Merge pull request #3873 from akohlmey/next_patch_release

Step version strings for next release

.github/CODEOWNERS

@@ -13,40 +13,45 @@ lib/kim/*             @ellio167
 lib/mesont/*          @iafoss
 
 # whole packages
+src/ADIOS/*           @pnorbert
 src/AMOEBA/*          @sjplimp
-src/COMPRESS/*        @rbberger
-src/GPU/*             @ndtrung81
-src/KOKKOS/*          @stanmoore1
-src/KIM/*             @ellio167
-src/LATTE/*           @cnegre
-src/MLIAP/*           @athomps
-src/SNAP/*            @athomps
-src/SPIN/*            @julient31
+src/BPM/*             @jtclemm
 src/BROWNIAN/*        @samueljmcameron
 src/CG-DNA/*          @ohenrich
 src/CG-SPICA/*        @yskmiyazaki
 src/COLVARS/*         @giacomofiorin
+src/COMPRESS/*        @rbberger
 src/DIELECTRIC/*      @ndtrung81
 src/ELECTRODE/*       @ludwig-ahrens
 src/FEP/*             @agiliopadua
-src/ML-HDNNP/*        @singraber
+src/GPU/*             @ndtrung81
+src/GRANULAR/*        @jtclemm @dsbolin
 src/INTEL/*           @wmbrownintel
+src/KIM/*             @ellio167
+src/KOKKOS/*          @stanmoore1
+src/LATTE/*           @cnegre
 src/MANIFOLD/*        @Pakketeretet2
-src/MDI/*             @taylor-a-barnes
+src/MDI/*             @taylor-a-barnes @sjplimp
 src/MEAM/*            @martok
 src/MESONT/*          @iafoss
+src/ML-HDNNP/*        @singraber
+src/ML-IAP/*          @athomps
+src/ML-PACE/*         @yury-lysogorskiy
+src/ML-POD/*          @exapde @rohskopf
 src/MOFFF/*           @hheenen
 src/MOLFILE/*         @akohlmey
 src/NETCDF/*          @pastewka
-src/ML-PACE/*         @yury-lysogorskiy
-src/PLUMED/*          @gtribello
-src/PHONON/*          @lingtikong
-src/PTM/*             @pmla
 src/OPENMP/*          @akohlmey
+src/PHONON/*          @lingtikong
+src/PLUGIN/*          @akohlmey
+src/PLUMED/*          @gtribello
+src/PTM/*             @pmla
 src/QMMM/*            @akohlmey
-src/REAXFF/*          @hasanmetin @stanmoore1
 src/REACTION/*        @jrgissing
+src/REAXFF/*          @hasanmetin @stanmoore1
 src/SCAFACOS/*        @rhalver
+src/SNAP/*            @athomps
+src/SPIN/*            @julient31
 src/TALLY/*           @akohlmey
 src/UEF/*             @danicholson
 src/VTK/*             @rbberger
@@ -58,7 +63,11 @@ src/MANYBODY/pair_vashishta_table.* @andeplane
 src/MANYBODY/pair_atm.*             @sergeylishchuk
 src/REPLICA/*_grem.*                @dstelter92
 src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
+src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps
 src/MISC/*_tracker.*                @jtclemm
+src/MC/fix_gcmc.*                   @athomps
+src/MC/fix_sgcmc.*                  @athomps
+src/REPLICA/fix_pimd_langevin.*     @Yi-FanLi
 
 # core LAMMPS classes
 src/lammps.*              @sjplimp
@@ -120,42 +129,46 @@ src/dump_movie.*          @akohlmey
 src/exceptions.h          @rbberger
 src/fix_nh.*              @athomps
 src/info.*                @akohlmey @rbberger
-src/timer.*               @akohlmey
 src/min*                  @sjplimp @stanmoore1
+src/platform.*            @akohlmey
+src/timer.*               @akohlmey
 src/utils.*               @akohlmey @rbberger
 src/verlet.*              @sjplimp @stanmoore1
 src/math_eigen_impl.h     @jewettaij
 
 # tools
-tools/msi2lmp/*       @akohlmey
+tools/coding_standard/* @akohlmey @rbberger
 tools/emacs/*         @HaoZeke
-tools/singularity/*   @akohlmey @rbberger
-tools/coding_standard/* @rbberger
-tools/valgrind/*      @akohlmey
-tools/swig/*          @akohlmey
+tools/lammps-shell/*  @akohlmey
+tools/msi2lmp/*       @akohlmey
 tools/offline/*       @rbberger
+tools/singularity/*   @akohlmey @rbberger
+tools/swig/*          @akohlmey
+tools/valgrind/*      @akohlmey
 tools/vim/*           @hammondkd
 
 # tests
-unittest/*            @akohlmey @rbberger
+unittest/*            @akohlmey
 
 # cmake
-cmake/*               @junghans @rbberger
-cmake/Modules/Packages/COLVARS.cmake @junghans @rbberger @giacomofiorin
-cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
+cmake/*               @rbberger
+cmake/Modules/LAMMPSInterfacePlugin.cmake @akohlmey
+cmake/Modules/MPI4WIN.cmake @akohlmey
+cmake/Modules/OpenCLLoader.cmake @akohlmey
+cmake/Modules/Packages/COLVARS.cmake @rbberger @giacomofiorin
+cmake/Modules/Packages/KIM.cmake @rbberger @ellio167
 cmake/presets/*.cmake @akohlmey
 
 # python
 python/*              @rbberger
 
 # fortran
-fortran/*             @akohlmey
+fortran/*             @akohlmey @hammondkd
 
 # docs
-doc/utils/*/*         @rbberger
-doc/Makefile          @rbberger
-doc/README            @rbberger
+doc/*                 @akohlmey
 examples/plugin/*     @akohlmey
+examples/PACKAGES/pace/plugin/*     @akohlmey
 
 # for releases
 src/version.h         @sjplimp

.github/CONTRIBUTING.md

@@ -1,6 +1,6 @@
 # Contributing to LAMMPS via GitHub
 
-Thank your for considering to contribute to the LAMMPS software project.
+Thank you for considering to contribute to the LAMMPS software project.
 
 The following is a set of guidelines as well as explanations of policies and work flows for contributing to the LAMMPS molecular dynamics software project. These guidelines focus on submitting issues or pull requests on the LAMMPS GitHub project.
 

.github/workflows/codeql-analysis.yml

@@ -49,7 +49,9 @@ jobs:
       shell: bash
       working-directory: build
       run: |
-        cmake -C ../cmake/presets/most.cmake ../cmake
+        cmake -C ../cmake/presets/most.cmake \
+              -D DOWNLOAD_POTENTIALS=off \
+              ../cmake
         cmake --build . --parallel 2
 
     - name: Perform CodeQL Analysis

.github/workflows/compile-msvc.yml

@@ -26,20 +26,25 @@ jobs:
     - name: Select Python version
       uses: actions/setup-python@v4
       with:
-        python-version: '3.10'
+        python-version: '3.11'
 
     - name: Building LAMMPS via CMake
       shell: bash
       run: |
         python3 -m pip install numpy
         python3 -m pip install pyyaml
+        nuget install MSMPIsdk
+        nuget install MSMPIDIST
         cmake -C cmake/presets/windows.cmake \
+              -D DOWNLOAD_POTENTIALS=off \
               -D PKG_PYTHON=on \
+              -D WITH_PNG=off \
+              -D WITH_JPEG=off \
               -S cmake -B build \
               -D BUILD_SHARED_LIBS=on \
               -D LAMMPS_EXCEPTIONS=on \
               -D ENABLE_TESTING=on
-        cmake --build build --config Release
+        cmake --build build --config Release --parallel 2
 
     - name: Run LAMMPS executable
       shell: bash
@@ -50,4 +55,4 @@ jobs:
     - name: Run Unit Tests
       working-directory: build
       shell: bash
-      run: ctest -V -C Release
+      run: ctest -V -C Release -E FixTimestep:python_move_nve

.github/workflows/unittest-macos.yml

@@ -47,6 +47,7 @@ jobs:
         python3 -m pip install pyyaml
         cmake -C ../cmake/presets/clang.cmake \
               -C ../cmake/presets/most.cmake \
+              -D DOWNLOAD_POTENTIALS=off \
               -D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
               -D CMAKE_C_COMPILER_LAUNCHER=ccache \
               -D ENABLE_TESTING=on \

.gitignore

@@ -55,3 +55,8 @@ out/RelWithDebInfo
 out/Release
 out/x86
 out/x64
+src/Makefile.package-e
+src/Makefile.package.settings-e
+/cmake/build/x64-Debug-Clang
+/install/x64-GUI-MSVC
+/install

SECURITY.md

@@ -30,18 +30,23 @@ for unicode characters and only all-ASCII source code is accepted.
 
 # Version Updates
 
-LAMMPS follows continuous release development model.  We aim to keep to
-keep the development version (develop branch) always fully functional
-and employ a variety of automatic testing procedures to detect failures
-of existing functionality from adding or modifying features.  Most of
-those tests are run on pull requests *before* merging to the development
-branch.  The develop branch is protected, so all changes *must* be
-submitted as a pull request and thus cannot avoid the automated tests.
+LAMMPS follows a continuous release development model.  We aim to keep
+the development version (`develop` branch) always fully functional and
+employ a variety of automatic testing procedures to detect failures of
+existing functionality from adding or modifying features.  Most of those
+tests are run on pull requests and must be passed *before* merging to
+the `develop` branch.  The `develop` branch is protected, so all changes
+*must* be submitted as a pull request and thus cannot avoid the
+automated tests.
 
 Additional tests are run *after* merging.  Before releases are made
 *all* tests must have cleared.  Then a release tag is applied and the
-release branch fast-forwarded to that tag.  Bug fixes and updates are
-applied to the current development branch and thus will be available in
-the next (patch) release.  For stable releases, selected bug fixes are
-back-ported and occasionally published as update releases.  There are
-only updates to the latest stable release.
+`release` branch is fast-forwarded to that tag.  This is referred to to
+as a "feature release".  Bug fixes and updates are applied first to the
+`develop` branch.  Later, they appear in the `release` branch when the
+next patch release occurs.  For stable releases, backported bug fixes
+and infrastructure updates are first applied to the `maintenance` branch
+and then merged to `stable` and published as "updates".  For a new
+stable release the `stable` branch is updated to the corresponding state
+of the `release` branch and a new stable tag is applied in addition to
+the release tag.

bench/in.chain

@@ -1,25 +1,25 @@
 # FENE beadspring benchmark
 
-units		lj
-atom_style	bond
+units           lj
+atom_style      bond
 special_bonds   fene
 
-read_data	data.chain
+read_data       data.chain
 
-neighbor	0.4 bin
-neigh_modify	every 1 delay 1
+neighbor        0.4 bin
+neigh_modify    every 1 delay 1
 
 bond_style      fene
-bond_coeff	1 30.0 1.5 1.0 1.0
+bond_coeff      1 30.0 1.5 1.0 1.0
 
-pair_style	lj/cut 1.12
-pair_modify	shift yes
-pair_coeff	1 1 1.0 1.0 1.12
+pair_style      lj/cut 1.12
+pair_modify     shift yes
+pair_coeff      1 1 1.0 1.0 1.12
 
-fix		1 all nve
-fix		2 all langevin 1.0 1.0 10.0 904297
+fix             1 all nve
+fix             2 all langevin 1.0 1.0 10.0 904297
 
 thermo          100
-timestep	0.012
+timestep        0.012
 
-run		100
+run             100

bench/in.chain.scaled

@@ -1,32 +1,32 @@
 # FENE beadspring benchmark
 
-variable	x index 1
-variable	y index 1
-variable	z index 1
+variable        x index 1
+variable        y index 1
+variable        z index 1
 
-units		lj
-atom_style	bond
-atom_modify	map hash
+units           lj
+atom_style      bond
+atom_modify     map hash
 special_bonds   fene
 
-read_data	data.chain
+read_data       data.chain
 
-replicate	$x $y $z
+replicate       $x $y $z
 
-neighbor	0.4 bin
-neigh_modify	every 1 delay 1
+neighbor        0.4 bin
+neigh_modify    every 1 delay 1
 
 bond_style      fene
-bond_coeff	1 30.0 1.5 1.0 1.0
+bond_coeff      1 30.0 1.5 1.0 1.0
 
-pair_style	lj/cut 1.12
-pair_modify	shift yes
-pair_coeff	1 1 1.0 1.0 1.12
+pair_style      lj/cut 1.12
+pair_modify     shift yes
+pair_coeff      1 1 1.0 1.0 1.12
 
-fix		1 all nve
-fix		2 all langevin 1.0 1.0 10.0 904297
+fix             1 all nve
+fix             2 all langevin 1.0 1.0 10.0 904297
 
 thermo          100
-timestep	0.012
+timestep        0.012
 
-run		100
+run             100

bench/in.chute

@@ -1,33 +1,33 @@
 # LAMMPS benchmark of granular flow
 # chute flow of 32000 atoms with frozen base at 26 degrees
 
-units		lj
-atom_style	sphere
-boundary	p p fs
-newton		off
-comm_modify	vel yes
+units           lj
+atom_style      sphere
+boundary        p p fs
+newton          off
+comm_modify     vel yes
 
-read_data	data.chute
+read_data       data.chute
 
-pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
-pair_coeff	* *
+pair_style      gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
+pair_coeff      * *
 
-neighbor	0.1 bin
-neigh_modify	every 1 delay 0
+neighbor        0.1 bin
+neigh_modify    every 1 delay 0
 
-timestep	0.0001
+timestep        0.0001
 
-group		bottom type 2
-group		active subtract all bottom
-neigh_modify	exclude group bottom bottom
+group           bottom type 2
+group           active subtract all bottom
+neigh_modify    exclude group bottom bottom
 
-fix		1 all gravity 1.0 chute 26.0
-fix		2 bottom freeze
-fix		3 active nve/sphere
+fix             1 all gravity 1.0 chute 26.0
+fix             2 bottom freeze
+fix             3 active nve/sphere
 
-compute		1 all erotate/sphere
-thermo_style	custom step atoms ke c_1 vol
-thermo_modify	norm no
-thermo		100
+compute         1 all erotate/sphere
+thermo_style    custom step atoms ke c_1 vol
+thermo_modify   norm no
+thermo          100
 
-run		100
+run             100

bench/in.chute.scaled

@@ -1,38 +1,38 @@
 # LAMMPS benchmark of granular flow
 # chute flow of 32000 atoms with frozen base at 26 degrees
 
-variable	x index 1
-variable	y index 1
+variable        x index 1
+variable        y index 1
 
-units		lj
-atom_style	sphere
-boundary	p p fs
-newton		off
-comm_modify	vel yes
+units           lj
+atom_style      sphere
+boundary        p p fs
+newton          off
+comm_modify     vel yes
 
-read_data	data.chute
+read_data       data.chute
 
-replicate	$x $y 1
+replicate       $x $y 1
 
-pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
-pair_coeff	* *
+pair_style      gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
+pair_coeff      * *
 
-neighbor	0.1 bin
-neigh_modify	every 1 delay 0
+neighbor        0.1 bin
+neigh_modify    every 1 delay 0
 
-timestep	0.0001
+timestep        0.0001
 
-group		bottom type 2
-group		active subtract all bottom
-neigh_modify	exclude group bottom bottom
+group           bottom type 2
+group           active subtract all bottom
+neigh_modify    exclude group bottom bottom
 
-fix		1 all gravity 1.0 chute 26.0
-fix		2 bottom freeze
-fix		3 active nve/sphere
+fix             1 all gravity 1.0 chute 26.0
+fix             2 bottom freeze
+fix             3 active nve/sphere
 
-compute		1 all erotate/sphere
-thermo_style	custom step atoms ke c_1 vol
-thermo_modify	norm no
-thermo		100
+compute         1 all erotate/sphere
+thermo_style    custom step atoms ke c_1 vol
+thermo_modify   norm no
+thermo          100
 
-run		100
+run             100

bench/in.eam

@@ -1,32 +1,32 @@
 # bulk Cu lattice
 
-variable	x index 1
-variable	y index 1
-variable	z index 1
+variable        x index 1
+variable        y index 1
+variable        z index 1
 
-variable	xx equal 20*$x
-variable	yy equal 20*$y
-variable	zz equal 20*$z
+variable        xx equal 20*$x
+variable        yy equal 20*$y
+variable        zz equal 20*$z
 
-units		metal
-atom_style	atomic
+units           metal
+atom_style      atomic
 
-lattice		fcc 3.615
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-create_box	1 box
-create_atoms	1 box
+lattice         fcc 3.615
+region          box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box      1 box
+create_atoms    1 box
 
-pair_style	eam
-pair_coeff	1 1 Cu_u3.eam
+pair_style      eam
+pair_coeff      1 1 Cu_u3.eam
 
-velocity	all create 1600.0 376847 loop geom
+velocity        all create 1600.0 376847 loop geom
 
-neighbor	1.0 bin
+neighbor        1.0 bin
 neigh_modify    every 1 delay 5 check yes
 
-fix		1 all nve
+fix             1 all nve
 
-timestep	0.005
-thermo		50
+timestep        0.005
+thermo          50
 
-run		100
+run             100

bench/in.lj

@@ -1,30 +1,30 @@
 # 3d Lennard-Jones melt
 
-variable	x index 1
-variable	y index 1
-variable	z index 1
+variable        x index 1
+variable        y index 1
+variable        z index 1
 
-variable	xx equal 20*$x
-variable	yy equal 20*$y
-variable	zz equal 20*$z
+variable        xx equal 20*$x
+variable        yy equal 20*$y
+variable        zz equal 20*$z
 
-units		lj
-atom_style	atomic
+units           lj
+atom_style      atomic
 
-lattice		fcc 0.8442
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-create_box	1 box
-create_atoms	1 box
-mass		1 1.0
+lattice         fcc 0.8442
+region          box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box      1 box
+create_atoms    1 box
+mass            1 1.0
 
-velocity	all create 1.44 87287 loop geom
+velocity        all create 1.44 87287 loop geom
 
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0 2.5
+pair_style      lj/cut 2.5
+pair_coeff      1 1 1.0 1.0 2.5
 
-neighbor	0.3 bin
-neigh_modify	delay 0 every 20 check no
+neighbor        0.3 bin
+neigh_modify    delay 0 every 20 check no
 
-fix		1 all nve
+fix             1 all nve
 
-run		100
+run             100

bench/in.rhodo

@@ -1,27 +1,27 @@
 # Rhodopsin model
 
-units           real  
-neigh_modify    delay 5 every 1   
+units           real
+neigh_modify    delay 5 every 1
 
