Merge branch 'develop' into new-pair_style-ylz

README

@@ -16,8 +16,8 @@ National Laboratories, a US Department of Energy facility, with
 funding from the DOE.  It is an open-source code, distributed freely
 under the terms of the GNU Public License (GPL) version 2.
 
-The primary author of the code is Steve Plimpton, who can be emailed
+The code is maintained by the LAMMPS development team who can be emailed
-at sjplimp@sandia.gov.  The LAMMPS WWW Site at www.lammps.org has
+at developers@lammps.org.  The LAMMPS WWW Site at www.lammps.org has
 more information about the code and its uses.
 
 The LAMMPS distribution includes the following files and directories:

cmake/CMakeLists.txt

@@ -727,18 +727,17 @@ list(FIND LANGUAGES "Fortran" _index)
 if(_index GREATER -1)
   target_link_libraries(lammps PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
 endif()
-set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h compute.h dihedral.h domain.h error.h fix.h force.h group.h improper.h
+set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h command.h compute.h dihedral.h domain.h
-  input.h info.h kspace.h lammps.h lattice.h library.h lmppython.h lmptype.h memory.h modify.h neighbor.h neigh_list.h output.h
+  error.h exceptions.h fix.h force.h group.h improper.h input.h info.h kspace.h lammps.h lattice.h
-  pair.h pointers.h region.h timer.h universe.h update.h utils.h variable.h)
+  library.h lmppython.h lmptype.h memory.h modify.h neighbor.h neigh_list.h output.h pair.h
-if(LAMMPS_EXCEPTIONS)
+  platform.h pointers.h region.h timer.h universe.h update.h utils.h variable.h)
-  list(APPEND LAMMPS_CXX_HEADERS exceptions.h)
+set(LAMMPS_FMT_HEADERS core.h format.h)
-endif()
 
 set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
 set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
 set_target_properties(lammps PROPERTIES PREFIX "lib")
 target_include_directories(lammps PUBLIC $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/lammps>)
-file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps)
+file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt)
 foreach(_HEADER ${LAMMPS_CXX_HEADERS})
   add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/${_HEADER})
   add_custom_target(${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER})
@@ -747,6 +746,14 @@ foreach(_HEADER ${LAMMPS_CXX_HEADERS})
     install(FILES ${LAMMPS_SOURCE_DIR}/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
   endif()
 endforeach()
+foreach(_HEADER ${LAMMPS_FMT_HEADERS})
+  add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER})
+  add_custom_target(fmt_${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt/${_HEADER})
+  add_dependencies(lammps fmt_${_HEADER})
+  if(BUILD_SHARED_LIBS)
+    install(FILES ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps/fmt)
+  endif()
+endforeach()
 target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/includes>)
 add_library(LAMMPS::lammps ALIAS lammps)
 get_target_property(LAMMPS_DEFINES lammps INTERFACE_COMPILE_DEFINITIONS)
@@ -969,9 +976,6 @@ if(PKG_GPU)
   endif()
   message(STATUS "GPU precision:            ${GPU_PREC}")
 endif()
-if(PKG_KOKKOS)
-  message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}")
-endif()
 if(PKG_KSPACE)
   message(STATUS "<<< FFT settings >>>
 -- Primary FFT lib:  ${FFT}")

cmake/Modules/FindClangFormat.cmake

@@ -1,5 +1,10 @@
 # Find clang-format
 find_program(ClangFormat_EXECUTABLE NAMES clang-format
+                                          clang-format-15.0
+                                          clang-format-14.0
+                                          clang-format-13.0
+                                          clang-format-12.0
+                                          clang-format-11.0
                                           clang-format-10.0
                                           clang-format-9.0
                                           clang-format-8.0
@@ -14,19 +19,27 @@ if(ClangFormat_EXECUTABLE)
                   OUTPUT_VARIABLE clang_format_version
                   ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
 
-
+  if(clang_format_version MATCHES "^(Ubuntu |)clang-format version .*")
-  if(clang_format_version MATCHES "^clang-format version .*")
+    # Arch Linux output:
-    # Arch Linux
     # clang-format version 10.0.0
-
+    #
-    # Ubuntu 18.04 LTS Output
+    # Ubuntu 18.04 LTS output:
     # clang-format version 6.0.0-1ubuntu2 (tags/RELEASE_600/final)
-    string(REGEX REPLACE "clang-format version ([0-9.]+).*"
+    #
-                         "\\1"
+    # Ubuntu 20.04 LTS output:
+    # clang-format version 10.0.0-4ubuntu1
+    #
+    # Ubuntu 22.04 LTS output:
+    # Ubuntu clang-format version 14.0.0-1ubuntu1
+    #
+    # Fedora 36 output:
+    # clang-format version 14.0.5 (Fedora 14.0.5-1.fc36)
+    string(REGEX REPLACE "^(Ubuntu |)clang-format version ([0-9.]+).*"
+                         "\\2"
                          ClangFormat_VERSION
                          "${clang_format_version}")
   elseif(clang_format_version MATCHES ".*LLVM version .*")
-    # CentOS 7 Output
+    # CentOS 7 output:
     # LLVM (http://llvm.org/):
     #   LLVM version 3.4.2
     #   Optimized build.

cmake/Modules/FindCythonize.cmake

@@ -22,7 +22,7 @@ endif()
 if(Python_EXECUTABLE)
   get_filename_component(_python_path ${Python_EXECUTABLE} PATH)
   find_program(Cythonize_EXECUTABLE
-    NAMES cythonize3 cythonize cythonize.bat
+    NAMES cythonize-${Python_VERSION_MAJOR}.${Python_VERSION_MINOR} cythonize3 cythonize cythonize.bat
     HINTS ${_python_path})
 endif()
 

cmake/Modules/Packages/ML-IAP.cmake

@@ -2,7 +2,13 @@
 set(MLIAP_ENABLE_PYTHON_DEFAULT OFF)
 if(PKG_PYTHON)
   find_package(Cythonize QUIET)
-  if(Cythonize_FOUND)
+  if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14)
+    find_package(Python COMPONENTS NumPy QUIET)
+  else()
+    # assume we have NumPy
+    set(Python_NumPy_FOUND ON)
+  endif()
+  if(Cythonize_FOUND AND Python_NumPy_FOUND)
     set(MLIAP_ENABLE_PYTHON_DEFAULT ON)
   endif()
 endif()
@@ -11,6 +17,9 @@ option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_EN
 
 if(MLIAP_ENABLE_PYTHON)
   find_package(Cythonize REQUIRED)
+  if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14)
+    find_package(Python COMPONENTS NumPy REQUIRED)
+  endif()
   if(NOT PKG_PYTHON)
     message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP")
   endif()

cmake/Modules/Packages/PLUMED.cmake

@@ -47,15 +47,15 @@ if(DOWNLOAD_PLUMED)
   endif()
   message(STATUS "PLUMED download requested - we will build our own")
   if(PLUMED_MODE STREQUAL "STATIC")
-    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumed.a")
+    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX}")
   elseif(PLUMED_MODE STREQUAL "SHARED")
-    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX};<INSTALL_DIR>/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX};<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
   elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
+    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_PREFIX}")
   endif()
 
