fixing merge conflicts, update to master

.gitattributes

@@ -2,3 +2,4 @@
 .gitignore export-ignore
 .github export-ignore
 .lgtm.yml export-ignore
+SECURITY.md export-ignore

.github/CODEOWNERS

@@ -13,29 +13,37 @@ lib/kim/*             @ellio167
 lib/mesont/*          @iafoss
 
 # whole packages
-src/COMPRESS/*        @akohlmey
+src/COMPRESS/*        @rbberger
 src/GPU/*             @ndtrung81
 src/KOKKOS/*          @stanmoore1
 src/KIM/*             @ellio167
 src/LATTE/*           @cnegre
 src/MESSAGE/*         @sjplimp
+src/MLIAP/*           @athomps
+src/SNAP/*            @athomps
 src/SPIN/*            @julient31
+src/USER-BROWNIAN/*   @samueljmcameron
 src/USER-CGDNA/*      @ohenrich
 src/USER-CGSDK/*      @akohlmey
 src/USER-COLVARS/*    @giacomofiorin
+src/USER-FEP/*        @agiliopadua
+src/USER-HDNNP/*      @singraber
 src/USER-INTEL/*      @wmbrownintel
 src/USER-MANIFOLD/*   @Pakketeretet2
+src/USER-MDI/*        @taylor-a-barnes
 src/USER-MEAMC/*      @martok
 src/USER-MESONT/*     @iafoss
 src/USER-MOFFF/*      @hheenen
 src/USER-MOLFILE/*    @akohlmey
 src/USER-NETCDF/*     @pastewka
+src/USER-PACE/*       @yury-lysogorskiy
 src/USER-PLUMED/*     @gtribello
 src/USER-PHONON/*     @lingtikong
 src/USER-PTM/*        @pmla
 src/USER-OMP/*        @akohlmey
 src/USER-QMMM/*       @akohlmey
 src/USER-REAXC/*      @hasanmetin
+src/USER-REACTION/*   @jrgissing
 src/USER-SCAFACOS/*   @rhalver
 src/USER-TALLY/*      @akohlmey
 src/USER-UEF/*        @danicholson
@@ -47,7 +55,6 @@ src/GPU/pair_vashishta_gpu.*        @andeplane
 src/KOKKOS/pair_vashishta_kokkos.*  @andeplane
 src/MANYBODY/pair_vashishta_table.* @andeplane
 src/MANYBODY/pair_atm.*             @sergeylishchuk
-src/USER-REACTION/fix_bond_react.*  @jrgissing
 src/USER-MISC/*_grem.*              @dstelter92
 src/USER-MISC/compute_stress_mop*.* @RomainVermorel
 
@@ -122,6 +129,8 @@ tools/emacs/*         @HaoZeke
 tools/singularity/*   @akohlmey @rbberger
 tools/code_standard/* @rbberger
 tools/valgrind/*      @akohlmey
+tools/swig/*          @akohlmey
+tools/offline/*       @rbberger
 
 # tests
 unittest/*            @akohlmey @rbberger
@@ -130,7 +139,7 @@ unittest/*            @akohlmey @rbberger
 cmake/*               @junghans @rbberger
 cmake/Modules/Packages/USER-COLVARS.cmake @junghans @rbberger @giacomofiorin
 cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
-cmake/presets/*.cmake @junghans @rbberger @akohlmey
+cmake/presets/*.cmake @akohlmey
 
 # python
 python/*              @rbberger
@@ -142,6 +151,7 @@ fortran/*             @akohlmey
 doc/utils/*/*         @rbberger
 doc/Makefile          @rbberger
 doc/README            @rbberger
+examples/plugin/*     @akohlmey
 
 # for releases
 src/version.h         @sjplimp

README

@@ -14,10 +14,10 @@ LAMMPS is a classical molecular dynamics simulation code designed to
 run efficiently on parallel computers.  It was developed 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).
+under the terms of the GNU Public License (GPL) version 2.
 
 The primary author of the code is Steve Plimpton, who can be emailed
-at sjplimp@sandia.gov.  The LAMMPS WWW Site at lammps.sandia.gov has
+at sjplimp@sandia.gov.  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:
@@ -37,14 +37,14 @@ tools                      pre- and post-processing tools
 
 Point your browser at any of these files to get started:
 
-https://lammps.sandia.gov/doc/Manual.html         LAMMPS manual
+https://docs.lammps.org/Manual.html         LAMMPS manual
-https://lammps.sandia.gov/doc/Intro.html          hi-level introduction
+https://docs.lammps.org/Intro.html          hi-level introduction
-https://lammps.sandia.gov/doc/Build.html          how to build LAMMPS
+https://docs.lammps.org/Build.html          how to build LAMMPS
-https://lammps.sandia.gov/doc/Run_head.html       how to run LAMMPS
+https://docs.lammps.org/Run_head.html       how to run LAMMPS
-https://lammps.sandia.gov/doc/Commands_all.html   Table of available commands
+https://docs.lammps.org/Commands_all.html   Table of available commands
-https://lammps.sandia.gov/doc/Library.html        LAMMPS library interfaces
+https://docs.lammps.org/Library.html        LAMMPS library interfaces
-https://lammps.sandia.gov/doc/Modify.html         how to modify and extend LAMMPS
+https://docs.lammps.org/Modify.html         how to modify and extend LAMMPS
-https://lammps.sandia.gov/doc/Developer.html      LAMMPS developer info
+https://docs.lammps.org/Developer.html      LAMMPS developer info
 
 You can also create these doc pages locally:
 

SECURITY.md

@@ -0,0 +1,35 @@
+# Security Policy
+
+LAMMPS is designed as a user-level application to conduct computer
+simulations for research using classical mechanics.  As such LAMMPS
+depends to some degrees on users providing correctly formatted input and
+LAMMPS needs to read and write files based on uncontrolled user input.
+As a parallel application for use in high-performance computing
+environments, performance critical steps are also done without checking
+data.
+
+LAMMPS also is interfaced to a number of external libraries, including
+libraries with experimental research software, that are not validated
+and tested by the LAMMPS developers, so it is easy to import bad
+behavior from calling functions in one of those libraries.
+
+Thus is is quite easy to crash LAMMPS through malicious input and do all
+kinds of filesystem manipulations.  And because of that LAMMPS should
+**NEVER** be compiled or **run** as superuser, either from a "root" or
+"administrator" account directly or indirectly via "sudo" or "su".
+
+Therefore what could be seen as a security vulnerability is usually
+either a user mistake or a bug in the code.  Bugs can be reported in
+the LAMMPS project
+[issue tracker on GitHub](https://github.com/lammps/lammps/issues).
+
+
+# Version Updates
+
+LAMMPS follows continuous release development model.  We aim to keep all
+release versions (stable or patch) fully functional and employ a variety
+of automatic testing procedures to detect failures of existing
+functionality from adding new features before releases are made.  Thus
+bugfixes and updates are only integrated into the current development
+branch and thus the next (patch) release and users are recommended to
+update regularly.

bench/POTENTIALS/README

@@ -1,7 +1,7 @@
 These are input scripts used to run benchmark tests for many of the
 interatomic potentials in LAMMPS.  The results of running these
 scripts on different machines are shown on the Potentials section of
-the Benchmark page of the LAMMPS WWW site (lammps.sandia.gov/bench).
+the Benchmark page of the LAMMPS WWW site (https://www.lammps.org/bench.html).
 
 Examples are shown below of how to run these scripts.  Log files for
 running them on 1 and 4 processors of a Linux box are included in the

bench/README

@@ -2,7 +2,7 @@ LAMMPS benchmark problems
 
 This directory contains 5 benchmark problems which are discussed in
 the Benchmark section of the LAMMPS documentation, and on the
-Benchmark page of the LAMMPS WWW site (lammps.sandia.gov/bench).
+Benchmark page of the LAMMPS WWW site (https://www.lammps.org/bench.html).
 
 This directory also has several sub-directories:
 
@@ -11,7 +11,7 @@ KEPLER          benchmark scripts for GPU cluster with Kepler GPUs
 POTENTIALS      benchmarks scripts for various potentials in LAMMPS
 
 The results for all of these benchmarks are displayed and discussed on
-the Benchmark page of the LAMMPS WWW site: lammps.sandia.gov/bench.
+the Benchmark page of the LAMMPS WWW site: https://www.lammps.org/bench.html
 
 The remainder of this file refers to the 5 problems in the top-level
 of this directory and how to run them on CPUs, either in serial or

cmake/CMakeLists.txt

@@ -7,6 +7,11 @@ cmake_minimum_required(VERSION 3.10)
 if(POLICY CMP0074)
   cmake_policy(SET CMP0074 NEW)
 endif()
+# set policy to silence warnings about missing executable permissions in
+# pythonx.y-config when cross-compiling. review occasionally if it may be set to NEW
+if(POLICY CMP0109)
+  cmake_policy(SET CMP0109 OLD)
+endif()
 ########################################
 
 project(lammps CXX)
@@ -72,7 +77,7 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
 include(CheckIncludeFileCXX)
 
 # set required compiler flags and compiler/CPU arch specific optimizations
-if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
+if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
   if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
     set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
@@ -86,6 +91,11 @@ set(CMAKE_CXX_STANDARD 11)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
 
+# export all symbols when building a .dll file on windows
+if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND BUILD_SHARED_LIBS)
+  set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
+endif()
+
 ########################################################################
 # User input options                                                   #
 ########################################################################
@@ -104,11 +114,23 @@ endif()
 option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
 option(BUILD_LAMMPS_SHELL "Build and install the LAMMPS shell" OFF)
 
+# allow enabling clang-tidy for C++ files
+set(ENABLE_CLANG_TIDY OFF CACHE BOOL "Include clang-tidy processing when compiling")
+if(ENABLE_CLANG_TIDY)
+  set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=*-header-filter=.*" CACHE STRING "")
+endif()
+
 include(GNUInstallDirs)
 file(GLOB ALL_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
 file(GLOB MAIN_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
 list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
 add_library(lammps ${ALL_SOURCES})
+
+# tell CMake to export all symbols to a .dll on Windows with MinGW cross-compilers
+if(BUILD_SHARED_LIBS AND (CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
+  set_target_properties(lammps PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols")
+endif()
+
 add_executable(lmp ${MAIN_SOURCES})
 target_link_libraries(lmp PRIVATE lammps)
 set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})
@@ -121,9 +143,9 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
   PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
   USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK
   USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
-  USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
+  USER-HDNNP USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESONT USER-MGPT USER-MISC
-  USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
+  USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
-  USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
+  USER-RANN USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
   USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE USER-BROWNIAN)
 
 set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP)
@@ -151,12 +173,13 @@ if(NOT CMAKE_CROSSCOMPILING)
   find_package(MPI QUIET)
   option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
 else()
+  set(MPI_CXX_SKIP_MPICXX TRUE)
   option(BUILD_MPI "Build MPI version" OFF)
 endif()
 
 if(BUILD_MPI)
   # We use a non-standard procedure to cross-compile with MPI on Windows
-  if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)
+  if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
     include(MPI4WIN)
     target_link_libraries(lammps PUBLIC MPI::MPI_CXX)
   else()
@@ -190,7 +213,7 @@ string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
 target_compile_definitions(lammps PUBLIC -DLAMMPS_${LAMMPS_SIZES})
 
 # posix_memalign is not available on Windows
-if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
   set(LAMMPS_MEMALIGN "0" CACHE STRING "posix_memalign() is not available on Windows" FORCE)
 else()
   set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS. Set to 0 to disable")
@@ -232,8 +255,9 @@ if(BUILD_OMP)
     message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
   endif()
 
-  if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
+  if(((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
       (CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR
+      ((CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
     # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
@@ -296,7 +320,7 @@ find_program(GZIP_EXECUTABLE gzip)
 find_package_handle_standard_args(GZIP REQUIRED_VARS GZIP_EXECUTABLE)
 option(WITH_GZIP "Enable GZIP support" ${GZIP_FOUND})
 if(WITH_GZIP)
-  if(GZIP_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING))
+  if(GZIP_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING))
     target_compile_definitions(lammps PRIVATE -DLAMMPS_GZIP)
   else()
     message(FATAL_ERROR "gzip executable not found")
@@ -307,7 +331,7 @@ find_program(FFMPEG_EXECUTABLE ffmpeg)
 find_package_handle_standard_args(FFMPEG REQUIRED_VARS FFMPEG_EXECUTABLE)
 option(WITH_FFMPEG "Enable FFMPEG support" ${FFMPEG_FOUND})
 if(WITH_FFMPEG)
-  if(FFMPEG_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING))
+  if(FFMPEG_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING))
     target_compile_definitions(lammps PRIVATE -DLAMMPS_FFMPEG)
   else()
     message(FATAL_ERROR "ffmpeg executable not found")
@@ -324,10 +348,10 @@ else()
   set(CUDA_REQUEST_PIC)
 endif()
 
-foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MDI USER-MOLFILE USER-NETCDF USER-PLUMED
+foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-HDNNP USER-MDI USER-MOLFILE USER-NETCDF USER-PLUMED
         USER-QMMM USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE)
   if(PKG_${PKG_WITH_INCL})
-    include(Packages/${PKG_WITH_INCL}) 
+    include(Packages/${PKG_WITH_INCL})
   endif()
 endforeach()
 
@@ -422,7 +446,7 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT)
   if(PKG_${SIMPLE_LIB})
     string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
     string(TOLOWER "${PKG_LIB}" PKG_LIB)
-    if(PKG_LIB STREQUAL mesont)
+    if(PKG_LIB STREQUAL "mesont")
       enable_language(Fortran)
       file(GLOB_RECURSE ${PKG_LIB}_SOURCES
         ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.f90)
@@ -434,9 +458,9 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT)
     add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
     set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE})
     target_link_libraries(lammps PRIVATE ${PKG_LIB})
-    if(PKG_LIB STREQUAL awpmd)
+    if(PKG_LIB STREQUAL "awpmd")
       target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)
-    elseif(PKG_LIB STREQUAL h5md)
+    elseif(PKG_LIB STREQUAL "h5md")
       target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include ${HDF5_INCLUDE_DIRS})
     else()
       target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB})
@@ -449,7 +473,7 @@ if(PKG_USER-AWPMD)
 endif()
 
 if(PKG_USER-ATC)
-  if(LAMMPS_SIZES STREQUAL BIGBIG)
+  if(LAMMPS_SIZES STREQUAL "BIGBIG")
     message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG")
   endif()
   target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES})
@@ -493,7 +517,7 @@ endif()
 # and the MPI library - if use - has to be linked right before those
 # and after everything else that is compiled locally
 ######################################################################
-if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
   target_link_libraries(lammps PRIVATE -lwsock32 -lpsapi)
 endif()
 
@@ -542,8 +566,8 @@ add_dependencies(lammps gitversion)
 # Actually add executable and lib to build
 ############################################
 get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
-list (FIND LANGUAGES "Fortran" _index)
+list(FIND LANGUAGES "Fortran" _index)
-if(${_index} GREATER -1)
+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
@@ -621,7 +645,7 @@ if(BUILD_SHARED_LIBS)
   else()
     find_package(Python COMPONENTS Interpreter)
   endif()
-  if (Python_EXECUTABLE)
+  if(Python_EXECUTABLE)
     add_custom_target(
       install-python ${CMAKE_COMMAND} -E remove_directory build
       COMMAND ${Python_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
@@ -654,7 +678,7 @@ if(BUILD_SHARED_LIBS OR PKG_PYTHON)
   else()
     find_package(Python COMPONENTS Interpreter)
   endif()
-  if (Python_EXECUTABLE)
+  if(Python_EXECUTABLE)
     file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python)
     install(CODE "execute_process(COMMAND ${Python_EXECUTABLE} setup.py build -b ${CMAKE_BINARY_DIR}/python install --prefix=${CMAKE_INSTALL_PREFIX} --root=\$ENV{DESTDIR}/ WORKING_DIRECTORY ${LAMMPS_PYTHON_DIR})")
   endif()
@@ -699,15 +723,15 @@ if(OPTIONS)
   message("      Options:       ${OPTIONS}")
 endif()
 get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
-list (FIND LANGUAGES "Fortran" _index)
+list(FIND LANGUAGES "Fortran" _index)
-if(${_index} GREATER -1)
+if(_index GREATER -1)
   message(STATUS "Fortran Compiler: ${CMAKE_Fortran_COMPILER}
       Type:          ${CMAKE_Fortran_COMPILER_ID}
       Version:       ${CMAKE_Fortran_COMPILER_VERSION}
       Fortran Flags:${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}")
 endif()
-list (FIND LANGUAGES "C" _index)
+list(FIND LANGUAGES "C" _index)
-if(${_index} GREATER -1)
+if(_index GREATER -1)
   message(STATUS "C compiler:       ${CMAKE_C_COMPILER}
       Type:          ${CMAKE_C_COMPILER_ID}
       Version:       ${CMAKE_C_COMPILER_VERSION}
@@ -772,7 +796,7 @@ if(PKG_KSPACE)
   endif()
   if(PKG_KOKKOS)
     if(Kokkos_ENABLE_CUDA)
-      if (${FFT} STREQUAL "KISS")
+      if(FFT STREQUAL "KISS")
         message(STATUS "Kokkos FFT: KISS")
       else()
         message(STATUS "Kokkos FFT: cuFFT")

cmake/Modules/CodingStandard.cmake

@@ -15,6 +15,11 @@ if(Python3_EXECUTABLE)
           ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .
           WORKING_DIRECTORY  ${LAMMPS_DIR}
           COMMENT "Check for whitespace errors")
+        add_custom_target(
+          check-homepage
+          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py .
+          WORKING_DIRECTORY  ${LAMMPS_DIR}
+          COMMENT "Check for homepage URL errors")
         add_custom_target(
           check-permissions
           ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py .
@@ -25,6 +30,11 @@ if(Python3_EXECUTABLE)
           ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py -f .
           WORKING_DIRECTORY  ${LAMMPS_DIR}
           COMMENT "Fix whitespace errors")
+        add_custom_target(
+          fix-homepage
+          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py -f .
+          WORKING_DIRECTORY  ${LAMMPS_DIR}
+          COMMENT "Fix homepage URL errors")
         add_custom_target(
           fix-permissions
           ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py -f .

