update to upstream

cmake/Modules/Packages/USER-MDI.cmake

@@ -12,37 +12,89 @@ if(DOWNLOAD_MDI)
   set(MDI_MD5 "ddfa46d6ee15b4e59cfd527ec7212184" CACHE STRING "MD5 checksum for MDI tarball")
   mark_as_advanced(MDI_URL)
   mark_as_advanced(MDI_MD5)
+  enable_language(C)
 
-  set(LAMMPS_LIB_MDI_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/mdi)
+  # only ON/OFF are allowed for "mpi" flag when building MDI library
+  # so translate boolean value of BUILD_MPI
+  # always disable MPI when cross-compiling to Windows.
+  if((BUILD_MPI) AND NOT((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING))
+    set(MDI_USE_MPI ON)
+  else()
+    set(MDI_USE_MPI OFF)
+  endif()
 
+  # detect if we have python development support and thus can enable python plugins
+  set(MDI_USE_PYTHON_PLUGINS OFF)
+  if(CMAKE_VERSION VERSION_LESS 3.12)
+    find_package(PythonLibs QUIET) # Deprecated since version 3.12
+    if (PYTHONLIBS_FOUND)
+      set(MDI_USE_PYTHON_PLUGINS ON)
+    endif()
+  else()
+    find_package(Python QUIET COMPONENTS Development)
+    if (Python_Development_FOUND)
+      set(MDI_USE_PYTHON_PLUGINS ON)
+    endif()
+  endif()
+
+  # download/ build MDI library
+  # always build static library with -fpic
+  # support cross-compilation and ninja-build
   include(ExternalProject)
-  message(STATUS "Building mdi.")
+  ExternalProject_Add(mdi_build
-  ExternalProject_Add(mdi_external
     URL     ${MDI_URL}
     URL_MD5 ${MDI_MD5}
-      UPDATE_COMMAND ""
     CMAKE_ARGS ${CMAKE_REQUEST_PIC}
-                 -DCMAKE_INSTALL_PREFIX=${LAMMPS_LIB_MDI_BIN_DIR}
+    -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+    -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
     -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-                 -DCMAKE_INSTALL_LIBDIR=${CMAKE_INSTALL_LIBDIR}
+    -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
-                 -DCMAKE_INSTALL_INCLUDEDIR=${CMAKE_INSTALL_INCLUDEDIR}
+    -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
-                 -DBUILD_SHARED_LIBS=${BUILD_SHARED_LIBS}
     -Dlanguage=C
-      CMAKE_CACHE_ARGS -DCMAKE_C_FLAGS:STRING=${CMAKE_C_FLAGS}
+    -Dlibtype=STATIC
-                       -DCMAKE_CXX_FLAGS:STRING=${CMAKE_CXX_FLAGS}
+    -Dmpi=${MDI_USE_MPI}
-                       -DTargetOpenMP_FIND_COMPONENTS:STRING=C;CXX)
+    -Dpython_plugins=${MDI_USE_PYTHON_PLUGINS}
+    UPDATE_COMMAND ""
+    INSTALL_COMMAND ""
+    BUILD_BYPRODUCTS "<BINARY_DIR>/MDI_Library/libmdi.a"
+    )
 
-  # Link the lammps library against MDI
+  # where is the compiled library?
-  target_include_directories(lammps PRIVATE ${LAMMPS_LIB_MDI_BIN_DIR}/${CMAKE_INSTALL_INCLUDEDIR}/mdi)
+  ExternalProject_get_property(mdi_build BINARY_DIR)
-  target_link_directories(lammps PRIVATE ${LAMMPS_LIB_MDI_BIN_DIR}/${CMAKE_INSTALL_LIBDIR}/mdi)
+  set(MDI_BINARY_DIR "${BINARY_DIR}/MDI_Library")
-  target_link_libraries(lammps PRIVATE mdi)
+  # workaround for older CMake versions
-  add_dependencies(lammps mdi_external)
+  file(MAKE_DIRECTORY ${MDI_BINARY_DIR})
 