-atom_style      full  
-bond_style      harmonic 
-angle_style     charmm 
-dihedral_style  charmm 
-improper_style  harmonic 
-pair_style      lj/charmm/coul/long 8.0 10.0 
-pair_modify     mix arithmetic 
-kspace_style    pppm 1e-4 
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+pair_style      lj/charmm/coul/long 8.0 10.0
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
 
 read_data       data.rhodo
 
 fix             1 all shake 0.0001 5 0 m 1.0 a 232
 fix             2 all npt temp 300.0 300.0 100.0 &
-		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
+                z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
 
 special_bonds   charmm
- 
+
 thermo          50
-thermo_style    multi 
+thermo_style    multi
 timestep        2.0
 
-run		100
+run             100

bench/in.rhodo.scaled

@@ -1,34 +1,34 @@
 # Rhodopsin model
 
-variable	x index 1
-variable	y index 1
-variable	z index 1
+variable        x index 1
+variable        y index 1
+variable        z index 1
 
-units           real  
-neigh_modify    delay 5 every 1   
+units           real
+neigh_modify    delay 5 every 1
 
-atom_style      full  
-atom_modify	map hash
-bond_style      harmonic 
-angle_style     charmm 
-dihedral_style  charmm 
-improper_style  harmonic 
-pair_style      lj/charmm/coul/long 8.0 10.0 
-pair_modify     mix arithmetic 
-kspace_style    pppm 1e-4 
+atom_style      full
+atom_modify     map hash
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+pair_style      lj/charmm/coul/long 8.0 10.0
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
 
 read_data       data.rhodo
 
-replicate	$x $y $z
+replicate       $x $y $z
 
 fix             1 all shake 0.0001 5 0 m 1.0 a 232
 fix             2 all npt temp 300.0 300.0 100.0 &
-		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
+                z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
 
 special_bonds   charmm
- 
+
 thermo          50
-thermo_style    multi 
+thermo_style    multi
 timestep        2.0
 
-run		100
+run             100

cmake/CMakeLists.jpeg

@@ -1,615 +0,0 @@
-cmake_minimum_required(VERSION 3.10)
-# When using CMake 3.4 and later, don't export symbols from executables unless
-# the CMAKE_ENABLE_EXPORTS variable is set.
-if(POLICY CMP0065)
-  cmake_policy(SET CMP0065 NEW)
-endif()
-if (POLICY CMP0077)
-  cmake_policy(SET CMP0077 NEW)
-endif()
-if(CMAKE_EXECUTABLE_SUFFIX)
-  set(CMAKE_EXECUTABLE_SUFFIX_TMP ${CMAKE_EXECUTABLE_SUFFIX})
-endif()
-
-project(libjpeg-turbo C)
-set(VERSION 2.1.3)
-set(COPYRIGHT_YEAR "1991-2022")
-string(REPLACE "." ";" VERSION_TRIPLET ${VERSION})
-list(GET VERSION_TRIPLET 0 VERSION_MAJOR)
-list(GET VERSION_TRIPLET 1 VERSION_MINOR)
-list(GET VERSION_TRIPLET 2 VERSION_REVISION)
-function(pad_number NUMBER OUTPUT_LEN)
-  string(LENGTH "${${NUMBER}}" INPUT_LEN)
-  if(INPUT_LEN LESS OUTPUT_LEN)
-    math(EXPR ZEROES "${OUTPUT_LEN} - ${INPUT_LEN} - 1")
-    set(NUM ${${NUMBER}})
-    foreach(C RANGE ${ZEROES})
-      set(NUM "0${NUM}")
-    endforeach()
-    set(${NUMBER} ${NUM} PARENT_SCOPE)
-  endif()
-endfunction()
-pad_number(VERSION_MINOR 3)
-pad_number(VERSION_REVISION 3)
-set(LIBJPEG_TURBO_VERSION_NUMBER ${VERSION_MAJOR}${VERSION_MINOR}${VERSION_REVISION})
-
-# CMake 3.14 and later sets CMAKE_MACOSX_BUNDLE to TRUE by default when
-# CMAKE_SYSTEM_NAME is iOS, tvOS, or watchOS, which breaks the libjpeg-turbo
-# build.  (Specifically, when CMAKE_MACOSX_BUNDLE is TRUE, executables for
-# Apple platforms are built as application bundles, which causes CMake to
-# complain that our install() directives for executables do not specify a
-# BUNDLE DESTINATION.  Even if CMake did not complain, building executables as
-# application bundles would break our iOS packages.)
-set(CMAKE_MACOSX_BUNDLE FALSE)
-
-string(TIMESTAMP DEFAULT_BUILD "%Y%m%d")
-set(BUILD ${DEFAULT_BUILD} CACHE STRING "Build string (default: ${DEFAULT_BUILD})")
-
-# NOTE: On Windows, this does nothing except when using MinGW or Cygwin.
-# CMAKE_BUILD_TYPE has no meaning in Visual Studio, and it always defaults to
-# Debug when using NMake.
-if(NOT CMAKE_BUILD_TYPE)
-  set(CMAKE_BUILD_TYPE Release)
-endif()
-message(STATUS "CMAKE_BUILD_TYPE = ${CMAKE_BUILD_TYPE}")
-
-message(STATUS "VERSION = ${VERSION}, BUILD = ${BUILD}")
-
-include(cmakescripts/PackageInfo.cmake)
-
-# Detect CPU type and whether we're building 64-bit or 32-bit code
-math(EXPR BITS "${CMAKE_SIZEOF_VOID_P} * 8")
-string(TOLOWER ${CMAKE_SYSTEM_PROCESSOR} CMAKE_SYSTEM_PROCESSOR_LC)
-set(COUNT 1)
-foreach(ARCH ${CMAKE_OSX_ARCHITECTURES})
-  if(COUNT GREATER 1)
-    message(FATAL_ERROR "The libjpeg-turbo build system does not support multiple values in CMAKE_OSX_ARCHITECTURES.")
-  endif()
-  math(EXPR COUNT "${COUNT}+1")
-endforeach()
-if(CMAKE_SYSTEM_PROCESSOR_LC MATCHES "x86_64" OR
-  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "amd64" OR
-  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "i[0-9]86" OR
-  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "x86" OR
-  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "ia32")
-  if(BITS EQUAL 64 OR CMAKE_C_COMPILER_ABI MATCHES "ELF X32")
-    set(CPU_TYPE x86_64)
-  else()
-    set(CPU_TYPE i386)
-  endif()
-  if(NOT CMAKE_SYSTEM_PROCESSOR STREQUAL ${CPU_TYPE})
-    set(CMAKE_SYSTEM_PROCESSOR ${CPU_TYPE})
-  endif()
-elseif(CMAKE_SYSTEM_PROCESSOR_LC STREQUAL "aarch64" OR
-  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "^arm")
-  if(BITS EQUAL 64)
-    set(CPU_TYPE arm64)
-  else()
-    set(CPU_TYPE arm)
-  endif()
-elseif(CMAKE_SYSTEM_PROCESSOR_LC MATCHES "^ppc" OR
-  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "^powerpc")
-  set(CPU_TYPE powerpc)
-else()
-  set(CPU_TYPE ${CMAKE_SYSTEM_PROCESSOR_LC})
-endif()
-if(CMAKE_OSX_ARCHITECTURES MATCHES "x86_64" OR
-  CMAKE_OSX_ARCHITECTURES MATCHES "arm64" OR
-  CMAKE_OSX_ARCHITECTURES MATCHES "i386")
-  set(CPU_TYPE ${CMAKE_OSX_ARCHITECTURES})
-endif()
-if(CMAKE_OSX_ARCHITECTURES MATCHES "ppc")
-  set(CPU_TYPE powerpc)
-endif()
-if(MSVC_IDE AND CMAKE_GENERATOR_PLATFORM MATCHES "arm64")
-  set(CPU_TYPE arm64)
-endif()
-
-message(STATUS "${BITS}-bit build (${CPU_TYPE})")
-
-macro(report_directory var)
-  if(CMAKE_INSTALL_${var} STREQUAL CMAKE_INSTALL_FULL_${var})
-    message(STATUS "CMAKE_INSTALL_${var} = ${CMAKE_INSTALL_${var}}")
-  else()
-    message(STATUS "CMAKE_INSTALL_${var} = ${CMAKE_INSTALL_${var}} (${CMAKE_INSTALL_FULL_${var}})")
-  endif()
-  mark_as_advanced(CLEAR CMAKE_INSTALL_${var})
-endmacro()
-
-set(DIRLIST "BINDIR;DATAROOTDIR;DOCDIR;INCLUDEDIR;LIBDIR")
-if(UNIX)
-  list(APPEND DIRLIST "MANDIR")
-endif()
-foreach(dir ${DIRLIST})
-  report_directory(${dir})
-endforeach()
-
-
-###############################################################################
-# CONFIGURATION OPTIONS
-###############################################################################
-
-macro(boolean_number var)
-  if(${var})
-    set(${var} 1 ${ARGN})
-  else()
-    set(${var} 0 ${ARGN})
-  endif()
-endmacro()
-
-option(ENABLE_SHARED "Build shared libraries" FALSE)
-boolean_number(ENABLE_SHARED)
-option(ENABLE_STATIC "Build static libraries" TRUE)
-boolean_number(ENABLE_STATIC)
-option(REQUIRE_SIMD "Generate a fatal error if SIMD extensions are not available for this platform (default is to fall back to a non-SIMD build)" FALSE)
-boolean_number(REQUIRE_SIMD)
-option(WITH_12BIT "Encode/decode JPEG images with 12-bit samples (implies WITH_ARITH_DEC=0 WITH_ARITH_ENC=0 WITH_JAVA=0 WITH_SIMD=0 WITH_TURBOJPEG=0 )" FALSE)
-boolean_number(WITH_12BIT)
-option(WITH_ARITH_DEC "Include arithmetic decoding support when emulating the libjpeg v6b API/ABI" TRUE)
-boolean_number(WITH_ARITH_DEC)
-option(WITH_ARITH_ENC "Include arithmetic encoding support when emulating the libjpeg v6b API/ABI" TRUE)
-boolean_number(WITH_ARITH_ENC)
-if(CMAKE_C_COMPILER_ABI MATCHES "ELF X32")
-  set(WITH_JAVA 0)
-else()
-  option(WITH_JAVA "Build Java wrapper for the TurboJPEG API library (implies ENABLE_SHARED=1)" FALSE)
-  boolean_number(WITH_JAVA)
-endif()
-option(WITH_JPEG7 "Emulate libjpeg v7 API/ABI (this makes ${CMAKE_PROJECT_NAME} backward-incompatible with libjpeg v6b)" FALSE)
-boolean_number(WITH_JPEG7)
-option(WITH_JPEG8 "Emulate libjpeg v8 API/ABI (this makes ${CMAKE_PROJECT_NAME} backward-incompatible with libjpeg v6b)" FALSE)
-boolean_number(WITH_JPEG8)
-option(WITH_MEM_SRCDST "Include in-memory source/destination manager functions when emulating the libjpeg v6b or v7 API/ABI" TRUE)
-boolean_number(WITH_MEM_SRCDST)
-option(WITH_SIMD "Include SIMD extensions, if available for this platform" FALSE)
-boolean_number(WITH_SIMD)
-option(WITH_TURBOJPEG "Include the TurboJPEG API library and associated test programs" FALSE)
-boolean_number(WITH_TURBOJPEG)
-option(WITH_FUZZ "Build fuzz targets" FALSE)
-
-macro(report_option var desc)
-  if(${var})
-    message(STATUS "${desc} enabled (${var} = ${${var}})")
-  else()
-    message(STATUS "${desc} disabled (${var} = ${${var}})")
-  endif()
-endmacro()
-
-if(WITH_JAVA)
-  set(ENABLE_SHARED 1)
-endif()
-
-# Explicitly setting CMAKE_POSITION_INDEPENDENT_CODE=FALSE disables PIC for all
-# targets, which will cause the shared library builds to fail.  Thus, if shared
-# libraries are enabled and CMAKE_POSITION_INDEPENDENT_CODE is explicitly set
-# to FALSE, we need to unset it, thus restoring the default behavior
-# (automatically using PIC for shared library targets.)
-if(DEFINED CMAKE_POSITION_INDEPENDENT_CODE AND
-  NOT CMAKE_POSITION_INDEPENDENT_CODE AND ENABLE_SHARED)
-  unset(CMAKE_POSITION_INDEPENDENT_CODE CACHE)
-endif()
-
-report_option(ENABLE_SHARED "Shared libraries")
-report_option(ENABLE_STATIC "Static libraries")
-
-if(ENABLE_SHARED)
-  set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR})
-endif()
-
-if(WITH_JPEG8 OR WITH_JPEG7)
-  set(WITH_ARITH_ENC 1)
-  set(WITH_ARITH_DEC 1)
-endif()
-if(WITH_JPEG8)
-  set(WITH_MEM_SRCDST 0)
-endif()
-
-if(WITH_12BIT)
-  set(WITH_ARITH_DEC 0)
-  set(WITH_ARITH_ENC 0)
-  set(WITH_JAVA 0)
-  set(WITH_SIMD 0)
-  set(WITH_TURBOJPEG 0)
-  set(BITS_IN_JSAMPLE 12)
-else()
-  set(BITS_IN_JSAMPLE 8)
-endif()
-report_option(WITH_12BIT "12-bit JPEG support")
-
-if(WITH_ARITH_DEC)
-  set(D_ARITH_CODING_SUPPORTED 1)
-endif()
-if(NOT WITH_12BIT)
-  report_option(WITH_ARITH_DEC "Arithmetic decoding support")
-endif()
-
-if(WITH_ARITH_ENC)
-  set(C_ARITH_CODING_SUPPORTED 1)
-endif()
-if(NOT WITH_12BIT)
-  report_option(WITH_ARITH_ENC "Arithmetic encoding support")
-endif()
-
-if(NOT WITH_12BIT)
-  report_option(WITH_TURBOJPEG "TurboJPEG API library")
-  report_option(WITH_JAVA "TurboJPEG Java wrapper")
-endif()
-
-if(WITH_MEM_SRCDST)
-  set(MEM_SRCDST_SUPPORTED 1)
-  set(MEM_SRCDST_FUNCTIONS "global:  jpeg_mem_dest;  jpeg_mem_src;")
-endif()
-if(NOT WITH_JPEG8)
-  report_option(WITH_MEM_SRCDST "In-memory source/destination managers")
-endif()
-
-set(SO_AGE 2)
-if(WITH_MEM_SRCDST)
-  set(SO_AGE 3)
-endif()
-
-if(WITH_JPEG8)
-  set(JPEG_LIB_VERSION 80)
-elseif(WITH_JPEG7)
-  set(JPEG_LIB_VERSION 70)
-else()
-  set(JPEG_LIB_VERSION 62)
-endif()
-
-math(EXPR JPEG_LIB_VERSION_DIV10 "${JPEG_LIB_VERSION} / 10")
-math(EXPR JPEG_LIB_VERSION_MOD10 "${JPEG_LIB_VERSION} % 10")
-if(JPEG_LIB_VERSION STREQUAL "62")
-  set(DEFAULT_SO_MAJOR_VERSION ${JPEG_LIB_VERSION})
-else()
-  set(DEFAULT_SO_MAJOR_VERSION ${JPEG_LIB_VERSION_DIV10})
-endif()
-if(JPEG_LIB_VERSION STREQUAL "80")
-  set(DEFAULT_SO_MINOR_VERSION 2)
-else()
-  set(DEFAULT_SO_MINOR_VERSION 0)
-endif()
-
-# This causes SO_MAJOR_VERSION/SO_MINOR_VERSION to reset to defaults if
-# WITH_JPEG7 or WITH_JPEG8 has changed.
-if((DEFINED WITH_JPEG7_INT AND NOT WITH_JPEG7 EQUAL WITH_JPEG7_INT) OR
-  (DEFINED WITH_JPEG8_INT AND NOT WITH_JPEG8 EQUAL WITH_JPEG8_INT))
-  set(FORCE_SO_VERSION "FORCE")
-endif()
-set(WITH_JPEG7_INT ${WITH_JPEG7} CACHE INTERNAL "")
-set(WITH_JPEG8_INT ${WITH_JPEG8} CACHE INTERNAL "")
-
-set(SO_MAJOR_VERSION ${DEFAULT_SO_MAJOR_VERSION} CACHE STRING
-  "Major version of the libjpeg API shared library (default: ${DEFAULT_SO_MAJOR_VERSION})"
-  ${FORCE_SO_VERSION})
-set(SO_MINOR_VERSION ${DEFAULT_SO_MINOR_VERSION} CACHE STRING
-  "Minor version of the libjpeg API shared library (default: ${DEFAULT_SO_MINOR_VERSION})"
-  ${FORCE_SO_VERSION})
-
-set(JPEG_LIB_VERSION_DECIMAL "${JPEG_LIB_VERSION_DIV10}.${JPEG_LIB_VERSION_MOD10}")