cmake/Modules/FindN2P2.cmake

@@ -0,0 +1,61 @@
+include(FindPackageHandleStandardArgs)
+
+# Check if N2P2_DIR is set manually.
+if (DEFINED ENV{N2P2_DIR})
+  set(N2P2_DIR "${N2P2_DIR}")
+# If not, try if directory "lib/hdnnp/n2p2" exists.
+else()
+  get_filename_component(_fullpath "${LAMMPS_LIB_SOURCE_DIR}/hdnnp/n2p2" REALPATH)
+  if (EXISTS ${_fullpath})
+    set(N2P2_DIR "${_fullpath}")
+  endif()
+endif()
+
+# Set path to include directory.
+find_path(N2P2_INCLUDE_DIR InterfaceLammps.h HINTS "${N2P2_DIR}/include")
+# Two libraries need to be linked: libnnp and libnnpif.
+find_library(N2P2_LIBNNP NAMES nnp HINTS "${N2P2_DIR}/lib")
+find_library(N2P2_LIBNNPIF NAMES nnpif HINTS "${N2P2_DIR}/lib")
+# Users could compile n2p2 with extra flags which are then also required for
+# pair_hdnnp.cpp compilation. To forward them to the LAMMPS build process n2p2
+# writes a file with cmake commands, e.g.
+#
+# target_compile_definitions(lammps PRIVATE -DN2P2_NO_SF_GROUPS)
+#
+# to "lib/lammps-extra.cmake" which is then included by USER-HDNNP.cmake.
+find_file(N2P2_CMAKE_EXTRA NAMES lammps-extra.cmake HINTS "${N2P2_DIR}/lib")
+
+find_package_handle_standard_args(N2P2 DEFAULT_MSG
+  N2P2_DIR
+  N2P2_INCLUDE_DIR
+  N2P2_LIBNNP
+  N2P2_LIBNNPIF
+  N2P2_CMAKE_EXTRA)
+
+if(N2P2_FOUND)
+  if (NOT TARGET N2P2::N2P2)
+    # n2p2 core library "libnnp"
+    add_library(N2P2::LIBNNP UNKNOWN IMPORTED)
+    set_target_properties(N2P2::LIBNNP PROPERTIES
+      INTERFACE_INCLUDE_DIRECTORIES ${N2P2_INCLUDE_DIR}
+      IMPORTED_LOCATION ${N2P2_LIBNNP})
+    # n2p2 interface library "libnnpif"
+    add_library(N2P2::LIBNNPIF UNKNOWN IMPORTED)
+    set_target_properties(N2P2::LIBNNPIF PROPERTIES
+      INTERFACE_INCLUDE_DIRECTORIES ${N2P2_INCLUDE_DIR}
+      IMPORTED_LOCATION ${N2P2_LIBNNPIF})
+    # Put libnnp, libnnpif and include directory together.
+    add_library(N2P2::N2P2 INTERFACE IMPORTED)
+    set_property(TARGET N2P2::N2P2 PROPERTY
+      INTERFACE_LINK_LIBRARIES N2P2::LIBNNPIF N2P2::LIBNNP)
+    set(N2P2_CMAKE_EXTRAS ${N2P2_CMAKE_EXTRA})
+  endif()
+endif()
+
+mark_as_advanced(
+  N2P2_DIR
+  N2P2_INCLUDE_DIR
+  N2P2_LIBNNP
+  N2P2_LIBNNPIF
+  N2P2_CMAKE_EXTRA
+)

cmake/Modules/GTest.cmake

@@ -1,6 +1,6 @@
 message(STATUS "Downloading and building Google Test library")
 
-if(CMAKE_BUILD_TYPE STREQUAL Debug)
+if(CMAKE_BUILD_TYPE STREQUAL "Debug")
   set(GTEST_LIB_POSTFIX d)
 else()
   set(GTEST_LIB_POSTFIX)

cmake/Modules/LAMMPSUtils.cmake

@@ -106,7 +106,7 @@ function(FetchPotentials pkgfolder potfolder)
 endfunction(FetchPotentials)
 
 # set CMAKE_LINUX_DISTRO and CMAKE_DISTRO_VERSION on Linux
-if((CMAKE_SYSTEM_NAME STREQUAL Linux) AND (EXISTS /etc/os-release))
+if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (EXISTS /etc/os-release))
   file(STRINGS /etc/os-release distro REGEX "^NAME=")
   string(REGEX REPLACE "NAME=\"?([^\"]*)\"?" "\\1" distro "${distro}")
   file(STRINGS /etc/os-release disversion REGEX "^VERSION_ID=")

cmake/Modules/Packages/GPU.cmake

@@ -48,7 +48,7 @@ if(GPU_API STREQUAL "CUDA")
 
   # ensure that no *cubin.h files exist from a compile in the lib/gpu folder
   file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
-  if (GPU_LIB_OLD_CUBIN_HEADERS)
+  if(GPU_LIB_OLD_CUBIN_HEADERS)
     message(FATAL_ERROR "########################################################################\n"
       "Found file(s) generated by the make-based build system in lib/gpu\n"
       "Please run\n"
@@ -154,7 +154,7 @@ elseif(GPU_API STREQUAL "OPENCL")
   endif()
   option(USE_STATIC_OPENCL_LOADER "Download and include a static OpenCL ICD loader" ${_opencl_static_default})
   mark_as_advanced(USE_STATIC_OPENCL_LOADER)
-  if (USE_STATIC_OPENCL_LOADER)
+  if(USE_STATIC_OPENCL_LOADER)
     include(OpenCLLoader)
   else()
     find_package(OpenCL REQUIRED)

cmake/Modules/Packages/KOKKOS.cmake

@@ -37,8 +37,8 @@ if(DOWNLOAD_KOKKOS)
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
   include(ExternalProject)
-  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.4.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.4.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "c2fdcedb6953e6160c765366f6045abb" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  set(KOKKOS_MD5 "4c84698917c93a18985b311bb6caf84f" CACHE STRING "MD5 checksum of KOKKOS tarball")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
   ExternalProject_Add(kokkos_build
@@ -58,7 +58,7 @@ if(DOWNLOAD_KOKKOS)
   target_link_libraries(lmp PRIVATE LAMMPS::KOKKOS)
   add_dependencies(LAMMPS::KOKKOS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 3.4.00 REQUIRED CONFIG)
+  find_package(Kokkos 3.4.01 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
   target_link_libraries(lmp PRIVATE Kokkos::kokkos)
 else()
@@ -99,7 +99,7 @@ if(PKG_KSPACE)
                                  ${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp
                                  ${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
   if(Kokkos_ENABLE_CUDA)
-    if(NOT ${FFT} STREQUAL "KISS")
+    if(NOT (FFT STREQUAL "KISS"))
       target_compile_definitions(lammps PRIVATE -DFFT_CUFFT)
       target_link_libraries(lammps PRIVATE cufft)
     endif()

cmake/Modules/Packages/MESSAGE.cmake

@@ -1,4 +1,4 @@
-if(LAMMPS_SIZES STREQUAL BIGBIG)
+if(LAMMPS_SIZES STREQUAL "BIGBIG")
   message(FATAL_ERROR "The MESSAGE Package is not compatible with -DLAMMPS_BIGBIG")
 endif()
 option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)

cmake/Modules/Packages/USER-HDNNP.cmake

@@ -0,0 +1,124 @@
+find_package(N2P2 QUIET)
+if(N2P2_FOUND)
+  set(DOWNLOAD_N2P2_DEFAULT OFF)
+else()
+  set(DOWNLOAD_N2P2_DEFAULT ON)
+endif()
+option(DOWNLOAD_N2P2 "Download n2p2 library instead of using an already installed one)" ${DOWNLOAD_N2P2_DEFAULT})
+if(DOWNLOAD_N2P2)
+  set(N2P2_URL "https://github.com/CompPhysVienna/n2p2/archive/v2.1.4.tar.gz" CACHE STRING "URL for n2p2 tarball")
+  set(N2P2_MD5 "9595b066636cd6b90b0fef93398297a5" CACHE STRING "MD5 checksum of N2P2 tarball")
+  mark_as_advanced(N2P2_URL)
+  mark_as_advanced(N2P2_MD5)
+
+  # adjust settings from detected compiler to compiler platform in n2p2 library
+  # set compiler specific flag to turn on C++11 syntax (required on macOS and CentOS 7)
+  if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang"))
+    set(N2P2_COMP llvm)
+    set(N2P2_CXX_STD "-std=c++11")
+  elseif(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+    set(N2P2_COMP intel)
+    set(N2P2_CXX_STD "-std=c++11")
+  elseif(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+    set(N2P2_COMP gnu)
+    set(N2P2_CXX_STD "-std=gnu++11")
+  elseif(CMAKE_CXX_COMPILER_ID STREQUAL "PGI")
+    set(N2P2_COMP gnu)
+    set(N2P2_CXX_STD "--c++11")
+  else() # default
+    set(N2P2_COMP "")
+  endif()
+
+  # pass on archive creator command. prefer compiler specific version, if set.
+  # important when using cross compiler.
+  if(CMAKE_CXX_COMPILER_AR)
+    set(N2P2_AR ${CMAKE_CXX_COMPILER_AR})
+  else()
+    set(N2P2_AR ${CMAKE_AR})
+  endif()
+
+  # adjust compilation of n2p2 library to whether MPI is requested in LAMMPS or not
+  # need special care for compiling for MPICH2 with Linux-to-Windows cross compiler.
+  if(NOT BUILD_MPI)
+    set(N2P2_PROJECT_OPTIONS "-DN2P2_NO_MPI")
+  else()
+    # get path to MPI include directory when cross-compiling to windows
+    if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)
+      get_target_property(N2P2_MPI_INCLUDE MPI::MPI_CXX INTERFACE_INCLUDE_DIRECTORIES)
+      set(N2P2_PROJECT_OPTIONS "-I ${N2P2_MPI_INCLUDE} -DMPICH_SKIP_MPICXX=1")
+      set(MPI_CXX_COMPILER ${CMAKE_CXX_COMPILER})
+    endif()
+    if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+      get_target_property(N2P2_MPI_INCLUDE MPI::MPI_CXX INTERFACE_INCLUDE_DIRECTORIES)
+      set(N2P2_PROJECT_OPTIONS "-I ${N2P2_MPI_INCLUDE} -DMPICH_SKIP_MPICXX=1")
+      set(MPI_CXX_COMPILER ${CMAKE_CXX_COMPILER})
+    endif()
+  endif()
+
+  # override compiler (optimization) flags in n2p2 library to flags used for LAMMPS
+  # specifically -march=native can result in problems when compiling on HPC clusters or with a cross compiler
+  # this convoluted way gets correct quoting/escaping when configuring the external project
+  string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
+  set(N2P2_BUILD_FLAGS "${CMAKE_SHARED_LIBRARY_CXX_FLAGS} ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}} ${N2P2_CXX_STD}")
+  set(N2P2_BUILD_OPTIONS INTERFACES=LAMMPS COMP=${N2P2_COMP} "PROJECT_OPTIONS=${N2P2_PROJECT_OPTIONS}" "PROJECT_DEBUG="
+    "PROJECT_CC=${CMAKE_CXX_COMPILER}" "PROJECT_MPICC=${MPI_CXX_COMPILER}" "PROJECT_CFLAGS=${N2P2_BUILD_FLAGS}"
+    "PROJECT_AR=${N2P2_AR}")
+  # echo final flag for debugging
+  message(STATUS "N2P2 BUILD OPTIONS: ${N2P2_BUILD_OPTIONS}")
+
+  # download compile n2p2 library. much patch MPI calls in LAMMPS interface to accommodate MPI-2 (e.g. for cross-compiling)
+  include(ExternalProject)
+  ExternalProject_Add(n2p2_build
+    URL     ${N2P2_URL}
+    URL_MD5 ${N2P2_MD5}
+    UPDATE_COMMAND ""
+    CONFIGURE_COMMAND ""
+    PATCH_COMMAND sed -i -e "s/\\(MPI_\\(P\\|Unp\\)ack(\\)/\\1(void *) /" src/libnnpif/LAMMPS/InterfaceLammps.cpp
+    BUILD_COMMAND make -f makefile libnnpif ${N2P2_BUILD_OPTIONS}
+    BUILD_ALWAYS YES
+    INSTALL_COMMAND ""
+    BUILD_IN_SOURCE 1
+    LOG_BUILD ON
+    SOURCE_SUBDIR src/
+    BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libnnp.a <SOURCE_DIR>/lib/libnnpif.a
+    )
+
+  # create imported target LAMMPS::N2P2 from two libraries nnp and nnpif
+  ExternalProject_get_property(n2p2_build SOURCE_DIR)
+  # n2p2 core library "libnnp"
+  add_library(LAMMPS::N2P2::LIBNNP UNKNOWN IMPORTED)
+  set_target_properties(LAMMPS::N2P2::LIBNNP PROPERTIES
+    IMPORTED_LOCATION "${SOURCE_DIR}/lib/libnnp.a"
+    INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include")
+  # n2p2 interface library "libnnpif"
+  add_library(LAMMPS::N2P2::LIBNNPIF UNKNOWN IMPORTED)
+  set_target_properties(LAMMPS::N2P2::LIBNNPIF PROPERTIES
+    IMPORTED_LOCATION "${SOURCE_DIR}/lib/libnnpif.a"
+    INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include")
+  # nnpif library has MPI calls if MPI is enabled, so we must link with MPI libs
+  if(BUILD_MPI)
+    set_target_properties(LAMMPS::N2P2::LIBNNPIF PROPERTIES
+      INTERFACE_LINK_LIBRARIES MPI::MPI_CXX)
+    if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)
+      add_dependencies(LAMMPS::N2P2::LIBNNPIF MPI::MPI_CXX)
+    endif()
+  endif()
+
+  # final step to define imported target
+  add_library(LAMMPS::N2P2 INTERFACE IMPORTED)
+  set_property(TARGET LAMMPS::N2P2 PROPERTY
+    INTERFACE_LINK_LIBRARIES LAMMPS::N2P2::LIBNNPIF LAMMPS::N2P2::LIBNNP)
+  target_link_libraries(lammps PRIVATE LAMMPS::N2P2)
+
+  add_dependencies(LAMMPS::N2P2 n2p2_build)
+  # work around issues with older CMake versions
+  file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
+  file(MAKE_DIRECTORY "${SOURCE_DIR}/lib")
+else()
+  find_package(N2P2)
+  if(NOT N2P2_FOUND)
+    message(FATAL_ERROR "n2p2 not found, help CMake to find it by setting N2P2_DIR, or set DOWNLOAD_N2P2=ON to download it")
+  endif()
+  target_link_libraries(lammps PRIVATE N2P2::N2P2)
+  include(${N2P2_CMAKE_EXTRAS})
+endif()

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     ${MDI_URL}
+    URL_MD5 ${MDI_MD5}
-      URL_MD5 ${MDI_MD5}
+    CMAKE_ARGS ${CMAKE_REQUEST_PIC}
-      UPDATE_COMMAND ""
+    -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
-      CMAKE_ARGS ${CMAKE_REQUEST_PIC}
+    -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-                 -DCMAKE_INSTALL_PREFIX=${LAMMPS_LIB_MDI_BIN_DIR}
+    -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-                 -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+    -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
-                 -DCMAKE_INSTALL_LIBDIR=${CMAKE_INSTALL_LIBDIR}
+    -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
-                 -DCMAKE_INSTALL_INCLUDEDIR=${CMAKE_INSTALL_INCLUDEDIR}
+    -Dlanguage=C
-                 -DBUILD_SHARED_LIBS=${BUILD_SHARED_LIBS}
+    -Dlibtype=STATIC
-                 -Dlanguage=C
+    -Dmpi=${MDI_USE_MPI}
-      CMAKE_CACHE_ARGS -DCMAKE_C_FLAGS:STRING=${CMAKE_C_FLAGS}
+    -Dpython_plugins=${MDI_USE_PYTHON_PLUGINS}
-                       -DCMAKE_CXX_FLAGS:STRING=${CMAKE_CXX_FLAGS}
+    UPDATE_COMMAND ""
-                       -DTargetOpenMP_FIND_COMPONENTS:STRING=C;CXX)
+    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/Modules/PreventInSourceBuilds.cmake

@@ -9,7 +9,7 @@ function(prevent_in_source_builds)
   get_filename_component(bindir "${CMAKE_BINARY_DIR}" REALPATH)
 
   # disallow in-source builds
-  if("${srcdir}" STREQUAL "${bindir}" OR "${srcdir2}" STREQUAL "${bindir}" OR "${srcdir3}" STREQUAL "${bindir}")
+  if(("${srcdir}" STREQUAL "${bindir}") OR ("${srcdir2}" STREQUAL "${bindir}") OR ("${srcdir3}" STREQUAL "${bindir}"))
     message(FATAL_ERROR "\
 
 CMake must not to be run in the source directory. \

cmake/Modules/Testing.cmake

@@ -19,11 +19,11 @@ if(ENABLE_TESTING)
   # we need to build and link a LOT of tester executables, so it is worth checking if
   # a faster linker is available. requires GNU or Clang compiler, newer CMake.
   # also only verified with Fedora Linux > 30 and Ubuntu <= 18.04 (Ubuntu 20.04 fails)
-  if((CMAKE_SYSTEM_NAME STREQUAL Linux) AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
+  if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
-      AND ((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
+      AND ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
-        OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")))
+        OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
-    if (((CMAKE_LINUX_DISTRO STREQUAL Ubuntu) AND (CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04))
+    if(((CMAKE_LINUX_DISTRO STREQUAL "Ubuntu") AND (CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04))
-        OR ((CMAKE_LINUX_DISTRO STREQUAL Fedora) AND (CMAKE_DISTRO_VERSION VERSION_GREATER 30)))
+        OR ((CMAKE_LINUX_DISTRO STREQUAL "Fedora") AND (CMAKE_DISTRO_VERSION VERSION_GREATER 30)))
       include(CheckCXXCompilerFlag)
       set(CMAKE_CUSTOM_LINKER_DEFAULT default)
       check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG)
@@ -58,7 +58,7 @@ if(ENABLE_TESTING)
 endif()
 
 # Compiler specific features for testing
-if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
+if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
   option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
   mark_as_advanced(ENABLE_COVERAGE)
   if(ENABLE_COVERAGE)
@@ -83,7 +83,7 @@ mark_as_advanced(ENABLE_IWYU)
 if(ENABLE_IWYU)
   # enforce these settings
   set(CMAKE_EXPORT_COMPILE_COMMANDS ON CACHE BOOL "Enable reporting compilation commands to compile_commands.json" FORCE)
-  if (NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")))
+  if(NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")))
     message(FATAL_ERROR "IWYU is only supported with Clang or GNU compilers")
   endif()
   # detect the "native" header folder so we can include them first
@@ -91,7 +91,7 @@ if(ENABLE_IWYU)
   string(REGEX REPLACE ".*libraries: *=([^:]+):.*" "\\1/include" IWYU_EXTRA_INCLUDE_DIR ${IWYU_SEARCH_PATHS})
   find_program(IWYU_EXE NAMES include-what-you-use iwyu)
   find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py)
-  if (IWYU_EXE AND IWYU_TOOL)
+  if(IWYU_EXE AND IWYU_TOOL)
     add_custom_target(
       iwyu
       ${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -I${IWYU_EXTRA_INCLUDE_DIR} -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp

cmake/Modules/Tools.cmake

@@ -45,7 +45,7 @@ if(BUILD_LAMMPS_SHELL)
   target_include_directories(lammps-shell PRIVATE ${LAMMPS_TOOLS_DIR}/lammps-shell)
 
   # workaround for broken readline pkg-config file on FreeBSD
-  if(CMAKE_SYSTEM_NAME STREQUAL FreeBSD)
+  if(CMAKE_SYSTEM_NAME STREQUAL "FreeBSD")
     target_include_directories(lammps-shell PRIVATE /usr/local/include)
   endif()
   target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE)

cmake/Modules/YAML.cmake

@@ -6,15 +6,27 @@ set(YAML_MD5 "bb15429d8fb787e7d3f1c83ae129a999" CACHE STRING "MD5 checksum of li
 mark_as_advanced(YAML_URL)
 mark_as_advanced(YAML_MD5)
 