-  # Link the lammps executable against MDI
+  # create imported target for the MDI library
-  target_include_directories(lmp PRIVATE ${LAMMPS_LIB_MDI_BIN_DIR}/${CMAKE_INSTALL_INCLUDEDIR}/mdi)
+  add_library(LAMMPS::MDI UNKNOWN IMPORTED)
-  target_link_directories(lmp PRIVATE ${LAMMPS_LIB_MDI_BIN_DIR}/${CMAKE_INSTALL_LIBDIR}/mdi)
+  add_dependencies(LAMMPS::MDI mdi_build)
-  target_link_libraries(lmp PRIVATE mdi)
+  set_target_properties(LAMMPS::MDI PROPERTIES
-  add_dependencies(lmp mdi_external)
+    IMPORTED_LOCATION "${MDI_BINARY_DIR}/libmdi.a"
+    INTERFACE_INCLUDE_DIRECTORIES ${MDI_BINARY_DIR}
+    )
+
+  set(MDI_DEP_LIBS "")
+  # if compiling with python plugins we need
+  # to add python libraries as dependency.
+  if(MDI_USE_PYTHON_PLUGINS)
+    if(CMAKE_VERSION VERSION_LESS 3.12)
+      list(APPEND MDI_DEP_LIBS ${PYTHON_LIBRARIES})
+    else()
+      list(APPEND MDI_DEP_LIBS Python::Python)
+    endif()
+
+  endif()
+  # need to add support for dlopen/dlsym, except when compiling for Windows.
+  if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+    list(APPEND MDI_DEP_LIBS "${CMAKE_DL_LIBS}")
+  endif()
+  if(MDI_DEP_LIBS)
+    set_target_properties(LAMMPS::MDI PROPERTIES
+      IMPORTED_LINK_INTERFACE_LIBRARIES "${MDI_DEP_LIBS}")
+  endif()
+
+  target_link_libraries(lammps PRIVATE LAMMPS::MDI)
+  target_link_libraries(lmp PRIVATE LAMMPS::MDI)
 
 else()
 

cmake/Modules/Packages/USER-PACE.cmake

@@ -14,13 +14,12 @@ execute_process(
   WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
 )
 
-
 file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE)
 file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE/*.cpp)
 list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp)
 
 add_library(pace STATIC ${PACE_EVALUATOR_SOURCES})
-set_target_properties(pace PROPERTIES OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
+set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
 target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR})
 target_link_libraries(lammps PRIVATE pace)
 

cmake/presets/all_off.cmake

@@ -5,13 +5,13 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
   GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE
   MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
   SRD VORONOI
-  USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
+  USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK
-  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-HDNNP
+  USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
-  USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MESONT
+  USER-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD
-  USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE
+  USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
-  USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION
+  USER-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
-  USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+  USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
-  USER-UEF USER-VTK USER-YAFF)
+  USER-TALLY USER-UEF USER-VTK USER-YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

cmake/presets/all_on.cmake

@@ -7,13 +7,13 @@ set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
   GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE
   MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
   SRD VORONOI
-  USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
+  USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK
-  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-HDNNP
+  USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
-  USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MESONT
+  USER-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD
-  USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE
+  USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
-  USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION
+  USER-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
-  USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+  USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
-  USER-UEF USER-VTK USER-YAFF)
+  USER-TALLY USER-UEF USER-VTK USER-YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)

cmake/presets/download.cmake

@@ -1,7 +1,7 @@
-# preset that turns on packages with automatic downloads of sources of potentials
+# Preset that turns on packages with automatic downloads of sources or potentials.
-# compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time.
+# Compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time.
 