-  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.4/plumed-src-2.7.4.tgz" CACHE STRING "URL for PLUMED tarball")
+  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.1/plumed-src-2.8.1.tgz" CACHE STRING "URL for PLUMED tarball")
-  set(PLUMED_MD5 "858e0b6aed173748fc85b6bc8a9dcb3e" CACHE STRING "MD5 checksum of PLUMED tarball")
+  set(PLUMED_MD5 "6bfe72ebdae63dc38a9ca27d9b0e08f8" CACHE STRING "MD5 checksum of PLUMED tarball")
 
   mark_as_advanced(PLUMED_URL)
   mark_as_advanced(PLUMED_MD5)
@@ -78,12 +78,12 @@ if(DOWNLOAD_PLUMED)
   add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
   add_dependencies(LAMMPS::PLUMED plumed_build)
   if(PLUMED_MODE STREQUAL "STATIC")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed.a INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
   elseif(PLUMED_MODE STREQUAL "SHARED")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
   elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumedWrapper.a INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}")
   endif()
   set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
   file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
@@ -96,7 +96,7 @@ else()
   elseif(PLUMED_MODE STREQUAL "SHARED")
     include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
   elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
     include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
   endif()
   set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")

cmake/Modules/Packages/VTK.cmake

@@ -1,4 +1,9 @@
 find_package(VTK REQUIRED NO_MODULE)
-include(${VTK_USE_FILE})
 target_compile_definitions(lammps PRIVATE -DLAMMPS_VTK)
+if (VTK_MAJOR_VERSION VERSION_LESS 9.0)
+  include(${VTK_USE_FILE})
   target_link_libraries(lammps PRIVATE ${VTK_LIBRARIES})
+else()
+  target_link_libraries(lammps PRIVATE VTK::CommonCore VTK::IOCore VTK::CommonDataModel VTK::IOXML VTK::IOLegacy VTK::IOParallelXML)
+  vtk_module_autoinit(TARGETS lammps MODULES VTK::CommonCore VTK::IOCore VTK::CommonDataModel VTK::IOXML VTK::IOLegacy VTK::IOParallelXML)
+endif()

doc/Makefile

@@ -38,16 +38,14 @@ endif
 # override settings for PIP commands
 # PIP_OPTIONS = --cert /etc/pki/ca-trust/extracted/openssl/ca-bundle.trust.crt --proxy http://proxy.mydomain.org
 
-#SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())') $(shell test -f $(BUILDDIR)/doxygen/xml/run.stamp && printf -- "-E")
-
 # temporarily disable caching so that the hack for the sphinx-tabs extensions to get proper non-html output works
-SPHINXEXTRA = -E -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
+SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
 
 # grab list of sources from doxygen config file.
 # we only want to use explicitly listed files.
 DOXYFILES      = $(shell sed -n -e 's/\#.*$$//' -e '/^ *INPUT \+=/,/^[A-Z_]\+ \+=/p' doxygen/Doxyfile.in | sed -e 's/@LAMMPS_SOURCE_DIR@/..\/src/g' -e 's/\\//g' -e 's/ \+/ /' -e 's/[A-Z_]\+ \+= *\(YES\|NO\|\)//') 
 
-.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check char_check xmlgen fasthtml
+.PHONY: help clean-all clean clean-spelling epub mobi html pdf spelling anchor_check style_check char_check xmlgen fasthtml
 
 # ------------------------------------------
 
@@ -89,6 +87,8 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
+		sphinx-build -E $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
+		touch $(RSTDIR)/Fortran.rst ;\
 		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
 		ln -sf Manual.html html/index.html;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
@@ -114,7 +114,9 @@ fasthtml: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@mkdir -p fasthtml
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
-		sphinx-build -j 4 -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
+		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
+		touch $(RSTDIR)/Fortran.rst ;\
+		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
 		deactivate ;\
 	)
 	@rm -rf fasthtml/_sources
@@ -144,6 +146,8 @@ epub: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@cp src/JPG/*.* epub/JPG
 	@(\
 		. $(VENV)/bin/activate ;\
+		sphinx-build -E $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
+		touch $(RSTDIR)/Fortran.rst ;\
 		sphinx-build $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		deactivate ;\
@@ -163,6 +167,8 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@if [ "$(HAS_PDFLATEX)" == "NO" ] ; then echo "PDFLaTeX or latexmk were not found! Please check README for further instructions" 1>&2; exit 1; fi
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
+		sphinx-build -E $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
+		touch $(RSTDIR)/Fortran.rst ;\
 		sphinx-build  $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		echo "############################################" ;\

doc/src/Build_development.rst

@@ -147,6 +147,16 @@ compile and will download and compile a specific recent version of the
 `Googletest <https://github.com/google/googletest/>`_ C++ test framework
 for implementing the tests.
 
+.. admonition:: Software version requirements for testing
+   :class: note
+
+   The compiler and library version requirements for the testing
+   framework are more strict than for the main part of LAMMPS.  For
+   example the default GNU C++ and Fortran compilers of RHEL/CentOS 7.x
+   (version 4.8.x) are not sufficient.  The CMake configuration will try
+   to detect compatible versions and either skip incompatible tests or
+   stop with an error.
+
 After compilation is complete, the unit testing is started in the build
 folder using the ``ctest`` command, which is part of the CMake software.
 The output of this command will be looking something like this::

doc/src/Developer_updating.rst

@@ -7,7 +7,7 @@ source files provided as a supplement to a publication) that are written
 for an older version of LAMMPS and thus need to be updated to be
 compatible with the current version of LAMMPS.  Due to the active
 development of LAMMPS it is likely to always be incomplete.  Please
-contact developer@lammps.org in case you run across an issue that is not
+contact developers@lammps.org in case you run across an issue that is not
 (yet) listed here.  Please also review the latest information about the
 LAMMPS :doc:`programming style conventions <Modify_style>`, especially
 if you are considering to submit the updated version for inclusion into

doc/src/Fortran.rst

@@ -1,11 +1,11 @@
 The ``LIBLAMMPS`` Fortran Module
 ********************************
 
-The ``LIBLAMMPS`` module provides an interface to call LAMMPS from Fortran.
+The ``LIBLAMMPS`` module provides an interface to call LAMMPS from
-It is based on the LAMMPS C library interface and
+Fortran.  It is based on the LAMMPS C library interface and requires a
-requires a Fortran 2003-compatible compiler to be compiled.  It is
+fully Fortran 2003-compatible compiler to be compiled.  It is designed
-designed to be self-contained and not require any support functions
+to be self-contained and not require any support functions written in C,
-written in C, C++, or Fortran other than those in the C library interface.
+C++, or Fortran other than those in the C library interface.
 
 While C libraries have a defined binary interface (ABI) and can thus be
 used from multiple compiler versions from different vendors as long
@@ -21,11 +21,11 @@ for a simple program using the Fortran interface would be:
    mpifort -o testlib.x lammps.f90 testlib.f90 -L. -llammps
 
 Please note that the MPI compiler wrapper is only required when the
-calling the library from an MPI-parallelized program.  Otherwise, using the
+calling the library from an MPI-parallelized program.  Otherwise, using
-fortran compiler (gfortran, ifort, flang, etc.) will suffice.  It may be
+the plain Fortran compiler (gfortran, ifort, flang, etc.) will suffice.
-necessary to link to additional libraries, depending on how LAMMPS was
+It may be necessary to link to additional libraries, depending on how
-configured and whether the LAMMPS library :doc:`was compiled as a static
+LAMMPS was configured and whether the LAMMPS library :doc:`was compiled
-or dynamic library <Build_link>`.
+as a static or dynamic library <Build_link>`.
 
 If the LAMMPS library itself has been compiled with MPI support, the
 resulting executable will still be able to run LAMMPS in parallel with
@@ -299,7 +299,7 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
       ``MPI_comm`` derived type to access the integer value of the
       communicator, such as in
 
-      .. code-block:: Fortran
+      .. code-block:: fortran
 
          PROGRAM testmpi
            USE LIBLAMMPS
@@ -446,7 +446,7 @@ Procedures Bound to the lammps Derived Type
    represents a properly-initialized LAMMPS instance, the following code will
    extract the periodic box settings into the variable "periodic":
 
-   .. code-block:: Fortran
+   .. code-block:: fortran
 
       ! code to start up
       logical :: periodic(3)
@@ -593,7 +593,7 @@ Procedures Bound to the lammps Derived Type
       but you can automatically reallocate it to the correct length after the
       function returns, viz.,
 
-      .. code-block :: Fortran
+      .. code-block :: fortran
 
          PROGRAM test
            USE LIBLAMMPS
@@ -670,7 +670,7 @@ Procedures Bound to the lammps Derived Type
        will print the *y*-coordinate of the sixth atom on this processor.
        Conversely,
 