-message(STATUS "Emulating libjpeg API/ABI v${JPEG_LIB_VERSION_DECIMAL} (WITH_JPEG7 = ${WITH_JPEG7}, WITH_JPEG8 = ${WITH_JPEG8})")
-message(STATUS "libjpeg API shared library version = ${SO_MAJOR_VERSION}.${SO_AGE}.${SO_MINOR_VERSION}")
-
-# Because the TurboJPEG API library uses versioned symbols and changes the
-# names of functions whenever they are modified in a backward-incompatible
-# manner, it is always backward-ABI-compatible with itself, so the major and
-# minor SO versions don't change.  However, we increase the middle number (the
-# SO "age") whenever functions are added to the API.
-set(TURBOJPEG_SO_MAJOR_VERSION 0)
-set(TURBOJPEG_SO_AGE 2)
-set(TURBOJPEG_SO_VERSION 0.${TURBOJPEG_SO_AGE}.0)
-
-
-###############################################################################
-# COMPILER SETTINGS
-###############################################################################
-
-if(MSVC)
-  option(WITH_CRT_DLL
-    "Link all ${CMAKE_PROJECT_NAME} libraries and executables with the C run-time DLL (msvcr*.dll) instead of the static C run-time library (libcmt*.lib.)  The default is to use the C run-time DLL only with the libraries and executables that need it."
-    FALSE)
-  if(NOT WITH_CRT_DLL)
-    # Use the static C library for all build types
-    foreach(var CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE
-      CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO)
-      if(${var} MATCHES "/MD")
-        string(REGEX REPLACE "/MD" "/MT" ${var} "${${var}}")
-      endif()
-    endforeach()
-  endif()
-  add_definitions(-D_CRT_NONSTDC_NO_WARNINGS)
-endif()
-
-if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_C_COMPILER_ID STREQUAL "Clang")
-  # Use the maximum optimization level for release builds
-  foreach(var CMAKE_C_FLAGS_RELEASE CMAKE_C_FLAGS_RELWITHDEBINFO)
-    if(${var} MATCHES "-O2")
-      string(REGEX REPLACE "-O2" "-O3" ${var} "${${var}}")
-    endif()
-  endforeach()
-endif()
-
-if(CMAKE_SYSTEM_NAME STREQUAL "SunOS")
-  if(CMAKE_C_COMPILER_ID MATCHES "SunPro")
-    # Use the maximum optimization level for release builds
-    foreach(var CMAKE_C_FLAGS_RELEASE CMAKE_C_FLAGS_RELWITHDEBINFO)
-      if(${var} MATCHES "-xO3")
-        string(REGEX REPLACE "-xO3" "-xO5" ${var} "${${var}}")
-      endif()
-      if(${var} MATCHES "-xO2")
-        string(REGEX REPLACE "-xO2" "-xO5" ${var} "${${var}}")
-      endif()
-    endforeach()
-  endif()
-endif()
-
-string(TOUPPER ${CMAKE_BUILD_TYPE} CMAKE_BUILD_TYPE_UC)
-
-set(EFFECTIVE_C_FLAGS "${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${CMAKE_BUILD_TYPE_UC}}")
-message(STATUS "Compiler flags = ${EFFECTIVE_C_FLAGS}")
-
-set(EFFECTIVE_LD_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS_${CMAKE_BUILD_TYPE_UC}}")
-message(STATUS "Linker flags = ${EFFECTIVE_LD_FLAGS}")
-
-include(CheckCSourceCompiles)
-include(CheckIncludeFiles)
-include(CheckTypeSize)
-
-check_type_size("size_t" SIZE_T)
-check_type_size("unsigned long" UNSIGNED_LONG)
-
-if(SIZE_T EQUAL UNSIGNED_LONG)
-  check_c_source_compiles("int main(int argc, char **argv) { unsigned long a = argc;  return __builtin_ctzl(a); }"
-    HAVE_BUILTIN_CTZL)
-endif()
-if(MSVC)
-  check_include_files("intrin.h" HAVE_INTRIN_H)
-endif()
-
-if(UNIX)
-  if(CMAKE_CROSSCOMPILING)
-    set(RIGHT_SHIFT_IS_UNSIGNED 0)
-  else()
-    include(CheckCSourceRuns)
-    check_c_source_runs("
-      #include <stdio.h>
-      #include <stdlib.h>
-      int is_shifting_signed (long arg) {
-        long res = arg >> 4;
-        if (res == -0x7F7E80CL)
-          return 1; /* right shift is signed */
-        /* see if unsigned-shift hack will fix it. */
-        /* we can't just test exact value since it depends on width of long... */
-        res |= (~0L) << (32-4);
-        if (res == -0x7F7E80CL)
-          return 0; /* right shift is unsigned */
-        printf(\"Right shift isn't acting as I expect it to.\\\\n\");
-        printf(\"I fear the JPEG software will not work at all.\\\\n\\\\n\");
-        return 0; /* try it with unsigned anyway */
-      }
-      int main (void) {
-        exit(is_shifting_signed(-0x7F7E80B1L));
-      }" RIGHT_SHIFT_IS_UNSIGNED)
-  endif()
-endif()
-
-if(MSVC)
-  set(INLINE_OPTIONS "__inline;inline")
-else()
-  set(INLINE_OPTIONS "__inline__;inline")
-endif()
-option(FORCE_INLINE "Force function inlining" TRUE)
-boolean_number(FORCE_INLINE)
-if(FORCE_INLINE)
-  if(MSVC)
-    list(INSERT INLINE_OPTIONS 0 "__forceinline")
-  else()
-    list(INSERT INLINE_OPTIONS 0 "inline __attribute__((always_inline))")
-    list(INSERT INLINE_OPTIONS 0 "__inline__ __attribute__((always_inline))")
-  endif()
-endif()
-foreach(inline ${INLINE_OPTIONS})
-  check_c_source_compiles("${inline} static int foo(void) { return 0; } int main(void) { return foo(); }"
-    INLINE_WORKS)
-  if(INLINE_WORKS)
-    set(INLINE ${inline})
-    break()
-  endif()
-endforeach()
-if(NOT INLINE_WORKS)
-  message(FATAL_ERROR "Could not determine how to inline functions.")
-endif()
-message(STATUS "INLINE = ${INLINE} (FORCE_INLINE = ${FORCE_INLINE})")
-
-if(WITH_TURBOJPEG)
-  if(MSVC)
-    set(THREAD_LOCAL "__declspec(thread)")
-  else()
-    set(THREAD_LOCAL "__thread")
-  endif()
-  check_c_source_compiles("${THREAD_LOCAL} int i;  int main(void) { i = 0;  return i; }" HAVE_THREAD_LOCAL)
-  if(HAVE_THREAD_LOCAL)
-    message(STATUS "THREAD_LOCAL = ${THREAD_LOCAL}")
-  else()
-    message(WARNING "Thread-local storage is not available.  The TurboJPEG API library's global error handler will not be thread-safe.")
-    unset(THREAD_LOCAL)
-  endif()
-endif()
-
-if(UNIX AND NOT APPLE)
-  file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/conftest.map "VERS_1 { global: *; };")
-  set(CMAKE_REQUIRED_FLAGS
-    "-Wl,--version-script,${CMAKE_CURRENT_BINARY_DIR}/conftest.map")
-  check_c_source_compiles("int main(void) { return 0; }" HAVE_VERSION_SCRIPT)
-  set(CMAKE_REQUIRED_FLAGS)
-  file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/conftest.map)
-  if(HAVE_VERSION_SCRIPT)
-    message(STATUS "Linker supports GNU-style version scripts")
-    set(MAPFLAG "-Wl,--version-script,")
-    set(TJMAPFLAG "-Wl,--version-script,")
-  else()
-    message(STATUS "Linker does not support GNU-style version scripts")
-    if(CMAKE_SYSTEM_NAME STREQUAL "SunOS")
-      # The Solaris linker doesn't like our version script for the libjpeg API
-      # library, but the version script for the TurboJPEG API library should
-      # still work.
-      file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/conftest.map
-        "VERS_1 { global: foo;  local: *; }; VERS_2 { global: foo2; } VERS_1;")
-      set(CMAKE_REQUIRED_FLAGS "-Wl,-M,${CMAKE_CURRENT_BINARY_DIR}/conftest.map -shared")
-      check_c_source_compiles("int foo() { return 0; } int foo2() { return 2; }"
-        HAVE_MAPFILE)
-      set(CMAKE_REQUIRED_FLAGS)
-      file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/conftest.map)
-      if(HAVE_MAPFILE)
-        message(STATUS "Linker supports mapfiles")
-        set(TJMAPFLAG "-Wl,-M,")
-      else()
-        message(STATUS "Linker does not support mapfiles")
-      endif()
-    endif()
-  endif()
-endif()
-
-# Generate files
-if(WIN32)
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/win/jconfig.h.in jconfig.h)
-else()
-  configure_file(jconfig.h.in jconfig.h)
-endif()
-configure_file(jconfigint.h.in jconfigint.h)
-configure_file(jversion.h.in jversion.h)
-if(UNIX)
-  configure_file(libjpeg.map.in libjpeg.map)
-endif()
-
-# Include directories and compiler definitions
-include_directories(${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_CURRENT_SOURCE_DIR})
-
-
-###############################################################################
-# TARGETS
-###############################################################################
-
-if(CMAKE_EXECUTABLE_SUFFIX_TMP)
-  set(CMAKE_EXECUTABLE_SUFFIX ${CMAKE_EXECUTABLE_SUFFIX_TMP})
-endif()
-message(STATUS "CMAKE_EXECUTABLE_SUFFIX = ${CMAKE_EXECUTABLE_SUFFIX}")
-
-set(JPEG_SOURCES jcapimin.c jcapistd.c jccoefct.c jccolor.c jcdctmgr.c jchuff.c
-  jcicc.c jcinit.c jcmainct.c jcmarker.c jcmaster.c jcomapi.c jcparam.c
-  jcphuff.c jcprepct.c jcsample.c jctrans.c jdapimin.c jdapistd.c jdatadst.c
-  jdatasrc.c jdcoefct.c jdcolor.c jddctmgr.c jdhuff.c jdicc.c jdinput.c
-  jdmainct.c jdmarker.c jdmaster.c jdmerge.c jdphuff.c jdpostct.c jdsample.c
-  jdtrans.c jerror.c jfdctflt.c jfdctfst.c jfdctint.c jidctflt.c jidctfst.c
-  jidctint.c jidctred.c jquant1.c jquant2.c jutils.c jmemmgr.c jmemnobs.c)
-
-if(WITH_ARITH_ENC OR WITH_ARITH_DEC)
-  set(JPEG_SOURCES ${JPEG_SOURCES} jaricom.c)
-endif()
-
-if(WITH_ARITH_ENC)
-  set(JPEG_SOURCES ${JPEG_SOURCES} jcarith.c)
-endif()
-
-if(WITH_ARITH_DEC)
-  set(JPEG_SOURCES ${JPEG_SOURCES} jdarith.c)
-endif()
-
-if(WITH_SIMD)
-  add_subdirectory(simd)
-  if(NEON_INTRINSICS)
-    add_definitions(-DNEON_INTRINSICS)
-  endif()
-elseif(NOT WITH_12BIT)
-  message(STATUS "SIMD extensions: None (WITH_SIMD = ${WITH_SIMD})")
-endif()
-if(WITH_SIMD)
-  message(STATUS "SIMD extensions: ${CPU_TYPE} (WITH_SIMD = ${WITH_SIMD})")
-  if(MSVC_IDE OR XCODE)
-    set_source_files_properties(${SIMD_OBJS} PROPERTIES GENERATED 1)
-  endif()
-else()
-  add_library(simd OBJECT jsimd_none.c)
-  if(NOT WIN32 AND (CMAKE_POSITION_INDEPENDENT_CODE OR ENABLE_SHARED))
-    set_target_properties(simd PROPERTIES POSITION_INDEPENDENT_CODE 1)
-  endif()
-endif()
-
-if(WITH_JAVA)
-  add_subdirectory(java)
-endif()
-
-if(ENABLE_SHARED)
-  add_subdirectory(sharedlib)
-endif()
-
-if(ENABLE_STATIC)
-  add_library(jpeg-static STATIC ${JPEG_SOURCES} $<TARGET_OBJECTS:simd>
-    ${SIMD_OBJS})
-  if(NOT MSVC)
-    set_target_properties(jpeg-static PROPERTIES OUTPUT_NAME jpeg)
-  endif()
-endif()
-
-if(WITH_TURBOJPEG)
-  if(ENABLE_SHARED)
-    set(TURBOJPEG_SOURCES ${JPEG_SOURCES} $<TARGET_OBJECTS:simd> ${SIMD_OBJS}
-      turbojpeg.c transupp.c jdatadst-tj.c jdatasrc-tj.c rdbmp.c rdppm.c
-      wrbmp.c wrppm.c)
-    set(TJMAPFILE ${CMAKE_CURRENT_SOURCE_DIR}/turbojpeg-mapfile)
-    if(WITH_JAVA)
-      set(TURBOJPEG_SOURCES ${TURBOJPEG_SOURCES} turbojpeg-jni.c)
-      include_directories(${JAVA_INCLUDE_PATH} ${JAVA_INCLUDE_PATH2})
-      set(TJMAPFILE ${CMAKE_CURRENT_SOURCE_DIR}/turbojpeg-mapfile.jni)
-    endif()
-    if(MSVC)
-      configure_file(${CMAKE_SOURCE_DIR}/win/turbojpeg.rc.in
-        ${CMAKE_BINARY_DIR}/win/turbojpeg.rc)
-      set(TURBOJPEG_SOURCES ${TURBOJPEG_SOURCES}
-        ${CMAKE_BINARY_DIR}/win/turbojpeg.rc)
-    endif()
-    add_library(turbojpeg SHARED ${TURBOJPEG_SOURCES})
-    set_property(TARGET turbojpeg PROPERTY COMPILE_FLAGS
-      "-DBMP_SUPPORTED -DPPM_SUPPORTED")
-    if(WIN32)
-      set_target_properties(turbojpeg PROPERTIES DEFINE_SYMBOL DLLDEFINE)
-    endif()
-    if(MINGW)
-      set_target_properties(turbojpeg PROPERTIES LINK_FLAGS -Wl,--kill-at)
-    endif()
-    if(APPLE AND (NOT CMAKE_OSX_DEPLOYMENT_TARGET OR
-                  CMAKE_OSX_DEPLOYMENT_TARGET VERSION_GREATER 10.4))
-      if(NOT CMAKE_SHARED_LIBRARY_RUNTIME_C_FLAG)
-        set(CMAKE_SHARED_LIBRARY_RUNTIME_C_FLAG "-Wl,-rpath,")
-      endif()
-      set_target_properties(turbojpeg PROPERTIES MACOSX_RPATH 1)
-    endif()
-    set_target_properties(turbojpeg PROPERTIES
-      SOVERSION ${TURBOJPEG_SO_MAJOR_VERSION} VERSION ${TURBOJPEG_SO_VERSION})
-    if(TJMAPFLAG)
-      set_target_properties(turbojpeg PROPERTIES
-        LINK_FLAGS "${TJMAPFLAG}${TJMAPFILE}")
-    endif()
-  endif()
-
-  if(ENABLE_STATIC)
-    add_library(turbojpeg-static STATIC ${JPEG_SOURCES} $<TARGET_OBJECTS:simd>
-      ${SIMD_OBJS} turbojpeg.c transupp.c jdatadst-tj.c jdatasrc-tj.c rdbmp.c
-      rdppm.c wrbmp.c wrppm.c)
-    set_property(TARGET turbojpeg-static PROPERTY COMPILE_FLAGS
-      "-DBMP_SUPPORTED -DPPM_SUPPORTED")
-    if(NOT MSVC)
-      set_target_properties(turbojpeg-static PROPERTIES OUTPUT_NAME turbojpeg)
-    endif()
-  endif()
-endif()
-
-if(WIN32)
-  set(USE_SETMODE "-DUSE_SETMODE")
-endif()
-if(WITH_12BIT)
-  set(COMPILE_FLAGS "-DGIF_SUPPORTED -DPPM_SUPPORTED ${USE_SETMODE}")
-else()
-  set(COMPILE_FLAGS "-DBMP_SUPPORTED -DGIF_SUPPORTED -DPPM_SUPPORTED -DTARGA_SUPPORTED ${USE_SETMODE}")
-  set(CJPEG_BMP_SOURCES rdbmp.c rdtarga.c)
-  set(DJPEG_BMP_SOURCES wrbmp.c wrtarga.c)
-endif()

