126,6 +126,78 @@ defaults to ``${HOME}/.local``.
    root) the `ldconfig` program to update the cache file for fast lookup
    of system shared libraries.
 
+.. admonition:: Using the installed library
+   :class: Hint
+
+   The CMake installation functionality is an experimental work in
+   progress and thus not without problems, especially when writing your
+   own program that is trying to use the LAMMPS C++ classes directly.
+
+   While there is a well-defined :ref:`C-language interface
+   <lammps_c_api>` with the ``library.h`` header file, there is no
+   equivalent for the C++ interface yet.  When installing LAMMPS,
+   only the core header files are copied into the installation folder
+   and thus only high-level access to C++ features is available.
+
+   The following is a minimal CMake example file for using the installed
+   LAMMPS package which represents the current state of development:
+
+   .. code-block:: cmake
+
+      cmake_minimum_required(VERSION 3.20)
+      project(simpleCC CXX)
+      # set this to the LAMMPS installation location
+      if(NOT CMAKE_PREFIX_PATH)
+        set(CMAKE_PREFIX_PATH $ENV{HOME}/.local)
+      endif()
+      find_package(LAMMPS REQUIRED)
+      add_executable(simpleCC simple.cpp)
+      target_link_libraries(simpleCC PRIVATE LAMMPS::LAMMPS)
+
+   The ``CMAKE_PREFIX_PATH`` setting tells CMake where to find the
+   generated CMake configuration files for the `find_package()
+   <https://cmake.org/cmake/help/latest/command/find_package.html>`_
+   CMake command.  You can also specify a required minimal version or
+   version range.  For that a numeric representation in the "YYYY.MM.DD"
+   format has to be used: the 10 September 2025 release thus becomes
+   version 2025.09.10.  The include statements in the ``simple.cpp``
+   source file have to be prefixed with ``lammps/`` as follows:
+
+   .. code-block:: C++
+
+      #include <lammps/lammps.h>
+      #include <lammps/input.h>
+      #include <lammps/atom.h>
+      #include <lammps/library.h>
+
+   Using the ``LAMMPS::LAMMPS`` target imported from the installed
+   LAMMPS CMake configuration files should set up the include and linker
+   flags and folders automatically.  Below is the output for an example
+   session (note how it checks for and includes MPI and OpenMP support
+   since that specific LAMMPS library was set up this way):
+
+   .. code-block:: console
+
+      $ cmake -S . -B build -D CMAKE_PREFIX_PATH=$HOME/Downloads/test-install
+      -- The CXX compiler identification is GNU 15.2.1
+      -- Detecting CXX compiler ABI info
+      -- Detecting CXX compiler ABI info - done
+      -- Check for working CXX compiler: /usr/lib64/ccache/c++ - skipped
+      -- Detecting CXX compile features
+      -- Detecting CXX compile features - done
+      -- Found MPI_CXX: /usr/lib64/mpich/lib/libmpicxx.so (found version "4.1")
+      -- Found MPI: TRUE (found version "4.1") found components: CXX
+      -- Found OpenMP_CXX: -fopenmp (found version "4.5")
+      -- Found OpenMP: TRUE (found version "4.5") found components: CXX
+      -- Found LAMMPS: /home/akohlmey/Downloads/test-install/lib64/liblammps.so.0
+      -- Configuring done (0.9s)
+      -- Generating done (0.0s)
+      -- Build files have been written to: /home/akohlmey/Downloads/test-simple/build
+      $ cmake --build build
+      [ 50%] Building CXX object CMakeFiles/simpleCC.dir/simple.cpp.o
+      [100%] Linking CXX executable simpleCC
+      [100%] Built target simpleCC
+
 .. _cmake_options:
 
 Configuration and build options

doc/src/Commands_compute.rst

@@ -161,7 +161,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`temp/asphere <compute_temp_asphere>`
    * :doc:`temp/body <compute_temp_body>`
    * :doc:`temp/chunk <compute_temp_chunk>`
-   * :doc:`temp/com <compute_temp_com>`
+   * :doc:`temp/com (k) <compute_temp_com>`
    * :doc:`temp/cs <compute_temp_cs>`
    * :doc:`temp/deform (k) <compute_temp_deform>`
    * :doc:`temp/deform/eff <compute_temp_deform_eff>`

doc/src/Run_formats.rst

@@ -78,7 +78,7 @@ For floating point numbers in scientific notation, the Fortran double
 precision notation "1.1d3" is not accepted; you have to use "1100",
 "1100.0" or "1.1e3".
 