-set(ALL_PACKAGES KIM LATTE MSCG VORONOI USER-PLUMED USER-SCAFACOS USER-SMD USER-MESONT)
+set(ALL_PACKAGES KIM LATTE MSCG VORONOI USER-PLUMED USER-SCAFACOS USER-SMD USER-MESONT USER-MDI USER-PACE)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)
@@ -9,9 +9,11 @@ endforeach()
 
 set(DOWNLOAD_KIM ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_LATTE ON CACHE BOOL "" FORCE)
+set(DOWNLOAD_MDI ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_MSCG ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
+set(DOWNLOAD_PACE ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_PLUMED ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_SCAFACOS ON CACHE BOOL "" FORCE)
 

cmake/presets/mingw-cross.cmake

@@ -1,11 +1,11 @@
 set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
                  GRANULAR KSPACE LATTE MANYBODY MC MISC MLIAP MOLECULE OPT
                  PERI POEMS QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
-                 USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
+                 USER-ATC USER-AWPMD USER-BOCS USER-BROWNIAN USER-CGDNA USER-CGSDK
                  USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
                  USER-FEP USER-INTEL USER-MANIFOLD USER-MEAMC USER-MESODPD
                  USER-MESONT USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP
-                 USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC
+                 USER-PACE USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC
                  USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
                  USER-YAFF)
 

cmake/presets/nolib.cmake

@@ -4,7 +4,7 @@
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MESSAGE MPIIO MSCG
   PYTHON VORONOI
   USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-HDNNP USER-LB USER-MOLFILE
-  USER-MESONT USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP
+  USER-MESONT USER-MDI USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP
   USER-SCAFACOS USER-SMD USER-VTK)
 
 foreach(PKG ${PACKAGES_WITH_LIB})

doc/src/Howto_mdi.rst

@@ -109,7 +109,7 @@ instructions on how to run the examples.
 If LAMMPS is used as a stand-alone engine it should set up the system
 it will be modeling in its input script, then invoke the
 :doc:`mdi/engine <mdi_engine>` command.  This will put LAMMPS into
-engine mode where it waits for messages and data from the driver.
+"engine mode" where it waits for messages and data from the driver.
 When the driver sends an "EXIT" command, LAMMPS will exit engine mode
 and the input script will continue.
 

doc/src/Run_options.rst

@@ -10,6 +10,7 @@ letter abbreviation can be used:
 * :ref:`-i or -in <file>`
 * :ref:`-k or -kokkos <run-kokkos>`
 * :ref:`-l or -log <log>`
+* :ref:`-mdi <mdi>`
 * :ref:`-m or -mpicolor <mpicolor>`
 * :ref:`-c or -cite <cite>`
 * :ref:`-nc or -nocite <nocite>`
@@ -196,9 +197,23 @@ Option -plog will override the name of the partition log files file.N.
 
 ----------
 
+.. _mdi:
+
+**-mdi 'multiple flags'**
+
+This flag is only recognized and used when LAMMPS has support for the MolSSI
+Driver Interface (MDI) included as part of the :ref:`USER-MDI <PKG-USER-MDI>`
+package.  This flag is specific to the MDI library and controls how LAMMPS
+interacts with MDI.  There are usually multiple flags that have to follow it
+and those have to be placed in quotation marks.  For more information about
+how to launch LAMMPS in MDI client/server mode please refer to the
+:doc:`MDI Howto <Howto_mdi>`.
+
+----------
+
 .. _mpicolor:
 
-**-mpicolor** color
+**-mpicolor color**
 
 If used, this must be the first command-line argument after the LAMMPS
 executable name.  It is only used when LAMMPS is launched by an mpirun
@@ -223,7 +238,7 @@ links with from the lib/message directory.  See the
 
 .. _cite:
 
-**-cite style or file name**
+**-cite style** or **file name**
 
 Select how and where to output a reminder about citing contributions
 to the LAMMPS code that were used during the run. Available styles are

doc/src/angle_table.rst

@@ -69,7 +69,6 @@ parenthesized comments):
    HAM                           (keyword is the first text on line)
    N 181 FP 0 0 EQ 90.0          (N, FP, EQ parameters)
                                  (blank line)
-   N 181 FP 0 0                  (N, FP parameters)
    1 0.0 200.5 2.5               (index, angle, energy, derivative)
    2 1.0 198.0 2.5
    ...

doc/src/pair_lj_cut_tip4p.rst

@@ -145,6 +145,22 @@ specified since a Coulombic cutoff cannot be specified for an individual I,J
 type pair. All type pairs use the same global Coulombic cutoff specified in
 the pair_style command.
 