+# support cross-compilation to windows
+if(CMAKE_CROSSCOMPILING AND (CMAKE_SYSTEM_NAME STREQUAL "Windows"))
+  if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86")
+    set(YAML_CROSS_HOST --host=i686-mingw64)
+  elseif(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+    set(YAML_CROSS_HOST --host=x86_64-mingw64)
+  else()
+    message(FATAL_ERROR "Unsupported cross-compilation "
+      " for ${CMAKE_SYSTEM_NAME}/${CMAKE_SYSTEM_PROCESSOR}"
+      " on ${CMAKE_HOST_SYSTEM}/${CMAKE_HOST_SYSTEM_PROCESSOR}")
+  endif()
+endif()
+
 ExternalProject_Add(libyaml
                     URL               ${YAML_URL}
                     URL_MD5           ${YAML_MD5}
                     SOURCE_DIR        "${CMAKE_BINARY_DIR}/yaml-src"
                     BINARY_DIR        "${CMAKE_BINARY_DIR}/yaml-build"
                     CONFIGURE_COMMAND <SOURCE_DIR>/configure ${CONFIGURE_REQUEST_PIC}
-                                      CXX=${CMAKE_CXX_COMPILER}
+                                      CXX=${CMAKE_CXX_COMPILER} CC=${CMAKE_C_COMPILER}
-                                      CC=${CMAKE_C_COMPILER}
+                                      --prefix=<INSTALL_DIR> --disable-shared ${YAML_CROSS_HOST}
-                                      --prefix=<INSTALL_DIR> --disable-shared
                     BUILD_BYPRODUCTS  <INSTALL_DIR>/lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX}
                     TEST_COMMAND      "")
 

cmake/pkgconfig/liblammps.pc.in

@@ -24,7 +24,7 @@ includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
 
 Name: liblammps@LAMMPS_MACHINE@
 Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
-URL: http://lammps.sandia.gov
+URL: https://www.lammps.org
 Version: @PROJECT_VERSION@
 Requires:
 Libs: -L${libdir} -llammps@LAMMPS_MACHINE@

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-INTEL
+  USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
-  USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MESONT USER-MGPT
+  USER-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD
-  USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE USER-PHONON
+  USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
-  USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION USER-REAXC
+  USER-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN
-  USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
+  USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
-  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-INTEL
+  USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
-  USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MESONT USER-MGPT
+  USER-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD
-  USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE USER-PHONON
+  USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
-  USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION USER-REAXC
+  USER-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN
-  USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
+  USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
-  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/clang.cmake

@@ -4,10 +4,18 @@ set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+
 set(MPI_CXX "clang++" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
-unset(HAVE_OMP_H_INCLUDE CACHE)
 
+unset(HAVE_OMP_H_INCLUDE CACHE)
 set(OpenMP_C "clang" CACHE STRING "" FORCE)
 set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
 set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" 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/intel.cmake

@@ -3,10 +3,20 @@
 set(CMAKE_CXX_COMPILER "icpc" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "icc" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_COMPILER "ifort" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+
 set(MPI_CXX "icpc" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
-unset(HAVE_OMP_H_INCLUDE CACHE)
 
+unset(HAVE_OMP_H_INCLUDE CACHE)
 set(OpenMP_C "icc" CACHE STRING "" FORCE)
 set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE)
 set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)

cmake/presets/mingw-cross.cmake

@@ -1,9 +1,9 @@
 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-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
-                 USER-FEP USER-INTEL USER-MANIFOLD USER-MEAMC USER-MESODPD
+                 USER-HDNNP USER-INTEL USER-MANIFOLD USER-MDI 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-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF

cmake/presets/nolib.cmake

@@ -3,9 +3,9 @@
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MESSAGE MPIIO MSCG
   PYTHON VORONOI
-  USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB USER-MOLFILE USER-MESONT
+  USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-HDNNP USER-LB USER-MOLFILE
-  USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS
+  USER-MESONT USER-MDI USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP
-  USER-SMD USER-VTK)
+  USER-SCAFACOS USER-SMD USER-VTK)
 
 foreach(PKG ${PACKAGES_WITH_LIB})
   set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

cmake/presets/oneapi.cmake

@@ -1,12 +1,22 @@
-# preset that will enable the LLVM based Intel compilers with support for MPI and OpenMP (on Linux boxes)
+# preset that will enable the LLVM based Intel compilers with support for MPI and OpenMP and Fortran (on Linux boxes)
 
 set(CMAKE_CXX_COMPILER "icpx" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "icx" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_COMPILER "ifx" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+
 set(MPI_CXX "icpx" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
-unset(HAVE_OMP_H_INCLUDE CACHE)
 
+unset(HAVE_OMP_H_INCLUDE CACHE)
 set(OpenMP_C "icx" CACHE STRING "" FORCE)
 set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE)
 set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)

doc/Makefile

@@ -10,7 +10,6 @@ endif
 BUILDDIR       = ${CURDIR}
 RSTDIR         = $(BUILDDIR)/src
 VENV           = $(BUILDDIR)/docenv
-TXT2RST        = $(VENV)/bin/txt2rst
 ANCHORCHECK    = $(VENV)/bin/rst_anchor_check
 SPHINXCONFIG   = $(BUILDDIR)/utils/sphinx-config
 MATHJAX        = $(SPHINXCONFIG)/_static/mathjax
@@ -59,7 +58,7 @@ SPHINXEXTRA = -E -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiproc
 # 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 xmlgen
+.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check char_check xmlgen
 
 # ------------------------------------------
 
@@ -68,7 +67,6 @@ help:
 	@echo "Please use \`make <target>' where <target> is one of"
 	@echo "  html          create HTML pages in html dir"
 	@echo "  pdf           create Manual.pdf in this dir"
-	@echo "  fetch         fetch HTML and PDF files from LAMMPS web site"
 	@echo "  epub          create ePUB format manual for e-book readers"
 	@echo "  mobi          convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
 	@echo "                      (requires ebook-convert tool from calibre)"
@@ -185,13 +183,6 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@rm -rf latex/PDF/.[sg]*
 	@echo "Build finished. Manual.pdf is in this directory."
 
-fetch:
-	@rm -rf html_www Manual_www.pdf
-	@curl -s -o Manual_www.pdf http://lammps.sandia.gov/doc/Manual.pdf
-	@curl -s -o lammps-doc.tar.gz http://lammps.sandia.gov/tars/lammps-doc.tar.gz
-	@tar xzf lammps-doc.tar.gz
-	@rm -f lammps-doc.tar.gz
-
 anchor_check : $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ;\
@@ -213,6 +204,9 @@ package_check : $(VENV)
 		deactivate ;\
 	)
 
+char_check :
+	@( env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst && exit 1 || : )
+
 xmlgen : doxygen/xml/index.xml
 
 doxygen/Doxyfile: doxygen/Doxyfile.in
@@ -238,7 +232,7 @@ $(VENV):
 $(MATHJAX):
 	@git clone -b 3.1.4 -c advice.detachedHead=0 --depth 1 git://github.com/mathjax/MathJax.git $@
 
-$(TXT2RST) $(ANCHORCHECK): $(VENV)
+$(ANCHORCHECK): $(VENV)
 	@( \
 		. $(VENV)/bin/activate; \
 		(cd utils/converters;\

doc/README

@@ -25,16 +25,11 @@ github-development-workflow.md   notes on the LAMMPS development workflow
 include-file-conventions.md      notes on LAMMPS' include file conventions
 documentation_conventions.md     notes on writing documentation for LAMMPS
 
-If you downloaded a LAMMPS tarball from lammps.sandia.gov, then the html
+If you downloaded a LAMMPS tarball from www.lammps.org, then the html
 folder and the PDF manual should be included. If you downloaded LAMMPS
-from GitHub then you either need to download them or build them.
+from GitHub then you either need to build them.
 
-(a) You can "fetch" the current HTML and PDF files from the LAMMPS web
+You can build the HTML and PDF files yourself, by typing "make html"
-site.  Just type "make fetch".  This should create a html_www directory
-and Manual_www.pdf file.  These will always represent the latest published
-patch/development version of LAMMPS.
-
-(b) You can build the HTML and PDF files yourself, by typing "make html"
 or by "make pdf", respectively.  This requires various tools and files.
 Some of them have to be installed (more on that below).  For the rest the
 build process will attempt to download and install into a python virtual
@@ -78,4 +73,4 @@ the tool 'ebook-convert' from the 'calibre' e-book management software
 ----------------
 
 More details this can be found in the manual itself. The online
-version is at: https://lammps.sandia.gov/doc/Manual_build.html
+version is at: https://docs.lammps.org/Build_manual.html

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "8 April 2021" "2021-04-08"
+.TH LAMMPS "27 May 2021" "2021-05-27"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.
@@ -34,7 +34,7 @@ semiconductors) and coarse-grained or mesoscopic systems. It can be used to
 model atoms or, more generically, as a parallel particle simulator at the
 atomic, meso, or continuum scale.
 
-See https://lammps.sandia.gov/ for more information and documentation.
+See https://www.lammps.org/ for more information and documentation.
 
 .SH EXECUTABLE NAME
 The

doc/src/Bibliography.rst

@@ -1129,6 +1129,9 @@ Bibliography
 **(Sutmann)**
    Sutmann, Arnold, Fahrenberger, et. al., Physical review / E 88(6), 063308 (2013)
 
+**(Sutmann)** G. Sutmann. ScaFaCoS - a Scalable library of Fast Coulomb Solvers for particle Systems.
+  In Bajaj, Zavattieri, Koslowski, Siegmund, Proceedings of the Society of Engineering Science 51st Annual Technical Meeting. 2014.
+
 **(Swinburne)**
    Swinburne and Marinica, Physical Review Letters, 120, 1 (2018)
 
@@ -1285,9 +1288,6 @@ Bibliography
 **(Wennberg)**
    Wennberg, Murtola, Hess, Lindahl, J Chem Theory Comput, 9, 3527 (2013).
 
-**(Who)**
-   Who, Author2, Author3, J of Long Range Solvers, 35, 164-177 (2012).
-
 **(Wicaksono1)**
    Wicaksono, Sinclair, Militzer, Computational Materials Science, 117, 397-405 (2016).
 

doc/src/Build_development.rst

@@ -28,6 +28,28 @@ variable VERBOSE set to 1:
 
 ----------
 
+.. _clang-tidy:
+
+Enable static code analysis with clang-tidy
+-------------------------------------------
+
+The `clang-tidy tool <https://clang.llvm.org/extra/clang-tidy/>`_ is a
+static code analysis tool to diagnose (and potentially fix) typical
+programming errors or coding style violations.  It has a modular framework
+of tests that can be adjusted to help identifying problems before they
+become bugs and also assist in modernizing large code bases (like LAMMPS).
+It can be enabled for all C++ code with the following CMake flag
+
+.. code-block:: bash
+
+   -D ENABLE_CLANG_TIDY=value    # value = no (default) or yes
+
+With this flag enabled all source files will be processed twice, first to
+be compiled and then to be analyzed. Please note that the analysis can be
+significantly more time consuming than the compilation itself.
+
+----------
+
 .. _iwyu_processing:
 
 Report missing and unneeded '#include' statements
@@ -447,12 +469,24 @@ The following options are available.
 
 .. code-block:: bash
 
-   make check-whitespace    # generate coverage report in HTML format
+   make check-whitespace    # search for files with whitespace issues
-   make fix-whitespace      # generate coverage report in XML format
+   make fix-whitespace      # correct whitespace issues in files
-   make check-permissions   # delete folder with HTML format coverage report
+   make check-homepage      # search for files with old LAMMPS homepage URLs
-   make fix-permissions     # delete all collected coverage data and HTML output
+   make fix-homepage        # correct LAMMPS homepage URLs in files
+   make check-permissions   # search for files with permissions issues
+   make fix-permissions     # correct permissions issues in files
 
-For the code in the ``unittest`` tree we are using the `clang-format`
+For the code in the ``unittest`` and ``src`` trees we are transitioning
-tool (Clang version 8.0 or later is required). If available, the source
+to use the `clang-format` tool to assist with having a consistent source
-code files in the ``unittest`` tree can be updated to conform to the
+code style.  The `clang-format` command bundled with Clang version 8.0
-formatting settings using ``make format-tests``.
+or later is required.  The configuration is in files ``.clang-format``
+in the respective folders.  Since the modifications from `clang-format`
+can be significant and - especially for "legacy style code" - also is
+not always improving readability, a large number of files currently have
+a ``// clang-format off`` at the top, which will disable the processing.
+Over time, files will be refactored and updated to that `clang-format`
+may be applied to them (at least in part).
+
+If `clang-format` is available, the source code files in the ``unittest``
+tree can be updated to conform to the formatting settings using
+``make format-tests`` and the files in ``src`` with ``make format-src``.

doc/src/Build_extras.rst

@@ -48,6 +48,7 @@ This is the list of packages that may require additional steps.
    * :ref:`USER-AWPMD <user-awpmd>`
    * :ref:`USER-COLVARS <user-colvars>`
    * :ref:`USER-H5MD <user-h5md>`
+   * :ref:`USER-HDNNP <user-hdnnp>`
    * :ref:`USER-INTEL <user-intel>`
    * :ref:`USER-MDI <user-mdi>`
    * :ref:`USER-MESONT <user-mesont>`
@@ -456,6 +457,9 @@ They must be specified in uppercase.
    *  - ZEN2
       - HOST
       - AMD Zen2 class CPU (AVX 2)
+   *  - ZEN3
+      - HOST
+      - AMD Zen3 class CPU (AVX 2)
    *  - ARMV80
       - HOST
       - ARMv8.0 Compatible CPU
@@ -559,7 +563,7 @@ They must be specified in uppercase.
       - GPU
       - Intel GPUs Gen9+
 
-This list was last updated for version 3.4 of the Kokkos library.
+This list was last updated for version 3.4.1 of the Kokkos library.
 
 .. tabs::
 
@@ -1470,6 +1474,60 @@ the HDF5 library.
 
 ----------
 
+.. _user-hdnnp:
+
+USER-HDNNP package
+---------------------------------
+
+To build with the USER-HDNNP package it is required to download and build the
+external `n2p2 <https://github.com/CompPhysVienna/n2p2>`__ library ``v2.1.4``
+(or higher). The LAMMPS build process offers an automatic download and
+compilation of *n2p2* or allows you to choose the installation directory of
+*n2p2* manually. Please see the boxes below for the CMake and traditional build
+system for detailed information.
+
+In case of a manual installation of *n2p2* you only need to build the *n2p2* core
+library ``libnnp`` and interface library ``libnnpif``. When using GCC it should
+suffice to execute ``make libnnpif`` in the *n2p2* ``src`` directory. For more
+details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
+<https://compphysvienna.github.io/n2p2/topics/build.html>`__.
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      .. code-block:: bash
+
+         -D DOWNLOAD_N2P2=value    # download n2p2 for build, value = no (default) or yes
+         -D N2P2_DIR=path          # n2p2 base directory (only needed if a custom location)
+
+      If ``DOWNLOAD_N2P2`` is set, the *n2p2* library will be downloaded and
+      built inside the CMake build directory.  If the *n2p2* library is already
+      on your system (in a location CMake cannot find it), set the ``N2P2_DIR``
+      to path where *n2p2* is located. If *n2p2* is located directly in
+      ``lib/hdnnp/n2p2`` it will be automatically found by CMake.
+
+   .. tab:: Traditional make
+
+      You can download and build the *n2p2* library manually if you prefer;
+      follow the instructions in ``lib/hdnnp/README``\ . You can also do it in
+      one step from the ``lammps/src`` dir, using a command like these, which
+      simply invoke the ``lib/hdnnp/Install.py`` script with the specified args:
+
+      .. code-block:: bash
+
+         $ make lib-hdnnp             # print help message
+         $ make lib-hdnnp args="-b"   # download and build in lib/hdnnp/n2p2-...
+         $ make lib-hdnnp args="-b -v 2.1.4" # download and build specific version
+         $ make lib-hdnnp args="-p /usr/local/n2p2" # use the existing n2p2 installation in /usr/local/n2p2
+
+      Note that 3 symbolic (soft) links, ``includelink``, ``liblink`` and
+      ``Makefile.lammps``, will be created in ``lib/hdnnp`` to point to
+      ``n2p2/include``, ``n2p2/lib`` and ``n2p2/lib/Makefile.lammps-extra``,
+      respectively. When LAMMPS is built in ``src`` it will use these links.
+
+----------
+
 .. _user-intel:
 
 USER-INTEL package

doc/src/Build_manual.rst

@@ -28,29 +28,18 @@ If you downloaded LAMMPS as a tarball from `the LAMMPS website <lws_>`_,
 the html folder and the PDF files should be included.
 
 If you downloaded LAMMPS from the public git repository, then the HTML
-and PDF files are not included.  Instead you need to create them, in one
+and PDF files are not included.  You can build the HTML or PDF files yourself,
-of two ways:
+by typing ``make html``  or ``make pdf`` in the ``doc`` folder.  This requires
-
+various tools and files.  Some of them have to be installed (see below).  For
-a. You can "fetch" the current HTML and PDF files from the LAMMPS web
+the rest the build process will attempt to download and install them into
-   site.  Just type ``make fetch``.  This should download a ``html_www``
+a python virtual environment and local folders.
-   directory and a ``Manual_www.pdf`` file.  Note that if new LAMMPS features
-   have been added more recently than the date of your LAMMPS version, the
-   fetched documentation will include those changes (but your source code
-   will not, unless you update your local repository).
-
-b. You can build the HTML or PDF files yourself, by typing ``make html``
-   or ``make pdf`` in the ``doc`` folder.  This requires various tools
-   and files.  Some of them have to be installed (see below).  For the
-   rest the build process will attempt to download and install them into
-   a python virtual environment and local folders.
 
 A current version of the manual (latest patch release, aka unstable
 branch) is is available online at:
-`https://lammps.sandia.gov/doc/Manual.html
+`https://docs.lammps.org/Manual.html <https://docs.lammps.org/Manual.html>`_.
-<https://lammps.sandia.gov/doc/Manual.html>`_ A version of the manual
+A version of the manual corresponding to the ongoing development (aka master branch)
-corresponding to the ongoing development (aka master branch) is
+is available online at: `https://docs.lammps.org/latest/
-available online at: `https://docs.lammps.org/
+<https://docs.lammps.org/latest/>`_
-<https://docs.lammps.org/>`_
 
 Build using GNU make
 --------------------
@@ -257,4 +246,4 @@ the file ``lammps/doc/utils/sphinx-config/false_positives.txt``.
 
