Merge pull request #2785 from akohlmey/next_patch_release

Step version string for next patch release

.gitattributes

@@ -1,3 +1,5 @@
 .gitattributes export-ignore
 .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

.github/CONTRIBUTING.md

@@ -26,11 +26,11 @@ __
 
 ## I don't want to read this whole thing I just have a question!
 
-> **Note:** Please do not file an issue to ask a general question about LAMMPS, its features, how to use specific commands, or how perform simulations or analysis in LAMMPS. Instead post your question to the ['lammps-users' mailing list](https://lammps.sandia.gov/mail.html). You do not need to be subscribed to post to the list (but a mailing list subscription avoids having your post delayed until it is approved by a mailing list moderator). Most posts to the mailing list receive a response within less than 24 hours. Before posting to the mailing list, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html). Following those guidelines will help greatly to get a helpful response. Always mention which LAMMPS version you are using.
+> **Note:** Please do not file an issue to ask a general question about LAMMPS, its features, how to use specific commands, or how perform simulations or analysis in LAMMPS. Instead post your question to either the ['lammps-users' mailing list](https://lammps.sandia.gov/mail.html) or the [LAMMPS Material Science Discourse forum](https://matsci.org/lammps). You do not need to be subscribed to post to the list (but a mailing list subscription avoids having your post delayed until it is approved by a mailing list moderator). Most posts to the mailing list receive a response within less than 24 hours. Before posting to the mailing list, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html). Following those guidelines will help greatly to get a helpful response. Always mention which LAMMPS version you are using. The LAMMPS forum was recently created as part of a larger effort to build a materials science community and have discussions not just about using LAMMPS. Thus the forum may be also used for discussions that would be off-topic for the mailing list. Those will just have to be moved to a more general category.
 
 ## How Can I Contribute?
 
-There are several ways how you can actively contribute to the LAMMPS project: you can discuss compiling and using LAMMPS, and solving LAMMPS related problems with other LAMMPS users on the lammps-users mailing list, you can report bugs or suggest enhancements by creating issues on GitHub (or posting them to the lammps-users mailing list), and you can contribute by submitting pull requests on GitHub or e-mail your code
+There are several ways how you can actively contribute to the LAMMPS project: you can discuss compiling and using LAMMPS, and solving LAMMPS related problems with other LAMMPS users on the lammps-users mailing list, you can report bugs or suggest enhancements by creating issues on GitHub (or posting them to the lammps-users mailing list or posting in the LAMMPS Materials Science Discourse forum), and you can contribute by submitting pull requests on GitHub or e-mail your code
 to one of the [LAMMPS core developers](https://lammps.sandia.gov/authors.html). As you may see from the aforementioned developer page, the LAMMPS software package includes the efforts of a very large number of contributors beyond the principal authors and maintainers.
 
 ### Discussing How To Use LAMMPS
@@ -42,6 +42,8 @@ Anyone can browse/search previous questions/answers in the archives. You do not
 
 If you post a message and you are a subscriber, your message will appear immediately. If you are not a subscriber, your message will be moderated, which typically takes one business day. Either way, when someone replies the reply will usually be sent to both, your personal email address and the mailing list. When replying to people, that responded to your post to the list, please always included the mailing list in your replies (i.e. use "Reply All" and **not** "Reply"). Responses will appear on the list in a few minutes, but it can take a few hours for postings and replies to show up in the SourceForge archive. Sending replies also to the mailing list is important, so that responses are archived and people with a similar issue can search for possible solutions in the mailing list archive.
 
+The LAMMPS Materials Science Discourse forum was created recently to facilitate discussion not just about LAMMPS and as part of a larger effort  towards building a materials science community. The forum contains a read-only sub-category with the continually updated mailing list archive, so you won't miss anything by joining only the forum and not the mailing list.
+
 ### Reporting Bugs
 
 While developers writing code for LAMMPS are careful to test their code, LAMMPS is such a large and complex software, that it is impossible to test for all combinations of features under all normal and not so normal circumstances. Thus bugs do happen, and if you suspect, that you have encountered one, please try to document it and report it as an [Issue](https://github.com/lammps/lammps/issues) on the LAMMPS GitHub project web page. However, before reporting a bug, you need to check whether this is something that may have already been corrected. The [Latest Features and Bug Fixes in LAMMPS](https://lammps.sandia.gov/bug.html) web page lists all significant changes to LAMMPS over the years. It also tells you what the current latest development version of LAMMPS is, and you should test whether your issue still applies to that version.

.github/codeql/cpp.yml

@@ -0,0 +1,4 @@
+paths:
+ - src
+ - lib
+ - tools

.github/codeql/python.yml

@@ -0,0 +1,5 @@
+paths:
+ - python/lammps
+
+queries:
+ - uses: security-and-quality

.github/workflows/codeql-analysis.yml

@@ -31,16 +31,18 @@ jobs:
       uses: github/codeql-action/init@v1
       with:
         languages: ${{ matrix.language }}
+        config-file: ./.github/codeql/${{ matrix.language }}.yml
 
     - name: Create Build Environment
-      run: cmake -E make_directory ${{github.workspace}}/build
+      if: ${{ matrix.language == 'cpp' }}
+      run: mkdir build
 
     - name: Building LAMMPS via CMake
       if: ${{ matrix.language == 'cpp' }}
       shell: bash
-      working-directory: ${{github.workspace}}/build
+      working-directory: build
       run: |
-        cmake -C $GITHUB_WORKSPACE/cmake/presets/most.cmake $GITHUB_WORKSPACE/cmake
+        cmake -C ../cmake/presets/most.cmake ../cmake
         cmake --build . --parallel 2
 
     - name: Perform CodeQL Analysis

.github/workflows/unittest-macos.yml

@@ -10,6 +10,8 @@ jobs:
     name: MacOS Unit Test
     if: ${{ github.repository == 'lammps/lammps' }}
     runs-on: macos-latest
+    env:
+      CCACHE_DIR: ${{ github.workspace }}/.ccache
 
     steps:
     - name: Checkout repository
@@ -17,20 +19,36 @@ jobs:
       with:
         fetch-depth: 2
 
+    - name: Install ccache
+      run: brew install ccache
+
     - name: Create Build Environment
-      run: cmake -E make_directory ${{github.workspace}}/build
+      run: mkdir build
+
+    - name: Set up ccache
+      uses: actions/cache@v2
+      with:
+        path: ${{ env.CCACHE_DIR }}
+        key: macos-ccache-${{ github.sha }}
+        restore-keys: macos-ccache-
 
     - name: Building LAMMPS via CMake
       shell: bash
-      working-directory: ${{github.workspace}}/build
+      working-directory: build
       run: |
-        cmake -C $GITHUB_WORKSPACE/cmake/presets/clang.cmake \
-              -C $GITHUB_WORKSPACE/cmake/presets/most.cmake \
-                 $GITHUB_WORKSPACE/cmake \
-              -DENABLE_TESTING=ON -DBUILD_SHARED_LIBS=ON -DLAMMPS_EXCEPTIONS=ON
+        ccache -z
+        cmake -C ../cmake/presets/clang.cmake \
+              -C ../cmake/presets/most.cmake \
+              -D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
+              -D CMAKE_C_COMPILER_LAUNCHER=ccache \
+              -D ENABLE_TESTING=on \
+              -D BUILD_SHARED_LIBS=on \
+              -D LAMMPS_EXCEPTIONS=on \
+              ../cmake
         cmake --build . --parallel 2
+        ccache -s
 
     - name: Run Tests
-      working-directory: ${{github.workspace}}/build
+      working-directory: build
       shell: bash
       run: ctest -V

.lgtm.yml

@@ -0,0 +1,14 @@
+extraction:
+  cpp:
+    configure:
+      command:
+      - "mkdir build"
+      - "cd build"
+      - "cmake -G Ninja -C ../cmake/presets/minimal.cmake ../cmake"
+    index:
+      build_command:
+      - "cd build"
+      - "ninja"
+  python:
+    python_setup:
+      version: 3

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://lammps.sandia.gov/doc/Intro.html          hi-level introduction
-https://lammps.sandia.gov/doc/Build.html          how to build LAMMPS
-https://lammps.sandia.gov/doc/Run_head.html       how to run LAMMPS
-https://lammps.sandia.gov/doc/Commands_all.html   Table of available commands
-https://lammps.sandia.gov/doc/Library.html        LAMMPS library interfaces
-https://lammps.sandia.gov/doc/Modify.html         how to modify and extend LAMMPS
-https://lammps.sandia.gov/doc/Developer.html      LAMMPS developer info
+https://docs.lammps.org/Manual.html         LAMMPS manual
+https://docs.lammps.org/Intro.html          hi-level introduction
+https://docs.lammps.org/Build.html          how to build LAMMPS
+https://docs.lammps.org/Run_head.html       how to run LAMMPS
+https://docs.lammps.org/Commands_all.html   Table of available commands
+https://docs.lammps.org/Library.html        LAMMPS library interfaces
+https://docs.lammps.org/Modify.html         how to modify and extend LAMMPS
+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})
@@ -121,10 +143,10 @@ 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-MEAMC USER-MESONT USER-MGPT USER-MISC 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-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF)
+  USER-HDNNP USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESONT USER-MGPT USER-MISC
+  USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
+  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.
@@ -245,68 +269,6 @@ if(BUILD_OMP)
   target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
 endif()
 
-# Compiler specific features for testing
-if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
-  option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
-  mark_as_advanced(ENABLE_COVERAGE)
-  if(ENABLE_COVERAGE)
-    if(CMAKE_VERSION VERSION_LESS 3.13)
-      if(CMAKE_CXX_FLAGS)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
-      else()
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage")
-      endif()
-    else()
-      target_compile_options(lammps PUBLIC --coverage)
-      target_link_options(lammps PUBLIC --coverage)
-    endif()
-  endif()
-endif()
-
-#######################################
-# add custom target for IWYU analysis
-#######################################
-set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool")
-mark_as_advanced(ENABLE_IWYU)
-if(ENABLE_IWYU)
-  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)
-    add_custom_target(
-      iwyu
-      ${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp
-      COMMENT "Running IWYU")
-    add_dependencies(iwyu lammps)
-  else()
-    message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable"
-      "and the iwyu-tool/iwyu_tool script installed in your PATH")
-  endif()
-endif()
-
-set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
-mark_as_advanced(ENABLE_SANITIZER)
-set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
-set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES})
-validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
-string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)
-if(NOT ENABLE_SANITIZER STREQUAL "none")
-  if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
-    if(CMAKE_VERSION VERSION_LESS 3.13)
-      if(CMAKE_CXX_FLAGS)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
-      else()
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
-      endif()
-    else()
-      target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
-      target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
-    endif()
-  else()
-    message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.")
-    set(ENABLE_SANITIZER "none")
-  endif()
-endif()
-
 if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
   enable_language(C)
   find_package(LAPACK)
@@ -358,7 +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")
@@ -369,7 +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")
@@ -386,8 +348,8 @@ else()
   set(CUDA_REQUEST_PIC)
 endif()
 
-foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM
-        USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS)
+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})
   endif()
@@ -484,7 +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)
@@ -496,9 +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})
@@ -511,7 +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 ${LAPACK_LIBRARIES})
@@ -555,7 +517,7 @@ endif()
 # and the MPI library - if use - has to be linked right before those
 # and after everything else that is compiled locally
 ######################################################################
-if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
   target_link_libraries(lammps PRIVATE -lwsock32 -lpsapi)
 endif()
 
@@ -604,8 +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)
-if(${_index} GREATER -1)
+list(FIND LANGUAGES "Fortran" _index)
+if(_index GREATER -1)
   target_link_libraries(lammps PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
 endif()
 set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h compute.h dihedral.h domain.h error.h fix.h force.h group.h improper.h
@@ -683,7 +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
@@ -716,7 +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()
@@ -730,7 +692,7 @@ get_target_property(DEFINES lammps COMPILE_DEFINITIONS)
 include(FeatureSummary)
 feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND)
 message(STATUS "<<< Build configuration >>>
-   Operating System: ${CMAKE_SYSTEM_NAME}
+   Operating System: ${CMAKE_SYSTEM_NAME} ${CMAKE_LINUX_DISTRO} ${CMAKE_DISTRO_VERSION}
    Build type:       ${CMAKE_BUILD_TYPE}
    Install path:     ${CMAKE_INSTALL_PREFIX}
    Generator:        ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}")
@@ -761,15 +723,15 @@ if(OPTIONS)
   message("      Options:       ${OPTIONS}")
 endif()
 get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
-list (FIND LANGUAGES "Fortran" _index)
-if(${_index} GREATER -1)
+list(FIND LANGUAGES "Fortran" _index)
+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)
-if(${_index} GREATER -1)
+list(FIND LANGUAGES "C" _index)
+if(_index GREATER -1)
   message(STATUS "C compiler:       ${CMAKE_C_COMPILER}
       Type:          ${CMAKE_C_COMPILER_ID}
       Version:       ${CMAKE_C_COMPILER_VERSION}
@@ -799,9 +761,12 @@ if(BUILD_MPI)
 endif()
 if(PKG_GPU)
   message(STATUS "<<< GPU package settings >>>
--- GPU API:          ${GPU_API}")
+-- GPU API:                  ${GPU_API}")
   if(GPU_API STREQUAL "CUDA")
+    message(STATUS "CUDA Compiler:            ${CUDA_NVCC_EXECUTABLE}")
     message(STATUS "GPU default architecture: ${GPU_ARCH}")
+    message(STATUS "GPU binning with CUDPP:   ${CUDPP_OPT}")
+    message(STATUS "CUDA MPS support:         ${CUDA_MPS_SUPPORT}")
   elseif(GPU_API STREQUAL "HIP")
     message(STATUS "HIP platform:     ${HIP_PLATFORM}")
     message(STATUS "HIP architecture: ${HIP_ARCH}")
@@ -811,7 +776,7 @@ if(PKG_GPU)
       message(STATUS "HIP GPU sorting: off")
     endif()
   endif()
-  message(STATUS "GPU precision:    ${GPU_PREC}")
+  message(STATUS "GPU precision:            ${GPU_PREC}")
 endif()
 if(PKG_KOKKOS)
   message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}")
@@ -831,7 +796,7 @@ if(PKG_KSPACE)
   endif()
   if(PKG_KOKKOS)
     if(Kokkos_ENABLE_CUDA)
-      if (${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/Documentation.cmake

@@ -55,8 +55,8 @@ if(BUILD_DOC)
     COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
   )
 
-  set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.2.tar.gz" CACHE STRING "URL for MathJax tarball")
-  set(MATHJAX_MD5 "a4a6a093a89bc2ccab1452d766b98e53" CACHE STRING "MD5 checksum of MathJax tarball")
+  set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.3.tar.gz" CACHE STRING "URL for MathJax tarball")
+  set(MATHJAX_MD5 "d1c98c746888bfd52ca8ebc10704f92f" CACHE STRING "MD5 checksum of MathJax tarball")
   mark_as_advanced(MATHJAX_URL)
 
   # download mathjax distribution and unpack to folder "mathjax"

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/GenerateOpenCLHeader.cmake

@@ -0,0 +1,3 @@
+# utility script to call WriteOpenCLHeader function
+include(${SOURCE_DIR}/Modules/OpenCLUtils.cmake)
+WriteOpenCLHeader(${VARNAME} ${HEADER_FILE} ${SOURCE_FILES})

cmake/Modules/LAMMPSUtils.cmake

@@ -104,3 +104,13 @@ function(FetchPotentials pkgfolder potfolder)
     endforeach()
   endif()
 endfunction(FetchPotentials)
+
+# set CMAKE_LINUX_DISTRO and CMAKE_DISTRO_VERSION on Linux
+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 "${distro}")
+  file(STRINGS /etc/os-release disversion REGEX "^VERSION_ID=")
+  string(REGEX REPLACE "VERSION_ID=\"?([^\"]*)\"?" "\\1" disversion "${disversion}")
+  set(CMAKE_LINUX_DISTRO ${distro})
+  set(CMAKE_DISTRO_VERSION ${disversion})
+endif()

cmake/Modules/OpenCLLoader.cmake

@@ -1,6 +1,6 @@
 message(STATUS "Downloading and building OpenCL loader library")
-set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2020.12.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
-set(OPENCL_LOADER_MD5 "011cdcbd41030be94f3fced6d763a52a" CACHE STRING "MD5 checksum of OpenCL loader tarball")
+set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.05.02.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
+set(OPENCL_LOADER_MD5 "29180b05056578afda92f0d394c3a373" CACHE STRING "MD5 checksum of OpenCL loader tarball")
 mark_as_advanced(OPENCL_LOADER_URL)
 mark_as_advanced(OPENCL_LOADER_MD5)
 

cmake/Modules/OpenCLUtils.cmake

@@ -1,10 +1,8 @@
-function(GenerateOpenCLHeader varname outfile files)
-    message("Creating ${outfile}...")
+function(WriteOpenCLHeader varname outfile files)
     file(WRITE ${outfile} "const char * ${varname} = \n")
-    math(EXPR ARG_END   "${ARGC}-1")
+    separate_arguments(files)
 
-    foreach(IDX RANGE 2 ${ARG_END})
-        list(GET ARGV ${IDX} filename)
+    foreach(filename ${files})
         file(READ ${filename} content)
         string(REGEX REPLACE "\\s*//[^\n]*\n" "\n" content "${content}")
         string(REGEX REPLACE "\\\\" "\\\\\\\\" content "${content}")
@@ -15,4 +13,16 @@ function(GenerateOpenCLHeader varname outfile files)
     endforeach()
 
     file(APPEND ${outfile} ";\n")
+endfunction(WriteOpenCLHeader)
+
+function(GenerateOpenCLHeader varname outfile files)
+    list(REMOVE_AT ARGV 0 1)
+    add_custom_command(OUTPUT ${outfile}
+      COMMAND ${CMAKE_COMMAND} -D SOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR}
+                               -D VARNAME=${varname}
+                               -D HEADER_FILE=${outfile}
+                               -D SOURCE_FILES="${ARGV}"
+                               -P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/GenerateOpenCLHeader.cmake
+      DEPENDS ${ARGV}
+      COMMENT "Generating ${outfile}...")
 endfunction(GenerateOpenCLHeader)

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"
@@ -112,10 +112,10 @@ if(GPU_API STREQUAL "CUDA")
   endif()
 
   cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
-          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
+          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
 
   cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
-          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
+          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
 
   foreach(CU_OBJ ${GPU_GEN_OBJS})
     get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
@@ -145,9 +145,16 @@ if(GPU_API STREQUAL "CUDA")
   target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
 
 elseif(GPU_API STREQUAL "OPENCL")
-  option(USE_STATIC_OPENCL_LOADER "Download and include a static OpenCL ICD loader" ON)
+  # the static OpenCL loader doesn't seem to work on macOS. use the system provided
+  # version by default instead (for as long as it will be available)
+  if("${CMAKE_SYSTEM_NAME}" STREQUAL "Darwin")
+    set(_opencl_static_default OFF)
+  else()
+    set(_opencl_static_default ON)
+  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)
@@ -289,18 +296,18 @@ elseif(GPU_API STREQUAL "HIP")
 
         if(HIP_COMPILER STREQUAL "clang")
           add_custom_command(OUTPUT ${CUBIN_FILE}
-            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
+            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
             DEPENDS ${CU_CPP_FILE}
             COMMENT "Generating ${CU_NAME}.cubin")
         else()
           add_custom_command(OUTPUT ${CUBIN_FILE}
-            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
+            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
             DEPENDS ${CU_CPP_FILE}
             COMMENT "Generating ${CU_NAME}.cubin")
         endif()
     elseif(HIP_PLATFORM STREQUAL "nvcc")
         add_custom_command(OUTPUT ${CUBIN_FILE}
-          VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE}
+          VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE}
           DEPENDS ${CU_FILE}
           COMMENT "Generating ${CU_NAME}.cubin")
     endif()

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/3.3.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "08201d1c7cf5bc458ce0f5b44a629d5a" CACHE STRING "MD5 checksum of 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 "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 3.3.01 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-INTEL.cmake

@@ -79,9 +79,11 @@ if(INTEL_ARCH STREQUAL "KNL")
 else()
   if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
     include(CheckCXXCompilerFlag)
-    foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
-      check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAG})
-      if(COMPILER_SUPPORTS${_FLAG})
+    foreach(_FLAG -O2 "-fp-model fast=2" -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
+      string(REGEX REPLACE "[ =\"]" "" _FLAGX ${_FLAG})
+      check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAGX})
+      if(COMPILER_SUPPORTS${_FLAGX})
+          separate_arguments(_FLAG UNIX_COMMAND "${_FLAG}")
           target_compile_options(lammps PRIVATE ${_FLAG})
       endif()
     endforeach()