-       .. code-block:: Fortran
+       .. code-block:: fortran
 
           TYPE(lammps) :: lmp
           REAL(c_double), DIMENSION(:,:), POINTER :: x => NULL()
@@ -720,7 +720,7 @@ Procedures Bound to the lammps Derived Type
        typical notation in C and C++, but not Fortran), you can create another
        pointer and associate it thus:
 
-       .. code-block:: Fortran
+       .. code-block:: fortran
 
           REAL(c_double), DIMENSION(:,:), POINTER :: x, x0
           x = lmp%extract_atom("x")
@@ -752,7 +752,7 @@ Procedures Bound to the lammps Derived Type
 
    For example,
 
-   .. code-block:: Fortran
+   .. code-block:: fortran
 
       TYPE(lammps) :: lmp
       REAL(c_double), DIMENSION(:), POINTER :: COM
@@ -938,7 +938,7 @@ Procedures Bound to the lammps Derived Type
 
    For example,
 
-   .. code-block:: Fortran
+   .. code-block:: fortran
 
       TYPE(lammps) :: lmp
       REAL(c_double) :: dr, dx, dy, dz
@@ -960,7 +960,7 @@ Procedures Bound to the lammps Derived Type
    appropriate size to match the internal data, and will be
    type/kind/rank-checked at the time of the assignment. For example,
 
-   .. code-block:: Fortran
+   .. code-block:: fortran
 
       TYPE(lammps) :: lmp
       REAL(c_double), DIMENSION(:), POINTER :: r
@@ -973,7 +973,7 @@ Procedures Bound to the lammps Derived Type
    array computed by :doc:`fix store/state <fix_store_state>` when three
    inputs are specified. Similarly,
 
-   .. code-block:: Fortran
+   .. code-block:: fortran
 
       TYPE(lammps) :: lmp
       REAL(c_double), DIMENSION(:), POINTER :: x
@@ -1059,7 +1059,7 @@ Procedures Bound to the lammps Derived Type
 
    For example,
 
-   .. code-block:: Fortran
+   .. code-block:: fortran
 
       TYPE(lammps) :: lmp
       REAL(c_double) :: area
@@ -1129,7 +1129,7 @@ Procedures Bound to the lammps Derived Type
       If you want data from this function to be accessible as a two-dimensional
       array, you can declare a rank-2 pointer and reassign it, like so:
 
-      .. code-block:: Fortran
+      .. code-block:: fortran
 
          USE, INTRINSIC :: ISO_C_BINDING
          USE LIBLAMMPS

doc/src/Packages_details.rst

@@ -1735,8 +1735,6 @@ must be installed.
 
 **Author:** Aidan Thompson (Sandia), Nicholas Lubbers (LANL).
 
-.. versionadded:: 30Jun2020
-
 .. versionadded:: 30Jun2020
 
 **Supporting info:**

doc/src/Run_output.rst

@@ -16,46 +16,47 @@ simulation.  An example set of statistics is shown here:
 
 .. parsed-literal::
 
-   Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms
+   Loop time of 0.942801 on 4 procs for 300 steps with 2004 atoms
 
-   Performance: 18.436 ns/day  1.302 hours/ns  106.689 timesteps/s
+   Performance: 54.985 ns/day, 0.436 hours/ns, 318.201 timesteps/s, 637.674 katom-step/s
-   97.0% CPU use with 4 MPI tasks x no OpenMP threads
+   195.2% CPU use with 2 MPI tasks x 2 OpenMP threads
 
-   MPI task timings breakdown:
+   MPI task timing breakdown:
    Section \|  min time  \|  avg time  \|  max time  \|%varavg\| %total
    ---------------------------------------------------------------
-   Pair    \| 1.9808     \| 2.0134     \| 2.0318     \|   1.4 \| 71.60
+   Pair    \| 0.61419    \| 0.62872    \| 0.64325    \|   1.8 \| 66.69
-   Bond    \| 0.0021894  \| 0.0060319  \| 0.010058   \|   4.7 \|  0.21
+   Bond    \| 0.0028608  \| 0.0028899  \| 0.002919   \|   0.1 \|  0.31
-   Kspace  \| 0.3207     \| 0.3366     \| 0.36616    \|   3.1 \| 11.97
+   Kspace  \| 0.12652    \| 0.14048    \| 0.15444    \|   3.7 \| 14.90
-   Neigh   \| 0.28411    \| 0.28464    \| 0.28516    \|   0.1 \| 10.12
+   Neigh   \| 0.10242    \| 0.10242    \| 0.10242    \|   0.0 \| 10.86
-   Comm    \| 0.075732   \| 0.077018   \| 0.07883    \|   0.4 \|  2.74
+   Comm    \| 0.026753   \| 0.027593   \| 0.028434   \|   0.5 \|  2.93
-   Output  \| 0.00030518 \| 0.00042665 \| 0.00078821 \|   1.0 \|  0.02
+   Output  \| 0.00018341 \| 0.00030942 \| 0.00043542 \|   0.0 \|  0.03
-   Modify  \| 0.086606   \| 0.086631   \| 0.086668   \|   0.0 \|  3.08
+   Modify  \| 0.039117   \| 0.039348   \| 0.039579   \|   0.1 \|  4.17
-   Other   \|            \| 0.007178   \|            \|       \|  0.26
+   Other   \|            \| 0.001041   \|            \|       \|  0.11
 
-   Nlocal:    501 ave 508 max 490 min
+   Nlocal:           1002 ave        1006 max         998 min
-   Histogram: 1 0 0 0 0 0 1 1 0 1
+   Histogram: 1 0 0 0 0 0 0 0 0 1
-   Nghost:    6586.25 ave 6628 max 6548 min
+   Nghost:         8670.5 ave        8691 max        8650 min
-   Histogram: 1 0 1 0 0 0 1 0 0 1
+   Histogram: 1 0 0 0 0 0 0 0 0 1
-   Neighs:    177007 ave 180562 max 170212 min
+   Neighs:         354010 ave      357257 max      350763 min
-   Histogram: 1 0 0 0 0 0 0 1 1 1
+   Histogram: 1 0 0 0 0 0 0 0 0 1
 
-   Total # of neighbors = 708028
+   Total # of neighbors = 708020
-   Ave neighs/atom = 353.307
+   Ave neighs/atom = 353.30339
-   Ave special neighs/atom = 2.34032
+   Ave special neighs/atom = 2.3403194
    Neighbor list builds = 26
    Dangerous builds = 0
 
 ----------
 
-The first section provides a global loop timing summary. The *loop
+The first section provides a global loop timing summary. The *loop time*
-time* is the total wall-clock time for the simulation to run.  The
+is the total wall-clock time for the simulation to run.  The
-*Performance* line is provided for convenience to help predict how
+*Performance* line is provided for convenience to help predict how long
-long it will take to run a desired physical simulation.  The *CPU use*
+it will take to run a desired physical simulation and to have numbers
-line provides the CPU utilization per MPI task; it should be close to
+useful for performance comparison between different simulation settings
-100% times the number of OpenMP threads (or 1 of not using OpenMP).
+or system sizes.  The *CPU use* line provides the CPU utilization per
-Lower numbers correspond to delays due to file I/O or insufficient
+MPI task; it should be close to 100% times the number of OpenMP threads
-thread utilization.
+(or 1 of not using OpenMP).  Lower numbers correspond to delays due to
+file I/O or insufficient thread utilization.
 
 ----------
 

doc/src/clear.rst

@@ -23,15 +23,16 @@ Description
 """""""""""
 
 This command deletes all atoms, restores all settings to their default
-values, and frees all memory allocated by LAMMPS.  Once a clear
+values, and frees all memory allocated by LAMMPS.  Once a clear command
-command has been executed, it is almost as if LAMMPS were starting
+has been executed, it is almost as if LAMMPS were starting over, with
-over, with only the exceptions noted below.  This command enables
+only the exceptions noted below.  This command enables multiple jobs to
-multiple jobs to be run sequentially from one input script.
+be run sequentially from one input script.
 