+.. warning::
+
+   Because of how these pair styles implement the coulomb interactions
+   by implicitly defining a fourth site for the negative charge
+   of the TIP4P and similar water models, special care must be taken
+   when using these pair styles with other computations that also use
+   charges.  Unless they are specially set up to also handle the implicit
+   definition of the 4th site, results are likely incorrect.  Example:
+   :doc:`compute dipole/chunk <compute_dipole_chunk>`.  For the same
+   reason, when using one of these pair styles with
+   :doc:`pair_style  hybrid <pair_hybrid>`, **all** coulomb interactions
+   should be handled by a single sub-style with TIP4P support. All other
+   instances and styles will "see" the M point charges at the position
+   of the Oxygen atom and thus compute incorrect forces and energies.
+   LAMMPS will print a warning when it detects one of these issues.
+
 ----------
 
 A version of these styles with a soft core, *lj/cut/tip4p/long/soft*\ , suitable

examples/ASPHERE/box/in.box

@@ -67,7 +67,7 @@ delete_atoms	overlap 1.0 small big
 
 reset_timestep	0
 
-neighbor	0.3 bin
+neighbor	0.3 multi
 neigh_modify	delay 0 every 1 check yes
 
 comm_modify	mode multi group big vel yes

examples/ASPHERE/box/in.box.mp

@@ -67,7 +67,7 @@ delete_atoms	overlap 1.0 small big
 
 reset_timestep	0
 
-neighbor	0.3 bin
+neighbor	0.3 multi
 neigh_modify	delay 0 every 1 check yes
 
 comm_modify	mode multi group big vel yes

examples/ASPHERE/dimer/in.dimer

@@ -61,7 +61,7 @@ delete_atoms	overlap 0.5 small big
 
 reset_timestep	0
 
-neighbor	0.3 bin
+neighbor	0.3 multi
 neigh_modify	delay 0 every 1 check yes
 
 comm_modify	mode multi group big vel yes

examples/ASPHERE/dimer/in.dimer.mp

@@ -61,7 +61,7 @@ delete_atoms	overlap 0.5 small big
 
 reset_timestep	0
 
-neighbor	0.3 bin
+neighbor	0.3 multi
 neigh_modify	delay 0 every 1 check yes
 
 comm_modify	mode multi group big vel yes

examples/ASPHERE/ellipsoid/in.ellipsoid

@@ -72,7 +72,7 @@ delete_atoms	overlap 1.6 small big
 
 reset_timestep	0
 
-neighbor	0.3 bin
+neighbor	0.3 multi
 neigh_modify	delay 0 every 1 check yes
 
 comm_modify	mode multi group big vel yes

examples/ASPHERE/ellipsoid/in.ellipsoid.mp

@@ -72,7 +72,7 @@ delete_atoms	overlap 1.6 small big
 
 reset_timestep	0
 
-neighbor	0.3 bin
+neighbor	0.3 multi
 neigh_modify	delay 0 every 1 check yes
 
 comm_modify	mode multi group big vel yes

examples/ASPHERE/line/in.line.srd

@@ -34,7 +34,7 @@ reset_timestep	0
 
 velocity	small create 1.44 87287 loop geom
 
-neighbor	0.3 bin
+neighbor	0.3 multi
 neigh_modify	delay 0 every 1 check yes
 neigh_modify	exclude molecule/intra big include big
 