cmake/Modules/Packages/USER-MDI.cmake

@@ -0,0 +1,118 @@
+find_package(mdi QUIET)
+if(${mdi_FOUND})
+  set(DOWNLOAD_MDI_DEFAULT OFF)
+else()
+  set(DOWNLOAD_MDI_DEFAULT ON)
+endif()
+option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an already installed one" ${DOWNLOAD_MDI_DEFAULT})
+
+if(DOWNLOAD_MDI)
+  message(STATUS "MDI download requested - we will build our own")
+  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.2.9.tar.gz" CACHE STRING "URL for MDI tarball")
+  set(MDI_MD5 "ddfa46d6ee15b4e59cfd527ec7212184" CACHE STRING "MD5 checksum for MDI tarball")
+  mark_as_advanced(MDI_URL)
+  mark_as_advanced(MDI_MD5)
+  enable_language(C)
+
+  # 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)
+  ExternalProject_Add(mdi_build
+    URL     ${MDI_URL}
+    URL_MD5 ${MDI_MD5}
+    CMAKE_ARGS ${CMAKE_REQUEST_PIC}
+    -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+    -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+    -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+    -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
+    -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
+    -Dlanguage=C
+    -Dlibtype=STATIC
+    -Dmpi=${MDI_USE_MPI}
+    -Dpython_plugins=${MDI_USE_PYTHON_PLUGINS}
+    UPDATE_COMMAND ""
+    INSTALL_COMMAND ""
+    BUILD_BYPRODUCTS "<BINARY_DIR>/MDI_Library/libmdi.a"
+    )
+
+  # where is the compiled library?
+  ExternalProject_get_property(mdi_build BINARY_DIR)
+  set(MDI_BINARY_DIR "${BINARY_DIR}/MDI_Library")
+  # workaround for older CMake versions
+  file(MAKE_DIRECTORY ${MDI_BINARY_DIR})
+
+  # create imported target for the MDI library
+  add_library(LAMMPS::MDI UNKNOWN IMPORTED)
+  add_dependencies(LAMMPS::MDI mdi_build)
+  set_target_properties(LAMMPS::MDI PROPERTIES
+    IMPORTED_LOCATION "${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()
+
+  find_package(mdi)
+  if(NOT mdi_FOUND)
+    message(FATAL_ERROR "MDI library not found. Help CMake to find it "
+      "by setting mdi_LIBRARY and mdi_INCLUDE_DIR, or set DOWNLOAD_MDI=ON "
+      "to download and compile it")
+  endif()
+
+  # Link the lammps library against MDI
+  target_include_directories(lammps PRIVATE ${mdi_INCLUDE_DIR})
+  target_link_libraries(lammps PRIVATE ${mdi_LIBRARY})
+
+  # Link the lammps executable against MDI
+  target_include_directories(lmp PRIVATE ${mdi_INCLUDE_DIR})
+  target_link_libraries(lmp PRIVATE ${mdi_LIBRARY})
+endif()
+
+target_compile_definitions(lammps PRIVATE -DLMP_USER_MDI)
+target_compile_definitions(lmp PRIVATE -DLMP_USER_MDI)

cmake/Modules/Packages/USER-PACE.cmake

@@ -0,0 +1,25 @@
+
+set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.4.9.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+set(PACELIB_MD5 "4db54962fbd6adcf8c18d46e1798ceb5" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+mark_as_advanced(PACELIB_URL)
+mark_as_advanced(PACELIB_MD5)
+
+# download library sources to build folder
+file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz SHOW_PROGRESS EXPECTED_HASH MD5=${PACELIB_MD5})
+
+# uncompress downloaded sources
+execute_process(
+  COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
+  COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
+  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 ${PACE_EVALUATOR_SOURCES})
+set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
+target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR})
+target_link_libraries(lammps PRIVATE pace)
+

cmake/Modules/Packages/USER-PLUMED.cmake

@@ -54,8 +54,9 @@ if(DOWNLOAD_PLUMED)
     set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
   endif()
 
-  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.0/plumed-src-2.7.0.tgz" CACHE STRING "URL for PLUMED tarball")
-  set(PLUMED_MD5 "95f29dd0c067577f11972ff90dfc7d12" CACHE STRING "MD5 checksum of PLUMED tarball")
+  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.1/plumed-src-2.7.1.tgz" CACHE STRING "URL for PLUMED tarball")
+  set(PLUMED_MD5 "4eac6a462ec84dfe0cec96c82421b8e8" CACHE STRING "MD5 checksum of PLUMED tarball")
+
   mark_as_advanced(PLUMED_URL)
   mark_as_advanced(PLUMED_MD5)
 

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

@@ -16,11 +16,14 @@ if(ENABLE_TESTING)
   set(MEMORYCHECK_COMMAND "${VALGRIND_BINARY}" CACHE FILEPATH "Memory Check Command")
   set(MEMORYCHECK_COMMAND_OPTIONS "${VALGRIND_DEFAULT_OPTIONS}" CACHE STRING "Memory Check Command Options")
 
-  # check if a faster linker is available.
-  # only verified with GNU and Clang compilers and new CMake
-  if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
-    if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
-        OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
+  # 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)
+      AND ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+        OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
+    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)))
       include(CheckCXXCompilerFlag)
       set(CMAKE_CUSTOM_LINKER_DEFAULT default)
       check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG)
@@ -53,3 +56,76 @@ if(ENABLE_TESTING)
   get_filename_component(LAMMPS_UNITTEST_BIN ${CMAKE_BINARY_DIR}/unittest ABSOLUTE)
   add_subdirectory(${LAMMPS_UNITTEST_DIR} ${LAMMPS_UNITTEST_BIN})
 endif()
+
+# Compiler specific features for testing
+if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+  option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
+  mark_as_advanced(ENABLE_COVERAGE)
+  if(ENABLE_COVERAGE)
+    if(CMAKE_VERSION VERSION_LESS 3.13)
+      if(CMAKE_CXX_FLAGS)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
+      else()
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage")
+      endif()
+    else()
+      target_compile_options(lammps PUBLIC --coverage)
+      target_link_options(lammps PUBLIC --coverage)
+    endif()
+  endif()
+endif()
+
+#######################################
+# add custom target for IWYU analysis
+#######################################
+set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool")
+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")))
+    message(FATAL_ERROR "IWYU is only supported with Clang or GNU compilers")
+  endif()
+  # detect the "native" header folder so we can include them first
+  execute_process(COMMAND ${CMAKE_CXX_COMPILER} --print-search-dirs OUTPUT_VARIABLE IWYU_SEARCH_PATHS)
+  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)
+    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
+      COMMENT "Running IWYU")
+    add_dependencies(iwyu lammps)
+  else()
+    message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable"
+      "and the iwyu-tool/iwyu_tool script installed in your PATH")
+  endif()
+endif()
+
+#######################################
+# select code sanitizer options
+#######################################
+set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
+mark_as_advanced(ENABLE_SANITIZER)
+set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
+set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES})
+validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
+string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)
+if(NOT ENABLE_SANITIZER STREQUAL "none")
+  if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
+    if(CMAKE_VERSION VERSION_LESS 3.13)
+      if(CMAKE_CXX_FLAGS)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
+      else()
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
+      endif()
+    else()
+      target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
+      target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
+    endif()
+  else()
+    message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.")
+    set(ENABLE_SANITIZER "none")
+  endif()
+endif()

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}
-                                      CC=${CMAKE_C_COMPILER}
-                                      --prefix=<INSTALL_DIR> --disable-shared
+                                      CXX=${CMAKE_CXX_COMPILER} CC=${CMAKE_C_COMPILER}
+                                      --prefix=<INSTALL_DIR> --disable-shared ${YAML_CROSS_HOST}
                     BUILD_BYPRODUCTS  <INSTALL_DIR>/lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX}
                     TEST_COMMAND      "")
 

cmake/Modules/generate_lmpgitversion.cmake

@@ -17,7 +17,7 @@ if(GIT_FOUND AND EXISTS ${LAMMPS_DIR}/.git)
     ERROR_QUIET
     WORKING_DIRECTORY ${LAMMPS_DIR}
     OUTPUT_STRIP_TRAILING_WHITESPACE)
-  execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified
+  execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified --always
     OUTPUT_VARIABLE temp_git_describe
     ERROR_QUIET
     WORKING_DIRECTORY ${LAMMPS_DIR}

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

@@ -2,16 +2,16 @@
 # an existing package selection without losing any other settings
 
 set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-        GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MLIAP
-        MOLECULE MPIIO MSCG OPT PERI 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-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
-        USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD
-        USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
-        USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
-        USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
-        USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)
+  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-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK
+  USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
+  USER-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD
+  USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
+  USER-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN
+  USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
+  USER-TALLY USER-UEF USER-VTK USER-YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

cmake/presets/all_on.cmake

@@ -4,16 +4,16 @@
 # with just a working C++ compiler and an MPI library.
 
 set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-        GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MLIAP
-        MOLECULE MPIIO MSCG OPT PERI 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-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
-        USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD
-        USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
-        USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
-        USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
-        USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)
+  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-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK
+  USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
+  USER-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD
+  USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
+  USER-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN
+  USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
+  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
-# compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time.
+# 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.
 
-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-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
-                 USER-FEP USER-INTEL USER-MANIFOLD USER-MEAMC USER-MESODPD
+                 USER-ATC USER-AWPMD USER-BOCS USER-BROWNIAN USER-CGDNA USER-CGSDK
+                 USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
+                 USER-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/most.cmake

@@ -5,9 +5,9 @@
 set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
         GRANULAR KSPACE MANYBODY MC MISC MLIAP MOLECULE OPT PERI
         PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
-        USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
-        USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC USER-MESODPD
-        USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
+        USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
+        USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC
+        USER-MESODPD USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
         USER-REAXC USER-SDPD USER-SPH USER-SMD USER-UEF USER-YAFF)
 
 foreach(PKG ${ALL_PACKAGES})

cmake/presets/nolib.cmake

@@ -1,10 +1,11 @@
 # preset that turns off all packages that require some form of external
 # library or special compiler (fortran or cuda) or equivalent.
 
-set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MPIIO MSCG PYTHON
-        VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB
-        USER-MOLFILE USER-MESONT USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP
-        USER-SCAFACOS USER-SMD USER-VTK)
+set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MESSAGE MPIIO MSCG
+  PYTHON VORONOI
+  USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-HDNNP USER-LB USER-MOLFILE
+  USER-MESONT USER-MDI USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP
+  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
@@ -236,9 +230,9 @@ $(VENV):
 	)
 
 $(MATHJAX):
-	@git clone --depth 1 git://github.com/mathjax/MathJax.git $@
+	@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
-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"
+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/graphviz/lammps-classes.dot

@@ -18,8 +18,8 @@ digraph lammps {
     Up [shape=box label="Update" color=blue]
     Un [shape=box label="Universe" color=blue]
     Ti [shape=box label="Timer" color=blue]
-    Lt [label="Lattice"]
     Rg [label="Region" color=red]
+    Lt [label="Lattice"]
     Rb [shape=box label="RegionBlock"]
     Rs [shape=box label="RegionSphere"]
     Av [label="AtomVec" color=red]
@@ -34,6 +34,7 @@ digraph lammps {
     Du [label="Dump" color=red]
     Fi [label="Fix" color=red]
     Cp [label="Compute" color=red]
+    Cm [label="Command" color=red]
     Th [label="Thermo"]
     Va [label="Variable"]
     Ew [shape=box label="Ewald"]
@@ -71,16 +72,19 @@ digraph lammps {
     Dg [shape=box label="DumpCFG"]
     Ve [shape=box label="Verlet"]
     Rr [shape=box label="Respa"]
+    Ru [shape=box label="Run"]
+    Se [shape=box label="Set"]
     Pt [shape=box label="PPPMTIP4P"]
     Vs [shape=box label="VerletSplit"]
     Ro [shape=box label="RespaOMP"]
     Mc [shape=box label="MinCG"]
     Mf [shape=box label="MinFire"]
     La -> {At Ci Co Do Er Fo Gr In Me Mo Ne Ou Ti Up Un} [penwidth=2]
-    Do -> {Lt Rg} [penwidth=2]
+    Do -> {Rg Lt} [penwidth=2]
     Rg -> {Rb Rs} [style=dashed penwidth=2]
     Co -> {Cb Ct} [style=dashed penwidth=2]
-    In -> Va [penwidth=2]
+    In -> {Va Cm} [penwidth=2]
+    Cm -> {Ru Se} [style=dashed penwidth=2]
     Mo -> {Fi Cp} [penwidth=2]
     Fo -> {Pa Bo An Di Im Ks} [penwidth=2]
     Ks -> {Ew Pp} [style=dashed penwidth=2]