cmake/CMakeLists.png

@@ -1,741 +0,0 @@
-# CMakeLists.txt
-
-# Copyright (C) 2018 Cosmin Truta
-# Copyright (C) 2007,2009-2018 Glenn Randers-Pehrson
-# Written by Christian Ehrlicher, 2007
-# Revised by Roger Lowman, 2009-2010
-# Revised by Clifford Yapp, 2011-2012,2017
-# Revised by Roger Leigh, 2016
-# Revised by Andreas Franek, 2016
-# Revised by Sam Serrels, 2017
-# Revised by Vadim Barkov, 2017
-# Revised by Vicky Pfau, 2018
-# Revised by Cameron Cawley, 2018
-# Revised by Cosmin Truta, 2018
-# Revised by Kyle Bentley, 2018
-
-# This code is released under the libpng license.
-# For conditions of distribution and use, see the disclaimer
-# and license in png.h
-
-cmake_minimum_required(VERSION 3.10)
-cmake_policy(VERSION 3.1)
-# When using CMake 3.4 and later, don't export symbols from executables unless
-# the CMAKE_ENABLE_EXPORTS variable is set.
-if(POLICY CMP0065)
-  cmake_policy(SET CMP0065 NEW)
-endif()
-if (POLICY CMP0077)
-  cmake_policy(SET CMP0077 NEW)
-endif()
-set(CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS ON)
-
-project(libpng C ASM)
-enable_testing()
-
-set(PNGLIB_MAJOR 1)
-set(PNGLIB_MINOR 6)
-set(PNGLIB_RELEASE 37)
-set(PNGLIB_NAME libpng${PNGLIB_MAJOR}${PNGLIB_MINOR})
-set(PNGLIB_VERSION ${PNGLIB_MAJOR}.${PNGLIB_MINOR}.${PNGLIB_RELEASE})
-
-include(GNUInstallDirs)
-
-# needed packages
-
-# Allow users to specify location of Zlib.
-# Useful if zlib is being built alongside this as a sub-project.
-option(PNG_BUILD_ZLIB "Custom zlib Location, else find_package is used" ON)
-
-if(NOT PNG_BUILD_ZLIB)
-  find_package(ZLIB REQUIRED)
-  include_directories(${ZLIB_INCLUDE_DIR})
-endif()
-
-if(UNIX AND NOT APPLE AND NOT BEOS AND NOT HAIKU)
-  find_library(M_LIBRARY m)
-else()
-  # libm is not needed and/or not available
-  set(M_LIBRARY "")
-endif()
-
-# COMMAND LINE OPTIONS
-option(PNG_SHARED "Build shared lib" OFF)
-option(PNG_STATIC "Build static lib" ON)
-option(PNG_TESTS  "Build libpng tests" OFF)
-
-# Many more configuration options could be added here
-option(PNG_FRAMEWORK "Build OS X framework" OFF)
-option(PNG_DEBUG "Build with debug output" OFF)
-option(PNG_HARDWARE_OPTIMIZATIONS "Enable hardware optimizations" OFF)
-
-set(PNG_PREFIX "" CACHE STRING "Prefix to add to the API function names")
-set(DFA_XTRA "" CACHE FILEPATH "File containing extra configuration settings")
-
-if(PNG_HARDWARE_OPTIMIZATIONS)
-
-# set definitions and sources for arm
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^arm" OR
-  CMAKE_SYSTEM_PROCESSOR MATCHES "^aarch64")
-  set(PNG_ARM_NEON_POSSIBLE_VALUES check on off)
-  set(PNG_ARM_NEON "check" CACHE STRING "Enable ARM NEON optimizations:
-     check: (default) use internal checking code;
-     off: disable the optimizations;
-     on: turn on unconditionally.")
-  set_property(CACHE PNG_ARM_NEON PROPERTY STRINGS
-     ${PNG_ARM_NEON_POSSIBLE_VALUES})
-  list(FIND PNG_ARM_NEON_POSSIBLE_VALUES ${PNG_ARM_NEON} index)
-  if(index EQUAL -1)
-    message(FATAL_ERROR
-            "PNG_ARM_NEON must be one of [${PNG_ARM_NEON_POSSIBLE_VALUES}]")
-  elseif(NOT ${PNG_ARM_NEON} STREQUAL "off")
-    set(libpng_arm_sources
-      arm/arm_init.c
-      arm/filter_neon.S
-      arm/filter_neon_intrinsics.c
-      arm/palette_neon_intrinsics.c)
-
-    if(${PNG_ARM_NEON} STREQUAL "on")
-      add_definitions(-DPNG_ARM_NEON_OPT=2)
-    elseif(${PNG_ARM_NEON} STREQUAL "check")
-      add_definitions(-DPNG_ARM_NEON_CHECK_SUPPORTED)
-    endif()
-  else()
-    add_definitions(-DPNG_ARM_NEON_OPT=0)
-  endif()
-endif()
-
-# set definitions and sources for powerpc
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^powerpc*" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "^ppc64*")
-  set(PNG_POWERPC_VSX_POSSIBLE_VALUES on off)
-  set(PNG_POWERPC_VSX "on" CACHE STRING "Enable POWERPC VSX optimizations:
-     off: disable the optimizations.")
-  set_property(CACHE PNG_POWERPC_VSX PROPERTY STRINGS
-     ${PNG_POWERPC_VSX_POSSIBLE_VALUES})
-  list(FIND PNG_POWERPC_VSX_POSSIBLE_VALUES ${PNG_POWERPC_VSX} index)
-  if(index EQUAL -1)
-    message(FATAL_ERROR
-            "PNG_POWERPC_VSX must be one of [${PNG_POWERPC_VSX_POSSIBLE_VALUES}]")
-  elseif(NOT ${PNG_POWERPC_VSX} STREQUAL "off")
-    set(libpng_powerpc_sources
-      powerpc/powerpc_init.c
-      powerpc/filter_vsx_intrinsics.c)
-    if(${PNG_POWERPC_VSX} STREQUAL "on")
-      add_definitions(-DPNG_POWERPC_VSX_OPT=2)
-    endif()
-  else()
-    add_definitions(-DPNG_POWERPC_VSX_OPT=0)
-  endif()
-endif()
-
-# set definitions and sources for intel
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^i?86" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "^x86_64*")
-  set(PNG_INTEL_SSE_POSSIBLE_VALUES on off)
-  set(PNG_INTEL_SSE "on" CACHE STRING "Enable INTEL_SSE optimizations:
-     off: disable the optimizations")
-  set_property(CACHE PNG_INTEL_SSE PROPERTY STRINGS
-     ${PNG_INTEL_SSE_POSSIBLE_VALUES})
-  list(FIND PNG_INTEL_SSE_POSSIBLE_VALUES ${PNG_INTEL_SSE} index)
-  if(index EQUAL -1)
-    message(FATAL_ERROR
-            "PNG_INTEL_SSE must be one of [${PNG_INTEL_SSE_POSSIBLE_VALUES}]")
-  elseif(NOT ${PNG_INTEL_SSE} STREQUAL "off")
-    set(libpng_intel_sources
-      intel/intel_init.c
-      intel/filter_sse2_intrinsics.c)
-    if(${PNG_INTEL_SSE} STREQUAL "on")
-      add_definitions(-DPNG_INTEL_SSE_OPT=1)
-    endif()
-  else()
-    add_definitions(-DPNG_INTEL_SSE_OPT=0)
-  endif()
-endif()
-
-# set definitions and sources for MIPS
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "mipsel*" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "mips64el*")
-  set(PNG_MIPS_MSA_POSSIBLE_VALUES on off)
-  set(PNG_MIPS_MSA "on" CACHE STRING "Enable MIPS_MSA optimizations:
-     off: disable the optimizations")
-  set_property(CACHE PNG_MIPS_MSA PROPERTY STRINGS
-     ${PNG_MIPS_MSA_POSSIBLE_VALUES})
-  list(FIND PNG_MIPS_MSA_POSSIBLE_VALUES ${PNG_MIPS_MSA} index)
-  if(index EQUAL -1)
-    message(FATAL_ERROR
-            "PNG_MIPS_MSA must be one of [${PNG_MIPS_MSA_POSSIBLE_VALUES}]")
-  elseif(NOT ${PNG_MIPS_MSA} STREQUAL "off")
-    set(libpng_mips_sources
-      mips/mips_init.c
-      mips/filter_msa_intrinsics.c)
-    if(${PNG_MIPS_MSA} STREQUAL "on")
-      add_definitions(-DPNG_MIPS_MSA_OPT=2)
-    endif()
-  else()
-    add_definitions(-DPNG_MIPS_MSA_OPT=0)
-  endif()
-endif()
-
-else(PNG_HARDWARE_OPTIMIZATIONS)
-
-# set definitions and sources for arm
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^arm" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "^aarch64")
-  add_definitions(-DPNG_ARM_NEON_OPT=0)
-endif()
-
-# set definitions and sources for powerpc
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^powerpc*" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "^ppc64*")
-  add_definitions(-DPNG_POWERPC_VSX_OPT=0)
-endif()
-
-# set definitions and sources for intel
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^i?86" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "^x86_64*")
-  add_definitions(-DPNG_INTEL_SSE_OPT=0)
-endif()
-
-# set definitions and sources for MIPS
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "mipsel*" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "mips64el*")
-  add_definitions(-DPNG_MIPS_MSA_OPT=0)
-endif()
-
-endif(PNG_HARDWARE_OPTIMIZATIONS)
-
-# SET LIBNAME
-set(PNG_LIB_NAME png${PNGLIB_MAJOR}${PNGLIB_MINOR})
-
-# to distinguish between debug and release lib
-set(CMAKE_DEBUG_POSTFIX "d")
-
-include(CheckCSourceCompiles)
-option(ld-version-script "Enable linker version script" ON)
-if(ld-version-script AND NOT APPLE)
-  # Check if LD supports linker scripts.
-  file(WRITE "${CMAKE_CURRENT_BINARY_DIR}/conftest.map" "VERS_1 {
-        global: sym;
-        local: *;
-};
-
-VERS_2 {
-        global: sym2;
-                main;
-} VERS_1;
-")
-  set(CMAKE_REQUIRED_FLAGS_SAVE ${CMAKE_REQUIRED_FLAGS})
-  set(CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS} "-Wl,--version-script='${CMAKE_CURRENT_BINARY_DIR}/conftest.map'")
-  check_c_source_compiles("void sym(void) {}
-void sym2(void) {}
-int main(void) {return 0;}
-" HAVE_LD_VERSION_SCRIPT)
-  if(NOT HAVE_LD_VERSION_SCRIPT)
-    set(CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS_SAVE} "-Wl,-M -Wl,${CMAKE_CURRENT_BINARY_DIR}/conftest.map")
-  check_c_source_compiles("void sym(void) {}
-void sym2(void) {}
-int main(void) {return 0;}
-" HAVE_SOLARIS_LD_VERSION_SCRIPT)
-  endif()
-  set(CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS_SAVE})
-  file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/conftest.map")
-endif()
-
-# Find symbol prefix.  Likely obsolete and unnecessary with recent
-# toolchains (it's not done in many other projects).
-function(symbol_prefix)
-  set(SYMBOL_PREFIX)
-
-  execute_process(COMMAND "${CMAKE_C_COMPILER}" "-E" "-"
-                  INPUT_FILE /dev/null
-                  OUTPUT_VARIABLE OUT
-                  RESULT_VARIABLE STATUS)
-
-  if(CPP_FAIL)
-    message(WARNING "Failed to run the C preprocessor")
-  endif()
-
-  string(REPLACE "\n" ";" OUT "${OUT}")
-  foreach(line ${OUT})
-    string(REGEX MATCH "^PREFIX=" found_match "${line}")
-    if(found_match)
-      string(REGEX REPLACE "^PREFIX=(.*\)" "\\1" prefix "${line}")
-      string(REGEX MATCH "__USER_LABEL_PREFIX__" found_match "${prefix}")
-      if(found_match)
-        string(REGEX REPLACE "(.*)__USER_LABEL_PREFIX__(.*)" "\\1\\2" prefix "${prefix}")
-      endif()
-      set(SYMBOL_PREFIX "${prefix}")
-    endif()
-  endforeach()
-
-  message(STATUS "Symbol prefix: ${SYMBOL_PREFIX}")
-  set(SYMBOL_PREFIX "${SYMBOL_PREFIX}" PARENT_SCOPE)
-endfunction()
-
-if(UNIX)
-  symbol_prefix()
-endif()
-
-find_program(AWK NAMES gawk awk)
-
-include_directories(${CMAKE_CURRENT_BINARY_DIR})
-
-if(NOT AWK OR ANDROID)
-  # No awk available to generate sources; use pre-built pnglibconf.h
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/scripts/pnglibconf.h.prebuilt
-                 ${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h)
-  add_custom_target(genfiles) # Dummy
-else()
-  include(CMakeParseArguments)
-  # Generate .chk from .out with awk
-  # generate_chk(INPUT inputfile OUTPUT outputfile [DEPENDS dep1 [dep2...]])
-  function(generate_chk)
-    set(options)
-    set(oneValueArgs INPUT OUTPUT)
-    set(multiValueArgs DEPENDS)
-    cmake_parse_arguments(_GC "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
-    if(NOT _GC_INPUT)
-      message(FATAL_ERROR "generate_chk: Missing INPUT argument")
-    endif()
-    if(NOT _GC_OUTPUT)
-      message(FATAL_ERROR "generate_chk: Missing OUTPUT argument")
-    endif()
-
-    add_custom_command(OUTPUT "${_GC_OUTPUT}"
-                       COMMAND "${CMAKE_COMMAND}"
-                               "-DINPUT=${_GC_INPUT}"
-                               "-DOUTPUT=${_GC_OUTPUT}"
-                               -P "${CMAKE_CURRENT_BINARY_DIR}/scripts/genchk.cmake"
-                       DEPENDS "${_GC_INPUT}" ${_GC_DEPENDS}
-                       WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
-  endfunction()
-
-  # Generate .out from .c with awk
-  # generate_out(INPUT inputfile OUTPUT outputfile [DEPENDS dep1 [dep2...]])
-  function(generate_out)
-    set(options)
-    set(oneValueArgs INPUT OUTPUT)
-    set(multiValueArgs DEPENDS)
-    cmake_parse_arguments(_GO "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
-    if(NOT _GO_INPUT)
-      message(FATAL_ERROR "generate_out: Missing INPUT argument")
-    endif()
-    if(NOT _GO_OUTPUT)
-      message(FATAL_ERROR "generate_out: Missing OUTPUT argument")
-    endif()
-
-    add_custom_command(OUTPUT "${_GO_OUTPUT}"
-                       COMMAND "${CMAKE_COMMAND}"
-                               "-DINPUT=${_GO_INPUT}"
-                               "-DOUTPUT=${_GO_OUTPUT}"
-                               -P "${CMAKE_CURRENT_BINARY_DIR}/scripts/genout.cmake"
-                       DEPENDS "${_GO_INPUT}" ${_GO_DEPENDS}
-                       WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
-  endfunction()
-
-  # Generate specific source file with awk
-  # generate_source(OUTPUT outputfile [DEPENDS dep1 [dep2...]])
-  function(generate_source)
-    set(options)
-    set(oneValueArgs OUTPUT)
-    set(multiValueArgs DEPENDS)
-    cmake_parse_arguments(_GSO "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
-    if(NOT _GSO_OUTPUT)
-      message(FATAL_ERROR "generate_source: Missing OUTPUT argument")
-    endif()
-
-    add_custom_command(OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/${_GSO_OUTPUT}"
-                       COMMAND "${CMAKE_COMMAND}"
-                               "-DOUTPUT=${_GSO_OUTPUT}"
-                               -P "${CMAKE_CURRENT_BINARY_DIR}/scripts/gensrc.cmake"
-                       DEPENDS ${_GSO_DEPENDS}
-                       WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
-  endfunction()
-
-  # Copy file
-  function(generate_copy source destination)
-    add_custom_command(OUTPUT "${destination}"
-                       COMMAND "${CMAKE_COMMAND}" -E remove "${destination}"
-                       COMMAND "${CMAKE_COMMAND}" -E copy "${source}"
-                                                          "${destination}"
-                       DEPENDS "${source}")
-  endfunction()
-
-  # Generate scripts/pnglibconf.h
-  generate_source(OUTPUT "scripts/pnglibconf.c"
-                  DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/scripts/pnglibconf.dfa"
-                          "${CMAKE_CURRENT_SOURCE_DIR}/scripts/options.awk"
-                          "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h")
-
-  # Generate pnglibconf.c
-  generate_source(OUTPUT "pnglibconf.c"
-                  DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/scripts/pnglibconf.dfa"
-                          "${CMAKE_CURRENT_SOURCE_DIR}/scripts/options.awk"
-                          "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h")
-
-  if(PNG_PREFIX)
-    set(PNGLIBCONF_H_EXTRA_DEPENDS
-        "${CMAKE_CURRENT_BINARY_DIR}/scripts/prefix.out"
-        "${CMAKE_CURRENT_SOURCE_DIR}/scripts/macro.lst")
-    set(PNGPREFIX_H_EXTRA_DEPENDS
-        "${CMAKE_CURRENT_BINARY_DIR}/scripts/intprefix.out")
-  endif()
-
-  generate_out(INPUT "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.c"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.out")
-
-  # Generate pnglibconf.h
-  generate_source(OUTPUT "pnglibconf.h"
-                  DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.out"
-                          ${PNGLIBCONF_H_EXTRA_DEPENDS})
-
-  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/intprefix.c"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/intprefix.out"
-               DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h")
-
-  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/prefix.c"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/prefix.out"
-               DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/png.h"
-                       "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h"
-                       "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.out")
-
-  # Generate pngprefix.h
-  generate_source(OUTPUT "pngprefix.h"
-                  DEPENDS ${PNGPREFIX_H_EXTRA_DEPENDS})
-
-  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/sym.c"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/sym.out"
-               DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h")
-
-  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/symbols.c"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.out"
-               DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/png.h"
-                       "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h"
-                       "${CMAKE_CURRENT_SOURCE_DIR}/scripts/pnglibconf.h.prebuilt")
-
-  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/vers.c"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/vers.out"
-               DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/png.h"
-                       "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h"
-                       "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h")
-
-  generate_chk(INPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.out"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.chk"
-               DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/scripts/checksym.awk"
-                       "${CMAKE_CURRENT_SOURCE_DIR}/scripts/symbols.def")
-
-  add_custom_target(symbol-check DEPENDS
-                    "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.chk")
-
-  generate_copy("${CMAKE_CURRENT_BINARY_DIR}/scripts/sym.out"
-                "${CMAKE_CURRENT_BINARY_DIR}/libpng.sym")
-  generate_copy("${CMAKE_CURRENT_BINARY_DIR}/scripts/vers.out"
-                "${CMAKE_CURRENT_BINARY_DIR}/libpng.vers")
-
-  add_custom_target(genvers DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/libpng.vers")
-  add_custom_target(gensym DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/libpng.sym")
-
-  add_custom_target("genprebuilt"
-                    COMMAND "${CMAKE_COMMAND}"
-                            "-DOUTPUT=scripts/pnglibconf.h.prebuilt"
-                            -P "${CMAKE_CURRENT_BINARY_DIR}/scripts/gensrc.cmake"
-                    WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
-
-  # A single target handles generation of all generated files.  If
-  # they are depended upon separately by multiple targets, this
-  # confuses parallel make (it would require a separate top-level
-  # target for each file to track the dependencies properly).
-  add_custom_target(genfiles DEPENDS
-    "${CMAKE_CURRENT_BINARY_DIR}/libpng.sym"
-    "${CMAKE_CURRENT_BINARY_DIR}/libpng.vers"
-    "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.c"
-    "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h"
-    "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.out"
-    "${CMAKE_CURRENT_BINARY_DIR}/pngprefix.h"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/intprefix.out"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/pnglibconf.c"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/prefix.out"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/sym.out"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.chk"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.out"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/vers.out")
-endif(NOT AWK OR ANDROID)
-
-# OUR SOURCES
-set(libpng_public_hdrs
-  png.h
-  pngconf.h
-  "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h"
-)
-set(libpng_private_hdrs
-  pngpriv.h
-  pngdebug.h
-  pnginfo.h
-  pngstruct.h
-)
-if(AWK AND NOT ANDROID)
-  list(APPEND libpng_private_hdrs "${CMAKE_CURRENT_BINARY_DIR}/pngprefix.h")
-endif()
-set(libpng_sources
-  ${libpng_public_hdrs}
-  ${libpng_private_hdrs}
-  png.c
-  pngerror.c
-  pngget.c
-  pngmem.c
-  pngpread.c
-  pngread.c
-  pngrio.c
-  pngrtran.c
-  pngrutil.c
-  pngset.c
-  pngtrans.c
-  pngwio.c
-  pngwrite.c
-  pngwtran.c
-  pngwutil.c
-  ${libpng_arm_sources}
-  ${libpng_intel_sources}
-  ${libpng_mips_sources}
-  ${libpng_powerpc_sources}
-)
-set(pngtest_sources
-  pngtest.c
-)
-set(pngvalid_sources
-  contrib/libtests/pngvalid.c
-)
-set(pngstest_sources
-  contrib/libtests/pngstest.c
-)
-set(pngunknown_sources
-  contrib/libtests/pngunknown.c
-)
-set(pngimage_sources
-  contrib/libtests/pngimage.c
-)
-set(pngfix_sources
-  contrib/tools/pngfix.c
-)
-set(png_fix_itxt_sources
-  contrib/tools/png-fix-itxt.c
-)
-
-if(MSVC)
-  add_definitions(-D_CRT_SECURE_NO_DEPRECATE)
-endif()
-
-if(PNG_DEBUG)
-  add_definitions(-DPNG_DEBUG)
-endif()
-
-# NOW BUILD OUR TARGET
-include_directories(${CMAKE_CURRENT_SOURCE_DIR} ${ZLIB_INCLUDE_DIR})
-
-unset(PNG_LIB_TARGETS)
-
-if(PNG_STATIC)
-  # does not work without changing name
-  set(PNG_LIB_NAME_STATIC png_static)
-  add_library(png_static STATIC ${libpng_sources})
-  add_dependencies(png_static genfiles)
-  # MSVC doesn't use a different file extension for shared vs. static
-  # libs.  We are able to change OUTPUT_NAME to remove the _static
-  # for all other platforms.
-  if(NOT MSVC)
-    set_target_properties(png_static PROPERTIES
-      OUTPUT_NAME "${PNG_LIB_NAME}"
-      CLEAN_DIRECT_OUTPUT 1)
-  else()
-    set_target_properties(png_static PROPERTIES
-      OUTPUT_NAME "${PNG_LIB_NAME}_static"
-      CLEAN_DIRECT_OUTPUT 1)
-  endif()
-  list(APPEND PNG_LIB_TARGETS png_static)
-  if(MSVC)
-    # msvc does not append 'lib' - do it here to have consistent name
-    set_target_properties(png_static PROPERTIES PREFIX "lib")
-  endif()
-  target_link_libraries(png_static ${M_LIBRARY})
-endif()
-
-if(NOT PNG_LIB_TARGETS)
-  message(SEND_ERROR
-    "No library variant selected to build. "
-    "Please enable at least one of the following options: "
-    "PNG_STATIC, PNG_SHARED, PNG_FRAMEWORK")
-endif()
-
-# Set a variable with CMake code which:
-# Creates a symlink from src to dest (if possible) or alternatively
-# copies if different.
-include(CMakeParseArguments)
-
-function(create_symlink DEST_FILE)
-
-  cmake_parse_arguments(S "" "FILE;TARGET" "" ${ARGN})
-
-  if(NOT S_TARGET AND NOT S_FILE)
-    message(FATAL_ERROR "create_symlink: Missing TARGET or FILE argument")
-  endif()
-
-  if(S_TARGET AND S_FILE)
-    message(FATAL_ERROR "create_symlink: Both source file ${S_FILE} and build target ${S_TARGET} arguments are present; can only have one.")
-  endif()
-
-  if(S_FILE)
-    # If we don't need to symlink something that's coming from a build target,
-    # we can go ahead and symlink/copy at configure time.
-    if(CMAKE_HOST_WIN32 AND NOT CYGWIN)
-      execute_process(
-        COMMAND "${CMAKE_COMMAND}" -E copy_if_different ${S_FILE} ${DEST_FILE}
-        WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
-    else()
-      execute_process(
-        COMMAND ${CMAKE_COMMAND} -E create_symlink ${S_FILE} ${DEST_FILE}
-        WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
-    endif()
-  endif()
-
-  if(S_TARGET)
-    # We need to use generator expressions, which can be a bit tricky, so for
-    # simplicity make the symlink a POST_BUILD step and use the TARGET
-    # signature of add_custom_command.
-    if(CMAKE_HOST_WIN32 AND NOT CYGWIN)
-      add_custom_command(TARGET ${S_TARGET} POST_BUILD
-        COMMAND "${CMAKE_COMMAND}" -E copy_if_different $<TARGET_LINKER_FILE_NAME:${S_TARGET}> $<TARGET_LINKER_FILE_DIR:${S_TARGET}>/${DEST_FILE})
-    else()
-      add_custom_command(TARGET ${S_TARGET} POST_BUILD
-        COMMAND "${CMAKE_COMMAND}" -E create_symlink $<TARGET_LINKER_FILE_NAME:${S_TARGET}> $<TARGET_LINKER_FILE_DIR:${S_TARGET}>/${DEST_FILE})
-    endif()
-  endif()
-
-endfunction()
-
-# Create source generation scripts.
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/scripts/genchk.cmake.in
-               ${CMAKE_CURRENT_BINARY_DIR}/scripts/genchk.cmake @ONLY)
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/scripts/genout.cmake.in
-               ${CMAKE_CURRENT_BINARY_DIR}/scripts/genout.cmake @ONLY)
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/scripts/gensrc.cmake.in
-               ${CMAKE_CURRENT_BINARY_DIR}/scripts/gensrc.cmake @ONLY)
-
-# libpng is a library so default to 'lib'
-if(NOT DEFINED CMAKE_INSTALL_LIBDIR)
-  set(CMAKE_INSTALL_LIBDIR lib)
-endif()
-
-# CREATE PKGCONFIG FILES
-# We use the same files like ./configure, so we have to set its vars.
-# Only do this on Windows for Cygwin - the files don't make much sense outside
-# of a UNIX look-alike.
-if(NOT WIN32 OR CYGWIN OR MINGW)
-  set(prefix      ${CMAKE_INSTALL_PREFIX})
-  set(exec_prefix ${CMAKE_INSTALL_PREFIX})
-  set(libdir      ${CMAKE_INSTALL_FULL_LIBDIR})
-  set(includedir  ${CMAKE_INSTALL_FULL_INCLUDEDIR})
-  set(LIBS        "-lz -lm")
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libpng.pc.in
-    ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}.pc @ONLY)
-  create_symlink(libpng.pc FILE ${PNGLIB_NAME}.pc)
-
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libpng-config.in
-    ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}-config @ONLY)
-  create_symlink(libpng-config FILE ${PNGLIB_NAME}-config)
-endif()
-
-# SET UP LINKS
-if(PNG_SHARED)
-  set_target_properties(png PROPERTIES
-#   VERSION 16.${PNGLIB_RELEASE}.1.6.37
-    VERSION 16.${PNGLIB_RELEASE}.0
-    SOVERSION 16
-    CLEAN_DIRECT_OUTPUT 1)
-endif()
-
-# INSTALL
-if(NOT SKIP_INSTALL_LIBRARIES AND NOT SKIP_INSTALL_ALL)
-  install(TARGETS ${PNG_LIB_TARGETS}
-          EXPORT libpng
-          RUNTIME DESTINATION bin
-          LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-          ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
-          FRAMEWORK DESTINATION ${CMAKE_INSTALL_LIBDIR})
-
-  if(PNG_SHARED)
-    # Create a symlink for libpng.dll.a => libpng16.dll.a on Cygwin
-    if(CYGWIN OR MINGW)
-      create_symlink(libpng${CMAKE_IMPORT_LIBRARY_SUFFIX} TARGET png)
-      install(FILES $<TARGET_LINKER_FILE_DIR:png>/libpng${CMAKE_IMPORT_LIBRARY_SUFFIX}
-              DESTINATION ${CMAKE_INSTALL_LIBDIR})
-    endif()
-
-    if(NOT WIN32)
-      create_symlink(libpng${CMAKE_SHARED_LIBRARY_SUFFIX} TARGET png)
-      install(FILES $<TARGET_LINKER_FILE_DIR:png>/libpng${CMAKE_SHARED_LIBRARY_SUFFIX}
-              DESTINATION ${CMAKE_INSTALL_LIBDIR})
-    endif()
-  endif()
-
-  if(PNG_STATIC)
-    if(NOT WIN32 OR CYGWIN OR MINGW)
-      create_symlink(libpng${CMAKE_STATIC_LIBRARY_SUFFIX} TARGET png_static)
-      install(FILES $<TARGET_LINKER_FILE_DIR:png_static>/libpng${CMAKE_STATIC_LIBRARY_SUFFIX}
-              DESTINATION ${CMAKE_INSTALL_LIBDIR})
-    endif()
-  endif()
-endif()
-
-if(NOT SKIP_INSTALL_HEADERS AND NOT SKIP_INSTALL_ALL)
-  install(FILES ${libpng_public_hdrs} DESTINATION include)
-  install(FILES ${libpng_public_hdrs} DESTINATION include/${PNGLIB_NAME})
-endif()
-if(NOT SKIP_INSTALL_EXECUTABLES AND NOT SKIP_INSTALL_ALL)
-  if(NOT WIN32 OR CYGWIN OR MINGW)
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/libpng-config DESTINATION bin)
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}-config DESTINATION bin)
-  endif()
-endif()
-
-if(NOT SKIP_INSTALL_PROGRAMS AND NOT SKIP_INSTALL_ALL)
-  install(TARGETS ${PNG_BIN_TARGETS}
-          RUNTIME DESTINATION bin)
-endif()
-
-if(NOT SKIP_INSTALL_FILES AND NOT SKIP_INSTALL_ALL)
-  # Install man pages
-  if(NOT PNG_MAN_DIR)
-    set(PNG_MAN_DIR "share/man")
-  endif()
-  install(FILES libpng.3 libpngpf.3 DESTINATION ${PNG_MAN_DIR}/man3)
-  install(FILES png.5 DESTINATION ${PNG_MAN_DIR}/man5)
-  # Install pkg-config files
-  if(NOT CMAKE_HOST_WIN32 OR CYGWIN OR MINGW)
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libpng.pc
-            DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/libpng-config
-            DESTINATION bin)
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}.pc
-            DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}-config
-            DESTINATION bin)
-  endif()
-endif()
-
-# Create an export file that CMake users can include() to import our targets.
-if(NOT SKIP_INSTALL_EXPORT AND NOT SKIP_INSTALL_ALL)
-  install(EXPORT libpng DESTINATION lib/libpng FILE lib${PNG_LIB_NAME}.cmake)
-endif()
-
-# what's with libpng-manual.txt and all the extra files?
-
-# UNINSTALL
-# do we need this?
-
-# DIST
-# do we need this?
-
-# to create msvc import lib for mingw compiled shared lib
-# pexports libpng.dll > libpng.def
-# lib /def:libpng.def /machine:x86