 .. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
 
-.. _lws: https://lammps.sandia.gov
+.. _lws: https://www.lammps.org

doc/src/Build_package.rst

@@ -30,17 +30,17 @@ steps, as explained on the :doc:`Build extras <Build_extras>` page.
 These links take you to the extra instructions for those select
 packages:
 
-+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
++--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
-| :ref:`COMPRESS <compress>`           | :ref:`GPU <gpu>`               | :ref:`KIM <kim>`                   | :ref:`KOKKOS <kokkos>`       | :ref:`LATTE <latte>`           | :ref:`MESSAGE <message>`             |
+| :ref:`COMPRESS <compress>`           | :ref:`GPU <gpu>`                     | :ref:`KIM <kim>`                   | :ref:`KOKKOS <kokkos>`           | :ref:`LATTE <latte>`           | :ref:`MESSAGE <message>`       |
-+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
++--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
-| :ref:`MSCG <mscg>`                   | :ref:`OPT <opt>`               | :ref:`POEMS <poems>`               | :ref:`PYTHON <python>`       | :ref:`VORONOI <voronoi>`       | :ref:`USER-ADIOS <user-adios>`       |
+| :ref:`MSCG <mscg>`                   | :ref:`OPT <opt>`                     | :ref:`POEMS <poems>`               | :ref:`PYTHON <python>`           | :ref:`VORONOI <voronoi>`       | :ref:`USER-ADIOS <user-adios>` |
-+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
++--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
-| :ref:`USER-ATC <user-atc>`           | :ref:`USER-AWPMD <user-awpmd>` | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>` | :ref:`USER-INTEL <user-intel>` | :ref:`USER-MOLFILE <user-molfile>`   |
+| :ref:`USER-ATC <user-atc>`           | :ref:`USER-AWPMD <user-awpmd>`       | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>`     | :ref:`USER-HDNNP <user-hdnnp>` | :ref:`USER-INTEL <user-intel>` |
-+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
++--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
-| :ref:`USER-NETCDF <user-netcdf>`     | :ref:`USER-PACE <user-pace>`   | :ref:`USER-PLUMED <user-plumed>`   | :ref:`USER-OMP <user-omp>`   | :ref:`USER-QMMM <user-qmmm>`   | :ref:`USER-QUIP <user-quip>`         |
+| :ref:`USER-MOLFILE <user-molfile>`   | :ref:`USER-NETCDF <user-netcdf>`     | :ref:`USER-PACE <user-pace>`       | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>`     | :ref:`USER-QMMM <user-qmmm>`   |
-+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
++--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
-| :ref:`USER-SCAFACOS <user-scafacos>` | :ref:`USER-SMD <user-smd>`     | :ref:`USER-VTK <user-vtk>`         |                              |                                |                                      |
+| :ref:`USER-QUIP <user-quip>`         | :ref:`USER-SCAFACOS <user-scafacos>` | :ref:`USER-SMD <user-smd>`         | :ref:`USER-VTK <user-vtk>`       |                                |                                |
-+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
++--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
 
 The mechanism for including packages is simple but different for CMake
 versus make.

doc/src/Commands_pair.rst

@@ -118,6 +118,7 @@ OPT.
    * :doc:`gw/zbl <pair_gw>`
    * :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
    * :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
+   * :doc:`hdnnp <pair_hdnnp>`
    * :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
    * :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
    * :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`
@@ -226,6 +227,7 @@ OPT.
    * :doc:`polymorphic <pair_polymorphic>`
    * :doc:`python <pair_python>`
    * :doc:`quip <pair_quip>`
+   * :doc:`rann <pair_rann>`
    * :doc:`reax/c (ko) <pair_reaxc>`
    * :doc:`rebo (io) <pair_airebo>`
    * :doc:`resquared (go) <pair_resquared>`

doc/src/Errors_bugs.rst

@@ -5,8 +5,8 @@ If you are confident that you have found a bug in LAMMPS, please follow
 the steps outlined below:
 
  * Check the `New features and bug fixes
-   <https://lammps.sandia.gov/bug.html>`_ section of the `LAMMPS WWW site
+   <https://www.lammps.org/bug.html>`_ section of the `LAMMPS WWW site
-   <https://lammps.sandia.gov>`_ or the
+   <https://www.lammps.org>`_ or the
    `GitHub Releases page <https://github.com/lammps/lammps/releases>`_ to
    see if the bug has already been addressed in a patch release.
  * Check that your issue can be reproduced with the latest development
@@ -17,7 +17,7 @@ the steps outlined below:
    if your issue has already been reported and if it is still open.
  * Check the `GitHub Pull Requests page <https://github.com/lammps/lammps/pulls>`_
    to see if there is already a fix for your bug pending.
- * Check the `mailing list archives <https://lammps.sandia.gov/mail.html>`_
+ * Check the `mailing list archives <https://www.lammps.org/mail.html>`_
    to see if the issue has been discussed before.
 
 If none of these steps yields any useful information, please file a new

doc/src/Errors_common.rst

@@ -39,7 +39,7 @@ figure out your physics or numerical mistakes, like choosing too big a
 timestep, specifying erroneous force field coefficients, or putting 2
 atoms on top of each other!  If you run into errors that LAMMPS
 does not catch that you think it should flag, please send an email to
-the `developers <https://lammps.sandia.gov/authors.html>`_.
+the `developers <https://www.lammps.org/authors.html>`_.
 
 If you get an error message about an invalid command in your input
 script, you can determine what command is causing the problem by

doc/src/Errors_messages.rst

@@ -3871,7 +3871,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
 *Fix orient/fcc found self twice*
    The neighbor lists used by fix orient/fcc are messed up.  If this
    error occurs, it is likely a bug, so send an email to the
-   `developers <https://lammps.sandia.gov/authors.html>`_.
+   `developers <https://www.lammps.org/authors.html>`_.
 
 *Fix peri neigh does not exist*
    Somehow a fix that the pair style defines has been deleted.

doc/src/Examples.rst

@@ -18,7 +18,7 @@ files and image files.
 
 If you uncomment the :doc:`dump <dump>` command in the input script, a
 text dump file will be produced, which can be animated by various
-`visualization programs <https://lammps.sandia.gov/viz.html>`_.
+`visualization programs <https://www.lammps.org/viz.html>`_.
 
 If you uncomment the :doc:`dump image <dump>` command in the input
 script, and assuming you have built LAMMPS with a JPG library, JPG
@@ -27,7 +27,7 @@ be quickly post-processed into a movie using commands described on the
 :doc:`dump image <dump_image>` doc page.
 
 Animations of many of the examples can be viewed on the Movies section
-of the `LAMMPS web site <https://lammps.sandia.gov/movies.html>`_.
+of the `LAMMPS web site <https://www.lammps.org/movies.html>`_.
 
 There are two kinds of sub-directories in the examples folder.  Lower
 case named directories contain one or a few simple, quick-to-run
@@ -168,7 +168,7 @@ Here is how you can run and visualize one of the sample problems:
 Running the simulation produces the files *dump.indent* and
 *log.lammps*\ .  You can visualize the dump file of snapshots with a
 variety of third-party tools highlighted on the
-`Visualization <https://lammps.sandia.gov/viz.html>`_ page of the LAMMPS
+`Visualization <https://www.lammps.org/viz.html>`_ page of the LAMMPS
 web site.
 
 If you uncomment the :doc:`dump image <dump_image>` line(s) in the input

doc/src/Howto.rst

@@ -3,7 +3,7 @@ Howto discussions
 
 These doc pages describe how to perform various tasks with LAMMPS,
 both for users and developers.  The
-`glossary <https://lammps.sandia.gov/glossary.html>`_ website page also lists MD
+`glossary <https://www.lammps.org/glossary.html>`_ website page also lists MD
 terminology with links to corresponding LAMMPS manual pages.  The
 example input scripts included in the examples directory of the LAMMPS
 distribution and highlighted on the :doc:`Examples <Examples>` doc page

doc/src/Howto_mdi.rst

@@ -1,7 +1,7 @@
 Using LAMMPS with the MDI library for code coupling
 ===================================================
 
-..note::
+.. note::
 
   This Howto doc page will eventually replace the
   :doc:`Howto client/server <Howto_client_server>` doc page.
@@ -65,8 +65,8 @@ how the 2 codes are launched to communicate by MPI:
 
 .. code-block:: bash
 
-% mpirun -np 2 lmp_mpi -mdi "-role DRIVER -name d -method MPI" \
+   % mpirun -np 2 lmp_mpi -mdi "-role DRIVER -name d -method MPI" \
-   -in in.aimd : -np 16 pw.x -in qe.in -mdi "-role ENGINE -name e -method MPI"
+     -in in.aimd : -np 16 pw.x -in qe.in -mdi "-role ENGINE -name e -method MPI"
 
 In this case LAMMPS runs on 2 processors (MPI tasks), ``pw.x`` runs on 16
 processors.
@@ -75,8 +75,8 @@ Here is how the 2 codes are launched to communicate by sockets:
 
 .. code-block:: bash
 
-% mpirun -np 2 lmp_mpi -mdi "-role DRIVER -name d -method TCP -port 8021" -in in.aimd
+   % mpirun -np 2 lmp_mpi -mdi "-role DRIVER -name d -method TCP -port 8021" -in in.aimd
-% mpirun -np 16 pw.x -in qe.in -mdi "-role ENGINE -name e -method TCP -port 8021 -hostname localhost"
+   % mpirun -np 16 pw.x -in qe.in -mdi "-role ENGINE -name e -method TCP -port 8021 -hostname localhost"
 
 These commands could be issued in different windows on a desktop
 machine.  Or in the same window, if the first command is ended with
@@ -99,7 +99,7 @@ Examples scripts for using LAMMPS as an MDI engine are in the
 examples/mdi directory.  See the README file in that directory for
 instructions on how to run the examples.
 
-..note::
+.. note::
 
   Work is underway to add commands that allow LAMMPS to be used as an
   MDI driver, e.g. for the AIMD example discussed above.  Example
@@ -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/Howto_wsl.rst

@@ -201,7 +201,7 @@ build configuration and any binaries generated during compilation.
 
 There are countless ways to compile LAMMPS. It is beyond the scope of this
 tutorial. If you want to find out more about what can be enabled, please
-consult the extensive `documentation <https://lammps.sandia.gov/doc/Build_cmake.html>`_.
+consult the extensive `documentation <https://docs.lammps.org/Build_cmake.html>`_.
 
 To compile a minimal version of LAMMPS, we're going to use a preset.
 Presets are a way to specify a collection of CMake options using a file.

doc/src/Install_git.rst

@@ -78,7 +78,7 @@ this is as follows.
    $ git checkout tagID
 
 Stable versions and what tagID to use for a particular stable version
-are discussed on `this page <https://lammps.sandia.gov/bug.html#version>`_.
+are discussed on `this page <https://www.lammps.org/bug.html#version>`_.
 Note that this command will print some warnings, because in order to get
 back to the latest revision and to be able to update with ``git pull``
 again, you will need to do ``git checkout unstable`` (or

doc/src/Install_patch.rst

@@ -10,7 +10,7 @@ If you prefer to download a tarball, as described on the
 :doc:`tarball download <Install_tarball>` page, you can stay current by
 downloading "patch files" when new patch releases are made.  A link to
 a patch file is posted on the
-`bug fixes and new feature page <https://lammps.sandia.gov/bug.html>`_
+`bug fixes and new feature page <https://www.lammps.org/bug.html>`_
 of the LAMMPS website, along
 with a list of changed files and details about what is in the new patch
 release.  This page explains how to apply the patch file to your local

doc/src/Install_tarball.rst

@@ -4,10 +4,10 @@ Download source and documentation as a tarball
 You can download a current LAMMPS tarball from the `download page <download_>`_
 of the `LAMMPS website <lws_>`_.
 
-.. _download: https://lammps.sandia.gov/download.html
+.. _download: https://www.lammps.org/download.html
-.. _bug: https://lammps.sandia.gov/bug.html
+.. _bug: https://www.lammps.org/bug.html
-.. _older: https://lammps.sandia.gov/tars
+.. _older: https://www.lammps.org/tars
-.. _lws: https://lammps.sandia.gov
+.. _lws: https://www.lammps.org
 
 You have two choices of tarballs, either the most recent stable
 release or the most current patch release.  Stable releases occur a

doc/src/Intro_authors.rst

@@ -11,14 +11,14 @@ University:
 * Richard Berger, richard.berger at temple.edu
 
 .. _sjp: http://www.cs.sandia.gov/~sjplimp
-.. _lws: https://lammps.sandia.gov
+.. _lws: https://www.lammps.org
 
 Past developers include Paul Crozier and Mark Stevens, both at Sandia,
 and Ray Shan, now at Materials Design.
 
 ----------
 
-The `Authors page <https://lammps.sandia.gov/authors.html>`_ of the
+The `Authors page <https://www.lammps.org/authors.html>`_ of the
 `LAMMPS website <lws_>`_ has a comprehensive list of all the individuals
 who have contributed code for a new feature or command or tool to
 LAMMPS.
@@ -46,7 +46,7 @@ general-purpose as it is without their expertise and efforts.
 
 ----------
 
-As discussed on the `History page <https://lammps.sandia.gov/history.html>`_ of the website, LAMMPS
+As discussed on the `History page <https://www.lammps.org/history.html>`_ of the website, LAMMPS
 originated as a cooperative project between DOE labs and industrial
 partners.  Folks involved in the design and testing of the original
 version of LAMMPS were the following:

doc/src/Intro_citing.rst

@@ -38,8 +38,8 @@ In addition there are DOIs for individual stable releases. Currently there are:
 Home page
 ^^^^^^^^^
 
-The LAMMPS website at `https://lammps.sandia.gov/
+The LAMMPS website at `https://www.lammps.org/
-<https://lammps.sandia.gov>`_ is the canonical location for information
+<https://www.lammps.org>`_ is the canonical location for information
 about LAMMPS and its features.
 
 Citing contributions

doc/src/Intro_nonfeatures.rst

@@ -33,7 +33,7 @@ Here are suggestions on how to perform these tasks:
   linear bead-spring polymer chains.  The moltemplate program is a true
   molecular builder that will generate complex molecular models.  See
   the :doc:`Tools <Tools>` doc page for details on tools packaged with
-  LAMMPS.  The `Pre/post processing page <http:/lammps.sandia.gov/prepost.html>`_ of the LAMMPS website
+  LAMMPS.  The `Pre/post processing page <http:/www.lammps.org/prepost.html>`_ of the LAMMPS website
   describes a variety of third party tools for this task.  Furthermore,
   some LAMMPS internal commands allow to reconstruct, or selectively add
   topology information, as well as provide the option to insert molecule
@@ -67,7 +67,7 @@ Here are suggestions on how to perform these tasks:
   them to an external program, `FFmpeg <https://www.ffmpeg.org>`_ to generate
   movies from them.  For high-quality, interactive visualization there are
   many excellent and free tools available.  See the
-  `Visualization Tools <https://lammps.sandia.gov/viz.html>`_ page of the
+  `Visualization Tools <https://www.lammps.org/viz.html>`_ page of the
   LAMMPS website for
   visualization packages that can process LAMMPS output data.
 * **Plotting:** See the next bullet about Pizza.py as well as the

doc/src/Intro_opensource.rst

@@ -2,18 +2,20 @@ LAMMPS open-source license
 --------------------------
 
 LAMMPS is a freely-available open-source code, distributed under the
-terms of the `GNU Public License <gnu_>`_, which means you can use or
+terms of the `GNU Public License Version 2 <gpl_>`_, which means you can
-modify the code however you wish.
+use or modify the code however you wish for your own purposes, but have
+to adhere to certain rules when redistributing it or software derived
+from it or that includes parts of it.
 
 LAMMPS comes with no warranty of any kind.  As each source file states
 in its header, it is a copyrighted code that is distributed free-of-
-charge, under the terms of the `GNU Public License <gnu_>`_ (GPL).  This
+charge, under the terms of the `GNU Public License Version 2 <gpl_>`_
-is often referred to as open-source distribution - see
+(GPLv2).  This is often referred to as open-source distribution - see
-`www.gnu.org <gnuorg_>`_ or `www.opensource.org <opensource_>`_.  The legal
+`www.gnu.org <gnuorg_>`_ or `www.opensource.org <opensource_>`_.  The
-text of the GPL is in the LICENSE file included in the LAMMPS
+legal text of the GPL is in the LICENSE file included in the LAMMPS
 distribution.
 
-.. _gnu: http://www.gnu.org/copyleft/gpl.html
+.. _gpl: https://github.com/lammps/lammps/blob/master/LICENSE
 
 .. _gnuorg: http://www.gnu.org
 
@@ -24,14 +26,14 @@ Here is a summary of what the GPL means for LAMMPS users:
 (1) Anyone is free to use, modify, or extend LAMMPS in any way they
 choose, including for commercial purposes.
 
-(2) If you distribute a modified version of LAMMPS, it must remain
+(2) If you **distribute** a modified version of LAMMPS, it must remain
-open-source, meaning you distribute it under the terms of the GPL.
+open-source, meaning you distribute **all** of it under the terms of
-You should clearly annotate such a code as a derivative version of
+the GPL.  You should clearly annotate such a code as a derivative version
-LAMMPS.
+of LAMMPS.
 
-(3) If you release any code that includes LAMMPS source code, then it
+(3) If you release any code that includes or uses LAMMPS source code,
-must also be open-sourced, meaning you distribute it under the terms
+then it must also be open-sourced, meaning you distribute it under
-of the GPL.
+the terms of the GPL.
 
 (4) If you give LAMMPS files to someone else, the GPL LICENSE file and
 source file headers (including the copyright and GPL notices) should

doc/src/Intro_overview.rst

@@ -16,10 +16,10 @@ shared-memory boxes and distributed-memory clusters and
 supercomputers.
 
 .. _mpi: https://en.wikipedia.org/wiki/Message_Passing_Interface
-.. _lws: https://lammps.sandia.gov
+.. _lws: https://www.lammps.org
 
 LAMMPS is written in C++.  Earlier versions were written in F77 and
-F90.  See the `History page <https://lammps.sandia.gov/history.html>`_ of
+F90.  See the `History page <https://www.lammps.org/history.html>`_ of
 the website for details.  All versions can be downloaded from the
 `LAMMPS website <lws_>`_.
 

doc/src/Intro_website.rst

@@ -5,31 +5,31 @@ The `LAMMPS website <lws_>`_ has a variety of additional info about
 LAMMPS, beyond what is in this manual.  Some other useful resources
 available online are listed below.
 
-.. _lws: https://lammps.sandia.gov
+.. _lws: https://www.lammps.org
 
 * `Brief intro and recently added significant features <lws_>`_
-* `List of features <https://lammps.sandia.gov/doc/Intro_features.html>`_
+* `List of features <https://docs.lammps.org/Intro_features.html>`_
-* `List of non-features <https://lammps.sandia.gov/doc/Intro_nonfeatures.html>`_
+* `List of non-features <https://docs.lammps.org/Intro_nonfeatures.html>`_
-* `Recent bug fixes and new features <https://lammps.sandia.gov/bug.html>`_
+* `Recent bug fixes and new features <https://www.lammps.org/bug.html>`_
 
-* `Download info <https://lammps.sandia.gov/download.html>`_
+* `Download info <https://www.lammps.org/download.html>`_
 * `GitHub site <https://github.com/lammps/lammps>`_
 * `SourceForge site <https://sourceforge.net/projects/lammps>`_
-* `LAMMPS open-source license <https://lammps.sandia.gov/doc/Intro_opensource.html>`_
+* `LAMMPS open-source license <https://docs.lammps.org/Intro_opensource.html>`_
 
-* `Glossary of terms relevant to LAMMPS <https://lammps.sandia.gov/glossary.html>`_
+* `Glossary of terms relevant to LAMMPS <https://www.lammps.org/glossary.html>`_
-* `LAMMPS highlights with images <https://lammps.sandia.gov/pictures.html>`_
+* `LAMMPS highlights with images <https://www.lammps.org/pictures.html>`_
-* `LAMMPS highlights with movies <https://lammps.sandia.gov/movies.html>`_
+* `LAMMPS highlights with movies <https://www.lammps.org/movies.html>`_
-* `Mail list <https://lammps.sandia.gov/mail.html>`_
+* `Mail list <https://www.lammps.org/mail.html>`_
-* `Workshops <https://lammps.sandia.gov/workshops.html>`_
+* `Workshops <https://www.lammps.org/workshops.html>`_
-* `Tutorials <https://lammps.sandia.gov/tutorials.html>`_
+* `Tutorials <https://www.lammps.org/tutorials.html>`_
 
-* `Pre- and post-processing tools for LAMMPS <https://lammps.sandia.gov/prepost.html>`_
+* `Pre- and post-processing tools for LAMMPS <https://www.lammps.org/prepost.html>`_
-* `Other software usable with LAMMPS <https://lammps.sandia.gov/offsite.html>`_
+* `Other software usable with LAMMPS <https://www.lammps.org/offsite.html>`_
-* `Viz tools usable with LAMMPS <https://lammps.sandia.gov/viz.html>`_
+* `Viz tools usable with LAMMPS <https://www.lammps.org/viz.html>`_
 
-* `Benchmark performance <https://lammps.sandia.gov/bench.html>`_
+* `Benchmark performance <https://www.lammps.org/bench.html>`_
-* `Publications that have cited LAMMPS <https://lammps.sandia.gov/papers.html>`_
+* `Publications that have cited LAMMPS <https://www.lammps.org/papers.html>`_
-* `Authors of LAMMPS <https://lammps.sandia.gov/authors.html>`_
+* `Authors of LAMMPS <https://www.lammps.org/authors.html>`_
-* `History of LAMMPS development <https://lammps.sandia.gov/history.html>`_
+* `History of LAMMPS development <https://www.lammps.org/history.html>`_
-* `Funding for LAMMPS <https://lammps.sandia.gov/funding.html>`_
+* `Funding for LAMMPS <https://www.lammps.org/funding.html>`_

doc/src/Manual.rst

@@ -1,6 +1,6 @@
-######################################
+########################################
-LAMMPS version |version| Documentation
+LAMMPS Documentation (|version| version)
-######################################
+########################################
 
 LAMMPS stands for **L**\ arge-scale **A**\ tomic/**M**\ olecular
 **M**\ assively **P**\ arallel **S**\ imulator.
@@ -11,11 +11,12 @@ computers.  It was developed originally at Sandia National
 Laboratories, a US Department of Energy facility.  The majority of
 funding for LAMMPS has come from the US Department of Energy (DOE).
 LAMMPS is an open-source code, distributed freely under the terms of
-the GNU Public License (GPL).
+the GNU Public License Version 2 (GPLv2).
 