 These settings are not affected by a clear command: the working
-directory (:doc:`shell <shell>` command), log file status
+directory (:doc:`shell <shell>` command), log file status (:doc:`log
-(:doc:`log <log>` command), echo status (:doc:`echo <echo>` command), and
+<log>` command), echo status (:doc:`echo <echo>` command), and input
-input script variables (:doc:`variable <variable>` command).
+script variables except for *atomfile* style variables (:doc:`variable
+<variable>` command).
 
 Restrictions
 """"""""""""

doc/src/dump.rst

@@ -202,7 +202,7 @@ or multiple smaller files).
    to a dump file may be slightly outside the simulation box.
    Re-neighbor timesteps will not typically coincide with the
    timesteps dump snapshots are written.  See the :doc:`dump_modify
-   pbc <dump_modify>` command if you with to force coordinates to be
+   pbc <dump_modify>` command if you wish to force coordinates to be
    strictly inside the simulation box.
 
 .. note::

doc/src/fix_bond_react.rst

@@ -404,6 +404,12 @@ atoms are present. The velocity of each created atom is initialized in
 a random direction with a magnitude calculated from the instantaneous
 temperature of the reaction site.
 
+.. note::
+
+   The 'Coords' section must be included in the post-reaction template
+   when creating atoms because these coordinates are used to determine
+   where new atoms are inserted.
+
 The handedness of atoms that are chiral centers can be enforced by
 listing their IDs in the ChiralIDs section. A chiral atom must be
 bonded to four atoms with mutually different atom types. This feature

doc/src/neigh_modify.rst

@@ -16,12 +16,12 @@ Syntax
 
      keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize* or *collection/type* or *collection/interval*
        *delay* value = N
-         N = delay building until this many steps since last build
+         N = delay building neighbor lists until this many steps since last build
        *every* value = M
-         M = build neighbor list every this many steps
+         M = consider building neighbor lists every this many steps
        *check* value = *yes* or *no*
-         *yes* = only build if some atom has moved half the skin distance or more
+         *yes* = only build if at least one atom has moved half the skin distance or more
-         *no* = always build on 1st step that *every* and *delay* are satisfied
+         *no* = always build on 1st step where *every* and *delay* are conditions are satisfied
        *once* value = *yes* or *no*
          *yes* = only build neighbor list once at start of run and never rebuild
          *no* = rebuild neighbor list according to other settings
@@ -71,30 +71,53 @@ Description
 """""""""""
 
 This command sets parameters that affect the building and use of
-pairwise neighbor lists.  Depending on what pair interactions and
+pairwise neighbor lists.  Depending on what pair interactions and other
-other commands are defined, a simulation may require one or more
+commands are defined, a simulation may require one or more neighbor
-neighbor lists.
+lists.
 
-The *every*, *delay*, *check*, and *once* options affect how often
+The *every*, *delay*, *check*, and *once* options affect how often lists
-lists are built as a simulation runs.  The *delay* setting means never
+are built as a simulation runs.  The *delay* setting means never build
-build new lists until at least N steps after the previous build.  The
+new lists until at least N steps after the previous build.  The *every*
-*every* setting means build lists every M steps (after the delay has
+setting means attempt to build lists every M steps (after the delay has
 passed).  If the *check* setting is *no*, the lists are built on the
 first step that satisfies the *delay* and *every* settings.  If the
 *check* setting is *yes*, then the *every* and *delay* settings
 determine when a build may possibly be performed, but an actual build
-only occurs if some atom has moved more than half the skin distance
+only occurs if at least one atom has moved more than half the neighbor
-(specified in the :doc:`neighbor <neighbor>` command) since the last
+skin distance (specified in the :doc:`neighbor <neighbor>` command)
-build.
+since the last neighbor list build.
 
-If the *once* setting is yes, then the neighbor list is only built
+.. admonition:: Impact of neighbor list settings
-once at the beginning of each run, and never rebuilt, except on steps
+   :class: note
-when a restart file is written, or steps when a fix forces a rebuild
+
-to occur (e.g. fixes that create or delete atoms, such as :doc:`fix deposit <fix_deposit>` or :doc:`fix evaporate <fix_evaporate>`).
+   The choice of neighbor list settings can have a significant impact on
-This setting should only be made if you are certain atoms will not
+   the (parallel) performance of LAMMPS and the correctness of the
-move far enough that the neighbor list should be rebuilt, e.g. running
+   simulation results.  Since building the neighbor lists is time
-a simulation of a cold crystal.  Note that it is not that expensive to
+   consuming, doing it less frequently can speed up a calculation.  If
-check if neighbor lists should be rebuilt.
+   the lists are rebuilt too infrequently, however, interacting pairs
+   may be missing and thus the resulting pairwise interactions
+   incorrect.  The optimal settings depend on many factors like the
+   properties of the simulated system (density, geometry, topology,
+   temperature, pressure), the force field parameters and settings, the
+   size of the timestep, neighbor list skin distance and more.  The
+   default settings are chosen to be very conservative to guarantee
+   correctness of the simulation.  They depend on the *check* flag
+   heuristics to reduce the number of neighbor list rebuilds at a minor
+   expense for executing the check.  Determining the correctness of a
+   specific choice of neighbor list settings is complicated by the fact
+   that a neighbor list rebuild changes the order in which pairwise
+   interactions are computed and thus
+   - due to the limitations of floating-point math - the trajectory.
+
+If the *once* setting is yes, then the neighbor list is only built once
+at the beginning of each run, and never rebuilt, except on steps when a
+restart file is written, or steps when a fix forces a rebuild to occur
+(e.g. fixes that create or delete atoms, such as :doc:`fix deposit
+<fix_deposit>` or :doc:`fix evaporate <fix_evaporate>`).  This setting
+should only be made if you are certain atoms will not move far enough
+that the neighbor list should be rebuilt, e.g. running a simulation of a
+cold crystal.  Note that it is not that expensive to check if neighbor
+lists should be rebuilt.
 
 When the rRESPA integrator is used (see the :doc:`run_style <run_style>`
 command), the *every* and *delay* parameters refer to the longest
@@ -234,11 +257,11 @@ depend on their atom type.
 Restrictions
 """"""""""""
 
-If the "delay" setting is non-zero, then it must be a multiple of the
+If the *delay* setting is non-zero, then it must be a multiple of the
-"every" setting.
+*every* setting.
 
-The molecule/intra and molecule/inter exclude options can only be used
+The *molecule/intra* and *molecule/inter* exclusion options can only
-with atom styles that define molecule IDs.
+be used with atom styles that define molecule IDs.
 
 The value of the *page* setting must be at least 10x larger than the
 *one* setting.  This insures neighbor pages are not mostly empty
@@ -252,6 +275,6 @@ Related commands
 Default
 """""""
 
-The option defaults are delay = 10, every = 1, check = yes, once = no,
+The option defaults are delay = 0, every = 1, check = yes, once = no,
 cluster = no, include = all (same as no include option defined),
 exclude = none, page = 100000, one = 2000, and binsize = 0.0.

doc/src/pair_dipole.rst

@@ -58,22 +58,26 @@ Examples
 
 .. code-block:: LAMMPS
 
-   pair_style lj/cut/dipole/cut 10.0
+   pair_style lj/cut/dipole/cut 2.5 5.0
    pair_coeff * * 1.0 1.0
-   pair_coeff 2 3 1.0 1.0 2.5 4.0
+   pair_coeff 2 3 0.8 1.0 2.5 4.0
 
    pair_style lj/sf/dipole/sf 9.0
    pair_coeff * * 1.0 1.0
    pair_coeff 2 3 1.0 1.0 2.5 4.0 scale 0.5
-   pair_coeff 2 3 1.0 1.0 2.5 4.0
+   pair_coeff 2 3 0.8 1.0 2.5 4.0
 
-   pair_style lj/cut/dipole/long 10.0
+   pair_style lj/cut/dipole/long 2.5 3.5
    pair_coeff * * 1.0 1.0
-   pair_coeff 2 3 1.0 1.0 2.5 4.0
+   pair_coeff 2 3 0.8 1.0 3.0
 