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 fix-whitespace      # generate coverage report in XML format
-   make check-permissions   # delete folder with HTML format coverage report
-   make fix-permissions     # delete all collected coverage data and HTML output
+   make check-whitespace    # search for files with whitespace issues
+   make fix-whitespace      # correct whitespace issues in files
+   make check-homepage      # search for files with old LAMMPS homepage URLs
+   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`
-tool (Clang version 8.0 or later is required). If available, the source
-code files in the ``unittest`` tree can be updated to conform to the
-formatting settings using ``make format-tests``.
+For the code in the ``unittest`` and ``src`` trees we are transitioning
+to use the `clang-format` tool to assist with having a consistent source
+code style.  The `clang-format` command bundled with Clang version 8.0
+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

@@ -48,10 +48,13 @@ 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>`
    * :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>`
@@ -454,6 +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
@@ -466,6 +472,9 @@ They must be specified in uppercase.
    *  - ARMV8_THUNDERX2
       - HOST
       - ARMv8 Cavium ThunderX2 CPU
+   *  - A64FX
+      - HOST
+      - ARMv8.2 with SVE Support
    *  - WSM
       - HOST
       - Intel Westmere CPU (SSE 4.2)
@@ -538,6 +547,9 @@ They must be specified in uppercase.
    *  - AMPERE80
       - GPU
       - NVIDIA Ampere generation CC 8.0 GPU
+   *  - AMPERE86
+      - GPU
+      - NVIDIA Ampere generation CC 8.6 GPU
    *  - VEGA900
       - GPU
       - AMD GPU MI25 GFX900
@@ -546,12 +558,12 @@ They must be specified in uppercase.
       - AMD GPU MI50/MI60 GFX906
    *  - VEGA908
       - GPU
-      - AMD GPU GFX908
+      - AMD GPU MI100 GFX908
    *  - INTEL_GEN
       - GPU
       - Intel GPUs Gen9+
 
-This list was last updated for version 3.3 of the Kokkos library.
+This list was last updated for version 3.4.1 of the Kokkos library.
 
 .. tabs::
 
@@ -1247,6 +1259,46 @@ be built for the most part with all major versions of the C++ language.
 
 ----------
 
+.. _user-pace:
+
+USER-PACE package
+-----------------------------
+
+This package requires a library that can be downloaded and built
+in lib/pace or somewhere else, which must be done before building
+LAMMPS with this package. The code for the library can be found
+at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps-user-pace/>`_
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      By default the library will be downloaded from the git repository
+      and built automatically when the USER-PACE package is enabled with
+      ``-D PKG_USER-PACE=yes``.  The location for the sources may be
+      customized by setting the variable ``PACELIB_URL`` when
+      configuring with CMake (e.g. to use a local archive on machines
+      without internet access).  Since CMake checks the validity of the
+      archive with ``md5sum`` you may also need to set ``PACELIB_MD5``
+      if you provide a different library version than what is downloaded
+      automatically.
+
+
+   .. tab:: Traditional make
+
+      You can download and build the USER-PACE library
+      in one step from the ``lammps/src`` dir, using these commands,
+      which invoke the ``lib/pace/Install.py`` script.
+
+      .. code-block:: bash
+
+         $ make lib-pace                          # print help message
+         $ make lib-pace args="-b"                # download and build the default version in lib/pace
+
+      You should not need to edit the ``lib/pace/Makefile.lammps`` file.
+
+----------
+
 .. _user-plumed:
 
 USER-PLUMED package
@@ -1422,6 +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
@@ -1492,6 +1598,35 @@ TBB and MKL.
 
 ----------
 
+.. _user-mdi:
+
+USER-MDI package
+-----------------------------
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      .. code-block:: bash
+
+         -D DOWNLOAD_MDI=value    # download MDI Library for build, value = no (default) or yes
+
+   .. tab:: Traditional make
+
+      Before building LAMMPS, you must build the MDI Library in
+      ``lib/mdi``\ .  You can do this by executing a command like one
+      of the following from the ``lib/mdi`` directory:
+
+      .. code-block:: bash
+
+         $ python Install.py -m gcc       # build using gcc compiler
+         $ python Install.py -m icc       # build using icc compiler
+
+      The build should produce two files: ``lib/mdi/includelink/mdi.h``
+      and ``lib/mdi/liblink/libmdi.so``\ .
+
+----------
+
 .. _user-mesont:
 
 USER-MESONT 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
-of two ways:
-
-a. You can "fetch" the current HTML and PDF files from the LAMMPS web
-   site.  Just type ``make fetch``.  This should download a ``html_www``
-   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.
+and PDF files are not included.  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://lammps.sandia.gov/doc/Manual.html>`_ A version of the manual
-corresponding to the ongoing development (aka master branch) is
-available online at: `https://docs.lammps.org/
-<https://docs.lammps.org/>`_
+`https://docs.lammps.org/Manual.html <https://docs.lammps.org/Manual.html>`_.
+A version of the manual corresponding to the ongoing development (aka master branch)
+is available online at: `https://docs.lammps.org/latest/
+<https://docs.lammps.org/latest/>`_
 
 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:`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-NETCDF <user-netcdf>` | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>`         | :ref:`USER-QMMM <user-qmmm>` | :ref:`USER-QUIP <user-quip>`   | :ref:`USER-SCAFACOS <user-scafacos>` |
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
-| :ref:`USER-SMD <user-smd>`       | :ref:`USER-VTK <user-vtk>`       |                                    |                              |                                |                                      |
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
++--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
+| :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:`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-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-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_all.rst

@@ -67,6 +67,7 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`lattice <lattice>`
    * :doc:`log <log>`
    * :doc:`mass <mass>`
+   * :doc:`mdi/engine <mdi_engine>`
    * :doc:`message <message>`
    * :doc:`minimize <minimize>`
    * :doc:`min_modify <min_modify>`

doc/src/Commands_fix.rst

@@ -39,6 +39,9 @@ OPT.
    * :doc:`ave/time <fix_ave_time>`
    * :doc:`aveforce <fix_aveforce>`
    * :doc:`balance <fix_balance>`
+   * :doc:`brownian <fix_brownian>`
+   * :doc:`brownian/asphere <fix_brownian>`
+   * :doc:`brownian/sphere <fix_brownian>`
    * :doc:`bocs <fix_bocs>`
    * :doc:`bond/break <fix_bond_break>`
    * :doc:`bond/create <fix_bond_create>`
@@ -46,6 +49,7 @@ OPT.
    * :doc:`bond/react <fix_bond_react>`
    * :doc:`bond/swap <fix_bond_swap>`
    * :doc:`box/relax <fix_box_relax>`
+   * :doc:`charge/regulation <fix_charge_regulation>`
    * :doc:`client/md <fix_client_md>`
    * :doc:`cmap <fix_cmap>`
    * :doc:`colvars <fix_colvars>`
@@ -97,6 +101,7 @@ OPT.
    * :doc:`lb/viscous <fix_lb_viscous>`
    * :doc:`lineforce <fix_lineforce>`
    * :doc:`manifoldforce <fix_manifoldforce>`
+   * :doc:`mdi/engine <fix_mdi_engine>`
    * :doc:`meso/move <fix_meso_move>`
    * :doc:`momentum (k) <fix_momentum>`
    * :doc:`momentum/chunk <fix_momentum>`

doc/src/Commands_pair.rst

@@ -26,6 +26,7 @@ OPT.
    * :doc:`zero <pair_zero>`
    * :doc:`hybrid (k) <pair_hybrid>`
    * :doc:`hybrid/overlay (k) <pair_hybrid>`
+   * :doc:`hybrid/scaled <pair_hybrid>`
    * :doc:`kim <pair_kim>`
    * :doc:`list <pair_list>`
    *
@@ -33,7 +34,6 @@ OPT.
    *
    *
    *
-   *
    * :doc:`adp (o) <pair_adp>`
    * :doc:`agni (o) <pair_agni>`
    * :doc:`airebo (io) <pair_airebo>`
@@ -69,6 +69,7 @@ OPT.
    * :doc:`comb3 <pair_comb>`
    * :doc:`cosine/squared <pair_cosine_squared>`
    * :doc:`coul/cut (gko) <pair_coul>`
+   * :doc:`coul/cut/global (o) <pair_coul>`
    * :doc:`coul/cut/soft (o) <pair_fep_soft>`
    * :doc:`coul/debye (gko) <pair_coul>`
    * :doc:`coul/diel (o) <pair_coul_diel>`
@@ -86,6 +87,8 @@ OPT.
    * :doc:`coul/wolf/cs <pair_cs>`
    * :doc:`dpd (gio) <pair_dpd>`
    * :doc:`dpd/fdt <pair_dpd_fdt>`
+   * :doc:`dpd/ext <pair_dpd_ext>`
+   * :doc:`dpd/ext/tstat <pair_dpd_ext>`
    * :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
    * :doc:`dpd/tstat (go) <pair_dpd>`
    * :doc:`dsmc <pair_dsmc>`
@@ -115,6 +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>`
@@ -168,7 +172,7 @@ OPT.
    * :doc:`lj/sdk/coul/long (go) <pair_sdk>`
    * :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
    * :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
-   * :doc:`lj/smooth (o) <pair_lj_smooth>`
+   * :doc:`lj/smooth (go) <pair_lj_smooth>`
    * :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`
    * :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
    * :doc:`lj96/cut (go) <pair_lj96>`
@@ -215,6 +219,7 @@ OPT.
    * :doc:`oxrna2/stk <pair_oxrna2>`
    * :doc:`oxrna2/xstk <pair_oxrna2>`
    * :doc:`oxrna2/coaxstk <pair_oxrna2>`
+   * :doc:`pace <pair_pace>`
    * :doc:`peri/eps <pair_peri>`
    * :doc:`peri/lps (o) <pair_peri>`
    * :doc:`peri/pmb (o) <pair_peri>`
@@ -222,6 +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/Developer_org.rst

@@ -49,8 +49,8 @@ underscore character '_' to separate words. Outside of bundled libraries
 which may have different conventions, all C and C++ header files have a
 ``.h`` extension, all C++ files have a ``.cpp`` extension, and C files a
 ``.c`` extension. A small number of C++ classes and utility functions
-are implemented with only a ``.h`` file. Examples are the Pointer class
-or the MathVec functions.
+are implemented with only a ``.h`` file. Examples are the Pointers and
+Commands classes or the MathVec functions.
 