 The `LAMMPS website <lws_>`_ has a variety of information about the
 code.  It includes links to an on-line version of this manual, a
-`mailing list <https://lammps.sandia.gov/mail.html>`_ where users can
+`mailing list <https://www.lammps.org/mail.html>`_ and
+`online forum <https://www.lammps.org/forum.html>`_  where users can
 post questions, and a `GitHub site <https://github.com/lammps/lammps>`_
 where all LAMMPS development is coordinated.
 
@@ -30,11 +31,13 @@ please :ref:`see this note <webbrowser>`.
 
 -----------
 
-The manual is organized in two parts:
+The manual is organized in three parts:
 1) the :ref:`User Guide <user_documentation>` for how to install
-and use LAMMPS and 2) the :ref:`Programmer Guide <programmer_documentation>`
+and use LAMMPS, 2) the :ref:`Programmer Guide <programmer_documentation>`
 for how to write programs using the LAMMPS library from different
-programming languages and how to modify and extend LAMMPS.
+programming languages and how to modify and extend LAMMPS, and 3) the
+:ref:`Command Reference <command_reference>` which includes detailed
+descriptions of all commands included in the LAMMPS code.
 
 .. only:: html
 
@@ -42,7 +45,7 @@ programming languages and how to modify and extend LAMMPS.
    :doc:`this page <Commands_all>` since it gives quick access
    the documentation for all LAMMPS commands.
 
-.. _lws: https://lammps.sandia.gov
+.. _lws: https://www.lammps.org
 
 ----------
 
@@ -89,10 +92,15 @@ Programmer Guide
    Modify
    Developer
 
+*****************
+Command Reference
+*****************
+
+.. _command_reference:
 .. toctree::
-   :caption: Index
+   :name: reference
-   :name: index
+   :maxdepth: 1
-   :hidden:
+   :caption: Command Reference
 
    commands_list
    fixes
@@ -118,10 +126,10 @@ Indices and tables
 .. admonition:: Web Browser Compatibility
 
    The HTML version of the manual makes use of advanced features present
-   int "modern" web browsers.  This can lead to incompatibilities with older
+   in "modern" web browsers.  This can lead to incompatibilities with older
    web browsers (released more than 4 years ago) and specific vendor browsers
    (e.g. Internet Explorer on Windows; Microsoft Edge works well though)
    where parts of the pages are not rendered as expected (e.g. the layout is
    broken or mathematical expressions not typeset).  In that case we
    recommend to install/use a different/newer web browser or use
-   the `PDF version of the manual <https://lammps.sandia.gov/doc/Manual.pdf>`_.
+   the `PDF version of the manual <https://docs.lammps.org/Manual.pdf>`_.

doc/src/Manual_version.rst

@@ -5,7 +5,7 @@ The LAMMPS "version" is the date when it was released, such as 1 May
 2014. LAMMPS is updated continuously.  Whenever we fix a bug or add a
 feature, we release it in the next *patch* release, which are
 typically made every couple of weeks.  Info on patch releases are on
-`this website page <https://lammps.sandia.gov/bug.html>`_. Every few
+`this website page <https://www.lammps.org/bug.html>`_. Every few
 months, the latest patch release is subjected to more thorough testing
 and labeled as a *stable* version.
 

doc/src/Modify_contribute.rst

@@ -2,7 +2,7 @@ Submitting new features for inclusion in LAMMPS
 ===============================================
 
 We encourage users to submit new features or modifications for LAMMPS to
-`the core developers <https://lammps.sandia.gov/authors.html>`_ so they
+`the core developers <https://www.lammps.org/authors.html>`_ so they
 can be added to the LAMMPS distribution. The preferred way to manage and
 coordinate this is via the LAMMPS project on `GitHub
 <https://github.com/lammps/lammps>`_.  Please see the :doc:`GitHub
@@ -10,15 +10,15 @@ Tutorial <Howto_github>` for a demonstration on how to do that.  An
 alternative is to contact the LAMMPS developers or the indicated
 developer of a package or feature directly and send in your contribution
 via e-mail, but that can add a significant delay on getting your
-contribution included, depending on how busy the developer is you
+contribution included, depending on how busy the respective developer
-contact, how complex a task it would be to integrate that code, and how
+is, how complex a task it would be to integrate that code, and how
 many - if any - changes are required before the code can be included.
 
 For any larger modifications or programming project, you are encouraged
-to contact the LAMMPS developers ahead of time, in order to discuss
+to contact the LAMMPS developers ahead of time in order to discuss
-implementation strategies and coding guidelines, that will make it
+implementation strategies and coding guidelines. That will make it
-easier to integrate your contribution and result in less work for
+easier to integrate your contribution and results in less work for
-everybody involved. You are also encouraged to search through the list
+everybody involved.  You are also encouraged to search through the list
 of `open issues on GitHub <https://github.com/lammps/lammps/issues>`_
 and submit a new issue for a planned feature, so you would not duplicate
 the work of others (and possibly get scooped by them) or have your work
@@ -31,21 +31,22 @@ send an e-mail to ``slack@lammps.org`` explaining what part of LAMMPS
 you are working on.  Only discussions related to LAMMPS development are
 tolerated, so this is **NOT** for people that look for help with compiling,
 installing, or using LAMMPS. Please contact the `lammps-users mailing
-list <https://lammps.sandia.gov/mail.html>`_ for those purposes instead.
+list <https://www.lammps.org/mail.html>`_ for those purposes instead.
 
 How quickly your contribution will be integrated depends largely on how
-much effort it will cause to integrate and test it, how much it requires
+much effort it will cause to integrate and test it, how many and what
-changes to the core codebase, and of how much interest it is to the
+kind of changes it requires to the core codebase, and of how much
-larger LAMMPS community.  Please see below for a checklist of typical
+interest it is to the larger LAMMPS community.  Please see below for a
-requirements. Once you have prepared everything, see the :doc:`LAMMPS GitHub
+checklist of typical requirements.  Once you have prepared everything,
-Tutorial <Howto_github>` page for instructions on
+see the :doc:`LAMMPS GitHub Tutorial <Howto_github>` page for
-how to submit your changes or new files through a GitHub pull
+instructions on how to submit your changes or new files through a GitHub
-request. If you prefer to submit patches or full files, you should first
+pull request.  If you prefer to submit patches or full files, you should
-make certain, that your code works correctly with the latest patch-level
+first make certain, that your code works correctly with the latest
-version of LAMMPS and contains all bug fixes from it. Then create a
+patch-level version of LAMMPS and contains all bug fixes from it.  Then
-gzipped tar file of all changed or added files or a corresponding patch
+create a gzipped tar file of all changed or added files or a
-file using 'diff -u' or 'diff -c' and compress it with gzip. Please only
+corresponding patch file using 'diff -u' or 'diff -c' and compress it
-use gzip compression, as this works well on all platforms.
+with gzip.  Please only use gzip compression, as this works well and is
+available on all platforms.
 
 If the new features/files are broadly useful we may add them as core
 files to LAMMPS or as part of a :doc:`standard package <Packages_standard>`.  Else we will add them as a
@@ -57,13 +58,16 @@ added to the LAMMPS distribution.  All the standard and user packages
 are listed and described on the :doc:`Packages details <Packages_details>` doc page.
 
 Note that by providing us files to release, you are agreeing to make
-them open-source, i.e. we can release them under the terms of the GPL,
+them open-source, i.e. we can release them under the terms of the GPL
-used as a license for the rest of LAMMPS.  See the :doc:`LAMMPS license
+(version 2), used as a license for the rest of LAMMPS.  And as part of
-<Intro_opensource>` doc page for details.
+a LGPL (version 2.1) distribution that we make available to developers
+on request only and with files that are authorized for that kind of
+distribution removed (e.g. interface to FFTW).  See the
+:doc:`LAMMPS license <Intro_opensource>` doc page for details.
 
 With user packages and files, all we are really providing (aside from
 the fame and fortune that accompanies having your name in the source
-code and on the `Authors page <https://lammps.sandia.gov/authors.html>`_
+code and on the `Authors page <https://www.lammps.org/authors.html>`_
 of the `LAMMPS WWW site <lws_>`_), is a means for you to distribute your
 work to the LAMMPS user community, and a mechanism for others to
 easily try out your new feature.  This may help you find bugs or make
@@ -77,13 +81,13 @@ unusual event).
    If you prefer to actively develop and support your add-on
    feature yourself, then you may wish to make it available for download
    from your own website, as a user package that LAMMPS users can add to
-   their copy of LAMMPS.  See the `Offsite LAMMPS packages and tools <https://lammps.sandia.gov/offsite.html>`_ page of the LAMMPS web
+   their copy of LAMMPS.  See the `Offsite LAMMPS packages and tools <https://www.lammps.org/offsite.html>`_ page of the LAMMPS web
    site for examples of groups that do this.  We are happy to advertise
    your package and web site from that page.  Simply email the
-   `developers <https://lammps.sandia.gov/authors.html>`_ with info about
+   `developers <https://www.lammps.org/authors.html>`_ with info about
    your package and we will post it there.
 
-.. _lws: https://lammps.sandia.gov
+.. _lws: https://www.lammps.org
 
 The previous sections of this doc page describe how to add new "style"
 files of various kinds to LAMMPS.  Packages are simply collections of
@@ -92,7 +96,7 @@ LAMMPS input script.  If designed correctly, these additions typically
 do not require changes to the main core of LAMMPS; they are simply
 add-on files.  If you think your new feature requires non-trivial
 changes in core LAMMPS files, you should `communicate with the
-developers <https://lammps.sandia.gov/authors.html>`_, since we may or
+developers <https://www.lammps.org/authors.html>`_, since we may or
 may not want to include those changes for some reason.  An example of a
 trivial change is making a parent-class method "virtual" when you derive
 a new child class from it.
@@ -112,7 +116,7 @@ packages in the src directory for examples. If you are uncertain, please ask.
   your contribution(s) to be added to main LAMMPS code or one of its
   standard packages, it needs to be written in a style compatible with
   other LAMMPS source files. This means: 2-character indentation per
-  level, **no tabs**\ , no lines over 80 characters. I/O is done via
+  level, **no tabs**\ , no lines over 100 characters. I/O is done via
   the C-style stdio library (mixing of stdio and iostreams is generally
   discouraged), class header files should not import any system headers
   outside of <cstdio>, STL containers should be avoided in headers,
@@ -131,6 +135,31 @@ packages in the src directory for examples. If you are uncertain, please ask.
   LAMMPS source files, including the use of the error class for error
   and warning messages.
 
+* To simplify reformatting contributed code in a way that is compatible
+  with the LAMMPS formatting styles, you can use clang-format (version 8
+  or later).  The LAMMPS distribution includes a suitable ``.clang-format``
+  file which will be applied if you run ``clang-format -i some_file.cpp``
+  on your files inside the LAMMPS src tree.  Please only reformat files
+  that you have contributed.  For header files containing a
+  ``SomeStyle(keyword, ClassName)`` macros it is required to have this
+  macro embedded with a pair of ``// clang-format off``, ``// clang-format on``
+  commends and the line must be terminated with a semi-colon (;).
+  Example:
+
+  .. code-block:: c++
+
+     #ifdef COMMAND_CLASS
+     // clang-format off
+     CommandStyle(run,Run);
+     // clang-format on
+     #else
+
+     #ifndef LMP_RUN_H
+     [...]
+
+  You may also use ``// clang-format on/off`` throughout your file
+  to protect sections of the file from being reformatted.
+
 * If you want your contribution to be added as a user-contributed
   feature, and it's a single file (actually a \*.cpp and \*.h file) it can
   rapidly be added to the USER-MISC directory.  Send us the one-line

doc/src/Packages_details.rst

@@ -79,6 +79,7 @@ page gives those details.
    * :ref:`USER-EFF <PKG-USER-EFF>`
    * :ref:`USER-FEP <PKG-USER-FEP>`
    * :ref:`USER-H5MD <PKG-USER-H5MD>`
+   * :ref:`USER-HDNNP <PKG-USER-HDNNP>`
    * :ref:`USER-INTEL <PKG-USER-INTEL>`
    * :ref:`USER-LB <PKG-USER-LB>`
    * :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>`
@@ -99,6 +100,7 @@ page gives those details.
    * :ref:`USER-QMMM <PKG-USER-QMMM>`
    * :ref:`USER-QTB <PKG-USER-QTB>`
    * :ref:`USER-QUIP <PKG-USER-QUIP>`
+   * :ref:`USER-RANN <PKG-USER-RANN>`
    * :ref:`USER-REACTION <PKG-USER-REACTION>`
    * :ref:`USER-REAXC <PKG-USER-REAXC>`
    * :ref:`USER-SCAFACOS <PKG-USER-SCAFACOS>`
@@ -133,8 +135,8 @@ particle models including ellipsoids, 2d lines, and 3d triangles.
 * `doc/PDF/pair_resquared_extra.pdf <PDF/pair_resquared_extra.pdf>`_
 * examples/ASPHERE
 * examples/ellipse
-* https://lammps.sandia.gov/movies.html#line
+* https://www.lammps.org/movies.html#line
-* https://lammps.sandia.gov/movies.html#tri
+* https://www.lammps.org/movies.html#tri
 
 ----------
 
@@ -330,7 +332,7 @@ This package has :ref:`specific installation instructions <gpu>` on the :doc:`Bu
 * :doc:`package gpu <package>`
 * :doc:`Commands <Commands_all>` pages (:doc:`pair <Commands_pair>`, :doc:`kspace <Commands_kspace>`)
   for styles followed by (g)
-* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
+* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
 
 ----------
 
@@ -356,11 +358,11 @@ potentials.
 * examples/granregion
 * examples/pour
 * bench/in.chute
-* https://lammps.sandia.gov/pictures.html#jamming
+* https://www.lammps.org/pictures.html#jamming
-* https://lammps.sandia.gov/movies.html#hopper
+* https://www.lammps.org/movies.html#hopper
-* https://lammps.sandia.gov/movies.html#dem
+* https://www.lammps.org/movies.html#dem
-* https://lammps.sandia.gov/movies.html#brazil
+* https://www.lammps.org/movies.html#brazil
-* https://lammps.sandia.gov/movies.html#granregion
+* https://www.lammps.org/movies.html#granregion
 
 ----------
 
@@ -447,7 +449,7 @@ time via the "-sf kk" or "-suffix kk" :doc:`command-line switches <Run_options>`
 :ref:`USER-INTEL <PKG-USER-INTEL>`, and :ref:`USER-OMP <PKG-USER-OMP>` packages, which
 have styles optimized for CPUs, KNLs, and GPUs.
 
-You must have a C++11 compatible compiler to use this package.
+You must have a C++14 compatible compiler to use this package.
 KOKKOS makes extensive use of advanced C++ features, which can
 expose compiler bugs, especially when compiling for maximum
 performance at high optimization levels. Please see the file
@@ -479,7 +481,7 @@ This package has :ref:`specific installation instructions <kokkos>` on the :doc:
 * Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,
   :doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`,
   :doc:`kspace <Commands_kspace>`) for styles followed by (k)
-* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
+* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
 
 ----------
 
@@ -603,7 +605,7 @@ bonds, for performing atomic swaps, and performing grand-canonical MC
 * :doc:`fix tfmc <fix_tfmc>`
 * :doc:`fix widom <fix_widom>`
 * :doc:`pair_style dsmc <pair_dsmc>`
-* https://lammps.sandia.gov/movies.html#gcmc
+* https://www.lammps.org/movies.html#gcmc
 
 ----------
 
@@ -660,8 +662,8 @@ listing, "ls src/MISC", to see the list of commands.
 * :doc:`fix viscosity <fix_viscosity>`
 * examples/KAPPA
 * examples/VISCOSITY
-* https://lammps.sandia.gov/pictures.html#ttm
+* https://www.lammps.org/pictures.html#ttm
-* https://lammps.sandia.gov/movies.html#evaporation
+* https://www.lammps.org/movies.html#evaporation
 
 ----------
 
@@ -816,7 +818,7 @@ This package has :ref:`specific installation instructions <opt>` on the :doc:`Bu
 * :doc:`OPT package <Speed_opt>`
 * :doc:`Section 2.6 -sf opt <Run_options>`
 * Search the :doc:`pair style <Commands_pair>` page for styles followed by (t)
-* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
+* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
 
 ----------
 
@@ -847,7 +849,7 @@ Foster (UTSA).
 * :doc:`compute damage/atom <compute_damage_atom>`
 * :doc:`compute plasticity/atom <compute_plasticity_atom>`
 * examples/peri
-* https://lammps.sandia.gov/movies.html#peri
+* https://www.lammps.org/movies.html#peri
 
 ----------
 
@@ -1008,8 +1010,8 @@ Also several computes which calculate properties of rigid bodies.
 * examples/ASPHERE
 * examples/rigid
 * bench/in.rhodo
-* https://lammps.sandia.gov/movies.html#box
+* https://www.lammps.org/movies.html#box
-* https://lammps.sandia.gov/movies.html#star
+* https://www.lammps.org/movies.html#star
 
 ----------
 
@@ -1110,9 +1112,9 @@ colloidal particles.
 * :doc:`fix wall/srd <fix_wall_srd>`
 * examples/srd
 * examples/ASPHERE
-* https://lammps.sandia.gov/movies.html#tri
+* https://www.lammps.org/movies.html#tri
-* https://lammps.sandia.gov/movies.html#line
+* https://www.lammps.org/movies.html#line
-* https://lammps.sandia.gov/movies.html#poly
+* https://www.lammps.org/movies.html#poly
 
 ----------
 
@@ -1204,7 +1206,7 @@ This package has :ref:`specific installation instructions <user-atc>` on the :do
 * src/USER-ATC/README
 * :doc:`fix atc <fix_atc>`
 * examples/USER/atc
-* https://lammps.sandia.gov/pictures.html#atc
+* https://www.lammps.org/pictures.html#atc
 
