lammps · akohlmey · Oct 13, 2023 · Oct 10, 2023 · Oct 10, 2023 · Oct 11, 2023
diff --git a/doc/src/Tools.rst b/doc/src/Tools.rst
@@ -702,11 +702,15 @@ Prerequisites and portability
 LAMMPS GUI is programmed in C++ based on the C++11 standard and using
 the `Qt GUI framework <https://www.qt.io/product/framework>`_.
 Currently, Qt version 5.12 or later is required; Qt 5.15LTS is
-recommended; Qt 6.x not (yet) supported.  Building LAMMPS with CMake is
-required.  The LAMMPS GUI has been successfully compiled and tested on:
+recommended; support for Qt version 6.x is under active development and
+thus far only tested with Qt 6.5LTS on Linux.  Building LAMMPS with
+CMake is required.
+
+The LAMMPS GUI has been successfully compiled and tested on:
 
 - Ubuntu Linux 20.04LTS x86_64 using GCC 9, Qt version 5.12
 - Fedora Linux 38 x86\_64 using GCC 13 and Clang 16, Qt version 5.15LTS
+- Fedora Linux 38 x86\_64 using GCC 13, Qt version 6.5LTS
 - Apple macOS 12 (Monterey) and macOS 13 (Ventura) with Xcode on arm64 and x86\_64, Qt version 5.15LTS
 - Windows 10 and 11 x86_64 with Visual Studio 2022 and Visual C++ 14.36, Qt version 5.15LTS
 - Windows 10 and 11 x86_64 with MinGW / GCC 10.0 cross-compiler on Fedora 38, Qt version 5.15LTS
@@ -717,7 +721,7 @@ required.  The LAMMPS GUI has been successfully compiled and tested on:
 Pre-compiled executables
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
-Pre-compiled LAMMPS executables including the GUI are currently
+Pre-compiled LAMMPS executable packages that include the GUI are currently
 available from https://download.lammps.org/static or
 https://github.com/lammps/lammps/releases.  You can unpack the archives
 (or mount the macOS disk image) and run the GUI directly in place. The
@@ -742,7 +746,10 @@ stored in a location where CMake can find them without additional help.
 Otherwise, the location of the Qt library installation must be indicated
 by setting ``-D Qt5_DIR=/path/to/qt5/lib/cmake/Qt5``, which is a path to
 a folder inside the Qt installation that contains the file
-``Qt5Config.cmake``.
+``Qt5Config.cmake``. Similarly, for Qt6 the location of the Qt library
+installation can be indicated by setting ``-D Qt6_DIR=/path/to/qt6/lib/cmake/Qt6``,
+if necessary.  When both, Qt5 and Qt6 are available, Qt6 will be preferred
+unless ``-D LAMMPS_GUI_USE_QT5=yes`` is set.
 
 It should be possible to build the LAMMPS GUI as a standalone
 compilation (e.g. when LAMMPS has been compiled with traditional make),

diff --git a/doc/src/fix_srd.rst b/doc/src/fix_srd.rst
@@ -71,14 +71,15 @@ imbue the SRD particles with fluid-like properties, including an
 effective viscosity.  Thus simulations with large solute particles can
 be run more quickly, to measure solute properties like diffusivity
 and viscosity in a background fluid.  The usual LAMMPS fixes for such
-simulations, such as :doc:`fix deform <fix_deform>`, :doc:`fix viscosity <fix_viscosity>`, and :doc:`fix nvt/sllod <fix_nvt_sllod>`,
+simulations, such as :doc:`fix deform <fix_deform>`,
+:doc:`fix viscosity <fix_viscosity>`, and :doc:`fix nvt/sllod <fix_nvt_sllod>`,
 can be used in conjunction with the SRD model.
 