-   pair_style lj/long/dipole/long long long 3.5 10.0
+   pair_style lj/long/dipole/long long long 3.5
    pair_coeff * * 1.0 1.0
-   pair_coeff 2 3 1.0 1.0 2.5 4.0
+   pair_coeff 2 3 0.8 1.0
+
+   pair_style lj/long/dipole/long cut long 2.5 3.5
+   pair_coeff * * 1.0 1.0
+   pair_coeff 2 3 0.8 1.0 3.0
 
 Description
 """""""""""
@@ -254,23 +258,28 @@ long-range LJ interactions, the :doc:`kspace_style ewald/disp
 
 ----------
 
-The following coefficients must be defined for each pair of atoms
+The following coefficients must be defined for each pair of atoms types
-types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
+via the :doc:`pair_coeff <pair_coeff>` command as in the examples above,
-above, or in the data file or restart files read by the
+or in the data file or restart files read by the :doc:`read_data
-:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
+<read_data>` or :doc:`read_restart <read_restart>` commands, or by
-commands, or by mixing as described below:
+mixing as described below:
 
 * :math:`\epsilon` (energy units)
 * :math:`\sigma` (distance units)
 * cutoff1 (distance units)
 * cutoff2 (distance units)
 
-The latter 2 coefficients are optional.  If not specified, the global
+The latter 2 coefficients are optional.  If not specified, the global LJ
-LJ and Coulombic cutoffs specified in the pair_style command are used.
+and Coulombic cutoffs specified in the pair_style command are used.  If
-If only one cutoff is specified, it is used as the cutoff for both LJ
+only one cutoff is specified, it is used as the cutoff for both LJ and
-and Coulombic interactions for this type pair.  If both coefficients
+Coulombic interactions for this type pair.  If both coefficients are
-are specified, they are used as the LJ and Coulombic cutoffs for this
+specified, they are used as the LJ and Coulombic cutoffs for this type
-type pair.
+pair.  When using a long-rang Coulomb solver, only a global Coulomb
+cutoff may be used and only the LJ cutoff may be changed with the
+:doc:`pair_coeff <pair_coeff>` command.  When using the
+*lj/long/dipole/long* pair style with *long* *long* setting, only a
+single global cutoff may be provided and no cutoff for the
+:doc:`pair_coeff <pair_coeff>` command.
 
 ----------
 

doc/src/pair_list.rst

@@ -57,7 +57,7 @@ The format of the list file is as follows:
        ID2 = atom ID of second atom
        style = style of interaction
        coeffs = list of coeffs
-       cutoff = cutoff for interaction (optional, except for style *quartic*)
+       cutoff = cutoff for interaction (optional)
 
 The cutoff parameter is optional for all but the *quartic* interactions.
 If it is not specified, the global cutoff is used.
@@ -71,7 +71,7 @@ Here is an example file:
    15 259 lj126     1.0 1.0      50.0
    15 603 morse    10.0 1.2 2.0  10.0 # and another comment
    18 470 harmonic 50.0 1.2       5.0
-   19 332 quartic   5.0 -1.2 1.2  5.0
+   19 332 quartic  10.0 5.0 -1.2 1.2
 
 The style *lj126* computes pairwise interactions with the formula
 
@@ -100,7 +100,7 @@ The style *harmonic* computes pairwise interactions with the formula
 
 .. math::
 
-   E = K (r - r_0)^2
+   E = K (r - r_0)^2 \qquad r < r_c
 
 and the coefficients:
 
@@ -113,16 +113,14 @@ The style *quartic* computes pairwise interactions with the formula
 
 .. math::
 
-   E = K (r - r_c)^2 (r - r_c -b_1) (r - r_c - b_2) \qquad r < r_c
+   E = K (r - r_0)^2 (r - r_0 -b_1) (r - r_0 - b_2) \qquad r < r_c
 
 and the coefficients:
 
 * :math:`K` (energy units)
+* :math:`r_0` (distance units)
 * :math:`b_1` (distance units)
 * :math:`b_2` (distance units)
-* :math:`r_c` (distance units)
-
-Note that the per list entry cutoff :math:`r_c` is **required** for *quartic* interactions.
 
 ----------
 

doc/src/pair_pace.rst

@@ -112,7 +112,6 @@ requests to compute `gamma`, as shown in example below:
     compute max_pace_gamma all reduce max f_pace_gamma
     variable dump_skip equal "c_max_pace_gamma < 5"
 
-
     dump pace_dump all custom 20 extrapolative_structures.dump id x y z f_pace_gamma
     dump_modify pace_dump skip v_dump_skip
 

doc/src/read_data.rst

@@ -71,8 +71,14 @@ Also see the explanation of the :doc:`-restart command-line switch
 
 This command can be used multiple times to add new atoms and their
 properties to an existing system by using the *add*, *offset*, and
-*shift* keywords.  See more details below, which includes the use case
+*shift* keywords.  However, it is important to understand that several
-for the *extra* keywords.
+system parameters, like the number of types of different kinds and per
+atom settings are **locked in** after the first *read_data* command,
+which means that no type ID (including its offset) may have a larger
+value when processing additional data files than what is set by the
+first data file and the corresponding *read_data* command options.  See
+more details on this situation below, which includes the use case for
+the *extra* keywords.
 
 The *group* keyword adds all the atoms in the data file to the
 specified group-ID.  The group will be created if it does not already

doc/src/run_style.rst

@@ -101,7 +101,7 @@ Py2 by Pz2, then Px1 must be an integer multiple of Px2, and similarly
 for Py1 a multiple of Py2, and Pz1 a multiple of Pz2.
 
 Typically the best way to do this is to let the first partition choose
-its onn optimal layout, then require the second partition's layout to
+its own optimal layout, then require the second partition's layout to
 match the integer multiple constraint.  See the
 :doc:`processors <processors>` command with its *part* keyword for a way
 to control this, e.g.

doc/src/variable.rst

@@ -213,6 +213,9 @@ from the list of active variables, and is thus available to be
 re-defined in a subsequent variable command.  The *delete* style does
 the same thing.
 
+Variables are **not** deleted by the :doc:`clear <clear>` command with
+the exception of atomfile-style variables.
+
 ----------
 
 The :doc:`Commands parse <Commands_parse>` page explains how
@@ -265,7 +268,7 @@ the first string is assigned to the variable.  Each time a
 string is assigned.  All processors assign the same string to the
 variable.
 
-*Index* style variables with a single string value can also be set by
+Index-style variables with a single string value can also be set by
 using the :doc:`command-line switch -var <Run_options>`.
 
 The *loop* style is identical to the *index* style except that the
@@ -285,7 +288,7 @@ be one string for each processor partition or "world".  LAMMPS can be
 run with multiple partitions via the :doc:`-partition command-line
 switch <Run_options>`.  This variable command assigns one string to
 each world.  All processors in the world are assigned the same string.
-The next command cannot be used with *equal* style variables, since
+The next command cannot be used with equal-style variables, since
 there is only one value per world.  This style of variable is useful
 when you wish to run different simulations on different partitions, or
 when performing a parallel tempering simulation (see the :doc:`temper
@@ -303,7 +306,7 @@ string.  This continues until all the variable strings are consumed.
 Thus, this command can be used to run 50 simulations on 8 processor
 partitions.  The simulations will be run one after the other on
 whatever partition becomes available, until they are all finished.
-*Universe* style variables are incremented using the files
+Universe-style variables are incremented using the files
 "tmp.lammps.variable" and "tmp.lammps.variable.lock" which you will
 see in your directory during such a LAMMPS run.
 
@@ -341,7 +344,9 @@ variable can be used to adapt the behavior of LAMMPS input scripts via
 environment variable settings, or to retrieve information that has
 been previously stored with the :doc:`shell putenv <shell>` command.
 Note that because environment variable settings are stored by the
-operating systems, they persist beyond a :doc:`clear <clear>` command.
+operating systems, they persist even if the corresponding *getenv*
+style variable is deleted, and also are set for sub-shells executed
+by the :doc:`shell <shell>` command.
 