 ----------
 
@@ -1337,7 +1339,7 @@ acids.
 * :doc:`pair_style lj/sdk/\* <pair_sdk>`
 * :doc:`angle_style sdk <angle_sdk>`
 * examples/USER/cgsdk
-* https://lammps.sandia.gov/pictures.html#cg
+* https://www.lammps.org/pictures.html#cg
 
 ----------
 
@@ -1574,7 +1576,7 @@ tools/eff; see its README file.
 * examples/USER/eff
 * tools/eff/README
 * tools/eff
-* https://lammps.sandia.gov/movies.html#eff
+* https://www.lammps.org/movies.html#eff
 
 ----------
 
@@ -1639,6 +1641,39 @@ This package has :ref:`specific installation instructions <user-h5md>` on the :d
 
 ----------
 
+.. _PKG-USER-HDNNP:
+
+USER-HDNNP package
+------------------
+
+**Contents:**
+
+A :doc:`pair_style hdnnp <pair_hdnnp>` command which allows to use
+high-dimensional neural network potentials (HDNNPs), a form of machine learning
+potentials. HDNNPs must be carefully trained prior to their application in a
+molecular dynamics simulation.
+
+.. _n2p2: https://github.com/CompPhysVienna/n2p2
+
+To use this package you must have the `n2p2 <n2p2_>`_ library installed and
+compiled on your system.
+
+**Author:** Andreas Singraber
+
+**Install:**
+
+This package has :ref:`specific installation instructions <user-hdnnp>` on the :doc:`Build extras <Build_extras>` page.
+
+**Supporting info:**
+
+* src/USER-HDNNP: filenames -> commands
+* src/USER-HDNNP/README
+* lib/hdnnp/README
+* :doc:`pair_style hdnnp <pair_hdnnp>`
+* examples/USER/hdnnp
+
+----------
+
 .. _PKG-USER-INTEL:
 
 USER-INTEL package
@@ -1683,7 +1718,7 @@ This package has :ref:`specific installation instructions <user-intel>` on the :
 * Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,
   :doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`, :doc:`kspace <Commands_kspace>`) for styles followed by (i)
 * src/USER-INTEL/TEST
-* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
+* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
 
 ----------
 
@@ -1788,7 +1823,7 @@ Waltham, MA, USA)
 * :doc:`fix nve/manifold/rattle <fix_nve_manifold_rattle>`
 * :doc:`fix nvt/manifold/rattle <fix_nvt_manifold_rattle>`
 * examples/USER/manifold
-* https://lammps.sandia.gov/movies.html#manifold
+* https://www.lammps.org/movies.html#manifold
 
 ----------
 
@@ -1866,10 +1901,10 @@ algorithm.
 * :doc:`pair_style tdpd <pair_mesodpd>`
 * :doc:`fix mvv/dpd <fix_mvv_dpd>`
 * examples/USER/mesodpd
-* https://lammps.sandia.gov/movies.html#mesodpd
+* https://www.lammps.org/movies.html#mesodpd
 
 * examples/USER/meso
-* http://lammps.sandia.gov/movies.html#mesodpd
+* http://www.lammps.org/movies.html#mesodpd
 
 ----------
 
@@ -2085,7 +2120,7 @@ This package has :ref:`specific installation instructions <user-omp>` on the :do
 * Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,
   :doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`,
   :doc:`kspace <Commands_kspace>`) for styles followed by (o)
-* `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of web site
+* `Benchmarks page <https://www.lammps.org/bench.html>`_ of web site
 
 ----------
 
@@ -2243,6 +2278,31 @@ This package has :ref:`specific installation instructions <user-quip>` on the :d
 
 ----------
 
+.. _PKG-USER-RANN:
+
+USER-RANN package
+-----------------
+
+**Contents:**
+
+A pair style for using rapid atomistic neural network (RANN) potentials.
+These neural network potentials work by first generating a series of symmetry
+functions from the neighbor list and then using these values as the input layer
+of a neural network.
+
+**Authors:**
+
+This package was written by Christopher Barrett
+with contributions by Doyl Dickel, Mississippi State University.
+
+**Supporting info:**
+
+* src/USER-RANN: filenames -> commands
+* :doc:`pair_style rann <pair_rann>`
+* examples/USER/rann
+
+----------
+
 .. _PKG-USER-REACTION:
 
 USER-REACTION package
@@ -2268,8 +2328,8 @@ molecules, and chiral-sensitive reactions.
 * src/USER-REACTION/README
 * :doc:`fix bond/react <fix_bond_react>`
 * examples/USER/reaction
-* `2017 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug17/pdf/gissinger.pdf>`_
+* `2017 LAMMPS Workshop <https://www.lammps.org/workshops/Aug17/pdf/gissinger.pdf>`_
-* `2019 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug19/talk_gissinger.pdf>`_
+* `2019 LAMMPS Workshop <https://www.lammps.org/workshops/Aug19/talk_gissinger.pdf>`_
 * reacter.org
 
 ----------
@@ -2396,7 +2456,7 @@ This package has :ref:`specific installation instructions <user-smd>` on the :do
 * src/USER-SMD/README
 * doc/PDF/SMD_LAMMPS_userguide.pdf
 * examples/USER/smd
-* https://lammps.sandia.gov/movies.html#smd
+* https://www.lammps.org/movies.html#smd
 
 ----------
 
@@ -2453,7 +2513,7 @@ Dynamics, Ernst Mach Institute, Germany).
 * src/USER-SPH/README
 * doc/PDF/SPH_LAMMPS_userguide.pdf
 * examples/USER/sph
-* https://lammps.sandia.gov/movies.html#sph
+* https://www.lammps.org/movies.html#sph
 
 ----------
 

doc/src/Packages_standard.rst

@@ -39,13 +39,13 @@ package:
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`DIPOLE <PKG-DIPOLE>`       | point dipole particles               | :doc:`pair_style lj/.../dipole <pair_dipole>`      | dipole                                               | no      |
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
-| :ref:`GPU <PKG-GPU>`             | GPU-enabled styles                   | :doc:`Section gpu <Speed_gpu>`                     | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | int     |
+| :ref:`GPU <PKG-GPU>`             | GPU-enabled styles                   | :doc:`Section gpu <Speed_gpu>`                     | `Benchmarks <https://www.lammps.org/bench.html>`_    | int     |
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`GRANULAR <PKG-GRANULAR>`   | granular systems                     | :doc:`Howto granular <Howto_granular>`             | pour                                                 | no      |
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`KIM <PKG-KIM>`             | OpenKIM wrapper                      | :doc:`pair_style kim <pair_kim>`                   | kim                                                  | ext     |
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
-| :ref:`KOKKOS <PKG-KOKKOS>`       | Kokkos-enabled styles                | :doc:`Speed kokkos <Speed_kokkos>`                 | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no      |
+| :ref:`KOKKOS <PKG-KOKKOS>`       | Kokkos-enabled styles                | :doc:`Speed kokkos <Speed_kokkos>`                 | `Benchmarks <https://www.lammps.org/bench.html>`_    | no      |
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`KSPACE <PKG-KSPACE>`       | long-range Coulombic solvers         | :doc:`kspace_style <kspace_style>`                 | peptide                                              | no      |
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
@@ -67,7 +67,7 @@ package:
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`MSCG <PKG-MSCG>`           | multi-scale coarse-graining wrapper  | :doc:`fix mscg <fix_mscg>`                         | mscg                                                 | ext     |
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
-| :ref:`OPT <PKG-OPT>`             | optimized pair styles                | :doc:`Speed opt <Speed_opt>`                       | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no      |
+| :ref:`OPT <PKG-OPT>`             | optimized pair styles                | :doc:`Speed opt <Speed_opt>`                       | `Benchmarks <https://www.lammps.org/bench.html>`_    | no      |
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`PERI <PKG-PERI>`           | Peridynamics models                  | :doc:`pair_style peri <pair_peri>`                 | peri                                                 | no      |
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+

doc/src/Packages_user.rst

@@ -59,7 +59,9 @@ package:
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-H5MD <PKG-USER-H5MD>`               | dump output via HDF5                                            | :doc:`dump h5md <dump_h5md>`                                                  | n/a                                                  | ext     |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
-| :ref:`USER-INTEL <PKG-USER-INTEL>`             | optimized Intel CPU and KNL styles                              | :doc:`Speed intel <Speed_intel>`                                              | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no      |
+| :ref:`USER-HDNNP <PKG-USER-HDNNP>`             | High-dimensional neural network potentials                      | :doc:`pair_style hdnnp <pair_hdnnp>`                                          | USER/hdnnp                                           | ext     |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
+| :ref:`USER-INTEL <PKG-USER-INTEL>`             | optimized Intel CPU and KNL styles                              | :doc:`Speed intel <Speed_intel>`                                              | `Benchmarks <https://www.lammps.org/bench.html>`_    | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-LB <PKG-USER-LB>`                   | Lattice Boltzmann fluid                                         | :doc:`fix lb/fluid <fix_lb_fluid>`                                            | USER/lb                                              | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
@@ -83,7 +85,7 @@ package:
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-NETCDF <PKG-USER-NETCDF>`           | dump output via NetCDF                                          | :doc:`dump netcdf <dump_netcdf>`                                              | n/a                                                  | ext     |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
-| :ref:`USER-OMP <PKG-USER-OMP>`                 | OpenMP-enabled styles                                           | :doc:`Speed omp <Speed_omp>`                                                  | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no      |
+| :ref:`USER-OMP <PKG-USER-OMP>`                 | OpenMP-enabled styles                                           | :doc:`Speed omp <Speed_omp>`                                                  | `Benchmarks <https://www.lammps.org/bench.html>`_    | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-PACE <PKG-USER-PACE>`               | Fast implementation of Atomic Cluster Expansion (ACE) potential | :doc:`pair pace <pair_pace>`                                                  | USER/pace                                            | ext     |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
@@ -99,6 +101,8 @@ package:
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-QUIP <PKG-USER-QUIP>`               | QUIP/libatoms interface                                         | :doc:`pair_style quip <pair_quip>`                                            | USER/quip                                            | ext     |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
+| :ref:`USER-RANN <PKG-USER-RANN>`               | rapid atomistic neural network (RANN) potentials                | :doc:`pair rann <pair_rann>`                                                  | USER/rann                                            | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-REACTION <PKG-USER-REACTION>`       | chemical reactions in classical MD                              | :doc:`fix bond/react <fix_bond_react>`                                        | USER/reaction                                        | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-REAXC <PKG-USER-REAXC>`             | ReaxFF potential (C/C++)                                        | :doc:`pair_style reaxc <pair_reaxc>`                                          | reax                                                 | no      |

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/Speed.rst

@@ -12,7 +12,7 @@ accelerator packages provided with LAMMPS that contain code optimized
 for certain kinds of hardware, including multi-core CPUs, GPUs, and
 Intel Xeon Phi co-processors.
 
-The `Benchmark page <https://lammps.sandia.gov/bench.html>`_ of the LAMMPS
+The `Benchmark page <https://www.lammps.org/bench.html>`_ of the LAMMPS
 web site gives performance results for the various accelerator
 packages discussed on the :doc:`Speed packages <Speed_packages>` doc
 page, for several of the standard LAMMPS benchmark problems, as a

doc/src/Speed_bench.rst

@@ -1,7 +1,7 @@
 Benchmarks
 ==========
 
-Current LAMMPS performance is discussed on the `Benchmarks page <https://lammps.sandia.gov/bench.html>`_ of the `LAMMPS website <lws_>`_
+Current LAMMPS performance is discussed on the `Benchmarks page <https://www.lammps.org/bench.html>`_ of the `LAMMPS website <lws_>`_
 where timings and parallel efficiency are listed.  The page has
 several sections, which are briefly described below:
 
@@ -43,11 +43,11 @@ to build LAMMPS and run on that kind of hardware.
 
 The bench/POTENTIALS directory has input files which correspond to the
 table of results on the
-`Potentials <https://lammps.sandia.gov/bench.html#potentials>`_ section of
+`Potentials <https://www.lammps.org/bench.html#potentials>`_ section of
 the Benchmarks web page.  So you can also run those test problems on
 your machine.
 
-The `billion-atom <https://lammps.sandia.gov/bench.html#billion>`_ section
+The `billion-atom <https://www.lammps.org/bench.html#billion>`_ section
 of the Benchmarks web page has performance data for very large
 benchmark runs of simple Lennard-Jones (LJ) models, which use the
 bench/in.lj input script.
@@ -73,4 +73,4 @@ estimate parallel performance for multi-node runs using the same logic
 as for all-MPI mode, except that now you will typically need many more
 atoms/node to achieve good scalability.
 
-.. _lws: https://lammps.sandia.gov
+.. _lws: https://www.lammps.org

doc/src/Speed_gpu.rst

@@ -152,7 +152,7 @@ in OpenCL mode on CPUs (which uses vectorization and multithreading) is
 usually resulting in inferior performance compared to using LAMMPS' native
 threading and vectorization support in the USER-OMP and USER-INTEL packages.
 
-See the `Benchmark page <https://lammps.sandia.gov/bench.html>`_ of the
+See the `Benchmark page <https://www.lammps.org/bench.html>`_ of the
 LAMMPS web site for performance of the GPU package on various
 hardware, including the Titan HPC platform at ORNL.
 

doc/src/Speed_kokkos.rst

@@ -406,7 +406,7 @@ Generally speaking, the following rules of thumb apply:
   package also can increase the vector length of vector instructions
   by switching to single or mixed precision mode.
 
-See the `Benchmark page <https://lammps.sandia.gov/bench.html>`_ of the
+See the `Benchmark page <https://www.lammps.org/bench.html>`_ of the
 LAMMPS web site for performance of the KOKKOS package on different
 hardware.
 

doc/src/Speed_packages.rst

@@ -145,7 +145,7 @@ sub-directories with Make.py commands and input scripts for using all
 the accelerator packages on various machines.  See the README files in
 those directories.
 
-As mentioned above, the `Benchmark page <https://lammps.sandia.gov/bench.html>`_ of the LAMMPS web site gives
+As mentioned above, the `Benchmark page <https://www.lammps.org/bench.html>`_ of the LAMMPS web site gives
 performance results for the various accelerator packages for several
 of the standard LAMMPS benchmark problems, as a function of problem
 size and number of compute nodes, on different hardware platforms.

doc/src/Tools.rst

@@ -6,15 +6,15 @@ molecular dynamics computations.  Additional pre- and post-processing
 steps are often necessary to setup and analyze a simulation.  A list
 of such tools can be found on the `LAMMPS webpage <lws_>`_ at these links:
 
-* `Pre/Post processing <https://lammps.sandia.gov/prepost.html>`_
+* `Pre/Post processing <https://www.lammps.org/prepost.html>`_
-* `Offsite LAMMPS packages & tools <https://lammps.sandia.gov/offsite.html>`_
+* `Offsite LAMMPS packages & tools <https://www.lammps.org/offsite.html>`_
 * `Pizza.py toolkit <pizza_>`_
 
 The last link for `Pizza.py <pizza_>`_ is a Python-based tool developed at
 Sandia which provides tools for doing setup, analysis, plotting, and
 visualization for LAMMPS simulations.
 
-.. _lws: https://lammps.sandia.gov
+.. _lws: https://www.lammps.org
 .. _pizza: https://pizza.sandia.gov
 .. _python: https://www.python.org
 

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/atom_modify.rst

@@ -80,7 +80,7 @@ LAMMPS commands require a map, even for atomic systems, and will
 generate an error if one does not exist.  The *map* keyword thus
 allows you to force the creation of a map.  The *yes* value will
 create either an *array* or *hash* style map, as explained in the next
-paragraph.  The *array* and *hash* values create an atom-style or
+paragraph.  The *array* and *hash* values create an array-style or
 hash-style map respectively.
 
 For an *array*\ -style map, each processor stores a lookup table of

doc/src/fix.rst

@@ -244,6 +244,7 @@ accelerated styles exist.
 * :doc:`lb/viscous <fix_lb_viscous>` -
 * :doc:`lineforce <fix_lineforce>` - constrain atoms to move in a line
 * :doc:`manifoldforce <fix_manifoldforce>` - restrain atoms to a manifold during minimization
+* :doc:`mdi/engine <fix_mdi_engine>` - connect LAMMPS to external programs via the MolSSI Driver Interface (MDI)
 * :doc:`meso/move <fix_meso_move>` - move mesoscopic SPH/SDPD particles in a prescribed fashion
 * :doc:`momentum <fix_momentum>` - zero the linear and/or angular momentum of a group of atoms
 * :doc:`momentum/chunk <fix_momentum>` - zero the linear and/or angular momentum of a chunk of atoms

doc/src/fix_bond_react.rst

@@ -17,7 +17,7 @@ Syntax
 * ID, group-ID are documented in :doc:`fix <fix>` command.
 * bond/react = style name of this fix command
 * the common keyword/values may be appended directly after 'bond/react'
-* this applies to all reaction specifications (below)
+* common keywords apply to all reaction specifications
 * common_keyword = *stabilization* or *reset_mol_ids*
 
   .. parsed-literal::
@@ -525,12 +525,12 @@ reaction can be imposed as follows:
 
 .. code-block:: LAMMPS
 
-compute 1 all pe/atom # in LAMMPS input script
+   compute 1 all pe/atom # in LAMMPS input script
-variable my_pe atom c_1 # in LAMMPS input script
+   variable my_pe atom c_1 # in LAMMPS input script
 
 .. code-block:: LAMMPS
 
-custom "rxnsum(v_my_pe) > 100" # in Constraints section of map file
+   custom "rxnsum(v_my_pe) > 100" # in Constraints section of map file
 
 The above example prevents the reaction from occurring unless the
 total potential energy of the reaction site is above 100. The variable

doc/src/fix_grem.rst

@@ -92,6 +92,11 @@ The :doc:`thermo_modify <thermo_modify>` *press* option is supported
 by this fix to add the rescaled kinetic pressure as part of
 :doc:`thermodynamic output <thermo_style>`.
 
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the effective
+temperature :math:`T_{eff}`.  The scalar value calculated by this
+fix is "intensive".
+
 Restrictions
 """"""""""""
 

doc/src/fix_mdi_engine.rst

@@ -1,4 +1,4 @@
-.. index:: fix move
+.. index:: fix mdi/engine
 
 fix mdi/engine command
 ======================

doc/src/fix_wall_gran_region.rst

@@ -65,7 +65,7 @@ non-granular particles and simpler wall geometries, respectively.
 
 Here are snapshots of example models using this command.  Corresponding
 input scripts can be found in examples/granregion.  Movies of these
-simulations are `here on the Movies page <https://lammps.sandia.gov/movies.html#granregion>`_
+simulations are `here on the Movies page <https://www.lammps.org/movies.html#granregion>`_
 of the LAMMPS web site.
 
 .. |wallgran1| image:: img/gran_funnel.png

doc/src/kspace_style.rst

@@ -278,7 +278,7 @@ pressure simulation with MSM will cause the code to run slower.
 ----------
 
 The *scafacos* style is a wrapper on the `ScaFaCoS Coulomb solver library <http://www.scafacos.de>`_ which provides a variety of solver
-methods which can be used with LAMMPS.  The paper by :ref:`(Who) <Who2012>`
+methods which can be used with LAMMPS.  The paper by :ref:`(Sutman) <Sutmann2014>`
 gives an overview of ScaFaCoS.
 
 ScaFaCoS was developed by a consortium of German research facilities
@@ -550,7 +550,7 @@ Illinois at Urbana-Champaign, (2006).
 