-Input file
+Input File
 ^^^^^^^^^^
 
 A LAMMPS input file is a text file with commands.  It is read
@@ -161,7 +161,7 @@ recommended to always have an empty line at the end of an input file.
 The specific details describing how LAMMPS input is processed and parsed
 are explained in :doc:`Commands_parse`.
 
-Data file
+Data File
 ^^^^^^^^^
 
 A LAMMPS data file contains a description of a system suitable for
@@ -302,7 +302,7 @@ Molecule-ID', one for each atom in the system.  For adding charges to
 atom style molecular with fix property/atom, the "Atoms" section is now
 formatted according to the atom style and a "Charges" section is added.
 
-Molecule file
+Molecule File
 ^^^^^^^^^^^^^
 
 Molecule files for use with the :doc:`molecule command <molecule>` look
@@ -376,7 +376,7 @@ if the molecule command is issued *before* the simulation box is
 defined.  Otherwise, the molecule command can derive the required
 settings internally.
 
-Restart file
+Restart File
 ^^^^^^^^^^^^
 
 LAMMPS restart files are binary files and not available in text format.
@@ -409,6 +409,69 @@ are in the ``lmprestart.h`` header file.
 LAMMPS restart files are not expected to be portable between platforms
 or LAMMPS versions, but changes to the file format are rare.
 
+.. _json-dump-files:
+
+JSON Dump Files
+^^^^^^^^^^^^^^^
+
+LAMMPS can print information about molecules and other sets of atoms during
+a run, in JSON format. Several fixes currently support dumping JSON files
+in the 'molecules' style, including :doc:`fix bond/react <fix_bond_react>`
+and the *delete* keyword of :doc:`fix reaxff/species <fix_reaxff_species>`.
+The JSON 'dump molecules' format lists sets of atoms in the style of the
+:doc:`JSON molecule file <molecule>`, where more discussion of JSON schema
+can be found. Here is an generic example of a JSON output file that dumped
+one water molecule on the first timestep:
+
+.. code-block:: json
+
+   {
+       "application": "LAMMPS",
+       "units": "real",
+       "format": "dump",
+       "style": "molecules",
+       "revision": 1,
+       "timesteps": [
+           {
+               "timestep": 1,
+               "molecules": [
+                   {
+                       "types": {
+                           "format": ["atom-id", "type"],
+                           "data": [
+                               [1368, "H"],
+                               [1366, "O"],
+                               [1367, "H"]
+                           ]
+                       },
+                       "coords": {
+                           "format": ["atom-id", "x", "y", "z"],
+                           "data": [
+                               [1368, 26.787767440427466, 29.785528640296768, 25.85197353660144],
+                               [1366, 26.641801222582824, 29.868106247702887, 24.91285138212243],
+                               [1367, 25.69611192416744, 30.093425787807448, 24.914380215672846]
+                           ]
+                       }
+                   }
+               ]
+           }
+       ]
+   }
+
+The required first-level keys of the JSON format output are "application",
+"format", "style", "revision", and "timesteps", and optional keys are
+"units" and "title".  The value of the "timesteps" key is an array of
+objects that contain data for each timestep on which a molecule was dumped,
+and the other first-level keys identify this JSON schema.  The objects in
+"timesteps" contains two mandatory keys, "timestep" and "molecules".  The
+"molecules" key is an array of :doc:`LAMMPS molecule JSON <molecule>`
+objects, and may contain other keys that contain metadata for each
+molecule.  The "format" keys within molecule JSON objects are only printed
+once per output file, for brevity.  The "atom-id" values are atom IDs from
+the simulation, and the "type" values are atom types.  In the above
+example, the types were reported as strings corresponding to elements using
+:doc:`type labels <labelmap>`.
+
 .. Native Dump file
 .. ^^^^^^^^^^^^^^^^
 ..