 Class topology
 --------------
@@ -144,7 +144,7 @@ implement specific commands that can be invoked before, after, or in
 between runs.  For these an instance of the class is created, its
 command() method called and then, after completion, the class instance
 deleted.  Examples for this are the create_box, create_atoms, minimize,
-run, or velocity command styles.
+run, set, or velocity command styles.
 
 For all those ``styles`` certain naming conventions are employed: for
 the fix nve command the class is called FixNVE and the source files are
@@ -175,11 +175,11 @@ follows:
 - The Input class reads and processes input input strings and files,
   stores variables, and invokes :doc:`commands <Commands_all>`.
 
-- As discussed above, command style classes are directly derived from
-  the Pointers class. They provide input script commands that perform
-  one-time operations before/after/between simulations or which invoke a
-  simulation.  They are instantiated from within the Input class,
-  invoked, then immediately destructed.
+- Command style classes are derived from the Command class. They provide
+  input script commands that perform one-time operations
+  before/after/between simulations or which invoke a simulation.  They
+  are usually instantiated from within the Input class, its ``command``
+  method invoked, and then immediately destructed.
 
 - The Finish class is instantiated to print statistics to the screen
   after a simulation is performed, by commands like run and minimize.

doc/src/Developer_plugins.rst

@@ -59,31 +59,25 @@ Members of ``lammpsplugin_t``
    * - author
      - String with the name and email of the author
    * - creator.v1
-     - Pointer to factory function for pair, bond, angle, dihedral, or improper styles
+     - Pointer to factory function for pair, bond, angle, dihedral, improper or command styles
    * - creator.v2
      - Pointer to factory function for compute, fix, or region styles
-   * - creator.v3
-     - Pointer to factory function for command styles
    * - handle
      - Pointer to the open DSO file handle
 
 Only one of the three alternate creator entries can be used at a time
-and which of those is determined by the style of plugin. The "creator.v1"
-element is for factory functions of supported styles computing forces (i.e.
-pair, bond, angle, dihedral, or improper styles) and the function takes
-as single argument the pointer to the LAMMPS instance. The factory function
-is cast to the ``lammpsplugin_factory1`` type before assignment.  The
-"creator.v2" element is for factory functions creating an instance of
-a fix, compute, or region style and takes three arguments: a pointer to
-the LAMMPS instance, an integer with the length of the argument list and
-a ``char **`` pointer to the list of arguments. The factory function pointer
-needs to be cast to the ``lammpsplugin_factory2`` type before assignment.
-The "creator.v3" element takes the same arguments as "creator.v3" but is
-specific to creating command styles: the factory function has to instantiate
-the command style locally passing the LAMMPS pointer as argument and then
-call its "command" member function with the number and list of arguments.
-The factory function pointer needs to be cast to the
-``lammpsplugin_factory3`` type before assignment.
+and which of those is determined by the style of plugin. The
+"creator.v1" element is for factory functions of supported styles
+computing forces (i.e.  command, pair, bond, angle, dihedral, or
+improper styles) and the function takes as single argument the pointer
+to the LAMMPS instance. The factory function is cast to the
+``lammpsplugin_factory1`` type before assignment.  The "creator.v2"
+element is for factory functions creating an instance of a fix, compute,
+or region style and takes three arguments: a pointer to the LAMMPS
+instance, an integer with the length of the argument list and a ``char
+**`` pointer to the list of arguments. The factory function pointer
+needs to be cast to the ``lammpsplugin_factory2`` type before
+assignment.
 
 Pair style example
 ^^^^^^^^^^^^^^^^^^
@@ -123,12 +117,12 @@ function would look like this:
 
 The factory function in this example is called ``morse2creator()``.  It
 receives a pointer to the LAMMPS class as only argument and thus has to
-be assigned to the *creator.v1* member of the plugin struct and cast to the
-``lammpsplugin_factory1`` pointer type.  It returns a
+be assigned to the *creator.v1* member of the plugin struct and cast to
+the ``lammpsplugin_factory1`` function pointer type.  It returns a
 pointer to the allocated class instance derived from the ``Pair`` class.
-This function may be declared static to avoid clashes with other plugins.
-The name of the derived class, ``PairMorse2``, must be unique inside
-the entire LAMMPS executable.
+This function may be declared static to avoid clashes with other
+plugins.  The name of the derived class, ``PairMorse2``, however must be
+unique inside the entire LAMMPS executable.
 
 Fix style example
 ^^^^^^^^^^^^^^^^^
@@ -169,9 +163,9 @@ Below is an example for that:
 
 Command style example
 ^^^^^^^^^^^^^^^^^^^^^
-For command styles there is a third variant of factory function as
+Command styles also use the first variant of factory function as
 demonstrated in the following example, which also shows that the
-implementation of the plugin class may also be within the same
+implementation of the plugin class may be within the same source
 file as the plugin interface code:
 
 .. code-block:: C++
@@ -180,15 +174,15 @@ file as the plugin interface code:
 
    #include "comm.h"
    #include "error.h"
-   #include "pointers.h"
+   #include "command.h"
    #include "version.h"
 
    #include <cstring>
 
    namespace LAMMPS_NS {
-     class Hello : protected Pointers {
+     class Hello : public Command {
       public:
-       Hello(class LAMMPS *lmp) : Pointers(lmp) {};
+       Hello(class LAMMPS *lmp) : Command(lmp) {};
        void command(int, char **);
      };
    }
@@ -202,10 +196,9 @@ file as the plugin interface code:
         utils::logmesg(lmp,fmt::format("Hello, {}!\n",argv[0]));
    }
 
-   static void hellocreator(LAMMPS *lmp, int argc, char **argv)
+   static void hellocreator(LAMMPS *lmp)
    {
-     Hello hello(lmp);
-     hello.command(argc,argv);
+     return new Hello(lmp);
    }
 
    extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
@@ -216,9 +209,9 @@ file as the plugin interface code:
      plugin.version = LAMMPS_VERSION;
      plugin.style   = "command";
      plugin.name    = "hello";
-     plugin.info    = "Hello world command v1.0";
+     plugin.info    = "Hello world command v1.1";
      plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
-     plugin.creator.v3 = (lammpsplugin_factory3 *) &hellocreator;
+     plugin.creator.v1 = (lammpsplugin_factory1 *) &hellocreator;
      plugin.handle  = handle;
      (*register_plugin)(&plugin,lmp);
    }

doc/src/Developer_utils.rst

@@ -9,14 +9,29 @@ reading or writing to files with error checking or translation of
 strings into specific types of numbers with checking for validity.  This
 reduces redundant implementations and encourages consistent behavior.
 
-I/O with status check
-^^^^^^^^^^^^^^^^^^^^^
+I/O with status check and similar functions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-These are wrappers around the corresponding C library calls like
-``fgets()`` or ``fread()``.  They will check if there were errors
-on reading or an unexpected end-of-file state was reached.  In that
-case, the functions will stop the calculation with an error message,
-indicating the name of the problematic file, if possible.
+The the first two functions are wrappers around the corresponding C
+library calls ``fgets()`` or ``fread()``.  They will check if there
+were errors on reading or an unexpected end-of-file state was reached.
+In that case, the functions will stop with an error message, indicating
+the name of the problematic file, if possible unless the *error* argument
+is a NULL pointer.
+
+The :cpp:func:`fgets_trunc` function will work similar for ``fgets()``
+but it will read in a whole line (i.e. until the end of line or end
+of file), but store only as many characters as will fit into the buffer
+including a final newline character and the terminating NULL byte.
+If the line in the file is longer it will thus be truncated in the buffer.
+This function is used by :cpp:func:`read_lines_from_file` to read individual
+lines but make certain they follow the size constraints.
+
+The :cpp:func:`read_lines_from_file` function will read the requested
+number of lines of a maximum length into a buffer and will return 0
+if successful or 1 if not. It also guarantees that all lines are
+terminated with a newline character and the entire buffer with a
+NULL character.
 
 ----------
 
@@ -26,6 +41,12 @@ indicating the name of the problematic file, if possible.
 .. doxygenfunction:: sfread
    :project: progguide
 
+.. doxygenfunction:: fgets_trunc
+   :project: progguide
+
+.. doxygenfunction:: read_lines_from_file
+   :project: progguide
+
 ----------
 
 String to number conversions with validity check
@@ -164,7 +185,10 @@ Argument processing
 Convenience functions
 ^^^^^^^^^^^^^^^^^^^^^
 
-.. doxygenfunction:: logmesg
+.. doxygenfunction:: logmesg(LAMMPS *lmp, const S &format, Args&&... args)
+   :project: progguide
+
+.. doxygenfunction:: logmesg(LAMMPS *lmp, const std::string &mesg)
    :project: progguide
 
 .. doxygenfunction:: getsyserror

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://lammps.sandia.gov>`_ or the
+   <https://www.lammps.org/bug.html>`_ section of the `LAMMPS WWW site
+   <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
@@ -108,6 +108,8 @@ Lowercase directories
 +-------------+------------------------------------------------------------------+
 | msst        | MSST shock dynamics                                              |
 +-------------+------------------------------------------------------------------+
+| multi       | multi neighboring for systems with large interaction disparities |
++-------------+------------------------------------------------------------------+
 | nb3b        | use of non-bonded 3-body harmonic pair style                     |
 +-------------+------------------------------------------------------------------+
 | neb         | nudged elastic band (NEB) calculation for barrier finding        |
@@ -164,7 +166,7 @@ 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
@@ -23,6 +23,7 @@ General howto
    Howto_library
    Howto_couple
    Howto_client_server
+   Howto_mdi
 
 Settings howto
 ==============

doc/src/Howto_drude2.rst

@@ -9,6 +9,8 @@ USER-DRUDE package activated. Then, the data file and input scripts
 have to be modified to include the Drude dipoles and how to handle
 them.
 