-For more details on how the SRD model is implemented in LAMMPS, :ref:`this paper <Petersen1>` describes the implementation and usage of pure SRD
-fluids.  :ref:`This paper <Lechman>`, which is nearly complete, describes
-the implementation and usage of mixture systems (solute particles in
-an SRD fluid).  See the examples/srd directory for sample input
-scripts using SRD particles in both settings.
+For more details on how the SRD model is implemented in LAMMPS,
+:ref:`(Petersen) <Petersen1>` describes the implementation and usage of
+pure SRD fluids.  See the ``examples/srd`` directory for sample input
+scripts using SRD particles for that and for mixture systems (solute
+particles in an SRD fluid).
 
 This fix does two things:
 
@@ -357,28 +358,28 @@ These are the 12 quantities.  All are values for the current timestep,
 except for quantity 5 and the last three, each of which are
 cumulative quantities since the beginning of the run.
 
-* (1) # of SRD/big collision checks performed
-* (2) # of SRDs which had a collision
-* (3) # of SRD/big collisions (including multiple bounces)
-* (4) # of SRD particles inside a big particle
-* (5) # of SRD particles whose velocity was rescaled to be < Vmax
-* (6) # of bins for collision searching
-* (7) # of bins for SRD velocity rotation
-* (8) # of bins in which SRD temperature was computed
-* (9) SRD temperature
-* (10) # of SRD particles which have undergone max # of bounces
-* (11) max # of bounces any SRD particle has had in a single step
-* (12) # of reneighborings due to SRD particles moving too far
+(1) # of SRD/big collision checks performed
+(2) # of SRDs which had a collision
+(3) # of SRD/big collisions (including multiple bounces)
+(4) # of SRD particles inside a big particle
+(5) # of SRD particles whose velocity was rescaled to be < Vmax
+(6) # of bins for collision searching
+(7) # of bins for SRD velocity rotation
+(8) # of bins in which SRD temperature was computed
+(9) SRD temperature
+(10) # of SRD particles which have undergone max # of bounces
+(11) max # of bounces any SRD particle has had in a single step
+(12) # of reneighborings due to SRD particles moving too far
 
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""
 
-This command can only be used if LAMMPS was built with the SRD
-package.  See the :doc:`Build package <Build_package>` doc
-page for more info.
+This command can only be used if LAMMPS was built with the SRD package.
+See the :doc:`Build package <Build_package>` doc page for more info.
 
 Related commands
 """"""""""""""""
@@ -403,7 +404,3 @@ no, and rescale = yes.
 
 **(Petersen)** Petersen, Lechman, Plimpton, Grest, in' t Veld, Schunk, J
 Chem Phys, 132, 174106 (2010).
-
-.. _Lechman:
-
-**(Lechman)** Lechman, et al, in preparation (2010).
diff --git a/doc/src/pair_ilp_tmd.rst b/doc/src/pair_ilp_tmd.rst
@@ -22,12 +22,12 @@ Examples
 .. code-block:: LAMMPS
 
    pair_style  hybrid/overlay ilp/tmd 16.0 1
-   pair_coeff  * * ilp/tmd  TMD.ILP Mo S S
+   pair_coeff  * * ilp/tmd  MoS2.ILP Mo S S
 
    pair_style  hybrid/overlay sw/mod sw/mod ilp/tmd 16.0
    pair_coeff  * * sw/mod 1  tmd.sw.mod Mo S S NULL NULL NULL
    pair_coeff  * * sw/mod 2  tmd.sw.mod NULL NULL NULL Mo S S
-   pair_coeff  * * ilp/tmd   TMD.ILP    Mo S S Mo S S
+   pair_coeff  * * ilp/tmd   MoS2.ILP   Mo S S Mo S S
 
 Description
 """""""""""
@@ -69,15 +69,15 @@ calculating the normals.
    each atom `i`, its six nearest neighboring atoms belonging to the same
    sub-layer are chosen to define the normal vector `{\bf n}_i`.
 