 For the *file* style, a filename is provided which contains a list of
 strings to assign to the variable, one per line.  The strings can be
@@ -373,7 +378,9 @@ This means the variable can then be evaluated as many times as desired
 and will return those values.  There are two ways to cause the next
 set of per-atom values from the file to be read: use the
 :doc:`next <next>` command or the next() function in an atom-style
-variable, as discussed below.
+variable, as discussed below.  Unlike most variable styles
+atomfile-style variables are **deleted** during a :doc:`clear <clear>`
+command.
 
 The rules for formatting the file are as follows.  Each time a set of
 per-atom values is read, a non-blank line is searched for in the file.

doc/utils/converters/lammpsdoc/txt2html.py

@@ -3,7 +3,7 @@
 #
 # Python rewrite of txt2html
 # The original txt2html was written in C by Steve Plimpton
-# (http://www.cs.sandia.gov/cgi-bin/sjplimp/)
+# (https://sjplimp.github.io/)
 #
 # Copyright (C) 2015 Richard Berger
 #

doc/utils/sphinx-config/conf.py.in

@@ -38,7 +38,7 @@ sys.path.append(os.path.join(LAMMPS_DOC_DIR, 'src', '_ext'))
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+needs_sphinx = '5.2.0'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
@@ -53,10 +53,6 @@ extensions = [
     'tab_or_note',
     'breathe',
 ]
-# 2017-12-07: commented out, since this package is broken with Sphinx 16.x
-#             yet we can no longer use Sphinx 15.x, since that breaks with
-#             newer version of the multiprocessor module.
-#    'sphinxcontrib.images',
 
 images_config = {
   'default_image_width' : '25%',
@@ -413,9 +409,9 @@ at Sandia National Laboratories, a US Department of Energy facility,
 with funding from the DOE.  It is an open-source code, distributed
 freely under the terms of the GNU Public License (GPL).
 
-The primary author of the code is Steve Plimpton, who can be emailed
+The LAMMPS developers can be contacted at developers@lammps.org.
-at sjplimp@sandia.gov.  The LAMMPS WWW Site at www.lammps.org has
+The LAMMPS WWW Site at www.lammps.org has more information about
-more information about the code and its uses.
+the code and its uses.
 """
 
 epub_author = 'The LAMMPS Developers'

doc/utils/sphinx-config/false_positives.txt

@@ -2541,7 +2541,6 @@ oneAPI
 onelevel
 oneway
 onlysalt
-onn
 ons
 OO
 Oord
@@ -2739,6 +2738,7 @@ Polym
 polymorph
 polymorphism
 Ponder
+Ponte
 popen
 Popoola
 Popov
@@ -3693,6 +3693,7 @@ vdw
 vdW
 vdwl
 vec
+Vecchio
 vectorial
 vectorization
 Vectorization

examples/COUPLE/fortran/libfwrapper.c

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov, 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

examples/COUPLE/fortran2/LAMMPS-wrapper.cpp

@@ -1,7 +1,7 @@
 /* -----------------------------------------------------------------------
     LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-    https://www.lammps.org/
+    https://www.lammps.org/, Sandia National Laboratories
-    Steve Plimpton, sjplimp@sandia.gov, 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

examples/COUPLE/fortran2/LAMMPS-wrapper.h

@@ -1,7 +1,7 @@
 /* -----------------------------------------------------------------------
     LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-    www.cs.sandia.gov/~sjplimp/lammps.html
+    https://www.lammps.org/, Sandia National Laboratories
-    Steve Plimpton, sjplimp@sandia.gov, 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

examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp

@@ -1,7 +1,7 @@
 /* -----------------------------------------------------------------------
     LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-    https://www.lammps.org/
+    https://www.lammps.org/, Sandia National Laboratories
-    Steve Plimpton, sjplimp@sandia.gov, 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

examples/COUPLE/fortran_dftb/LAMMPS-wrapper.h

@@ -1,7 +1,7 @@
 /* -----------------------------------------------------------------------
     LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-    www.cs.sandia.gov/~sjplimp/lammps.html
+    https://www.lammps.org/, Sandia National Laboratories
-    Steve Plimpton, sjplimp@sandia.gov, 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

examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp

@@ -1,7 +1,7 @@
 /* -----------------------------------------------------------------------
     LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-    https://www.lammps.org/
+    https://www.lammps.org/, Sandia National Laboratories
-    Steve Plimpton, sjplimp@sandia.gov, 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

examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.h

@@ -1,7 +1,7 @@
 /* -----------------------------------------------------------------------
     LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-    www.cs.sandia.gov/~sjplimp/lammps.html
+    https://www.lammps.org/, Sandia National Laboratories
-    Steve Plimpton, sjplimp@sandia.gov, 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

examples/COUPLE/multiple/multiple.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   https://www.lammps.org/
+   https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov, 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

examples/COUPLE/plugin/liblammpsplugin.c

@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   https://www.lammps.org/ Sandia National Laboratories
+   https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

examples/COUPLE/plugin/liblammpsplugin.h

@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   https://www.lammps.org/ Sandia National Laboratories
+   https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

examples/COUPLE/plugin/simple.c

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   https://www.lammps.org, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov, 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

examples/COUPLE/simple/simple.c

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov, 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

examples/COUPLE/simple/simple.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   https://www.lammps.org/
+   https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov, 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

examples/COUPLE/simple/simple.f90

@@ -1,6 +1,6 @@
 !  LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-!  www.cs.sandia.gov/~sjplimp/lammps.html
+!  https://www.lammps.org/, Sandia National Laboratories
-!  Steve Plimpton, sjplimp@sandia.gov, 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

examples/COUPLE/simple/simple_f77.f90

@@ -1,6 +1,6 @@
 !  LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-!  www.cs.sandia.gov/~sjplimp/lammps.html
+!  https://www.lammps.org/, Sandia National Laboratories
-!  Steve Plimpton, sjplimp@sandia.gov, 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

examples/PACKAGES/cgdna/examples/oxDNA2/unique_bp/generate_unique.py

@@ -3,7 +3,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/ Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

examples/PACKAGES/cgdna/util/generate.py

@@ -3,7 +3,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/ Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

examples/plugins/angle_zero2.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

examples/plugins/angle_zero2.h

@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/ Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

examples/plugins/bond_zero2.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

examples/plugins/bond_zero2.h

@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/ Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

examples/plugins/dihedral_zero2.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

examples/plugins/dihedral_zero2.h

@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/ Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

examples/plugins/fix_nve2.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

examples/plugins/fix_nve2.h

@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/ Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

examples/plugins/improper_zero2.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

examples/plugins/improper_zero2.h

@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/ Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

examples/plugins/pair_morse2.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

examples/plugins/pair_morse2.h

@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/ Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

examples/plugins/pair_morse2_omp.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   LAMMPS development team: developers@lammps.org
 
    This software is distributed under the GNU General Public License.
 

examples/plugins/pair_morse2_omp.h

@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/ Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

examples/plugins/pair_zero2.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

examples/plugins/pair_zero2.h

@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/ Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

fortran/lammps.f90

@@ -1,7 +1,7 @@
 ! -------------------------------------------------------------------------
 !   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
 !   https://www.lammps.org/ Sandia National Laboratories
-!   Steve Plimpton, sjplimp@sandia.gov
+!   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
@@ -19,8 +19,12 @@
 !   Karl D. Hammond <hammondkd@missouri.edu>
 !   University of Missouri, 2012-2020
 !
+! Contributing authors:
+!  - Axel Kohlmeyer <akohlmey@gmail.com>, Temple University, 2020-2022
+!  - Karl D. Hammond <hammondkd@missouri.edu> University of Missouri, 2022
+!
 ! The Fortran module tries to follow the API of the C library interface
-! closely, but like the Python wrapper it employs an object-oriented
+! closely, but like the Python wrapper, it employs an object-oriented
 ! approach.  To accommodate the object-oriented approach, all exported
 ! subroutines and functions have to be implemented in Fortran and
 ! call the interfaced C-style functions with adapted calling conventions