examples/ASPHERE/poly/in.poly

@@ -70,7 +70,7 @@ delete_atoms	overlap 1.0 small big
 
 reset_timestep	0
 
-neighbor	0.3 bin
+neighbor	0.3 multi
 neigh_modify	delay 0 every 1 check yes
 
 comm_modify	mode multi group big vel yes

examples/ASPHERE/poly/in.poly.mp

@@ -70,7 +70,7 @@ delete_atoms	overlap 1.0 small big
 
 reset_timestep	0
 
-neighbor	0.3 bin
+neighbor	0.3 multi
 neigh_modify	delay 0 every 1 check yes
 
 comm_modify	mode multi group big vel yes

examples/ASPHERE/star/in.star

@@ -67,7 +67,7 @@ delete_atoms	overlap 0.5 small big
 
 reset_timestep	0
 
-neighbor	0.3 bin
+neighbor	0.3 multi
 neigh_modify	delay 0 every 1 check yes
 
 comm_modify	mode multi group big vel yes

examples/ASPHERE/star/in.star.mp

@@ -67,7 +67,7 @@ delete_atoms	overlap 0.5 small big
 
 reset_timestep	0
 
-neighbor	0.3 bin
+neighbor	0.3 multi
 neigh_modify	delay 0 every 1 check yes
 
 comm_modify	mode multi group big vel yes

examples/ASPHERE/tri/in.tri.srd

@@ -33,7 +33,7 @@ reset_timestep	0
 
 velocity	small create 1.44 87287 loop geom
 
-neighbor	0.3 bin
+neighbor	0.3 multi
 neigh_modify	delay 0 every 1 check yes
 neigh_modify	exclude molecule/intra big include big
 

examples/USER/cgsdk/sds-monolayer/in.sds-hybrid

@@ -37,10 +37,11 @@ atom_modify     first charged
 kspace_style    pppm/cg 0.00001
 kspace_modify   order 3 
 
-comm_modify     mode multi
 neighbor        2.0 multi
 neigh_modify    delay 4 every 2 check yes
 
+comm_modify     mode multi
+
 timestep        10.0
 
 fix             1 all nvt temp 310.0 310.0 100.0

src/KOKKOS/memory_kokkos.h

@@ -253,7 +253,7 @@ TYPE grow_kokkos(TYPE &data, typename TYPE::value_type **&array,
   data.resize(n1);
 
   bigint nbytes = ((bigint) sizeof(typename TYPE::value_type *)) * n1;
-  array = (typename TYPE::value_type **) smalloc(nbytes,name);
+  array = (typename TYPE::value_type **) srealloc(array,nbytes,name);
 
   for (int i = 0; i < n1; i++)
     if (data.h_view.extent(1)==0)

src/KOKKOS/pair_table_kokkos.cpp

@@ -52,6 +52,14 @@ PairTableKokkos<DeviceType>::~PairTableKokkos()
 {
   if (copymode) return;
 
+  if (allocated) {
+    memoryKK->destroy_kokkos(k_eatom,eatom);
+    memoryKK->destroy_kokkos(k_vatom,vatom);
+    memory->destroy(setflag);
+    memoryKK->destroy_kokkos(d_table->cutsq,cutsq);
+    memoryKK->destroy_kokkos(d_table->tabindex,tabindex);
+  }
+
   delete h_table;
   h_table = nullptr;
   delete d_table;

src/KOKKOS/pair_table_rx_kokkos.cpp

@@ -166,10 +166,10 @@ PairTableRXKokkos<DeviceType>::~PairTableRXKokkos()
   delete [] site1;
   delete [] site2;
 
+  if (allocated) {
     memoryKK->destroy_kokkos(k_eatom,eatom);
     memoryKK->destroy_kokkos(k_vatom,vatom);
-
+    memory->destroy(setflag);
-  if (allocated) {
     memoryKK->destroy_kokkos(d_table->cutsq,cutsq);
     memoryKK->destroy_kokkos(d_table->tabindex,tabindex);
   }

src/KOKKOS/sna_kokkos_impl.h

@@ -55,6 +55,7 @@ SNAKokkos<DeviceType, real_type, vector_length>::SNAKokkos(real_type rfac0_in,
   ncoeff = compute_ncoeff();
 
   nmax = 0;
+  natom = 0;
 
   build_indexlist();
 

src/USER-QTB/fix_qbmsst.cpp

@@ -221,7 +221,7 @@ FixQBMSST::FixQBMSST(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
   // create a new compute potential energy compute
 
   id_pe = utils::strdup(std::string(id) + "_pe");
-  modify->add_compute(fmt::format("{} all pe",id_temp));
+  modify->add_compute(fmt::format("{} all pe",id_pe));
   peflag = 1;
 