-The parameter file (e.g. TMD.ILP), is intended for use with *metal*
+The parameter file (e.g. MoS2.ILP), is intended for use with *metal*
 :doc:`units <units>`, with energies in meV. Two additional parameters,
 *S*, and *rcut* are included in the parameter file. *S* is designed to
 facilitate scaling of energies. *rcut* is designed to build the neighbor
 list for calculating the normals for each atom pair.
 
 .. note::
 
-   The parameters presented in the parameter file (e.g. TMD.ILP),
+   The parameters presented in the parameter file (e.g. MoS2.ILP),
    are fitted with taper function by setting the cutoff equal to 16.0
    Angstrom.  Using different cutoff or taper function should be careful.
    These parameters provide a good description in both short- and long-range
@@ -133,10 +133,10 @@ if LAMMPS was built with that package.  See the :doc:`Build package
 This pair style requires the newton setting to be *on* for pair
 interactions.
 
-The TMD.ILP potential file provided with LAMMPS (see the potentials
+The MoS2.ILP potential file provided with LAMMPS (see the potentials
 directory) are parameterized for *metal* units.  You can use this
 potential with any LAMMPS units, but you would need to create your own
-custom TMD.ILP potential file with coefficients listed in the appropriate
+custom MoS2.ILP potential file with coefficients listed in the appropriate
 units, if your simulation does not use *metal* units.
 
 Related commands

diff --git a/doc/src/pair_reaxff.rst b/doc/src/pair_reaxff.rst
@@ -43,22 +43,22 @@ Examples
 Description
 """""""""""
 
-Style *reaxff* computes the ReaxFF potential of van Duin, Goddard and
-co-workers.  ReaxFF uses distance-dependent bond-order functions to
+Pair style *reaxff* computes the ReaxFF potential of van Duin, Goddard
+and co-workers.  ReaxFF uses distance-dependent bond-order functions to
 represent the contributions of chemical bonding to the potential
-energy. There is more than one version of ReaxFF. The version
+energy.  There is more than one version of ReaxFF.  The version
 implemented in LAMMPS uses the functional forms documented in the
 supplemental information of the following paper:
-:ref:`(Chenoweth et al., 2008) <Chenoweth_20082>`.  The version integrated
-into LAMMPS matches the version of ReaxFF From Summer 2010.  For more
-technical details about the pair reaxff implementation of ReaxFF, see
-the :ref:`(Aktulga) <Aktulga>` paper. The *reaxff* style was initially
-implemented as a stand-alone C code and is now converted to C++ and
-integrated into LAMMPS as a package.
+:ref:`(Chenoweth et al., 2008) <Chenoweth_20082>` and matches the
+version of the reference ReaxFF implementation from Summer 2010.  For
+more technical details about the implementation of ReaxFF in pair style
+*reaxff*, see the :ref:`(Aktulga) <Aktulga>` paper. The *reaxff* style
+was initially implemented as a stand-alone C code and is now converted
+to C++ and integrated into LAMMPS as a package.
 
 The *reaxff/kk* style is a Kokkos version of the ReaxFF potential that
-is derived from the *reaxff* style. The Kokkos version can run on GPUs
-and can also use OpenMP multithreading. For more information about the
+is derived from the *reaxff* style.  The Kokkos version can run on GPUs
+and can also use OpenMP multithreading.  For more information about the
 Kokkos package, see :doc:`Packages details <Packages_details>` and
 :doc:`Speed kokkos <Speed_kokkos>` doc pages.  One important
 consideration when using the *reaxff/kk* style is the choice of either

@@ -32,6 +32,7 @@ namespace LAMMPS_NS {
 // get access to number of threads and per-thread data structures via FixOMP
 #define NPAIR_OMP_INIT                 \
   const int nthreads = comm->nthreads; \
+  omp_set_num_threads(nthreads); \
   const int ifix = modify->find_fix("package_omp")
 
 // get thread id and then assign each thread a fixed chunk of atoms

diff --git a/src/compute_msd_chunk.cpp b/src/compute_msd_chunk.cpp
@@ -27,8 +27,8 @@ using namespace LAMMPS_NS;
 /* ---------------------------------------------------------------------- */
 