lib/gpu/geryon/ocl_device.h

@@ -184,7 +184,7 @@ class UCL_Device {
       _cq.back()=clCreateCommandQueueWithProperties(_context, _cl_device, props,
                                                     &errorv);
     } else {
-      cl_queue_properties props[] = {CL_QUEUE_PROPERTIES, 0};
+      cl_queue_properties props[] = {0};
       _cq.back()=clCreateCommandQueueWithProperties(_context, _cl_device, props,
                                                     &errorv);
     }

lib/gpu/lal_device.cpp

@@ -741,6 +741,7 @@ void DeviceT::estimate_gpu_overhead(const int kernel_calls,
   }
   gpu_overhead/=10.0;
   gpu_driver_overhead/=10.0;
+  gpu->sync();
 
   if (_data_in_estimate>0) {
     delete [] host_data_in;
@@ -793,6 +794,7 @@ void DeviceT::output_times(UCL_Timer &time_pair, Answer<numtyp,acctyp> &ans,
   #ifdef USE_OPENCL
   // Workaround for timing issue on Intel OpenCL
   if (times[0] > 80e6) times[0]=0.0;
+  if (times[1] > 80e6) times[1]=0.0;
   if (times[3] > 80e6) times[3]=0.0;
   if (times[5] > 80e6) times[5]=0.0;
   #endif
@@ -806,9 +808,8 @@ void DeviceT::output_times(UCL_Timer &time_pair, Answer<numtyp,acctyp> &ans,
       fprintf(screen,"--------------------------------\n");
 
       if (time_device() && (times[3] > 0.0)) {
-        if (times[0] > 0.0)
+        if (times[0] > 0.0) fprintf(screen,"Data Transfer:   %.4f s.\n",times[0]/_replica_size);
-          fprintf(screen,"Data Transfer:   %.4f s.\n",times[0]/_replica_size);
+        if (times[1] > 0.0) fprintf(screen,"Neighbor copy:   %.4f s.\n",times[1]/_replica_size);
-        fprintf(screen,"Neighbor copy:   %.4f s.\n",times[1]/_replica_size);
         if (nbor.gpu_nbor() > 0.0)
           fprintf(screen,"Neighbor build:  %.4f s.\n",times[2]/_replica_size);
         else
@@ -862,32 +863,34 @@ void DeviceT::output_kspace_times(UCL_Timer &time_in,
   double max_mb=mpi_max_bytes/(1024.0*1024.0);
   #ifdef USE_OPENCL
   // Workaround for timing issue on Intel OpenCL
+  if (times[0] > 80e6) times[0]=0.0;
+  if (times[1] > 80e6) times[1]=0.0;
   if (times[3] > 80e6) times[3]=0.0;
+  if (times[5] > 80e6) times[5]=0.0;
   #endif
 
 
   if (replica_me()==0)
-    if (screen && times[6]>0.0) {
+    if (screen && (times[6] > 0.0)) {
       fprintf(screen,"\n\n-------------------------------------");
       fprintf(screen,"--------------------------------\n");
       fprintf(screen,"    Device Time Info (average) for kspace: ");
       fprintf(screen,"\n-------------------------------------");
       fprintf(screen,"--------------------------------\n");
 
-      if (time_device() && times[3]>0) {
+      if (time_device() && (times[3] > 0.0)) {
-        fprintf(screen,"Data Out:        %.4f s.\n",times[0]/_replica_size);
+        if (times[0] > 0.0) fprintf(screen,"Data Out:        %.4f s.\n",times[0]/_replica_size);
-        fprintf(screen,"Data In:         %.4f s.\n",times[1]/_replica_size);
+        if (times[1] > 0.0) fprintf(screen,"Data In:         %.4f s.\n",times[1]/_replica_size);
         fprintf(screen,"Kernel (map):    %.4f s.\n",times[2]/_replica_size);
         fprintf(screen,"Kernel (rho):    %.4f s.\n",times[3]/_replica_size);
         fprintf(screen,"Force interp:    %.4f s.\n",times[4]/_replica_size);
-        fprintf(screen,"Total rho:       %.4f s.\n",
+        if (times[0] > 0.0)
-                (times[0]+times[2]+times[3])/_replica_size);
+          fprintf(screen,"Total rho:       %.4f s.\n", (times[0]+times[2]+times[3])/_replica_size);
-        fprintf(screen,"Total interp:    %.4f s.\n",
+        if (times[1] > 0.0)
-                (times[1]+times[4])/_replica_size);
+          fprintf(screen,"Total interp:    %.4f s.\n", (times[1]+times[4])/_replica_size);
-        fprintf(screen,"Force copy:      %.4f s.\n",times[5]/_replica_size);
+        if (times[5] > 0.0) fprintf(screen,"Force copy:      %.4f s.\n",times[5]/_replica_size);
         fprintf(screen,"Total:           %.4f s.\n",
-                (times[0]+times[1]+times[2]+times[3]+times[4]+times[5])/
+                (times[0]+times[1]+times[2]+times[3]+times[4]+times[5])/_replica_size);
-                _replica_size);
       }
       fprintf(screen,"CPU Poisson:     %.4f s.\n",times[6]/_replica_size);
       fprintf(screen,"CPU Data Cast:   %.4f s.\n",times[8]/_replica_size);

lib/gpu/lal_lj_tip4p_long.cu

@@ -257,7 +257,7 @@ __kernel void k_lj_tip4p_reneigh(
     }
     if (i<inum && itype == typeH) {
       if (hneigh[i*4+2] != -1) {
-        int iI, iH;
+        int iI;
         iI = atom_mapping(map,tag[i] - 1);
         iO  = closest_image(i,iI,sametag, x_);
         numtyp4 iIx; fetch4(iIx,iO,pos_tex); //x_[iI];

lib/mesont/CNTPot.f90

@@ -1,7 +1,7 @@
 ! ------------ ----------------------------------------------------------
 !   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
 !   https://www.lammps.org/ Sandia National Laboratories
-!   Steve Plimpton, sjplimp@sandia.gov
+!   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

lib/mesont/ExportCNT.f90

@@ -1,7 +1,7 @@
 ! ------------ ----------------------------------------------------------
 !   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
 !   https://www.lammps.org/ Sandia National Laboratories
-!   Steve Plimpton, sjplimp@sandia.gov
+!   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

lib/mesont/LinFun2.f90

@@ -1,7 +1,7 @@
 ! ------------ ----------------------------------------------------------
 !   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
 !   https://www.lammps.org/ Sandia National Laboratories
-!   Steve Plimpton, sjplimp@sandia.gov
+!   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

lib/mesont/Spline1.f90

@@ -1,7 +1,7 @@
 ! ------------ ----------------------------------------------------------
 !   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
 !   https://www.lammps.org/ Sandia National Laboratories
-!   Steve Plimpton, sjplimp@sandia.gov
+!   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

lib/mesont/Spline2.f90

@@ -1,7 +1,7 @@
 ! ------------ ----------------------------------------------------------
 !   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
 !   https://www.lammps.org/ Sandia National Laboratories
-!   Steve Plimpton, sjplimp@sandia.gov
+!   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

lib/mesont/TPMForceField.f90

@@ -1,7 +1,7 @@
 ! ------------ ----------------------------------------------------------
 !   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
 !   https://www.lammps.org/ Sandia National Laboratories
-!   Steve Plimpton, sjplimp@sandia.gov
+!   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

lib/mesont/TPMGeom.f90

@@ -1,7 +1,7 @@
 ! ------------ ----------------------------------------------------------
 !   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
 !   https://www.lammps.org/ Sandia National Laboratories
-!   Steve Plimpton, sjplimp@sandia.gov
+!   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

lib/mesont/TPMLib.f90

@@ -1,7 +1,7 @@
 ! ------------ ----------------------------------------------------------
 !   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
 !   https://www.lammps.org/ Sandia National Laboratories
-!   Steve Plimpton, sjplimp@sandia.gov
+!   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

lib/mesont/TPMM0.f90

@@ -1,7 +1,7 @@
 ! ------------ ----------------------------------------------------------
 !   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
 !   https://www.lammps.org/ Sandia National Laboratories
-!   Steve Plimpton, sjplimp@sandia.gov
+!   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