doc/src/compute_temp_com.rst

@@ -1,8 +1,11 @@
 .. index:: compute temp/com
+.. index:: compute temp/com/kk
 
 compute temp/com command
 ========================
 
+Accelerator Variants: *temp/com/kk*
+
 Syntax
 """"""
 
@@ -82,6 +85,12 @@ See the :doc:`Howto thermostat <Howto_thermostat>` page for a
 discussion of different ways to compute temperature and perform
 thermostatting.
 
+----------
+
+.. include:: accel_styles.rst
+
+----------
+
 Output info
 """""""""""
 

doc/src/fix_bond_react.rst

@@ -41,6 +41,8 @@ Syntax
          Nlimit = maximum total number of reactions allowed to occur
        *shuffle_seed* value = seed
          seed = random # seed (positive integer) for choosing between eligible reactions
+       *file* value = filename
+         filename = name of the JSON file that records reaction occurrences
 
 * react = mandatory argument indicating new reaction specification
 * react-ID = user-assigned name for the reaction
@@ -244,6 +246,52 @@ if available; reactions are chosen deterministically if a positive integer
 is specified for the 'shuffle_seed' keyword. Multiple *max_rxn* keywords
 can be specified.
 
+The *file* keyword can be used to dump information about each reaction that
+occurs during the simulation. The atom IDs, types, and coordinates of all
+atoms in the reaction site are printed out on the timestep that the
+reaction is initiated. The output file follows the :ref:`JSON dump
+molecules format <json-dump-files>`, with one extra key added to each
+molecule object to identify the reaction. The added key is "reaction" and
+its value is the reaction name (react-ID). Here is an example output for a
+hypothetical reaction involving one water molecule:
+
+.. code-block:: json
+
+   {
+       "application": "LAMMPS",
+       "units": "real",
+       "format": "dump",
+       "style": "molecules",
+       "revision": 1,
+       "title": "fix bond/react",
+       "timesteps": [
+           {
+               "timestep": 1,
+               "molecules": [
+                   {
+                       "reaction": "water_dissociation",
+                       "types": {
+                           "format": ["atom-id", "type"],
+                           "data": [
+                               [1368, "H"],
+                               [1366, "O"],
+                               [1367, "H"]
+                           ]
+                       },
+                       "coords": {
+                           "format": ["atom-id", "x", "y", "z"],
+                           "data": [
+                               [1368, 26.787767440427466, 29.785528640296768, 25.85197353660144],
+                               [1366, 26.641801222582824, 29.868106247702887, 24.91285138212243],
+                               [1367, 25.69611192416744, 30.093425787807448, 24.914380215672846]
+                           ]
+                       }
+                   }
+               ]
+           }
+       ]
+   }
+
 The following comments pertain to each *react* argument (in other
 words, they can be customized for each reaction, or reaction step):
 

src/KOKKOS/Install.sh

@@ -114,6 +114,8 @@ action compute_sna_grid_local_kokkos.h compute_sna_grid_local.h
 action compute_sna_grid_local_kokkos_impl.h compute_sna_grid_local.cpp
 action compute_gaussian_grid_local_kokkos.cpp compute_gaussian_grid_local.cpp
 action compute_gaussian_grid_local_kokkos.h compute_gaussian_grid_local.h
+action compute_temp_com_kokkos.cpp
+action compute_temp_com_kokkos.h
 action compute_temp_deform_kokkos.cpp
 action compute_temp_deform_kokkos.h
 action compute_temp_kokkos.cpp