Merge branch 'develop' into cg-dna

.github/CODEOWNERS

@@ -38,6 +38,7 @@ src/ML-HDNNP/*        @singraber
 src/ML-IAP/*          @athomps
 src/ML-PACE/*         @yury-lysogorskiy
 src/ML-POD/*          @exapde
+src/ML-UF3/*          @monk-04
 src/MOFFF/*           @hheenen
 src/MOLFILE/*         @akohlmey
 src/NETCDF/*          @pastewka
@@ -72,6 +73,8 @@ src/MC/fix_sgcmc.*                  @athomps
 src/REAXFF/compute_reaxff_atom.*    @rbberger
 src/KOKKOS/compute_reaxff_atom_kokkos.*    @rbberger
 src/REPLICA/fix_pimd_langevin.*     @Yi-FanLi
+src/DPD-BASIC/pair_dpd_coul_slater_long.* @Eddy-Barraud
+src/GPU/pair_dpd_coul_slater_long.* @Eddy-Barraud
 
 # core LAMMPS classes
 src/lammps.*              @sjplimp

cmake/CMakeLists.txt

@@ -256,6 +256,7 @@ set(STANDARD_PACKAGES
   DRUDE
   EFF
   ELECTRODE
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -285,6 +286,7 @@ set(STANDARD_PACKAGES
   ML-RANN
   ML-SNAP
   ML-POD
+  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE
@@ -689,7 +691,7 @@ endif()
 # packages which selectively include variants based on enabled styles
 # e.g. accelerator packages
 ######################################################################
-foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
+foreach(PKG_WITH_INCL CORESHELL DPD-BASIC DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()

cmake/Modules/Packages/DPD-BASIC.cmake

@@ -0,0 +1,9 @@
+# pair style dpd/coul/slater/long may only be installed if also KSPACE is installed
+if(NOT PKG_KSPACE)
+  get_property(LAMMPS_PAIR_HEADERS GLOBAL PROPERTY PAIR)
+  list(REMOVE_ITEM LAMMPS_PAIR_HEADERS ${LAMMPS_SOURCE_DIR}/DPD-BASIC/pair_dpd_coul_slater_long.h)
+  set_property(GLOBAL PROPERTY PAIR "${LAMMPS_PAIR_HEADERS}")
+  get_target_property(LAMMPS_SOURCES lammps SOURCES)
+  list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/DPD-BASIC/pair_dpd_coul_slater_long.cpp)
+  set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
+endif()

cmake/Modules/Packages/PLUMED.cmake

@@ -1,5 +1,9 @@
 # Plumed2 support for PLUMED package
 
+# for supporting multiple concurrent plumed2 installations for debugging and testing
+set(PLUMED_SUFFIX "" CACHE STRING "Suffix for Plumed2 library")
+mark_as_advanced(PLUMED_SUFFIX)
+
 if(BUILD_MPI)
   set(PLUMED_CONFIG_MPI "--enable-mpi")
   set(PLUMED_CONFIG_CC  ${CMAKE_MPI_C_COMPILER})
@@ -21,9 +25,11 @@ else()
   set(PLUMED_CONFIG_OMP "--disable-openmp")
 endif()
 
-set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.3/plumed-src-2.8.3.tgz"
+# Note: must also adjust check for supported API versions in
+# fix_plumed.cpp when version changes from v2.n.x to v2.n+1.y
+set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.9.1/plumed-src-2.9.1.tgz"
   CACHE STRING "URL for PLUMED tarball")
-set(PLUMED_MD5 "76d23cd394eba9e6530316ed1184e219" CACHE STRING "MD5 checksum of PLUMED tarball")
+set(PLUMED_MD5 "c3b2d31479c1e9ce211719d40e9efbd7" CACHE STRING "MD5 checksum of PLUMED tarball")
 
 mark_as_advanced(PLUMED_URL)
 mark_as_advanced(PLUMED_MD5)
@@ -151,15 +157,15 @@ else()
     file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
   else()
     find_package(PkgConfig REQUIRED)
-    pkg_check_modules(PLUMED REQUIRED plumed)
+    pkg_check_modules(PLUMED REQUIRED plumed${PLUMED_SUFFIX})
     add_library(LAMMPS::PLUMED INTERFACE IMPORTED)
     if(PLUMED_MODE STREQUAL "STATIC")
-      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
+      include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.static)
     elseif(PLUMED_MODE STREQUAL "SHARED")
-      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
+      include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.shared)
     elseif(PLUMED_MODE STREQUAL "RUNTIME")
-      set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+      set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${PLUMED_SUFFIX}Kernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
-      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
+      include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.runtime)
     endif()
     set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")
     set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_INCLUDE_DIRS}")

cmake/packaging/build_linux_tgz.sh

@@ -59,12 +59,14 @@ done
 
 echo "Set up wrapper script"
 MYDIR=$(dirname "$0")
+cp ${MYDIR}/xdg-open ${DESTDIR}/bin
 cp ${MYDIR}/linux_wrapper.sh ${DESTDIR}/bin
 for s in ${DESTDIR}/bin/*
 do \
         EXE=$(basename $s)
         test ${EXE} = linux_wrapper.sh && continue
         test ${EXE} = qt.conf && continue
+        test ${EXE} = xdg-open && continue
         ln -s bin/linux_wrapper.sh ${DESTDIR}/${EXE}
 done
 

cmake/packaging/linux_wrapper.sh

@@ -4,15 +4,17 @@
 # reset locale to avoid problems with decimal numbers
 export LC_ALL=C
 
-BASEDIR=$(dirname "$0")
+BASEDIR="$(dirname "$0")"
-EXENAME=$(basename "$0")
+EXENAME="$(basename "$0")"
+
+PATH="${BASEDIR}/bin:${PATH}"
 
 # append to LD_LIBRARY_PATH to prefer local (newer) libs
-LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${BASEDIR}/lib
+LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${BASEDIR}/lib"
 
 # set some environment variables for LAMMPS etc.
-LAMMPS_POTENTIALS=${BASEDIR}/share/lammps/potentials
+LAMMPS_POTENTIALS="${BASEDIR}/share/lammps/potentials"
-MSI2LMP_LIBRARY=${BASEDIR}/share/lammps/frc_files
+MSI2LMP_LIBRARY="${BASEDIR}/share/lammps/frc_files"
-export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY
+export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY PATH
 
 exec "${BASEDIR}/bin/${EXENAME}" "$@"

cmake/presets/all_off.cmake

@@ -28,6 +28,7 @@ set(ALL_PACKAGES
   DRUDE
   ELECTRODE
   EFF
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -60,6 +61,7 @@ set(ALL_PACKAGES
   ML-QUIP
   ML-RANN
   ML-SNAP
+  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE

cmake/presets/all_on.cmake

@@ -30,6 +30,7 @@ set(ALL_PACKAGES
   DRUDE
   ELECTRODE
   EFF
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -62,6 +63,7 @@ set(ALL_PACKAGES
   ML-QUIP
   ML-RANN
   ML-SNAP
+  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE

cmake/presets/mingw-cross.cmake

@@ -24,6 +24,7 @@ set(WIN_PACKAGES
   DRUDE
   ELECTRODE
   EFF
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -50,6 +51,7 @@ set(WIN_PACKAGES
   ML-POD
   ML-RANN
   ML-SNAP
+  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE

cmake/presets/most.cmake

@@ -26,6 +26,7 @@ set(ALL_PACKAGES
   DRUDE
   EFF
   ELECTRODE
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -45,6 +46,7 @@ set(ALL_PACKAGES
   ML-IAP
   ML-POD
   ML-SNAP
+  ML-UF3
   MOFFF
   MOLECULE
   OPENMP

cmake/presets/windows.cmake

@@ -22,6 +22,7 @@ set(WIN_PACKAGES
   DRUDE
   EFF
   ELECTRODE
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -42,6 +43,7 @@ set(WIN_PACKAGES
   ML-IAP
   ML-POD
   ML-SNAP
+  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE

doc/src/Commands_bond.rst

@@ -27,7 +27,7 @@ OPT.
 
    * :doc:`none <bond_none>`
    * :doc:`zero <bond_zero>`
-   * :doc:`hybrid <bond_hybrid>`
+   * :doc:`hybrid (k) <bond_hybrid>`
    *
    *
    *
@@ -72,7 +72,7 @@ OPT.
 
    * :doc:`none <angle_none>`
    * :doc:`zero <angle_zero>`
-   * :doc:`hybrid (k) <angle_hybrid>`
+   * :doc:`hybrid <angle_hybrid>`
    *
    *
    *

doc/src/Commands_pair.rst

@@ -25,16 +25,16 @@ OPT.
 
    * :doc:`none <pair_none>`
    * :doc:`zero <pair_zero>`
-   * :doc:`hybrid (k) <pair_hybrid>`
+   * :doc:`hybrid (ko) <pair_hybrid>`
-   * :doc:`hybrid/overlay (k) <pair_hybrid>`
+   * :doc:`hybrid/molecular (o) <pair_hybrid>`
-   * :doc:`hybrid/scaled <pair_hybrid>`
+   * :doc:`hybrid/overlay (ko) <pair_hybrid>`
+   * :doc:`hybrid/scaled (o) <pair_hybrid>`
    * :doc:`kim <pair_kim>`
    * :doc:`list <pair_list>`
    * :doc:`tracker <pair_tracker>`
    *
    *
    *
-   *
    * :doc:`adp (ko) <pair_adp>`
    * :doc:`agni (o) <pair_agni>`
    * :doc:`aip/water/2dm (t) <pair_aip_water_2dm>`
@@ -94,9 +94,10 @@ OPT.
    * :doc:`coul/wolf (ko) <pair_coul>`
    * :doc:`coul/wolf/cs <pair_cs>`
    * :doc:`dpd (giko) <pair_dpd>`
-   * :doc:`dpd/fdt <pair_dpd_fdt>`
+   * :doc:`dpd/coul/slater/long (g) <pair_dpd_coul_slater_long>`
    * :doc:`dpd/ext (ko) <pair_dpd_ext>`
    * :doc:`dpd/ext/tstat (ko) <pair_dpd_ext>`
+   * :doc:`dpd/fdt <pair_dpd_fdt>`
    * :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
    * :doc:`dpd/tstat (gko) <pair_dpd>`
    * :doc:`dsmc <pair_dsmc>`
@@ -269,7 +270,7 @@ OPT.
    * :doc:`smd/ulsph <pair_smd_ulsph>`
    * :doc:`smtbq <pair_smtbq>`
    * :doc:`snap (ik) <pair_snap>`
-   * :doc:`soft (go) <pair_soft>`
+   * :doc:`soft (gko) <pair_soft>`
    * :doc:`sph/heatconduction (g) <pair_sph_heatconduction>`
    * :doc:`sph/idealgas <pair_sph_idealgas>`
    * :doc:`sph/lj (g) <pair_sph_lj>`
@@ -303,6 +304,7 @@ OPT.
    * :doc:`tip4p/long/soft (o) <pair_fep_soft>`
    * :doc:`tri/lj <pair_tri_lj>`
    * :doc:`ufm (got) <pair_ufm>`
+   * :doc:`uf3 (k) <pair_uf3>`
    * :doc:`vashishta (gko) <pair_vashishta>`
    * :doc:`vashishta/table (o) <pair_vashishta>`
    * :doc:`wf/cut <pair_wf_cut>`

doc/src/Packages_details.rst

@@ -52,6 +52,7 @@ page gives those details.
    * :ref:`DRUDE <PKG-DRUDE>`
    * :ref:`EFF <PKG-EFF>`
    * :ref:`ELECTRODE <PKG-ELECTRODE>`
+   * :ref:`EXTRA-COMMAND <PKG-EXTRA-COMMAND>`
    * :ref:`EXTRA-COMPUTE <PKG-EXTRA-COMPUTE>`
    * :ref:`EXTRA-DUMP <PKG-EXTRA-DUMP>`
    * :ref:`EXTRA-FIX <PKG-EXTRA-FIX>`
@@ -84,6 +85,7 @@ page gives those details.
    * :ref:`ML-QUIP <PKG-ML-QUIP>`
    * :ref:`ML-RANN <PKG-ML-RANN>`
    * :ref:`ML-SNAP <PKG-ML-SNAP>`
+   * :ref:`ML-UF3 <PKG-ML-UF3>`
    * :ref:`MOFFF <PKG-MOFFF>`
    * :ref:`MOLECULE <PKG-MOLECULE>`
    * :ref:`MOLFILE <PKG-MOLFILE>`
@@ -677,7 +679,12 @@ DPD-BASIC package
 Pair styles for the basic dissipative particle dynamics (DPD) method
 and DPD thermostatting.
 
-**Author:** Kurt Smith (U Pittsburgh), Martin Svoboda, Martin Lisal (ICPF and UJEP)
+Pair style :doc:`dpd/coul/slater/long <pair_dpd_coul_slater_long>` also
+includes smeared charges for coulomb interactions and thus requires the
+:ref:`KSPACE <PKG-KSPACE>` package to be installed to handle the long-range
+Coulomb part of the interactions.
+
+**Authors:** Kurt Smith (U Pittsburgh), Martin Svoboda, Martin Lisal (ICPF and UJEP), Eddy Barraud (IFPEN)
 
 **Supporting info:**
 
@@ -686,6 +693,7 @@ and DPD thermostatting.
 * :doc:`pair_style dpd/tstat <pair_dpd>`
 * :doc:`pair_style dpd/ext <pair_dpd_ext>`
 * :doc:`pair_style dpd/ext/tstat <pair_dpd_ext>`
+* :doc:`pair_style dpd/coul/slater/long <pair_dpd_coul_slater_long>`
 * examples/PACKAGES/dpd-basic
 
 ----------
@@ -887,6 +895,22 @@ This package has :ref:`specific installation instructions <electrode>` on the
 
 ----------
 
+.. _PKG-EXTRA-COMMAND:
+
+EXTRA-COMMAND package
+---------------------
+
+**Contents:**
+
+Additional command styles that are less commonly used.
+
+**Supporting info:**
+
+* src/EXTRA-COMMAND: filenames -> commands
+* :doc:`general commands <Commands_all>`
+
+----------
+
 .. _PKG-EXTRA-COMPUTE:
 
 EXTRA-COMPUTE package
@@ -1926,6 +1950,31 @@ computes which analyze attributes of the potential.
 
 ----------
 
+.. _PKG-ML-UF3:
+
+ML-UF3 package
+--------------
+
+**Contents:**
+
+A pair style for the ultra-fast force field potentials (UF3). UF3 is a
+methodology for deriving a highly accurate classical potential which is
+fast to evaluate and is fitted to a large archives of quantum mechanical
+(DFT) data.  The use of b-spline basis set in UF3 enables the rapid
+evaluation of 2-body and 3-body interactions.
+
+**Authors:** Ajinkya C Hire (University of Florida),
+Hendrik Krass (University of Constance),
+Matthias Rupp (Luxembourg Institute of Science and Technology),
+Richard Hennig (University of Florida)
+
+**Supporting info:**
+
+* src/ML-UF3: filenames -> commands
+* :doc:`pair_style uf3 <pair_uf3>`
+* examples/uf3
+* https://github.com/uf3/uf3
+
 .. _PKG-MOFFF:
 
 MOFFF package

doc/src/Packages_list.rst

@@ -158,6 +158,11 @@ whether an extra library is needed to build and use the package:
      - :doc:`fix electrode/conp <fix_electrode>`
      - PACKAGES/electrode
      - no
+   * - :ref:`EXTRA-COMMAND <PKG-EXTRA-COMMAND>`
+     - additional command styles
+     - :doc:`general commands <Commands_all>`
+     - n/a
+     - no
    * - :ref:`EXTRA-COMPUTE <PKG-EXTRA-COMPUTE>`
      - additional compute styles
      - :doc:`compute <compute>`
@@ -318,6 +323,11 @@ whether an extra library is needed to build and use the package:
      - :doc:`pair_style snap <pair_snap>`
      - snap
      - no
+   * - :ref:`ML-UF3 <PKG-ML-UF3>`
+     - quantum-fitted ultra fast potentials
+     - :doc:`pair_style uf3 <pair_uf3>`
+     - PACKAGES/uf3
+     - no
    * - :ref:`MOFFF <PKG-MOFFF>`
      - styles for `MOF-FF <MOFplus_>`_ force field
      - :doc:`pair_style buck6d/coul/gauss <pair_buck6d_coul_gauss>`

doc/src/Tools.rst

@@ -728,8 +728,8 @@ 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 40 x86\_64 using GCC 14 and Clang 17, Qt version 5.15LTS
-- Fedora Linux 38 x86\_64 using GCC 13, Qt version 6.5LTS
+- Fedora Linux 40 x86\_64 using GCC 14, 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
@@ -771,22 +771,23 @@ 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),
+compilation (e.g. when LAMMPS has been compiled with traditional make).
-then the CMake configuration needs to be told where to find the LAMMPS
+Then the CMake configuration needs to be told where to find the LAMMPS
 headers and the LAMMPS library, via ``-D
 LAMMPS_SOURCE_DIR=/path/to/lammps/src``.  CMake will try to guess a
 build folder with the LAMMPS library from that path, but it can also be
 set with ``-D LAMMPS_LIB_DIR=/path/to/lammps/lib``.
 
 Rather than linking to the LAMMPS library during compilation, it is also
-possible to compile the GUI with a plugin loader library that will load
+possible to compile the GUI with a plugin loader that will load
 the LAMMPS library dynamically at runtime during the start of the GUI
 from a shared library; e.g. ``liblammps.so`` or ``liblammps.dylib`` or
 ``liblammps.dll`` (depending on the operating system).  This has the
-advantage that the LAMMPS library can be updated LAMMPS without having
+advantage that the LAMMPS library can be built from updated or modified
-to recompile the GUI.  The ABI of the LAMMPS C-library interface is very
+LAMMPS source without having to recompile the GUI.  The ABI of the
-stable and generally backward compatible.  This feature is enabled by
+LAMMPS C-library interface is very stable and generally backward
-setting ``-D LAMMPS_GUI_USE_PLUGIN=on`` and then ``-D
+compatible.  This feature is enabled by setting
+``-D LAMMPS_GUI_USE_PLUGIN=on`` and then ``-D
 LAMMPS_PLUGINLIB_DIR=/path/to/lammps/plugin/loader``. Typically, this
 would be the ``examples/COUPLE/plugin`` folder of the LAMMPS
 distribution.
@@ -798,8 +799,8 @@ macOS
 """""
 
 When building on macOS, the build procedure will try to manufacture a
-drag-n-drop installer, LAMMPS-macOS-multiarch.dmg, when using the 'dmg'
+drag-n-drop installer, ``LAMMPS-macOS-multiarch.dmg``, when using the
-target (i.e. ``cmake --build <build dir> --target dmg`` or ``make dmg``.
+'dmg' target (i.e. ``cmake --build <build dir> --target dmg`` or ``make dmg``.
 
 To build multi-arch executables that will run on both, arm64 and x86_64
 architectures natively, it is necessary to set the CMake variable ``-D
@@ -839,11 +840,11 @@ and LAMMPS GUI can be launched from anywhere from the command line.
 The standard CMake build procedure can be applied and the
 ``mingw-cross.cmake`` preset used. By using ``mingw64-cmake`` the CMake
 command will automatically include a suitable CMake toolset file (the
-regular cmake command can be used after that).  After building the
+regular cmake command can be used after that to modify the configuration
-libraries and executables, you can build the target 'zip'
+settings, if needed).  After building the libraries and executables,
-(i.e. ``cmake --build <build dir> --target zip`` or ``make zip``
+you can build the target 'zip' (i.e. ``cmake --build <build dir> --target zip``
-to stage all installed files into a LAMMPS_GUI folder and then
+or ``make zip`` to stage all installed files into a LAMMPS_GUI folder
-run a script to copy all required dependencies, some other files,
+and then run a script to copy all required dependencies, some other files,
 and create a zip file from it.
 
 Linux

doc/src/fix_deform.rst

@@ -64,6 +64,8 @@ Syntax
                  effectively an engineering shear strain rate
            *erate* value = R
              R = engineering shear strain rate (1/time units)
+           *erate/rescale* value = R (ONLY available in :doc:`fix deform/pressure <fix_deform_pressure>` command)
+             R = engineering shear strain rate (1/time units)
            *trate* value = R
              R = true shear strain rate (1/time units)
            *wiggle* values = A Tp

doc/src/fix_sgcmc.rst

@@ -15,7 +15,7 @@ Syntax
 * every_nsteps = number of MD steps between MC cycles
 * swap_fraction = fraction of a full MC cycle carried out at each call (a value of 1.0 will perform as many trial moves as there are atoms)
 * temperature = temperature that enters Boltzmann factor in Metropolis criterion (usually the same as MD temperature)
-* deltamu = chemical potential difference(s) (`N-1` values must be provided, with `N` being the number of elements)
+* deltamu = `N-1` chemical potential differences :math:`\mu_1-\mu_2, \ldots, \mu_1-\mu_N` (`N` is the number of atom types)
 * Zero or more keyword/value pairs may be appended to fix definition line:
 
   .. parsed-literal::
@@ -23,7 +23,7 @@ Syntax
      keyword = *variance* or *randseed* or *window_moves* or *window_size*
        *variance* kappa conc1 [conc2] ... [concN]
          kappa = variance constraint parameter
-         conc1,conc2,...  = target concentration(s) in the range 0.0-1.0 (*N-1* values must be provided, with *N* being the number of elements)
+         `c_2`, `c_3`,..., `c_N` = `N-1` target concentration fractions
        *randseed* N
          N = seed for pseudo random number generator
        *window_moves* N
@@ -90,11 +90,10 @@ the simulation, e.g., to speed up equilibration at low temperatures.
 
 ------------
 
-The parameter *deltamu* is used to set the chemical potential difference
+The parameter *deltamu* is used to set the chemical potential differences
-in the SGC MC algorithm (see Eq. 16 in :ref:`Sadigh1 <Sadigh1>`). By
+in the SGC MC algorithm (see Eq. 16 in :ref:`Sadigh1 <Sadigh1>`).
-convention it is the difference of the chemical potentials of elements
+The `N-1` differences are defined as :math:`\mu_1-\mu_2, \ldots, \mu_1-\mu_N`,
-`B`, `C` ..., with respect to element A. When the simulation includes
+where `N` is the number of atom types.
-`N` elements, `N-1` values must be specified.
 
 ------------
 
@@ -104,12 +103,12 @@ the effective average constraint in the parallel VC-SGC MC algorithm
 (parameter :math:`\delta\mu_0` in Eq. (20) of :ref:`Sadigh1
 <Sadigh1>`). The parameter *kappa* specifies the variance constraint
 (see Eqs. (20-21) in :ref:`Sadigh1 <Sadigh1>`).
-
+The parameter *conc* sets the `N-1` target atomic concentration
-The parameter *conc* sets the target concentration (parameter
+fractions (parameter :math:`c_0` in Eqs.  (20-21) of :ref:`Sadigh1 <Sadigh1>`)
-:math:`c_0` in Eqs.  (20-21) of :ref:`Sadigh1 <Sadigh1>`). The atomic
+:math:`0 \le c_2, \ldots, c_N \le 1`, with
-concentrations refer to components `B`, `C` ..., with `A` being set
+:math:`c_1 = 1 - \Sigma_{i=2}^N c_i`.
-automatically. When the simulation includes `N` elements, `N-1`
+When the simulation includes `N` atom types (elements),
-concentration values must be specified.
+`N-1` concentration values must be specified.
 
 ------------
 
@@ -143,10 +142,10 @@ components of the vector represent the following quantities:
 
 * 1 = The absolute number of accepted trial swaps during the last MC step
 * 2 = The absolute number of rejected trial swaps during the last MC step
-* 3 = The current global concentration of species *A* (= number of atoms of type 1 / total number of atoms)
+* 3 = Current global concentration `c_1` (= number of atoms of type 1 / total number of atoms)
-* 4 = The current global concentration of species *B* (= number of atoms of type 2 / total number of atoms)
+* 4 = Current global concentration `c_2` (= number of atoms of type 2 / total number of atoms)
 * ...
-* N+2: The current global concentration of species *X* (= number of atoms of type *N* / total number of atoms)
+* N+2: Current global concentration `c_N` (= number of atoms of type *N* / total number of atoms)
 
 The vector values calculated by this fix are "intensive".
 

doc/src/fix_wall_gran.rst

@@ -115,6 +115,18 @@ friction and twisting friction supported by the :doc:`pair_style granular <pair_
 supported for walls. These are discussed in greater detail on the doc
 page for :doc:`pair_style granular <pair_granular>`.
 
+.. note::
+   When *fstyle* *granular* is specified, the associated *fstyle_params* are taken as
+   those for a wall/particle interaction. For example, for the *hertz/material* normal
+   contact model with :math:`E = 960` and :math:`\nu = 0.2`, the effective Young's
+   modulus for a wall/particle interaction is computed as
+   :math:`E_{eff} = \frac{960}{2(1-0.2^2)} = 500`. Any pair coefficients defined by
+   :doc:`pair_style granular <pair_granular>` are not taken into consideration. To
+   model different wall/particle interactions for particles of different material
+   types, the user may define multiple fix wall/gran commands operating on separate
+   groups (e.g. based on particle type) each with a different wall/particle effective
+   Young's modulus.
+
 Note that you can choose a different force styles and/or different
 values for the wall/particle coefficients than for particle/particle
 interactions.  E.g. if you wish to model the wall as a different

doc/src/group2ndx.rst

@@ -34,32 +34,66 @@ Description
 Write or read a Gromacs style index file in text format that associates
 atom IDs with the corresponding group definitions. This index file can be
 used with in combination with Gromacs analysis tools or to import group
-definitions into the :doc:`fix colvars <fix_colvars>` input file. It can
+definitions into the :doc:`fix colvars <fix_colvars>` input file.
-also be used to save and restore group definitions for static groups.
+
+It can also be used to save and restore group definitions for static groups
+using the individual atom IDs. This may be important if the original
+group definition depends on a region or otherwise on the geometry and thus
+cannot be easily recreated.
+
+Another application would be to import atom groups defined for Gromacs
+simulation into LAMMPS.  When translating Gromacs topology and geometry
+data to LAMMPS.
 
 The *group2ndx* command will write group definitions to an index file.
-Without specifying any group IDs, all groups will be written to the index
+Without specifying any group IDs, all groups will be written to the
-file. When specifying group IDs, only those groups will be written to the
+index file.  When specifying group IDs, only those groups will be
-index file. In order to follow the Gromacs conventions, the group *all*
+written to the index file.  In order to follow the Gromacs conventions,
-will be renamed to *System* in the index file.
+the group *all* will be renamed to *System* in the index file.
 
-The *ndx2group* command will create of update group definitions from those
+The *ndx2group* command will create of update group definitions from
-stored in an index file. Without specifying any group IDs, all groups except
+those stored in an index file.  Without specifying any group IDs, all
-*System* will be read from the index file and the corresponding groups
+groups except *System* will be read from the index file and the
-recreated. If a group of the same name already exists, it will be completely
+corresponding groups recreated.  If a group of the same name already
-reset. When specifying group IDs, those groups, if present, will be read
+exists, it will be completely reset.  When specifying group IDs, those
-from the index file and restored.
+groups, if present, will be read from the index file and restored.
+
+File Format
+"""""""""""
+
+The file format is equivalent and compatible with what is produced by
+the `Gromacs make_ndx command <https://manual.gromacs.org/current/onlinehelp/gmx-make_ndx.html>`_.
+and follows the `Gromacs definition of an ndx file <https://manual.gromacs.org/current/reference-manual/file-formats.html#ndx>`_
+
+Each group definition begins with the group name in square brackets with
+blanks, e.g. \[ water \] and is then followed by the list of atom
+indices, which may be spread over multiple lines.  Here is a small
+example file:
+
+.. code-block:: ini
+
+   [ Oxygen ]
+   1  4  7
+   [ Hydrogen ]
+   2  3  5  6
+   8  9
+   [ Water ]
+   1 2 3 4 5 6 7 8 9
+
+The index file defines 3 groups: Oxygen, Hydrogen, and Water and the
+latter happens to be the union of the first two.
 
 ----------
 
 Restrictions
 """"""""""""
 
-This command requires that atoms have atom IDs, since this is the
+These commands require that atoms have atom IDs, since this is the
 information that is written to the index file.
 
-These commands are part of the COLVARS package.  They are only
+These commands are part of the EXTRA-COMMAND package.  They are only
-enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+enabled if LAMMPS was built with that package.  See the
+:doc:`Build package <Build_package>` page for more info.
 
 Related commands
 """"""""""""""""

doc/src/pair_dpd_coul_slater_long.rst

@@ -0,0 +1,179 @@
+.. index:: pair_style dpd/coul/slater/long
+.. index:: pair_style dpd/coul/slater/long/gpu
+
+pair_style dpd/coul/slater/long command
+=======================================
+
+Accelerator Variants: *dpd/coul/slater/long/gpu*
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style dpd/coul/slater/long T cutoff_DPD seed lambda cutoff_coul
+
+   pair_coeff I J a_IJ Gamma is_charged
+
+* T = temperature (temperature units) (dpd only)
+* cutoff_DPD = global cutoff for DPD interactions (distance units)
+* seed = random # seed (positive integer)
+* lambda = decay length of the charge (distance units)
+* cutoff_coul = real part cutoff for Coulombic interactions (distance units)
+* I,J = numeric atom types, or type labels
+* Gamma = DPD Gamma coefficient
+* is_charged (boolean) set to yes if I and J are charged beads
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style dpd/coul/slater/long 1.0 2.5 34387 0.25 3.0
+   pair_coeff 1 1 78.0 4.5 # not charged by default
+   pair_coeff 2 2 78.0 4.5 yes
+
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+Style *dpd/coul/slater/long* computes a force field for dissipative particle dynamics
+(DPD) following the exposition in :ref:`(Groot) <Groot5>` with the addition of
+electrostatic interactions. The coulombic forces in mesoscopic models
+employ potentials without explicit excluded-volume interactions.
+The goal is to prevent artificial ionic pair formation by including a charge
+distribution in the Coulomb potential, following the formulation of
+:ref:`(Melchor) <Melchor1>`:
+
+The force on bead I due to bead J is given as a sum
+of 4 terms
+
+.. math::
+
+   \vec{f}  = & (F^C + F^D + F^R + F^E) \hat{r_{ij}} \\
+   F^C      = & A w(r) \qquad \qquad \qquad \qquad \qquad r < r_c \\
+   F^D      = & - \gamma w^2(r) (\hat{r_{ij}} \bullet \vec{v}_{ij}) \qquad \qquad r < r_c \\
+   F^R      = & \sigma w(r) \alpha (\Delta t)^{-1/2} \qquad \qquad \qquad r < r_c \\
+   w(r)     = & 1 - \frac{r}{r_c} \\
+   F^E      = & \frac{Cq_iq_j}{\epsilon r^2} \left( 1- exp\left( \frac{2r_{ij}}{\lambda} \right) \left( 1 + \frac{2r_{ij}}{\lambda} \left( 1 + \frac{r_{ij}}{\lambda} \right)\right) \right)
+
+where :math:`F^C` is a conservative force, :math:`F^D` is a dissipative
+force, :math:`F^R` is a random force, and :math:`F^E` is an electrostatic force.
+:math:`\hat{r_{ij}}` is a unit vector in the direction
+:math:`r_i - r_j`, :math:`\vec{v}_{ij}` is
+the vector difference in velocities of the two atoms :math:`\vec{v}_i -
+\vec{v}_j`, :math:`\alpha` is a Gaussian random number with zero mean
+and unit variance, *dt* is the timestep size, and :math:`w(r)` is a
+weighting factor that varies between 0 and 1.  :math:`r_c` is the
+pairwise cutoff.  :math:`\sigma` is set equal to :math:`\sqrt{2 k_B T
+\gamma}`, where :math:`k_B` is the Boltzmann constant and *T* is the
+temperature parameter in the pair_style command.
+C is the same Coulomb conversion factor as in the pair_styles
+coul/cut and coul/long. In this way the Coulomb
+interaction between ions is corrected at small distances r, and
+the long-range interactions are computed either by the Ewald or the PPPM technique.
+
+
+The following parameters must be defined for each
+pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command as in
+the examples above, or in the data file or restart files read by the
+:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
+commands:
+
+* A (force units)
+* :math:`\gamma` (force/velocity units)
+* is_charged (boolean)
+
+
+.. note::
+
+   This style is the combination of :doc:`pair_style dpd <pair_dpd>` and :doc:`pair_style coul/slater/long <pair_coul_slater>`.
+
+----------
+
+.. include:: accel_styles.rst
+
+----------
+
+Mixing, shift, table, tail correction, restart, rRESPA info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+This pair style does not support mixing.  Thus, coefficients for all
+I,J pairs must be specified explicitly.
+
+This pair style does not support the :doc:`pair_modify <pair_modify>`
+shift option for the energy of the pair interaction.
+
+The :doc:`pair_modify <pair_modify>` table option is not relevant
+for this pair style.
+
+This pair style does not support the :doc:`pair_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style writes its information to :doc:`binary restart files
+<restart>`, so pair_style and pair_coeff commands do not need to be
+specified in an input script that reads a restart file.  Note that the
+user-specified random number seed is stored in the restart file, so when
+a simulation is restarted, each processor will re-initialize its random
+number generator the same way it did initially.  This means the random
+forces will be random, but will not be the same as they would have been
+if the original simulation had continued past the restart time.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run_style respa <run_style>` command.  They do not support the
+*inner*, *middle*, *outer* keywords.
+
+
+----------
+
+Restrictions
+""""""""""""
+
+This style is part of the DPD-BASIC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
+
+The default frequency for rebuilding neighbor lists is every 10 steps
+(see the :doc:`neigh_modify <neigh_modify>` command). This may be too
+infrequent since particles move rapidly and
+can overlap by large amounts.  If this setting yields a non-zero number
+of "dangerous" reneighborings (printed at the end of a simulation), you
+should experiment with forcing reneighboring more often and see if
+system energies/trajectories change.
+
+This pair style requires you to use the :doc:`comm_modify vel yes
+<comm_modify>` command so that velocities are stored by ghost atoms.
+
+This pair style also requires the long-range solvers included in the KSPACE package.
+
+
+This pair style will not restart exactly when using the
+:doc:`read_restart <read_restart>` command, though they should provide
+statistically similar results.  This is because the forces they compute
+depend on atom velocities.  See the :doc:`read_restart <read_restart>`
+command for more details.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair_style dpd <pair_dpd>`, :doc:`pair_style coul/slater/long <pair_coul_slater>`,
+:doc:`pair_coeff <pair_coeff>`, :doc:`fix nvt <fix_nh>`, :doc:`fix langevin <fix_langevin>`,
+:doc:`pair_style srp <pair_srp>`, :doc:`fix mvv/dpd <fix_mvv_dpd>`.
+
+Default
+"""""""
+
+is_charged = no
+
+----------
+
+.. _Groot5:
+
+**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
+
+.. _Melchor1:
+
+**(Melchor)** Gonzalez-Melchor, Mayoral, Velazquez, and Alejandre, J Chem Phys, 125, 224107 (2006).

doc/src/pair_granular.rst

@@ -111,7 +111,7 @@ For the *hertz* model, the normal component of force is given by:
 
    \mathbf{F}_{ne, Hertz} = k_n R_{eff}^{1/2}\delta_{ij}^{3/2} \mathbf{n}
 
-Here, :math:`R_{eff} = \frac{R_i R_j}{R_i + R_j}` is the effective
+Here, :math:`R_{eff} = R = \frac{R_i R_j}{R_i + R_j}` is the effective
 radius, denoted for simplicity as *R* from here on.  For *hertz*, the
 units of the spring constant :math:`k_n` are *force*\ /\ *length*\ \^2, or
 equivalently *pressure*\ .
@@ -120,13 +120,14 @@ For the *hertz/material* model, the force is given by:
 
 .. math::
 
-   \mathbf{F}_{ne, Hertz/material} = \frac{4}{3} E_{eff} R_{eff}^{1/2}\delta_{ij}^{3/2} \mathbf{n}
+   \mathbf{F}_{ne, Hertz/material} = \frac{4}{3} E_{eff} R^{1/2}\delta_{ij}^{3/2} \mathbf{n}
 
-Here, :math:`E_{eff} = E = \left(\frac{1-\nu_i^2}{E_i} + \frac{1-\nu_j^2}{E_j}\right)^{-1}` is the effective Young's
+Here, :math:`E_{eff} = E = \left(\frac{1-\nu_i^2}{E_i} + \frac{1-\nu_j^2}{E_j}\right)^{-1}`
-modulus, with :math:`\nu_i, \nu_j` the Poisson ratios of the particles of
+is the effective Young's modulus, with :math:`\nu_i, \nu_j` the Poisson ratios
-types *i* and *j*\ . Note that if the elastic modulus and the shear
+of the particles of types *i* and *j*. :math:`E_{eff}` is denoted as *E* from here on.
-modulus of the two particles are the same, the *hertz/material* model
+Note that if the elastic modulus and the shear modulus of the two particles are the
-is equivalent to the *hertz* model with :math:`k_n = 4/3 E_{eff}`
+same, the *hertz/material* model is equivalent to the *hertz* model with
+:math:`k_n = 4/3 E`
 
 The *dmt* model corresponds to the
 :ref:`(Derjaguin-Muller-Toporov) <DMT1975>` cohesive model, where the force
@@ -270,7 +271,8 @@ where :math:`k_n = \frac{4}{3} E_{eff}` for the *hertz/material* model. Since
 *coeff_restitution* accounts for the effective mass, effective radius, and
 pairwise overlaps (except when used with the *hooke* normal model) when calculating
 the damping coefficient, it accurately reproduces the specified coefficient of
-restitution for both monodisperse and polydisperse particle pairs.
+restitution for both monodisperse and polydisperse particle pairs.  This damping
+model is not compatible with cohesive normal models such as *JKR* or *DMT*.
 