lib/mesont/TPMM1.f90

@@ -1,7 +1,7 @@
 ! ------------ ----------------------------------------------------------
 !   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
 !   https://www.lammps.org/ Sandia National Laboratories
-!   Steve Plimpton, sjplimp@sandia.gov
+!   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

lib/mesont/TubePotBase.f90

@@ -1,7 +1,7 @@
 ! ------------ ----------------------------------------------------------
 !   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
 !   https://www.lammps.org/ Sandia National Laboratories
-!   Steve Plimpton, sjplimp@sandia.gov
+!   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

lib/mesont/TubePotMono.f90

@@ -1,7 +1,7 @@
 ! ------------ ----------------------------------------------------------
 !   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
 !   https://www.lammps.org/ Sandia National Laboratories
-!   Steve Plimpton, sjplimp@sandia.gov
+!   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

lib/mesont/TubePotTrue.f90

@@ -1,7 +1,7 @@
 ! ------------ ----------------------------------------------------------
 !   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
 !   https://www.lammps.org/ Sandia National Laboratories
-!   Steve Plimpton, sjplimp@sandia.gov
+!   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

lib/plumed/Install.py

@@ -17,7 +17,7 @@ parser = ArgumentParser(prog='Install.py',
 
 # settings
 
-version = "2.7.4"
+version = "2.8.1"
 mode = "static"
 
 # help message
@@ -58,7 +58,9 @@ checksums = { \
         '2.7.2' : 'cfa0b4dd90a81c25d3302e8d97bfeaea', \
         '2.7.3' : 'f00cc82edfefe6bb3df934911dbe32fb', \
         '2.7.4' : 'f858e0b6aed173748fc85b6bc8a9dcb3', \
+        '2.7.5' : '2aca1986d6c1ca3ba7e9eb51b1102792', \
         '2.8.0' : '489b23daba70da78cf0506cbc31689c6', \
+        '2.8.1' : '6bfe72ebdae63dc38a9ca27d9b0e08f8', \
         }
 
 # parse and process arguments

python/examples/pizza/gl.py

@@ -1,5 +1,5 @@
 # Pizza.py toolkit, https://lammps.github.io/pizza
-# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
+# LAMMPS Development team: developers@lammps.org, Sandia National Laboratories
 #
 # Copyright (2005) Sandia Corporation.  Under the terms of Contract
 # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

python/examples/pizza/vizinfo.py

@@ -1,5 +1,5 @@
 # Pizza.py toolkit, https://lammps.github.io/pizza
-# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
+# LAMMPS Development team: developers@lammps.org, Sandia National Laboratories
 #
 # Copyright (2005) Sandia Corporation.  Under the terms of Contract
 # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

python/examples/pizza/vmd.py

@@ -1,5 +1,5 @@
 # Pizza.py toolkit, https://lammps.github.io/pizza
-# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
+# LAMMPS Development team: developers@lammps.org, Sandia National Laboratories
 #
 # Copyright (2005) Sandia Corporation.  Under the terms of Contract
 # DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

python/lammps/constants.py

@@ -1,7 +1,7 @@
 # ----------------------------------------------------------------------
 #   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
 #   https://www.lammps.org/ Sandia National Laboratories
-#   Steve Plimpton, sjplimp@sandia.gov
+#   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

python/lammps/core.py

@@ -1,7 +1,7 @@
 # ----------------------------------------------------------------------
 #   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
 #   https://www.lammps.org/ Sandia National Laboratories
-#   Steve Plimpton, sjplimp@sandia.gov
+#   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
@@ -265,6 +265,7 @@ class lammps(object):
 
     self.lib.lammps_encode_image_flags.restype = self.c_imageint
 
+    self.lib.lammps_config_has_package.argtypes = [c_char_p]
     self.lib.lammps_config_package_name.argtypes = [c_int, c_char_p, c_int]
     self.lib.lammps_config_accelerator.argtypes = [c_char_p, c_char_p, c_char_p]
 
@@ -1627,6 +1628,23 @@ class lammps(object):
 
   # -------------------------------------------------------------------------
 
+  def has_package(self, name):
+    """ Report if the named package has been enabled in the LAMMPS shared library.
+
+    This is a wrapper around the :cpp:func:`lammps_config_has_package`
+    function of the library interface.
+
+    .. versionadded:: TBD
+
+    :param name: name of the package
+    :type  name: string
+
+    :return: state of package availability
+    :rtype: bool
+    """
+    return self.lib.lammps_config_has_package(name.encode()) != 0
+  # -------------------------------------------------------------------------
+
   @property
   def accelerator_config(self):
     """ Return table with available accelerator configuration settings.

python/lammps/data.py

@@ -1,7 +1,7 @@
 # ----------------------------------------------------------------------
 #   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
 #   https://www.lammps.org/ Sandia National Laboratories
-#   Steve Plimpton, sjplimp@sandia.gov
+#   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

python/lammps/formats.py

@@ -1,7 +1,7 @@
 # ----------------------------------------------------------------------
 #   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
 #   https://www.lammps.org/ Sandia National Laboratories
-#   Steve Plimpton, sjplimp@sandia.gov
+#   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

python/lammps/mliap/__init__.py

@@ -10,15 +10,15 @@ import warnings
 py_ver = sysconfig.get_config_vars('VERSION')[0]
 OS_name = platform.system()
 
-if OS_name == "Linux":
+if OS_name == "Darwin":
-    SHLIB_SUFFIX = '.so'
-    library = 'libpython' + py_ver + SHLIB_SUFFIX
-elif OS_name == "Darwin":
     SHLIB_SUFFIX = '.dylib'
     library = 'libpython' + py_ver + SHLIB_SUFFIX
 elif OS_name == "Windows":
     SHLIB_SUFFIX = '.dll'
     library = 'python' + py_ver + SHLIB_SUFFIX
+else:
+    SHLIB_SUFFIX = '.so'
+    library = 'libpython' + py_ver + SHLIB_SUFFIX
 
 try:
     pylib = ctypes.CDLL(library)

python/lammps/mliap/loader.py

@@ -1,7 +1,7 @@
 # ----------------------------------------------------------------------
 #   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
 #   https://www.lammps.org/ Sandia National Laboratories
-#   Steve Plimpton, sjplimp@sandia.gov
+#   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

python/lammps/mliap/pytorch.py

@@ -1,7 +1,7 @@
 # ----------------------------------------------------------------------
 #   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
 #   https://www.lammps.org/ Sandia National Laboratories
-#   Steve Plimpton, sjplimp@sandia.gov
+#   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

python/lammps/numpy_wrapper.py

@@ -1,7 +1,7 @@
 # ----------------------------------------------------------------------
 #   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
 #   https://www.lammps.org/ Sandia National Laboratories
-#   Steve Plimpton, sjplimp@sandia.gov
+#   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

python/lammps/pylammps.py

@@ -1,7 +1,7 @@
 # ----------------------------------------------------------------------
 #   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
 #   https://www.lammps.org/ Sandia National Laboratories
-#   Steve Plimpton, sjplimp@sandia.gov
+#   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

python/setup.py

@@ -46,8 +46,8 @@ else:
 setup(
     name = "lammps",
     version = get_lammps_version(),
-    author = "Steve Plimpton",
+    author = "The LAMMPS Developers",
-    author_email = "sjplimp@sandia.gov",
+    author_email = "developers@lammps.org",
     url = "https://www.lammps.org",
     project_urls = {
         "Bug Tracker": "https://github.com/lammps/lammps/issues",

src/ADIOS/adios_common.h

@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

src/ADIOS/dump_atom_adios.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

src/ADIOS/dump_atom_adios.h

@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

src/ADIOS/dump_custom_adios.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

src/ADIOS/dump_custom_adios.h

@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

src/ADIOS/reader_adios.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

src/ADIOS/reader_adios.h

@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

src/AMOEBA/amoeba_charge_transfer.cpp

@@ -2,7 +2,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/ Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

src/AMOEBA/amoeba_convolution.cpp

@@ -2,7 +2,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/ Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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

src/AMOEBA/amoeba_convolution.h

@@ -1,7 +1,7 @@
 /* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/ Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
+   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