+Example input scripts available: examples/USER/drude
+
 ----------
 
 **Overview of Drude induced dipoles**

doc/src/Howto_mdi.rst

@@ -0,0 +1,132 @@
+Using LAMMPS with the MDI library for code coupling
+===================================================
+
+.. note::
+
+  This Howto doc page will eventually replace the
+  :doc:`Howto client/server <Howto_client_server>` doc page.
+
+Client/server coupling of two codes is where one code is the "client"
+and sends request messages (data) to a "server" code.  The server
+responds to each request with a reply message.  This enables the two
+codes to work in tandem to perform a simulation.  LAMMPS can act as
+either a client or server code; it does this by using the `MolSSI
+Driver Interface (MDI) library
+<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_,
+developed by the `Molecular Sciences Software Institute (MolSSI)
+<https://molssi.org>`_.
+
+Alternate methods for code coupling with LAMMPS are described on the
+:doc:`Howto couple <Howto_couple>` doc page.
+
+Some advantages of client/server coupling are that the two codes can run
+as stand-alone executables; they need not be linked together.  Thus
+neither code needs to have a library interface.  This also makes it easy
+to run the two codes on different numbers of processors.  If a message
+protocol (format and content) is defined for a particular kind of
+simulation, then in principle any code which implements the client-side
+protocol can be used in tandem with any code which implements the
+server-side protocol.  Neither code needs to know what specific other
+code it is working with.
+
+In MDI nomenclature, a client code is the "driver", and a server code is
+an "engine".  One driver code can communicate with one or more instances
+of one or more engine codes.  Driver and engine codes can be written in
+any language: C, C++, Fortran, Python, etc.
+
+In addition to allowing driver and engine(s) running to run as
+stand-alone executables, MDI also enables a server code to be a
+"plugin" to the client code.  In this scenario, server code(s) are
+compiled as shared libraries, and one (or more) instances of the
+server are instantiated by the driver code.  If the driver code runs
+in parallel, it can split its MPI communicator into multiple
+sub-communicators, and launch each plugin engine instance on a
+sub-communicator.  Driver processors in that sub-communicator exchange
+messages with that engine instance, and can also send MPI messages to
+other processors in the driver.  The driver code can also destroy
+engine instances and re-instantiate them.
+
+The way that a driver communicates with an engine is by making
+MDI_Send() and MDI_Recv() calls, which are conceptually similar to
+MPI_Send() and MPI_Recv() calls.  Each send or receive has a string
+which identifies the command name, and optionally some data, which can
+be a single value or vector of values of any data type.  Inside the
+MDI library, data is exchanged between the driver and engine via MPI
+calls or sockets.  This a run-time choice by the user.
+
+-------------
+
+As an example, LAMMPS and the ``pw.x`` command from Quantum Espresso (a
+suite of quantum DFT codes), can work together via the MDI library to
+perform an ab initio MD (AIMD) simulation, where LAMMPS runs an MD
+simulation and sends a message each timestep to ``pw.x`` asking it to
+compute quantum forces on the current configuration of atoms.  Here is
+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" \
+     -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.
+
+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 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
+"&" so as to run in the background.  If "localhost" is replaced by an
+IP address, ``pw.x`` could be run on another machine on the same network, or
+even on another machine across the country.
+
+After both codes initialize themselves to model the same system, this is
+what occurs each timestep:
+
+* LAMMPS send a ">COORDS" message to ``pw.x`` with a 3*N vector of current atom coords
+* ``pw.x`` receives the message/coords and computes quantum forces on all the atoms
+* LAMMPS send a "<FORCES" message to ``pw.x`` and waits for the result
+* ``pw.x`` receives the message (after its computation finishes) and sends a 3*N vector of forces
+* LAMMPS receives the forces and time integrates to complete a single timestep
+
+-------------
+
+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::
+
+  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
+  scripts for this usage mode will be added the same directory when
+  available.
+
+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.
+When the driver sends an "EXIT" command, LAMMPS will exit engine mode
+and the input script will continue.
+
+If LAMMPS is used as a plugin engine it operates the same way, except
+that the driver will pass LAMMPS an input script to initialize itself.
+Upon receiving the "EXIT" command, LAMMPS will exit engine mode and the
+input script will continue.  After finishing execution of the input
+script, the instance of LAMMPS will be destroyed.
+
+LAMMPS supports the full set of MD-appropriate engine commands defined
+by the MDI library.  See the :doc:`mdi/engine <mdi_engine>` doc page for
+a list of these.
+
+If those commands are not sufficient for a user-developed driver to use
+LAMMPS as an engine, then new commands can be easily added.  See these
+two files which implement the definition of MDI commands and the logic
+for responding to them:
+
+* src/MDI/mdi_engine.cpp
+* src/MDI/fix_mdi_engine.cpp

doc/src/Howto_spins.rst

@@ -21,8 +21,8 @@ orientations and their associated inter-atomic distances.
 
 The command :doc:`fix precession/spin <fix_precession_spin>` allows to
 apply a constant magnetic torque on all the spins in the system. This
-torque can be an external magnetic field (Zeeman interaction), or an
-uniaxial magnetic anisotropy.
+torque can be an external magnetic field (Zeeman interaction), and an
+uniaxial or cubic magnetic anisotropy.
 
 A Langevin thermostat can be applied to those magnetic spins using
 :doc:`fix langevin/spin <fix_langevin_spin>`. Typically, this thermostat

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
-.. _bug: https://lammps.sandia.gov/bug.html
-.. _older: https://lammps.sandia.gov/tars
-.. _lws: https://lammps.sandia.gov
+.. _download: https://www.lammps.org/download.html
+.. _bug: https://www.lammps.org/bug.html
+.. _older: https://www.lammps.org/tars
+.. _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/
-<https://lammps.sandia.gov>`_ is the canonical location for information
+The LAMMPS website at `https://www.lammps.org/
+<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
-modify the code however you wish.
+terms of the `GNU Public License Version 2 <gpl_>`_, which means you can
+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
-is often referred to as open-source distribution - see
-`www.gnu.org <gnuorg_>`_ or `www.opensource.org <opensource_>`_.  The legal
-text of the GPL is in the LICENSE file included in the LAMMPS
+charge, under the terms of the `GNU Public License Version 2 <gpl_>`_
+(GPLv2).  This is often referred to as open-source distribution - see
+`www.gnu.org <gnuorg_>`_ or `www.opensource.org <opensource_>`_.  The
+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
-open-source, meaning you distribute it under the terms of the GPL.
-You should clearly annotate such a code as a derivative version of
-LAMMPS.
+(2) If you **distribute** a modified version of LAMMPS, it must remain
+open-source, meaning you distribute **all** of it under the terms of
+the GPL.  You should clearly annotate such a code as a derivative version
+of LAMMPS.
 
-(3) If you release any code that includes LAMMPS source code, then it
-must also be open-sourced, meaning you distribute it under the terms
-of the GPL.
+(3) If you release any code that includes or uses LAMMPS source code,
+then it must also be open-sourced, meaning you distribute it under
+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 non-features <https://lammps.sandia.gov/doc/Intro_nonfeatures.html>`_
-* `Recent bug fixes and new features <https://lammps.sandia.gov/bug.html>`_
+* `List of features <https://docs.lammps.org/Intro_features.html>`_
+* `List of non-features <https://docs.lammps.org/Intro_nonfeatures.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>`_
-* `LAMMPS highlights with images <https://lammps.sandia.gov/pictures.html>`_
-* `LAMMPS highlights with movies <https://lammps.sandia.gov/movies.html>`_
-* `Mail list <https://lammps.sandia.gov/mail.html>`_
-* `Workshops <https://lammps.sandia.gov/workshops.html>`_
-* `Tutorials <https://lammps.sandia.gov/tutorials.html>`_
+* `Glossary of terms relevant to LAMMPS <https://www.lammps.org/glossary.html>`_
+* `LAMMPS highlights with images <https://www.lammps.org/pictures.html>`_
+* `LAMMPS highlights with movies <https://www.lammps.org/movies.html>`_
+* `Mail list <https://www.lammps.org/mail.html>`_
+* `Workshops <https://www.lammps.org/workshops.html>`_
+* `Tutorials <https://www.lammps.org/tutorials.html>`_
 
-* `Pre- and post-processing tools for LAMMPS <https://lammps.sandia.gov/prepost.html>`_
-* `Other software usable with LAMMPS <https://lammps.sandia.gov/offsite.html>`_
-* `Viz tools usable with LAMMPS <https://lammps.sandia.gov/viz.html>`_
+* `Pre- and post-processing tools for LAMMPS <https://www.lammps.org/prepost.html>`_
+* `Other software usable with LAMMPS <https://www.lammps.org/offsite.html>`_
+* `Viz tools usable with LAMMPS <https://www.lammps.org/viz.html>`_
 
-* `Benchmark performance <https://lammps.sandia.gov/bench.html>`_
-* `Publications that have cited LAMMPS <https://lammps.sandia.gov/papers.html>`_
-* `Authors of LAMMPS <https://lammps.sandia.gov/authors.html>`_
-* `History of LAMMPS development <https://lammps.sandia.gov/history.html>`_
-* `Funding for LAMMPS <https://lammps.sandia.gov/funding.html>`_
+* `Benchmark performance <https://www.lammps.org/bench.html>`_
+* `Publications that have cited LAMMPS <https://www.lammps.org/papers.html>`_
+* `Authors of LAMMPS <https://www.lammps.org/authors.html>`_
+* `History of LAMMPS development <https://www.lammps.org/history.html>`_
+* `Funding for LAMMPS <https://www.lammps.org/funding.html>`_

doc/src/Library_config.rst

@@ -15,6 +15,8 @@ This section documents the following functions:
 - :cpp:func:`lammps_config_package_count`
 - :cpp:func:`lammps_config_package_name`
 - :cpp:func:`lammps_config_accelerator`
+- :cpp:func:`lammps_has_gpu_device`
+- :cpp:func:`lammps_gpu_device_info`
 - :cpp:func:`lammps_has_style`
 - :cpp:func:`lammps_style_count`
 - :cpp:func:`lammps_style_name`
@@ -132,6 +134,16 @@ approach.
 
 -----------------------
 
+.. doxygenfunction:: lammps_has_gpu_device
+   :project: progguide
+
+-----------------------
+
+.. doxygenfunction:: lammps_get_gpu_device_info
+   :project: progguide
+
+-----------------------
+
 .. doxygenfunction:: lammps_has_style
    :project: progguide
 

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: index
-   :hidden:
+   :name: reference
+   :maxdepth: 1
+   :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_command.rst

@@ -1,14 +1,15 @@
 Input script command style
 ==========================
 
-New commands can be added to LAMMPS input scripts by adding new
-classes that have a "command" method.  For example, the create_atoms,
-read_data, velocity, and run commands are all implemented in this
-fashion.  When such a command is encountered in the LAMMPS input
-script, LAMMPS simply creates a class with the corresponding name,
-invokes the "command" method of the class, and passes it the arguments
-from the input script.  The command method can perform whatever
-operations it wishes on LAMMPS data structures.
+New commands can be added to LAMMPS input scripts by adding new classes
+that are derived from the Command class and thus must have a "command"
+method.  For example, the create_atoms, read_data, velocity, and run
+commands are all implemented in this fashion.  When such a command is
+encountered in the LAMMPS input script, LAMMPS simply creates a class
+instance with the corresponding name, invokes the "command" method of
+the class, and passes it the arguments from the input script.  The
+command method can perform whatever operations it wishes on LAMMPS data
+structures.
 