cmake/CMakeLists.txt

@@ -3,6 +3,7 @@
 # This file is part of LAMMPS
 # Created by Christoph Junghans and Richard Berger
 cmake_minimum_required(VERSION 3.10)
+########################################
 # set policy to silence warnings about ignoring <PackageName>_ROOT but use it
 if(POLICY CMP0074)
   cmake_policy(SET CMP0074 NEW)
@@ -20,7 +21,13 @@ endif()
 if(POLICY CMP0135)
   cmake_policy(SET CMP0135 OLD)
 endif()
-
+########################################
+# Use CONFIGURE_DEPENDS as option for file(GLOB...) when available
+if(CMAKE_VERSION VERSION_LESS 3.12)
+  unset(CONFIGURE_DEPENDS)
+else()
+  set(CONFIGURE_DEPENDS CONFIGURE_DEPENDS)
+endif()
 ########################################
 
 project(lammps CXX)
@@ -161,8 +168,8 @@ endif()
 ########################################################################
 # User input options                                                   #
 ########################################################################
-# set path to python interpreter and thus enforcing python version if
-# when in a virtual environment and PYTHON_EXECUTABLE is not set on command line
+# set path to python interpreter and thus enforcing python version when
+# in a virtual environment and PYTHON_EXECUTABLE is not set on command line
 if(DEFINED ENV{VIRTUAL_ENV} AND NOT PYTHON_EXECUTABLE)
   if(CMAKE_HOST_SYSTEM_NAME STREQUAL "Windows")
     set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/Scripts/python.exe")
@@ -185,6 +192,7 @@ option(BUILD_SHARED_LIBS "Build shared library" OFF)
 option(CMAKE_POSITION_INDEPENDENT_CODE "Create object compatible with shared libraries" ON)
 option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
 option(BUILD_LAMMPS_SHELL "Build and install the LAMMPS shell" OFF)
+option(BUILD_LAMMPS_GUI "Build and install the LAMMPS GUI" OFF)
 
 # Support using clang-tidy for C++ files with selected options
 set(ENABLE_CLANG_TIDY OFF CACHE BOOL "Include clang-tidy processing when compiling")
@@ -195,8 +203,8 @@ else()
 endif()
 
 include(GNUInstallDirs)
-file(GLOB ALL_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
-file(GLOB MAIN_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
+file(GLOB ALL_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
+file(GLOB MAIN_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/main.cpp)
 list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
 add_library(lammps ${ALL_SOURCES})
 
@@ -250,7 +258,7 @@ set(STANDARD_PACKAGES
   KIM
   KSPACE
   LATBOLTZ
-  LATTE
+  LEPTON
   MACHDYN
   MANIFOLD
   MANYBODY
@@ -266,6 +274,7 @@ set(STANDARD_PACKAGES
   ML-QUIP
   ML-RANN
   ML-SNAP
+  ML-POD
   MOFFF
   MOLECULE
   MOLFILE
@@ -316,6 +325,15 @@ if(PKG_ADIOS)
   # script that defines the MPI::MPI_C target
   enable_language(C)
   find_package(ADIOS2 REQUIRED)
+  if(BUILD_MPI)
+    if(NOT ADIOS2_HAVE_MPI)
+      message(FATAL_ERROR "ADIOS2 must be built with MPI support when LAMMPS has MPI enabled")
+    endif()
+  else()
+    if(ADIOS2_HAVE_MPI)
+      message(FATAL_ERROR "ADIOS2 must be built without MPI support when LAMMPS has MPI disabled")
+    endif()
+  endif()
   target_link_libraries(lammps PRIVATE adios2::adios2)
 endif()
 
@@ -423,23 +441,19 @@ if(BUILD_OMP)
   target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
 endif()
 
-if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE OR PKG_ELECTRODE)
+if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_TOOLS)
   enable_language(C)
   if (NOT USE_INTERNAL_LINALG)
     find_package(LAPACK)
     find_package(BLAS)
   endif()
   if(NOT LAPACK_FOUND OR NOT BLAS_FOUND OR USE_INTERNAL_LINALG)
-    include(CheckGeneratorSupport)
-    if(NOT CMAKE_GENERATOR_SUPPORT_FORTRAN)
-      status(FATAL_ERROR "Cannot build internal linear algebra library as CMake build tool lacks Fortran support")
-    endif()
-    enable_language(Fortran)
-    file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
-    add_library(linalg STATIC ${LAPACK_SOURCES})
+    file(GLOB LINALG_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.cpp)
+    add_library(linalg STATIC ${LINALG_SOURCES})
     set_target_properties(linalg PROPERTIES OUTPUT_NAME lammps_linalg${LAMMPS_MACHINE})
     set(BLAS_LIBRARIES "$<TARGET_FILE:linalg>")
     set(LAPACK_LIBRARIES "$<TARGET_FILE:linalg>")
+    target_link_libraries(lammps PRIVATE linalg)
   else()
     list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
   endif()
@@ -507,7 +521,7 @@ else()
 endif()
 
 foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
-        PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM LATTE MSCG COMPRESS ML-PACE)
+        PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM MSCG COMPRESS ML-PACE LEPTON)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
@@ -524,7 +538,10 @@ set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler and machine
 separate_arguments(CMAKE_TUNE_FLAGS)
 foreach(_FLAG ${CMAKE_TUNE_FLAGS})
   target_compile_options(lammps PRIVATE ${_FLAG})
-  target_compile_options(lmp PRIVATE ${_FLAG})
+  # skip these flags when linking the main executable
+  if(NOT (("${_FLAG}" STREQUAL "-Xcudafe") OR (("${_FLAG}" STREQUAL "--diag_suppress=unrecognized_pragma"))))
+    target_compile_options(lmp PRIVATE ${_FLAG})
+  endif()
 endforeach()
 ########################################################################
 # Basic system tests (standard libraries, headers, functions, types)   #
@@ -552,6 +569,8 @@ RegisterStyles(${LAMMPS_SOURCE_DIR})
 ########################################################
 # Fetch missing external files and archives for packages
 ########################################################
+option(DOWNLOAD_POTENTIALS "Automatically download large potential files" ON)
+mark_as_advanced(DOWNLOAD_POTENTIALS)
 foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
   if(PKG_${PKG})
     FetchPotentials(${LAMMPS_SOURCE_DIR}/${PKG} ${LAMMPS_POTENTIALS_DIR})
@@ -564,8 +583,8 @@ endforeach()
 foreach(PKG ${STANDARD_PACKAGES})
   set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
 
-  file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
-  file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/[^.]*.h)
+  file(GLOB ${PKG}_SOURCES ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
+  file(GLOB ${PKG}_HEADERS ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.h)
 
   # check for package files in src directory due to old make system
   DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
@@ -592,8 +611,8 @@ endforeach()
 foreach(PKG ${SUFFIX_PACKAGES})
   set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
 
-  file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
-  file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/[^.]*.h)
+  file(GLOB ${PKG}_SOURCES ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
+  file(GLOB ${PKG}_HEADERS ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.h)
 
   # check for package files in src directory due to old make system
   DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
@@ -604,18 +623,11 @@ endforeach()
 ##############################################
 # add lib sources of (simple) enabled packages
 ############################################
-foreach(PKG_LIB POEMS ATC AWPMD H5MD MESONT)
+foreach(PKG_LIB POEMS ATC AWPMD H5MD)
   if(PKG_${PKG_LIB})
     string(TOLOWER "${PKG_LIB}" PKG_LIB)
-    if(PKG_LIB STREQUAL "mesont")
-      enable_language(Fortran)
-      file(GLOB_RECURSE ${PKG_LIB}_SOURCES
-        ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.f90)
-    else()
-      file(GLOB_RECURSE ${PKG_LIB}_SOURCES
-        ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c
-        ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
-    endif()
+    file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${CONFIGURE_DEPENDS}
+      ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
     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})
@@ -629,7 +641,7 @@ foreach(PKG_LIB POEMS ATC AWPMD H5MD MESONT)
   endif()
 endforeach()
 
-if(PKG_ELECTRODE)
+if(PKG_ELECTRODE OR PKG_ML-POD)
   target_link_libraries(lammps PRIVATE ${LAPACK_LIBRARIES})
 endif()
 
@@ -658,7 +670,7 @@ endif()
 # packages which selectively include variants based on enabled styles
 # e.g. accelerator packages
 ######################################################################
-foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
+foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
@@ -784,9 +796,11 @@ include(Tools)
 include(Documentation)
 
 ###############################################################################
-# Install potential and force field files in data directory
+# Install bench, potential and force field files in data directory
 ###############################################################################
-set(LAMMPS_INSTALL_DATADIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps)
+set(LAMMPS_INSTALL_DATADIR ${CMAKE_INSTALL_DATADIR}/lammps)
+
+install(DIRECTORY ${LAMMPS_DIR}/bench DESTINATION ${LAMMPS_INSTALL_DATADIR})
 install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_DATADIR})
 if(BUILD_TOOLS)
   install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files DESTINATION ${LAMMPS_INSTALL_DATADIR})
@@ -829,9 +843,8 @@ if(BUILD_SHARED_LIBS)
   set(LIBLAMMPS_SHARED_BINARY ${MY_BUILD_DIR}/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX})
   if(Python_EXECUTABLE)
     add_custom_target(
-      install-python ${CMAKE_COMMAND} -E remove_directory build
-      COMMAND ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps
-              -l ${LIBLAMMPS_SHARED_BINARY} -w ${MY_BUILD_DIR}
+      install-python ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps
+      -l ${LIBLAMMPS_SHARED_BINARY} -w ${MY_BUILD_DIR} -v ${LAMMPS_SOURCE_DIR}/version.h
       COMMENT "Installing LAMMPS Python module")
   else()
     add_custom_target(
@@ -844,35 +857,6 @@ else()
     ${CMAKE_COMMAND} -E echo "Must build LAMMPS as a shared library to use the Python module")
 endif()
 