 The total normal force is computed as the sum of the elastic and
 damping components:
@@ -441,11 +443,11 @@ discussion above. To match the Mindlin solution, one should set
 
    G_{eff} = \left(\frac{2-\nu_i}{G_i} + \frac{2-\nu_j}{G_j}\right)^{-1}
 
-where :math:`G` is the shear modulus, related to Young's modulus :math:`E`
+where :math:`G_i` is the shear modulus of a particle of type :math:`i`, related to Young's
-and Poisson's ratio :math:`\nu` by :math:`G = E/(2(1+\nu))`. This can also be
+modulus :math:`E_i` and Poisson's ratio :math:`\nu_i` by :math:`G_i = E_i/(2(1+\nu_i))`.
-achieved by specifying *NULL* for :math:`k_t`, in which case a
+This can also be achieved by specifying *NULL* for :math:`k_t`, in which case a
-normal contact model that specifies material parameters :math:`E` and
+normal contact model that specifies material parameters :math:`E_i` and
-:math:`\nu` is required (e.g. *hertz/material*, *dmt* or *jkr*\ ). In this
+:math:`\nu_i` is required (e.g. *hertz/material*, *dmt* or *jkr*\ ). In this
 case, mixing of the shear modulus for different particle types *i* and
 *j* is done according to the formula above.
 
@@ -575,7 +577,7 @@ opposite torque on each particle, according to:
 
 .. math::
 
-   \tau_{roll,i} =  R_{eff} \mathbf{n} \times \mathbf{F}_{roll}
+   \tau_{roll,i} =  R \mathbf{n} \times \mathbf{F}_{roll}
 
 .. math::
 

doc/src/pair_hybrid.rst

@@ -1,28 +1,41 @@
 .. index:: pair_style hybrid
 .. index:: pair_style hybrid/kk
+.. index:: pair_style hybrid/omp
+.. index:: pair_style hybrid/molecular
+.. index:: pair_style hybrid/molecular/omp
 .. index:: pair_style hybrid/overlay
+.. index:: pair_style hybrid/overlay/omp
 .. index:: pair_style hybrid/overlay/kk
 .. index:: pair_style hybrid/scaled
+.. index:: pair_style hybrid/scaled/omp
 
 pair_style hybrid command
 =========================
 
-Accelerator Variants: *hybrid/kk*
+Accelerator Variants: *hybrid/kk*, *hybrid/omp*
+
+pair_style hybrid/molecular command
+===================================
+
+Accelerator Variant: *hybrid/molecular/omp*
 
 pair_style hybrid/overlay command
 =================================
 
-Accelerator Variants: *hybrid/overlay/kk*
+Accelerator Variants: *hybrid/overlay/kk*, *hybrid/overlay/omp*
 
 pair_style hybrid/scaled command
 ==================================
 
+Accelerator Variant: *hybrid/scaled/omp*
+
 Syntax
 """"""
 
 .. code-block:: LAMMPS
 
    pair_style hybrid style1 args style2 args ...
+   pair_style hybrid/molecular factor1 style1 args factor2 style 2 args
    pair_style hybrid/overlay style1 args style2 args ...
    pair_style hybrid/scaled factor1 style1 args factor2 style 2 args ...
 
@@ -47,6 +60,10 @@ Examples
    pair_coeff * * tersoff Si.tersoff Si
    pair_coeff * * sw Si.sw Si
 
+   pair_style hybrid/molecular lj/cut 2.5 lj/cut 2.5
+   pair_coeff * * lj/cut 1 1.0 1.0
+   pair_coeff * * lj/cut 2 1.5 1.0
+
    variable one equal ramp(1.0,0.0)
    variable two equal 1.0-v_one
    pair_style hybrid/scaled v_one lj/cut 2.5 v_two morse 2.5
@@ -56,17 +73,26 @@ Examples
 Description
 """""""""""
 
-The *hybrid*, *hybrid/overlay*, and *hybrid/scaled* styles enable the
+The *hybrid*, *hybrid/overlay*, *hybrid/molecular*, and *hybrid/scaled*
-use of multiple pair styles in one simulation.  With the *hybrid* style,
+styles enable the use of multiple pair styles in one simulation.  With
-exactly one pair style is assigned to each pair of atom types.  With the
+the *hybrid* style, exactly one pair style is assigned to each pair of
-*hybrid/overlay* and *hybrid/scaled* styles, one or more pair styles can
+atom types.  With the *hybrid/overlay* and *hybrid/scaled* styles, one
-be assigned to each pair of atom types.  The assignment of pair styles
+or more pair styles can be assigned to each pair of atom types.  With
-to type pairs is made via the :doc:`pair_coeff <pair_coeff>` command.
+the hybrid/molecular style, pair styles are assigned to either intra-
-The major difference between the *hybrid/overlay* and *hybrid/scaled*
+or inter-molecular interactions.
-styles is that the *hybrid/scaled* adds a scale factor for each
+
-sub-style contribution to forces, energies and stresses.  Because of the
+The assignment of pair styles to type pairs is made via the
-added complexity, the *hybrid/scaled* style has more overhead and thus
+:doc:`pair_coeff <pair_coeff>` command.  The major difference between
-may be slower than *hybrid/overlay*.
+the *hybrid/overlay* and *hybrid/scaled* styles is that the
+*hybrid/scaled* adds a scale factor for each sub-style contribution to
+forces, energies and stresses.  Because of the added complexity, the
+*hybrid/scaled* style has more overhead and thus may be slower than
+*hybrid/overlay*.
+
+The *hybrid/molecular* pair style accepts *only* two sub-styles: the
+first is assigned to intra-molecular interactions (i.e. both atoms
+have the same molecule ID), the second to inter-molecular interactions
+(i.e. interacting atoms have different molecule IDs).
 
 Here are two examples of hybrid simulations.  The *hybrid* style could
 be used for a simulation of a metal droplet on a LJ surface.  The metal
@@ -476,6 +502,8 @@ the same or else LAMMPS will generate an error.
 Pair style *hybrid/scaled* currently only works for non-accelerated
 pair styles and pair styles from the OPT package.
 
+Pair style *hybrid/molecular* is not compatible with manybody potentials.
+
 When using pair styles from the GPU package they must not be listed
 multiple times.  LAMMPS will detect this and abort.
 

doc/src/pair_soft.rst

@@ -1,11 +1,12 @@
 .. index:: pair_style soft
 .. index:: pair_style soft/gpu
+.. index:: pair_style soft/kk
 .. index:: pair_style soft/omp
 
 pair_style soft command
 =======================
 
-Accelerator Variants: *soft/gpu*, *soft/omp*
+Accelerator Variants: *soft/gpu*, *soft/kk*, *soft/omp*
 
 Syntax
 """"""

doc/src/pair_style.rst

@@ -108,6 +108,7 @@ accelerated styles exist.
 
 * :doc:`none <pair_none>` - turn off pairwise interactions
 * :doc:`hybrid <pair_hybrid>` - multiple styles of pairwise interactions
+* :doc:`hybrid/molecular <pair_hybrid>` - different pair styles for intra- and inter-molecular interactions
 * :doc:`hybrid/overlay <pair_hybrid>` - multiple styles of superposed pairwise interactions
 * :doc:`hybrid/scaled <pair_hybrid>` - multiple styles of scaled superposed pairwise interactions
 * :doc:`zero <pair_zero>` - neighbor list but no interactions
@@ -171,6 +172,7 @@ accelerated styles exist.
 * :doc:`coul/wolf <pair_coul>` - Coulomb via Wolf potential
 * :doc:`coul/wolf/cs <pair_cs>` - Coulomb via Wolf potential with core/shell adjustments
 * :doc:`dpd <pair_dpd>` - dissipative particle dynamics (DPD)
+* :doc:`dpd/coul/slater/long <pair_dpd_coul_slater_long>` - dissipative particle dynamics (DPD) with electrostatic interactions
 * :doc:`dpd/ext <pair_dpd_ext>` - generalized force field for DPD
 * :doc:`dpd/ext/tstat <pair_dpd_ext>` - pairwise DPD thermostatting  with generalized force field
 * :doc:`dpd/fdt <pair_dpd_fdt>` - DPD for constant temperature and pressure
@@ -382,6 +384,7 @@ accelerated styles exist.
 * :doc:`tracker <pair_tracker>` - monitor information about pairwise interactions
 * :doc:`tri/lj <pair_tri_lj>` - LJ potential between triangles
 * :doc:`ufm <pair_ufm>` -
+* :doc:`uf3 <pair_uf3>` - UF3 machine-learning potential
 * :doc:`vashishta <pair_vashishta>` - Vashishta 2-body and 3-body potential
 * :doc:`vashishta/table <pair_vashishta>` -
 * :doc:`wf/cut <pair_wf_cut>` - Wang-Frenkel Potential for short-ranged interactions

doc/src/pair_uf3.rst

@@ -0,0 +1,213 @@
+.. index:: pair_style uf3
+.. index:: pair_style uf3/kk
+
+pair_style uf3 command
+======================
+
+Accelerator Variants: *uf3/kk*
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+    pair_style style BodyFlag
+
+* style = *uf3* or *uf3/kk*
+
+  .. parsed-literal::
+
+       BodyFlag = Indicates whether to calculate only 2-body or 2 and 3-body interactions. Possible values: 2 or 3
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+    pair_style uf3 3
+    pair_coeff * * Nb.uf3 Nb
+
+    pair_style uf3 2
+    pair_coeff * * NbSn.uf3 Nb Sn
+
+    pair_style uf3 3
+    pair_coeff * * NbSn.uf3 Nb Sn
+
+Description
+"""""""""""
+
+.. versionadded:: TBD
+
+The *uf3* style computes the :ref:`Ultra-Fast Force Fields (UF3)
+<Xie23>` potential, a machine-learning interatomic potential. In UF3,
+the total energy of the system is defined via two- and three-body
+interactions:
+
+.. math::
+
+   E & = \sum_{i,j} V_2(r_{ij}) + \sum_{i,j,k} V_3 (r_{ij},r_{ik},r_{jk}) \\
+   V_2(r_{ij}) & = \sum_{n=0}^N c_n B_n(r_{ij}) \\
+   V_3 (r_{ij},r_{ik},r_{jk}) & = \sum_{l=0}^{N_l} \sum_{m=0}^{N_m} \sum_{n=0}^{N_n} c_{l,m,n} B_l(r_{ij}) B_m(r_{ik}) B_n(r_{jk})
+
+where :math:`V_2(r_{ij})` and :math:`V_3 (r_{ij},r_{ik},r_{jk})` are the
+two- and three-body interactions, respectively. For the two-body the
+summation is over all neighbors J and for the three-body the summation
+is over all neighbors J and K of atom I within a cutoff distance
+determined from the potential files. :math:`B_n(r_{ij})` are the cubic
+b-spline basis, :math:`c_n` and :math:`c_{l,m,n}` are the machine-learned
+interaction parameters and :math:`N`, :math:`N_l`, :math:`N_m`, and
+:math:`N_n` denote the number of basis functions per spline or tensor
+spline dimension.
+
+With *uf3* style only a single pair_coeff command is used to indicate the
+UF3 LAMMPS potential file containing all the two- and three-body interactions
+followed by N additional arguments specifying the mapping of UF3 elements to
+LAMMPS atom types, where N is the number of LAMMPS atom types:
+
+* UF3 LAMMPS potential file
+* N elements names = mapping of UF3 elements to atom types
+
+As an example, if a LAMMPS simulation contains 2 atom types (elements
+'A' and 'B'), the pair_coeff command will be:
+
+.. code-block:: LAMMPS
+
+   pair_style uf3 3
+   pair_coeff * * AB.uf3 A B
+
+The AB.uf3 file should contain all two-body (A-A, A-B, B-B) and three-body
+(A-A-A, A-A-B, A-B-B, B-A-A, B-A-B, B-B-B).
+
+If a value of "2" is specified in the :code:`pair_style uf3` command,
+only the two-body potentials are needed. For 3-body interaction the
+first atom type is the central atom. We recommend using the
+:code:`generate_uf3_lammps_pots.py` script (found `here
+<https://github.com/uf3/uf3/tree/develop/lammps_plugin/scripts>`_) for
+generating the UF3 LAMMPS potential file from the UF3 JSON potentials.
+
+----------
+
+UF3 LAMMPS potential file in the *potentials* directory of the LAMMPS
+distribution have a ".uf3" suffix. The interaction block in UF3 LAMMPS potential
+file should start with :code:`#UF3 POT` and end with :code:`#` characters.
+Following shows the format of a generic 2-body and 3-body potential block in
+UF3 LAMMPS potential file-
+
+.. code-block:: LAMMPS
+
+   #UF3 POT UNITS: units DATE: POT_GEN_DATE AUTHOR: AUTHOR_NAME CITATION: CITE
+   2B ELEMENT1 ELEMENT2 LEADING_TRIM TRAILING_TRIM
+   Rij_CUTOFF NUM_OF_KNOTS
+   BSPLINE_KNOTS
+   NUM_OF_COEFF
+   COEFF
+   #
+   #UF3 POT UNITS: units DATE: POT_GEN_DATE AUTHOR: AUTHOR_NAME CITATION: CITE
+   3B ELEMENT1 ELEMENT2 ELEMENT3 LEADING_TRIM TRAILING_TRIM
+   Rjk_CUTOFF Rik_CUTOFF Rij_CUTOFF NUM_OF_KNOTS_JK NUM_OF_KNOTS_IK NUM_OF_KNOTS_IJ
+   BSPLINE_KNOTS_FOR_JK
+   BSPLINE_KNOTS_FOR_IK
+   BSPLINE_KNOTS_FOR_IJ
+   SHAPE_OF_COEFF_MATRIX[I][J][K]
+   COEFF_MATRIX[0][0][K]
+   COEFF_MATRIX[0][1][K]
+   COEFF_MATRIX[0][2][K]
+   .
+   .
+   .
+   COEFF_MATRIX[1][0][K]
+   COEFF_MATRIX[1][1][K]
+   COEFF_MATRIX[1][2][K]
+   .
+   .
+   .
+   #
+
+The second line indicates whether the block contains data for 2-body
+(:code:`2B`) or 3-body (:code:`3B`) interaction. This is followed by element
+combination interaction, :code:`LEADING_TRIM` and :code:`TRAILING_TRIM`
+number on the same line. The current implementation is only tested for
+:code:`LEADING_TRIM=0` and :code:`TRAILING_TRIM=3`.
+If other values are used LAMMPS is terminated after issuing an error message.
+The :code:`Rij_CUTOFF` sets the 2-body cutoff for the interaction described
+by the potential block. :code:`NUM_OF_KNOTS` is the number of knots
+(or the length of the knot vector) present on the very next line. The
+:code:`BSPLINE_KNOTS` line should contain all the knots in ascending order.
+:code:`NUM_OF_COEFF` is the number of coefficients in the :code:`COEFF` line.
+All the numbers in the BSPLINE_KNOTS and COEFF line should be space-separated.
+Similar to the 2-body potential block, the third line sets the cutoffs and
+length of the knots. The cutoff distance between atom-type I and J is
+:code:`Rij_CUTOFF`, atom-type I and K is :code:`Rik_CUTOFF` and between
+J and K is :code:`Rjk_CUTOFF`.
+
+.. note::
+
+   The current implementation only works for UF3 potentials with cutoff
+   distances for 3-body interactions that follows
+   :code:`2Rij_CUTOFF=2Rik_CUTOFF=Rjk_CUTOFF` relation.
+
+The :code:`BSPLINE_KNOTS_FOR_JK`, :code:`BSPLINE_KNOTS_FOR_IK`, and
+:code:`BSPLINE_KNOTS_FOR_IJ` lines (note the order) contain the knots in
+increasing order for atoms J and K, I and K, and atoms I and J
+respectively. The number of knots is defined by the
+:code:`NUM_OF_KNOTS_*` characters in the previous line.  The shape of
+the coefficient matrix is defined on the
+:code:`SHAPE_OF_COEFF_MATRIX[I][J][K]` line followed by the columns of
+the coefficient matrix, one per line, as shown above. For example, if
+the coefficient matrix has the shape of 8x8x13, then
+:code:`SHAPE_OF_COEFF_MATRIX[I][J][K]` will be :code:`8 8 13` followed
+by 64 (8x8) lines each containing 13 coefficients separated by space.
+
+----------
+
+.. include:: accel_styles.rst
+
+----------
+
+Mixing, shift, table, tail correction, restart, rRESPA info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS as described
+above from values in the potential file.
+
+This pair style does not support the :doc:`pair_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart
+files <restart>`, since it is stored in potential file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run_style respa <run_style>` command.  It does not support the
+*inner*, *middle*, *outer* keywords.
+
+Restrictions
+""""""""""""
+
+The 'uf3' pair style is part of the ML-UF3 package. It is only enabled
+if LAMMPS was built with that package. See the :doc:`Build package
+<Build_package>` page for more info.
+
+This pair style requires the :doc:`newton <newton>` setting to be "on".
+
+The UF3 LAMMPS potential file provided with LAMMPS (see the potentials
+directory) are parameterized for metal :doc:`units <units>`.
+
+The single() function of 'uf3' pair style only return the 2-body
+interaction energy.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair_coeff <pair_coeff>`
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _Xie23:
+
+**(Xie23)** Xie, S.R., Rupp, M. & Hennig, R.G. Ultra-fast interpretable machine-learning potentials. npj Comput Mater 9, 162 (2023). https://doi.org/10.1038/s41524-023-01092-7

doc/src/run_style.rst

@@ -327,10 +327,12 @@ Restrictions
 """"""""""""
 
 The *verlet/split* style can only be used if LAMMPS was built with the
-REPLICA package. Correspondingly the *respa/omp* style is available
+REPLICA package.  Correspondingly the *respa/omp* style is available
 only if the OPENMP package was included. See the :doc:`Build package
-<Build_package>` page for more info.  It is not compatible with
+<Build_package>` page for more info.
-kspace styles from the INTEL package.
+
+Run style *verlet/split* is not compatible with kspace styles from
+the INTEL package and it is not compatible with any TIP4P styles.
 
 Whenever using rRESPA, the user should experiment with trade-offs in
 speed and accuracy for their system, and verify that they are

doc/utils/requirements.txt

@@ -1,4 +1,4 @@
-Sphinx >= 5.3.0, <7.3
+Sphinx >= 5.3.0, <8.0
 sphinxcontrib-spelling
 sphinxcontrib-jquery
 git+https://github.com/akohlmey/sphinx-fortran@parallel-read

doc/utils/sphinx-config/false_positives.txt

@@ -1434,6 +1434,7 @@ Hendrik
 Henin
 Henkelman
 Henkes
+Hennig
 henrich
 Henrich
 Hermitian
@@ -1595,6 +1596,7 @@ interlayer
 intermolecular
 interoperable
 Interparticle
+interpretable
 interstitials
 intertube
 Intr
@@ -1817,6 +1819,7 @@ Koziol
 Kp
 kradius
 Kraker
+Krass
 Kraus
 Kremer
 Kress
@@ -2959,6 +2962,7 @@ Priya
 proc
 Proc
 procs
+proggrid
 progguide
 Prony
 ps
@@ -3271,6 +3275,7 @@ Rudranarayan
 Rudzinski
 Runge
 runtime
+Rupp
 Rutuparna
 rx
 rxd
@@ -3820,6 +3825,8 @@ uChem
 uCond
 uef
 UEF
+uf
+uf3
 ufm
 Uhlenbeck
 Ui

examples/PACKAGES/dpd-basic/README

@@ -14,3 +14,5 @@ pair styles from the DPD-BASIC package.
 4)  'dpdext_tstat' - coarse-grained SPC/E water example for 'dpd/ext/tstat' pair style
     (in.dpdext_tstat), an initial configuration (dpdext.data) and tabulated potential
     (cg_spce_table.pot) obtained by bottom-up coarse-graining of the atomistic SPC/E water.
+
+5)  'dpd_coul_slater_long' - simple example (DPD ionic fluid) for 'dpd/coul/slater/long' pair style (in.dpd_coul_slater_long).

examples/PACKAGES/dpd-basic/dpd_coul_slater_long/data.dpd_coul_slater_long

@@ -0,0 +1,779 @@
+LAMMPS data file via write_data, version 17 Apr 2024, timestep = 1394, units = lj
+
+375 atoms
+3 atom types
+
+0 5 xlo xhi
+0 5 ylo yhi
+0 5 zlo zhi
+
+Masses
+
+1 1
+2 1
+3 1
+
+PairIJ Coeffs # dpd/coul/slater/long
+
+1 1 78 4.5 yes 1
+1 2 78 4.5 yes 1
+1 3 78 4.5 yes 1
+2 2 78 4.5 no 1
+2 3 78 4.5 no 1
+3 3 78 4.5 no 1
+
+Atoms # full
+
+189 0 1 0 0.8621554018960034 1.5213257556560191 0.4064444607843129 0 1 0
+107 0 1 0 2.040249318291146 0.3862591116608294 1.8661957131854634 0 0 0
+253 0 1 0 3.511834308089607 0.7338273870464224 0.801173549802059 0 1 1
+163 0 1 0 2.303289649738226 0.6809493239075631 0.7383435796468727 0 1 0
+26 0 1 0 0.03534770106704549 1.4889933012536283 1.4815498922617432 0 0 0
+27 0 1 0 4.170525658289272 1.8438490221677797 2.1918634082517614 -1 0 0
+56 0 1 0 2.9501314702448633 2.322938987390429 0.6158870411938201 0 0 0
+167 0 1 0 1.948558457807243 0.1261294591496785 0.039492485708843984 0 1 0
+364 0 3 -1 4.538825953029656 0.2655458359259118 2.131668601530241 0 1 0
+61 0 1 0 4.645784299395809 0.3574274125207269 1.7056474795918568 -1 0 0
+222 0 1 0 4.41481966340897 2.262979887349817 1.1679075968940398 0 0 0
+332 0 2 1 3.853874714249102 0.1758912358513287 0.8799773810713412 0 1 0
+1 0 1 0 4.608301143657016 1.4090100132224024 1.218887039455649 -1 0 0
+319 0 2 1 3.732213186171727 0.981827023519373 2.3857377768158727 -1 0 0
+53 0 1 0 2.380311878254328 0.953677113042391 1.8268738776443192 0 0 0
+68 0 1 0 0.33279009298924916 1.0106375746131884 0.7038515854567269 0 0 0
+220 0 1 0 1.1094848303775686 2.378414106514282 1.4793246435196352 1 0 0
+44 0 1 0 0.12449238274832848 1.7475396894040345 0.5495194876290164 0 0 0
+55 0 1 0 0.1451415441609303 2.337329820574407 0.940744164662616 0 0 0
+362 0 3 -1 1.2987762452744613 1.8352325797868587 1.1809674941775483 0 0 0
+165 0 1 0 0.6610209400465688 2.22554349560855 1.971912177574677 0 0 0
+60 0 1 0 1.8643313870571518 0.6352678895179578 1.4416996493100478 0 0 0
+202 0 1 0 0.007896731087640774 1.5385720917803027 0.18965671583085075 0 1 0
+85 0 1 0 1.5630176980330266 1.1482985441214197 2.019916217302335 1 0 0
+73 0 1 0 0.5556133646182337 1.6170466333456652 2.101792903006452 0 0 0
+96 0 1 0 1.6611967219346682 0.07688637034882238 0.46572063062814617 0 0 1
+30 0 1 0 0.46644353751713447 1.8254820637852556 1.2380479793915407 1 0 0
+67 0 1 0 3.4270812515248483 2.350996339385886 1.77527952461483 0 0 0
+349 0 3 -1 1.7935506583370944 1.7235931740659332 0.4478371869612185 1 0 0
+132 0 1 0 4.951074988035153 1.5039089286454406 2.4219801232797398 -1 0 0
+328 0 2 1 0.8958492991096989 1.2809413147557527 1.0440931858570435 0 0 1
+161 0 1 0 4.798276598985588 0.9882558902185279 2.462987088497934 0 1 0
+185 0 1 0 0.6126520391294695 0.04940161418784647 0.6135262263024062 0 1 0
+219 0 1 0 1.647872968759676 2.305100092833184 2.0217182617222096 0 0 0
+8 0 1 0 2.8077478718165207 0.7661158156519451 1.3602857540877684 0 0 0
+69 0 1 0 2.8568644931819835 0.13340029053585767 2.106212637519767 0 0 0
+3 0 1 0 1.908450187819087 2.298808713848062 0.4221817812562634 0 0 0
+7 0 1 0 1.8799145446976495 0.9814789886011673 0.955308672406064 0 0 0
+329 0 2 1 0.9727877144189607 0.8906662949552561 1.4472553696387669 0 1 0
+174 0 1 0 3.9905681672951636 0.6401683928312465 1.0284041192891435 -1 1 0
+20 0 1 0 3.392515194191721 2.0774851454870427 0.8812446323305514 0 0 0
+57 0 1 0 4.874212056539195 0.13899230379169403 0.7199140773346149 0 0 0
+325 0 2 1 1.362093021934204 2.3422237404192465 0.6655225660551776 0 0 1
+40 0 1 0 4.306473534903154 1.7047871476017826 0.8560715024613603 0 0 0
+51 0 1 0 2.297377802384159 0.11499650506694176 1.4731005354419167 0 0 0
+54 0 1 0 2.971300335884777 1.8792385205105047 1.3973014092900102 0 0 0
+186 0 1 0 3.583414064904102 1.7542346893771112 0.35130247738019466 0 0 0
+289 0 1 0 2.5651653875350906 1.4858962835620086 0.6587351599193196 0 0 1
+75 0 1 0 3.132107705055228 0.19794042232605677 0.44488993973642094 0 0 1
+48 0 1 0 3.4384178020381717 0.7217742755424055 1.7304812232062636 0 0 0
+66 0 1 0 3.191389133037332 1.1674191637093172 1.7413707516914332 0 0 0
+52 0 1 0 1.856006413772654 1.871405713016935 1.5164995404363106 0 0 0
+158 0 1 0 3.725559226243618 1.2320067990055215 0.4240371305587515 -1 1 0
+330 0 2 1 0.4226192821951129 0.22648053650193767 0.04025715930862768 1 1 0
+359 0 3 -1 4.4476116877707925 0.8271711042623823 1.1688054720798116 0 1 0
+366 0 3 -1 0.13989896192253948 0.6502137062351493 0.845841913773404 1 1 0
+196 0 1 0 0.21878194805964699 2.4139077401885523 1.602735237996178 1 0 0
+128 0 1 0 2.474112780481313 1.5036993910540244 1.234391076605564 0 0 1
+118 0 1 0 0.1703454662324439 0.9401878407982331 0.17224714060344348 0 0 1
+43 0 1 0 3.708324777814944 2.4767443359210524 0.5791362456922102 0 0 0
+184 0 1 0 0.4061592126934206 0.22209165285150972 1.3598048859115588 0 1 0
+360 0 3 -1 1.225690366400486 0.4472136514952278 1.0864811555493794 0 1 0
+64 0 1 0 2.6116937036965266 1.793563094424563 2.091822223631947 0 0 0
+285 0 1 0 0.7747031518566616 0.24118573693540882 2.1434463705260494 0 1 0
+58 0 1 0 1.598997109049339 1.2355543729347458 1.1437352681100093 0 0 0
+257 0 1 0 0.02882436640692898 0.8179392413775496 1.6880006059524528 1 1 0
+356 0 3 -1 2.0441963785801733 1.236982129976697 2.2147135788798726 0 0 0
+100 0 1 0 3.653446945164378 0.3462603812889145 1.6428480228892703 0 0 0
+121 0 1 0 3.3427026587713 1.3818800793465942 1.0715223415915789 0 0 1
+130 0 1 0 3.3647959804349648 1.6468424783155522 2.142743574286686 0 0 1
+238 0 1 0 1.3459228411155364 0.633596613028775 2.1301210835283637 0 1 0
+211 0 1 0 0.6615598402766512 2.33271179551025 0.47581804017205676 1 0 0
+208 0 1 0 2.962020456626749 0.2159270527386094 1.30534135402314 0 1 0
+63 0 1 0 1.3612122125160733 0.010635376740000254 1.5982897032081793 0 0 0
+22 0 1 0 4.210300352056279 0.36529901441609736 0.22595511161653342 0 0 0
+355 0 3 -1 1.2042503283777344 1.597276477439138 1.9589099368399292 0 0 0
+70 0 1 0 4.378695647703822 2.2211752925991073 0.5054248018357668 0 0 0
+65 0 1 0 4.730200694542147 1.8860651406962996 1.9541188923646609 0 0 0
+182 0 1 0 0.6006579892093956 1.0766698682185656 1.8982320873119558 0 1 0
+188 0 1 0 3.968278800401347 2.2778420975676017 1.5855956915283134 -1 0 0
+35 0 1 0 2.223480574739111 2.044750380955685 1.1501174861326973 0 0 0
+6 0 1 0 4.393818207857278 0.9691596735067866 0.4973738964333318 0 0 0
+346 0 3 -1 1.799292171051204 0.9378491451956622 0.32819450450408366 0 0 0
+14 0 1 0 4.116276227278533 0.9144868046413738 1.9001996318293624 0 0 0
+15 0 1 0 4.057083687324151 1.5512296337030849 1.8388944544921122 0 0 0
+16 0 1 0 3.82411370026405 1.5506478336832812 1.2725337401183239 0 0 0
+287 0 1 0 2.6387027215894454 1.893079917045916 0.49300315071401646 0 0 1
+81 0 1 0 0.23374890251430025 0.34479122000015083 2.377074044522331 1 0 0
+114 0 1 0 2.97788308248854 0.8029642133737654 0.43679357743492564 0 0 1
+232 0 1 0 1.1637120121074183 0.7914170906883582 0.5169414304881136 1 1 1
+50 0 1 0 1.3582030484899448 1.733969902734067 2.475757370252963 0 0 -1
+79 0 1 0 4.002398001699839 2.453310546669259 2.3569732163529196 0 0 0
+74 0 1 0 2.5693171940612936 0.3236751012125613 0.052755933881527994 0 0 1
+194 0 1 0 2.8970695996535842 1.3203227830648074 2.4866087995688972 0 0 0
+133 0 1 0 2.6178632265286743 1.0115830273791913 0.19081692003348572 0 0 1
+311 0 1 0 3.3683313684704523 1.1471203834722834 0.04523595785096113 0 1 1
+115 0 1 0 0.43505007353257874 2.385803272207332 0.02841287624716582 0 0 1
+4 0 1 0 4.3073950086925725 2.400627067573385 4.56127636601268 -1 0 -1
+151 0 1 0 0.6919123879927325 2.1849820555988084 3.5078472275384267 0 0 0
+306 0 1 0 0.5589151617318056 0.058029533314856774 4.427085995859885 0 1 0
+138 0 1 0 1.7147207261520883 1.4323880737092538 3.757478681577442 0 0 0
+110 0 1 0 1.3876397037618702 1.3714565550984217 4.5219172301432895 0 0 0
+251 0 1 0 2.788428291071368 2.3409448558940977 3.4381375025566263 0 0 0
+331 0 2 1 2.838525921735314 0.09442598845901452 3.3146265769160324 0 1 0
+243 0 1 0 4.489290143790526 2.26853729359999 3.7839844553823094 0 0 0
+156 0 1 0 0.23302160032454478 1.3603287603692662 4.342729568698205 1 1 -1
+32 0 1 0 2.081389395149717 0.4938421510915584 2.707994013583073 0 0 0
+205 0 1 0 0.09940021857353744 2.408012210772126 3.2074615425616426 0 0 0
+41 0 1 0 4.323708181823033 0.4958928465474822 2.525689303250374 0 0 0
+28 0 1 0 4.717322170568759 1.0215969335342936 3.32138298357052 -1 0 -1
+322 0 2 1 2.2029274368349303 2.0230576314539634 3.254975041225457 0 0 0
+103 0 1 0 3.4039994449255992 0.5284405133705601 4.809880920488395 0 0 0
+353 0 3 -1 1.1636351711418296 1.6849823280188108 3.628904996363181 0 0 0
+295 0 1 0 2.015582444660267 2.152457218882018 4.802270482662931 0 0 0
+365 0 3 -1 0.1355221924615853 0.6843479265638512 3.832358314244189 0 0 0
+98 0 1 0 2.5146420394624114 1.4050031824562241 2.965312255745623 0 0 0
+33 0 1 0 2.3626541269063335 0.301607887792709 4.126675184172655 0 0 0
+39 0 1 0 1.0864796756700101 0.14884263883618853 3.538403788545902 0 0 -1
+343 0 2 1 1.4514575528852092 0.7274022675751877 4.022000140293159 0 1 0
+259 0 1 0 3.655779855306037 1.3576945405765304 3.834017837247726 0 0 0
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examples/PACKAGES/dpd-basic/dpd_coul_slater_long/in.dpd_coul_slater_long

@@ -0,0 +1,58 @@
+# DPD Ionic Fluid
+
+variable    T           equal 1.0
+variable    cut_DPD     equal 1.0
+variable    seed        equal 165412
+variable    lambda      equal 0.25
+variable    cut_coul    equal 2.0
+
+#-------------------------------------------------------------------------------
+# Initialize LAMMPS run for 3-d periodic
+#-------------------------------------------------------------------------------
+
+units                   lj
+boundary                p p p # periodic at all axes
+atom_style              full
+dimension    3
+
+bond_style              none
+angle_style             none
+dihedral_style          none
+improper_style          none
+
+newton on
+comm_modify vel yes # store info of ghost atoms btw processors
+
+#-------------------------------------------------------------------------------
+# Box creation and configuration
+#-------------------------------------------------------------------------------
+
+# Define pair style and coefficients
+pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
+
+read_data data.dpd_coul_slater_long
+
+# Enable long range electrostatics solver
+kspace_style    pppm       1e-04
+
+# Construct neighbors every steps
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+#-------------------------------------------------------------------------------
+# Run the simulation
+#-------------------------------------------------------------------------------
+
+thermo_style            custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
+thermo_modify norm no
+thermo                  100
+
+timestep     0.01
+run_style    verlet
+
+fix                     1 all nve
+
+run                     1000
+
+unfix           1
+

examples/PACKAGES/dpd-basic/dpd_coul_slater_long/log.19Jun24.dpd_coul_slater.g++.1