 **(Cerda)** Cerda, Ballenegger, Lenz, Holm, J Chem Phys 129, 234104 (2008)
 
-.. _Who2012:
+.. _Sutmann2014:
 
-**(Who)** Who, Author2, Author3, J of Long Range Solvers, 35, 164-177
+**(Sutmann)** G. Sutmann. ScaFaCoS - a Scalable library of Fast Coulomb Solvers for particle Systems.
-(2012).
+  In Bajaj, Zavattieri, Koslowski, Siegmund, Proceedings of the Society of Engineering Science 51st Annual Technical Meeting. 2014.

doc/src/mdi_engine.rst

@@ -1,4 +1,4 @@
-.. index:: mdi_engine
+.. index:: mdi/engine
 
 mdi_engine command
 ==================

doc/src/pair_hdnnp.rst

@@ -0,0 +1,230 @@
+.. index:: pair_style hdnnp
+
+pair_style hdnnp command
+========================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style hdnnp cutoff keyword value ...
+
+* cutoff = short-range cutoff of HDNNP (maximum symmetry function cutoff radius)
+* zero or more keyword/value pairs may be appended
+* keyword = *dir* or *showew* or *showewsum* or *maxew* or *resetew* or *cflength* or *cfenergy*
+* value depends on the preceding keyword:
+
+.. parsed-literal::
+
+   *dir* value = directory
+       directory = Path to HDNNP configuration files
+   *showew* value = *yes* or *no*
+   *showewsum* value = summary
+             summary = Write EW summary every this many timesteps (*0* turns summary off)
+   *maxew* value = threshold
+         threshold = Maximum number of EWs allowed
+   *resetew* value = *yes* or *no*
+   *cflength* value = length
+            length = Length unit conversion factor
+   *cfenergy* value = energy
+            energy = Energy unit conversion factor
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style hdnnp 6.35 showew yes showewsum 100 maxew 1000 resetew yes cflength 1.8897261328 cfenergy 0.0367493254
+   pair_coeff * * H O
+
+   pair_style hdnnp 6.01 dir "./" showewsum 10000
+   pair_coeff * * S Cu NULL Cu
+
+Description
+"""""""""""
+
+This pair style adds an interaction based on the high-dimensional neural network
+potential (HDNNP) method as presented in :ref:`(Behler and Parrinello 2007)
+<Behler_Parrinello_2007>`. HDNNPs are machine learning potentials which require
+careful training of neural networks prior to application in MD simulations. The
+pair style uses an interface to the *n2p2* library :ref:`(Singraber, Behler and
+Dellago 2019) <Singraber_Behler_Dellago_2019>` which is available on Github
+`here <https://github.com/CompPhysVienna/n2p2>`__. Please see the *n2p2*
+`documentation <https://compphysvienna.github.io/n2p2/>`__ for further details.
+*n2p2* (and hence this pair style) is compatible with neural network potentials
+trained with its own tools :ref:`(Singraber et al 2019) <Singraber_et_al_2019>`
+and with `RuNNer <https://www.uni-goettingen.de/de/560580.html>`__.
+
+Only a single *pair_coeff* command with two asterisk wild-cards is used with this
+pair style. Its additional arguments define the mapping of LAMMPS atom types to
+n2p2 elements.
+
+.. code-block:: LAMMPS
+
+   pair_coeff * * H O
+
+In the above example LAMMPS types 1 and 2 are mapped to the elements "H" and "O"
+in n2p2, respectively. Multiple types may map to the same element, or some types
+may not be mapped at all. For example, if the LAMMPS simulation has four atom
+types, the command
+
+.. code-block:: LAMMPS
+
+   pair_coeff * * H H O NULL
+
+maps atom types 1 and 2 to the element "H", type 3 to "O" and type 4 is not mapped
+(indicated by NULL).  Atoms mapped to NULL are ignored by the HDNNP calculation,
+i.e. they do not contribute in any way to the evaluation of HDNNP energies and forces.
+This may be useful in a setup with :doc:`hybrid pair styles <pair_hybrid>`.
+
+----
+
+The mandatory pair style argument *cutoff* must match the short-range cutoff radius
+of the HDNNP.  This corresponds to the maximum cutoff radius of all symmetry
+functions (the atomic environment descriptors of HDNNPs) used.
+
+.. note::
+
+   The cutoff must be given in LAMMPS length units, even if the neural network
+   potential has been trained using a different unit system (see remarks about the
+   *cflength* and *cfenergy* keywords below for details).
+
+The numeric value may be slightly larger than the actual maximum symmetry
+function cutoff radius (to account for rounding errors when converting units),
+but must not be smaller.
+
+Use the *dir* keyword to specify the directory containing the HDNNP configuration
+files. The directory must contain ``input.nn`` with neural network and symmetry
+function setup, ``scaling.data`` with symmetry function scaling data and
+``weights.???.data`` with weight parameters for each element.
+
+The keyword *showew* can be used to turn on/off the display of extrapolation
+warnings (EWs) which are issued whenever a symmetry function value is out of
+bounds defined by minimum/maximum values in ``scaling.data``. An extrapolation
+warning may look like this:
+
+.. code-block:: LAMMPS
+
+   ### NNP EXTRAPOLATION WARNING ### STRUCTURE:      0 ATOM:       119 ELEMENT: Cu SYMFUNC:   32 TYPE:  3 VALUE:  2.166E-02 MIN:  2.003E-05 MAX:  1.756E-02
+
+stating that the value 2.166E-02 of symmetry function 32 of type 3 (Narrow Angular symmetry function), element Cu (see the log file for a symmetry function listing) was out
+of bounds (maximum in ``scaling.data`` is 1.756E-02) for atom 119. Here, the
+atom index refers to the LAMMPS tag (global index) and the structure index is
+used to print out the MPI rank the atom belongs to.
+
+.. note::
+
+   The *showew* keyword should only be set to *yes* for debugging purposes.
+   Extrapolation warnings may add lots of overhead as they are communicated each
+   timestep. Also, if the simulation is run in a region where the HDNNP was not
+   correctly trained, lots of extrapolation warnings may clog log files and the
+   console. In a production run use *showewsum* instead.
+
+The keyword *showewsum* can be used to get an overview of extrapolation warnings
+occurring during an MD simulation. The argument specifies the interval at which
+extrapolation warning summaries are displayed and logged. An EW summary may look
+like this:
+
+.. code-block:: LAMMPS
+
+   ### NNP EW SUMMARY ### TS:        100 EW         11 EWPERSTEP  1.100E-01
+
+Here, at timestep 100 the occurrence of 11 extrapolation warnings since the last
+summary is reported, which corresponds to an EW rate of 0.11 per timestep.
+Setting *showewsum* to 0 deactivates the EW summaries.
+
+A maximum number of allowed extrapolation warnings can be specified with the
+*maxew* keyword. If the number of EWs exceeds the *maxew* argument the
+simulation is stopped. Note however that this is merely an approximate threshold
+since the check is only performed at the end of each timestep and each MPI
+process counts individually to minimize communication overhead.
+
+The keyword *resetew* alters the behavior of the above mentioned *maxew*
+threshold. If *resetew* is set to *yes* the threshold is applied on a
+per-timestep basis and the internal EW counters are reset at the beginning of
+each timestep. With *resetew* set to *no* the counters accumulate EWs along the
+whole trajectory.
+
+If the training of a neural network potential has been performed with different
+physical units for length and energy than those set in LAMMPS, it is still
+possible to use the potential when the unit conversion factors are provided via
+the *cflength* and *cfenergy* keywords. If for example, the HDNNP was
+parameterized with Bohr and Hartree training data and symmetry function
+parameters (i.e. distances and energies in "input.nn" are given in Bohr and
+Hartree) but LAMMPS is set to use *metal* units (Angstrom and eV) the correct
+conversion factors are:
+
+.. code-block:: LAMMPS
+
+   cflength 1.8897261328
+
+   cfenergy 0.0367493254
+
+Thus, arguments of *cflength* and *cfenergy* are the multiplicative factors
+required to convert lengths and energies given in LAMMPS units to respective
+quantities in native HDNNP units (1 Angstrom = 1.8897261328 Bohr, 1 eV =
+0.0367493254 Hartree).
+
+----
+
+Mixing, shift, table, tail correction, restart, rRESPA info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+This style does not support mixing. The :doc:`pair_coeff <pair_coeff>` command
+should only be invoked with asterisk wild cards (see above).
+
+This style does not support the :doc:`pair_modify <pair_modify>`
+shift, table, and tail options.
+
+This style does not write information to :doc:`binary restart files <restart>`.
+Thus, you need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+
+This style can only be used via the *pair* keyword of the :doc:`run_style respa
+<run_style>` command.  It does not support the *inner*\ , *middle*\ , *outer*
+keywords.
+
+Restrictions
+""""""""""""
+
+This pair style is part of the USER-HDNNP package.  It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package <Build_package>` doc
+page for more info.
+
+Please report bugs and feature requests to the `n2p2 GitHub issue page
+<https://github.com/CompPhysVienna/n2p2/issues>`__.
+
+Related commands
+^^^^^^^^^^^^^^^^
+
+:doc:`pair_coeff <pair_coeff>`, :doc:`pair_hybrid <pair_hybrid>`, :doc:`units <units>`
+
+Default
+^^^^^^^
+
+The default options are *dir* = "hdnnp/", *showew* = yes, *showewsum* = 0, *maxew*
+= 0, *resetew* = no, *cflength* = 1.0, *cfenergy* = 1.0.
+
+----
+
+.. _Behler_Parrinello_2007:
+
+**(Behler and Parrinello 2007)** `Behler, J.; Parrinello, M. Generalized
+Neural-Network Representation of High-Dimensional Potential-Energy Surfaces.
+Phys. Rev. Lett.  2007, 98 (14), 146401.
+<https://doi.org/10.1103/PhysRevLett.98.146401>`__
+
+.. _Singraber_Behler_Dellago_2019:
+
+**(Singraber, Behler and Dellago 2019)** `Singraber, A.; Behler, J.; Dellago, C.
+Library-Based LAMMPS Implementation of High-Dimensional Neural Network
+Potentials. J. Chem.  Theory Comput. 2019, 15 (3), 1827-1840
+<https://doi.org/10.1021/acs.jctc.8b00770>`__
+
+.. _Singraber_et_al_2019:
+
+**(Singraber et al 2019)** `Singraber, A.; Morawietz, T.; Behler, J.; Dellago,
+C. Parallel Multistream Training of High-Dimensional Neural Network Potentials.
+J. Chem. Theory Comput.  2019, 15 (5), 3075-3092.
+<https://doi.org/10.1021/acs.jctc.8b01092>`__

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

doc/src/pair_rann.rst

@@ -0,0 +1,412 @@
+.. index:: pair_style rann
+
+pair_style rann command
+=======================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style rann
+   pair_coeff file Type1_element Type2_element Type3_element...
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+    pair_style rann
+    pair_coeff ** Mg.rann Mg
+    pair_coeff ** MgAlalloy.rann Mg Mg Al Mg
+
+Description
+"""""""""""
+
+Pair style *rann* computes pairwise interactions for a variety of
+materials using rapid atomistic neural network (RANN) potentials
+(:ref:`Dickel <Dickel>` , :ref:`Nitol <Nitol>`).  Neural network
+potentials work by first generating a series of symmetry functions
+i.e. structural fingerprints from the neighbor list and then using these
+values as the input layer of a neural network.  There is a single output
+neuron in the final layer which is the energy.  Atomic forces are found
+by analytical derivatives computed via back-propagation.  For alloy
+systems, each element has a unique network.
+
+Potential file syntax
+"""""""""""""""""""""
+
+The RANN potential is defined by a single text file which contains all
+the fitting parameters for the alloy system.  The potential file also
+defines the active fingerprints, network architecture, activation
+functions, etc.  The potential file is divided into several sections
+which are identified by one of the following keywords:
+
+* atomtypes
+* mass
+* fingerprintsperelement
+* fingerprints
+* fingerprintconstants
+* screening (optional)
+* networklayers
+* layersize
+* weight
+* bias
+* activationfunctions
+* calibrationparameters (ignored)
+
+The '#' character is treated as a comment marker, similar to LAMMPS
+input scripts.  Sections are not required to follow a rigid ordering,
+but do require previous definition of prerequisite information.  E.g.,
+fingerprintconstants for a particular fingerprint must follow the
+fingerprints definition; layersize for a particular layer must follow
+the declaration of network layers.
+
+*atomtypes* are defined as follows using element keywords separated by spaces.
+
+.. code-block::
+
+    atomtypes:
+    Fe Mg Al etc.
+
+*mass* must be specified for each element keyword as follows:
+
+.. code-block::
+
+    mass:Mg:
+    24.305
+    mass:Fe:
+    55.847
+    mass:Al:
+    26.982
+
+*fingerprintsperelement* specifies how many fingerprints are active for
+computing the energy of a given atom.  This number must be specified for
+each element keyword.  Active elements for each fingerprint depend upon
+the type of the central atom and the neighboring atoms.  Pairwise
+fingerprints may be defined for a Mg atom based exclusively on its Al
+neighbors, for example.  Bond fingerprints may use two neighbor lists of
+different element types.  In computing fingerprintsperelement from all
+defined fingerprints, only the fingerprints defined for atoms of a
+particular element should be considered, regardless of the elements used
+in its neighbor list.  In the following code, for example, some
+fingerprints may compute pairwise fingerprints summing contributions
+about Fe atoms based on a neighbor list of exclusively Al atoms, but if
+there are no fingerprints summing contributions of all neighbors about a
+central Al atom, then fingerprintsperelement of Al is zero:
+
+.. code-block::
+
+    fingerprintsperelement:Mg:
+    5
+    fingerprintsperelement:Fe:
+    2
+    fingerprintsperelement:Al:
+    0
+
+*fingerprints* specifies the active fingerprints for a certain element
+combination.  Pair fingerprints are specified for two elements, while
+bond fingerprints are specified for three elements.  Only one
+fingerprints header should be used for an individual combination of
+elements.  The ordering of the fingerprints in the network input layer
+is determined by the order of element combinations specified by
+subsequent *fingerprints* lines, and the order of the fingerprints
+defined for each element combination.  Multiple fingerprints of the same
+style or different ones may be specified.  If the same style and element
+combination is used for multiple fingerprints, they should have
+different id numbers.  The first element specifies the atoms for which
+this fingerprint is computed while the other(s) specify which atoms to
+use in the neighbor lists for the computation.  Switching the second and
+third element type in bond fingerprints has no effect on the
+computation:
+
+.. code-block::
+
+    fingerprints:Mg_Mg:
+    radial_0 radialscreened_0 radial_1
+    fingerprints:Mg_Al_Fe:
+    bond_0 bondspin_0
+    fingerprints:Mg_Al:
+    radial_0 radialscreened_0
+
+The following fingerprint styles are currently defined.  See the
+:ref:`formulation section <fingerprints>` below for their definitions:
+
+* radial
+* radialscreened
+* radialspin
+* radialscreenedspin
+* bond
+* bondscreened
+* bondspin
+* bondscreenedspin
+
+*fingerprintconstants*  specifies the meta-parameters for a defined fingerprint.  For all radial styles, re, rc,
+alpha, dr, o, and n must be specified.  re should usually be the stable interatomic distance, rc is the cutoff
+radius, dr is the cutoff smoothing distance, o is the lowest radial power term (which may be negative), and n
+is the highest power term.  The total length of the fingerprint vector is (n-o+1).  alpha is a list of decay parameters
+used for exponential decay of radial contributions.  It may be set proportionally to the bulk modulus similarly
+to MEAM potentials, but other values may provided better fitting in special cases.  Bond style fingerprints require
+specification of re, rc, alphak, dr, k, and m.  Here m is the power of the bond cosines and k is the number of
+decay parameters.  Cosine powers go from 0 to m-1 and are each computed for all values of alphak.  Thus the total
+length of the fingerprint vector is m*k.
+
+.. code-block::
+
+   fingerprintconstants:Mg_Mg:radialscreened_0:re:
+   3.193592
+   fingerprintconstants:Mg_Mg:radialscreened_0:rc:
+   6.000000
+   fingerprintconstants:Mg_Mg:radialscreened_0:alpha:
+   5.520000 5.520000 5.520000 5.520000 5.520000
+   fingerprintconstants:Mg_Mg:radialscreened_0:dr:
+   2.806408
+   fingerprintconstants:Mg_Mg:radialscreened_0:o:
+   -1
+   fingerprintconstants:Mg_Mg:radialscreened_0:n:
+   3
+
+*screening* specifies the Cmax and Cmin values used in the screening
+fingerprints. Contributions form neighbors to the fingerprint are
+omitted if they are blocked by a closer neighbor, and reduced if they
+are partially blocked.  Larger values of Cmin correspond to neighbors
+being blocked more easily.  Cmax cannot be greater than 3, and Cmin
+cannot be greater than Cmax or less than zero.  Screening may be omitted
+in which case the default values Cmax = 2.8, Cmin = 0.8 are used.  Since
+screening is a bond computation, it is specified separately for each
+combination of three elements in which the latter two may be
+interchanged with no effect.
+
+.. code-block::
+
+    screening:Mg_Mg_Mg:Cmax:
+    2.700000
+    screening:Mg_Mg_Mg:Cmin:
+    0.400000
+
+*networklayers* species the size of the neural network for each atom.
+It counts both the input and output layer and so is 2 + \<hidden layers\>.
+
+.. code-block::
+
+   networklayers:Mg:
+   3
+
+*layersize* specifies the length of each layer, including the input
+layer and output layer.  The input layer is layer 0.  The size of the
+input layer size must match the summed length of all the fingerprints
+for that element, and the output layer size must be 1:
+
+.. code-block::
+
+    layersize:Mg:0:
+    14
+    layersize:Mg:1:
+    20
+    layersize:Mg:2:
+    1
+
+
+*weight* specifies the weight for a given element and layer.  Weight
+cannot be specified for the output layer.  The weight of layer i is a
+*m* x *n* matrix where *m* is the layer size of *i* and *n* is the layer size of
+*i*\ +1:
+
+.. code-block::
+
+   weight:Mg:0:
+   w11 w12 w13 ...
+   w21 w22 w23 ...
+   ...
+
+*bias* specifies the bias for a given element and layer.  Bias cannot be
+specified for the output layer.  The bias of layer i is a nx1 vector
+where n is the layer size of i+1:
+
+.. code-block::
+
+   bias:Mg:0:
+   b1
+   b2
+   b3
+   ...
+
+*activationfunctions* specifies the activation function for a given
+element and layer.  Activation functions cannot be specified for the
+output layer:
+
+.. code-block::
+
+    activationfunctions:Mg:0:
+    sigI
+    activationfunctions:Mg:1:
+    linear
+
+The following activation styles are currently specified.  See the
+:ref:`formulation section <activations>` below for their definitions.
+
+* sigI
+
+* linear
+
+*calibrationparameters* specifies a number of parameters used to calibrate the potential. These are ignored
+by LAMMPS.
+
+Formulation
+"""""""""""
+
+In the RANN formulation, the total energy of a system of atoms
+is given by:
+
+.. math::
+
+    E = \sum_{\alpha} E^{\alpha}\\\\
+    E^{\alpha} = {}^{N}\!A^{\alpha}\\\\
+    {}^{n+1}\!A_i^{\alpha} = {}^{n}\!F\left({}^{n}\!W_{ij}{\;}^{n}\!A_j^{\alpha}+{}^{n}\!B_i\right)\\\\
+    {}^{0}\!A_i^{\alpha} = \left[\begin{array}{c} {}^1\!S\!f^\alpha\\ {}^2\!S\!f^\alpha \\...\\\end{array}\right]
+
+Here :math:`E^\alpha` is the energy of atom :math:`\alpha`,
+:math:`{}^n\!F()`, :math:`{}^n\!W_{ij}` and :math:`{}^n\!B_i` are the
+activation function, weight matrix and bias vector of the n-th layer
+respectively.  The inputs to the first layer are a collection of
+structural fingerprints which are collected and reshaped into a single
+long vector.  The individual fingerprints may be defined in any order
+and have various shapes and sizes.  Multiple fingerprints of the same
+type and varying parameters may also be defined in the input layer.
+
+Eight types of structural fingerprints are currently defined.  In the
+following, :math:`\beta` and :math:`\gamma` span the full neighbor list
+of atom :math:`\alpha`.  :math:`\delta_i` are decay meta-parameters, and
+:math:`r_e` is a meta-parameter roughly proportional to the first
+neighbor distance.  :math:`r_c` and :math:`dr` are the neighbor cutoff
+distance and cutoff smoothing distance respectively.
+:math:`S^{\alpha\beta}` is the MEAM screening function :ref:`(Baskes)
+<Baskes97>`, :math:`s_i^\alpha` and :math:`s_i^\beta` are the atom spin
+vectors :ref:`(Tranchida) <Tranchida7>`.  :math:`r^{\alpha\beta}` is the
+distance from atom :math:`\alpha` to atom :math:`\beta`, and
+:math:`\theta^{\alpha\beta\gamma}` is the bond angle:
+
+.. math ::
+
+    cos\left(\theta^{\alpha\beta\gamma}\right)=\frac{\mathbf{r}^{\alpha\beta} \cdot \mathbf{r}^{\alpha\gamma}}{r^{\alpha\beta}r^{\alpha\gamma}}
+
+:math:`S^{\alpha\beta}` is defined as :ref:`(Baskes) <Baskes97>`:
+
+.. math::
+
+    X^{\gamma\beta} = \left(\frac{r^{\gamma\beta}}{r^{\alpha\beta}}\right)^2\\
+    \\
+    X^{\alpha\gamma} = \left(\frac{r^{\alpha\gamma}}{r^{\alpha\beta}}\right)^2\\
+    \\
+    C = \frac{2\left(X^{\alpha\gamma}+X^{\gamma\beta}\right)-\left(X^{\alpha\gamma}-X^{\gamma\beta}\right)^2-1}{1-\left(X^{\alpha\gamma}-X^{\gamma\beta}\right)^2}\\
+    \\
+    f_c(x) = \left[\begin{array}{l}  1 \; \: x \geq 1\\ \left(1-\left(1-x\right)^4\right)^2 \; \: 0<x<1\\0\; \; x\leq0\end{array}\right.\\
+    \\
+    S^{\alpha\beta\gamma} = f_c\left(\frac{C-C_{min}}{C_{max}-C_{min}}\right)\\
+    \\
+    S^{\alpha\beta} = \prod_\gamma S^{\alpha\beta\gamma}\\
+
+
+The structural fingerprints are computed as follows:
+
+.. _fingerprints:
+
+* **radial**
+
+.. math::
+
+    {}^r\!S\!f_i^\alpha = \sum_{\beta} \left(\frac{r^{\alpha\beta}}{r_e}\right)^ie^{-\delta_i \frac{r^{\alpha\beta}}{r_e}}f_c\left(\frac{r_c-r^{\alpha\beta}}{dr}\right)
+
+* **bond**
+
+.. math::
+
+    {}^b\!S\!f_{ij}^\alpha = \sum_{\beta}\sum_{\gamma} \left(cos(\theta_{\alpha\beta\gamma})\right)^ie^{-\delta_j \frac{r^{\alpha\beta}}{r_e}}e^{-\delta_j \frac{r^{\alpha\gamma}}{r_e}}f_c\left(\frac{r_c-r^{\alpha\beta}}{dr}\right)f_c\left(\frac{r_c-r^{\alpha\gamma}}{dr}\right)
+
+* **radialscreened**
+
+.. math::
+
+    {}^{rsc}\!S\!f_i^\alpha = \sum_{\beta} \left(\frac{r^{\alpha\beta}}{r_e}\right)^ie^{-\delta_i \frac{r^{\alpha\beta}}{r_e}}S^{\alpha\beta}f_c\left(\frac{r_c-r^{\alpha\beta}}{dr}\right)
+
+* **bondscreened**
+
+.. math::
+
+    {}^{bsc}\!S\!f_{ij}^\alpha = \sum_{\beta}\sum_{\gamma} \left(cos(\theta_{\alpha\beta\gamma})\right)^ie^{-\delta_j \frac{r^{\alpha\beta}}{r_e}}e^{-\delta_j \frac{r^{\alpha\gamma}}{r_e}}S^{\alpha\beta}S^{\alpha\gamma}f_c\left(\frac{r_c-r^{\alpha\beta}}{dr}\right)f_c\left(\frac{r_c-r^{\alpha\gamma}}{dr}\right)
+
+* **radialspin**
+
+.. math::
+
+    {}^{rsp}\!S\!f_i^\alpha = \sum_{\beta} \left(\frac{r^{\alpha\beta}}{r_e}\right)^ie^{-\delta_i \frac{r^{\alpha\beta}}{r_e}}\left(\mathbf{s^\alpha \cdot s^\beta}\right)f_c\left(\frac{r_c-r^{\alpha\beta}}{dr}\right)
+
+*  **bondspin**
+
+.. math::
+
+   {}^{bsp}\!S\!f_{ij}^\alpha = \sum_{\beta}\sum_{\gamma} \left(cos(\theta_{\alpha\beta\gamma})\right)^ie^{-\delta_j \frac{r^{\alpha\beta}}{r_e}}e^{-\delta_j \frac{r^{\alpha\gamma}}{r_e}}\left(\mathbf{s^\alpha \cdot s^\beta}\right)\left(\mathbf{s^\alpha \cdot s^\gamma}\right)f_c\left(\frac{r_c-r^{\alpha\beta}}{dr}\right)f_c\left(\frac{r_c-r^{\alpha\gamma}}{dr}\right)
+
+* **radialscreenedspin**
+
+.. math::
+
+    {}^{rscsp}\!S\!f_i^\alpha = \sum_{\beta} \left(\frac{r^{\alpha\beta}}{r_e}\right)^ie^{-\delta_i \frac{r^{\alpha\beta}}{r_e}}S^{\alpha\beta}\left(\mathbf{s^\alpha \cdot s^\beta}\right)f_c\left(\frac{r_c-r^{\alpha\beta}}{dr}\right)
+
+* **bondscreenedspin**
+
+.. math::
+
+    {}^{bscsp}\!S\!f_{ij}^\alpha = \sum_{\beta}\sum_{\gamma} \left(cos(\theta_{\alpha\beta\gamma})\right)^ie^{-\delta_j \frac{r^{\alpha\beta}}{r_e}}e^{-\delta_j \frac{r^{\alpha\gamma}}{r_e}}S^{\alpha\beta}S^{\alpha\gamma}\left(\mathbf{s^\alpha \cdot s^\beta}\right)\left(\mathbf{s^\alpha \cdot s^\gamma}\right)f_c\left(\frac{r_c-r^{\alpha\beta}}{dr}\right)f_c\left(\frac{r_c-r^{\alpha\gamma}}{dr}\right)
+
+The activation functions are computed as follows:
+
+.. _activations:
+
+* **sigI**
+
+.. math::
+
+    F^{sigI}(x) = 0.1x+0.9ln\left(e^x+1\right)
+
+* **linear**
+
+.. math::
+
+   F^{linear}(x) = x
+
+Restrictions
+""""""""""""
+
+Pair style *rann* is part of the USER-RANN package.  It is only enabled if LAMMPS was built with that
+package.  Additionally, if any spin fingerprint styles are used LAMMPS must be built with the SPIN
+package as well.
+
+Defaults
+""""""""""""
+
+Cmin = 0.8, Cmax = 2.8.
+
+----------
+
+
+.. _Baskes97:
+
+**(Baskes)** Baskes,
+Materials Chemistry and Physics, 50(2), 152-158, (1997).
+
+.. _Dickel:
+
+**(Dickel)** Dickel, Francis, and Barrett,
+Computational Materials Science 171 (2020): 109157.
+
+.. _Nitol:
+
+**(Nitol)** Nitol, Dickel, and Barrett,
+Computational Materials Science 188 (2021): 110207.
+
+.. _Tranchida7:
+
+**(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson,
+Journal of Computational Physics, 372, 406-425, (2018).
+