-###############################################################################
-# Add LAMMPS python module to "install" target. This is taylored for building
-# LAMMPS for package managers and with different prefix settings.
-# This requires either a shared library or that the PYTHON package is included.
-###############################################################################
-if(BUILD_SHARED_LIBS OR PKG_PYTHON)
-  if(CMAKE_VERSION VERSION_LESS 3.12)
-    # adjust so we find Python 3 versions before Python 2 on old systems with old CMake
-    set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
-    find_package(PythonInterp) # Deprecated since version 3.12
-    if(PYTHONINTERP_FOUND)
-      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
-    endif()
-  else()
-    # backward compatibility
-    if(PYTHON_EXECUTABLE)
-      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
-    endif()
-    find_package(Python COMPONENTS Interpreter)
-  endif()
-  if(Python_EXECUTABLE)
-    file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python/lib)
-    file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python/src)
-    file(COPY ${LAMMPS_SOURCE_DIR}/version.h  DESTINATION ${CMAKE_BINARY_DIR}/python/src)
-    file(COPY ${LAMMPS_PYTHON_DIR}/README ${LAMMPS_PYTHON_DIR}/pyproject.toml ${LAMMPS_PYTHON_DIR}/setup.py ${LAMMPS_PYTHON_DIR}/lammps  DESTINATION ${CMAKE_BINARY_DIR}/python/lib)
-    install(CODE "if(\"\$ENV{DESTDIR}\" STREQUAL \"\")\n execute_process(COMMAND ${Python_EXECUTABLE} -m pip install -v ${CMAKE_BINARY_DIR}/python/lib --prefix=${CMAKE_INSTALL_PREFIX})\n else()\n execute_process(COMMAND ${Python_EXECUTABLE} -m pip install -v ${CMAKE_BINARY_DIR}/python/lib --prefix=${CMAKE_INSTALL_PREFIX} --root=\$ENV{DESTDIR})\n endif()")
-  endif()
-endif()
-
 include(Testing)
 include(CodeCoverage)
 include(CodingStandard)
@@ -884,6 +868,23 @@ if(ClangFormat_FOUND)
     WORKING_DIRECTORY ${LAMMPS_SOURCE_DIR})
 endif()
 
+# extract Kokkos compilation settings
+get_cmake_property(_allvars VARIABLES)
+foreach(_var ${_allvars})
+  if(${_var})
+    string(REGEX MATCH "Kokkos_ENABLE_(SERIAL|THREADS|OPENMP|CUDA|HIP|SYCL|OPENMPTARGET|HPX)" _match ${_var})
+    if(_match)
+      string(REGEX REPLACE "Kokkos_ENABLE_(OPENMP|SERIAL|CUDA|HIP|SYCL)" "\\1" _match ${_var})
+      list(APPEND KOKKOS_DEVICE ${_match})
+    endif()
+    string(REGEX MATCH "Kokkos_ARCH" _match ${_var})
+    if(_match)
+      string(REGEX REPLACE "Kokkos_ARCH_(.*)" "\\1" _match ${_var})
+      list(APPEND KOKKOS_ARCH ${_match})
+    endif()
+  endif()
+endforeach()
+
 get_target_property(DEFINES lammps COMPILE_DEFINITIONS)
 if(BUILD_IS_MULTI_CONFIG)
   set(LAMMPS_BUILD_TYPE "Multi-Config")
@@ -895,6 +896,7 @@ feature_summary(DESCRIPTION "The following tools and libraries have been found a
 message(STATUS "<<< Build configuration >>>
    LAMMPS Version:   ${PROJECT_VERSION}
    Operating System: ${CMAKE_SYSTEM_NAME} ${CMAKE_LINUX_DISTRO} ${CMAKE_DISTRO_VERSION}
+   CMake Version:    ${CMAKE_VERSION}
    Build type:       ${LAMMPS_BUILD_TYPE}
    Install path:     ${CMAKE_INSTALL_PREFIX}
    Generator:        ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}")
@@ -980,6 +982,12 @@ if(PKG_GPU)
   endif()
   message(STATUS "GPU precision:            ${GPU_PREC}")
 endif()
+if(PKG_KOKKOS)
+  message(STATUS "Kokkos Devices: ${KOKKOS_DEVICE}")
+  if(KOKKOS_ARCH)
+    message(STATUS "Kokkos Architecture: ${KOKKOS_ARCH}")
+  endif()
+endif()
 if(PKG_KSPACE)
   message(STATUS "<<< FFT settings >>>
 -- Primary FFT lib:  ${FFT}")

cmake/CMakeLists.zlib

@@ -1,195 +0,0 @@
-cmake_minimum_required(VERSION 3.10)
-# When using CMake 3.4 and later, don't export symbols from executables unless
-# the CMAKE_ENABLE_EXPORTS variable is set.
-if(POLICY CMP0065)
-  cmake_policy(SET CMP0065 NEW)
-endif()
-if (POLICY CMP0077)
-  cmake_policy(SET CMP0077 NEW)
-endif()
-set(CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS ON)
-
-project(zlib C)
-
-set(VERSION "1.2.11")
-
-option(ASM686 "Enable building i686 assembly implementation" OFF)
-option(AMD64 "Enable building amd64 assembly implementation" OFF)
-
-set(INSTALL_BIN_DIR "${CMAKE_INSTALL_PREFIX}/bin" CACHE PATH "Installation directory for executables")
-set(INSTALL_LIB_DIR "${CMAKE_INSTALL_PREFIX}/lib" CACHE PATH "Installation directory for libraries")
-set(INSTALL_INC_DIR "${CMAKE_INSTALL_PREFIX}/include" CACHE PATH "Installation directory for headers")
-set(INSTALL_MAN_DIR "${CMAKE_INSTALL_PREFIX}/share/man" CACHE PATH "Installation directory for manual pages")
-set(INSTALL_PKGCONFIG_DIR "${CMAKE_INSTALL_PREFIX}/share/pkgconfig" CACHE PATH "Installation directory for pkgconfig (.pc) files")
-
-include(CheckTypeSize)
-include(CheckFunctionExists)
-include(CheckIncludeFile)
-include(CheckCSourceCompiles)
-
-check_include_file(sys/types.h HAVE_SYS_TYPES_H)
-check_include_file(stdint.h    HAVE_STDINT_H)
-check_include_file(stddef.h    HAVE_STDDEF_H)
-
-#
-# Check to see if we have large file support
-#
-set(CMAKE_REQUIRED_DEFINITIONS -D_LARGEFILE64_SOURCE=1)
-# We add these other definitions here because CheckTypeSize.cmake
-# in CMake 2.4.x does not automatically do so and we want
-# compatibility with CMake 2.4.x.
-if(HAVE_SYS_TYPES_H)
-    list(APPEND CMAKE_REQUIRED_DEFINITIONS -DHAVE_SYS_TYPES_H)
-endif()
-if(HAVE_STDINT_H)
-    list(APPEND CMAKE_REQUIRED_DEFINITIONS -DHAVE_STDINT_H)
-endif()
-if(HAVE_STDDEF_H)
-    list(APPEND CMAKE_REQUIRED_DEFINITIONS -DHAVE_STDDEF_H)
-endif()
-check_type_size(off64_t OFF64_T)
-check_type_size(off64_t OFF64_T)
-if(HAVE_OFF64_T)
-   add_definitions(-D_LARGEFILE64_SOURCE=1)
-endif()
-set(CMAKE_REQUIRED_DEFINITIONS) # clear variable
-
-#
-# Check for fseeko
-#
-check_function_exists(fseeko HAVE_FSEEKO)
-if(NOT HAVE_FSEEKO)
-    add_definitions(-DNO_FSEEKO)
-endif()
-
-#
-# Check for unistd.h
-#
-check_include_file(unistd.h Z_HAVE_UNISTD_H)
-
-if(MSVC)
-    set(CMAKE_DEBUG_POSTFIX "d")
-    add_definitions(-D_CRT_SECURE_NO_DEPRECATE)
-    add_definitions(-D_CRT_NONSTDC_NO_DEPRECATE)
-    include_directories(${CMAKE_CURRENT_SOURCE_DIR})
-endif()
-
-if(NOT CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_CURRENT_BINARY_DIR)
-    # If we're doing an out of source build and the user has a zconf.h
-    # in their source tree...
-    if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h)
-        file(RENAME ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h.included)
-  endif()
-endif()
-
-set(ZLIB_PC ${CMAKE_CURRENT_BINARY_DIR}/zlib.pc)
-configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/zlib.pc.cmakein
-		${ZLIB_PC} @ONLY)
-configure_file(	${CMAKE_CURRENT_SOURCE_DIR}/zconf.h.cmakein
-		${CMAKE_CURRENT_BINARY_DIR}/zconf.h @ONLY)
-include_directories(${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_SOURCE_DIR})
-
-
-#============================================================================
-# zlib
-#============================================================================
-
-set(ZLIB_PUBLIC_HDRS
-    ${CMAKE_CURRENT_BINARY_DIR}/zconf.h
-    zlib.h
-)
-set(ZLIB_PRIVATE_HDRS
-    crc32.h
-    deflate.h
-    gzguts.h
-    inffast.h
-    inffixed.h
-    inflate.h
-    inftrees.h
-    trees.h
-    zutil.h
-)
-set(ZLIB_SRCS
-    adler32.c
-    compress.c
-    crc32.c
-    deflate.c
-    gzclose.c
-    gzlib.c
-    gzread.c
-    gzwrite.c
-    inflate.c
-    infback.c
-    inftrees.c
-    inffast.c
-    trees.c
-    uncompr.c
-    zutil.c
-)
-
-if(NOT MINGW)
-    set(ZLIB_DLL_SRCS
-        win32/zlib1.rc # If present will override custom build rule below.
-    )
-endif()
-
-if(CMAKE_COMPILER_IS_GNUCC)
-    if(ASM686)
-        set(ZLIB_ASMS contrib/asm686/match.S)
-    elseif (AMD64)
-        set(ZLIB_ASMS contrib/amd64/amd64-match.S)
-    endif ()
-
-	if(ZLIB_ASMS)
-		add_definitions(-DASMV)
-		set_source_files_properties(${ZLIB_ASMS} PROPERTIES LANGUAGE C COMPILE_FLAGS -DNO_UNDERLINE)
-	endif()
-endif()
-
-if(MSVC)
-    if(ASM686)
-		ENABLE_LANGUAGE(ASM_MASM)
-        set(ZLIB_ASMS
-			contrib/masmx86/inffas32.asm
-			contrib/masmx86/match686.asm
-		)
-    elseif (AMD64)
-		ENABLE_LANGUAGE(ASM_MASM)
-        set(ZLIB_ASMS
-			contrib/masmx64/gvmat64.asm
-			contrib/masmx64/inffasx64.asm
-		)
-    endif()
-
-	if(ZLIB_ASMS)
-		add_definitions(-DASMV -DASMINF)
-	endif()
-endif()
-
-# parse the full version number from zlib.h and include in ZLIB_FULL_VERSION
-file(READ ${CMAKE_CURRENT_SOURCE_DIR}/zlib.h _zlib_h_contents)
-string(REGEX REPLACE ".*#define[ \t]+ZLIB_VERSION[ \t]+\"([-0-9A-Za-z.]+)\".*"
-    "\\1" ZLIB_FULL_VERSION ${_zlib_h_contents})
-
-if(MINGW)
-    # This gets us DLL resource information when compiling on MinGW.
-    if(NOT CMAKE_RC_COMPILER)
-        set(CMAKE_RC_COMPILER windres.exe)
-    endif()
-
-    add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/zlib1rc.obj
-                       COMMAND ${CMAKE_RC_COMPILER}
-                            -D GCC_WINDRES
-                            -I ${CMAKE_CURRENT_SOURCE_DIR}
-                            -I ${CMAKE_CURRENT_BINARY_DIR}
-                            -o ${CMAKE_CURRENT_BINARY_DIR}/zlib1rc.obj
-                            -i ${CMAKE_CURRENT_SOURCE_DIR}/win32/zlib1.rc)
-    set(ZLIB_DLL_SRCS ${CMAKE_CURRENT_BINARY_DIR}/zlib1rc.obj)
-endif(MINGW)
-
-add_library(zlibstatic STATIC ${ZLIB_SRCS} ${ZLIB_ASMS} ${ZLIB_PUBLIC_HDRS} ${ZLIB_PRIVATE_HDRS})
-
-if(UNIX)
-    # On unix-like platforms the library is almost always called libz
-   set_target_properties(zlibstatic PROPERTIES OUTPUT_NAME z)
-endif()

cmake/CMakeSettings.json

@@ -63,6 +63,11 @@
           "name": "ENABLE_TESTING",
           "value": "True",
           "type": "BOOL"
+        },
+        {
+          "name": "BUILD_LAMMPS_GUI",
+          "value": "False",
+          "type": "BOOL"
         }
       ]
     },
@@ -72,7 +77,7 @@
       "configurationType": "Debug",
       "buildRoot": "${workspaceRoot}\\build\\${name}",
       "installRoot": "${workspaceRoot}\\install\\${name}",
-      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe",
+      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe -DBUILD_MPI=off",
       "buildCommandArgs": "",
       "ctestCommandArgs": "",
       "inheritEnvironments": [ "clang_cl_x64" ],
@@ -105,7 +110,7 @@
       "configurationType": "Release",
       "buildRoot": "${workspaceRoot}\\build\\${name}",
       "installRoot": "${workspaceRoot}\\install\\${name}",
-      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe",
+      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe -DBUILD_MPI=off",
       "buildCommandArgs": "",
       "ctestCommandArgs": "-V",
       "inheritEnvironments": [ "clang_cl_x64" ],
@@ -303,6 +308,54 @@
           "type": "STRING"
         }
       ]
+    },
+    {
+      "name": "x64-GUI-MSVC",
+      "generator": "Ninja",
+      "configurationType": "Release",
+      "buildRoot": "${workspaceRoot}\\build\\${name}",
+      "installRoot": "${workspaceRoot}\\install\\${name}",
+      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -D QT_DIR=C:\\Qt\\5.15.2\\msvc2019_64\\lib\\cmake\\Qt5  -D Qt5_DIR=C:\\Qt\\5.15.2\\msvc2019_64\\lib\\cmake\\Qt5",
+      "buildCommandArgs": "",
+      "ctestCommandArgs": "-V",
+      "inheritEnvironments": [ "msvc_x64_x64" ],
+      "variables": [
+        {
+          "name": "BUILD_SHARED_LIBS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_TOOLS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "LAMMPS_EXCEPTIONS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "ENABLE_TESTING",
+          "value": "False",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_MPI",
+          "value": "False",
+          "type": "BOOL"
+        },
+        {
+          "name": "WITH_PNG",
+          "value": "False",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_LAMMPS_GUI",
+          "value": "True",
+          "type": "BOOL"
+        }
+      ]
     }
   ]
-}
+}

cmake/Modules/CodingStandard.cmake

@@ -5,6 +5,10 @@ if(CMAKE_VERSION VERSION_LESS 3.12)
         set(Python3_VERSION ${PYTHON_VERSION_STRING})
     endif()
 else()
+    # use default (or custom) Python executable, if version is sufficient
+    if(Python_VERSION VERSION_GREATER_EQUAL 3.5)
+      set(Python3_EXECUTABLE ${Python_EXECUTABLE})
+    endif()
     find_package(Python3 COMPONENTS Interpreter QUIET)
 endif()
 

cmake/Modules/DetectHIPInstallation.cmake

@@ -0,0 +1,16 @@
+if(NOT DEFINED HIP_PATH)
+    if(NOT DEFINED ENV{HIP_PATH})
+        message(FATAL_ERROR "HIP support requires HIP_PATH to be defined.\n"
+        "Either pass the HIP_PATH as a CMake option via -DHIP_PATH=... or set the HIP_PATH environment variable.")
+    else()
+        set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to HIP installation")
+    endif()
+endif()
+if(NOT DEFINED ROCM_PATH)
+    if(NOT DEFINED ENV{ROCM_PATH})
+        set(ROCM_PATH "/opt/rocm" CACHE PATH "Path to ROCm installation")
+    else()
+        set(ROCM_PATH $ENV{ROCM_PATH} CACHE PATH "Path to ROCm installation")
+    endif()
+endif()
+list(APPEND CMAKE_PREFIX_PATH ${HIP_PATH} ${ROCM_PATH})

cmake/Modules/Documentation.cmake

@@ -4,20 +4,24 @@
 option(BUILD_DOC "Build LAMMPS HTML documentation" OFF)
 
 if(BUILD_DOC)
-  # Sphinx 3.x requires at least Python 3.5
+  # Current Sphinx versions require at least Python 3.8
   if(CMAKE_VERSION VERSION_LESS 3.12)
-    find_package(PythonInterp 3.5 REQUIRED)
+    find_package(PythonInterp 3.8 REQUIRED)
     set(VIRTUALENV ${PYTHON_EXECUTABLE} -m venv)
   else()
+    # use default (or custom) Python executable, if version is sufficient
+    if(Python_VERSION VERSION_GREATER_EQUAL 3.8)
+      set(Python3_EXECUTABLE ${Python_EXECUTABLE})
+    endif()
     find_package(Python3 REQUIRED COMPONENTS Interpreter)
-    if(Python3_VERSION VERSION_LESS 3.5)
-      message(FATAL_ERROR "Python 3.5 and up is required to build the HTML documentation")
+    if(Python3_VERSION VERSION_LESS 3.8)
+      message(FATAL_ERROR "Python 3.8 and up is required to build the HTML documentation")
     endif()
     set(VIRTUALENV ${Python3_EXECUTABLE} -m venv)
   endif()
   find_package(Doxygen 1.8.10 REQUIRED)
 
-  file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
+  file(GLOB DOC_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
 
 
   add_custom_command(
@@ -56,16 +60,27 @@ if(BUILD_DOC)
   )
 
   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")
+  set(MATHJAX_MD5 "b81661c6e6ba06278e6ae37b30b0c492" CACHE STRING "MD5 checksum of MathJax tarball")
   mark_as_advanced(MATHJAX_URL)
+  GetFallbackURL(MATHJAX_URL MATHJAX_FALLBACK)
 