@@ -0,0 +1,147 @@
+LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-262-g0aff26705c-modified)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# DPD Ionic Fluid
+
+variable    T           equal 1.0
+variable    cut_DPD     equal 1.0
+variable    seed        equal 165412
+variable    lambda      equal 0.25
+variable    cut_coul    equal 2.0
+
+#-------------------------------------------------------------------------------
+# Initialize LAMMPS run for 3-d periodic
+#-------------------------------------------------------------------------------
+
+units                   lj
+boundary                p p p # periodic at all axes
+atom_style              full
+dimension    3
+
+bond_style              none
+angle_style             none
+dihedral_style          none
+improper_style          none
+
+newton on
+comm_modify vel yes # store info of ghost atoms btw processors
+
+#-------------------------------------------------------------------------------
+# Box creation and configuration
+#-------------------------------------------------------------------------------
+
+# Define pair style and coefficients
+pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
+pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul}
+pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul}
+pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul}
+pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul}
+pair_style dpd/coul/slater/long 1 1 165412 0.25 2
+
+read_data data.dpd_coul_slater_long
+Reading data file ...
+  orthogonal box = (0 0 0) to (5 5 5)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  375 atoms
+  reading velocities ...
+  375 velocities
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     0 = max # of 1-2 neighbors
+     0 = max # of 1-3 neighbors
+     0 = max # of 1-4 neighbors
+     1 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.003 seconds
+
+# Enable long range electrostatics solver
+kspace_style    pppm       1e-04
+
+# Construct neighbors every steps
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+#-------------------------------------------------------------------------------
+# Run the simulation
+#-------------------------------------------------------------------------------
+
+thermo_style            custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
+thermo_modify norm no
+thermo                  100
+
+timestep     0.01
+run_style    verlet
+
+fix                     1 all nve
+
+run                     1000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
+  G vector (1/distance) = 1.4828454
+  grid = 20 20 20
+  stencil order = 5
+  estimated absolute RMS force accuracy = 7.7240141e-05
+  estimated relative force accuracy = 7.7240141e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 24389 8000
+Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3
+  ghost atom cutoff = 3
+  binsize = 1.5, bins = 4 4 4
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair dpd/coul/slater/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 8.359 | 8.359 | 8.359 Mbytes
+   Step          Temp          Press          Volume         E_vdwl         E_coul         E_long         PotEng         KinEng         Fnorm           Fmax     
+         0   0.9849949      69.271905      125            4673.0443      0             -30.365103      4642.6792      552.58214      646.76798      65.851035    
+       100   1.0614027      69.794624      125            4659.0139      0             -31.906319      4627.1075      595.44692      612.94396      60.338653    
+       200   0.9422517      68.721098      125            4687.8862      0             -33.81531       4654.0709      528.6032       620.25627      62.726994    
+       300   0.8956649      69.323482      125            4721.0824      0             -33.854275      4687.2281      502.46801      670.22699      73.087908    
+       400   0.99584547     69.670416      125            4713.9086      0             -30.783633      4683.125       558.66931      607.65881      59.224652    
+       500   1.0565931      69.497816      125            4701.2584      0             -26.80545       4674.4529      592.74873      646.18907      71.398122    
+       600   1.0071523      70.26222       125            4659.2061      0             -29.98909       4629.217       565.01243      630.00244      58.264115    
+       700   1.0507355      67.920078      125            4695.255       0             -32.649209      4662.6058      589.46259      651.80459      70.573524    
+       800   0.98561942     68.279591      125            4745.7603      0             -28.98491       4716.7754      552.9325       627.14371      67.196483    
+       900   0.96470105     70.742864      125            4706.3605      0             -30.271633      4676.0889      541.19729      644.43036      79.474998    
+      1000   1.0204819      70.164419      125            4654.6077      0             -27.797433      4626.8103      572.49035      624.19728      71.825307    
+Loop time of 2.10153 on 1 procs for 1000 steps with 375 atoms
+
+Performance: 411128.483 tau/day, 475.843 timesteps/s, 178.441 katom-step/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.1779     | 1.1779     | 1.1779     |   0.0 | 56.05
+Bond    | 6.507e-05  | 6.507e-05  | 6.507e-05  |   0.0 |  0.00
+Kspace  | 0.74636    | 0.74636    | 0.74636    |   0.0 | 35.51
+Neigh   | 0.12903    | 0.12903    | 0.12903    |   0.0 |  6.14
+Comm    | 0.039726   | 0.039726   | 0.039726   |   0.0 |  1.89
+Output  | 0.00027587 | 0.00027587 | 0.00027587 |   0.0 |  0.01
+Modify  | 0.0037596  | 0.0037596  | 0.0037596  |   0.0 |  0.18
+Other   |            | 0.004451   |            |       |  0.21
+
+Nlocal:            375 ave         375 max         375 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           3613 ave        3613 max        3613 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          62354 ave       62354 max       62354 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 62354
+Ave neighs/atom = 166.27733
+Ave special neighs/atom = 0
+Neighbor list builds = 65
+Dangerous builds = 0
+
+unfix           1
+
+Total wall time: 0:00:02

examples/PACKAGES/dpd-basic/dpd_coul_slater_long/log.19Jun24.dpd_coul_slater.g++.4

@@ -0,0 +1,147 @@
+LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-262-g0aff26705c-modified)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# DPD Ionic Fluid
+
+variable    T           equal 1.0
+variable    cut_DPD     equal 1.0
+variable    seed        equal 165412
+variable    lambda      equal 0.25
+variable    cut_coul    equal 2.0
+
+#-------------------------------------------------------------------------------
+# Initialize LAMMPS run for 3-d periodic
+#-------------------------------------------------------------------------------
+
+units                   lj
+boundary                p p p # periodic at all axes
+atom_style              full
+dimension    3
+
+bond_style              none
+angle_style             none
+dihedral_style          none
+improper_style          none
+
+newton on
+comm_modify vel yes # store info of ghost atoms btw processors
+
+#-------------------------------------------------------------------------------
+# Box creation and configuration
+#-------------------------------------------------------------------------------
+
+# Define pair style and coefficients
+pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
+pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul}
+pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul}
+pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul}
+pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul}
+pair_style dpd/coul/slater/long 1 1 165412 0.25 2
+
+read_data data.dpd_coul_slater_long
+Reading data file ...
+  orthogonal box = (0 0 0) to (5 5 5)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  375 atoms
+  reading velocities ...
+  375 velocities
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     0 = max # of 1-2 neighbors
+     0 = max # of 1-3 neighbors
+     0 = max # of 1-4 neighbors
+     1 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.003 seconds
+
+# Enable long range electrostatics solver
+kspace_style    pppm       1e-04
+
+# Construct neighbors every steps
+neighbor 1.0 bin
+neigh_modify every 1 delay 0 check yes
+
+#-------------------------------------------------------------------------------
+# Run the simulation
+#-------------------------------------------------------------------------------
+
+thermo_style            custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
+thermo_modify norm no
+thermo                  100
+
+timestep     0.01
+run_style    verlet
+
+fix                     1 all nve
+
+run                     1000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
+  G vector (1/distance) = 1.4828454
+  grid = 20 20 20
+  stencil order = 5
+  estimated absolute RMS force accuracy = 7.7240141e-05
+  estimated relative force accuracy = 7.7240141e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 10469 2000
+Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3
+  ghost atom cutoff = 3
+  binsize = 1.5, bins = 4 4 4
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair dpd/coul/slater/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.208 | 7.208 | 7.209 Mbytes
+   Step          Temp          Press          Volume         E_vdwl         E_coul         E_long         PotEng         KinEng         Fnorm           Fmax     
+         0   0.9849949      69.076433      125            4673.0443      0             -30.365103      4642.6792      552.58214      613.18374      70.700582    
+       100   0.95374867     69.110009      125            4681.1097      0             -31.260804      4649.8489      535.053        629.95109      62.05418     
+       200   1.0076152      69.824904      125            4670.7458      0             -28.382203      4642.3636      565.27213      656.8501       72.049813    
+       300   1.0014752      69.666331      125            4696.454       0             -26.943577      4669.5105      561.8276       631.49861      74.737274    
+       400   0.98863876     69.731774      125            4700.7552      0             -23.816077      4676.9391      554.62634      637.74742      68.928573    
+       500   0.95782852     68.588075      125            4698.588       0             -29.249543      4669.3385      537.3418       646.31897      68.800569    
+       600   0.97443232     70.864079      125            4674.8821      0             -26.415644      4648.4664      546.65653      606.50755      78.664429    
+       700   0.98783988     68.908299      125            4692.5536      0             -28.092022      4664.4616      554.17817      638.98401      69.691814    
+       800   0.98000145     69.83977       125            4706.6365      0             -29.648365      4676.9881      549.78082      626.84362      73.133934    
+       900   1.0526251      69.466078      125            4671.9648      0             -30.941117      4641.0237      590.52269      618.1049       62.333546    
+      1000   0.98340746     69.527121      125            4728.2894      0             -31.869907      4696.4195      551.69159      630.14208      61.392611    
+Loop time of 0.928543 on 4 procs for 1000 steps with 375 atoms
+
+Performance: 930490.137 tau/day, 1076.956 timesteps/s, 403.859 katom-step/s
+98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.30761    | 0.34974    | 0.38864    |   4.9 | 37.67
+Bond    | 8.4633e-05 | 9.0539e-05 | 9.9184e-05 |   0.0 |  0.01
+Kspace  | 0.39038    | 0.42976    | 0.47215    |   4.4 | 46.28
+Neigh   | 0.033986   | 0.035576   | 0.036791   |   0.5 |  3.83
+Comm    | 0.10247    | 0.10324    | 0.10481    |   0.3 | 11.12
+Output  | 0.00024145 | 0.00027404 | 0.00036867 |   0.0 |  0.03
+Modify  | 0.0022402  | 0.0025068  | 0.0026343  |   0.3 |  0.27
+Other   |            | 0.007356   |            |       |  0.79
+
+Nlocal:          93.75 ave          96 max          93 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+Nghost:        2289.75 ave        2317 max        2271 min
+Histogram: 1 1 0 0 1 0 0 0 0 1
+Neighs:        15590.2 ave       16765 max       14540 min
+Histogram: 1 0 1 0 0 1 0 0 0 1
+
+Total # of neighbors = 62361
+Ave neighs/atom = 166.296
+Ave special neighs/atom = 0
+Neighbor list builds = 64
+Dangerous builds = 0
+
+unfix           1
+
+Total wall time: 0:00:00

examples/PACKAGES/uf3/Nb.uf3

@@ -0,0 +1 @@
+../../../potentials/Nb.uf3

examples/PACKAGES/uf3/in.uf3.Nb

@@ -0,0 +1,46 @@
+# Demonstrate UF3 W potential
+
+# # ============= Initialize simulation
+
+variable        nsteps index 100
+variable        nrep equal 4
+variable        a equal 3.3005
+units           metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable        nx equal ${nrep}
+variable        ny equal ${nrep}
+variable        nz equal ${nrep}
+
+boundary        p p p
+
+lattice         bcc $a
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+create_box      1 box
+create_atoms    1 box
+
+mass            1 92.906
+
+# # ============= set pair style
+
+pair_style      uf3 3
+pair_coeff      * * Nb.uf3 Nb
+
+
+# # ============= Setup output
+
+thermo          10
+thermo_modify   norm yes
+
+# # ============= Set up NVE run
+
+timestep        0.5e-3
+neighbor        1.0 bin
+neigh_modify    once no every 1 delay 0 check yes
+
+# # ============= Run MD
+
+velocity        all create 300.0 2367804 loop geom
+fix             1 all nve
+run             ${nsteps}

examples/PACKAGES/uf3/log.13May24.Nb.uf3.g++.1

@@ -0,0 +1,118 @@
+LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-199-g49f20229ad-modified)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# Demonstrate UF3 W potential
+
+# # ============= Initialize simulation
+
+variable        nsteps index 100
+variable        nrep equal 4
+variable        a equal 3.3005
+units           metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable        nx equal ${nrep}
+variable        nx equal 4
+variable        ny equal ${nrep}
+variable        ny equal 4
+variable        nz equal ${nrep}
+variable        nz equal 4
+
+boundary        p p p
+
+lattice         bcc $a
+lattice         bcc 3.3005
+Lattice spacing in x,y,z = 3.3005 3.3005 3.3005
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+region          box block 0 4 0 ${ny} 0 ${nz}
+region          box block 0 4 0 4 0 ${nz}
+region          box block 0 4 0 4 0 4
+create_box      1 box
+Created orthogonal box = (0 0 0) to (13.202 13.202 13.202)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 box
+Created 128 atoms
+  using lattice units in orthogonal box = (0 0 0) to (13.202 13.202 13.202)
+  create_atoms CPU = 0.000 seconds
+
+mass            1 92.906
+
+# # ============= set pair style
+
+pair_style      uf3 3
+pair_coeff      * * Nb.uf3 Nb
+Reading potential file Nb.uf3 with DATE: 2024-04-02
+
+
+# # ============= Setup output
+
+thermo          10
+thermo_modify   norm yes
+
+# # ============= Set up NVE run
+
+timestep        0.5e-3
+neighbor        1.0 bin
+neigh_modify    once no every 1 delay 0 check yes
+
+# # ============= Run MD
+
+velocity        all create 300.0 2367804 loop geom
+fix             1 all nve
+run             ${nsteps}
+run             100
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 9
+  ghost atom cutoff = 9
+  binsize = 4.5, bins = 3 3 3
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair uf3, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.376 | 3.376 | 3.376 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press     
+         0   300           -4.4256832      0             -4.3872081      90756.437    
+        10   294.36659     -4.4249607      0             -4.3872081      91006.427    
+        20   277.9021      -4.422849       0             -4.387208       91716.126    
+        30   251.88303     -4.4195119      0             -4.3872078      92789.12     
+        40   218.42803     -4.4152211      0             -4.3872076      94118.45     
+        50   180.40641     -4.4103445      0             -4.3872073      95579.009    
+        60   141.2326      -4.4053202      0             -4.3872071      97031.816    
+        70   104.54429     -4.4006146      0             -4.3872068      98332.882    
+        80   73.787889     -4.3966699      0             -4.3872066      99351.332    
+        90   51.759956     -4.3938446      0             -4.3872064      99992.934    
+       100   40.209821     -4.3923633      0             -4.3872064      100211.98    
+Loop time of 0.385575 on 1 procs for 100 steps with 128 atoms
+
+Performance: 11.204 ns/day, 2.142 hours/ns, 259.353 timesteps/s, 33.197 katom-step/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.38403    | 0.38403    | 0.38403    |   0.0 | 99.60
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00090609 | 0.00090609 | 0.00090609 |   0.0 |  0.23
+Output  | 0.00017626 | 0.00017626 | 0.00017626 |   0.0 |  0.05
+Modify  | 0.00018204 | 0.00018204 | 0.00018204 |   0.0 |  0.05
+Other   |            | 0.0002795  |            |       |  0.07
+
+Nlocal:            128 ave         128 max         128 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           1601 ave        1601 max        1601 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:        21504 ave       21504 max       21504 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 21504
+Ave neighs/atom = 168
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/PACKAGES/uf3/log.13May24.Nb.uf3.g++.4

@@ -0,0 +1,118 @@
+LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-199-g49f20229ad-modified)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# Demonstrate UF3 W potential
+
+# # ============= Initialize simulation
+
+variable        nsteps index 100
+variable        nrep equal 4
+variable        a equal 3.3005
+units           metal
+
+# generate the box and atom positions using a BCC lattice
+
+variable        nx equal ${nrep}
+variable        nx equal 4
+variable        ny equal ${nrep}
+variable        ny equal 4
+variable        nz equal ${nrep}
+variable        nz equal 4
+
+boundary        p p p
+
+lattice         bcc $a
+lattice         bcc 3.3005
+Lattice spacing in x,y,z = 3.3005 3.3005 3.3005
+region          box block 0 ${nx} 0 ${ny} 0 ${nz}
+region          box block 0 4 0 ${ny} 0 ${nz}
+region          box block 0 4 0 4 0 ${nz}
+region          box block 0 4 0 4 0 4
+create_box      1 box
+Created orthogonal box = (0 0 0) to (13.202 13.202 13.202)
+  1 by 2 by 2 MPI processor grid
+create_atoms    1 box
+Created 128 atoms
+  using lattice units in orthogonal box = (0 0 0) to (13.202 13.202 13.202)
+  create_atoms CPU = 0.001 seconds
+
+mass            1 92.906
+
+# # ============= set pair style
+
+pair_style      uf3 3
+pair_coeff      * * Nb.uf3 Nb
+Reading potential file Nb.uf3 with DATE: 2024-04-02
+
+
+# # ============= Setup output
+
+thermo          10
+thermo_modify   norm yes
+
+# # ============= Set up NVE run
+
+timestep        0.5e-3
+neighbor        1.0 bin
+neigh_modify    once no every 1 delay 0 check yes
+
+# # ============= Run MD
+
+velocity        all create 300.0 2367804 loop geom
+fix             1 all nve
+run             ${nsteps}
+run             100
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 9
+  ghost atom cutoff = 9
+  binsize = 4.5, bins = 3 3 3
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair uf3, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.351 | 3.351 | 3.351 Mbytes
+   Step          Temp          E_pair         E_mol          TotEng         Press     
+         0   300           -4.4256832      0             -4.3872081      90756.437    
+        10   294.36659     -4.4249607      0             -4.3872081      91006.427    
+        20   277.9021      -4.422849       0             -4.387208       91716.126    
+        30   251.88303     -4.4195119      0             -4.3872078      92789.12     
+        40   218.42803     -4.4152211      0             -4.3872076      94118.45     
+        50   180.40641     -4.4103445      0             -4.3872073      95579.009    
+        60   141.2326      -4.4053202      0             -4.3872071      97031.816    
+        70   104.54429     -4.4006146      0             -4.3872068      98332.882    
+        80   73.787889     -4.3966699      0             -4.3872066      99351.332    
+        90   51.759956     -4.3938446      0             -4.3872064      99992.934    
+       100   40.209821     -4.3923633      0             -4.3872064      100211.98    
+Loop time of 0.11881 on 4 procs for 100 steps with 128 atoms
+
+Performance: 36.361 ns/day, 0.660 hours/ns, 841.679 timesteps/s, 107.735 katom-step/s
+99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.10673    | 0.10875    | 0.11236    |   0.7 | 91.53
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.0057324  | 0.0093477  | 0.011375   |   2.4 |  7.87
+Output  | 0.00016629 | 0.00018236 | 0.00022483 |   0.0 |  0.15
+Modify  | 9.4948e-05 | 0.00010621 | 0.00012066 |   0.0 |  0.09
+Other   |            | 0.0004263  |            |       |  0.36
+
+Nlocal:             32 ave          32 max          32 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:           1049 ave        1049 max        1049 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:         5376 ave        5376 max        5376 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 21504
+Ave neighs/atom = 168
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

lib/gpu/lal_base_dpd.cpp

@@ -57,7 +57,7 @@ int BaseDPDT::init_atomic(const int nlocal, const int nall,
                           const double cell_size, const double gpu_split,
                           FILE *_screen, const void *pair_program,
                           const char *k_name, const int onetype,
-                          const int extra_fields) {
+                          const int extra_fields, bool need_charges) {
   screen=_screen;
 
   int gpu_nbor=0;
@@ -73,7 +73,7 @@ int BaseDPDT::init_atomic(const int nlocal, const int nall,
 
   _threads_per_atom=device->threads_per_atom();
 
-  bool charge = false;
+  bool charge = need_charges;
   bool rot = false;
   bool vel = true;
   _extra_fields = extra_fields;

lib/gpu/lal_base_dpd.h

@@ -53,7 +53,8 @@ class BaseDPD {
                   const int maxspecial, const double cell_size,
                   const double gpu_split, FILE *screen,
                   const void *pair_program, const char *k_name,
-                  const int onetype=0, const int extra_fields=0);
+                  const int onetype=0, const int extra_fields=0,
+                  bool need_charges=false);
 
   /// Estimate the overhead for GPU context changes and CPU driver
   void estimate_gpu_overhead();

lib/gpu/lal_dpd_coul_slater_long.cpp

@@ -0,0 +1,238 @@
+/***************************************************************************
+                                 lal_dpd_coul_slater_long.cpp
+                             -------------------
+                            Eddy BARRAUD (IFPEN/Sorbonne)
+
+  Class for acceleration of the dpd/coul/slater/long pair style.
+
+ __________________________________________________________________________
+    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+ __________________________________________________________________________
+
+    begin                : May 28, 2024
+    email                : eddy.barraud@outlook.fr
+ ***************************************************************************/
+
+#if defined(USE_OPENCL)
+#include "dpd_coul_slater_long_cl.h"
+#elif defined(USE_CUDART)
+const char *dpd_coul_slater_long=0;
+#else
+#include "dpd_coul_slater_long_cubin.h"
+#endif
+
+#include "lal_dpd_coul_slater_long.h"
+#include <cassert>
+namespace LAMMPS_AL {
+#define DPDCoulSlaterLongT DPDCoulSlaterLong<numtyp, acctyp>
+
+extern Device<PRECISION,ACC_PRECISION> device;
+
+template <class numtyp, class acctyp>
+DPDCoulSlaterLongT::DPDCoulSlaterLong() : BaseDPD<numtyp,acctyp>(), _allocated(false) {
+}
+
+template <class numtyp, class acctyp>
+DPDCoulSlaterLongT::~DPDCoulSlaterLong() {
+  clear();
+}
+
+template <class numtyp, class acctyp>
+int DPDCoulSlaterLongT::bytes_per_atom(const int max_nbors) const {
+  return this->bytes_per_atom_atomic(max_nbors);
+}
+
+template <class numtyp, class acctyp>
+int DPDCoulSlaterLongT::init(const int ntypes,
+               double **host_cutsq, double **host_a0,
+               double **host_gamma, double **host_sigma,
+               double **host_cut_dpd, double **host_cut_dpdsq,
+               double **host_cut_slatersq, double *host_special_lj,
+               const bool tstat_only,
+               const int nlocal, const int nall,
+               const int max_nbors, const int maxspecial,
+               const double cell_size,
+               const double gpu_split, FILE *_screen, double *host_special_coul,
+               const double qqrd2e, const double g_ewald, double lamda) {
+  const int max_shared_types=this->device->max_shared_types();
+
+  int onetype=0;
+  #ifdef USE_OPENCL
+  if (maxspecial==0)
+    for (int i=1; i<ntypes; i++)
+      for (int j=i; j<ntypes; j++)
+        if (host_cutsq[i][j]>0) {
+          if (onetype>0)
+            onetype=-1;
+          else if (onetype==0)
+            onetype=i*max_shared_types+j;
+        }
+  if (onetype<0) onetype=0;
+  #endif
+  int extra_fields = 4; // round up to accomodate quadruples of numtyp values
+                        // q
+  int success;
+  bool need_charges = true;
+  success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,
+                            gpu_split,_screen,dpd_coul_slater_long,"k_dpd_coul_slater_long",onetype, extra_fields, need_charges);
+
+  if (success!=0)
+    return success;
+
+  // If atom type constants fit in shared memory use fast kernel
+  int lj_types=ntypes;
+  shared_types=false;
+  if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) {
+    lj_types=max_shared_types;
+    shared_types=true;
+  }
+
+  // Allocate a host write buffer for data initialization
+  UCL_H_Vec<numtyp> host_write_coul(lj_types*lj_types*32,*(this->ucl_device),
+                               UCL_WRITE_ONLY);
+  sp_cl.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
+  for (int i=0; i<4; i++) {
+    host_write_coul[i]=host_special_coul[i];
+  }
+  ucl_copy(sp_cl,host_write_coul,4,false);
+
+  _lj_types=lj_types;
+  _qqrd2e=qqrd2e;
+  _g_ewald=g_ewald;
+  _lamda=lamda;
+
+  // Allocate a host write buffer for data initialization
+  UCL_H_Vec<numtyp> host_write(lj_types*lj_types*32,*(this->ucl_device),
+                               UCL_WRITE_ONLY);
+
+  for (int i=0; i<lj_types*lj_types; i++)
+    host_write[i]=0.0;
+
+  coeff.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
+  this->atom->type_pack4(ntypes,lj_types,coeff,host_write,host_a0,host_gamma,
+                         host_sigma,host_cut_dpd);
+
+  cutsq.alloc(lj_types*lj_types,*(this->ucl_device),UCL_READ_ONLY);
+  this->atom->type_pack4(ntypes,lj_types,cutsq,host_write,host_cutsq,
+                          host_cut_dpdsq,host_cut_slatersq);
+
+  double special_sqrt[4];
+  special_sqrt[0] = sqrt(host_special_lj[0]);
+  special_sqrt[1] = sqrt(host_special_lj[1]);
+  special_sqrt[2] = sqrt(host_special_lj[2]);
+  special_sqrt[3] = sqrt(host_special_lj[3]);
+
+  UCL_H_Vec<double> dview;
+  sp_lj.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
+  dview.view(host_special_lj,4,*(this->ucl_device));
+  ucl_copy(sp_lj,dview,false);
+  sp_sqrt.alloc(4,*(this->ucl_device),UCL_READ_ONLY);
+  dview.view(special_sqrt,4,*(this->ucl_device));
+  ucl_copy(sp_sqrt,dview,false);
+
+  _tstat_only = 0;
+  if (tstat_only) _tstat_only=1;
+
+  _allocated=true;
+  this->_max_bytes=coeff.row_bytes()+cutsq.row_bytes()+sp_lj.row_bytes()+sp_sqrt.row_bytes();
+  return 0;
+}
+
+template <class numtyp, class acctyp>
+void DPDCoulSlaterLongT::clear() {
+  if (!_allocated)
+    return;
+  _allocated=false;
+
+  coeff.clear();
+  cutsq.clear();
+  sp_lj.clear();
+  sp_sqrt.clear();
+  this->clear_atomic();
+}
+
+template <class numtyp, class acctyp>
+double DPDCoulSlaterLongT::host_memory_usage() const {
+  return this->host_memory_usage_atomic()+sizeof(DPDCoulSlaterLong<numtyp,acctyp>);
+}
+
+// ---------------------------------------------------------------------------
+// Calculate energies, forces, and torques
+// ---------------------------------------------------------------------------
+template <class numtyp, class acctyp>
+int DPDCoulSlaterLongT::loop(const int eflag, const int vflag) {
+
+  int nall = this->atom->nall();
+  // signal that we need to transfer extra data from the host
+
+  this->atom->extra_data_unavail();
+
+  numtyp4 *pextra=reinterpret_cast<numtyp4*>(&(this->atom->extra[0]));
+
+  int n = 0;
+  int nstride = 1;
+  for (int i = 0; i < nall; i++) {
+    int idx = n+i*nstride;
+    numtyp4 v;
+    v.x = q[i];
+    v.y = 0;
+    v.z = 0;
+    v.w = 0;
+    pextra[idx] = v;
+  }
+  this->atom->add_extra_data();
+
+  // Compute the block size and grid size to keep all cores busy
+  const int BX=this->block_size();
+  int GX=static_cast<int>(ceil(static_cast<double>(this->ans->inum())/
+                               (BX/this->_threads_per_atom)));
+
+  int ainum=this->ans->inum();
+  int nbor_pitch=this->nbor->nbor_pitch();
+  this->time_pair.start();
+  if (shared_types) {
+    this->k_pair_sel->set_size(GX,BX);
+    this->k_pair_sel->run(&this->atom->x, &this->atom->extra, &coeff, &sp_lj, &sp_cl, &sp_sqrt,
+                          &this->nbor->dev_nbor, &this->_nbor_data->begin(),
+                          &this->ans->force, &this->ans->engv, &eflag,
+                          &vflag, &ainum, &nbor_pitch, &this->atom->v, &cutsq,
+                          &this->_dtinvsqrt, &this->_seed, &this->_timestep,
+                          &_qqrd2e, &_g_ewald, &_lamda,
+                          &this->_tstat_only, &this->_threads_per_atom);
+  } else {
+    this->k_pair.set_size(GX,BX);
+    this->k_pair.run(&this->atom->x, &this->atom->extra, &coeff, &_lj_types, &sp_lj, &sp_cl, &sp_sqrt,
+                     &this->nbor->dev_nbor, &this->_nbor_data->begin(),
+                     &this->ans->force, &this->ans->engv, &eflag, &vflag,
+                     &ainum, &nbor_pitch, &this->atom->v, &cutsq, &this->_dtinvsqrt,
+                     &this->_seed, &this->_timestep,
+                     &_qqrd2e, &_g_ewald, &_lamda,
+                     &this->_tstat_only, &this->_threads_per_atom);
+  }
+  this->time_pair.stop();
+  return GX;
+}
+
+template <class numtyp, class acctyp>
+void DPDCoulSlaterLongT::update_coeff(int ntypes, double **host_a0, double **host_gamma,
+                        double **host_sigma, double **host_cut_dpd)
+{
+  UCL_H_Vec<numtyp> host_write(_lj_types*_lj_types*32,*(this->ucl_device),
+                               UCL_WRITE_ONLY);
+  this->atom->type_pack4(ntypes,_lj_types,coeff,host_write,host_a0,host_gamma,
+                         host_sigma,host_cut_dpd);
+}
+
+// ---------------------------------------------------------------------------
+// Get the extra data pointers from host
+// ---------------------------------------------------------------------------
+
+template <class numtyp, class acctyp>
+void DPDCoulSlaterLongT::get_extra_data(double *host_q) {
+  q = host_q;
+}
+
+template class DPDCoulSlaterLong<PRECISION,ACC_PRECISION>;
+}
+
+