doc/src/pair_style.rst

@@ -182,6 +182,7 @@ accelerated styles exist.
 * :doc:`gw/zbl <pair_gw>` - Gao-Weber potential with a repulsive ZBL core
 * :doc:`hbond/dreiding/lj <pair_hbond_dreiding>` - DREIDING hydrogen bonding LJ potential
 * :doc:`hbond/dreiding/morse <pair_hbond_dreiding>` - DREIDING hydrogen bonding Morse potential
+* :doc:`hdnnp <pair_hdnnp>` - High-dimensional neural network potential
 * :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>` - registry-dependent interlayer potential (ILP)
 * :doc:`kim <pair_kim>` - interface to potentials provided by KIM project
 * :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>` - Kolmogorov-Crespi (KC) potential with no simplifications
@@ -290,6 +291,7 @@ accelerated styles exist.
 * :doc:`polymorphic <pair_polymorphic>` - polymorphic 3-body potential
 * :doc:`python <pair_python>` -
 * :doc:`quip <pair_quip>` -
+* :doc:`rann <pair_rann>` -
 * :doc:`reax/c <pair_reaxc>` - ReaxFF potential in C
 * :doc:`rebo <pair_airebo>` - second generation REBO potential of Brenner
 * :doc:`resquared <pair_resquared>` - Everaers RE-Squared ellipsoidal potential

doc/utils/converters/lammpsdoc/rst_anchor_check.py

@@ -1,4 +1,4 @@
-#! /usr/bin/env python3
+#!/usr/bin/env python3
 # LAMMPS Documentation Utilities
 #
 # Scan for duplicate anchor labels in documentation files

doc/utils/converters/setup.py

@@ -1,7 +1,7 @@
 from setuptools import setup
 
 setup(name='LAMMPS Documentation Utilities',
-      version='2.0.0',
+      version='2.0.1',
       description='Utilities to convert existing LAMMPS documentation text files into ReStructured Text',
       url='https://github.com/rbberger/lammps-doc-utils',
       author='Richard Berger',
@@ -11,8 +11,6 @@ setup(name='LAMMPS Documentation Utilities',
       test_suite='nose.collector',
       tests_require=['nose'],
       entry_points = {
-          "console_scripts": ['txt2html = lammpsdoc.txt2html:main',
+          "console_scripts": ['rst_anchor_check = lammpsdoc.rst_anchor_check:main ']
-                              'txt2rst  = lammpsdoc.txt2rst:main',
-                              'rst_anchor_check = lammpsdoc.rst_anchor_check:main ']
       },
 )

doc/utils/sphinx-config/_static/css/lammps.css

@@ -35,6 +35,10 @@ hr {
      display: none;
 }
 
+#command-reference.section h2 {
+     display: none;
+}
+
 .ui.tabular.menu .item {
     padding-right: 1em;
     padding-left: 1em;

doc/utils/sphinx-config/_themes/lammps_theme/layout.html

@@ -134,14 +134,8 @@
           </a>
 
           {% if theme_display_version %}
-            {%- set nav_version = version %}
+              <div class="lammps_version">Version: <b>{{ current_version }}</b></div>
-            {% if READTHEDOCS and current_version %}
-              {%- set nav_version = current_version %}
-            {% endif %}
-            {% if nav_version %}
-              <div class="lammps_version">Version: <b>{{ nav_version }}</b></div>
               <div class="lammps_release">git info: {{ release }}</div>
-            {% endif %}
           {% endif %}
 
           {% include "searchbox.html" %}

doc/utils/sphinx-config/_themes/lammps_theme/versions.html

@@ -1,9 +1,9 @@
-{% if READTHEDOCS %}
+{% if READTHEDOCS or display_manual_versions %}
 {# Add rst-badge after rst-versions for small badge style. #}
   <div class="rst-versions" data-toggle="rst-versions" role="note" aria-label="versions">
     <span class="rst-current-version" data-toggle="rst-current-version">
-      <span class="fa fa-book"> Read the Docs</span>
+      <span class="fa fa-book"> Version</span>
-      v: {{ current_version }}
+      {{ current_version }}
       <span class="fa fa-caret-down"></span>
     </span>
     <div class="rst-other-versions">
@@ -20,14 +20,8 @@
         {% endfor %}
       </dl>
       <dl>
-        {# Translators: The phrase "Read the Docs" is not translated #}
+        <dt>Git Info</dt>
-        <dt>{{ _('On Read the Docs') }}</dt>
+        <dd><a href="https://github.com/lammps/lammps/tree/{{ git_commit }}" target="_blank">{{ release }}</a></dd>
-          <dd>
-            <a href="//{{ PRODUCTION_DOMAIN }}/projects/{{ slug }}/?fromdocs={{ slug }}">{{ _('Project Home') }}</a>
-          </dd>
-          <dd>
-            <a href="//{{ PRODUCTION_DOMAIN }}/builds/{{ slug }}/?fromdocs={{ slug }}">{{ _('Builds') }}</a>
-          </dd>
       </dl>
     </div>
   </div>

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

@@ -99,6 +99,16 @@ def get_git_info():
         pass
     return git_n_date
 
+def get_git_commit():
+    import subprocess,time
+    try:
+        commit = subprocess.run(['git','rev-parse','HEAD'],stdout=subprocess.PIPE,stderr=subprocess.PIPE)
+        if commit.returncode == 0:
+            return commit.stdout.decode()
+    except:
+        pass
+    return ''
+
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
@@ -108,6 +118,8 @@ version = get_lammps_version()
 # The full version, including alpha/beta/rc tags.
 release = get_git_info()
 
+git_commit = get_git_commit()
+
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 #language = None
@@ -241,7 +253,7 @@ html_show_sourcelink = False
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'LAMMPSdoc'
 
-html_add_permalinks = ''
+html_permalinks = True
 
 if 'epub' in sys.argv:
   html_math_renderer = 'imgmath'
@@ -348,7 +360,7 @@ 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
-at sjplimp@sandia.gov.  The LAMMPS WWW Site at lammps.sandia.gov has
+at sjplimp@sandia.gov.  The LAMMPS WWW Site at www.lammps.org has
 more information about the code and its uses.
 """
 
@@ -389,3 +401,20 @@ breathe_domain_by_extension = { 'h'   : 'cpp',
                                 'cpp' : 'cpp',
                                 'c'   : 'c',
                                 }
+
+# allows showing multiple versions
+try:
+   html_context
+except NameError:
+   html_context = dict()
+
+is_website_build = os.environ.get('LAMMPS_WEBSITE_BUILD', '0') != '0'
+
+html_context['display_manual_versions'] = is_website_build
+html_context['current_version'] = os.environ.get('LAMMPS_WEBSITE_BUILD_VERSION', version)
+html_context['git_commit'] = git_commit
+html_context['versions'] = [
+  ('latest', 'https://docs.lammps.org/latest/'),
+  (version, 'https://docs.lammps.org/')
+]
+html_context['downloads'] = [('PDF', 'Manual.pdf')]

doc/utils/sphinx-config/false_positives.txt

@@ -23,6 +23,7 @@ acolor
 acos
 Acta
 actinide
+activationfunctions
 acylindricity
 addforce
 Addington
@@ -75,6 +76,7 @@ allocaters
 allosws
 AlO
 Alonso
+alphak
 alphashrink
 amap
 Amatrix
@@ -153,6 +155,7 @@ atomfile
 AtomicPairStyle
 atomID
 atomistic
+atomtypes
 attogram
 attograms
 attrac
@@ -187,6 +190,7 @@ backends
 Baczewski
 Bagi
 Bagnold
+Bajaj
 Bkappa
 Bal
 balancer
@@ -287,6 +291,9 @@ BondAngle
 BondBond
 bondchk
 bondmax
+bondscreened
+bondscreenedspin
+bondspin
 bondtype
 Bonet
 Bonomi
@@ -339,6 +346,8 @@ bz
 cadetblue
 Cagin
 calc
+calibrationfunctions
+calibrationparameters
 calibre
 caltech
 Caltech
@@ -669,6 +678,7 @@ diagonalized
 diagonalizers
 diagonalizing
 Diallo
+Dickel
 diel
 differentiable
 diffusively
@@ -721,6 +731,7 @@ doxygenclass
 doxygenfunction
 downarrow
 Doye
+Doyl
 dpd
 DPD
 dpdTheta
@@ -1228,6 +1239,8 @@ hbn
 hbnewflag
 hbond
 hcp
+hdnnp
+HDNNP
 heatconduction
 Hebbeker
 Hebenstreit
@@ -1570,6 +1583,7 @@ Koning
 Kooser
 Korn
 Koskinen
+Koslowski
 Kosovan
 Koster
 Kosztin
@@ -1634,6 +1648,7 @@ Laupretre
 Lauriat
 lavenderblush
 lawngreen
+layersize
 lB
 lbfgs
 lbl
@@ -2160,6 +2175,7 @@ nemd
 netcdf
 netstat
 Nettleton
+networklayers
 Neumann
 Nevent
 nevery
@@ -2194,6 +2210,7 @@ Ninteger
 NiO
 Nissila
 nist
+Nitol
 nitride
 nitrides
 niu
@@ -2668,6 +2685,9 @@ qw
 qx
 qy
 qz
+radialscreened
+radialscreenedspin
+radialspin
 radian
 radians
 Rafferty
@@ -2680,6 +2700,8 @@ ramping
 Ramprasad
 Randisi
 randomizations
+rann
+RANN
 Raphson
 Rappe
 Ravelo
@@ -2850,6 +2872,8 @@ Runge
 runtime
 Rutuparna
 rx
+rxnave
+rxnsum
 ry
 rz
 Ryckaert
@@ -2951,8 +2975,10 @@ shrinkexceed
 Shugaev
 si
 SiC
+Siegmund
 Siepmann
 Sievers
+sigI
 sigmoid
 Sij
 Sikandar
@@ -3616,6 +3642,7 @@ yx
 yy
 yz
 Zannoni
+Zavattieri
 zbl
 ZBL
 Zc
@@ -3653,6 +3680,8 @@ zz
 Zm
 PowerShell
 filesystems
+fingerprintconstants
+fingerprintsperelement
 zincblende
 Zstandard
 Zstd

examples/ASPHERE/README

@@ -10,7 +10,7 @@ systems.  Some of the directories include a Python script, which can
 be used with the Pizza.py tool to create the data file, e.g. for
 collections of rigid bodies.
 
-The web site for Pizza.py is http://pizza.sandia.gov
+The web site for Pizza.py is https://pizza.sandia.gov
 
 For example, If you have Pizza.py installed you can type "pizza.py -f
 box.py", which creates the data.box data file in the box dir.
@@ -18,7 +18,7 @@ box.py", which creates the data.box data file in the box dir.
 If you uncomment the dump or dump image lines in the input scripts the
 runs will produce dump files or JPG images which you can view or
 animate.  See the Movies page of the LAMMPS web site
-(http://lammps.sandia.gov/movies.html), for animations of these
+(https://www.lammps.org/movies.html), for animations of these
 scripts.  Most were done using the dump image command.  A few were
 done using the gl tool in Pizza.py; the Pizza.py scripts that do the
 animation are given in the directory, e.g. as line.viz.py.

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