 The single method your new class must define is as follows:
 

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
-contact, how complex a task it would be to integrate that code, and how
+contribution included, depending on how busy the respective developer
+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
-implementation strategies and coding guidelines, that will make it
-easier to integrate your contribution and result in less work for
-everybody involved. You are also encouraged to search through the list
+to contact the LAMMPS developers ahead of time in order to discuss
+implementation strategies and coding guidelines. That will make it
+easier to integrate your contribution and results in less work for
+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
-changes to the core codebase, and of how much interest it is to the
-larger LAMMPS community.  Please see below for a checklist of typical
-requirements. Once you have prepared everything, see the :doc:`LAMMPS GitHub
-Tutorial <Howto_github>` page for instructions on
-how to submit your changes or new files through a GitHub pull
-request. If you prefer to submit patches or full files, you should first
-make certain, that your code works correctly with the latest patch-level
-version of LAMMPS and contains all bug fixes from it. Then create a
-gzipped tar file of all changed or added files or a corresponding patch
-file using 'diff -u' or 'diff -c' and compress it with gzip. Please only
-use gzip compression, as this works well on all platforms.
+much effort it will cause to integrate and test it, how many and what
+kind of changes it requires to the core codebase, and of how much
+interest it is to the larger LAMMPS community.  Please see below for a
+checklist of typical requirements.  Once you have prepared everything,
+see the :doc:`LAMMPS GitHub Tutorial <Howto_github>` page for
+instructions on how to submit your changes or new files through a GitHub
+pull request.  If you prefer to submit patches or full files, you should
+first make certain, that your code works correctly with the latest
+patch-level version of LAMMPS and contains all bug fixes from it.  Then
+create a gzipped tar file of all changed or added files or a
+corresponding patch file using 'diff -u' or 'diff -c' and compress it
+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,
-used as a license for the rest of LAMMPS.  See the :doc:`LAMMPS license
-<Intro_opensource>` doc page for details.
+them open-source, i.e. we can release them under the terms of the GPL
+(version 2), used as a license for the rest of LAMMPS.  And as part of
+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

@@ -69,6 +69,7 @@ page gives those details.
    * :ref:`USER-ATC <PKG-USER-ATC>`
    * :ref:`USER-AWPMD <PKG-USER-AWPMD>`
    * :ref:`USER-BOCS <PKG-USER-BOCS>`
+   * :ref:`USER-BROWNIAN <PKG-USER-BROWNIAN>`
    * :ref:`USER-CGDNA <PKG-USER-CGDNA>`
    * :ref:`USER-CGSDK <PKG-USER-CGSDK>`
    * :ref:`USER-COLVARS <PKG-USER-COLVARS>`
@@ -78,9 +79,11 @@ 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>`
+   * :ref:`USER-MDI <PKG-USER-MDI>`
    * :ref:`USER-MEAMC <PKG-USER-MEAMC>`
    * :ref:`USER-MESODPD <PKG-USER-MESODPD>`
    * :ref:`USER-MESONT <PKG-USER-MESONT>`
@@ -90,12 +93,14 @@ page gives those details.
    * :ref:`USER-MOLFILE <PKG-USER-MOLFILE>`
    * :ref:`USER-NETCDF <PKG-USER-NETCDF>`
    * :ref:`USER-OMP <PKG-USER-OMP>`
+   * :ref:`USER-PACE <PKG-USER-PACE>`
    * :ref:`USER-PHONON <PKG-USER-PHONON>`
    * :ref:`USER-PLUMED <PKG-USER-PLUMED>`
    * :ref:`USER-PTM <PKG-USER-PTM>`
    * :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>`
@@ -130,8 +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://lammps.sandia.gov/movies.html#tri
+* https://www.lammps.org/movies.html#line
+* https://www.lammps.org/movies.html#tri
 
 ----------
 
@@ -327,7 +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
 
 ----------
 
@@ -353,11 +358,11 @@ potentials.
 * examples/granregion
 * examples/pour
 * bench/in.chute
-* https://lammps.sandia.gov/pictures.html#jamming
-* https://lammps.sandia.gov/movies.html#hopper
-* https://lammps.sandia.gov/movies.html#dem
-* https://lammps.sandia.gov/movies.html#brazil
-* https://lammps.sandia.gov/movies.html#granregion
+* https://www.lammps.org/pictures.html#jamming
+* https://www.lammps.org/movies.html#hopper
+* https://www.lammps.org/movies.html#dem
+* https://www.lammps.org/movies.html#brazil
+* https://www.lammps.org/movies.html#granregion
 
 ----------
 
@@ -444,7 +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
@@ -476,7 +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
 
 ----------
 
@@ -585,7 +590,7 @@ MC package
 Several fixes and a pair style that have Monte Carlo (MC) or MC-like
 attributes.  These include fixes for creating, breaking, and swapping
 bonds, for performing atomic swaps, and performing grand-canonical MC
-(GCMC) in conjunction with dynamics.
+(GCMC) or similar processes in conjunction with dynamics.
 
 **Supporting info:**
 
@@ -593,10 +598,14 @@ bonds, for performing atomic swaps, and performing grand-canonical MC
 * :doc:`fix atom/swap <fix_atom_swap>`
 * :doc:`fix bond/break <fix_bond_break>`
 * :doc:`fix bond/create <fix_bond_create>`
+* :doc:`fix bond/create/angle <fix_bond_create>`
 * :doc:`fix bond/swap <fix_bond_swap>`
+* :doc:`fix charge/regulation <fix_charge_regulation>`
 * :doc:`fix gcmc <fix_gcmc>`
+* :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
 
 ----------
 
@@ -653,8 +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://lammps.sandia.gov/movies.html#evaporation
+* https://www.lammps.org/pictures.html#ttm
+* https://www.lammps.org/movies.html#evaporation
 
 ----------
 
@@ -809,7 +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
 
 ----------
 
@@ -840,7 +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
 
 ----------
 
@@ -1001,8 +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://lammps.sandia.gov/movies.html#star
+* https://www.lammps.org/movies.html#box
+* https://www.lammps.org/movies.html#star
 
 ----------
 
@@ -1103,9 +1112,9 @@ colloidal particles.
 * :doc:`fix wall/srd <fix_wall_srd>`
 * examples/srd
 * examples/ASPHERE
-* https://lammps.sandia.gov/movies.html#tri
-* https://lammps.sandia.gov/movies.html#line
-* https://lammps.sandia.gov/movies.html#poly
+* https://www.lammps.org/movies.html#tri
+* https://www.lammps.org/movies.html#line
+* https://www.lammps.org/movies.html#poly
 
 ----------
 
@@ -1197,7 +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
 
 ----------
 
@@ -1261,6 +1270,26 @@ Example inputs are in the examples/USER/bocs folder.
 
 ----------
 
+.. _PKG-USER-BROWNIAN:
+
+USER-BROWNIAN package
+---------------------
+
+**Contents:**
+
+This package provides :doc:`fix brownian, fix brownian/sphere, and
+fix brownian/asphere <fix_brownian>` as well as
+:doc:`fix propel/self <fix_propel_self>` which allow to do Brownian
+Dynamics time integration of point, spherical and aspherical particles
+and also support self-propelled particles.
+
+**Authors:** Sam Cameron (University of Bristol),
+Stefan Paquay (while at Brandeis University) (initial version of fix propel/self)
+
+Example inputs are in the examples/USER/brownian folder.
+
+----------
+
 .. _PKG-USER-CGDNA:
 
 USER-CGDNA package
@@ -1310,7 +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
 
 ----------
 
@@ -1349,6 +1378,46 @@ This package has :ref:`specific installation instructions <user-colvars>` on the
 
 ----------
 
+.. _PKG-USER-PACE:
+
+USER-PACE package
+-------------------
+
+**Contents:**
+
+A pair style for the Atomic Cluster Expansion potential (ACE).
+ACE is a methodology for deriving a highly accurate classical potential
+fit to a large archive of quantum mechanical (DFT) data. The USER-PACE
+package provides an efficient implementation for running simulations
+with ACE potentials.
+
+**Authors:**
+
+This package was written by Yury Lysogorskiy^1,
+Cas van der Oord^2, Anton Bochkarev^1,
+Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
+Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1.
+
+ ^1: Ruhr-University Bochum, Bochum, Germany
+
+ ^2: University of Cambridge, Cambridge, United Kingdom
+
+ ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
+
+ ^4: University of British Columbia, Vancouver, BC, Canada
+
+**Install:**
+
+This package has :ref:`specific installation instructions <user-pace>` on the :doc:`Build extras <Build_extras>` page.
+
+**Supporting info:**
+
+* src/USER-PACE: filenames -> commands
+* :doc:`pair_style pace <pair_pace>`
+* examples/USER/pace
+
+----------
+
 .. _PKG-USER-PLUMED:
 
 USER-PLUMED package
@@ -1507,7 +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
 
 ----------
 
@@ -1572,6 +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
@@ -1616,7 +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
 
 ----------
 
@@ -1721,7 +1823,29 @@ 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
+
+----------
+
+.. _PKG-USER-MDI:
+
+USER-MDI package
+----------------
+
+**Contents:**
+
+A LAMMPS command and fix to allow client-server coupling of LAMMPS to
+other atomic or molecular simulation codes via the `MolSSI Driver Interface
+(MDI) library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_.
+
+**Author:** Taylor Barnes - MolSSI, taylor.a.barnes at gmail.com
+
+**Supporting info:**
+
+* src/USER-MDI/README
+* :doc:`mdi/engine <mdi_engine>`
+* :doc:`fix mdi/engine <fix_mdi_engine>`
+* examples/USER/mdi
 
 ----------
 
@@ -1777,10 +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
 
 ----------
 
@@ -1996,7 +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
 
 ----------
 
@@ -2154,6 +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
@@ -2179,8 +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>`_
-* `2019 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug19/talk_gissinger.pdf>`_
+* `2017 LAMMPS Workshop <https://www.lammps.org/workshops/Aug17/pdf/gissinger.pdf>`_
+* `2019 LAMMPS Workshop <https://www.lammps.org/workshops/Aug19/talk_gissinger.pdf>`_
 * reacter.org
 
 ----------
@@ -2307,7 +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
 
 ----------
 
@@ -2364,7 +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

@@ -39,6 +39,8 @@ package:
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-BOCS <PKG-USER-BOCS>`               | BOCS bottom up coarse graining                                  | :doc:`fix bocs <fix_bocs>`                                                    | USER/bocs                                            | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
+| :ref:`USER-BROWNIAN <PKG-USER-BROWNIAN>`       | Brownian dynamics and self-propelled particles                  | :doc:`fix brownian <fix_brownian>`, :doc:`fix propel/self <fix_propel_self>`  | USER/brownian                                        | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-CGDNA <PKG-USER-CGDNA>`             | coarse-grained DNA force fields                                 | src/USER-CGDNA/README                                                         | USER/cgdna                                           | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-CGSDK <PKG-USER-CGSDK>`             | SDK coarse-graining model                                       | :doc:`pair_style lj/sdk <pair_sdk>`                                           | USER/cgsdk                                           | no      |
@@ -57,12 +59,16 @@ 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      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>`       | motion on 2d surfaces                                           | :doc:`fix manifoldforce <fix_manifoldforce>`                                  | USER/manifold                                        | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
+| :ref:`USER-MDI <PKG-USER-MDI>`                 | client-server coupling                                          | :doc:`MDI Howto <Howto_mdi>`                                                  | USER/mdi                                             | ext     |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-MEAMC <PKG-USER-MEAMC>`             | modified EAM potential (C++)                                    | :doc:`pair_style meam/c <pair_meamc>`                                         | meamc                                                | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-MESODPD <PKG-USER-MESODPD>`         | mesoscale DPD models                                            | :doc:`pair_style edpd <pair_mesodpd>`                                         | USER/mesodpd                                         | no      |
@@ -79,7 +85,9 @@ 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     |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-PHONON <PKG-USER-PHONON>`           | phonon dynamical matrix                                         | :doc:`fix phonon <fix_phonon>`                                                | USER/phonon                                          | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
@@ -93,6 +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>`_
-* `Offsite LAMMPS packages & tools <https://lammps.sandia.gov/offsite.html>`_
+* `Pre/Post processing <https://www.lammps.org/prepost.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
 
@@ -94,6 +94,7 @@ Miscellaneous tools
    * :ref:`kate <kate>`
    * :ref:`LAMMPS shell <lammps_shell>`
    * :ref:`LAMMPS magic patterns for file(1) <magic>`
+   * :ref:`Offline build tool <offline>`
    * :ref:`singularity <singularity_tool>`
    * :ref:`SWIG interface <swig>`
    * :ref:`vim <vim>`
@@ -756,6 +757,103 @@ See the README file in the tools/msi2lmp folder for more information.
 