lib/gpu/lal_dpd_coul_slater_long.cu

@@ -0,0 +1,523 @@
+// **************************************************************************
+//                                   dpd.cu
+//                             -------------------
+//                           Eddy BARRAUD (IFPEN/Sorbonne)
+//                           Trung Dac Nguyen (U Chicago)
+//
+//  Device code for acceleration of the dpd/coul/slater/long pair style
+//
+// __________________________________________________________________________
+//    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+// __________________________________________________________________________
+//
+//    begin                : May 28, 2024
+//    email                : eddy.barraud@outlook.fr
+// ***************************************************************************
+
+#if defined(NV_KERNEL) || defined(USE_HIP)
+#include "lal_aux_fun1.h"
+#ifndef _DOUBLE_DOUBLE
+_texture( pos_tex,float4);
+_texture( vel_tex,float4);
+#else
+_texture_2d( pos_tex,int4);
+_texture_2d( vel_tex,int4);
+#endif
+#else
+#define pos_tex x_
+#define vel_tex v_
+#endif
+
+#define EPSILON (numtyp)1.0e-10
+
+//#define _USE_UNIFORM_SARU_LCG
+//#define _USE_UNIFORM_SARU_TEA8
+//#define _USE_GAUSSIAN_SARU_LCG
+
+#if !defined(_USE_UNIFORM_SARU_LCG) && !defined(_USE_UNIFORM_SARU_TEA8) && !defined(_USE_GAUSSIAN_SARU_LCG)
+#define _USE_UNIFORM_SARU_LCG
+#endif
+
+// References:
+// 1. Y. Afshar, F. Schmid, A. Pishevar, S. Worley, Comput. Phys. Comm. 184 (2013), 1119–1128.
+// 2. C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput. Phys. Comm. 230 (2011), 7191-7201.
+// PRNG period = 3666320093*2^32 ~ 2^64 ~ 10^19
+
+#define LCGA 0x4beb5d59 /* Full period 32 bit LCG */
+#define LCGC 0x2600e1f7
+#define oWeylPeriod 0xda879add /* Prime period 3666320093 */
+#define oWeylOffset 0x8009d14b
+#define TWO_N32 0.232830643653869628906250e-9f /* 2^-32 */
+
+// specifically implemented for steps = 1; high = 1.0; low = -1.0
+// returns uniformly distributed random numbers u in [-1.0;1.0]
+// using the inherent LCG, then multiply u with sqrt(3) to "match"
+// with a normal random distribution.
+// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
+// Curly brackets to make variables local to the scope.
+#ifdef _USE_UNIFORM_SARU_LCG
+#define SQRT3 (numtyp)1.7320508075688772935274463
+#define saru(seed1, seed2, seed, timestep, randnum) {                         \
+  unsigned int seed3 = seed + timestep;                                       \
+  seed3^=(seed1<<7)^(seed2>>6);                                               \
+  seed2+=(seed1>>4)^(seed3>>15);                                              \
+  seed1^=(seed2<<9)+(seed3<<8);                                               \
+  seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1));                               \
+  seed2+=0x72BE1579*((seed1<<4)  ^ (seed3>>16));                              \
+  seed1^=0x3F38A6ED*((seed3>>5)  ^ (((signed int)seed2)>>22));                \
+  seed2+=seed1*seed3;                                                         \
+  seed1+=seed3 ^ (seed2>>2);                                                  \
+  seed2^=((signed int)seed2)>>17;                                             \
+  unsigned int state  = 0x79dedea3*(seed1^(((signed int)seed1)>>14));         \
+  unsigned int wstate = (state + seed2) ^ (((signed int)state)>>8);           \
+  state  = state + (wstate*(wstate^0xdddf97f5));                              \
+  wstate = 0xABCB96F7 + (wstate>>1);                                          \
+  state = LCGA*state + LCGC;                                                  \
+  wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod);   \
+  unsigned int v = (state ^ (state>>26)) + wstate;                            \
+  unsigned int s = (signed int)((v^(v>>20))*0x6957f5a7);                      \
+  randnum = SQRT3*(s*TWO_N32*(numtyp)2.0-(numtyp)1.0);                        \
+}
+#endif
+
+// specifically implemented for steps = 1; high = 1.0; low = -1.0
+// returns uniformly distributed random numbers u in [-1.0;1.0] using TEA8
+// then multiply u with sqrt(3) to "match" with a normal random distribution
+// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
+#ifdef _USE_UNIFORM_SARU_TEA8
+#define SQRT3 (numtyp)1.7320508075688772935274463
+#define k0 0xA341316C
+#define k1 0xC8013EA4
+#define k2 0xAD90777D
+#define k3 0x7E95761E
+#define delta 0x9e3779b9
+#define rounds 8
+#define saru(seed1, seed2, seed, timestep, randnum) {                         \
+  unsigned int seed3 = seed + timestep;                                       \
+  seed3^=(seed1<<7)^(seed2>>6);                                               \
+  seed2+=(seed1>>4)^(seed3>>15);                                              \
+  seed1^=(seed2<<9)+(seed3<<8);                                               \
+  seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1));                               \
+  seed2+=0x72BE1579*((seed1<<4)  ^ (seed3>>16));                              \
+  seed1^=0x3F38A6ED*((seed3>>5)  ^ (((signed int)seed2)>>22));                \
+  seed2+=seed1*seed3;                                                         \
+  seed1+=seed3 ^ (seed2>>2);                                                  \
+  seed2^=((signed int)seed2)>>17;                                             \
+  unsigned int state  = 0x79dedea3*(seed1^(((signed int)seed1)>>14));         \
+  unsigned int wstate = (state + seed2) ^ (((signed int)state)>>8);           \
+  state  = state + (wstate*(wstate^0xdddf97f5));                              \
+  wstate = 0xABCB96F7 + (wstate>>1);                                          \
+  unsigned int sum = 0;                                                       \
+  for (int i=0; i < rounds; i++) {                                            \
+    sum += delta;                                                             \
+    state += ((wstate<<4) + k0)^(wstate + sum)^((wstate>>5) + k1);            \
+    wstate += ((state<<4) + k2)^(state + sum)^((state>>5) + k3);              \
+  }                                                                           \
+  unsigned int v = (state ^ (state>>26)) + wstate;                            \
+  unsigned int s = (signed int)((v^(v>>20))*0x6957f5a7);                      \
+  randnum = SQRT3*(s*TWO_N32*(numtyp)2.0-(numtyp)1.0);                        \
+}
+#endif
+
+// specifically implemented for steps = 1; high = 1.0; low = -1.0
+// returns two uniformly distributed random numbers r1 and r2 in [-1.0;1.0],
+// and uses the polar method (Marsaglia's) to transform to a normal random value
+// This is used to compared with CPU DPD using RandMars::gaussian()
+#ifdef _USE_GAUSSIAN_SARU_LCG
+#define saru(seed1, seed2, seed, timestep, randnum) {                         \
+  unsigned int seed3 = seed + timestep;                                       \
+  seed3^=(seed1<<7)^(seed2>>6);                                               \
+  seed2+=(seed1>>4)^(seed3>>15);                                              \
+  seed1^=(seed2<<9)+(seed3<<8);                                               \
+  seed3^=0xA5366B4D*((seed2>>11) ^ (seed1<<1));                               \
+  seed2+=0x72BE1579*((seed1<<4)  ^ (seed3>>16));                              \
+  seed1^=0x3F38A6ED*((seed3>>5)  ^ (((signed int)seed2)>>22));                \
+  seed2+=seed1*seed3;                                                         \
+  seed1+=seed3 ^ (seed2>>2);                                                  \
+  seed2^=((signed int)seed2)>>17;                                             \
+  unsigned int state=0x12345678;                                              \
+  unsigned int wstate=12345678;                                               \
+  state  = 0x79dedea3*(seed1^(((signed int)seed1)>>14));                      \
+  wstate = (state + seed2) ^ (((signed int)state)>>8);                        \
+  state  = state + (wstate*(wstate^0xdddf97f5));                              \
+  wstate = 0xABCB96F7 + (wstate>>1);                                          \
+  unsigned int v, s;                                                          \
+  numtyp r1, r2, rsq;                                                         \
+  while (1) {                                                                 \
+    state = LCGA*state + LCGC;                                                \
+    wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
+    v = (state ^ (state>>26)) + wstate;                                       \
+    s = (signed int)((v^(v>>20))*0x6957f5a7);                                 \
+    r1 = s*TWO_N32*(numtyp)2.0-(numtyp)1.0;                                   \
+    state = LCGA*state + LCGC;                                                \
+    wstate = wstate + oWeylOffset+((((signed int)wstate)>>31) & oWeylPeriod); \
+    v = (state ^ (state>>26)) + wstate;                                       \
+    s = (signed int)((v^(v>>20))*0x6957f5a7);                                 \
+    r2 = s*TWO_N32*(numtyp)2.0-(numtyp)1.0;                                   \
+    rsq = r1 * r1 + r2 * r2;                                                  \
+    if (rsq < (numtyp)1.0) break;                                             \
+  }                                                                           \
+  numtyp fac = ucl_sqrt((numtyp)-2.0*log(rsq)/rsq);                           \
+  randnum = r2*fac;                                                           \
+}
+#endif
+
+__kernel void k_dpd_coul_slater_long(const __global numtyp4 *restrict x_,
+                    const __global numtyp4 *restrict extra,
+                    const __global numtyp4 *restrict coeff,
+                    const int lj_types,
+                    const __global numtyp *restrict sp_lj,
+                    const __global numtyp *restrict sp_cl_in,
+                    const __global numtyp *restrict sp_sqrt,
+                    const __global int * dev_nbor,
+                    const __global int * dev_packed,
+                    __global acctyp3 *restrict ans,
+                    __global acctyp *restrict engv,
+                    const int eflag, const int vflag, const int inum,
+                    const int nbor_pitch,
+                    const __global numtyp4 *restrict v_,
+                    const __global numtyp4 *restrict cutsq,
+                    const numtyp dtinvsqrt, const int seed,
+                    const int timestep, const numtyp qqrd2e, 
+                    const numtyp g_ewald, const numtyp lamda,
+                    const int tstat_only,
+                    const int t_per_atom) {
+  int tid, ii, offset;
+  atom_info(t_per_atom,ii,tid,offset);
+
+  __local numtyp sp_cl[4];
+  ///local_allocate_store_charge();
+
+  sp_cl[0]=sp_cl_in[0];
+  sp_cl[1]=sp_cl_in[1];
+  sp_cl[2]=sp_cl_in[2];
+  sp_cl[3]=sp_cl_in[3];
+
+  int n_stride;
+  local_allocate_store_pair();
+
+  acctyp3 f;
+  f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
+  acctyp e_coul, energy, virial[6];
+  if (EVFLAG) {
+    energy=(acctyp)0;
+    e_coul=(acctyp)0;
+    for (int i=0; i<6; i++) virial[i]=(acctyp)0;
+  }
+
+  if (ii<inum) {
+    int i, numj, nbor, nbor_end;
+    nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
+              n_stride,nbor_end,nbor);
+
+    numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
+    int itype=ix.w;
+    numtyp4 iv; fetch4(iv,i,vel_tex); //v_[i];
+    int itag=iv.w;
+
+    numtyp qtmp = extra[i].x; // q[i]
+    numtyp lamdainv = ucl_recip(lamda);
+
+    numtyp factor_dpd, factor_sqrt;
+    for ( ; nbor<nbor_end; nbor+=n_stride) {
+      ucl_prefetch(dev_packed+nbor+n_stride);
+
+      int j=dev_packed[nbor];
+      factor_dpd = sp_lj[sbmask(j)];
+      factor_sqrt = sp_sqrt[sbmask(j)];
+      numtyp factor_coul;
+      factor_coul = (numtyp)1.0-sp_cl[sbmask(j)];
+      j &= NEIGHMASK;
+
+      numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
+      int jtype=jx.w;
+      numtyp4 jv; fetch4(jv,j,vel_tex); //v_[j];
+      int jtag=jv.w;
+
+      // Compute r12
+      numtyp delx = ix.x-jx.x;
+      numtyp dely = ix.y-jx.y;
+      numtyp delz = ix.z-jx.z;
+      numtyp rsq = delx*delx+dely*dely+delz*delz;
+
+      int mtype=itype*lj_types+jtype;
+
+      // cutsq[mtype].x -> global squared cutoff
+      if (rsq<cutsq[mtype].x) {
+        numtyp r=ucl_sqrt(rsq);
+        numtyp force_dpd = (numtyp)0.0;
+        numtyp force_coul = (numtyp)0.0;
+
+        // apply DPD force if distance below DPD cutoff
+        // cutsq[mtype].y -> DPD squared cutoff
+        if (rsq < cutsq[mtype].y && r > EPSILON) {
+
+          numtyp rinv=ucl_recip(r);
+          numtyp delvx = iv.x - jv.x;
+          numtyp delvy = iv.y - jv.y;
+          numtyp delvz = iv.z - jv.z;
+          numtyp dot = delx*delvx + dely*delvy + delz*delvz;
+          numtyp wd = (numtyp)1.0 - r/coeff[mtype].w;
+
+          unsigned int tag1=itag, tag2=jtag;
+          if (tag1 > tag2) {
+            tag1 = jtag; tag2 = itag;
+          }
+
+          numtyp randnum = (numtyp)0.0;
+          saru(tag1, tag2, seed, timestep, randnum);
+
+          // conservative force = a0 * wd, or 0 if tstat only
+          // drag force = -gamma * wd^2 * (delx dot delv) / r
+          // random force = sigma * wd * rnd * dtinvsqrt;
+
+          if (!tstat_only) force_dpd = coeff[mtype].x*wd;
+          force_dpd -= coeff[mtype].y*wd*wd*dot*rinv;
+          force_dpd *= factor_dpd;
+          force_dpd += factor_sqrt*coeff[mtype].z*wd*randnum*dtinvsqrt;
+          force_dpd *=rinv;
+
+          if (EVFLAG && eflag) {
+            // unshifted eng of conservative term:
+            // evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]);
+            // eng shifted to 0.0 at cutoff
+            numtyp e = (numtyp)0.5*coeff[mtype].x*coeff[mtype].w * wd*wd;
+            energy += factor_dpd*e;
+          }
+
+        }// if cut_dpdsq
+      
+        // apply Slater electrostatic force if distance below Slater cutoff 
+        // and the two species have a slater coeff
+        // cutsq[mtype].z -> Coulombic squared cutoff
+        if ( cutsq[mtype].z != 0.0 && rsq < cutsq[mtype].z){
+          numtyp r2inv=ucl_recip(rsq);
+          numtyp _erfc;
+          numtyp grij = g_ewald * r;
+          numtyp expm2 = ucl_exp(-grij*grij);
+          numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij);
+          _erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+          numtyp prefactor = extra[j].x;
+          prefactor *= qqrd2e * cutsq[mtype].z * qtmp/r;
+          numtyp rlamdainv = r * lamdainv;
+          numtyp exprlmdainv = ucl_exp((numtyp)-2.0*rlamdainv);
+          numtyp slater_term = exprlmdainv*((numtyp)1.0 + ((numtyp)2.0*rlamdainv*((numtyp)1.0+rlamdainv)));
+          force_coul = prefactor*(_erfc + EWALD_F*grij*expm2-slater_term);
+          if (factor_coul > (numtyp)0) force_coul -= factor_coul*prefactor*((numtyp)1.0-slater_term);
+          force_coul *= r2inv;
+
+          if (EVFLAG && eflag) {
+            numtyp e_slater = ((numtyp)1.0 + rlamdainv)*exprlmdainv;
+            numtyp e = prefactor*(_erfc-e_slater);
+            if (factor_coul > (numtyp)0) e -= factor_coul*prefactor*((numtyp)1.0 - e_slater);
+            e_coul += e;
+          }
+        } // if cut_coulsq
+
+        numtyp force = force_coul + force_dpd;
+        f.x += delx*force;
+        f.y += dely*force;
+        f.z += delz*force;
+
+        if (EVFLAG && vflag) {
+          virial[0] += delx*delx*force;
+          virial[1] += dely*dely*force;
+          virial[2] += delz*delz*force;
+          virial[3] += delx*dely*force;
+          virial[4] += delx*delz*force;
+          virial[5] += dely*delz*force;
+        }
+      
+      } // if cutsq
+
+    } // for nbor
+  } // if ii
+  store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag,
+                ans,engv);
+}
+
+__kernel void k_dpd_coul_slater_long_fast(const __global numtyp4 *restrict x_,
+                         const __global numtyp4 *restrict extra,
+                         const __global numtyp4 *restrict coeff_in,
+                         const __global numtyp *restrict sp_lj_in,
+                         const __global numtyp *restrict sp_cl_in,
+                         const __global numtyp *restrict sp_sqrt_in,
+                         const __global int * dev_nbor,
+                         const __global int * dev_packed,
+                         __global acctyp3 *restrict ans,
+                         __global acctyp *restrict engv,
+                         const int eflag, const int vflag, const int inum,
+                         const int nbor_pitch,
+                         const __global numtyp4 *restrict v_,
+                         const __global numtyp4 *restrict cutsq_in,
+                         const numtyp dtinvsqrt, const int seed,
+                         const int timestep, const numtyp qqrd2e, 
+                         const numtyp g_ewald, const numtyp lamda,
+                         const int tstat_only,
+                         const int t_per_atom) {
+  int tid, ii, offset;
+  atom_info(t_per_atom,ii,tid,offset);
+
+  __local numtyp4 coeff[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
+  __local numtyp4 cutsq[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
+  __local numtyp sp_lj[4];
+  __local numtyp sp_sqrt[4];
+  /// COUL Init
+  __local numtyp sp_cl[4];
+  if (tid<4) {
+    sp_lj[tid]=sp_lj_in[tid];
+    sp_sqrt[tid]=sp_sqrt_in[tid];
+    sp_cl[tid]=sp_cl_in[tid];
+  }
+  if (tid<MAX_SHARED_TYPES*MAX_SHARED_TYPES) {
+    coeff[tid]=coeff_in[tid];
+    cutsq[tid]=cutsq_in[tid];
+  }
+
+  __syncthreads();
+  
+
+  int n_stride;
+  local_allocate_store_pair();
+
+  acctyp3 f;
+  f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0;
+  acctyp e_coul, energy, virial[6];
+  if (EVFLAG) {
+    energy=(acctyp)0;
+    e_coul=(acctyp)0;
+    for (int i=0; i<6; i++) virial[i]=(acctyp)0;
+  }
+
+  if (ii<inum) {
+    int i, numj, nbor, nbor_end;
+    nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
+              n_stride,nbor_end,nbor);
+
+    numtyp4 ix; fetch4(ix,i,pos_tex); //x_[i];
+    int iw=ix.w;
+    int itype=fast_mul((int)MAX_SHARED_TYPES,iw);
+    numtyp4 iv; fetch4(iv,i,vel_tex); //v_[i];
+    int itag=iv.w;
+
+    numtyp qtmp = extra[i].x; // q[i]
+    numtyp lamdainv = ucl_recip(lamda);
+
+    numtyp factor_dpd, factor_sqrt;
+    for ( ; nbor<nbor_end; nbor+=n_stride) {
+      ucl_prefetch(dev_packed+nbor+n_stride);
+
+      int j=dev_packed[nbor];
+      factor_dpd = sp_lj[sbmask(j)];
+      factor_sqrt = sp_sqrt[sbmask(j)];
+      numtyp factor_coul;
+      factor_coul = (numtyp)1.0-sp_cl[sbmask(j)];
+      j &= NEIGHMASK;
+
+      numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
+      numtyp4 jv; fetch4(jv,j,vel_tex); //v_[j];
+      int jtag=jv.w;
+
+      // Compute r12
+      numtyp delx = ix.x-jx.x;
+      numtyp dely = ix.y-jx.y;
+      numtyp delz = ix.z-jx.z;
+      numtyp rsq = delx*delx+dely*dely+delz*delz;
+
+      int mtype=itype+jx.w;
+      
+      /// cutsq.x = cutsq, cutsq.y = cut_dpdsq, cutsq.z = cut_slatersq
+      if (rsq<cutsq[mtype].x) {
+        numtyp r=ucl_sqrt(rsq);
+        numtyp force_dpd = (numtyp)0.0;
+        numtyp force_coul = (numtyp)0.0;
+
+        // apply DPD force if distance below DPD cutoff
+        // cutsq[mtype].y -> DPD squared cutoff
+        if (rsq < cutsq[mtype].y && r > EPSILON) {
+
+          numtyp rinv=ucl_recip(r);
+          numtyp delvx = iv.x - jv.x;
+          numtyp delvy = iv.y - jv.y;
+          numtyp delvz = iv.z - jv.z;
+          numtyp dot = delx*delvx + dely*delvy + delz*delvz;
+          numtyp wd = (numtyp)1.0 - r/coeff[mtype].w;
+
+          unsigned int tag1=itag, tag2=jtag;
+          if (tag1 > tag2) {
+            tag1 = jtag; tag2 = itag;
+          }
+
+          numtyp randnum = (numtyp)0.0;
+          saru(tag1, tag2, seed, timestep, randnum);
+
+          // conservative force = a0 * wd, or 0 if tstat only
+          // drag force = -gamma * wd^2 * (delx dot delv) / r
+          // random force = sigma * wd * rnd * dtinvsqrt;
+          /// coeff.x = a0, coeff.y = gamma, coeff.z = sigma, coeff.w = cut_dpd
+
+          if (!tstat_only) force_dpd = coeff[mtype].x*wd;
+          force_dpd -= coeff[mtype].y*wd*wd*dot*rinv;
+          force_dpd *= factor_dpd;
+          force_dpd += factor_sqrt*coeff[mtype].z*wd*randnum*dtinvsqrt;
+          force_dpd *=rinv;
+
+          if (EVFLAG && eflag) {
+            // unshifted eng of conservative term:
+            // evdwl = -a0[itype][jtype]*r * (1.0-0.5*r/cut[itype][jtype]);
+            // eng shifted to 0.0 at cutoff
+            numtyp e = (numtyp)0.5*coeff[mtype].x*coeff[mtype].w * wd*wd;
+            energy += factor_dpd*e;
+          }
+
+        }// if cut_dpdsq
+      
+        // apply Slater electrostatic force if distance below Slater cutoff 
+        // and the two species have a slater coeff
+        // cutsq[mtype].z -> Coulombic squared cutoff
+        if ( cutsq[mtype].z != 0.0 && rsq < cutsq[mtype].z){
+          numtyp r2inv=ucl_recip(rsq);
+          numtyp _erfc;
+          numtyp grij = g_ewald * r;
+          numtyp expm2 = ucl_exp(-grij*grij);
+          numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij);
+          _erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+          numtyp prefactor = extra[j].x;
+          prefactor *= qqrd2e * cutsq[mtype].z * qtmp/r;
+          numtyp rlamdainv = r * lamdainv;
+          numtyp exprlmdainv = ucl_exp((numtyp)-2.0*rlamdainv);
+          numtyp slater_term = exprlmdainv*((numtyp)1.0 + ((numtyp)2.0*rlamdainv*((numtyp)1.0+rlamdainv)));
+          force_coul = prefactor*(_erfc + EWALD_F*grij*expm2-slater_term);
+          if (factor_coul > (numtyp)0) force_coul -= factor_coul*prefactor*((numtyp)1.0-slater_term);
+          force_coul *= r2inv;
+
+          if (EVFLAG && eflag) {
+            numtyp e_slater = ((numtyp)1.0 + rlamdainv)*exprlmdainv;
+            numtyp e_sf = prefactor*(_erfc-e_slater);
+            if (factor_coul > (numtyp)0) e_sf -= factor_coul*prefactor*((numtyp)1.0 - e_slater);
+            e_coul += e_sf;
+          }
+        } // if cut_coulsq
+
+        numtyp force = force_coul + force_dpd;
+        f.x += delx*force;
+        f.y += dely*force;
+        f.z += delz*force;
+
+        if (EVFLAG && vflag) {
+          virial[0] += delx*delx*force;
+          virial[1] += dely*dely*force;
+          virial[2] += delz*delz*force;
+          virial[3] += delx*dely*force;
+          virial[4] += delx*delz*force;
+          virial[5] += dely*delz*force;
+        }
+      
+      } // if cutsq
+
+    } // for nbor
+  } // if ii
+  store_answers_q(f,energy,e_coul,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag,
+                ans,engv);
+}
+

lib/gpu/lal_dpd_coul_slater_long.h

@@ -0,0 +1,100 @@
+/***************************************************************************
+                                 lal_dpd_coul_slater_long.h
+                             -------------------
+                            Eddy BARRAUD (IFPEN/Sorbonne)
+
+  Class for acceleration of the dpd/coul/slater/long pair style.
+
+ __________________________________________________________________________
+    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+ __________________________________________________________________________
+
+    begin                : May 28, 2024
+    email                : eddy.barraud@outlook.fr
+ ***************************************************************************/
+
+#ifndef LAL_DPD_CHARGED_H
+#define LAL_DPD_CHARGED_H
+
+#include "lal_base_dpd.h"
+
+namespace LAMMPS_AL {
+
+template <class numtyp, class acctyp>
+class DPDCoulSlaterLong : public BaseDPD<numtyp, acctyp> {
+ public:
+  DPDCoulSlaterLong();
+  ~DPDCoulSlaterLong();
+
+  /// Clear any previous data and set up for a new LAMMPS run
+  /** \param max_nbors initial number of rows in the neighbor matrix
+    * \param cell_size cutoff + skin
+    * \param gpu_split fraction of particles handled by device
+    *
+    * Returns:
+    * -  0 if successful
+    * - -1 if fix gpu not found
+    * - -3 if there is an out of memory error
+    * - -4 if the GPU library was not compiled for GPU
+    * - -5 Double precision is not supported on card **/
+  int init(const int ntypes, double **host_cutsq, double **host_a0, double **host_gamma,
+           double **host_sigma, double **host_cut_dpd, double **host_cut_dpdsq,
+           double **host_cut_slatersq, double *host_special_lj, bool tstat_only, const int nlocal,
+           const int nall, const int max_nbors, const int maxspecial, const double cell_size,
+           const double gpu_split, FILE *screen, double *host_special_coul, const double qqrd2e,
+           const double g_ewald, const double lamda);
+
+  /// Clear all host and device data
+  /** \note This is called at the beginning of the init() routine **/
+  void clear();
+
+  /// Returns memory usage on device per atom
+  int bytes_per_atom(const int max_nbors) const;
+
+  /// Total host memory used by library for pair style
+  double host_memory_usage() const;
+
+  /// Update coeff if needed (tstat only)
+  void update_coeff(int ntypes, double **host_a0, double **host_gamma,
+                    double **host_sigma, double **host_cut_dpd );
+
+  void get_extra_data(double *host_q);
+
+  // --------------------------- TYPE DATA --------------------------
+
+  /// coeff.x = a0, coeff.y = gamma, coeff.z = sigma, coeff.w = cut_dpd
+  UCL_D_Vec<numtyp4> coeff;
+
+  /// cutsq.x = cutsq, cutsq.y = cut_dpdsq, cutsq.w = cut_slatersq
+  UCL_D_Vec<numtyp4> cutsq;
+
+  /// Special LJ values
+  UCL_D_Vec<numtyp> sp_lj, sp_sqrt;
+
+  /// Special Coul values [0-3]
+  UCL_D_Vec<numtyp> sp_cl;
+
+
+  /// If atom type constants fit in shared memory, use fast kernels
+  bool shared_types;
+
+  /// Number of atom types
+  int _lj_types;
+
+  /// Only used for thermostat
+  int _tstat_only;
+
+  /// Coulombic terms
+  numtyp _qqrd2e, _g_ewald, _lamda;
+
+  /// pointer to host data for atom charge
+  double *q;
+
+ private:
+  bool _allocated;
+  int loop(const int eflag, const int vflag);
+};
+
+}
+
+#endif

lib/gpu/lal_dpd_coul_slater_long_ext.cpp

@@ -0,0 +1,142 @@
+/***************************************************************************
+                                 lal_dpd_coul_slater_long_ext.cpp
+                             -------------------
+                            Eddy BARRAUD (IFPEN/Sorbonne)
+
+  Functions for LAMMPS access to dpd/coul/slater/long acceleration routines.
+
+ __________________________________________________________________________
+    This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
+ __________________________________________________________________________
+
+    begin                : May 28, 2024
+    email                : eddy.barraud@outlook.fr
+ ***************************************************************************/
+
+#include <iostream>
+#include <cassert>
+#include <cmath>
+
+#include "lal_dpd_coul_slater_long.h"
+
+using namespace std;
+using namespace LAMMPS_AL;
+
+static DPDCoulSlaterLong<PRECISION,ACC_PRECISION> DPDCMF;
+
+// ---------------------------------------------------------------------------
+// Allocate memory on host and device and copy constants to device
+// ---------------------------------------------------------------------------
+int dpd_coul_slater_long_gpu_init(const int ntypes, double **host_cutsq, double **host_a0,
+                                  double **host_gamma, double **host_sigma, double **host_cut_dpd,
+                                  double **host_cut_dpdsq, double **host_cut_slatersq,
+                                  double *special_lj, const int inum, const int nall,
+                                  const int max_nbors, const int maxspecial,
+                                  const double cell_size, int &gpu_mode, FILE *screen,
+                                  double *host_special_coul, const double qqrd2e,
+                                  const double g_ewald, const double lamda) {
+  DPDCMF.clear();
+  gpu_mode=DPDCMF.device->gpu_mode();
+  double gpu_split=DPDCMF.device->particle_split();
+  int first_gpu=DPDCMF.device->first_device();
+  int last_gpu=DPDCMF.device->last_device();
+  int world_me=DPDCMF.device->world_me();
+  int gpu_rank=DPDCMF.device->gpu_rank();
+  int procs_per_gpu=DPDCMF.device->procs_per_gpu();
+
+  DPDCMF.device->init_message(screen,"dpd",first_gpu,last_gpu);
+
+  bool message=false;
+  if (DPDCMF.device->replica_me()==0 && screen)
+    message=true;
+
+  if (message) {
+    fprintf(screen,"Initializing Device and compiling on process 0...");
+    fflush(screen);
+  }
+
+  int init_ok=0;
+  if (world_me==0)
+    init_ok=DPDCMF.init(ntypes, host_cutsq, host_a0, host_gamma, host_sigma, host_cut_dpd,
+                        host_cut_dpdsq, host_cut_slatersq, special_lj, false, inum, nall,
+                        max_nbors, maxspecial, cell_size, gpu_split, screen, host_special_coul,
+                        qqrd2e, g_ewald, lamda);
+
+  DPDCMF.device->world_barrier();
+  if (message)
+    fprintf(screen,"Done.\n");
+
+  for (int i=0; i<procs_per_gpu; i++) {
+    if (message) {
+      if (last_gpu-first_gpu==0)
+        fprintf(screen,"Initializing Device %d on core %d...",first_gpu,i);
+      else
+        fprintf(screen,"Initializing Devices %d-%d on core %d...",first_gpu,
+                last_gpu,i);
+      fflush(screen);
+    }
+    if (gpu_rank==i && world_me!=0)
+      init_ok=DPDCMF.init(ntypes, host_cutsq, host_a0, host_gamma, host_sigma, host_cut_dpd,
+                          host_cut_dpdsq, host_cut_slatersq, special_lj, false, inum, nall,
+                          max_nbors, maxspecial, cell_size, gpu_split, screen, host_special_coul,
+                          qqrd2e, g_ewald, lamda);
+
+    DPDCMF.device->serialize_init();
+    if (message)
+      fprintf(screen,"Done.\n");
+  }
+  if (message)
+    fprintf(screen,"\n");
+
+  if (init_ok==0)
+    DPDCMF.estimate_gpu_overhead();
+  return init_ok;
+}
+
+void dpd_coul_slater_long_gpu_clear() {
+  DPDCMF.clear();
+}
+
+int ** dpd_coul_slater_long_gpu_compute_n(const int ago, const int inum_full, const int nall,
+                         double **host_x, int *host_type, double *sublo,
+                         double *subhi, tagint *tag, int **nspecial,
+                         tagint **special, const bool eflag, const bool vflag,
+                         const bool eatom, const bool vatom, int &host_start,
+                         int **ilist, int **jnum, const double cpu_time, bool &success,
+                         double **host_v, const double dtinvsqrt,
+                         const int seed, const int timestep,
+                         double *boxlo, double *prd) {
+  return DPDCMF.compute(ago, inum_full, nall, host_x, host_type, sublo,
+                       subhi, tag, nspecial, special, eflag, vflag, eatom,
+                       vatom, host_start, ilist, jnum, cpu_time, success,
+                       host_v, dtinvsqrt, seed, timestep, boxlo, prd);
+}
+
+void dpd_coul_slater_long_gpu_compute(const int ago, const int inum_full, const int nall,
+                     double **host_x, int *host_type, int *ilist, int *numj,
+                     int **firstneigh, const bool eflag, const bool vflag,
+                     const bool eatom, const bool vatom, int &host_start,
+                     const double cpu_time, bool &success, tagint *tag,
+                     double **host_v, const double dtinvsqrt,
+                     const int seed, const int timestep,
+                     const int nlocal, double *boxlo, double *prd) {
+  DPDCMF.compute(ago, inum_full, nall, host_x, host_type, ilist, numj,
+                firstneigh, eflag, vflag, eatom, vatom, host_start, cpu_time, success,
+                tag, host_v, dtinvsqrt, seed, timestep, nlocal, boxlo, prd);
+}
+
+void dpd_coul_slater_long_gpu_update_coeff(int ntypes, double **host_a0, double **host_gamma,
+                          double **host_sigma, double **host_cut_dpd)
+{
+   DPDCMF.update_coeff(ntypes,host_a0,host_gamma,host_sigma, host_cut_dpd);
+}
+
+void dpd_coul_slater_long_gpu_get_extra_data(double *host_q) {
+  DPDCMF.get_extra_data(host_q);
+}
+
+double dpd_coul_slater_long_gpu_bytes() {
+  return DPDCMF.host_memory_usage();
+}
+
+

lib/plumed/Install.py

@@ -16,8 +16,10 @@ parser = ArgumentParser(prog='Install.py',
                         description="LAMMPS library build wrapper script")
 
 # settings
+# Note: must also adjust check for supported API versions in
+# fix_plumed.cpp when version changes from v2.n.x to v2.n+1.y
 
-version = "2.8.3"
+version = "2.9.1"
 mode = "static"
 
 # help message
@@ -46,7 +48,9 @@ checksums = { \
         '2.8.1' : '6bfe72ebdae63dc38a9ca27d9b0e08f8', \
         '2.8.2' : '599092b6a0aa6fff992612537ad98994', \
         '2.8.3' : '76d23cd394eba9e6530316ed1184e219', \
+        '2.8.4' : '9f59c4f9bda86fe5bef19543c295a981', \
         '2.9.0' : '661eabeebee05cf84bbf9dc23d7d5f46', \
+        '2.9.1' : 'c3b2d31479c1e9ce211719d40e9efbd7', \
         }
 
 # parse and process arguments

potentials/Nb.uf3

@@ -0,0 +1,136 @@
+#UF3 POT UNITS: metal DATE: 2024-04-02 12:18:15.359106 AUTHOR: Ajinkya_Hire CITATION:
+2B Nb Nb 0 3 nk
+8.0 31
+0.001 0.001 0.001 0.001 0.33429166666666665 0.66758333333333331 1.000875 1.3341666666666665 1.6674583333333333 2.00075 2.3340416666666663 2.6673333333333331 3.0006249999999999 3.3339166666666666 3.667208333333333 4.0004999999999997 4.3337916666666665 4.6670833333333333 5.000375 5.3336666666666668 5.6669583333333335 6.0002500000000003 6.3335416666666671 6.6668333333333338 7.0001249999999997 7.3334166666666665 7.6667083333333332 8 8 8 8
+27
+79.140244588519465 79.140244588519465 55.85833391113556 36.597903318706138 21.358952811231141 12.290000872768841 1.9593931914091953 -0.65697974623243804 -0.85177956270573463 -0.68929688239869991 -0.46787243412973262 -0.27624655899523165 -0.11912921944351409 -0.056302369393035338 -0.0049812809608429064 0.0085637634684603507 0.0034716161454604712 -0.0058751075573311978 -0.005453415412748467 -0.0015123194244718201 0.0011577919587182201 0.001583772506713282 -0.00049823976100720228 -0.0013902809146717273 0 0 0
+#
+#UF3 POT UNITS: metal DATE: 2024-04-02 12:18:15.359106 AUTHOR: Ajinkya_Hire CITATION:
+3B Nb Nb Nb 0 3 nk
+8.0 4.0 4.0 23 15 15
+0.001 0.001 0.001 0.001 0.50093749999999992 1.000875 1.5008124999999999 2.00075 2.5006874999999997 3.0006249999999999 3.5005624999999996 4.0004999999999997 4.5004375000000003 5.000375 5.5003124999999997 6.0002500000000003 6.5001875 7.0001249999999997 7.5000625000000003 8 8 8 8
+0.001 0.001 0.001 0.001 0.50087499999999996 1.00075 1.5006249999999999 2.0005000000000002 2.500375 3.0002499999999999 3.5001250000000002 4 4 4 4
+0.001 0.001 0.001 0.001 0.50087499999999996 1.00075 1.5006249999999999 2.0005000000000002 2.500375 3.0002499999999999 3.5001250000000002 4 4 4 4
+11 11 19
+-1.1790416072105636e-06 6.589114265858035e-08 2.1094970065385374e-06 4.7014910818419987e-07 8.288423734406254e-06 0.000186151370764668 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
+3.2366723157260956e-05 2.6208783380066457e-05 1.0239981836366566e-05 1.8487993936404763e-05 2.1943710009352506e-05 2.6899947783571087e-07 5.002786118380638e-06 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
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+4.1934884152796484e-05 0.0035902058234846823 0.0005824017329515572 0.01441762880686721 0.6293209695433368 0.09572421881003676 0.08586090788885907 0.031601835145355577 0.06121858995657405 0.07315778164682188 -0.0013308261229131521 0.012882908917780034 0.13273058077548822 0.2035107778991338 0.1961396131043037 -0.04170252478795313 0.0 0.0 0.0
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+#

potentials/README

@@ -118,4 +118,5 @@ sw            Stillinger-Weber potential
 tersoff       Tersoff potential
 tersoff.mod   modified Tersoff potential
 tersoff.zbl   Tersoff with ZBL core
+uf3           UF3 potential
 vashishta     Vashishta 2-body and 3-body potential

python/lammps/core.py

@@ -891,7 +891,7 @@ class lammps(object):
     # set length of vector for items that are not a scalar
     vec_dict = { 'boxlo':3, 'boxhi':3, 'sublo':3, 'subhi':3,
                  'sublo_lambda':3, 'subhi_lambda':3, 'periodicity':3,
-                 'special_lj':4, 'special_coul':4 }
+                 'special_lj':4, 'special_coul':4, 'procgrid':3 }
     if name in vec_dict:
       veclen = vec_dict[name]
     elif name == 'respa_dt':

python/lammps/pylammps.py

@@ -796,18 +796,16 @@ class PyLammps(object):
     comm = {}
     comm['nprocs'] = self.lmp.extract_setting("world_size")
     comm['nthreads'] = self.lmp.extract_setting("nthreads")
+    comm['proc_grid'] = comm['procgrid'] = self.lmp.extract_global("procgrid")
+    idx = self.lmp.extract_setting("comm_style")
+    comm['comm_style'] = ('brick', 'tiled')[idx]
+    idx = self.lmp.extract_setting("comm_style")
+    comm['comm_layout'] = ('uniform', 'nonuniform', 'irregular')[idx]
+    comm['ghost_velocity'] = self.lmp.extract_setting("ghost_velocity") == 1
 
     for line in output:
       if line.startswith("MPI library"):
         comm['mpi_version'] = line.split(':')[1].strip()
-      elif line.startswith("Comm style"):
-        parts = self._split_values(line)
-        comm['comm_style'] = self._get_pair(parts[0])[1]
-        comm['comm_layout'] = self._get_pair(parts[1])[1]
-      elif line.startswith("Processor grid"):
-        comm['proc_grid'] = [int(x) for x in self._get_pair(line)[1].split('x')]
-      elif line.startswith("Communicate velocities for ghost atoms"):
-        comm['ghost_velocity'] = (self._get_pair(line)[1] == "yes")
     return comm
 
   def _parse_element_list(self, output):

src/.gitignore

@@ -169,6 +169,17 @@
 /rann_*.cpp
 /rann_*.h
 
+/pair_uf3.cpp
+/pair_uf3.h
+/uf3_bspline_basis2.cpp
+/uf3_bspline_basis2.h
+/uf3_bspline_basis3.cpp
+/uf3_bspline_basis3.h
+/uf3_pair_bspline.cpp
+/uf3_pair_bspline.h
+/uf3_triplet_bspline.cpp
+/uf3_triplet_bspline.h
+
 /compute_test_nbl.cpp
 /compute_test_nbl.h
 /pair_multi_lucy.cpp
@@ -1706,6 +1717,8 @@
 /pair_dpd.h
 /pair_dpd_tstat.cpp
 /pair_dpd_tstat.h
+/pair_dpd_coul_slater_long.cpp
+/pair_dpd_coul_slater_long.h
 /pair_dpd_ext.cpp
 /pair_dpd_ext.h
 /pair_dpd_ext_tstat.cpp

src/BPM/bond_bpm.cpp

@@ -352,19 +352,32 @@ void BondBPM::process_broken(int i, int j)
 {
   if (!break_flag)
     error->one(FLERR, "BPM bond broke with break no option");
-  if (fix_store_local) {
-    for (int n = 0; n < nvalues; n++) (this->*pack_choice[n])(n, i, j);
 
-    fix_store_local->add_data(output_data, i, j);
+  int nlocal = atom->nlocal;
+  if (fix_store_local) {
+    // If newton off, bond can break on two procs so only record if proc owns lower tag
+    //    (BPM bond styles should sort so i -> atom with lower tag)
+    if (force->newton_bond || (i < nlocal)) {
+      for (int n = 0; n < nvalues; n++) (this->*pack_choice[n])(n, i, j);
+      fix_store_local->add_data(output_data, i, j);
+    }
   }
 
-  if (fix_update_special_bonds) fix_update_special_bonds->add_broken_bond(i, j);
+  if (fix_update_special_bonds) {
+    // If this processor owns two copies of the bond (i.e. if the domain is periodic and 1 proc thick),
+    //   skip instance where larger tag (j) owned
+    int check = 1;
+    if (i >= nlocal) {
+      int imap = atom->map(atom->tag[i]);
+      if (imap < nlocal) check = 0;
+    }
+    if (check) fix_update_special_bonds->add_broken_bond(i, j);
+  }
 
   // Manually search and remove from atom arrays
   // need to remove in case special bonds arrays rebuilt
-  int m, n;
-  int nlocal = atom->nlocal;
 
+  int m, n;
   tagint *tag = atom->tag;
   tagint **bond_atom = atom->bond_atom;
   int **bond_type = atom->bond_type;

src/BPM/compute_nbond_atom.cpp

@@ -65,14 +65,13 @@ void ComputeNBondAtom::compute_peratom()
   tagint **bond_atom = atom->bond_atom;
   int **bond_type = atom->bond_type;
 
-  int ntotal = nlocal;
-  if (force->newton) ntotal += atom->nghost;
-
   // set local nbond array
   int i, j, k;
   int *num_bond = atom->num_bond;
   int newton_bond = force->newton_bond;
 
+  int ntotal = nlocal;
+  if (newton_bond) ntotal += atom->nghost;
   for (i = 0; i < ntotal; i++) nbond[i] = 0;
 
   for (i = 0; i < nlocal; i++) {
@@ -88,7 +87,7 @@ void ComputeNBondAtom::compute_peratom()
   }
 
   // communicate ghost nbond between neighbor procs
-  if (force->newton) comm->reverse_comm(this);
+  if (newton_bond) comm->reverse_comm(this);
 