 ComputeMSDChunk::ComputeMSDChunk(LAMMPS *lmp, int narg, char **arg) :
-    ComputeChunk(lmp, narg, arg), id_fix(nullptr), massproc(nullptr), masstotal(nullptr),
-    com(nullptr), comall(nullptr), msd(nullptr)
+    ComputeChunk(lmp, narg, arg), id_fix(nullptr), fix(nullptr), massproc(nullptr),
+    masstotal(nullptr), com(nullptr), comall(nullptr), msd(nullptr)
 {
   if (narg != 4) error->all(FLERR, "Illegal compute msd/chunk command");
 
@@ -196,6 +196,12 @@ void ComputeMSDChunk::compute_array()
 void ComputeMSDChunk::allocate()
 {
   ComputeChunk::allocate();
+  memory->destroy(massproc);
+  memory->destroy(masstotal);
+  memory->destroy(com);
+  memory->destroy(comall);
+  memory->destroy(msd);
+
   memory->create(massproc, nchunk, "msd/chunk:massproc");
   memory->create(masstotal, nchunk, "msd/chunk:masstotal");
   memory->create(com, nchunk, 3, "msd/chunk:com");

diff --git a/tools/lammps-gui/CMakeLists.txt b/tools/lammps-gui/CMakeLists.txt
@@ -11,6 +11,42 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
 option(LAMMPS_GUI_USE_PLUGIN "Load LAMMPS library dynamically at runtime" OFF)
 mark_as_advanced(LAMMPS_GUI_USE_PLUGIN)
+option(LAMMPS_GUI_USE_QT5 "Prefer using Qt5 over Qt6" OFF)
+
+include(CheckIncludeFileCXX)
+# helper function to check for usable omp.h header
+function(check_omp_h_include)
+  find_package(OpenMP COMPONENTS CXX QUIET)
+  if(OpenMP_CXX_FOUND)
+    set(CMAKE_REQUIRED_FLAGS ${OpenMP_CXX_FLAGS})
+    set(CMAKE_REQUIRED_INCLUDES ${OpenMP_CXX_INCLUDE_DIRS})
+    set(CMAKE_REQUIRED_LINK_OPTIONS ${OpenMP_CXX_FLAGS})
+    set(CMAKE_REQUIRED_LIBRARIES ${OpenMP_CXX_LIBRARIES})
+    check_include_file_cxx(omp.h _have_omp_h)
+  else()
+    set(_have_omp_h FALSE)
+  endif()
+  set(HAVE_OMP_H_INCLUDE ${_have_omp_h} PARENT_SCOPE)
+endfunction()
+
+# detect if we may enable OpenMP support by default
+set(BUILD_OMP_DEFAULT OFF)
+find_package(OpenMP COMPONENTS CXX QUIET)
+if(OpenMP_CXX_FOUND)
+  check_omp_h_include()
+  if(HAVE_OMP_H_INCLUDE)
+    set(BUILD_OMP_DEFAULT ON)
+  endif()
+endif()
+
+option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT})
+if(BUILD_OMP)
+  find_package(OpenMP COMPONENTS CXX REQUIRED)
+  check_omp_h_include()
+  if(NOT HAVE_OMP_H_INCLUDE)
+    message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
+  endif()
+endif()
 
 # checks
 # when this file is included as subdirectory in the LAMMPS build, many settings are directly imported
@@ -73,7 +109,15 @@ if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
 endif()
 