   # download mathjax distribution and unpack to folder "mathjax"
   if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/mathjax/es5)
-    file(DOWNLOAD ${MATHJAX_URL}
-      "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
-      EXPECTED_MD5 ${MATHJAX_MD5})
+    if(EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz)
+      file(MD5 ${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz)
+    endif()
+    if(NOT "${DL_MD5}" STREQUAL "${MATHJAX_MD5}")
+      file(DOWNLOAD ${MATHJAX_URL} "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz" STATUS DL_STATUS SHOW_PROGRESS)
+      file(MD5 ${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz DL_MD5)
+      if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${MATHJAX_MD5}"))
+        message(WARNING "Download from primary URL ${MATHJAX_URL} failed\nTrying fallback URL ${MATHJAX_FALLBACK}")
+        file(DOWNLOAD ${MATHJAX_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${MATHJAX_MD5} SHOW_PROGRESS)
+      endif()
+    else()
+      message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
+    endif()
     execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
-    file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
+    file(GLOB MATHJAX_VERSION_DIR ${CONFIGURE_DEPENDS} ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
     execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax)
   endif()
 

cmake/Modules/ExternalCMakeProject.cmake

@@ -9,8 +9,22 @@ function(ExternalCMakeProject target url hash basedir cmakedir cmakefile)
 
   get_filename_component(archive ${url} NAME)
   file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/_deps/src)
-  message(STATUS "Downloading ${url}")
-  file(DOWNLOAD ${url} ${CMAKE_BINARY_DIR}/_deps/${archive} EXPECTED_HASH MD5=${hash} SHOW_PROGRESS)
+  if(EXISTS ${CMAKE_BINARY_DIR}/_deps/${archive})
+    file(MD5 ${CMAKE_BINARY_DIR}/_deps/${archive} DL_MD5)
+  endif()
+  if(NOT "${DL_MD5}" STREQUAL "${hash}")
+    message(STATUS "Downloading ${url}")
+    file(DOWNLOAD ${url} ${CMAKE_BINARY_DIR}/_deps/${archive} STATUS DL_STATUS SHOW_PROGRESS)
+    file(MD5 ${CMAKE_BINARY_DIR}/_deps/${archive} DL_MD5)
+    if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${hash}"))
+      set(${target}_URL ${url})
+      GetFallbackURL(${target}_URL fallback)
+      message(WARNING "Download from primary URL ${url} failed\nTrying fallback URL ${fallback}")
+      file(DOWNLOAD ${fallback} ${CMAKE_BINARY_DIR}/_deps/${archive} EXPECTED_HASH MD5=${hash} SHOW_PROGRESS)
+    endif()
+  else()
+    message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/_deps/${archive}")
+  endif()
   message(STATUS "Unpacking and configuring ${archive}")
   execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf ${CMAKE_BINARY_DIR}/_deps/${archive}
     WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/_deps/src)

cmake/Modules/FindZMQ.cmake

@@ -1,19 +0,0 @@
-find_path(ZMQ_INCLUDE_DIR zmq.h)
-find_library(ZMQ_LIBRARY NAMES zmq)
-
-include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(ZMQ DEFAULT_MSG ZMQ_LIBRARY ZMQ_INCLUDE_DIR)
-
-# Copy the results to the output variables and target.
-if(ZMQ_FOUND)
-  set(ZMQ_LIBRARIES ${ZMQ_LIBRARY})
-  set(ZMQ_INCLUDE_DIRS ${ZMQ_INCLUDE_DIR})
-
-  if(NOT TARGET ZMQ::ZMQ)
-    add_library(ZMQ::ZMQ UNKNOWN IMPORTED)
-    set_target_properties(ZMQ::ZMQ PROPERTIES
-      IMPORTED_LINK_INTERFACE_LANGUAGES "C"
-      IMPORTED_LOCATION "${ZMQ_LIBRARY}"
-      INTERFACE_INCLUDE_DIRECTORIES "${ZMQ_INCLUDE_DIR}")
-  endif()
-endif()

cmake/Modules/LAMMPSInterfacePlugin.cmake

@@ -65,7 +65,7 @@ endfunction(validate_option)
 
 # helper function for getting the most recently modified file or folder from a glob pattern
 function(get_newest_file path variable)
-  file(GLOB _dirs ${path})
+  file(GLOB _dirs ${CONFIGURE_DEPENDS} ${path})
   set(_besttime 2000-01-01T00:00:00)
   set(_bestfile "<unknown>")
   foreach(_dir ${_dirs})
@@ -88,6 +88,18 @@ function(get_lammps_version version_header variable)
     set(${variable} "${date}" PARENT_SCOPE)
 endfunction()
 
+# determine canonical URL for downloading backup copy from download.lammps.org/thirdparty
+function(GetFallbackURL input output)
+  string(REPLACE "_URL" "" _tmp ${input})
+  string(TOLOWER ${_tmp} libname)
+  string(REGEX REPLACE "^https://.*/([^/]+gz)" "${LAMMPS_THIRDPARTY_URL}/${libname}-\\1" newurl "${${input}}")
+  if ("${newurl}" STREQUAL "${${input}}")
+    set(${output} "" PARENT_SCOPE)
+  else()
+    set(${output} ${newurl} PARENT_SCOPE)
+  endif()
+endfunction(GetFallbackURL)
+
 #################################################################################
 # LAMMPS C++ interface. We only need the header related parts except on windows.
 add_library(lammps INTERFACE)
@@ -112,45 +124,76 @@ if(BUILD_MPI)
   set(MPI_CXX_SKIP_MPICXX TRUE)
   # We use a non-standard procedure to cross-compile with MPI on Windows
   if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
-    # Download and configure custom MPICH files for Windows
-    message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
-    set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
-    set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball")
-    set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
-    set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball")
-    mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
-    mark_as_advanced(MPICH2_WIN32_DEVEL_URL)
-    mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
-    mark_as_advanced(MPICH2_WIN32_DEVEL_MD5)
+    # Download and configure MinGW compatible MPICH development files for Windows
+    option(USE_MSMPI "Use Microsoft's MS-MPI SDK instead of MPICH2-1.4.1" OFF)
+    if(USE_MSMPI)
+      message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
+      set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
+      set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
+      mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
+      mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
 
-    include(ExternalProject)
-    if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
-      ExternalProject_Add(mpi4win_build
-        URL     ${MPICH2_WIN64_DEVEL_URL}
-        URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
-        CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
-        BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+      include(ExternalProject)
+      if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+        ExternalProject_Add(mpi4win_build
+          URL     ${MPICH2_WIN64_DEVEL_URL}
+          URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
+          CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+          BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
+      else()
+        message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
+      endif()
+
+      ExternalProject_get_property(mpi4win_build SOURCE_DIR)
+      file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
+      add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
+      set_target_properties(MPI::MPI_CXX PROPERTIES
+        IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
+        INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
+        INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+      add_dependencies(MPI::MPI_CXX mpi4win_build)
+
+      # set variables for status reporting at the end of CMake run
+      set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
+      set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+      set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")
     else()
-      ExternalProject_Add(mpi4win_build
-        URL     ${MPICH2_WIN32_DEVEL_URL}
-        URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
-        CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
-        BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+      # Download and configure custom MPICH files for Windows
+      message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
+      set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
+      set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
+      mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
+      mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
+
+      include(ExternalProject)
+      if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+        ExternalProject_Add(mpi4win_build
+          URL     ${MPICH2_WIN64_DEVEL_URL}
+          URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
+          CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+          BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+      else()
+        ExternalProject_Add(mpi4win_build
+          URL     ${MPICH2_WIN32_DEVEL_URL}
+          URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
+          CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+          BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+      endif()
+
+      ExternalProject_get_property(mpi4win_build SOURCE_DIR)
+      file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
+      add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
+      set_target_properties(MPI::MPI_CXX PROPERTIES
+        IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
+        INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
+        INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+      add_dependencies(MPI::MPI_CXX mpi4win_build)
+
+      # set variables for status reporting at the end of CMake run
+      set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
+      set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+      set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
     endif()
-
-    ExternalProject_get_property(mpi4win_build SOURCE_DIR)
-    file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
-    add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
-    set_target_properties(MPI::MPI_CXX PROPERTIES
-      IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
-      INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
-      INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
-    add_dependencies(MPI::MPI_CXX mpi4win_build)
-
-    # set variables for status reporting at the end of CMake run
-    set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
-    set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
-    set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
   else()
     find_package(MPI REQUIRED)
     option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)

cmake/Modules/LAMMPSUtils.cmake

@@ -41,7 +41,7 @@ endfunction()
 
 # helper function for getting the most recently modified file or folder from a glob pattern
 function(get_newest_file path variable)
-  file(GLOB _dirs ${path})
+  file(GLOB _dirs ${CONFIGURE_DEPENDS} ${path})
   set(_besttime 2000-01-01T00:00:00)
   set(_bestfile "<unknown>")
   foreach(_dir ${_dirs})
@@ -80,8 +80,8 @@ endfunction()
 
 function(check_for_autogen_files source_dir)
     message(STATUS "Running check for auto-generated files from make-based build system")
-    file(GLOB SRC_AUTOGEN_FILES ${source_dir}/style_*.h)
-    file(GLOB SRC_AUTOGEN_PACKAGES ${source_dir}/packages_*.h)
+    file(GLOB SRC_AUTOGEN_FILES ${CONFIGURE_DEPENDS} ${source_dir}/style_*.h)
+    file(GLOB SRC_AUTOGEN_PACKAGES ${CONFIGURE_DEPENDS} ${source_dir}/packages_*.h)
     list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/lmpinstalledpkgs.h ${source_dir}/lmpgitversion.h)
     list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/mliap_model_python_couple.h ${source_dir}/mliap_model_python_couple.cpp)
     foreach(_SRC ${SRC_AUTOGEN_FILES})
@@ -99,8 +99,15 @@ function(check_for_autogen_files source_dir)
 endfunction()
 
 macro(pkg_depends PKG1 PKG2)
-  if(PKG_${PKG1} AND NOT (PKG_${PKG2} OR BUILD_${PKG2}))
-    message(FATAL_ERROR "The ${PKG1} package needs LAMMPS to be build with the ${PKG2} package")
+  if(DEFINED BUILD_${PKG2})
+    if(PKG_${PKG1} AND NOT BUILD_${PKG2})
+      message(FATAL_ERROR "The ${PKG1} package needs LAMMPS to be built with -D BUILD_${PKG2}=ON")
+    endif()
+  elseif(DEFINED PKG_${PKG2})
+    if(PKG_${PKG1} AND NOT PKG_${PKG2})
+      message(WARNING "The ${PKG1} package depends on the ${PKG2} package. Enabling it.")
+      set(PKG_${PKG2} ON CACHE BOOL "" FORCE)
+    endif()
   endif()
 endmacro()
 
@@ -118,34 +125,48 @@ endfunction(GenerateBinaryHeader)
 
 # fetch missing potential files
 function(FetchPotentials pkgfolder potfolder)
-  if(EXISTS "${pkgfolder}/potentials.txt")
-    file(STRINGS "${pkgfolder}/potentials.txt" linelist REGEX "^[^#].")
-    foreach(line ${linelist})
-      string(FIND ${line} " " blank)
-      math(EXPR plusone "${blank}+1")
-      string(SUBSTRING ${line} 0 ${blank} pot)
-      string(SUBSTRING ${line} ${plusone} -1 sum)
-      if(EXISTS "${LAMMPS_POTENTIALS_DIR}/${pot}")
-        file(MD5 "${LAMMPS_POTENTIALS_DIR}/${pot}" oldsum)
-      endif()
-      if(NOT sum STREQUAL oldsum)
-        message(STATUS "Downloading external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
-        string(MD5 TMP_EXT "${CMAKE_BINARY_DIR}")
-        file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${CMAKE_BINARY_DIR}/${pot}.${TMP_EXT}"
-          EXPECTED_HASH MD5=${sum} SHOW_PROGRESS)
-        file(COPY "${CMAKE_BINARY_DIR}/${pot}.${TMP_EXT}" DESTINATION "${LAMMPS_POTENTIALS_DIR}")
-        file(RENAME "${LAMMPS_POTENTIALS_DIR}/${pot}.${TMP_EXT}" "${LAMMPS_POTENTIALS_DIR}/${pot}")
-      endif()
-    endforeach()
+  if(DOWNLOAD_POTENTIALS)
+    if(EXISTS "${pkgfolder}/potentials.txt")
+      file(STRINGS "${pkgfolder}/potentials.txt" linelist REGEX "^[^#].")
+      foreach(line ${linelist})
+        string(FIND ${line} " " blank)
+        math(EXPR plusone "${blank}+1")
+        string(SUBSTRING ${line} 0 ${blank} pot)
+        string(SUBSTRING ${line} ${plusone} -1 sum)
+        if(EXISTS "${LAMMPS_POTENTIALS_DIR}/${pot}")
+          file(MD5 "${LAMMPS_POTENTIALS_DIR}/${pot}" oldsum)
+        endif()
+        if(NOT sum STREQUAL oldsum)
+          message(STATUS "Downloading external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
+          string(RANDOM LENGTH 10 TMP_EXT)
+          file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${CMAKE_BINARY_DIR}/${pot}.${TMP_EXT}"
+            EXPECTED_HASH MD5=${sum} SHOW_PROGRESS)
+          file(COPY "${CMAKE_BINARY_DIR}/${pot}.${TMP_EXT}" DESTINATION "${LAMMPS_POTENTIALS_DIR}")
+          file(RENAME "${LAMMPS_POTENTIALS_DIR}/${pot}.${TMP_EXT}" "${LAMMPS_POTENTIALS_DIR}/${pot}")
+        endif()
+      endforeach()
+    endif()
   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 "${distro}")
+  string(REGEX REPLACE "NAME=\"?([^ ]+).*\"?" "\\1" distro "${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()
+
+# determine canonical URL for downloading backup copy from download.lammps.org/thirdparty
+function(GetFallbackURL input output)
+  string(REPLACE "_URL" "" _tmp ${input})
+  string(TOLOWER ${_tmp} libname)
+  string(REGEX REPLACE "^https://.*/([^/]+gz)" "${LAMMPS_THIRDPARTY_URL}/${libname}-\\1" newurl "${${input}}")
+  if ("${newurl}" STREQUAL "${${input}}")
+    set(${output} "" PARENT_SCOPE)
+  else()
+    set(${output} ${newurl} PARENT_SCOPE)
+  endif()
+endfunction(GetFallbackURL)

cmake/Modules/MPI4WIN.cmake

@@ -1,39 +1,74 @@
-# Download and configure custom MPICH files for Windows
-message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
-set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
-set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball")
-set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
-set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball")
-mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
-mark_as_advanced(MPICH2_WIN32_DEVEL_URL)
-mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
-mark_as_advanced(MPICH2_WIN32_DEVEL_MD5)
+# Download and configure MinGW compatible MPICH development files for Windows
+option(USE_MSMPI "Use Microsoft's MS-MPI SDK instead of MPICH2-1.4.1" OFF)
 
-include(ExternalProject)
-if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
-  ExternalProject_Add(mpi4win_build
-    URL     ${MPICH2_WIN64_DEVEL_URL}
-    URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
-    CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
-    BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+if(USE_MSMPI)
+  message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
+  set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
+  set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
+  mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
+  mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
+
+  include(ExternalProject)
+  if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+    ExternalProject_Add(mpi4win_build
+      URL     ${MPICH2_WIN64_DEVEL_URL}
+      URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
+      CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+      BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
+  else()
+    message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
+  endif()
+
+  ExternalProject_get_property(mpi4win_build SOURCE_DIR)
+  file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
+  add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
+  set_target_properties(MPI::MPI_CXX PROPERTIES
+    IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
+    INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
+    INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+  add_dependencies(MPI::MPI_CXX mpi4win_build)
+
+  # set variables for status reporting at the end of CMake run
+  set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
+  set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+  set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")
 else()
-  ExternalProject_Add(mpi4win_build
-    URL     ${MPICH2_WIN32_DEVEL_URL}
-    URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
-    CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
-    BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+  message(STATUS "Downloading and configuring MPICH2-1.4.1 for Windows cross-compilation")
+  set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
+  set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball")
+  set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
+  set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball")
+  mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
+  mark_as_advanced(MPICH2_WIN32_DEVEL_URL)
+  mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
+  mark_as_advanced(MPICH2_WIN32_DEVEL_MD5)
+
+  include(ExternalProject)
+  if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+    ExternalProject_Add(mpi4win_build
+      URL     ${MPICH2_WIN64_DEVEL_URL}
+      URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
+      CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+      BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+  else()
+    ExternalProject_Add(mpi4win_build
+      URL     ${MPICH2_WIN32_DEVEL_URL}
+      URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
+      CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+      BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+  endif()
+
+  ExternalProject_get_property(mpi4win_build SOURCE_DIR)
+  file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
+  add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
+  set_target_properties(MPI::MPI_CXX PROPERTIES
+    IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
+    INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
+    INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+  add_dependencies(MPI::MPI_CXX mpi4win_build)
+
+  # set variables for status reporting at the end of CMake run
+  set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
+  set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+  set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
 endif()
-
-ExternalProject_get_property(mpi4win_build SOURCE_DIR)
-file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
-add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
-set_target_properties(MPI::MPI_CXX PROPERTIES
-  IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
-  INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
-  INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
-add_dependencies(MPI::MPI_CXX mpi4win_build)
-
-# set variables for status reporting at the end of CMake run
-set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
-set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
-set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")

cmake/Modules/Packages/COLVARS.cmake

@@ -1,20 +1,15 @@
 set(COLVARS_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars)
 
-file(GLOB COLVARS_SOURCES ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
+file(GLOB COLVARS_SOURCES ${CONFIGURE_DEPENDS} ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
 
-option(COLVARS_DEBUG "Debugging messages for Colvars (quite verbose)" OFF)
+option(COLVARS_DEBUG "Enable debugging messages for Colvars (quite verbose)" OFF)
 