   // zero nbond of atoms not in group
   // only do this after comm since ghost contributions must be included

src/BPM/fix_update_special_bonds.cpp

@@ -100,6 +100,7 @@ void FixUpdateSpecialBonds::pre_exchange()
       n1 = nspecial[i][0];
       for (m = 0; m < n1; m++)
         if (slist[m] == tagj) break;
+      if (m == n1) error->one(FLERR, "Special bond {} {} not found", tagi, tagj);
       for (; m < n1 - 1; m++) slist[m] = slist[m + 1];
       nspecial[i][0]--;
       nspecial[i][1] = nspecial[i][2] = nspecial[i][0];
@@ -110,6 +111,7 @@ void FixUpdateSpecialBonds::pre_exchange()
       n1 = nspecial[j][0];
       for (m = 0; m < n1; m++)
         if (slist[m] == tagi) break;
+      if (m == n1) error->one(FLERR, "Special bond {} {} not found", tagi, tagj);
       for (; m < n1 - 1; m++) slist[m] = slist[m + 1];
       nspecial[j][0]--;
       nspecial[j][1] = nspecial[j][2] = nspecial[j][0];

src/COLVARS/ndx_group.cpp

@@ -1,199 +0,0 @@
-// clang-format off
-// -*- c++ -*-
-
-/* ----------------------------------------------------------------------
-   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   https://www.lammps.org/, Sandia National Laboratories
-   LAMMPS development team: developers@lammps.org
-
-   Copyright (2003) Sandia Corporation.  Under the terms of Contract
-   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-   certain rights in this software.  This software is distributed under
-   the GNU General Public License.
-
-   See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-/* ----------------------------------------------------------------------
-   Contributing author:  Axel Kohlmeyer (Temple U)
-------------------------------------------------------------------------- */
-
-#include "ndx_group.h"
-
-#include "atom.h"
-#include "comm.h"
-#include "error.h"
-#include "group.h"
-#include "tokenizer.h"
-
-using namespace LAMMPS_NS;
-static constexpr int BUFLEN = 4096;
-
-// read file until next section "name" or any next section if name == ""
-
-static std::string find_section(FILE *fp, const std::string &name)
-{
-  char linebuf[BUFLEN];
-
-  std::string pattern = "^\\s*\\[\\s+\\S+\\s+\\]\\s*$";
-  if (!name.empty())
-    pattern = fmt::format("^\\s*\\[\\s+{}\\s+\\]\\s*$",name);
-
-  fgets(linebuf,BUFLEN,fp);
-  while (!feof(fp)) {
-    if (utils::strmatch(linebuf,pattern))
-      return Tokenizer(linebuf).as_vector()[1];
-    fgets(linebuf,BUFLEN,fp);
-  }
-  return "";
-}
-
-static std::vector<tagint> read_section(FILE *fp, std::string &name)
-{
-  char linebuf[BUFLEN];
-  std::vector<tagint> tagbuf;
-  std::string pattern = "^\\s*\\[\\s+\\S+\\s+\\]\\s*$";
-
-  while (fgets(linebuf,BUFLEN,fp)) {
-    // start of new section. we are done, update "name"
-    if (utils::strmatch(linebuf,pattern)) {
-      name = Tokenizer(linebuf).as_vector()[1];
-      return tagbuf;
-    }
-    ValueTokenizer values(linebuf);
-    while (values.has_next())
-      tagbuf.push_back(values.next_tagint());
-  }
-  // set empty name to indicate end of file
-  name = "";
-  return tagbuf;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Ndx2Group::command(int narg, char **arg)
-{
-  int len;
-  bigint num;
-  FILE *fp;
-  std::string name, next;
-
-  if (narg < 1) error->all(FLERR,"Illegal ndx2group command");
-  if (atom->tag_enable == 0)
-    error->all(FLERR,"Must have atom IDs for ndx2group command");
-  if (atom->map_style == Atom::MAP_NONE)
-    error->all(FLERR,"Must have an atom map for ndx2group command");
-  if (comm->me == 0) {
-    fp = fopen(arg[0], "r");
-    if (fp == nullptr)
-      error->one(FLERR,"Cannot open index file for reading: {}",
-                                   utils::getsyserror());
-    utils::logmesg(lmp,"Reading groups from index file {}:\n",arg[0]);
-  }
-
-  if (narg == 1) {              // restore all groups
-
-    if (comm->me == 0) {
-      name = find_section(fp,"");
-      while (!name.empty()) {
-
-        // skip over group "all", which is called "System" in gromacs
-        if (name == "System") {
-          name = find_section(fp,"");
-          continue;
-        }
-
-        utils::logmesg(lmp," Processing group '{}'\n",name);
-        len = name.size()+1;
-        MPI_Bcast(&len,1,MPI_INT,0,world);
-        if (len > 1) {
-          MPI_Bcast((void *)name.c_str(),len,MPI_CHAR,0,world);
-
-          // read tags for atoms in group and broadcast
-          std::vector<tagint> tags = read_section(fp,next);
-          num = tags.size();
-          MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world);
-          MPI_Bcast((void *)tags.data(),num,MPI_LMP_TAGINT,0,world);
-          create(name,tags);
-          name = next;
-        }
-      }
-      len = -1;
-      MPI_Bcast(&len,1,MPI_INT,0,world);
-
-    } else {
-
-      while (true) {
-        MPI_Bcast(&len,1,MPI_INT,0,world);
-        if (len < 0) break;
-        if (len > 1) {
-          char *buf = new char[len];
-          MPI_Bcast(buf,len,MPI_CHAR,0,world);
-          MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world);
-          tagint *tbuf = new tagint[num];
-          MPI_Bcast(tbuf,num,MPI_LMP_TAGINT,0,world);
-          create(buf,std::vector<tagint>(tbuf,tbuf+num));
-          delete[] buf;
-          delete[] tbuf;
-        }
-      }
-    }
-
-  } else {            // restore selected groups
-
-    for (int idx=1; idx < narg; ++idx) {
-      if (comm->me == 0) {
-
-        // find named section, search from beginning of file
-        rewind(fp);
-        name = find_section(fp,arg[idx]);
-        utils::logmesg(lmp," {} group '{}'\n", name.size()
-                       ? "Processing" : "Skipping",arg[idx]);
-        len = name.size()+1;
-        MPI_Bcast(&len,1,MPI_INT,0,world);
-        if (len > 1) {
-          MPI_Bcast((void *)name.c_str(),len,MPI_CHAR,0,world);
-
-          // read tags for atoms in group and broadcast
-          std::vector<tagint> tags = read_section(fp,next);
-          num = tags.size();
-          MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world);
-          MPI_Bcast((void *)tags.data(),num,MPI_LMP_TAGINT,0,world);
-          create(name,tags);
-          name = next;
-        }
-      } else {
-        MPI_Bcast(&len,1,MPI_INT,0,world);
-        if (len > 1) {
-          char *buf = new char[len];
-          MPI_Bcast(buf,len,MPI_CHAR,0,world);
-          MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world);
-          tagint *tbuf = new tagint[num];
-          MPI_Bcast(tbuf,num,MPI_LMP_TAGINT,0,world);
-          create(buf,std::vector<tagint>(tbuf,tbuf+num));
-          delete[] buf;
-          delete[] tbuf;
-        }
-      }
-    }
-  }
-  if (comm->me == 0) fclose(fp);
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Ndx2Group::create(const std::string &name, const std::vector<tagint> &tags)
-{
-  // wipe out all members if the group exists. gid==0 is group "all"
-  int gid = group->find(name);
-  if (gid > 0) group->assign(name + " clear");
-
-  // map from global to local
-  const int nlocal = atom->nlocal;
-  int *flags = (int *)calloc(nlocal,sizeof(int));
-  for (bigint i=0; i < (int)tags.size(); ++i) {
-    const int id = atom->map(tags[i]);
-    if (id < nlocal && id >= 0) flags[id] = 1;
-  }
-  group->create(name,flags);
-  free(flags);
-}

src/DPD-BASIC/Install.sh

@@ -0,0 +1,39 @@
+# Install/unInstall package files in LAMMPS
+# mode = 0/1/2 for uninstall/install/update
+
+mode=$1
+
+# enforce using portable C locale
+LC_ALL=C
+export LC_ALL
+
+# arg1 = file, arg2 = file it depends on
+
+action () {
+  if (test $mode = 0) then
+    rm -f ../$1
+  elif (! cmp -s $1 ../$1) then
+    if (test -z "$2" || test -e ../$2) then
+      cp $1 ..
+      if (test $mode = 2) then
+        echo "  updating src/$1"
+      fi
+    fi
+  elif (test -n "$2") then
+    if (test ! -e ../$2) then
+      rm -f ../$1
+    fi
+  fi
+}
+
+# list of files with optional dependcies
+action pair_dpd_coul_slater_long.cpp  pppm.cpp
+action pair_dpd_coul_slater_long.h  pppm.h
+action pair_dpd.cpp
+action pair_dpd_ext.cpp
+action pair_dpd_ext.h
+action pair_dpd_ext_tstat.cpp
+action pair_dpd_ext_tstat.h
+action pair_dpd.h
+action pair_dpd_tstat.cpp
+action pair_dpd_tstat.h

src/DPD-BASIC/pair_dpd_coul_slater_long.cpp

@@ -0,0 +1,544 @@
+// clang-format off
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Eddy BARRAUD (IFPEN/Sorbonne)
+------------------------------------------------------------------------- */
+
+#include "pair_dpd_coul_slater_long.h"
+
+#include "atom.h"
+#include "comm.h"
+#include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "neighbor.h"
+#include "random_mars.h"
+#include "update.h"
+
+#include "ewald_const.h"
+#include "kspace.h"
+
+#include <cmath>
+#include <cstring>
+
+using namespace LAMMPS_NS;
+using namespace EwaldConst;
+
+static constexpr double EPSILON = 1.0e-10;
+
+/* ---------------------------------------------------------------------- */
+
+PairDPDCoulSlaterLong::PairDPDCoulSlaterLong(LAMMPS *lmp) :
+    Pair(lmp), cut_dpd(nullptr), cut_dpdsq(nullptr), cut_slatersq(nullptr),
+    a0(nullptr), gamma(nullptr), sigma(nullptr), random(nullptr)
+{
+  writedata = 1;
+  ewaldflag = pppmflag = 1;
+  respa_enable = 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairDPDCoulSlaterLong::~PairDPDCoulSlaterLong()
+{
+  if (copymode) return;
+
+  if (allocated) {
+    memory->destroy(setflag);
+    memory->destroy(cutsq);
+    memory->destroy(cut_dpd);
+    memory->destroy(cut_dpdsq);
+    memory->destroy(cut_slatersq);
+
+    memory->destroy(cut);
+    memory->destroy(a0);
+    memory->destroy(gamma);
+    memory->destroy(sigma);
+  }
+
+  if (random) delete random;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairDPDCoulSlaterLong::compute(int eflag, int vflag)
+{
+  int i,j,ii,jj,inum,jnum,itype,jtype;
+  double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
+  double vxtmp,vytmp,vztmp,delvx,delvy,delvz;
+  double r2inv,forcedpd,forcecoul,factor_coul;
+  double grij,expm2,prefactor,t,erfc;
+  double rsq,r,rinv,dot,wd,randnum,factor_dpd,factor_sqrt;
+  int *ilist,*jlist,*numneigh,**firstneigh;
+  double slater_term;
+
+  evdwl = ecoul = 0.0;
+  ev_init(eflag,vflag);
+
+  double **x = atom->x;
+  double **v = atom->v;
+  double **f = atom->f;
+  int *type = atom->type;
+  int nlocal = atom->nlocal;
+  double *special_lj = force->special_lj;
+  int newton_pair = force->newton_pair;
+  double dtinvsqrt = 1.0/sqrt(update->dt);
+
+  double *q = atom->q;
+  double *special_coul = force->special_coul;
+  double qqrd2e = force->qqrd2e;
+
+  inum = list->inum;
+  ilist = list->ilist;
+  numneigh = list->numneigh;
+  firstneigh = list->firstneigh;
+
+  // loop over neighbors of my atoms
+
+  for (ii = 0; ii < inum; ii++) {
+    i = ilist[ii];
+    qtmp = q[i];
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+    vxtmp = v[i][0];
+    vytmp = v[i][1];
+    vztmp = v[i][2];
+    itype = type[i];
+    jlist = firstneigh[i];
+    jnum = numneigh[i];
+
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+      factor_dpd = special_lj[sbmask(j)];
+      factor_sqrt = special_sqrt[sbmask(j)];
+      factor_coul = special_coul[sbmask(j)];
+      j &= NEIGHMASK;
+
+      delx = xtmp - x[j][0];
+      dely = ytmp - x[j][1];
+      delz = ztmp - x[j][2];
+      rsq = delx*delx + dely*dely + delz*delz;
+      jtype = type[j];
+
+      // forces if below maximum cutoff
+      if (rsq < cutsq[itype][jtype]) {
+        r = sqrt(rsq);
+        if (evflag) evdwl = ecoul = 0.0;
+
+        // apply DPD force if distance below DPD cutoff
+        if (rsq < cut_dpdsq[itype][jtype] && r > EPSILON) {
+          rinv = 1.0/r;
+          delvx = vxtmp - v[j][0];
+          delvy = vytmp - v[j][1];
+          delvz = vztmp - v[j][2];
+          dot = delx*delvx + dely*delvy + delz*delvz;
+          wd = 1.0 - r/cut_dpd[itype][jtype];
+          randnum = random->gaussian();
+
+          // conservative force = a0 * wd
+          // drag force = -gamma * wd^2 * (delx dot delv) / r
+          // random force = sigma * wd * rnd * dtinvsqrt;
+          // random force must be scaled by sqrt(factor_dpd)
+
+          forcedpd = a0[itype][jtype]*wd;
+          forcedpd -= gamma[itype][jtype]*wd*wd*dot*rinv;
+          forcedpd *= factor_dpd;
+          forcedpd += factor_sqrt*sigma[itype][jtype]*wd*randnum*dtinvsqrt;
+          forcedpd *= rinv;
+
+          if (eflag) {
+            // eng shifted to 0.0 at cutoff
+            evdwl = 0.5*a0[itype][jtype]*cut_dpd[itype][jtype] * wd*wd;
+            evdwl *= factor_dpd;
+          }
+
+        } else forcedpd = 0.0;
+
+        // apply Slater electrostatic force if distance below Slater cutoff
+        // and the two species are charged
+        if (rsq < cut_slatersq[itype][jtype]){
+          r2inv = 1.0/rsq;
+          grij = g_ewald * r;
+          expm2 = exp(-grij*grij);
+          t = 1.0 / (1.0 + EWALD_P*grij);
+          erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+          slater_term = exp(-2*r/lamda)*(1 + (2*r/lamda*(1+r/lamda)));
+          prefactor = qqrd2e * qtmp*q[j]/r;
+          forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - slater_term);
+          if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor*(1-slater_term);
+          forcecoul *= r2inv;
+
+          if (eflag) {
+            ecoul = prefactor*(erfc - (1 + r/lamda)*exp(-2*r/lamda));
+            if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor*(1.0-(1 + r/lamda)*exp(-2*r/lamda));
+          }
+
+        } else forcecoul = 0.0;
+
+        fpair = forcedpd + forcecoul;
+
+        f[i][0] += delx*fpair;
+        f[i][1] += dely*fpair;
+        f[i][2] += delz*fpair;
+        if (newton_pair || j < nlocal) {
+          f[j][0] -= delx*fpair;
+          f[j][1] -= dely*fpair;
+          f[j][2] -= delz*fpair;
+        }
+
+
+        if (evflag) ev_tally(i,j,nlocal,newton_pair,
+                             evdwl,ecoul,fpair,delx,dely,delz);
+      }
+    }
+  }
+
+  if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ----------------------------------------------------------------------
+   allocate all arrays
+------------------------------------------------------------------------- */
+
+void PairDPDCoulSlaterLong::allocate()
+{
+  int i,j;
+  allocated = 1;
+  int n = atom->ntypes;
+
+  memory->create(setflag,n+1,n+1,"pair:setflag");
+  for (i = 1; i <= n; i++)
+    for (j = i; j <= n; j++)
+      setflag[i][j] = 0;
+
+  memory->create(cutsq,n+1,n+1,"pair:cutsq");
+  memory->create(cut,n+1,n+1,"pair:cut");
+  memory->create(cut_dpd,n+1,n+1,"pair:cut_dpd");
+  memory->create(cut_dpdsq,n+1,n+1,"pair:cut_dpdsq");
+  memory->create(cut_slatersq,n+1,n+1,"pair:cut_slatersq");
+  memory->create(a0,n+1,n+1,"pair:a0");
+  memory->create(gamma,n+1,n+1,"pair:gamma");
+  memory->create(sigma,n+1,n+1,"pair:sigma");
+  for (i = 0; i <= atom->ntypes; i++)
+    for (j = 0; j <= atom->ntypes; j++)
+      sigma[i][j] = gamma[i][j] = 0.0;
+}
+
+/* ----------------------------------------------------------------------
+   global settings
+------------------------------------------------------------------------- */
+
+void PairDPDCoulSlaterLong::settings(int narg, char **arg)
+{
+  // params : T cut_dpd seed lambda cut_coul
+  if (narg != 5) error->all(FLERR,"Illegal pair_style command");
+
+  temperature = utils::numeric(FLERR,arg[0],false,lmp);
+  cut_global = utils::numeric(FLERR,arg[1],false,lmp);
+  seed = utils::inumeric(FLERR,arg[2],false,lmp);
+  lamda = utils::numeric(FLERR,arg[3],false,lmp);
+  cut_coul = utils::numeric(FLERR,arg[4],false,lmp);
+
+  // initialize Marsaglia RNG with processor-unique seed
+
+  if (seed <= 0)
+    error->all(FLERR,"Invalid random seed {} for pair_style dpd/coul/slater/long command", seed);
+  delete random;
+  random = new RanMars(lmp,seed + comm->me);
+
+  // reset cutoffs that have been explicitly set
+
+  if (allocated) {
+    int i,j;
+    for (i = 1; i <= atom->ntypes; i++)
+      for (j = i; j <= atom->ntypes; j++)
+        if (setflag[i][j]) cut_dpd[i][j] = MAX(cut_global,cut_coul);
+  }
+}
+
+/* ----------------------------------------------------------------------
+   set coeffs for one or more type pairs
+------------------------------------------------------------------------- */
+
+void PairDPDCoulSlaterLong::coeff(int narg, char **arg)
+{
+  if (narg < 4 || narg > 6)
+    error->all(FLERR,"Incorrect args for pair coefficients");
+  if (!allocated) allocate();
+
+  int ilo,ihi,jlo,jhi;
+  utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
+  utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
+
+  double a0_one = utils::numeric(FLERR,arg[2],false,lmp);
+  double gamma_one = utils::numeric(FLERR,arg[3],false,lmp);
+
+  double cut_one = cut_global;
+  double cut_two = 0.0;
+
+  if (narg > 4) {
+    bool do_slater = utils::logical(FLERR,arg[4],false,lmp);
+    if (do_slater) cut_two = cut_coul;
+  }
+
+  if (narg > 5) cut_one = utils::numeric(FLERR,arg[5],false,lmp);
+
+  int count = 0;
+  for (int i = ilo; i <= ihi; i++) {
+    for (int j = MAX(jlo,i); j <= jhi; j++) {
+      a0[i][j] = a0_one;
+      gamma[i][j] = gamma_one;
+      cut_dpd[i][j] = cut_one;
+      cut_slatersq[i][j] = cut_two * cut_two;
+      cut[i][j] = MAX(cut_one, cut_two);
+      setflag[i][j] = 1;
+      count++;
+    }
+  }
+
+  if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+   init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairDPDCoulSlaterLong::init_style()
+{
+  if (comm->ghost_velocity == 0)
+    error->all(FLERR,"Pair dpd requires ghost atoms store velocity");
+  if (!atom->q_flag)
+    error->all(FLERR,"Pair style coul/slater/long requires atom attribute q");
+
+  // if newton off, forces between atoms ij will be double computed
+  // using different random numbers
+
+  if (force->newton_pair == 0 && comm->me == 0)
+    error->warning(FLERR, "Pair dpd needs newton pair on for momentum conservation");
+
+  neighbor->add_request(this);
+
+  // precompute random force scaling factors
+
+  for (int i = 0; i < 4; ++i) special_sqrt[i] = sqrt(force->special_lj[i]);
+
+
+  // ensure use of KSpace long-range solver, set g_ewald
+
+ if (force->kspace == nullptr)
+    error->all(FLERR,"Pair style requires a KSpace style");
+  g_ewald = force->kspace->g_ewald;
+}
+
+/* ----------------------------------------------------------------------
+   init for one type pair i,j and corresponding j,i
+   return the maximum cutoff between Slater or DPD cutoff if charged
+   return the DPD cutoff for uncharged
+------------------------------------------------------------------------- */
+
+double PairDPDCoulSlaterLong::init_one(int i, int j)
+{
+  if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+
+  sigma[i][j] = sqrt(2.0*force->boltz*temperature*gamma[i][j]);
+
+  cut_dpdsq[i][j] = cut_dpd[i][j] * cut_dpd[i][j];
+
+  a0[j][i] = a0[i][j];
+  gamma[j][i] = gamma[i][j];
+  sigma[j][i] = sigma[i][j];
+  cut_dpd[j][i] = cut_dpd[i][j];
+  cut[j][i] = cut[i][j];
+  cut_dpdsq[j][i] = cut_dpdsq[i][j];
+  cut_slatersq[j][i] = cut_slatersq[i][j];
+
+  return MAX(cut_dpd[i][j], sqrt(cut_slatersq[i][j]));
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairDPDCoulSlaterLong::write_restart(FILE *fp)
+{
+  write_restart_settings(fp);
+
+  int i,j;
+  for (i = 1; i <= atom->ntypes; i++) {
+    for (j = i; j <= atom->ntypes; j++) {
+      fwrite(&setflag[i][j],sizeof(int),1,fp);
+      if (setflag[i][j]) {
+        fwrite(&a0[i][j],sizeof(double),1,fp);
+        fwrite(&gamma[i][j],sizeof(double),1,fp);
+        fwrite(&cut[i][j],sizeof(double),1,fp);
+        fwrite(&cut_dpd[i][j],sizeof(double),1,fp);
+        fwrite(&cut_slatersq[i][j],sizeof(double),1,fp);
+      }
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairDPDCoulSlaterLong::read_restart(FILE *fp)
+{
+  read_restart_settings(fp);
+
+  allocate();
+
+  int i,j;
+  int me = comm->me;
+  for (i = 1; i <= atom->ntypes; i++) {
+    for (j = i; j <= atom->ntypes; j++) {
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error);
+      MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
+      if (setflag[i][j]) {
+        if (me == 0) {
+          utils::sfread(FLERR,&a0[i][j],sizeof(double),1,fp,nullptr,error);
+          utils::sfread(FLERR,&gamma[i][j],sizeof(double),1,fp,nullptr,error);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error);
+          utils::sfread(FLERR,&cut_dpd[i][j],sizeof(double),1,fp,nullptr,error);
+          utils::sfread(FLERR,&cut_slatersq[i][j],sizeof(double),1,fp,nullptr,error);
+        }
+        MPI_Bcast(&a0[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_dpd[i][j],1,MPI_DOUBLE,0,world);
+        MPI_Bcast(&cut_slatersq[i][j],1,MPI_DOUBLE,0,world);
+      }
+    }
+  }
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairDPDCoulSlaterLong::write_restart_settings(FILE *fp)
+{
+  fwrite(&temperature,sizeof(double),1,fp);
+  fwrite(&cut_global,sizeof(double),1,fp);
+  fwrite(&seed,sizeof(int),1,fp);
+  fwrite(&lamda,sizeof(double),1,fp);
+  fwrite(&cut_coul,sizeof(double),1,fp);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairDPDCoulSlaterLong::read_restart_settings(FILE *fp)
+{
+  if (comm->me == 0) {
+    utils::sfread(FLERR,&temperature,sizeof(double),1,fp,nullptr,error);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error);
+    utils::sfread(FLERR,&seed,sizeof(int),1,fp,nullptr,error);
+    utils::sfread(FLERR,&lamda,sizeof(double),1,fp,nullptr,error);
+    utils::sfread(FLERR,&cut_coul,sizeof(double),1,fp,nullptr,error);
+  }
+  MPI_Bcast(&temperature,1,MPI_DOUBLE,0,world);
+  MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
+  MPI_Bcast(&seed,1,MPI_INT,0,world);
+  MPI_Bcast(&lamda,1,MPI_DOUBLE,0,world);
+  MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
+
+  // initialize Marsaglia RNG with processor-unique seed
+  // same seed that pair_style command initially specified
+
+  if (random) delete random;
+  random = new RanMars(lmp,seed + comm->me);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void PairDPDCoulSlaterLong::write_data(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    fprintf(fp,"%d %g %g\n",i,a0[i][i],gamma[i][i]);
+}
+
+/* ----------------------------------------------------------------------
+   proc 0 writes all pairs to data file
+------------------------------------------------------------------------- */
+
+void PairDPDCoulSlaterLong::write_data_all(FILE *fp)
+{
+  for (int i = 1; i <= atom->ntypes; i++)
+    for (int j = i; j <= atom->ntypes; j++)
+      fprintf(fp,"%d %d %g %g %s %g\n",i,j,a0[i][j],gamma[i][j],
+              (cut_slatersq[i][j] == 0.0) ? "yes" : "no", cut_dpd[i][j]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairDPDCoulSlaterLong::single(int i, int j, int itype, int jtype, double rsq,
+                                     double factor_coul, double factor_dpd, double &fforce)
+{
+  double r,rinv,wd,phi;
+  double r2inv,grij,expm2,t,erfc,prefactor;
+  double slater_term;
+  double forcecoul,phicoul;
+
+  double energy = 0.0;
+  fforce = 0.0;
+
+  r = sqrt(rsq);
+
+  // compute DPD force and energy
+  if (rsq < cut_dpdsq[itype][jtype] && r > EPSILON) {
+    rinv = 1.0/r;
+    wd = 1.0 - r/cut_dpd[itype][jtype];
+    fforce += a0[itype][jtype]*wd * factor_dpd*rinv;
+
+    phi = 0.5*a0[itype][jtype]*cut_dpd[itype][jtype] * wd*wd;
+    energy += factor_dpd*phi;
+  }
+
+  // compute Slater coulombic force and energy
+  if (atom->q[i]*atom->q[j] != 0.0 && rsq < cut_slatersq[itype][jtype]) {
+    r2inv = 1.0/rsq;
+    grij = g_ewald * r;
+    expm2 = exp(-grij*grij);
+    t = 1.0 / (1.0 + EWALD_P*grij);
+    erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+    slater_term = exp(-2*r/lamda)*(1 + (2*r/lamda*(1+r/lamda)));
+    prefactor = force->qqrd2e * atom->q[i]*atom->q[j]/r;
+    forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - slater_term);
+    if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+    fforce += forcecoul * r2inv;
+    phicoul = prefactor*(erfc - (1 + r/lamda)*exp(-2*r/lamda));
+    if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
+    energy += phicoul;
+  }
+
+  return energy;
+}
+
+void *PairDPDCoulSlaterLong::extract(const char *str, int &dim)
+{
+  dim = 0;
+  if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
+  if (strcmp(str,"lamda") == 0) return (void *) &lamda;
+  dim = 2;
+  if (strcmp(str,"a0") == 0) return (void *) a0;
+  if (strcmp(str,"gamma") == 0) return (void *) gamma;
+  return nullptr;
+}

src/DPD-BASIC/pair_dpd_coul_slater_long.h

@@ -0,0 +1,64 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+// clang-format off
+PairStyle(dpd/coul/slater/long,PairDPDCoulSlaterLong);
+// clang-format on
+#else
+
+#ifndef LMP_PAIR_DPD_COUL_SLATER_LONG_H
+#define LMP_PAIR_DPD_COUL_SLATER_LONG_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairDPDCoulSlaterLong : public Pair {
+ public:
+  PairDPDCoulSlaterLong(class LAMMPS *);
+  ~PairDPDCoulSlaterLong() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  void init_style() override;
+  double init_one(int, int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_restart_settings(FILE *) override;
+  void read_restart_settings(FILE *) override;
+  void write_data(FILE *) override;
+  void write_data_all(FILE *) override;
+  double single(int, int, int, int, double, double, double, double &) override;
+  void *extract(const char *, int &) override;
+
+ protected:
+  double cut_global, temperature;
+  double special_sqrt[4];
+  int seed;
+  double **cut;
+  double **cut_dpd, **cut_dpdsq, **cut_slatersq;
+  double **a0, **gamma;
+  double **sigma;
+  class RanMars *random;
+  double cut_coul, qdist;
+  double lamda;
+  double g_ewald;
+
+  virtual void allocate();
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif

src/Depend.sh

@@ -116,6 +116,7 @@ if (test $1 = "KSPACE") then
   depend CG-SPICA
   depend CORESHELL
   depend DIELECTRIC
+  depend DPD-BASIC
   depend GPU
   depend KOKKOS
   depend OPT

src/EXTRA-COMMAND/group_ndx.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 // -*- c++ -*-
 
 /* ----------------------------------------------------------------------
@@ -34,12 +33,15 @@ using namespace LAMMPS_NS;
 
 static int cmptagint(const void *p1, const void *p2)
 {
-  const tagint i1 = * static_cast<const tagint *>(p1);
+  const tagint i1 = *static_cast<const tagint *>(p1);
-  const tagint i2 = * static_cast<const tagint *>(p2);
+  const tagint i2 = *static_cast<const tagint *>(p2);
-  if (i1 == i2) return 0;
+  if (i1 == i2)
+    return 0;
   else {
-    if (i1 < i2) return -1;
+    if (i1 < i2)
-    else return 1;
+      return -1;
+    else
+      return 1;
   }
 }
 
@@ -49,27 +51,24 @@ void Group2Ndx::command(int narg, char **arg)
 {
   FILE *fp = nullptr;
 
-  if (narg < 1) error->all(FLERR,"Illegal group2ndx command");
+  if (narg < 1) utils::missing_cmd_args(FLERR, "group2ndx", error);
 
-  if (atom->tag_enable == 0)
+  if (atom->tag_enable == 0) error->all(FLERR, "Must have atom IDs for group2ndx command");
-      error->all(FLERR,"Must have atom IDs for group2ndx command");
 
   if (comm->me == 0) {
     fp = fopen(arg[0], "w");
     if (fp == nullptr)
-      error->one(FLERR,"Cannot open index file for writing: {}", utils::getsyserror());
+      error->one(FLERR, "Cannot open index file for writing: {}", utils::getsyserror());
-    utils::logmesg(lmp,"Writing groups to index file {}:\n",arg[0]);
+    utils::logmesg(lmp, "Writing groups to index file {}:\n", arg[0]);
   }
 
-  if (narg == 1) { // write out all groups
+  if (narg == 1) {    // write out all groups
-    for (int i=0; i < group->ngroup; ++i) {
+    for (int i = 0; i < group->ngroup; ++i) { write_group(fp, i); }
-      write_group(fp,i);
+  } else {    // write only selected groups
-    }
+    for (int i = 1; i < narg; ++i) {
-  } else { // write only selected groups
-    for (int i=1; i < narg; ++i) {
       int gid = group->find(arg[i]);
       if (gid < 0) error->all(FLERR, "Non-existing group requested");
-      write_group(fp,gid);
+      write_group(fp, gid);
     }
   }
 
@@ -85,22 +84,26 @@ void Group2Ndx::write_group(FILE *fp, int gid)
   bigint gcount = group->count(gid);
   int lnum, width, cols;
 
+  if (utils::strmatch(group->names[gid], "\\s+")) {
+    if (fp) utils::logmesg(lmp, " skipping group {}...done", group->names[gid]);
+    return;
+  }
   if (fp) {
-    utils::logmesg(lmp," writing group {}...",group->names[gid]);
+    utils::logmesg(lmp, " writing group {}...", group->names[gid]);
 
     // the "all" group in LAMMPS is called "System" in Gromacs
     if (gid == 0) {
       fputs("[ System ]\n", fp);
     } else {
-      fmt::print(fp,"[ {} ]\n", group->names[gid]);
+      fmt::print(fp, "[ {} ]\n", group->names[gid]);
     }
-    width = log10((double) atom->natoms)+2;
+    width = log10((double) atom->natoms) + 2;
     cols = 80 / width;
   }
 
   if (gcount > 0) {
-    const int * const mask = atom->mask;
+    const int *const mask = atom->mask;
-    const tagint * const tag = atom->tag;
+    const tagint *const tag = atom->tag;
     const int groupbit = group->bitmask[gid];
     const int nlocal = atom->nlocal;
     int i;
@@ -111,45 +114,45 @@ void Group2Ndx::write_group(FILE *fp, int gid)
     for (i = 0; i < nlocal; i++)
       if (mask[i] & groupbit) sendlist[lnum++] = tag[i];
 
-    int nrecv=0;
+    int nrecv = 0;
     bigint allrecv;
     if (comm->me == 0) {
       MPI_Status status;
       MPI_Request request;
 
-      for (i=0; i < lnum; i++)
+      for (i = 0; i < lnum; i++) recvlist[i] = sendlist[i];
-        recvlist[i] = sendlist[i];
 
       allrecv = lnum;
-      for (i=1; i < comm->nprocs; ++i) {
+      for (i = 1; i < comm->nprocs; ++i) {
-        MPI_Irecv(recvlist+allrecv,gcount-allrecv,MPI_LMP_TAGINT,i,0, world,&request);
+        MPI_Irecv(recvlist + allrecv, gcount - allrecv, MPI_LMP_TAGINT, i, 0, world, &request);
-        MPI_Send(&nrecv,0,MPI_INT,i,0,world); // block rank "i" until we are ready to receive
+        // block rank "i" until we are ready to receive
-        MPI_Wait(&request,&status);
+        MPI_Send(&nrecv, 0, MPI_INT, i, 0, world);
-        MPI_Get_count(&status,MPI_LMP_TAGINT,&nrecv);
+        MPI_Wait(&request, &status);
+        MPI_Get_count(&status, MPI_LMP_TAGINT, &nrecv);
         allrecv += nrecv;
       }
 