   // allocate qbmsst

src/compute_dipole_chunk.cpp

@@ -15,9 +15,11 @@
 #include "compute_dipole_chunk.h"
 
 #include "atom.h"
+#include "comm.h"
 #include "compute_chunk_atom.h"
 #include "domain.h"
 #include "error.h"
+#include "force.h"
 #include "math_special.h"
 #include "memory.h"
 #include "modify.h"
@@ -95,6 +97,10 @@ void ComputeDipoleChunk::init()
   cchunk = (ComputeChunkAtom *) modify->compute[icompute];
   if (strcmp(cchunk->style,"chunk/atom") != 0)
     error->all(FLERR,"Compute dipole/chunk does not use chunk/atom compute");
+
+  if ((force->pair_match("/tip4p/",0) != nullptr) && (comm->me == 0))
+    error->warning(FLERR,"Computed dipole moments may be incorrect when "
+                   "using a tip4p pair style");
 }
 
 /* ---------------------------------------------------------------------- */

src/fix_wall_region.cpp

@@ -397,7 +397,7 @@ void FixWallRegion::morse(double r)
 {
   double dr = r - sigma;
   double dexp = exp(-alpha * dr);
-  fwall = coeff1 * (dexp*dexp - dexp) / r;
+  fwall = coeff1 * (dexp*dexp - dexp);
   eng = epsilon * (dexp*dexp - 2.0*dexp) - offset;
 }
 

src/lammps.cpp

@@ -1142,6 +1142,7 @@ void _noopt LAMMPS::help()
           "-in none/filename           : read input from file or stdin (default) (-i)\n"
           "-kokkos on/off ...          : turn KOKKOS mode on or off (-k)\n"
           "-log none/filename          : where to send log output (-l)\n"
+          "-mdi '<mdi flags>'          : pass flags to the MolSSI Driver Interface\n"
           "-mpicolor color             : which exe in a multi-exe mpirun cmd (-m)\n"
           "-cite                       : select citation reminder style (-c)\n"
           "-nocite                     : disable citation reminder (-nc)\n"

src/pair_hybrid.cpp

@@ -341,6 +341,8 @@ void PairHybrid::settings(int narg, char **arg)
 
   // multiple[i] = 1 to M if sub-style used multiple times, else 0
 
+  int num_tip4p = 0, num_coul = 0; // count sub-styles with tip4p and coulomb
+
   for (int i = 0; i < nstyles; i++) {
     int count = 0;
     for (int j = 0; j < nstyles; j++) {
@@ -348,8 +350,22 @@ void PairHybrid::settings(int narg, char **arg)
       if (j == i) multiple[i] = count;
     }
     if (count == 1) multiple[i] = 0;
+
+    if (utils::strmatch(keywords[i],"/tip4p/")) ++num_tip4p;
+    if (utils::strmatch(keywords[i],"/coul/")
+        || utils::strmatch(keywords[i],"^comb")
+        || utils::strmatch(keywords[i],"^reax/c")) ++num_coul;
   }
 
+  if ((num_tip4p > 1) && (comm->me == 0))
+    error->warning(FLERR,"Using multiple tip4p sub-styles can result in "
+                   "inconsistent calculation of coulomb interactions");
+
+  if ((num_tip4p > 0) && (num_coul > 0) && (comm->me == 0))
+    error->warning(FLERR,"Using a tip4p sub-style with other sub-styles "
+                   "that include coulomb interactions can result in "
+                   "inconsistent calculation of the coulomb interactions");
+
   // set pair flags from sub-style flags
 
   flags();