 # we require Qt 5 and at least version 5.12 at that.
-find_package(Qt5 5.12 REQUIRED COMPONENTS Widgets Charts)
+if(NOT LAMMPS_GUI_USE_QT5)
+  find_package(Qt6 6.2 COMPONENTS Widgets Charts)
+endif()
+if(NOT Qt6_FOUND)
+  find_package(Qt5 5.12 REQUIRED COMPONENTS Widgets Charts)
+  set(QT_VERSION_MAJOR "5")
+else()
+  set(QT_VERSION_MAJOR "6")
+endif()
 
 set(PROJECT_SOURCES
   main.cpp
@@ -105,18 +149,34 @@ set(PROJECT_SOURCES
   ${PLUGIN_LOADER_SRC}
   ${ICON_RC_FILE}
 )
-qt5_add_resources(PROJECT_SOURCES lammpsgui.qrc)
+if(QT_VERSION_MAJOR EQUAL 6)
+  qt6_add_resources(PROJECT_SOURCES lammpsgui.qrc)
+else()
+  qt5_add_resources(PROJECT_SOURCES lammpsgui.qrc)
+endif()
 
 if(APPLE)
   set(MACOSX_ICON_FILE ${LAMMPS_DIR}/cmake/packaging/lammps.icns)
   set(MACOSX_README_FILE ${LAMMPS_DIR}/cmake/packaging/README.macos)
   set(MACOSX_BACKGROUND_FILE ${LAMMPS_DIR}/cmake/packaging/LAMMPS_DMG_Background.png)
 endif()
 
-add_executable(lammps-gui
-  ${MACOSX_ICON_FILE}
-  ${PROJECT_SOURCES}
-)
+if(QT_VERSION_MAJOR EQUAL 6)
+  qt_add_executable(lammps-gui
+    MANUAL_FINALIZATION
+    ${MACOSX_ICON_FILE}
+    ${PROJECT_SOURCES}
+  )
+else()
+  add_executable(lammps-gui
+    ${MACOSX_ICON_FILE}
+    ${PROJECT_SOURCES}
+  )
+endif()
+
+if(QT_VERSION_MAJOR EQUAL 6)
+    qt_finalize_executable(lammps-gui)
+endif()
 
 # compilation settings
 if(LAMMPS_GUI_USE_PLUGIN)
@@ -128,7 +188,7 @@ else()
 endif()
 target_include_directories(lammps-gui PRIVATE ${CMAKE_CURRENT_SOURCE_DIR})
 target_compile_definitions(lammps-gui PRIVATE LAMMPS_GUI_VERSION="${PROJECT_VERSION}")
-target_link_libraries(lammps-gui PRIVATE Qt5::Widgets Qt5::Charts)
+target_link_libraries(lammps-gui PRIVATE Qt${QT_VERSION_MAJOR}::Widgets Qt${VERSION_MAJOR}::Charts)
 if(BUILD_OMP)
   find_package(OpenMP COMPONENTS CXX REQUIRED)
   target_link_libraries(lammps-gui PRIVATE OpenMP::OpenMP_CXX)
@@ -209,7 +269,7 @@ elseif((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
     COMMENT "Create zip file with windows binaries"
     BYPRODUCT LAMMPS-Win10-amd64.zip
     WORKING_DIRECTORY ${CMAKE_BINARY_DIR})
-elseif(CMAKE_SYSTEM_NAME STREQUAL "Linux")
+elseif((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND NOT LAMMPS_GUI_USE_PLUGIN)
   install(TARGETS lammps-gui DESTINATION ${CMAKE_INSTALL_BINDIR})
   install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/lammps-gui.desktop DESTINATION ${CMAKE_INSTALL_DATADIR}/applications/)
   install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/lammps-input.xml DESTINATION ${CMAKE_INSTALL_DATADIR}/mime/packages/)

diff --git a/tools/lammps-gui/TODO.md b/tools/lammps-gui/TODO.md
@@ -23,7 +23,6 @@ LAMMPS-GUI TODO list:
 
 # Long term ideas (v2.x)
 - rewrite entire application to build the App and its layout manually
-- port to Qt6 (with compatibility to Qt5?)
 - also a rewrite should establish consistent naming conventions. now we have a mix of LAMMPS style, Qt style, and others.
 - add option to attach a debugger to the running program (highly non-portable, need customization support in preferences)
 - write a "wizard" dialog that can be used for beginners to create an input file template for a few typical use scenarios