       // sort received list
-      qsort((void *)recvlist, allrecv, sizeof(tagint), cmptagint);
+      qsort((void *) recvlist, allrecv, sizeof(tagint), cmptagint);
     } else {
-      MPI_Recv(&nrecv,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE);
+      MPI_Recv(&nrecv, 0, MPI_INT, 0, 0, world, MPI_STATUS_IGNORE);
-      MPI_Rsend(sendlist,lnum,MPI_LMP_TAGINT,0,0,world);
+      MPI_Rsend(sendlist, lnum, MPI_LMP_TAGINT, 0, 0, world);
     }
-    delete [] sendlist;
+    delete[] sendlist;
   }
 
   if (fp) {
     int i, j;
-    for (i=0, j=0; i < gcount; ++i) {
+    for (i = 0, j = 0; i < gcount; ++i) {
-      fmt::print(fp,"{:>{}}",recvlist[i],width);
+      fmt::print(fp, "{:>{}}", recvlist[i], width);
       ++j;
       if (j == cols) {
-        fputs("\n",fp);
+        fputs("\n", fp);
         j = 0;
       }
     }
-    if (j > 0) fputs("\n",fp);
+    if (j > 0) fputs("\n", fp);
-    utils::logmesg(lmp,"done\n");
+    utils::logmesg(lmp, "done\n");
   }
   if (gcount > 0) delete[] recvlist;
 }

src/EXTRA-COMMAND/ndx_group.cpp

@@ -0,0 +1,220 @@
+// -*- c++ -*-
+
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   Contributing author:  Axel Kohlmeyer (Temple U)
+------------------------------------------------------------------------- */
+
+#include "ndx_group.h"
+
+#include "atom.h"
+#include "comm.h"
+#include "error.h"
+#include "group.h"
+#include "tokenizer.h"
+
+using namespace LAMMPS_NS;
+static constexpr int BUFLEN = 4096;
+
+// read file until next section "name" or any next section if name == ""
+
+static std::string find_section(FILE *fp, const std::string &name)
+{
+  char linebuf[BUFLEN];
+
+  fgets(linebuf, BUFLEN, fp);
+  while (!feof(fp)) {
+    if (utils::strmatch(linebuf, "^\\s*\\[.*\\]\\s*$")) {
+      auto words = Tokenizer(linebuf).as_vector();
+      if (words.size() != 3)
+        throw TokenizerException("Invalid group name in index file",
+                                 utils::trim(utils::strfind(linebuf, "[^\\[^\\]]+")));
+      if (name.empty() || (name == words[1])) return words[1];
+    }
+    fgets(linebuf, BUFLEN, fp);
+  }
+  return "";
+}
+
+static std::vector<tagint> read_section(FILE *fp, std::string &name)
+{
+  char linebuf[BUFLEN];
+  std::vector<tagint> tagbuf;
+
+  while (fgets(linebuf, BUFLEN, fp)) {
+    // start of new section. we are done, update "name"
+    if (utils::strmatch(linebuf, "^\\s*\\[.*\\]\\s*$")) {
+      auto words = Tokenizer(linebuf).as_vector();
+      if (words.size() != 3)
+        throw TokenizerException("Invalid group name in index file",
+                                 utils::trim(utils::strfind(linebuf, "[^\\[^\\]]+")));
+      name = words[1];
+      return tagbuf;
+    }
+    ValueTokenizer values(linebuf);
+    while (values.has_next()) tagbuf.push_back(values.next_tagint());
+  }
+  // set empty name to indicate end of file
+  name = "";
+  return tagbuf;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Ndx2Group::command(int narg, char **arg)
+{
+  int len;
+  bigint num;
+  FILE *fp;
+  std::string name, next;
+
+  if (narg < 1) utils::missing_cmd_args(FLERR, "ndx2group", error);
+  if (atom->tag_enable == 0) error->all(FLERR, "Must have atom IDs for ndx2group command");
+  if (atom->map_style == Atom::MAP_NONE)
+    error->all(FLERR, "Must have an atom map for ndx2group command");
+  if (comm->me == 0) {
+    fp = fopen(arg[0], "r");
+    if (fp == nullptr)
+      error->one(FLERR, "Cannot open index file for reading: {}", utils::getsyserror());
+    utils::logmesg(lmp, "Reading groups from index file {}:\n", arg[0]);
+  }
+
+  if (narg == 1) {    // restore all groups
+
+    if (comm->me == 0) {
+      try {
+        name = find_section(fp, "");
+      } catch (std::exception &e) {
+        error->one(FLERR, e.what());
+      }
+
+      while (!name.empty()) {
+        // skip over group "all", which is called "System" in gromacs
+        if (name == "System") {
+          try {
+            name = find_section(fp, "");
+          } catch (std::exception &e) {
+            error->one(FLERR, e.what());
+          }
+          continue;
+        }
+
+        utils::logmesg(lmp, " Processing group '{}'\n", name);
+        len = name.size() + 1;
+        MPI_Bcast(&len, 1, MPI_INT, 0, world);
+        if (len > 1) {
+          MPI_Bcast((void *) name.c_str(), len, MPI_CHAR, 0, world);
+
+          // read tags for atoms in group and broadcast
+          std::vector<tagint> tags;
+          try {
+            tags = read_section(fp, next);
+          } catch (std::exception &e) {
+            error->one(FLERR, e.what());
+          }
+          num = tags.size();
+          MPI_Bcast(&num, 1, MPI_LMP_BIGINT, 0, world);
+          MPI_Bcast((void *) tags.data(), num, MPI_LMP_TAGINT, 0, world);
+          create(name, tags);
+          name = next;
+        }
+      }
+      len = -1;
+      MPI_Bcast(&len, 1, MPI_INT, 0, world);
+
+    } else {
+
+      while (true) {
+        MPI_Bcast(&len, 1, MPI_INT, 0, world);
+        if (len < 0) break;
+        if (len > 1) {
+          char *buf = new char[len];
+          MPI_Bcast(buf, len, MPI_CHAR, 0, world);
+          MPI_Bcast(&num, 1, MPI_LMP_BIGINT, 0, world);
+          tagint *tbuf = new tagint[num];
+          MPI_Bcast(tbuf, num, MPI_LMP_TAGINT, 0, world);
+          create(buf, std::vector<tagint>(tbuf, tbuf + num));
+          delete[] buf;
+          delete[] tbuf;
+        }
+      }
+    }
+
+  } else {    // restore selected groups
+
+    for (int idx = 1; idx < narg; ++idx) {
+      if (comm->me == 0) {
+
+        // find named section, search from beginning of file
+        rewind(fp);
+        try {
+          name = find_section(fp, arg[idx]);
+        } catch (std::exception &e) {
+          error->one(FLERR, e.what());
+        }
+        utils::logmesg(lmp, " {} group '{}'\n", name.size() ? "Processing" : "Skipping", arg[idx]);
+        len = name.size() + 1;
+        MPI_Bcast(&len, 1, MPI_INT, 0, world);
+        if (len > 1) {
+          MPI_Bcast((void *) name.c_str(), len, MPI_CHAR, 0, world);
+
+          // read tags for atoms in group and broadcast
+          std::vector<tagint> tags;
+          try {
+            tags = read_section(fp, next);
+          } catch (std::exception &e) {
+            error->one(FLERR, e.what());
+          }
+          num = tags.size();
+          MPI_Bcast(&num, 1, MPI_LMP_BIGINT, 0, world);
+          MPI_Bcast((void *) tags.data(), num, MPI_LMP_TAGINT, 0, world);
+          create(name, tags);
+          name = next;
+        }
+      } else {
+        MPI_Bcast(&len, 1, MPI_INT, 0, world);
+        if (len > 1) {
+          char *buf = new char[len];
+          MPI_Bcast(buf, len, MPI_CHAR, 0, world);
+          MPI_Bcast(&num, 1, MPI_LMP_BIGINT, 0, world);
+          tagint *tbuf = new tagint[num];
+          MPI_Bcast(tbuf, num, MPI_LMP_TAGINT, 0, world);
+          create(buf, std::vector<tagint>(tbuf, tbuf + num));
+          delete[] buf;
+          delete[] tbuf;
+        }
+      }
+    }
+  }
+  if (comm->me == 0) fclose(fp);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Ndx2Group::create(const std::string &name, const std::vector<tagint> &tags)
+{
+  // wipe out all members if the group exists. gid==0 is group "all"
+  int gid = group->find(name);
+  if (gid > 0) group->assign(name + " clear");
+
+  // map from global to local
+  const int nlocal = atom->nlocal;
+  int *flags = (int *) calloc(nlocal, sizeof(int));
+  for (bigint i = 0; i < (int) tags.size(); ++i) {
+    const int id = atom->map(tags[i]);
+    if (id < nlocal && id >= 0) flags[id] = 1;
+  }
+  group->create(name, flags);
+  free(flags);
+}

src/EXTRA-PAIR/pair_coul_slater_long.cpp

@@ -39,7 +39,6 @@ using namespace EwaldConst;
 PairCoulSlaterLong::PairCoulSlaterLong(LAMMPS *lmp) : Pair(lmp)
 {
   ewaldflag = pppmflag = 1;
-  qdist = 0.0;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -232,7 +231,7 @@ void PairCoulSlaterLong::init_style()
 double PairCoulSlaterLong::init_one(int i, int j)
 {
   scale[j][i] = scale[i][j];
-  return cut_coul+2.0*qdist;
+  return cut_coul;
 }
 
 /* ----------------------------------------------------------------------

src/EXTRA-PAIR/pair_coul_slater_long.h

@@ -41,9 +41,7 @@ class PairCoulSlaterLong : public Pair {
   void *extract(const char *, int &) override;
 
  protected:
-  double cut_coul, cut_coulsq, qdist;
+  double cut_coul, cut_coulsq, lamda, g_ewald;
-  double lamda;
-  double g_ewald;
   double **scale;
 
   virtual void allocate();

src/GPU/pair_dpd_coul_slater_long_gpu.cpp

@@ -0,0 +1,474 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Eddy BARRAUD (IFPEN/Sorbonne)
+------------------------------------------------------------------------- */
+
+#include "pair_dpd_coul_slater_long_gpu.h"
+
+#include "atom.h"
+#include "comm.h"
+#include "domain.h"
+#include "error.h"
+#include "force.h"
+#include "gpu_extra.h"
+#include "neigh_list.h"
+#include "neighbor.h"
+#include "suffix.h"
+#include "update.h"
+
+#include "ewald_const.h"
+#include "kspace.h"
+
+#include <cmath>
+#include <cstring>
+
+using namespace LAMMPS_NS;
+using namespace EwaldConst;
+
+// External functions from cuda library for atom decomposition
+
+int dpd_coul_slater_long_gpu_init(const int ntypes, double **cutsq, double **host_a0,
+                                  double **host_gamma, double **host_sigma, double **host_cut_dpd,
+                                  double **host_cut_dpdsq, double **host_cut_slatersq,
+                                  double *special_lj, const int inum, const int nall,
+                                  const int max_nbors, const int maxspecial,
+                                  const double cell_size, int &gpu_mode, FILE *screen,
+                                  double *host_special_coul, const double qqrd2e,
+                                  const double g_ewald, const double lamda);
+void dpd_coul_slater_long_gpu_clear();
+int **dpd_coul_slater_long_gpu_compute_n(const int ago, const int inum_full, const int nall,
+                                         double **host_x, int *host_type, double *sublo,
+                                         double *subhi, tagint *tag, int **nspecial,
+                                         tagint **special, const bool eflag, const bool vflag,
+                                         const bool eatom, const bool vatom, int &host_start,
+                                         int **ilist, int **jnum, const double cpu_time,
+                                         bool &success, double **host_v, const double dtinvsqrt,
+                                         const int seed, const int timestep, double *boxlo,
+                                         double *prd);
+void dpd_coul_slater_long_gpu_compute(const int ago, const int inum_full, const int nall,
+                                      double **host_x, int *host_type, int *ilist, int *numj,
+                                      int **firstneigh, const bool eflag, const bool vflag,
+                                      const bool eatom, const bool vatom, int &host_start,
+                                      const double cpu_time, bool &success, tagint *tag,
+                                      double **host_v, const double dtinvsqrt, const int seed,
+                                      const int timestep, const int nlocal, double *boxlo,
+                                      double *prd);
+
+void dpd_coul_slater_long_gpu_get_extra_data(double *host_q);
+
+double dpd_coul_slater_long_gpu_bytes();
+
+static constexpr double EPSILON = 1.0e-10;
+
+//#define _USE_UNIFORM_SARU_LCG
+//#define _USE_UNIFORM_SARU_TEA8
+//#define _USE_GAUSSIAN_SARU_LCG
+
+#if !defined(_USE_UNIFORM_SARU_LCG) && !defined(_USE_UNIFORM_SARU_TEA8) && \
+    !defined(_USE_GAUSSIAN_SARU_LCG)
+#define _USE_UNIFORM_SARU_LCG
+#endif
+
+// References:
+// 1. Y. Afshar, F. Schmid, A. Pishevar, S. Worley, Comput. Phys. Comm. 184 (2013), 1119–1128.
+// 2. C. L. Phillips, J. A. Anderson, S. C. Glotzer, Comput. Phys. Comm. 230 (2011), 7191-7201.
+// PRNG period = 3666320093*2^32 ~ 2^64 ~ 10^19
+
+#define LCGA 0x4beb5d59    // Full period 32 bit LCG
+#define LCGC 0x2600e1f7
+#define oWeylPeriod 0xda879add    // Prime period 3666320093
+#define oWeylOffset 0x8009d14b
+#define TWO_N32 0.232830643653869628906250e-9f /* 2^-32 */
+
+// specifically implemented for steps = 1; high = 1.0; low = -1.0
+// returns uniformly distributed random numbers u in [-1.0;1.0]
+// using the inherent LCG, then multiply u with sqrt(3) to "match"
+// with a normal random distribution.
+// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
+// Curly brackets to make variables local to the scope.
+#ifdef _USE_UNIFORM_SARU_LCG
+#define numtyp double
+#define SQRT3 (numtyp) 1.7320508075688772935274463
+#define saru(seed1, seed2, seed, timestep, randnum)                                \
+  {                                                                                \
+    unsigned int seed3 = seed + timestep;                                          \
+    seed3 ^= (seed1 << 7) ^ (seed2 >> 6);                                          \
+    seed2 += (seed1 >> 4) ^ (seed3 >> 15);                                         \
+    seed1 ^= (seed2 << 9) + (seed3 << 8);                                          \
+    seed3 ^= 0xA5366B4D * ((seed2 >> 11) ^ (seed1 << 1));                          \
+    seed2 += 0x72BE1579 * ((seed1 << 4) ^ (seed3 >> 16));                          \
+    seed1 ^= 0x3F38A6ED * ((seed3 >> 5) ^ (((signed int) seed2) >> 22));           \
+    seed2 += seed1 * seed3;                                                        \
+    seed1 += seed3 ^ (seed2 >> 2);                                                 \
+    seed2 ^= ((signed int) seed2) >> 17;                                           \
+    unsigned int state = 0x79dedea3 * (seed1 ^ (((signed int) seed1) >> 14));      \
+    unsigned int wstate = (state + seed2) ^ (((signed int) state) >> 8);           \
+    state = state + (wstate * (wstate ^ 0xdddf97f5));                              \
+    wstate = 0xABCB96F7 + (wstate >> 1);                                           \
+    state = LCGA * state + LCGC;                                                   \
+    wstate = wstate + oWeylOffset + ((((signed int) wstate) >> 31) & oWeylPeriod); \
+    unsigned int v = (state ^ (state >> 26)) + wstate;                             \
+    unsigned int s = (signed int) ((v ^ (v >> 20)) * 0x6957f5a7);                  \
+    randnum = SQRT3 * (s * TWO_N32 * (numtyp) 2.0 - (numtyp) 1.0);                 \
+  }
+#endif
+
+// specifically implemented for steps = 1; high = 1.0; low = -1.0
+// returns uniformly distributed random numbers u in [-1.0;1.0] using TEA8
+// then multiply u with sqrt(3) to "match" with a normal random distribution
+// Afshar et al. mutlplies u in [-0.5;0.5] with sqrt(12)
+#ifdef _USE_UNIFORM_SARU_TEA8
+#define numtyp double
+#define SQRT3 (numtyp) 1.7320508075688772935274463
+#define k0 0xA341316C
+#define k1 0xC8013EA4
+#define k2 0xAD90777D
+#define k3 0x7E95761E
+#define delta 0x9e3779b9
+#define rounds 8
+#define saru(seed1, seed2, seed, timestep, randnum)                           \
+  {                                                                           \
+    unsigned int seed3 = seed + timestep;                                     \
+    seed3 ^= (seed1 << 7) ^ (seed2 >> 6);                                     \
+    seed2 += (seed1 >> 4) ^ (seed3 >> 15);                                    \
+    seed1 ^= (seed2 << 9) + (seed3 << 8);                                     \
+    seed3 ^= 0xA5366B4D * ((seed2 >> 11) ^ (seed1 << 1));                     \
+    seed2 += 0x72BE1579 * ((seed1 << 4) ^ (seed3 >> 16));                     \
+    seed1 ^= 0x3F38A6ED * ((seed3 >> 5) ^ (((signed int) seed2) >> 22));      \
+    seed2 += seed1 * seed3;                                                   \
+    seed1 += seed3 ^ (seed2 >> 2);                                            \
+    seed2 ^= ((signed int) seed2) >> 17;                                      \
+    unsigned int state = 0x79dedea3 * (seed1 ^ (((signed int) seed1) >> 14)); \
+    unsigned int wstate = (state + seed2) ^ (((signed int) state) >> 8);      \
+    state = state + (wstate * (wstate ^ 0xdddf97f5));                         \
+    wstate = 0xABCB96F7 + (wstate >> 1);                                      \
+    unsigned int sum = 0;                                                     \
+    for (int i = 0; i < rounds; i++) {                                        \
+      sum += delta;                                                           \
+      state += ((wstate << 4) + k0) ^ (wstate + sum) ^ ((wstate >> 5) + k1);  \
+      wstate += ((state << 4) + k2) ^ (state + sum) ^ ((state >> 5) + k3);    \
+    }                                                                         \
+    unsigned int v = (state ^ (state >> 26)) + wstate;                        \
+    unsigned int s = (signed int) ((v ^ (v >> 20)) * 0x6957f5a7);             \
+    randnum = SQRT3 * (s * TWO_N32 * (numtyp) 2.0 - (numtyp) 1.0);            \
+  }
+#endif
+
+// specifically implemented for steps = 1; high = 1.0; low = -1.0
+// returns two uniformly distributed random numbers r1 and r2 in [-1.0;1.0],
+// and uses the polar method (Marsaglia's) to transform to a normal random value
+// This is used to compared with CPU DPD using RandMars::gaussian()
+#ifdef _USE_GAUSSIAN_SARU_LCG
+#define numtyp double
+#define saru(seed1, seed2, seed, timestep, randnum)                                  \
+  {                                                                                  \
+    unsigned int seed3 = seed + timestep;                                            \
+    seed3 ^= (seed1 << 7) ^ (seed2 >> 6);                                            \
+    seed2 += (seed1 >> 4) ^ (seed3 >> 15);                                           \
+    seed1 ^= (seed2 << 9) + (seed3 << 8);                                            \
+    seed3 ^= 0xA5366B4D * ((seed2 >> 11) ^ (seed1 << 1));                            \
+    seed2 += 0x72BE1579 * ((seed1 << 4) ^ (seed3 >> 16));                            \
+    seed1 ^= 0x3F38A6ED * ((seed3 >> 5) ^ (((signed int) seed2) >> 22));             \
+    seed2 += seed1 * seed3;                                                          \
+    seed1 += seed3 ^ (seed2 >> 2);                                                   \
+    seed2 ^= ((signed int) seed2) >> 17;                                             \
+    unsigned int state = 0x12345678;                                                 \
+    unsigned int wstate = 12345678;                                                  \
+    state = 0x79dedea3 * (seed1 ^ (((signed int) seed1) >> 14));                     \
+    wstate = (state + seed2) ^ (((signed int) state) >> 8);                          \
+    state = state + (wstate * (wstate ^ 0xdddf97f5));                                \
+    wstate = 0xABCB96F7 + (wstate >> 1);                                             \
+    unsigned int v, s;                                                               \
+    numtyp r1, r2, rsq;                                                              \
+    while (1) {                                                                      \
+      state = LCGA * state + LCGC;                                                   \
+      wstate = wstate + oWeylOffset + ((((signed int) wstate) >> 31) & oWeylPeriod); \
+      v = (state ^ (state >> 26)) + wstate;                                          \
+      s = (signed int) ((v ^ (v >> 20)) * 0x6957f5a7);                               \
+      r1 = s * TWO_N32 * (numtyp) 2.0 - (numtyp) 1.0;                                \
+      state = LCGA * state + LCGC;                                                   \
+      wstate = wstate + oWeylOffset + ((((signed int) wstate) >> 31) & oWeylPeriod); \
+      v = (state ^ (state >> 26)) + wstate;                                          \
+      s = (signed int) ((v ^ (v >> 20)) * 0x6957f5a7);                               \
+      r2 = s * TWO_N32 * (numtyp) 2.0 - (numtyp) 1.0;                                \
+      rsq = r1 * r1 + r2 * r2;                                                       \
+      if (rsq < (numtyp) 1.0) break;                                                 \
+    }                                                                                \
+    numtyp fac = sqrt((numtyp) -2.0 * log(rsq) / rsq);                               \
+    randnum = r2 * fac;                                                              \
+  }
+#endif
+
+/* ---------------------------------------------------------------------- */
+
+PairDPDCoulSlaterLongGPU::PairDPDCoulSlaterLongGPU(LAMMPS *lmp) : PairDPDCoulSlaterLong(lmp), gpu_mode(GPU_FORCE)
+{
+  respa_enable = 0;
+  reinitflag = 0;
+  cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
+  GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
+}
+
+/* ----------------------------------------------------------------------
+   free all arrays
+------------------------------------------------------------------------- */
+
+PairDPDCoulSlaterLongGPU::~PairDPDCoulSlaterLongGPU()
+{
+  dpd_coul_slater_long_gpu_clear();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairDPDCoulSlaterLongGPU::compute(int eflag, int vflag)
+{
+  ev_init(eflag, vflag);
+
+  int nall = atom->nlocal + atom->nghost;
+  int inum, host_start;
+
+  double dtinvsqrt = 1.0 / sqrt(update->dt);
+
+  bool success = true;
+  int *ilist, *numneigh, **firstneigh;
+
+  double *q = atom->q;
+  dpd_coul_slater_long_gpu_get_extra_data(q);
+
+  if (gpu_mode != GPU_FORCE) {
+    double sublo[3], subhi[3];
+    if (domain->triclinic == 0) {
+      sublo[0] = domain->sublo[0];
+      sublo[1] = domain->sublo[1];
+      sublo[2] = domain->sublo[2];
+      subhi[0] = domain->subhi[0];
+      subhi[1] = domain->subhi[1];
+      subhi[2] = domain->subhi[2];
+    } else {
+      domain->bbox(domain->sublo_lamda, domain->subhi_lamda, sublo, subhi);
+    }
+    inum = atom->nlocal;
+    firstneigh = dpd_coul_slater_long_gpu_compute_n(
+        neighbor->ago, inum, nall, atom->x, atom->type, sublo, subhi, atom->tag, atom->nspecial,
+        atom->special, eflag, vflag, eflag_atom, vflag_atom, host_start, &ilist, &numneigh,
+        cpu_time, success, atom->v, dtinvsqrt, seed, update->ntimestep, domain->boxlo, domain->prd);
+  } else {
+    inum = list->inum;
+    ilist = list->ilist;
+    numneigh = list->numneigh;
+    firstneigh = list->firstneigh;
+    dpd_coul_slater_long_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh,
+                    eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time, success, atom->tag,
+                    atom->v, dtinvsqrt, seed, update->ntimestep, atom->nlocal, domain->boxlo,
+                    domain->prd);
+  }
+  if (!success) error->one(FLERR, "Insufficient memory on accelerator");
+
+  if (atom->molecular != Atom::ATOMIC && neighbor->ago == 0)
+    neighbor->build_topology();
+  if (host_start < inum) {
+    cpu_time = platform::walltime();
+    cpu_compute(host_start, inum, eflag, vflag, ilist, numneigh, firstneigh);
+    cpu_time = platform::walltime() - cpu_time;
+  }
+}
+
+/* ----------------------------------------------------------------------
+   init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairDPDCoulSlaterLongGPU::init_style()
+{
+
+  if (comm->ghost_velocity == 0)
+    error->all(FLERR,"Pair dpd requires ghost atoms store velocity");
+  if (!atom->q_flag)
+    error->all(FLERR,"Pair style coul/slater/long requires atom attribute q");
+  // ensure use of KSpace long-range solver, set g_ewald
+  if (force->kspace == nullptr) error->all(FLERR, "Pair style requires a KSpace style");
+  g_ewald = force->kspace->g_ewald;
+
+  // Repeat cutsq calculation because done after call to init_style
+  double maxcut = -1.0;
+  double mcut;
+  for (int i = 1; i <= atom->ntypes; i++) {
+    for (int j = i; j <= atom->ntypes; j++) {
+      if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
+        mcut = init_one(i, j);
+        mcut *= mcut;
+        if (mcut > maxcut) maxcut = mcut;
+        cutsq[i][j] = cutsq[j][i] = mcut;
+      } else
+        cutsq[i][j] = cutsq[j][i] = 0.0;
+    }
+  }
+  double cell_size = sqrt(maxcut) + neighbor->skin;
+
+  int maxspecial = 0;
+  if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial;
+  int mnf = 5e-2 * neighbor->oneatom;
+  int success =
+      dpd_coul_slater_long_gpu_init(atom->ntypes + 1, cutsq, a0, gamma, sigma,
+                   cut_dpd, cut_dpdsq, cut_slatersq, force->special_lj, atom->nlocal,
+                   atom->nlocal + atom->nghost, mnf, maxspecial, cell_size, gpu_mode, screen,
+                   force->special_coul, force->qqrd2e, g_ewald, lamda);
+  GPU_EXTRA::check_flag(success, error, world);
+
+  if (gpu_mode == GPU_FORCE) neighbor->add_request(this, NeighConst::REQ_FULL);
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairDPDCoulSlaterLongGPU::memory_usage()
+{
+  double bytes = Pair::memory_usage();
+  return bytes + dpd_coul_slater_long_gpu_bytes();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairDPDCoulSlaterLongGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */, int *ilist,
+                             int *numneigh, int **firstneigh)
+{
+  int i, j, ii, jj, jnum, itype, jtype;
+  double qtmp, xtmp, ytmp, ztmp, delx, dely, delz, evdwl, ecoul, fpair;
+  double vxtmp, vytmp, vztmp, delvx, delvy, delvz;
+  double r2inv,forcedpd,forcecoul,factor_coul;
+  double grij,expm2,prefactor,t,erfc;
+  double rsq,r,rinv,dot,wd,randnum,factor_dpd,factor_sqrt;
+  int *jlist;
+  double slater_term;
+
+  tagint itag, jtag;
+
+  double *q = atom->q;
+  double *special_coul = force->special_coul;
+  double qqrd2e = force->qqrd2e;
+
+  evdwl = 0.0;
+  ecoul = 0.0;
+
+  double **x = atom->x;
+  double **v = atom->v;
+  double **f = atom->f;
+  int *type = atom->type;
+  tagint *tag = atom->tag;
+  double *special_lj = force->special_lj;
+  double dtinvsqrt = 1.0 / sqrt(update->dt);
+  int timestep = (int) update->ntimestep;
+
+  // loop over neighbors of my atoms
+
+  for (ii = start; ii < inum; ii++) {
+    i = ilist[ii];
+    qtmp = q[i];
+    xtmp = x[i][0];
+    ytmp = x[i][1];
+    ztmp = x[i][2];
+    vxtmp = v[i][0];
+    vytmp = v[i][1];
+    vztmp = v[i][2];
+    itype = type[i];
+    itag = tag[i];
+    jlist = firstneigh[i];
+    jnum = numneigh[i];
+
+    for (jj = 0; jj < jnum; jj++) {
+      j = jlist[jj];
+      factor_dpd = special_lj[sbmask(j)];
+      factor_sqrt = special_sqrt[sbmask(j)];
+      factor_coul = special_coul[sbmask(j)];
+      j &= NEIGHMASK;
+
+      delx = xtmp - x[j][0];
+      dely = ytmp - x[j][1];
+      delz = ztmp - x[j][2];
+      rsq = delx * delx + dely * dely + delz * delz;
+      jtype = type[j];
+      jtag = tag[j];
+
+      // forces if below maximum cutoff
+      if (rsq < cutsq[itype][jtype]) {
+        r = sqrt(rsq);
+        if (evflag) evdwl = ecoul = 0.0;
+        // apply DPD force if distance below DPD cutoff
+        if (rsq < cut_dpdsq[itype][jtype] && r > EPSILON ) {
+          rinv = 1.0 / r;
+          delvx = vxtmp - v[j][0];
+          delvy = vytmp - v[j][1];
+          delvz = vztmp - v[j][2];
+          dot = delx * delvx + dely * delvy + delz * delvz;
+          wd = 1.0 - r / cut[itype][jtype];
+
+          unsigned int tag1 = itag, tag2 = jtag;
+          if (tag1 > tag2) {
+            tag1 = jtag;
+            tag2 = itag;
+          }
+
+          randnum = 0.0;
+          saru(tag1, tag2, seed, timestep, randnum);
+
+          // conservative force = a0 * wd
+          // drag force = -gamma * wd^2 * (delx dot delv) / r
+          // random force = sigma * wd * rnd * dtinvsqrt;
+          forcedpd = a0[itype][jtype]*wd;
+          forcedpd -= gamma[itype][jtype]*wd*wd*dot*rinv;
+          forcedpd *= factor_dpd;
+          forcedpd += factor_sqrt*sigma[itype][jtype]*wd*randnum*dtinvsqrt;
+          forcedpd *= rinv;
+
+          if (eflag) {
+            // eng shifted to 0.0 at cutoff
+            evdwl = 0.5*a0[itype][jtype]*cut_dpd[itype][jtype] * wd*wd;
+            evdwl *= factor_dpd;
+          }
+
+        } else forcedpd = 0.0;
+
+        // apply Slater electrostatic force if distance below Slater cutoff
+        // and the two species are charged
+        if (rsq < cut_slatersq[itype][jtype]){
+          r2inv = 1.0/rsq;
+          grij = g_ewald * r;
+          expm2 = exp(-grij*grij);
+          t = 1.0 / (1.0 + EWALD_P*grij);
+          erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+          slater_term = exp(-2*r/lamda)*(1 + (2*r/lamda*(1+r/lamda)));
+          prefactor = qqrd2e * qtmp*q[j]/r;
+          forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - slater_term);
+          if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor*(1-slater_term);
+          forcecoul *= r2inv;
+
+          if (eflag) {
+            ecoul = prefactor*(erfc - (1 + r/lamda)*exp(-2*r/lamda));
+            if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor*(1.0-(1 + r/lamda)*exp(-2*r/lamda));
+          }
+
+        } else forcecoul = 0.0;
+
+        fpair = forcedpd + forcecoul;
+
+        f[i][0] += delx * fpair;
+        f[i][1] += dely * fpair;
+        f[i][2] += delz * fpair;
+
+        if (evflag) ev_tally_full(i, evdwl, ecoul, fpair, delx, dely, delz);
+      }
+    }
+  }
+}

src/GPU/pair_dpd_coul_slater_long_gpu.h

@@ -0,0 +1,45 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+// clang-format off
+PairStyle(dpd/coul/slater/long/gpu,PairDPDCoulSlaterLongGPU);
+// clang-format on
+#else
+
+#ifndef LMP_PAIR_DPD_COUL_SLATER_LONG_GPU_H
+#define LMP_PAIR_DPD_COUL_SLATER_LONG_GPU_H
+
+#include "pair_dpd_coul_slater_long.h"
+
+namespace LAMMPS_NS {
+
+class PairDPDCoulSlaterLongGPU : public PairDPDCoulSlaterLong {
+ public:
+  PairDPDCoulSlaterLongGPU(LAMMPS *lmp);
+  ~PairDPDCoulSlaterLongGPU() override;
+  void cpu_compute(int, int, int, int, int *, int *, int **);
+  void compute(int, int) override;
+  void init_style() override;
+  double memory_usage() override;
+
+  enum { GPU_FORCE, GPU_NEIGH, GPU_HYB_NEIGH };
+
+ private:
+  int gpu_mode;
+  double cpu_time;
+};
+
+}    // namespace LAMMPS_NS
+#endif
+#endif

src/GRANULAR/gran_sub_mod_damping.cpp

@@ -156,6 +156,7 @@ double GranSubModDampingTsuji::calculate_forces()
 GranSubModDampingCoeffRestitution::GranSubModDampingCoeffRestitution(GranularModel *gm, LAMMPS *lmp) :
     GranSubModDamping(gm, lmp)
 {
+  allow_cohesion = 0;
 }
 
 void GranSubModDampingCoeffRestitution::init()
@@ -173,6 +174,12 @@ void GranSubModDampingCoeffRestitution::init()
 
 double GranSubModDampingCoeffRestitution::calculate_forces()
 {
-  damp_prefactor = damp * sqrt(gm->meff * gm->Fnormal / gm->delta);
+  // in case argument <= 0 due to precision issues
+  double sqrt1;
+  if (gm->delta > 0.0)
+    sqrt1 = MAX(0.0, gm->meff * gm->Fnormal / gm->delta);
+  else
+    sqrt1 = 0.0;
+  damp_prefactor = damp * sqrt(sqrt1);
   return -damp_prefactor * gm->vnnr;
 }

src/INTEL/npair_skip_intel.cpp

@@ -74,9 +74,13 @@ void NPairSkipIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
   const int nlocal = atom->nlocal;
   const int e_nall = nlocal + atom->nghost;
   const int * _noalias const type = atom->type;
+  const tagint * _noalias const molecule = atom->molecule;
+
   int * _noalias const ilist = list->ilist;
   int * _noalias const numneigh = list->numneigh;
   int ** _noalias const firstneigh = (int ** const)list->firstneigh;  // NOLINT
+  const int molskip = list->molskip;
+
   const int * _noalias const ilist_skip = list->listskip->ilist;
   const int * _noalias const numneigh_skip = list->listskip->numneigh;
   const int ** _noalias const firstneigh_skip = (const int ** const)list->listskip->firstneigh;  // NOLINT
@@ -110,7 +114,7 @@ void NPairSkipIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
     for (int ii = ifrom; ii < ito; ii++) {
       const int i = ilist_skip[ii];
       const int itype = type[i];
-      if (iskip[itype]) continue;
+      if (!molskip && iskip[itype]) continue;
 
       int n = 0;
       int *neighptr = ipage.vget();
@@ -142,7 +146,11 @@ void NPairSkipIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
         for (int jj = 0; jj < jnum; jj++) {
           const int joriginal = jlist[jj];
           const int j = joriginal & NEIGHMASK;
-          if (!ijskip[itype][type[j]]) neighptr[n++] = joriginal;
+          if (!molskip && ijskip[itype][type[j]]) continue;
+          if ((molskip == NeighRequest::INTRA) && (molecule[i] != molecule[j])) continue;
+          if ((molskip == NeighRequest::INTER) && (molecule[i] == molecule[j])) continue;
+
+          neighptr[n++] = joriginal;
         }
       }
 
@@ -269,9 +277,13 @@ void NPairSkipTrimIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
   const int e_nall = nlocal + atom->nghost;
   const ATOM_T * _noalias const x = buffers->get_x();
   const int * _noalias const type = atom->type;
+  const tagint * _noalias const molecule = atom->molecule;
+
   int * _noalias const ilist = list->ilist;
   int * _noalias const numneigh = list->numneigh;
   int ** _noalias const firstneigh = (int ** const)list->firstneigh;  // NOLINT
+  const int molskip = list->molskip;
+
   const int * _noalias const ilist_skip = list->listskip->ilist;
   const int * _noalias const numneigh_skip = list->listskip->numneigh;
   const int ** _noalias const firstneigh_skip = (const int ** const)list->listskip->firstneigh;  // NOLINT
@@ -306,7 +318,7 @@ void NPairSkipTrimIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
     for (int ii = ifrom; ii < ito; ii++) {
       const int i = ilist_skip[ii];
       const int itype = type[i];
-      if (iskip[itype]) continue;
+      if (!molskip && iskip[itype]) continue;
 
       const flt_t xtmp = x[i].x;
       const flt_t ytmp = x[i].y;
@@ -370,7 +382,9 @@ void NPairSkipTrimIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh,
           const int j = joriginal & NEIGHMASK;
 
           int addme = 1;
-          if (ijskip[itype][type[j]]) addme = 0;
+          if (!molskip && ijskip[itype][type[j]]) addme = 0;
+          if ((molskip == NeighRequest::INTRA) && (molecule[i] != molecule[j])) addme = 0;
+          if ((molskip == NeighRequest::INTER) && (molecule[i] == molecule[j])) addme = 0;
 