 ----------
 
+.. _offline:
+
+Scripts for building LAMMPS when offline
+----------------------------------------
+
+In some situations it might be necessary to build LAMMPS on a system
+without direct internet access. The scripts in ``tools/offline`` folder
+allow you to pre-load external dependencies for both the documentation
+build and for building LAMMPS with CMake.
+
+It does so by
+
+ #. downloading necessary ``pip`` packages,
+ #. cloning ``git`` repositories
+ #. downloading tarballs
+
+to a designated cache folder.
+
+As of April 2021, all of these downloads make up around 600MB. By
+default, the offline scripts will download everything into the
+``$HOME/.cache/lammps`` folder, but this can be changed by setting the
+``LAMMPS_CACHING_DIR`` environment variable.
+
+Once the caches have been initialized, they can be used for building the
+LAMMPS documentation or compiling LAMMPS using CMake on an offline
+system.
+
+The ``use_caches.sh`` script must be sourced into the current shell
+to initialize the offline build environment. Note that it must use
+the same ``LAMMPS_CACHING_DIR``. This script does the following:
+
+ #. Set up environment variables that modify the behavior of both,
+    ``pip`` and ``git``
+ #. Start a simple local HTTP server using Python to host files for CMake
+
+Afterwards, it will print out instruction on how to modify the CMake
+command line to make sure it uses the local HTTP server.
+
+To undo the environment changes and shutdown the local HTTP server,
+run the ``deactivate_caches`` command.
+
+Examples
+^^^^^^^^
+
+For all of the examples below, you first need to create the cache, which
+requires an internet connection.
+
+.. code-block:: bash
+
+   ./tools/offline/init_caches.sh
+
+Afterwards, you can disconnect or copy the contents of the
+``LAMMPS_CACHING_DIR`` folder to an offline system.
+
+Documentation Build
+^^^^^^^^^^^^^^^^^^^
+
+The documentation build will create a new virtual environment that
+typically first installs dependencies from ``pip``. With the offline
+environment loaded, these installations will instead grab the necessary
+packages from your local cache.
+
+.. code-block:: bash
+
+   # if LAMMPS_CACHING_DIR is different from default, make sure to set it first
+   # export LAMMPS_CACHING_DIR=path/to/folder
+   source tools/offline/use_caches.sh
+   cd doc/
+   make html
+
+   deactivate_caches
+
+CMake Build
+^^^^^^^^^^^
+
+When compiling certain packages with external dependencies, the CMake
+build system will download necessary files or sources from the web. For
+more flexibility the CMake configuration allows users to specify the URL
+of each of these dependencies.  What the ``init_caches.sh`` script does
+is create a CMake "preset" file, which sets the URLs for all of the known
+dependencies and redirects the download to the local cache.
+
+.. code-block:: bash
+
+   # if LAMMPS_CACHING_DIR is different from default, make sure to set it first
+   # export LAMMPS_CACHING_DIR=path/to/folder
+   source tools/offline/use_caches.sh
+
+   mkdir build
+   cd build
+   cmake -D LAMMPS_DOWNLOADS_URL=${HTTP_CACHE_URL} -C "${LAMMPS_HTTP_CACHE_CONFIG}" -C ../cmake/presets/most.cmake ../cmake
+   make -j 8
+
+   deactivate_caches
+
+----------
+
 .. _phonon:
 
 phonon tool

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/atom_style.rst

@@ -27,7 +27,7 @@ Syntax
            template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command
          *hybrid* args = list of one or more sub-styles, each with their args
 
-* accelerated styles (with same args) = *angle/kk* or *atomic/kk* or *bond/kk* or *charge/kk* or *full/kk* or *molecular/kk*
+* accelerated styles (with same args) = *angle/kk* or *atomic/kk* or *bond/kk* or *charge/kk* or *full/kk* or *molecular/kk* or *spin/kk*
 
 Examples
 """"""""

doc/src/balance.rst

@@ -257,7 +257,7 @@ factor, similar to how the :doc:`fix balance shift <fix_balance>`
 command operates.
 
 The *dimstr* argument is a string of characters, each of which must be
-an "x" or "y" or "z".  Eacn character can appear zero or one time,
+an "x" or "y" or "z". Each character can appear zero or one time,
 since there is no advantage to balancing on a dimension more than
 once.  You should normally only list dimensions where you expect there
 to be a density variation in the particles.
@@ -285,7 +285,7 @@ plane gets closer to the target value.
 
 After the balanced plane positions are determined, if any pair of
 adjacent planes are closer together than the neighbor skin distance
-(as specified by the :doc`neigh_modify <neigh_modify>` command), then
+(as specified by the :doc:`neigh_modify <neigh_modify>` command), then
 the plane positions are shifted to separate them by at least this
 amount.  This is to prevent particles being lost when dynamics are run
 with processor sub-domains that are too narrow in one or more

doc/src/comm_modify.rst

@@ -11,13 +11,17 @@ Syntax
    comm_modify keyword value ...
 
 * zero or more keyword/value pairs may be appended
-* keyword = *mode* or *cutoff* or *cutoff/multi* or *group* or *vel*
+* keyword = *mode* or *cutoff* or *cutoff/multi* or *multi/reduce* or *group* or *vel*
 
   .. parsed-literal::
 
-       *mode* value = *single* or *multi* = communicate atoms within a single or multiple distances
+       *mode* value = *single*, *multi*, or *multi/old* = communicate atoms within a single or multiple distances
        *cutoff* value = Rcut (distance units) = communicate atoms from this far away
-       *cutoff/multi* type value
+       *cutoff/multi* collection value
+          collection = atom collection or collection range (supports asterisk notation)
+          value = Rcut (distance units) = communicate atoms for selected types from this far away
+       *reduce/multi* arg = none = reduce number of communicated ghost atoms for multi style
+       *cutoff/multi/old* type value
           type = atom type or type range (supports asterisk notation)
           value = Rcut (distance units) = communicate atoms for selected types from this far away
        *group* value = group-ID = only communicate atoms in the group
@@ -28,9 +32,9 @@ Examples
 
 .. code-block:: LAMMPS
 
-   comm_modify mode multi
+   comm_modify mode multi reduce/multi
    comm_modify mode multi group solvent
-   comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0
+   comm_modify mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0
    comm_modify vel yes
    comm_modify mode single cutoff 5.0 vel yes
    comm_modify cutoff/multi * 0.0
@@ -62,12 +66,18 @@ sub-domain.  The distance is by default the maximum of the neighbor
 cutoff across all atom type pairs.
 
 For many systems this is an efficient algorithm, but for systems with
-widely varying cutoffs for different type pairs, the *multi* mode can
-be faster.  In this case, each atom type is assigned its own distance
+widely varying cutoffs for different type pairs, the *multi* or *multi/old* mode can
+be faster.  In *multi*, each atom is assigned to a collection which should
+correspond to a set of atoms with similar interaction cutoffs.
+In this case, each atom collection is assigned its own distance
 cutoff for communication purposes, and fewer atoms will be
-communicated.  See the :doc:`neighbor multi <neighbor>` command for a
-neighbor list construction option that may also be beneficial for
-simulations of this kind.
+communicated. in *multi/old*, a similar technique is used but atoms
+are grouped by atom type. See the :doc:`neighbor multi <neighbor>`  and
+:doc:`neighbor multi/old <neighbor>` commands for
+neighbor list construction options that may also be beneficial for
+simulations of this kind. The *multi* communication mode is only compatible
+with the *multi* neighbor style. The *multi/old* communication mode is comparable
+with both the *multi* and *multi/old* neighbor styles.
 
 The *cutoff* keyword allows you to extend the ghost cutoff distance
 for communication mode *single*\ , which is the distance from the borders
@@ -87,12 +97,26 @@ warning is printed, if this bond based estimate is larger than the
 communication cutoff used.
 
 The *cutoff/multi* option is equivalent to *cutoff*\ , but applies to
-communication mode *multi* instead. Since in this case the communication
-cutoffs are determined per atom type, a type specifier is needed and
-cutoff for one or multiple types can be extended. Also ranges of types
-using the usual asterisk notation can be given. For granular pair styles,
-the default cutoff is set to the sum of the current maximum atomic radii
-for each type.
+communication mode *multi* instead. Since the communication cutoffs are
+determined per atom collections, a collection specifier is needed and
+cutoff for one or multiple collections can be extended. Also ranges of
+collections using the usual asterisk notation can be given.  Collections
+are indexed from 1 to N where N is the total number of collections.
+Note that the arguments for *cutoff/multi* are parsed right before each
+simulation to account for potential changes in the number of
+collections.  Custom cutoffs are preserved between runs but if
+collections are redefined, one may want to re-specify the communication
+cutoffs.  For granular pair styles,the default cutoff is set to the sum
+of the current maximum atomic radii for each collection.  The
+*cutoff/multi/old* option is similar to *cutoff/multi* except it
+operates on atom types as opposed to collections.
+
+The *reduce/multi* option applies to *multi* and sets the communication
+cutoff for a particle equal to the maximum interaction distance between particles
+in the same collection. This reduces the number of
+ghost atoms that need to be communicated. This method is only compatible with the
+*multi* neighbor style and requires a half neighbor list and Newton on.
+See the :doc:`neighbor multi <neighbor>` command for more information.
 
 These are simulation scenarios in which it may be useful or even
 necessary to set a ghost cutoff > neighbor cutoff:
@@ -123,7 +147,7 @@ ghost cutoff should be set.
 In the last scenario, a :doc:`fix <fix>` or :doc:`compute <compute>` or
 :doc:`pairwise potential <pair_style>` needs to calculate with ghost
 atoms beyond the normal pairwise cutoff for some computation it
-performs (e.g. locate neighbors of ghost atoms in a multibody pair
+performs (e.g. locate neighbors of ghost atoms in a manybody pair
 potential).  Setting the ghost cutoff appropriately can insure it will
 find the needed atoms.
 

doc/src/commands_list.rst

@@ -59,6 +59,7 @@ Commands
    lattice
    log
    mass
+   mdi_engine
    message
    min_modify
    min_spin

doc/src/compute_fep.rst

@@ -48,6 +48,8 @@ Examples
    compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes
    compute 1 all fep 300 atom charge 2 v_delta
 
+Example input scripts available: examples/USER/fep
+
 Description
 """""""""""