           // trim to shorter cutoff
 

src/KOKKOS/Install.sh

@@ -365,6 +365,8 @@ action pair_reaxff_kokkos.h pair_reaxff.h
 action pair_snap_kokkos_impl.h pair_snap.cpp
 action pair_snap_kokkos.cpp pair_snap.cpp
 action pair_snap_kokkos.h pair_snap.h
+action pair_soft_kokkos.cpp
+action pair_soft_kokkos.h
 action pair_sw_kokkos.cpp pair_sw.cpp
 action pair_sw_kokkos.h pair_sw.h
 action pair_table_kokkos.cpp

src/KOKKOS/pair_soft_kokkos.cpp

@@ -0,0 +1,255 @@
+// clang-format off
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "pair_soft_kokkos.h"
+
+#include "atom_kokkos.h"
+#include "atom_masks.h"
+#include "error.h"
+#include "force.h"
+#include "kokkos.h"
+#include "math_const.h"
+#include "memory_kokkos.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+#include "respa.h"
+#include "update.h"
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+PairSoftKokkos<DeviceType>::PairSoftKokkos(LAMMPS *lmp) : PairSoft(lmp)
+{
+  respa_enable = 0;
+
+  kokkosable = 1;
+  atomKK = (AtomKokkos *) atom;
+  execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
+  datamask_read = X_MASK | F_MASK | TYPE_MASK | ENERGY_MASK | VIRIAL_MASK;
+  datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+PairSoftKokkos<DeviceType>::~PairSoftKokkos()
+{
+  if (copymode) return;
+
+  if (allocated) {
+    memoryKK->destroy_kokkos(k_eatom,eatom);
+    memoryKK->destroy_kokkos(k_vatom,vatom);
+    memoryKK->destroy_kokkos(k_cutsq,cutsq);
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairSoftKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
+{
+  eflag = eflag_in;
+  vflag = vflag_in;
+
+  if (neighflag == FULL) no_virial_fdotr_compute = 1;
+
+  ev_init(eflag,vflag,0);
+
+  // reallocate per-atom arrays if necessary
+
+  if (eflag_atom) {
+    memoryKK->destroy_kokkos(k_eatom,eatom);
+    memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
+    d_eatom = k_eatom.view<DeviceType>();
+  }
+  if (vflag_atom) {
+    memoryKK->destroy_kokkos(k_vatom,vatom);
+    memoryKK->create_kokkos(k_vatom,vatom,maxvatom,"pair:vatom");
+    d_vatom = k_vatom.view<DeviceType>();
+  }
+
+  atomKK->sync(execution_space,datamask_read);
+  k_cutsq.template sync<DeviceType>();
+  k_params.template sync<DeviceType>();
+  if (eflag || vflag) atomKK->modified(execution_space,datamask_modify);
+  else atomKK->modified(execution_space,F_MASK);
+
+  x = atomKK->k_x.view<DeviceType>();
+  c_x = atomKK->k_x.view<DeviceType>();
+  f = atomKK->k_f.view<DeviceType>();
+  type = atomKK->k_type.view<DeviceType>();
+  nlocal = atom->nlocal;
+  nall = atom->nlocal + atom->nghost;
+  newton_pair = force->newton_pair;
+  special_lj[0] = force->special_lj[0];
+  special_lj[1] = force->special_lj[1];
+  special_lj[2] = force->special_lj[2];
+  special_lj[3] = force->special_lj[3];
+
+  // loop over neighbors of my atoms
+
+  copymode = 1;
+
+  EV_FLOAT ev = pair_compute<PairSoftKokkos<DeviceType>,void >(this,(NeighListKokkos<DeviceType>*)list);
+
+  if (eflag_global) eng_vdwl += ev.evdwl;
+  if (vflag_global) {
+    virial[0] += ev.v[0];
+    virial[1] += ev.v[1];
+    virial[2] += ev.v[2];
+    virial[3] += ev.v[3];
+    virial[4] += ev.v[4];
+    virial[5] += ev.v[5];
+  }
+
+  if (eflag_atom) {
+    k_eatom.template modify<DeviceType>();
+    k_eatom.template sync<LMPHostType>();
+  }
+
+  if (vflag_atom) {
+    k_vatom.template modify<DeviceType>();
+    k_vatom.template sync<LMPHostType>();
+  }
+
+  if (vflag_fdotr) pair_virial_fdotr_compute(this);
+
+  copymode = 0;
+}
+
+template<class DeviceType>
+template<bool STACKPARAMS, class Specialisation>
+KOKKOS_INLINE_FUNCTION
+F_FLOAT PairSoftKokkos<DeviceType>::
+compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const {
+  (void) i;
+  const F_FLOAT r = sqrt(rsq);
+  const F_FLOAT cut_ij = STACKPARAMS?m_params[itype][jtype].cut:params(itype,jtype).cut;
+  const F_FLOAT prefactor_ij = STACKPARAMS?m_params[itype][jtype].prefactor:params(itype,jtype).prefactor;
+  const F_FLOAT arg = MY_PI*r/cut_ij;
+
+  F_FLOAT fpair = 0.0;
+  if (r > 0.0) fpair = prefactor_ij *
+                 sin(arg) * MY_PI/cut_ij/r;
+
+  return fpair;
+}
+
+template<class DeviceType>
+template<bool STACKPARAMS, class Specialisation>
+KOKKOS_INLINE_FUNCTION
+F_FLOAT PairSoftKokkos<DeviceType>::
+compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const {
+  (void) i;
+  const F_FLOAT r = sqrt(rsq);
+  const F_FLOAT cut_ij = STACKPARAMS?m_params[itype][jtype].cut:params(itype,jtype).cut;
+  const F_FLOAT prefactor_ij = STACKPARAMS?m_params[itype][jtype].prefactor:params(itype,jtype).prefactor;
+  const F_FLOAT arg = MY_PI*r/cut_ij;
+
+  return prefactor_ij*(1.0+cos(arg));
+}
+
+/* ----------------------------------------------------------------------
+   allocate all arrays
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairSoftKokkos<DeviceType>::allocate()
+{
+  PairSoft::allocate();
+
+  int n = atom->ntypes;
+  memory->destroy(cutsq);
+  memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
+  d_cutsq = k_cutsq.template view<DeviceType>();
+  k_params = Kokkos::DualView<params_soft**,Kokkos::LayoutRight,DeviceType>("PairSoft::params",n+1,n+1);
+  params = k_params.template view<DeviceType>();
+}
+
+/* ----------------------------------------------------------------------
+   global settings
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairSoftKokkos<DeviceType>::settings(int narg, char **arg)
+{
+  if (narg > 2) error->all(FLERR,"Illegal pair_style command");
+
+  PairSoft::settings(1,arg);
+}
+
+/* ----------------------------------------------------------------------
+   init specific to this pair style
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairSoftKokkos<DeviceType>::init_style()
+{
+  PairSoft::init_style();
+
+  // error if rRESPA with inner levels
+
+  if (update->whichflag == 1 && utils::strmatch(update->integrate_style,"^respa")) {
+    int respa = 0;
+    if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
+    if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
+    if (respa)
+      error->all(FLERR,"Cannot use Kokkos pair style with rRESPA inner/middle");
+  }
+
+  // adjust neighbor list request for KOKKOS
+
+  neighflag = lmp->kokkos->neighflag;
+  auto request = neighbor->find_request(this);
+  request->set_kokkos_host(std::is_same_v<DeviceType,LMPHostType> &&
+                           !std::is_same_v<DeviceType,LMPDeviceType>);
+  request->set_kokkos_device(std::is_same_v<DeviceType,LMPDeviceType>);
+  if (neighflag == FULL) request->enable_full();
+}
+
+/* ----------------------------------------------------------------------
+   init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+double PairSoftKokkos<DeviceType>::init_one(int i, int j)
+{
+  double cutone = PairSoft::init_one(i,j);
+
+  k_params.h_view(i,j).prefactor = prefactor[i][j];
+  k_params.h_view(i,j).cut = cutone;
+  k_params.h_view(i,j).cutsq = cutone*cutone;
+  k_params.h_view(j,i) = k_params.h_view(i,j);
+  if (i<MAX_TYPES_STACKPARAMS+1 && j<MAX_TYPES_STACKPARAMS+1) {
+    m_params[i][j] = m_params[j][i] = k_params.h_view(i,j);
+    m_cutsq[j][i] = m_cutsq[i][j] = cutone*cutone;
+  }
+
+  k_cutsq.h_view(i,j) = k_cutsq.h_view(j,i) = cutone*cutone;
+  k_cutsq.template modify<LMPHostType>();
+  k_params.template modify<LMPHostType>();
+
+  return cutone;
+}
+
+namespace LAMMPS_NS {
+template class PairSoftKokkos<LMPDeviceType>;
+#ifdef LMP_KOKKOS_GPU
+template class PairSoftKokkos<LMPHostType>;
+#endif
+}
+

src/KOKKOS/pair_soft_kokkos.h

@@ -0,0 +1,114 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+// clang-format off
+PairStyle(soft/kk,PairSoftKokkos<LMPDeviceType>);
+PairStyle(soft/kk/device,PairSoftKokkos<LMPDeviceType>);
+PairStyle(soft/kk/host,PairSoftKokkos<LMPHostType>);
+// clang-format on
+#else
+
+// clang-format off
+#ifndef LMP_PAIR_SOFT_KOKKOS_H
+#define LMP_PAIR_SOFT_KOKKOS_H
+
+#include "pair_kokkos.h"
+#include "pair_soft.h"
+#include "neigh_list_kokkos.h"
+
+namespace LAMMPS_NS {
+
+template<class DeviceType>
+class PairSoftKokkos : public PairSoft {
+ public:
+  enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF};
+  enum {COUL_FLAG=0};
+  typedef DeviceType device_type;
+  typedef ArrayTypes<DeviceType> AT;
+  PairSoftKokkos(class LAMMPS *);
+  ~PairSoftKokkos() override;
+
+  void compute(int, int) override;
+
+  void settings(int, char **) override;
+  void init_style() override;
+  double init_one(int, int) override;
+
+  struct params_soft{
+    KOKKOS_INLINE_FUNCTION
+    params_soft() {cutsq=0,cut=0,prefactor=0;};
+    KOKKOS_INLINE_FUNCTION
+    params_soft(int /*i*/) {cutsq=0,cut=0,prefactor=0;};
+    F_FLOAT cutsq,cut,prefactor;
+  };
+
+ protected:
+  template<bool STACKPARAMS, class Specialisation>
+  KOKKOS_INLINE_FUNCTION
+  F_FLOAT compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const;
+
+  template<bool STACKPARAMS, class Specialisation>
+  KOKKOS_INLINE_FUNCTION
+  F_FLOAT compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const;
+
+  template<bool STACKPARAMS, class Specialisation>
+  KOKKOS_INLINE_FUNCTION
+  F_FLOAT compute_ecoul(const F_FLOAT& /*rsq*/, const int& /*i*/, const int& /*j*/,
+                        const int& /*itype*/, const int& /*jtype*/) const { return 0; }
+
+  Kokkos::DualView<params_soft**,Kokkos::LayoutRight,DeviceType> k_params;
+  typename Kokkos::DualView<params_soft**,Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
+  params_soft m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];  // hardwired to space for 12 atom types
+  F_FLOAT m_cutsq[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
+  typename AT::t_x_array_randomread x;
+  typename AT::t_x_array c_x;
+  typename AT::t_f_array f;
+  typename AT::t_int_1d_randomread type;
+
+  DAT::tdual_efloat_1d k_eatom;
+  DAT::tdual_virial_array k_vatom;
+  typename AT::t_efloat_1d d_eatom;
+  typename AT::t_virial_array d_vatom;
+
+  int newton_pair;
+  double special_lj[4];
+
+  typename AT::tdual_ffloat_2d k_cutsq;
+  typename AT::t_ffloat_2d d_cutsq;
+
+  int neighflag;
+  int nlocal,nall,eflag,vflag;
+
+  void allocate() override;
+  friend struct PairComputeFunctor<PairSoftKokkos,FULL,true,0>;
+  friend struct PairComputeFunctor<PairSoftKokkos,FULL,true,1>;
+  friend struct PairComputeFunctor<PairSoftKokkos,HALF,true>;
+  friend struct PairComputeFunctor<PairSoftKokkos,HALFTHREAD,true>;
+  friend struct PairComputeFunctor<PairSoftKokkos,FULL,false,0>;
+  friend struct PairComputeFunctor<PairSoftKokkos,FULL,false,1>;
+  friend struct PairComputeFunctor<PairSoftKokkos,HALF,false>;
+  friend struct PairComputeFunctor<PairSoftKokkos,HALFTHREAD,false>;
+  friend EV_FLOAT pair_compute_neighlist<PairSoftKokkos,FULL,0>(PairSoftKokkos*,NeighListKokkos<DeviceType>*);
+  friend EV_FLOAT pair_compute_neighlist<PairSoftKokkos,FULL,1>(PairSoftKokkos*,NeighListKokkos<DeviceType>*);
+  friend EV_FLOAT pair_compute_neighlist<PairSoftKokkos,HALF>(PairSoftKokkos*,NeighListKokkos<DeviceType>*);
+  friend EV_FLOAT pair_compute_neighlist<PairSoftKokkos,HALFTHREAD>(PairSoftKokkos*,NeighListKokkos<DeviceType>*);
+  friend EV_FLOAT pair_compute<PairSoftKokkos>(PairSoftKokkos*,NeighListKokkos<DeviceType>*);
+  friend void pair_virial_fdotr_compute<PairSoftKokkos>(PairSoftKokkos*);
+};
+
+}
+
+#endif
+#endif
+

src/KOKKOS/pair_uf3_kokkos.h

@@ -0,0 +1,187 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Ajinkya Hire (Univ. of Florida),
+                        Hendrik Kraß (Univ. of Constance),
+                        Matthias Rupp (Luxembourg Institute of Science and Technology),
+                        Richard Hennig (Univ of Florida)
+---------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+// clang-format off
+PairStyle(uf3/kk,PairUF3Kokkos<LMPDeviceType>)
+PairStyle(uf3/kk/device,PairUF3Kokkos<LMPDeviceType>)
+// clang-format on
+#else
+
+#ifndef LMP_PAIR_UF3_KOKKOS_H
+#define LMP_PAIR_UF3_KOKKOS_H
+
+#include "kokkos.h"
+#include "pair_kokkos.h"
+#include "pair_uf3.h"
+
+template <int NEIGHFLAG, int EVFLAG> struct TagPairUF3ComputeFullA {};
+struct TagPairUF3ComputeShortNeigh {};
+
+namespace LAMMPS_NS {
+
+template <class DeviceType> class PairUF3Kokkos : public PairUF3 {
+ public:
+  PairUF3Kokkos(class LAMMPS *);
+  ~PairUF3Kokkos() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  void allocate();
+  void init_style() override;
+  void init_list(int, class NeighList *) override;    // needed for ptr to full neigh list
+  double init_one(int, int) override;                 // needed for cutoff radius for neighbour list
+  double single(int, int, int, int, double, double, double, double &) override;
+
+  template <typename T, typename V> void copy_2d(V &d, T **h, int m, int n);
+  template <typename T, typename V> void copy_3d(V &d, T ***h, int m, int n, int o);
+
+  template <int NEIGHFLAG, int EVFLAG>
+  KOKKOS_INLINE_FUNCTION void operator()(TagPairUF3ComputeFullA<NEIGHFLAG, EVFLAG>, const int &,
+                                         EV_FLOAT &) const;
+
+  template <int NEIGHFLAG, int EVFLAG>
+  KOKKOS_INLINE_FUNCTION void operator()(TagPairUF3ComputeFullA<NEIGHFLAG, EVFLAG>,
+                                         const int &) const;
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()(TagPairUF3ComputeShortNeigh, const int &) const;
+
+  enum { EnabledNeighFlags = FULL };
+  enum { COUL_FLAG = 0 };
+  typedef DeviceType device_type;
+  typedef ArrayTypes<DeviceType> AT;
+  typedef EV_FLOAT value_type;
+
+ protected:
+  typename AT::tdual_ffloat_2d k_cutsq;//Create a DualView, defination of tdual_ffloat_2d in kokkos_type.h
+  typename AT::t_ffloat_2d d_cutsq; //t_ffloat_2d = t_dev ==> Creates a new View d_cutsq
+  //the type of d_cutsq is decided by the Device(not host) type for the DualView k_cutsq
+  //Meaning the memory location of d_cutsq is the same as the Device(not host) memory location of
+  //k_cutsq
+  typedef Kokkos::DualView<F_FLOAT***, Kokkos::LayoutRight, DeviceType> tdual_ffloat_3d;
+  typedef Kokkos::DualView<F_FLOAT****, Kokkos::LayoutRight, DeviceType> tdual_ffloat_4d;
+  tdual_ffloat_3d k_cut_3b;
+  tdual_ffloat_4d k_min_cut_3b;
+  typename tdual_ffloat_3d::t_dev d_cut_3b;
+  typename tdual_ffloat_4d::t_dev d_min_cut_3b;
+  template <typename TYPE> void destroy_3d(TYPE data, typename TYPE::value_type*** &array);
+  template <typename TYPE> void destroy_4d(TYPE data, typename TYPE::value_type**** &array);
+  Kokkos::View<F_FLOAT **, LMPDeviceType::array_layout, LMPDeviceType> /*d_cutsq,*/ d_cut_3b_list;
+  //Kokkos::View<F_FLOAT ***, LMPDeviceType::array_layout, LMPDeviceType> d_cut_3b;
+
+  Kokkos::View<F_FLOAT **, LMPDeviceType::array_layout, LMPDeviceType> d_coefficients_2b;
+  Kokkos::View<F_FLOAT **, LMPDeviceType::array_layout, LMPDeviceType> d_dncoefficients_2b;
+  Kokkos::View<F_FLOAT **, LMPDeviceType::array_layout, LMPDeviceType> d_n2b_knot;
+  Kokkos::View<F_FLOAT *, LMPDeviceType::array_layout, LMPDeviceType> d_n2b_knot_spacings;
+  Kokkos::View<int **, LMPDeviceType::array_layout, LMPDeviceType> map2b;
+  Kokkos::View<F_FLOAT[4][4], LMPDeviceType::array_layout, LMPDeviceType> constants;
+  Kokkos::View<F_FLOAT[3][3], LMPDeviceType::array_layout, LMPDeviceType> dnconstants;
+  Kokkos::View<F_FLOAT ***, LMPDeviceType::array_layout, LMPDeviceType> d_n3b_knot_matrix;
+  Kokkos::View<F_FLOAT ****, LMPDeviceType::array_layout, LMPDeviceType> d_coefficients_3b;
+  Kokkos::View<F_FLOAT *****, LMPDeviceType::array_layout, LMPDeviceType> d_dncoefficients_3b;
+  Kokkos::View<F_FLOAT **, LMPDeviceType::array_layout, LMPDeviceType> d_n3b_knot_spacings;
+  Kokkos::View<F_FLOAT **, LMPDeviceType::array_layout, LMPDeviceType> d_n3b_knot_matrix_spacings;
+  Kokkos::View<int ***, LMPDeviceType::array_layout, LMPDeviceType> map3b;
+
+  Kokkos::View<F_FLOAT **[16], LMPDeviceType::array_layout, LMPDeviceType> constants_2b;
+  Kokkos::View<F_FLOAT **[9], LMPDeviceType::array_layout, LMPDeviceType> dnconstants_2b;
+  Kokkos::View<F_FLOAT ***[16], LMPDeviceType::array_layout, LMPDeviceType> constants_3b;
+  Kokkos::View<F_FLOAT ***[9], LMPDeviceType::array_layout, LMPDeviceType> dnconstants_3b;
+
+  std::vector<F_FLOAT> get_constants(double *knots, double coefficient);
+  std::vector<F_FLOAT> get_dnconstants(double *knots, double coefficient);
+
+  int coefficients_created = 0;
+  void create_coefficients();
+  void create_3b_coefficients();
+  void create_2b_coefficients();
+  std::vector<F_FLOAT> get_coefficients(const double *knots, const double coefficient) const;
+  std::vector<F_FLOAT> get_dncoefficients(const double *knots, const double coefficient) const;
+
+  template <int EVFLAG>
+  void twobody(const int itype, const int jtype, const F_FLOAT r, F_FLOAT &evdwl,
+               F_FLOAT &fpair) const;
+  template <int EVFLAG>
+  void threebody(const int itype, const int jtype, const int ktype, const F_FLOAT value_rij,
+                 const F_FLOAT value_rik, const F_FLOAT value_rjk, F_FLOAT &evdwl3,
+                 F_FLOAT (&fforce)[3]) const;
+
+  template <int NEIGHFLAG>
+  KOKKOS_INLINE_FUNCTION void
+  ev_tally(EV_FLOAT &ev, const int &i, const int &j, const F_FLOAT &epair, const F_FLOAT &fpair,
+           const F_FLOAT &delx, const F_FLOAT &dely, const F_FLOAT &delz) const;
+
+  template <int NEIGHFLAG>
+  KOKKOS_INLINE_FUNCTION void ev_tally3(EV_FLOAT &ev, const int &i, const int &j, int &k,
+                                        const F_FLOAT &evdwl, const F_FLOAT &ecoul, F_FLOAT *fj,
+                                        F_FLOAT *fk, F_FLOAT *drji, F_FLOAT *drki) const;
+
+  typename AT::t_x_array_randomread x;
+  typename AT::t_f_array f;
+  typename AT::t_tagint_1d tag;
+  typename AT::t_int_1d_randomread type;
+
+  DAT::tdual_efloat_1d k_eatom;
+  DAT::tdual_virial_array k_vatom;
+  typename AT::t_efloat_1d d_eatom;
+  typename AT::t_virial_array d_vatom;
+
+  using ScatterFType = Kokkos::Experimental::ScatterView<F_FLOAT *[3], Kokkos::LayoutRight,
+                                                         typename DeviceType::memory_space>;
+  ScatterFType fscatter;
+  using ScatterVType = Kokkos::Experimental::ScatterView<F_FLOAT *[6], Kokkos::LayoutRight,
+                                                         typename DeviceType::memory_space>;
+  ScatterVType vscatter;
+  using ScatterCVType = Kokkos::Experimental::ScatterView<F_FLOAT *[9], Kokkos::LayoutRight,
+                                                          typename DeviceType::memory_space>;
+  ScatterCVType cvscatter;
+  using ScatterEType = Kokkos::Experimental::ScatterView<E_FLOAT *, LMPDeviceType::array_layout,
+                                                         typename DeviceType::memory_space>;
+  ScatterEType escatter;
+
+  typename AT::t_neighbors_2d d_neighbors;
+  typename AT::t_int_1d_randomread d_ilist;
+  typename AT::t_int_1d_randomread d_numneigh;
+
+  int neighflag, newton_pair;
+  int nlocal, nall, eflag, vflag;
+
+  int inum;
+  Kokkos::View<int **, DeviceType> d_neighbors_short;
+  Kokkos::View<int *, DeviceType> d_numneigh_short;
+
+  friend void pair_virial_fdotr_compute<PairUF3Kokkos>(PairUF3Kokkos *);
+};
+
+KOKKOS_INLINE_FUNCTION int min(int i, int j)
+{
+  return i < j ? i : j;
+}
+KOKKOS_INLINE_FUNCTION int max(int i, int j)
+{
+  return i > j ? i : j;
+}
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif
+

src/MANYBODY/pair_sw.cpp

@@ -250,6 +250,7 @@ void PairSW::settings(int narg, char ** arg)
       // pair_coeff * * and can enable the single function.
       one_coeff = skip_threebody_flag ? 0 : 1;
       single_enable = skip_threebody_flag ? 1 : 0;
+      manybody_flag = skip_threebody_flag ? 0 : 1;
       iarg += 2;
     } else error->all(FLERR, "Illegal pair_style sw keyword: {}", arg[iarg]);
   }

src/MC/fix_gcmc.cpp

@@ -2233,7 +2233,8 @@ void FixGCMC::attempt_molecule_insertion_full()
 }
 
 /* ----------------------------------------------------------------------
-   compute particle's interaction energy with the rest of the system
+   compute particle's interaction energy with the rest of the system by
+   looping over all atoms in the sub-domain including ghosts.
 ------------------------------------------------------------------------- */
 
 double FixGCMC::energy(int i, int itype, tagint imolecule, double *coord)

src/MC/fix_widom.cpp

@@ -973,7 +973,8 @@ void FixWidom::attempt_molecule_insertion_full()
 }
 
 /* ----------------------------------------------------------------------
-   compute particle's interaction energy with the rest of the system
+   compute particle's interaction energy with the rest of the system by
+   looping over all atoms in the sub-domain including ghosts.
 ------------------------------------------------------------------------- */
 
 double FixWidom::energy(int i, int itype, tagint imolecule, double *coord)

src/ML-IAP/mliap_descriptor_ace.cpp

@@ -136,7 +136,6 @@ void MLIAPDescriptorACE::compute_descriptors(class MLIAPData *data)
   int nei = 0;
   int jtmp = 0;
   for (int iitmp = 0; iitmp < data->nlistatoms; iitmp++) {
-    int itmp = data->iatoms[iitmp];
     jtmp = data->numneighs[iitmp];
     nei = nei + jtmp;
     if (jtmp > max_jnum) { max_jnum = jtmp; }
@@ -144,7 +143,6 @@ void MLIAPDescriptorACE::compute_descriptors(class MLIAPData *data)
 
   for (int ii = 0; ii < data->nlistatoms; ii++) {
     const int i = data->iatoms[ii];
-    const int ielemx = data->ielems[ii];
     const int jnum = data->numneighs[ii];
 
     delete acemlimpl->ace;
@@ -184,7 +182,6 @@ void MLIAPDescriptorACE::compute_forces(class MLIAPData *data)
   int nei = 0;
   int jtmp = 0;
   for (int iitmp = 0; iitmp < data->nlistatoms; iitmp++) {
-    int itmp = data->iatoms[iitmp];
     jtmp = data->numneighs[iitmp];
     nei = nei + jtmp;
     if (jtmp > max_jnum) { max_jnum = jtmp; }
@@ -193,7 +190,6 @@ void MLIAPDescriptorACE::compute_forces(class MLIAPData *data)
   // BEGIN force loop
   for (int ii = 0; ii < data->nlistatoms; ii++) {
     const int i = data->iatoms[ii];
-    const int ielem = data->ielems[ii];
     delete acemlimpl->ace;
     acemlimpl->ace = new ACECTildeEvaluator(*acemlimpl->basis_set);
     acemlimpl->ace->compute_projections = 1;
@@ -268,7 +264,6 @@ void MLIAPDescriptorACE::compute_force_gradients(class MLIAPData *data)
   int nei = 0;
   int jtmp = 0;
   for (int iitmp = 0; iitmp < data->nlistatoms; iitmp++) {
-    int itmp = data->iatoms[iitmp];
     jtmp = data->numneighs[iitmp];
     nei = nei + jtmp;
     if (jtmp > max_jnum) { max_jnum = jtmp; }
@@ -276,7 +271,6 @@ void MLIAPDescriptorACE::compute_force_gradients(class MLIAPData *data)
 
   for (int ii = 0; ii < data->nlistatoms; ii++) {
     const int i = data->iatoms[ii];
-    const int ielem = data->ielems[ii];
     delete acemlimpl->ace;
     acemlimpl->ace = new ACECTildeEvaluator(*acemlimpl->basis_set);
     acemlimpl->ace->compute_projections = 1;
@@ -327,14 +321,12 @@ void MLIAPDescriptorACE::compute_descriptor_gradients(class MLIAPData *data)
   int nei = 0;
   int jtmp = 0;
   for (int iitmp = 0; iitmp < data->nlistatoms; iitmp++) {
-    int itmp = data->iatoms[iitmp];
     jtmp = data->numneighs[iitmp];
     nei = nei + jtmp;
     if (jtmp > max_jnum) { max_jnum = jtmp; }
   }
   for (int ii = 0; ii < data->nlistatoms; ii++) {
     const int i = data->iatoms[ii];
-    const int ielem = data->ielems[ii];
     delete acemlimpl->ace;
     acemlimpl->ace = new ACECTildeEvaluator(*acemlimpl->basis_set);
     acemlimpl->ace->compute_projections = 1;
@@ -349,7 +341,6 @@ void MLIAPDescriptorACE::compute_descriptor_gradients(class MLIAPData *data)
       }
     }
 
-    const int *const jlist = data->lmp_firstneigh[ii];
     const int jnum = data->numneighs[ii];
     acemlimpl->ace->resize_neighbours_cache(jnum);
     acemlimpl->ace->compute_atom(i, atom->x, atom->type, data->numneighs[ii],
@@ -363,11 +354,6 @@ void MLIAPDescriptorACE::compute_descriptor_gradients(class MLIAPData *data)
 
     ij = ij0;
     for (int jj = 0; jj < data->numneighs[ii]; jj++) {
-      const int jt = data->jatoms[ij];
-
-      const int j = jlist[jj];
-      int yoffset = ndescriptors;
-      int zoffset = ndescriptors * 2;
       for (int iicoeff = 0; iicoeff < ndescriptors; iicoeff++) {
         DOUBLE_TYPE fx_dB = acemlimpl->ace->neighbours_dB(iicoeff, jj, 0);
         DOUBLE_TYPE fy_dB = acemlimpl->ace->neighbours_dB(iicoeff, jj, 1);

src/ML-UF3/pair_uf3.h

@@ -0,0 +1,95 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Ajinkya Hire (Univ. of Florida),
+                        Hendrik Kraß (Univ. of Constance),
+                        Matthias Rupp (Luxembourg Institute of Science and Technology),
+                        Richard Hennig (Univ of Florida)
+---------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+// clang-format off
+PairStyle(uf3,PairUF3);
+// clang-format on
+#else
+
+#ifndef LMP_PAIR_UF3_H
+#define LMP_PAIR_UF3_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairUF3 : public Pair {
+ public:
+  PairUF3(class LAMMPS *);
+  ~PairUF3() override;
+  void compute(int, int) override;
+  void settings(int, char **) override;
+  void coeff(int, char **) override;
+  void init_style() override;
+  void init_list(int, class NeighList *) override;    // needed for ptr to full neigh list
+  double init_one(int, int) override;                 // needed for cutoff radius for neighbour list
+  double single(int, int, int, int, double, double, double, double &) override;
+
+  double memory_usage() override;
+
+ protected:
+  int ***setflag_3b, **knot_spacing_type_2b, ***knot_spacing_type_3b;
+  double **cut, ***cut_3b, **cut_3b_list, ****min_cut_3b;
+  double **knot_spacing_2b, ****knot_spacing_3b;
+
+  double ***n2b_knots_array, ***n2b_coeff_array;
+  int **n2b_knots_array_size, **n2b_coeff_array_size;
+  double ****cached_constants_2b, ****cached_constants_2b_deri;
+
+  int ***map_3b;
+  double ***n3b_knots_array, ****n3b_coeff_array;
+  int **n3b_knots_array_size, **n3b_coeff_array_size;
+  double ****coeff_for_der_jk, ****coeff_for_der_ik,****coeff_for_der_ij;
+  double ****cached_constants_3b, ****cached_constants_3b_deri;
+
+  int *neighshort, maxshort;    // short neighbor list array for 3body interaction
+
+  void uf3_read_unified_pot_file(char *potf_name);
+  void communicate();
+  int bsplines_created;
+  bool pot_3b;
+  virtual void allocate();
+  void create_bsplines();
+  void create_cached_constants_2b();
+  void create_cached_constants_3b();
+
+  int get_starting_index_uniform_2b(int i, int j, double r);
+  int get_starting_index_uniform_3b(int i, int j, int k, double r, int knot_dim);
+
+  int get_starting_index_nonuniform_2b(int i, int j, double r);
+  int get_starting_index_nonuniform_3b(int i, int j, int k, double r, int knot_dim);
+
+  int (PairUF3::*get_starting_index_2b)(int i, int j, double r);
+  int (PairUF3::*get_starting_index_3b)(int i, int j, int k, double r, int knot_dim);
+
+  int nbody_flag = 3;
+  int max_num_knots_2b = 0;
+  int max_num_coeff_2b = 0;
+  int max_num_knots_3b = 0;
+  int max_num_coeff_3b = 0;
+  int tot_interaction_count_3b = 0;
+};
+
+}    // namespace LAMMPS_NS
+
+#endif
+#endif
+

src/ML-UF3/uf3_bspline_basis2.cpp

@@ -0,0 +1,111 @@
+// clang-format off
+/* ----------------------------------------------------------------------
+   lammps - large-scale atomic/molecular massively parallel simulator
+   https://www.lammps.org/, sandia national laboratories
+   lammps development team: developers@lammps.org
+
+   copyright (2003) sandia corporation.  under the terms of contract
+   de-ac04-94al85000 with sandia corporation, the u.s. government retains
+   certain rights in this software.  this software is distributed under
+   the gnu general public license.
+
+   see the readme file in the top-level lammps directory.
+------------------------------------------------------------------------- */
+
+#include "uf3_bspline_basis2.h"
+
+#include "math_special.h"
+
+using namespace LAMMPS_NS;
+using MathSpecial::square;
+
+// Constructor
+// Initializes coefficients and knots
+// Requires [knots] to have length 4
+uf3_bspline_basis2::uf3_bspline_basis2(LAMMPS *ulmp, const double *knots, double coefficient)
+{
+  lmp = ulmp;
+
+  double c0, c1, c2;
+
+  c0 = coefficient
+    * (square(knots[0])
+       / (square(knots[0]) - knots[0] * knots[1] - knots[0] * knots[2] + knots[1] * knots[2]));
+  c1 = coefficient *
+      (-2.0 * knots[0] /
+       (square(knots[0]) - knots[0] * knots[1] - knots[0] * knots[2] + knots[1] * knots[2]));
+  c2 = coefficient *
+      (1.0 / (square(knots[0]) - knots[0] * knots[1] - knots[0] * knots[2] + knots[1] * knots[2]));
+  //constants.push_back(c0);
+  //constants.push_back(c1);
+  //constants.push_back(c2);
+  constants[0] = c0;
+  constants[1] = c1;
+  constants[2] = c2;
+  c0 = coefficient *
+      (-knots[1] * knots[3] /
+           (square(knots[1]) - knots[1] * knots[2] - knots[1] * knots[3] + knots[2] * knots[3]) -
+       knots[0] * knots[2] /
+           (knots[0] * knots[1] - knots[0] * knots[2] - knots[1] * knots[2] + square(knots[2])));
+  c1 = coefficient *
+      (knots[1] /
+           (square(knots[1]) - knots[1] * knots[2] - knots[1] * knots[3] + knots[2] * knots[3]) +
+       knots[3] /
+           (square(knots[1]) - knots[1] * knots[2] - knots[1] * knots[3] + knots[2] * knots[3]) +
+       knots[0] /
+           (knots[0] * knots[1] - knots[0] * knots[2] - knots[1] * knots[2] + square(knots[2])) +
+       knots[2] /
+           (knots[0] * knots[1] - knots[0] * knots[2] - knots[1] * knots[2] + square(knots[2])));
+  c2 = coefficient *
+      (-1.0 / (square(knots[1]) - knots[1] * knots[2] - knots[1] * knots[3] + knots[2] * knots[3]) -
+       1.0 / (knots[0] * knots[1] - knots[0] * knots[2] - knots[1] * knots[2] + square(knots[2])));
+  //constants.push_back(c0);
+  //constants.push_back(c1);
+  //constants.push_back(c2);
+  constants[3] = c0;
+  constants[4] = c1;
+  constants[5] = c2;
+  c0 = coefficient *
+      (square(knots[3]) /
+       (knots[1] * knots[2] - knots[1] * knots[3] - knots[2] * knots[3] + square(knots[3])));
+  c1 = coefficient *
+      (-2.0 * knots[3] /
+       (knots[1] * knots[2] - knots[1] * knots[3] - knots[2] * knots[3] + square(knots[3])));
+  c2 = coefficient *
+      (1.0 / (knots[1] * knots[2] - knots[1] * knots[3] - knots[2] * knots[3] + square(knots[3])));
+  //constants.push_back(c0);
+  //constants.push_back(c1);
+  //constants.push_back(c2);
+  constants[6] = c0;
+  constants[7] = c1;
+  constants[8] = c2;
+}
+
+uf3_bspline_basis2::~uf3_bspline_basis2() {}
+
+// Evaluate outer-left part of spline
+double uf3_bspline_basis2::eval0(double rsq, double r)
+{
+  return rsq * constants[2] + r * constants[1] + constants[0];
+}
+
+// Evaluate center-left part of spline
+double uf3_bspline_basis2::eval1(double rsq, double r)
+{
+  return rsq * constants[5] + r * constants[4] + constants[3];
+}
+
+// Evaluate center-right part of spline
+double uf3_bspline_basis2::eval2(double rsq, double r)
+{
+  return rsq * constants[8] + r * constants[7] + constants[6];
+}
+
+double uf3_bspline_basis2::memory_usage()
+{
+  double bytes = 0;
+
+  bytes += (double)9*sizeof(double);
+
+  return bytes;
+}

src/ML-UF3/uf3_bspline_basis2.h

@@ -0,0 +1,41 @@
+// clang-format off
+/* ----------------------------------------------------------------------
+   lammps - large-scale atomic/molecular massively parallel simulator
+   https://www.lammps.org/, sandia national laboratories
+   lammps development team: developers@lammps.org
+
+   copyright (2003) sandia corporation.  under the terms of contract
+   de-ac04-94al85000 with sandia corporation, the u.s. government retains
+   certain rights in this software.  this software is distributed under
+   the gnu general public license.
+
+   see the readme file in the top-level lammps directory.
+------------------------------------------------------------------------- */
+#include "pointers.h"
+
+#include <vector>
+
+#ifndef UF3_BSPLINE_BASIS2_H
+#define UF3_BSPLINE_BASIS2_H
+
+namespace LAMMPS_NS {
+
+class uf3_bspline_basis2 {
+ private:
+  LAMMPS *lmp;
+  //std::vector<double> constants;
+
+ public:
+  uf3_bspline_basis2(LAMMPS *ulmp, const double *knots, double coefficient);
+  ~uf3_bspline_basis2();
+  //std::vector<double> constants;
+  double constants[9] = {};
+  double eval0(double, double);
+  double eval1(double, double);
+  double eval2(double, double);
+
+  double memory_usage();
+};
+
+}    // namespace LAMMPS_NS
+#endif

src/ML-UF3/uf3_bspline_basis3.cpp

@@ -0,0 +1,355 @@
+// clang-format off
+/* ----------------------------------------------------------------------
+   lammps - large-scale atomic/molecular massively parallel simulator
+   https://www.lammps.org/, sandia national laboratories
+   lammps development team: developers@lammps.org
+
+   copyright (2003) sandia corporation.  under the terms of contract
+   de-ac04-94al85000 with sandia corporation, the u.s. government retains
+   certain rights in this software.  this software is distributed under
+   the gnu general public license.
+
+   see the readme file in the top-level lammps directory.
+------------------------------------------------------------------------- */
+
+#include "uf3_bspline_basis3.h"
+
+#include "math_special.h"
+
+using namespace LAMMPS_NS;
+using MathSpecial::cube;
+using MathSpecial::square;
+
+// Constructor
+// Initializes coefficients and knots
+// [knots] needs to have length 4
+uf3_bspline_basis3::uf3_bspline_basis3(LAMMPS *ulmp, const double *knots, double coefficient)
+{
+  lmp = ulmp;
+
+  double c0, c1, c2, c3;
+
+  c0 = coefficient *
+      (-cube(knots[0]) /
+       (-cube(knots[0]) + square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
+        square(knots[0]) * knots[3] - knots[0] * knots[1] * knots[2] -
+        knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
+        knots[1] * knots[2] * knots[3]));
+  c1 = coefficient *
+      (3.0 * square(knots[0]) /
+       (-cube(knots[0]) + square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
+        square(knots[0]) * knots[3] - knots[0] * knots[1] * knots[2] -
+        knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
+        knots[1] * knots[2] * knots[3]));
+  c2 = coefficient *
+      (-3.0 * knots[0] /
+       (-cube(knots[0]) + square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
+        square(knots[0]) * knots[3] - knots[0] * knots[1] * knots[2] -
+        knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
+        knots[1] * knots[2] * knots[3]));
+  c3 = coefficient *
+      (1.0 /
+       (-cube(knots[0]) + square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
+        square(knots[0]) * knots[3] - knots[0] * knots[1] * knots[2] -
+        knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
+        knots[1] * knots[2] * knots[3]));
+  //constants.push_back(c0);
+  //constants.push_back(c1);
+  //constants.push_back(c2);
+  //constants.push_back(c3);
+  constants[0] = c0;
+  constants[1] = c1;
+  constants[2] = c2;
+  constants[3] = c3;
+  c0 = coefficient *
+      (square(knots[1]) * knots[4] /
+           (-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
+            square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] -
+            knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
+            knots[2] * knots[3] * knots[4]) +
+       square(knots[0]) * knots[2] /
+           (-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
+            knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] -
+            knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] -
+            knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) +
+       knots[0] * knots[1] * knots[3] /
+           (-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] +
+            knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
+            square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] -
+            knots[1] * square(knots[3]) + knots[2] * square(knots[3])));
+  c1 = coefficient *
+      (-square(knots[1]) /
+           (-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
+            square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] -
+            knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
+            knots[2] * knots[3] * knots[4]) -
+       2.0 * knots[1] * knots[4] /
+           (-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
+            square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] -
+            knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
+            knots[2] * knots[3] * knots[4]) -
+       square(knots[0]) /
+           (-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
+            knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] -
+            knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] -
+            knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) -
+       2.0 * knots[0] * knots[2] /
+           (-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
+            knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] -
+            knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] -
+            knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) -
+       knots[0] * knots[1] /
+           (-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] +
+            knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
+            square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] -
+            knots[1] * square(knots[3]) + knots[2] * square(knots[3])) -
+       knots[0] * knots[3] /
+           (-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] +
+            knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
+            square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] -
+            knots[1] * square(knots[3]) + knots[2] * square(knots[3])) -
+       knots[1] * knots[3] /
+           (-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] +
+            knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
+            square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] -
+            knots[1] * square(knots[3]) + knots[2] * square(knots[3])));
+  c2 = coefficient *
+      (2.0 * knots[1] /
+           (-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
+            square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] -
+            knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
+            knots[2] * knots[3] * knots[4]) +
+       knots[4] /
+           (-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
+            square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] -
+            knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
+            knots[2] * knots[3] * knots[4]) +
+       2.0 * knots[0] /
+           (-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
+            knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] -
+            knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] -
+            knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) +
+       knots[2] /
+           (-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
+            knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] -
+            knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] -
+            knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) +
+       knots[0] /
+           (-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] +
+            knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
+            square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] -
+            knots[1] * square(knots[3]) + knots[2] * square(knots[3])) +
+       knots[1] /
+           (-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] +
+            knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
+            square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] -
+            knots[1] * square(knots[3]) + knots[2] * square(knots[3])) +
+       knots[3] /
+           (-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] +
+            knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
+            square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] -
+            knots[1] * square(knots[3]) + knots[2] * square(knots[3])));
+  c3 = coefficient *
+      (-1.0 /
+           (-cube(knots[1]) + square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
+            square(knots[1]) * knots[4] - knots[1] * knots[2] * knots[3] -
+            knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
+            knots[2] * knots[3] * knots[4]) -
+       1.0 /
+           (-square(knots[0]) * knots[1] + square(knots[0]) * knots[2] +
+            knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] -
+            knots[0] * square(knots[2]) - knots[0] * knots[2] * knots[3] -
+            knots[1] * knots[2] * knots[3] + square(knots[2]) * knots[3]) -
+       1.0 /
+           (-knots[0] * square(knots[1]) + knots[0] * knots[1] * knots[2] +
+            knots[0] * knots[1] * knots[3] - knots[0] * knots[2] * knots[3] +
+            square(knots[1]) * knots[3] - knots[1] * knots[2] * knots[3] -
+            knots[1] * square(knots[3]) + knots[2] * square(knots[3])));
+  //constants.push_back(c0);
+  //constants.push_back(c1);
+  //constants.push_back(c2);
+  //constants.push_back(c3);
+  constants[4] = c0;
+  constants[5] = c1;
+  constants[6] = c2;
+  constants[7] = c3;
+  c0 = coefficient *
+      (-knots[0] * square(knots[3]) /
+           (-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] +
+            knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) +
+            knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) -
+            knots[2] * square(knots[3]) + cube(knots[3])) -
+       knots[1] * knots[3] * knots[4] /
+           (-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
+            knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] -
+            knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] -
+            knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) -
+       knots[2] * square(knots[4]) /
+           (-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] +
+            knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
+            square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] -
+            knots[2] * square(knots[4]) + knots[3] * square(knots[4])));
+  c1 = coefficient *
+      (2.0 * knots[0] * knots[3] /
+           (-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] +
+            knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) +
+            knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) -
+            knots[2] * square(knots[3]) + cube(knots[3])) +
+       square(knots[3]) /
+           (-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] +
+            knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) +
+            knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) -
+            knots[2] * square(knots[3]) + cube(knots[3])) +
+       knots[1] * knots[3] /
+           (-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
+            knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] -
+            knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] -
+            knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) +
+       knots[1] * knots[4] /
+           (-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
+            knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] -
+            knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] -
+            knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) +
+       knots[3] * knots[4] /
+           (-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
+            knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] -
+            knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] -
+            knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) +
+       2.0 * knots[2] * knots[4] /
+           (-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] +
+            knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
+            square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] -
+            knots[2] * square(knots[4]) + knots[3] * square(knots[4])) +
+       square(knots[4]) /
+           (-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] +
+            knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
+            square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] -
+            knots[2] * square(knots[4]) + knots[3] * square(knots[4])));
+  c2 = coefficient *
+      (-knots[0] /
+           (-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] +
+            knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) +
+            knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) -
+            knots[2] * square(knots[3]) + cube(knots[3])) -
+       2.0 * knots[3] /
+           (-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] +
+            knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) +
+            knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) -
+            knots[2] * square(knots[3]) + cube(knots[3])) -
+       knots[1] /
+           (-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
+            knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] -
+            knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] -
+            knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) -
+       knots[3] /
+           (-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
+            knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] -
+            knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] -
+            knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) -
+       knots[4] /
+           (-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
+            knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] -
+            knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] -
+            knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) -
+       knots[2] /
+           (-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] +
+            knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
+            square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] -
+            knots[2] * square(knots[4]) + knots[3] * square(knots[4])) -
+       2.0 * knots[4] /
+           (-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] +
+            knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
+            square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] -
+            knots[2] * square(knots[4]) + knots[3] * square(knots[4])));
+  c3 = coefficient *
+      (1.0 /
+           (-knots[0] * knots[1] * knots[2] + knots[0] * knots[1] * knots[3] +
+            knots[0] * knots[2] * knots[3] - knots[0] * square(knots[3]) +
+            knots[1] * knots[2] * knots[3] - knots[1] * square(knots[3]) -
+            knots[2] * square(knots[3]) + cube(knots[3])) +
+       1.0 /
+           (-square(knots[1]) * knots[2] + square(knots[1]) * knots[3] +
+            knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] -
+            knots[1] * square(knots[3]) - knots[1] * knots[3] * knots[4] -
+            knots[2] * knots[3] * knots[4] + square(knots[3]) * knots[4]) +
+       1.0 /
+           (-knots[1] * square(knots[2]) + knots[1] * knots[2] * knots[3] +
+            knots[1] * knots[2] * knots[4] - knots[1] * knots[3] * knots[4] +
+            square(knots[2]) * knots[4] - knots[2] * knots[3] * knots[4] -
+            knots[2] * square(knots[4]) + knots[3] * square(knots[4])));
+  //constants.push_back(c0);
+  //constants.push_back(c1);
+  //constants.push_back(c2);
+  //constants.push_back(c3);
+  constants[8] = c0;
+  constants[9] = c1;
+  constants[10] = c2;
+  constants[11] = c3;
+  c0 = coefficient *
+      (cube(knots[4]) /
+       (-knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] +
+        knots[1] * knots[3] * knots[4] - knots[1] * square(knots[4]) +
+        knots[2] * knots[3] * knots[4] - knots[2] * square(knots[4]) - knots[3] * square(knots[4]) +
+        cube(knots[4])));
+  c1 = coefficient *
+      (-3.0 * square(knots[4]) /
+       (-knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] +
+        knots[1] * knots[3] * knots[4] - knots[1] * square(knots[4]) +
+        knots[2] * knots[3] * knots[4] - knots[2] * square(knots[4]) - knots[3] * square(knots[4]) +
+        cube(knots[4])));
+  c2 = coefficient *
+      (3.0 * knots[4] /
+       (-knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] +
+        knots[1] * knots[3] * knots[4] - knots[1] * square(knots[4]) +
+        knots[2] * knots[3] * knots[4] - knots[2] * square(knots[4]) - knots[3] * square(knots[4]) +
+        cube(knots[4])));
+  c3 = coefficient *
+      (-1.0 /
+       (-knots[1] * knots[2] * knots[3] + knots[1] * knots[2] * knots[4] +
+        knots[1] * knots[3] * knots[4] - knots[1] * square(knots[4]) +
+        knots[2] * knots[3] * knots[4] - knots[2] * square(knots[4]) - knots[3] * square(knots[4]) +
+        cube(knots[4])));
+  //constants.push_back(c0);
+  //constants.push_back(c1);
+  //constants.push_back(c2);
+  //constants.push_back(c3);
+  constants[12] = c0;
+  constants[13] = c1;
+  constants[14] = c2;
+  constants[15] = c3;
+}
+
+uf3_bspline_basis3::~uf3_bspline_basis3() {}
+
+// Evaluate outer-left part of spline
+double uf3_bspline_basis3::eval0(double rth, double rsq, double r)
+{
+  return rth * constants[3] + rsq * constants[2] + r * constants[1] + constants[0];
+}
+
+// Evaluate center-left part of spline
+double uf3_bspline_basis3::eval1(double rth, double rsq, double r)
+{
+  return rth * constants[7] + rsq * constants[6] + r * constants[5] + constants[4];
+}
+
+// Evaluate center-right part of spline
+double uf3_bspline_basis3::eval2(double rth, double rsq, double r)
+{
+  return rth * constants[11] + rsq * constants[10] + r * constants[9] + constants[8];
+}
+
+// Evaluate outer-right part of spline
+double uf3_bspline_basis3::eval3(double rth, double rsq, double r)
+{
+  return rth * constants[15] + rsq * constants[14] + r * constants[13] + constants[12];
+}
+
+double uf3_bspline_basis3::memory_usage()
+{
+  double bytes = 0;
+
+  bytes += (double)16*sizeof(double);
+
+  return bytes;
+}

src/ML-UF3/uf3_bspline_basis3.h

@@ -0,0 +1,42 @@
+// clang-format off
+/* ----------------------------------------------------------------------
+   lammps - large-scale atomic/molecular massively parallel simulator
+   https://www.lammps.org/, sandia national laboratories
+   lammps development team: developers@lammps.org
+
+   copyright (2003) sandia corporation.  under the terms of contract
+   de-ac04-94al85000 with sandia corporation, the u.s. government retains
+   certain rights in this software.  this software is distributed under
+   the gnu general public license.
+
+   see the readme file in the top-level lammps directory.
+------------------------------------------------------------------------- */
+
+#include "pointers.h"
+
+#include <vector>
+
+#ifndef UF3_BSPLINE_BASIS3_H
+#define UF3_BSPLINE_BASIS3_H
+
+namespace LAMMPS_NS {
+
+class uf3_bspline_basis3 {
+ private:
+  LAMMPS *lmp;
+  //std::vector<double> constants;
+
+ public:
+  uf3_bspline_basis3(LAMMPS *ulmp, const double *knots, double coefficient);
+  ~uf3_bspline_basis3();
+  double constants[16] = {};
+  double eval0(double, double, double);
+  double eval1(double, double, double);
+  double eval2(double, double, double);
+  double eval3(double, double, double);
+
+  double memory_usage();
+};
+
+}    // namespace LAMMPS_NS
+#endif

src/Makefile

@@ -74,6 +74,7 @@ PACKAGE = \
 	dpd-smooth \
 	drude \
 	eff \
+	extra-command \
 	extra-compute \
 	extra-dump \
 	extra-fix \
@@ -104,6 +105,7 @@ PACKAGE = \
 	ml-quip \
 	ml-rann \
 	ml-snap \
+	ml-uf3 \
 	mofff \
 	molfile \
 	netcdf \
@@ -167,6 +169,7 @@ PACKMOST = \
 	dpd-smooth \
 	drude \
 	eff \
+	extra-command \
 	extra-compute \
 	extra-dump \
 	extra-fix \

src/OPENMP/fix_omp.cpp

@@ -229,7 +229,13 @@ void FixOMP::init()
   check_hybrid = 0;                                                     \
   if (force->name) {                                                    \
     if ( (strcmp(force->name ## _style,"hybrid") == 0) ||               \
-         (strcmp(force->name ## _style,"hybrid/overlay") == 0) )        \
+         (strcmp(force->name ## _style,"hybrid/overlay") == 0) ||       \
+         (strcmp(force->name ## _style,"hybrid/scaled") == 0) ||        \
+         (strcmp(force->name ## _style,"hybrid/molecular") == 0) ||     \
+         (strcmp(force->name ## _style,"hybrid/omp") == 0) ||           \
+         (strcmp(force->name ## _style,"hybrid/overlay/omp") == 0) ||   \
+         (strcmp(force->name ## _style,"hybrid/scaled/omp") == 0) ||    \
+         (strcmp(force->name ## _style,"hybrid/molecular/omp") == 0) )  \
       check_hybrid=1;                                                   \
     if (force->name->suffix_flag & Suffix::OMP) {                       \
       last_force_name = (const char *) #name;                           \

src/OPENMP/npair_skip_omp.h

@@ -19,14 +19,12 @@
 
 NPairStyle(skip/omp,
            NPairSkip,
-           NP_SKIP | NP_HALF | NP_FULL |
+           NP_SKIP | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
-           NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
            NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP);
 
 NPairStyle(skip/half/respa/omp,
            NPairSkipRespa,
-           NP_SKIP | NP_RESPA | NP_HALF | NP_FULL |
+           NP_SKIP | NP_RESPA | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
-           NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
            NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP);
 
 NPairStyle(skip/half/size/omp,
@@ -36,32 +34,27 @@ NPairStyle(skip/half/size/omp,
 
 NPairStyle(skip/size/off2on/omp,
            NPairSkipSizeOff2on,
-           NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF |
+           NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
-           NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_MULTI_OLD |
            NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP);
 
 NPairStyle(skip/size/off2on/oneside/omp,
            NPairSkipSizeOff2onOneside,
-           NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF |
+           NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
-           NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF |
+           NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP);
-           NP_ORTHO | NP_TRI | NP_OMP);
 
 NPairStyle(skip/ghost/omp,
            NPairSkip,
-           NP_SKIP | NP_HALF | NP_FULL |
+           NP_SKIP | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
-           NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
            NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP | NP_GHOST);
 
 NPairStyle(skip/trim/omp,
            NPairSkipTrim,
-           NP_SKIP | NP_HALF | NP_FULL |
+           NP_SKIP | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
-           NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
            NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
 
 NPairStyle(skip/trim/half/respa/omp,
            NPairSkipTrimRespa,
-           NP_SKIP | NP_RESPA | NP_HALF | NP_FULL |
+           NP_SKIP | NP_RESPA | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
-           NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
            NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
 
 NPairStyle(skip/trim/half/size/omp,
@@ -71,20 +64,17 @@ NPairStyle(skip/trim/half/size/omp,
 
 NPairStyle(skip/trim/size/off2on/omp,
            NPairSkipTrimSizeOff2on,
-           NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF |
+           NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
-           NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_MULTI_OLD |
            NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
 
 NPairStyle(skip/trim/size/off2on/oneside/omp,
            NPairSkipTrimSizeOff2onOneside,
-           NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF |
+           NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
-           NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF |
+           NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
-           NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP);
 
 NPairStyle(skip/trim/ghost/omp,
            NPairSkipTrim,
-           NP_SKIP | NP_HALF | NP_FULL |
+           NP_SKIP | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
-           NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
            NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_TRIM | NP_OMP | NP_GHOST);
 // clang-format off
 #endif

src/PLUMED/fix_plumed.cpp

@@ -77,9 +77,9 @@ FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) :
 
   int api_version=0;
   p->cmd("getApiVersion",&api_version);
-  if ((api_version < 5) || (api_version > 9))
+  if ((api_version < 5) || (api_version > 10))
     error->all(FLERR,"Incompatible API version for PLUMED in fix plumed. "
-               "Only Plumed 2.4.x, 2.5.x, 2.6.x, 2.7.x, 2.8.x are tested and supported.");
+               "Only Plumed 2.4.x, 2.5.x, 2.6.x, 2.7.x, 2.8.x, 2.9.x are tested and supported.");
 
 #if !defined(MPI_STUBS)
   // If the -partition option is activated then enable
@@ -205,6 +205,7 @@ FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) :
   double dt=update->dt;
   p->cmd("setTimestep",&dt);
 
+  extscalar = 1;
   scalar_flag = 1;
   energy_global_flag = virial_global_flag = 1;
   thermo_energy = thermo_virial = 1;

src/QEQ/fix_qeq_shielded.cpp

@@ -55,29 +55,53 @@ void FixQEqShielded::init()
 
   neighbor->add_request(this, NeighConst::REQ_FULL);
 
-  int ntypes = atom->ntypes;
+  const int ntypes = atom->ntypes;
   memory->create(shld, ntypes + 1, ntypes + 1, "qeq:shielding");
 
   init_shielding();
 
-  int i;
+  // check if valid parameters for all atom types in the fix group are provided
-  for (i = 1; i <= ntypes; i++) {
+  const int *type = atom->type;
-    if (gamma[i] == 0.0) error->all(FLERR, "Invalid param file for fix qeq/shielded");
+  const int *mask = atom->mask;
+  int tmp = 0, tmp_all = 0;
+  for (int i = 0; i < nlocal; ++i) {
+    if (mask[i] & groupbit) {
+      if (gamma[type[i]] == 0.0)
+        tmp = type[i];
+    }
   }
+  MPI_Allreduce(&tmp, &tmp_all, 1, MPI_INT, MPI_MAX, world);
+  if (tmp_all)
+    error->all(FLERR, "Invalid QEq parameters for atom type {} provided", tmp_all);
 }
 
 /* ---------------------------------------------------------------------- */
 
 void FixQEqShielded::extract_reax()
 {
-  Pair *pair = force->pair_match("^reax..", 0);
+  const int nlocal = atom->nlocal;
-  if (pair == nullptr) error->all(FLERR, "No pair reaxff for fix qeq/shielded");
+  const int *mask = atom->mask;
-  int tmp;
+  const int *type = atom->type;
+
+  Pair *pair = force->pair_match("^reaxff", 0);
+  if (pair == nullptr) error->all(FLERR, "No reaxff pair style for fix qeq/shielded");
+  int tmp, tmp_all;
   chi = (double *) pair->extract("chi", tmp);
   eta = (double *) pair->extract("eta", tmp);
   gamma = (double *) pair->extract("gamma", tmp);
-  if (chi == nullptr || eta == nullptr || gamma == nullptr)
+  if ((chi == nullptr) || (eta == nullptr) || (gamma == nullptr))
-    error->all(FLERR, "Fix qeq/shielded could not extract params from pair reaxff");
+    error->all(FLERR, "Fix qeq/shielded could not extract all QEq parameters from pair reaxff");
+
+  tmp = tmp_all = 0;
+  for (int i = 0; i < nlocal; ++i) {
+    if (mask[i] & groupbit) {
+      if ((chi[type[i]] == 0.0) && (eta[type[i]] == 0.0) && (gamma[type[i]] == 0.0))
+        tmp = type[i];
+    }
+  }
+  MPI_Allreduce(&tmp, &tmp_all, 1, MPI_INT, MPI_MAX, world);
+  if (tmp_all)
+    error->all(FLERR, "No QEq parameters for atom type {} provided by pair reaxff", tmp_all);
 }
 
 // clang-format off

src/REAXFF/fix_qeq_reaxff.cpp

@@ -205,25 +205,41 @@ int FixQEqReaxFF::setmask()
 
 void FixQEqReaxFF::pertype_parameters(char *arg)
 {
+  const int nlocal = atom->nlocal;
+  const int *mask = atom->mask;
+  const int *type = atom->type;
+
   if (utils::strmatch(arg,"^reaxff")) {
     reaxflag = 1;
     Pair *pair = force->pair_match("^reaxff",0);
     if (!pair) error->all(FLERR,"No reaxff pair style for fix qeq/reaxff");
 
-    int tmp;
+    int tmp, tmp_all;
     chi = (double *) pair->extract("chi",tmp);
     eta = (double *) pair->extract("eta",tmp);
     gamma = (double *) pair->extract("gamma",tmp);
-    if (chi == nullptr || eta == nullptr || gamma == nullptr)
+    if ((chi == nullptr) || (eta == nullptr) || (gamma == nullptr))
-      error->all(FLERR, "Fix qeq/reaxff could not extract params from pair reaxff");
+      error->all(FLERR, "Fix qeq/reaxff could not extract all QEq parameters from pair reaxff");
+    tmp = tmp_all = 0;
+    for (int i = 0; i < nlocal; ++i) {
+      if (mask[i] & groupbit) {
+        if ((chi[type[i]] == 0.0) && (eta[type[i]] == 0.0) && (gamma[type[i]] == 0.0))
+          tmp = type[i];
+      }
+    }
+    MPI_Allreduce(&tmp, &tmp_all, 1, MPI_INT, MPI_MAX, world);
+    if (tmp_all)
+      error->all(FLERR, "No QEq parameters for atom type {} provided by pair reaxff", tmp_all);
     return;
   } else if (utils::strmatch(arg,"^reax/c")) {
     error->all(FLERR, "Fix qeq/reaxff keyword 'reax/c' is obsolete; please use 'reaxff'");
+  } else {
+    error->all(FLERR, "Unknown fix qeq/reaxff keyword {}", arg);
   }
 
   reaxflag = 0;
-  const int ntypes = atom->ntypes;
 
+  const int ntypes = atom->ntypes;
   memory->create(chi,ntypes+1,"qeq/reaxff:chi");
   memory->create(eta,ntypes+1,"qeq/reaxff:eta");
   memory->create(gamma,ntypes+1,"qeq/reaxff:gamma");

src/REAXFF/pair_reaxff.cpp

@@ -694,24 +694,28 @@ void *PairReaxFF::extract(const char *str, int &dim)
 {
   dim = 1;
   if (strcmp(str,"chi") == 0 && chi) {
+    chi[0] = 0.0;
     for (int i = 1; i <= atom->ntypes; i++)
       if (map[i] >= 0) chi[i] = api->system->reax_param.sbp[map[i]].chi;
       else chi[i] = 0.0;
     return (void *) chi;
   }
   if (strcmp(str,"eta") == 0 && eta) {
+    eta[0] = 0.0;
     for (int i = 1; i <= atom->ntypes; i++)
       if (map[i] >= 0) eta[i] = api->system->reax_param.sbp[map[i]].eta;
       else eta[i] = 0.0;
     return (void *) eta;
   }
   if (strcmp(str,"gamma") == 0 && gamma) {
+    gamma[0] = 0.0;
     for (int i = 1; i <= atom->ntypes; i++)
       if (map[i] >= 0) gamma[i] = api->system->reax_param.sbp[map[i]].gamma;
       else gamma[i] = 0.0;
     return (void *) gamma;
    }
    if (strcmp(str,"bcut_acks2") == 0 && bcut_acks2) {
+    bcut_acks2[0] = 0.0;
     for (int i = 1; i <= atom->ntypes; i++)
       if (map[i] >= 0) bcut_acks2[i] = api->system->reax_param.sbp[map[i]].bcut_acks2;
       else bcut_acks2[i] = 0.0;

src/delete_atoms.cpp

@@ -22,6 +22,7 @@
 #include "comm.h"
 #include "domain.h"
 #include "error.h"
+#include "fix_bond_history.h"
 #include "force.h"
 #include "group.h"
 #include "input.h"
@@ -754,6 +755,10 @@ void DeleteAtoms::bondring(int nbuf, char *cbuf, void *ptr)
 
   int nlocal = daptr->atom->nlocal;
 
+  // find instances of bond history to delete data
+  auto histories = daptr->modify->get_fix_by_style("BOND_HISTORY");
+  int n_histories = histories.size();
+
   // cbuf = list of N deleted atom IDs from other proc, put them in hash
 
   hash->clear();
@@ -771,6 +776,11 @@ void DeleteAtoms::bondring(int nbuf, char *cbuf, void *ptr)
         if (hash->find(bond_atom[i][m]) != hash->end()) {
           bond_type[i][m] = bond_type[i][n - 1];
           bond_atom[i][m] = bond_atom[i][n - 1];
+          if (n_histories > 0)
+            for (auto &ihistory: histories) {
+              dynamic_cast<FixBondHistory *>(ihistory)->shift_history(i,m,n-1);
+              dynamic_cast<FixBondHistory *>(ihistory)->delete_history(i,n-1);
+            }
           n--;
         } else
           m++;

src/fix_bond_history.h

@@ -44,6 +44,7 @@ class FixBondHistory : public Fix {
 
   void update_atom_value(int, int, int, double);
   double get_atom_value(int, int, int);
+  int get_ndata() const { return ndata; }
 
   // methods to reorder/delete elements of atom->bond_atom
   void delete_history(int, int);

src/input.cpp

@@ -888,6 +888,7 @@ void Input::clear()
   lmp->destroy();
   lmp->create();
   lmp->post_create();
+  variable->clear_in_progress();
 }
 
 /* ---------------------------------------------------------------------- */

src/library.cpp

@@ -1198,14 +1198,31 @@ internally by the :doc:`Fortran interface <Fortran>` and are not likely to be us
    * - triclinic
      - 1 if the the simulation box is triclinic, 0 if orthogonal.
        See :doc:`change_box`.
+
+**Communication status**
+
+.. list-table::
+   :header-rows: 1
+   :widths: auto
+
+   * - Keyword
+     - Description / Return value
    * - universe_rank
      - MPI rank on LAMMPS' universe communicator (0 <= universe_rank < universe_size)
    * - universe_size
      - Number of ranks on LAMMPS' universe communicator (world_size <= universe_size)
    * - world_rank
-     - MPI rank on LAMMPS' world communicator (0 <= world_rank < world_size)
+     - MPI rank on LAMMPS' world communicator (0 <= world_rank < world_size, aka comm->me)
    * - world_size
-     - Number of ranks on LAMMPS' world communicator
+     - Number of ranks on LAMMPS' world communicator (aka comm->nprocs)
+   * - comm_style
+     - communication style (0 = BRICK, 1 = TILED)
+   * - comm_layout
+     - communication layout (0 = LAYOUT_UNIFORM, 1 = LAYOUT_NONUNIFORM, 2 = LAYOUT_TILED)
+   * - comm_mode
+     - communication mode (0 = SINGLE, 1 = MULTI, 2 = MULTIOLD)
+   * - ghost_velocity
+     - whether velocities are communicated for ghost atoms (0 = no, 1 = yes)
 
 .. _extract_system_sizes:
 
@@ -1310,6 +1327,10 @@ int lammps_extract_setting(void *handle, const char *keyword)
   if (strcmp(keyword,"world_rank") == 0) return lmp->comm->me;
   if (strcmp(keyword,"world_size") == 0) return lmp->comm->nprocs;
   if (strcmp(keyword,"nthreads") == 0) return lmp->comm->nthreads;
+  if (strcmp(keyword,"comm_style") == 0) return lmp->comm->style;
+  if (strcmp(keyword,"comm_layout") == 0) return lmp->comm->layout;
+  if (strcmp(keyword,"comm_mode") == 0) return lmp->comm->mode;
+  if (strcmp(keyword,"ghost_velocity") == 0) return lmp->comm->ghost_velocity;
 
   if (strcmp(keyword,"nlocal") == 0) return lmp->atom->nlocal;
   if (strcmp(keyword,"nghost") == 0) return lmp->atom->nghost;
@@ -1386,6 +1407,7 @@ int lammps_extract_global_datatype(void * /*handle*/, const char *name)
   if (strcmp(name,"xy") == 0) return LAMMPS_DOUBLE;
   if (strcmp(name,"xz") == 0) return LAMMPS_DOUBLE;
   if (strcmp(name,"yz") == 0) return LAMMPS_DOUBLE;
+  if (strcmp(name,"procgrid") == 0) return LAMMPS_INT;
 
   if (strcmp(name,"natoms") == 0) return LAMMPS_BIGINT;
   if (strcmp(name,"nbonds") == 0) return LAMMPS_BIGINT;
@@ -1604,6 +1626,10 @@ report the "native" data type.  The following tables are provided:
      - double
      - 1
      - triclinic tilt factor. See :doc:`Howto_triclinic`.
+   * - procgrid
+     - int
+     - 3
+     - processor count assigned to each dimension of 3d grid. See :doc:`processors`.
 
 .. _extract_system_settings:
 
@@ -1861,6 +1887,9 @@ void *lammps_extract_global(void *handle, const char *name)
   if (strcmp(name,"xy") == 0) return (void *) &lmp->domain->xy;
   if (strcmp(name,"xz") == 0) return (void *) &lmp->domain->xz;
   if (strcmp(name,"yz") == 0) return (void *) &lmp->domain->yz;
+  if (((lmp->comm->layout == Comm::LAYOUT_UNIFORM) ||
+       (lmp->comm->layout == Comm::LAYOUT_NONUNIFORM)) && (strcmp(name,"procgrid") == 0))
+    return (void *) &lmp->comm->procgrid;
 
   if (strcmp(name,"natoms") == 0) return (void *) &lmp->atom->natoms;
   if (strcmp(name,"ntypes") == 0) return (void *) &lmp->atom->ntypes;

src/neigh_list.cpp

@@ -148,6 +148,7 @@ void NeighList::post_constructor(NeighRequest *nq)
   copy = nq->copy;
   trim = nq->trim;
   id = nq->id;
+  molskip = nq->molskip;
 
   if (nq->copy) {
     listcopy = neighbor->lists[nq->copylist];
@@ -157,14 +158,16 @@ void NeighList::post_constructor(NeighRequest *nq)
 
   if (nq->skip) {
     listskip = neighbor->lists[nq->skiplist];
-    int ntypes = atom->ntypes;
+    if (!molskip) {
-    iskip = new int[ntypes+1];
+      int ntypes = atom->ntypes;
-    memory->create(ijskip,ntypes+1,ntypes+1,"neigh_list:ijskip");
+      iskip = new int[ntypes+1];
-    int i,j;
+      memory->create(ijskip,ntypes+1,ntypes+1,"neigh_list:ijskip");
-    for (i = 1; i <= ntypes; i++) iskip[i] = nq->iskip[i];
+      int i,j;
-    for (i = 1; i <= ntypes; i++)
+      for (i = 1; i <= ntypes; i++) iskip[i] = nq->iskip[i];
-      for (j = 1; j <= ntypes; j++)
+      for (i = 1; i <= ntypes; i++)
-        ijskip[i][j] = nq->ijskip[i][j];
+        for (j = 1; j <= ntypes; j++)
+          ijskip[i][j] = nq->ijskip[i][j];
+    }
   }
 
   if (nq->halffull)

src/neigh_list.h

@@ -46,6 +46,7 @@ class NeighList : protected Pointers {
   int kk2cpu;         // 1 if this list is copied from Kokkos to CPU
   int copymode;       // 1 if this is a Kokkos on-device copy
   int id;             // copied from neighbor list request
+  int molskip;        // 1/2 if this is an intra-/inter-molecular skip list
 
   // data structs to store neighbor pairs I,J and associated values
 

src/neigh_request.cpp

@@ -76,6 +76,7 @@ NeighRequest::NeighRequest(LAMMPS *_lmp) : Pointers(_lmp)
   skip = 0;
   iskip = nullptr;
   ijskip = nullptr;
+  molskip = REGULAR;
 
   // only set when command = 1;
 
@@ -183,6 +184,8 @@ int NeighRequest::identical(NeighRequest *other)
 
 int NeighRequest::same_skip(NeighRequest *other)
 {
+  if (molskip != other->molskip) return 0;
+
   const int ntypes = atom->ntypes;
   int same = 1;
 
@@ -307,6 +310,12 @@ void NeighRequest::set_skip(int *_iskip, int **_ijskip)
   ijskip = _ijskip;
 }
 
+void NeighRequest::set_molskip(int _molskip)
+{
+  skip = 1;
+  molskip = _molskip;
+}
+
 void NeighRequest::enable_full()
 {
   half = 0;

src/neigh_request.h

@@ -29,6 +29,9 @@ class NeighRequest : protected Pointers {
   friend class NPairSkipTrimIntel;
   friend class FixIntel;
 
+ public:
+  enum { REGULAR, INTRA, INTER };
+
  protected:
   void *requestor;           // class that made request
   int requestor_instance;    // instance of that class (only Fix, Compute, Pair)
@@ -88,6 +91,7 @@ class NeighRequest : protected Pointers {
   int skip;        // 1 if this list skips atom types from another list
   int *iskip;      // iskip[i] if atoms of type I are not in list
   int **ijskip;    // ijskip[i][j] if pairs of type I,J are not in list
+  int molskip;     // 0 reqular list, 1 keep only intra-molecular entries, 2 keep inter-molecular
 
   // command_style only set if command = 1
   // allows print_pair_info() to access command name
@@ -137,6 +141,7 @@ class NeighRequest : protected Pointers {
   void set_kokkos_device(int);
   void set_kokkos_host(int);
   void set_skip(int *, int **);
+  void set_molskip(int);
   void enable_full();
   void enable_ghost();
   void enable_intel();

src/neighbor.cpp

@@ -1800,10 +1800,17 @@ void Neighbor::print_pairwise_info()
       else
         out += fmt::format(", half/full from ({})",rq->halffulllist+1);
     } else if (rq->skip) {
-      if (rq->trim)
+      if (rq->molskip) {
-        out += fmt::format(", skip trim from ({})",rq->skiplist+1);
+        if (rq->trim)
-      else
+          out += fmt::format(", molskip trim from ({})",rq->skiplist+1);
-        out += fmt::format(", skip from ({})",rq->skiplist+1);
+        else
+          out += fmt::format(", molskip from ({})",rq->skiplist+1);
+      } else {
+        if (rq->trim)
+          out += fmt::format(", skip trim from ({})",rq->skiplist+1);
+        else
+          out += fmt::format(", skip from ({})",rq->skiplist+1);
+      }
     }
     out += "\n";