-# Build Lepton by default
-option(COLVARS_LEPTON "Build and link the Lepton library" ON)
+option(COLVARS_LEPTON "Use the Lepton library for custom expressions" ON)
 
 if(COLVARS_LEPTON)
-  set(LEPTON_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton)
-  file(GLOB LEPTON_SOURCES ${LEPTON_DIR}/src/[^.]*.cpp)
-  add_library(lepton STATIC ${LEPTON_SOURCES})
-  # Change the define below to LEPTON_BUILDING_SHARED_LIBRARY when linking Lepton as a DLL with MSVC
-  target_compile_definitions(lepton PRIVATE -DLEPTON_BUILDING_STATIC_LIBRARY)
-  set_target_properties(lepton PROPERTIES OUTPUT_NAME lammps_lepton${LAMMPS_MACHINE})
-  target_include_directories(lepton PRIVATE ${LEPTON_DIR}/include)
+  if(NOT LEPTON_SOURCE_DIR)
+    include(Packages/LEPTON)
+  endif()
 endif()
 
 add_library(colvars STATIC ${COLVARS_SOURCES})
@@ -30,14 +25,11 @@ target_include_directories(colvars PRIVATE ${LAMMPS_SOURCE_DIR})
 target_link_libraries(lammps PRIVATE colvars)
 
 if(COLVARS_DEBUG)
-  # Need to export the macro publicly to also affect the proxy
+  # Need to export the define publicly to be valid in interface code
   target_compile_definitions(colvars PUBLIC -DCOLVARS_DEBUG)
 endif()
 
 if(COLVARS_LEPTON)
-  target_link_libraries(lammps PRIVATE lepton)
   target_compile_definitions(colvars PRIVATE -DLEPTON)
-  # Disable the line below when linking Lepton as a DLL with MSVC
-  target_compile_definitions(colvars PRIVATE -DLEPTON_USE_STATIC_LIBRARIES)
-  target_include_directories(colvars PUBLIC ${LEPTON_DIR}/include)
+  target_link_libraries(colvars PUBLIC lepton)
 endif()

cmake/Modules/Packages/COMPRESS.cmake

@@ -1,4 +1,9 @@
-find_package(ZLIB REQUIRED)
+find_package(ZLIB)
+if(NOT ZLIB_FOUND)
+  message(WARNING "No Zlib development support found. Disabling COMPRESS package...")
+  set(PKG_COMPRESS OFF CACHE BOOL "" FORCE)
+  return()
+endif()
 target_link_libraries(lammps PRIVATE ZLIB::ZLIB)
 
 find_package(PkgConfig QUIET)

cmake/Modules/Packages/GPU.cmake

@@ -26,7 +26,20 @@ elseif(GPU_PREC STREQUAL "SINGLE")
   set(GPU_PREC_SETTING "SINGLE_SINGLE")
 endif()
 
-file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
+option(GPU_DEBUG "Enable debugging code of the GPU package" OFF)
+mark_as_advanced(GPU_DEBUG)
+
+if(PKG_AMOEBA AND FFT_SINGLE)
+  message(FATAL_ERROR "GPU acceleration of AMOEBA is not (yet) compatible with single precision FFT")
+endif()
+
+if (PKG_AMOEBA)
+  list(APPEND GPU_SOURCES
+              ${GPU_SOURCES_DIR}/amoeba_convolution_gpu.h
+              ${GPU_SOURCES_DIR}/amoeba_convolution_gpu.cpp)
+endif()
+
+file(GLOB GPU_LIB_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
 file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
 
 if(GPU_API STREQUAL "CUDA")
@@ -47,15 +60,17 @@ if(GPU_API STREQUAL "CUDA")
   option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
   if(CUDA_MPS_SUPPORT)
     if(CUDPP_OPT)
-      message(FATAL_ERROR "Must use -DCUDPP_OPT=OFF with -DGPU_CUDA_MPS_SUPPORT=ON")
+      message(FATAL_ERROR "Must use -DCUDPP_OPT=OFF with -DCUDA_MPS_SUPPORT=ON")
     endif()
-    set(GPU_CUDA_MPS_FLAGS "-DCUDA_PROXY")
+    set(GPU_CUDA_MPS_FLAGS "-DCUDA_MPS_SUPPORT")
   endif()
+  option(CUDA_BUILD_MULTIARCH "Enable building CUDA kernels for all supported GPU architectures" ON)
+  mark_as_advanced(GPU_BUILD_MULTIARCH)
 
   set(GPU_ARCH "sm_50" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
 
   # 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)
+  file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
   if(GPU_LIB_OLD_CUBIN_HEADERS)
     message(FATAL_ERROR "########################################################################\n"
       "Found file(s) generated by the make-based build system in lib/gpu\n"
@@ -65,69 +80,74 @@ if(GPU_API STREQUAL "CUDA")
       "########################################################################")
   endif()
 
-  file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
+  file(GLOB GPU_LIB_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
   list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
 
   cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
 
   if(CUDPP_OPT)
     cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
-    file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
-    file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
+    file(GLOB GPU_LIB_CUDPP_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
+    file(GLOB GPU_LIB_CUDPP_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
   endif()
 
   # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
   # --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
   set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH}")
 
-  # apply the following to build "fat" CUDA binaries only for known CUDA toolkits since version 8.0
-  # only the Kepler achitecture and beyond is supported
-  if(CUDA_VERSION VERSION_LESS 8.0)
-    message(FATAL_ERROR "CUDA Toolkit version 8.0 or later is required")
-  elseif(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
-    message(WARNING "Untested CUDA Toolkit version ${CUDA_VERSION}. Use at your own risk")
-    set(GPU_CUDA_GENCODE "-arch=all")
-  else()
-    # Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
-    if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] ")
+  if(CUDA_BUILD_MULTIARCH)
+    # apply the following to build "fat" CUDA binaries only for known CUDA toolkits since version 8.0
+    # only the Kepler achitecture and beyond is supported
+    # comparison chart according to: https://en.wikipedia.org/wiki/CUDA#GPUs_supported
+    if(CUDA_VERSION VERSION_LESS 8.0)
+      message(FATAL_ERROR "CUDA Toolkit version 8.0 or later is required")
+    elseif(CUDA_VERSION VERSION_GREATER_EQUAL "13.0")
+      message(WARNING "Untested CUDA Toolkit version ${CUDA_VERSION}. Use at your own risk")
+      set(GPU_CUDA_GENCODE "-arch=all")
+    elseif(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
+      set(GPU_CUDA_GENCODE "-arch=all")
+    else()
+      # Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
+      if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] ")
+      endif()
+      # Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
+      if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_35,code=[sm_35,compute_35]")
+      endif()
+      # Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")
+      endif()
+      # Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")
+      endif()
+      # Volta (GPU Arch 7.0) is supported by CUDA 9 and later
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
+      endif()
+      # Turing (GPU Arch 7.5) is supported by CUDA 10 and later
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
+      endif()
+      # Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
+      endif()
+      # Ampere (GPU Arch 8.6) is supported by CUDA 11.1 and later
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
+      endif()
+      # Lovelace (GPU Arch 8.9) is supported by CUDA 11.8 and later
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "11.8")
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
+      endif()
+      # Hopper (GPU Arch 9.0) is supported by CUDA 12.0 and later
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
+      endif()
     endif()
-    # Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
-    if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_35,code=[sm_35,compute_35]")
-    endif()
-    # Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
-    if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")
-    endif()
-    # Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
-    if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")
-    endif()
-    # Volta (GPU Arch 7.0) is supported by CUDA 9 and later
-    if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
-    endif()
-    # Turing (GPU Arch 7.5) is supported by CUDA 10 and later
-    if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
-    endif()
-    # Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
-    if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
-    endif()
-    # Ampere (GPU Arch 8.6) is supported by CUDA 11.1 and later
-    if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
-    endif()
-    # Hopper (GPU Arch 9.0) is supported by CUDA 12.0? and later
-    if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
-    endif()
-    #    # Lovelace (GPU Arch 9.x) is supported by CUDA 12.0? and later
-    #if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
-    #  string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_9x,code=[sm_9x,compute_9x]")
-    #endif()
   endif()
 
   cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
@@ -150,14 +170,17 @@ if(GPU_API STREQUAL "CUDA")
   add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
   target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
   target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
-  target_compile_definitions(gpu PRIVATE -DUSE_CUDA -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
+  target_compile_definitions(gpu PRIVATE -DUSE_CUDA -D_${GPU_PREC_SETTING} ${GPU_CUDA_MPS_FLAGS})
+  if(GPU_DEBUG)
+    target_compile_definitions(gpu PRIVATE -DUCL_DEBUG -DGERYON_KERNEL_DUMP)
+  else()
+    target_compile_definitions(gpu PRIVATE -DMPI_GERYON -DUCL_NO_EXIT)
+  endif()
   if(CUDPP_OPT)
     target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
     target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
   endif()
 
-  target_link_libraries(lammps PRIVATE gpu)
-
   add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
   target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR)
   target_link_libraries(nvc_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
@@ -182,7 +205,7 @@ elseif(GPU_API STREQUAL "OPENCL")
   include(OpenCLUtils)
   set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
 
-  file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
+  file(GLOB GPU_LIB_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
   list(REMOVE_ITEM GPU_LIB_CU
     ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu
     ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu
@@ -191,6 +214,7 @@ elseif(GPU_API STREQUAL "OPENCL")
     ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu
     ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu
     ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu
+    ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_hippo.cu
   )
 
   foreach(GPU_KERNEL ${GPU_LIB_CU})
@@ -207,6 +231,7 @@ elseif(GPU_API STREQUAL "OPENCL")
   GenerateOpenCLHeader(tersoff ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu)
   GenerateOpenCLHeader(tersoff_zbl ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu)
   GenerateOpenCLHeader(tersoff_mod ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu)
+  GenerateOpenCLHeader(hippo ${CMAKE_CURRENT_BINARY_DIR}/gpu/hippo_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_hippo_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_hippo.cu)
 
   list(APPEND GPU_LIB_SOURCES
     ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h
@@ -216,37 +241,26 @@ elseif(GPU_API STREQUAL "OPENCL")
     ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h
     ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h
     ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h
+    ${CMAKE_CURRENT_BINARY_DIR}/gpu/hippo_cl.h
   )
 
   add_library(gpu STATIC ${GPU_LIB_SOURCES})
   target_link_libraries(gpu PRIVATE OpenCL::OpenCL)
   target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu)
-  target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT)
-  target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
-
-  target_link_libraries(lammps PRIVATE gpu)
+  target_compile_definitions(gpu PRIVATE -DUSE_OPENCL -D_${GPU_PREC_SETTING})
+  if(GPU_DEBUG)
+    target_compile_definitions(gpu PRIVATE -DUCL_DEBUG -DGERYON_KERNEL_DUMP)
+  else()
+    target_compile_definitions(gpu PRIVATE -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT)
+  endif()
 
   add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
   target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
   target_link_libraries(ocl_get_devices PRIVATE OpenCL::OpenCL)
   add_dependencies(ocl_get_devices OpenCL::OpenCL)
+
 elseif(GPU_API STREQUAL "HIP")
-  if(NOT DEFINED HIP_PATH)
-      if(NOT DEFINED ENV{HIP_PATH})
-          message(FATAL_ERROR "GPU_API=HIP requires HIP_PATH to be defined.\n"
-          "Either pass the HIP_PATH as a CMake option via -DHIP_PATH=... or set the HIP_PATH environment variable.")
-      else()
-          set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to HIP installation")
-      endif()
-  endif()
-  if(NOT DEFINED ROCM_PATH)
-      if(NOT DEFINED ENV{ROCM_PATH})
-          set(ROCM_PATH "/opt/rocm" CACHE PATH "Path to ROCm installation")
-      else()
-          set(ROCM_PATH $ENV{ROCM_PATH} CACHE PATH "Path to ROCm installation")
-      endif()
-  endif()
-  list(APPEND CMAKE_PREFIX_PATH ${HIP_PATH} ${ROCM_PATH})
+  include(DetectHIPInstallation)
   find_package(hip REQUIRED)
   option(HIP_USE_DEVICE_SORT "Use GPU sorting" ON)
 
@@ -260,7 +274,7 @@ elseif(GPU_API STREQUAL "HIP")
 
   set(ENV{HIP_PLATFORM} ${HIP_PLATFORM})
 
-  if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
+  if(HIP_PLATFORM STREQUAL "amd")
     set(HIP_ARCH "gfx906" CACHE STRING "HIP target architecture")
   elseif(HIP_PLATFORM STREQUAL "spirv")
     set(HIP_ARCH "spirv" CACHE STRING "HIP target architecture")
@@ -276,6 +290,7 @@ elseif(GPU_API STREQUAL "HIP")
     else()
       # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
       # --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
+      # comparison chart according to: https://en.wikipedia.org/wiki/CUDA#GPUs_supported
       set(HIP_CUDA_GENCODE "-arch=${HIP_ARCH}")
       # Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
       if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
@@ -305,14 +320,22 @@ elseif(GPU_API STREQUAL "HIP")
       if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
         string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
       endif()
-      # Hopper (GPU Arch 9.0) is supported by CUDA 12.0? and later
+      # Ampere (GPU Arch 8.6) is supported by CUDA 11.1 and later
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
+        string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
+      endif()
+      # Lovelace (GPU Arch 8.9) is supported by CUDA 11.8 and later
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "11.8")
+        string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
+      endif()
+      # Hopper (GPU Arch 9.0) is supported by CUDA 12.0 and later
       if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
-        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
+        string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
       endif()
     endif()
   endif()
 
-  file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
+  file(GLOB GPU_LIB_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
   list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
 
   set(GPU_LIB_CU_HIP "")
@@ -324,7 +347,7 @@ elseif(GPU_API STREQUAL "HIP")
     set(CUBIN_FILE   "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}.cubin")
     set(CUBIN_H_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h")
 
-    if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
+    if(HIP_PLATFORM STREQUAL "amd")
         configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY)
 
         if(HIP_COMPILER STREQUAL "clang")
@@ -364,8 +387,12 @@ elseif(GPU_API STREQUAL "HIP")
 
   add_library(gpu STATIC ${GPU_LIB_SOURCES})
   target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu)
-  target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT)
-  target_compile_definitions(gpu PRIVATE -DUSE_HIP)
+  target_compile_definitions(gpu PRIVATE -DUSE_HIP -D_${GPU_PREC_SETTING})
+  if(GPU_DEBUG)
+    target_compile_definitions(gpu PRIVATE -DUCL_DEBUG -DGERYON_KERNEL_DUMP)
+  else()
+    target_compile_definitions(gpu PRIVATE -DMPI_GERYON -DUCL_NO_EXIT)
+  endif()
   target_link_libraries(gpu PRIVATE hip::host)
 
   if(HIP_USE_DEVICE_SORT)
@@ -374,7 +401,8 @@ elseif(GPU_API STREQUAL "HIP")
       set_property(TARGET gpu PROPERTY CXX_STANDARD 14)
     endif()
     # add hipCUB
-    target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
+    find_package(hipcub REQUIRED)
+    target_link_libraries(gpu PRIVATE hip::hipcub)
     target_compile_definitions(gpu PRIVATE -DUSE_HIP_DEVICE_SORT)
 
     if(HIP_PLATFORM STREQUAL "nvcc")
@@ -390,15 +418,17 @@ elseif(GPU_API STREQUAL "HIP")
 
       if(DOWNLOAD_CUB)
         message(STATUS "CUB download requested")
-        set(CUB_URL "https://github.com/NVlabs/cub/archive/1.12.0.tar.gz" CACHE STRING "URL for CUB tarball")
+        # TODO: test update to current version 1.17.2
+        set(CUB_URL "https://github.com/nvidia/cub/archive/1.12.0.tar.gz" CACHE STRING "URL for CUB tarball")
         set(CUB_MD5 "1cf595beacafff104700921bac8519f3" CACHE STRING "MD5 checksum of CUB tarball")
         mark_as_advanced(CUB_URL)
         mark_as_advanced(CUB_MD5)
+        GetFallbackURL(CUB_URL CUB_FALLBACK)
 
         include(ExternalProject)
 
         ExternalProject_Add(CUB
-          URL     ${CUB_URL}
+          URL     ${CUB_URL} ${CUB_FALLBACK}
           URL_MD5 ${CUB_MD5}
           PREFIX "${CMAKE_CURRENT_BINARY_DIR}"
           CONFIGURE_COMMAND ""
@@ -421,35 +451,25 @@ elseif(GPU_API STREQUAL "HIP")
 
   add_executable(hip_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
   target_compile_definitions(hip_get_devices PRIVATE -DUCL_HIP)
-  target_link_libraries(hip_get_devices hip::host)
+  target_link_libraries(hip_get_devices PRIVATE hip::host)
 
   if(HIP_PLATFORM STREQUAL "nvcc")
     target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_NVCC__)
-    target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
     target_include_directories(gpu PRIVATE ${CUDA_INCLUDE_DIRS})
     target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
 
     target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_NVCC__)
-    target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/include)
     target_include_directories(hip_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
     target_link_libraries(hip_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
-  elseif(HIP_PLATFORM STREQUAL "hcc")
-    target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_HCC__)
-    target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
-
-    target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_HCC__)
-    target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include)
-  elseif(HIP_PLATFORM STREQUAL "amd")
-    target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_AMD__)
-    target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
-
-    target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_AMD__)
-    target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include)
   endif()
-
-  target_link_libraries(lammps PRIVATE gpu)
 endif()
 
+if(BUILD_OMP)
+  find_package(OpenMP COMPONENTS CXX REQUIRED)
+  target_link_libraries(gpu PRIVATE OpenMP::OpenMP_CXX)
+endif()
+target_link_libraries(lammps PRIVATE gpu)
+
 set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
 # detect styles which have a GPU version
 RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)

cmake/Modules/Packages/INTEL.cmake

@@ -112,9 +112,5 @@ if(PKG_KSPACE)
   RegisterIntegrateStyle(${INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
 endif()
 
-if(PKG_ELECTRODE)
-  list(APPEND INTEL_SOURCES ${INTEL_SOURCES_DIR}/electrode_accel_intel.cpp)
-endif()
-
 target_sources(lammps PRIVATE ${INTEL_SOURCES})
 target_include_directories(lammps PRIVATE ${INTEL_SOURCES_DIR})

cmake/Modules/Packages/KIM.cmake

@@ -19,7 +19,7 @@ if(CURL_FOUND)
     target_compile_definitions(lammps PRIVATE -DLMP_NO_SSL_CHECK)
   endif()
 endif()
-set(KIM_EXTRA_UNITTESTS OFF CACHE STRING "Set extra unit tests verbose mode on/off. If on, extra tests are included.")
+option(KIM_EXTRA_UNITTESTS "Enable extra unit tests for the KIM package." OFF)
 mark_as_advanced(KIM_EXTRA_UNITTESTS)
 find_package(PkgConfig QUIET)
 set(DOWNLOAD_KIM_DEFAULT ON)

cmake/Modules/Packages/KOKKOS.cmake

@@ -3,6 +3,7 @@
 if(CMAKE_CXX_STANDARD LESS 14)
   message(FATAL_ERROR "The KOKKOS package requires the C++ standard to be set to at least C++14")
 endif()
+
 ########################################################################
 # consistency checks and Kokkos options/settings required by LAMMPS
 if(Kokkos_ENABLE_CUDA)
@@ -15,8 +16,8 @@ if(Kokkos_ENABLE_OPENMP)
   if(NOT BUILD_OMP)
     message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP")
   else()
-    # NVHPC does not seem to provide a detectable OpenMP version, but is far beyond version 3.1
-    if((OpenMP_CXX_VERSION VERSION_LESS 3.1) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC"))
+    # NVHPC/(AMD)Clang does not seem to provide a detectable OpenMP version, but is far beyond version 3.1
+    if((OpenMP_CXX_VERSION VERSION_LESS 3.1) AND NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
       message(FATAL_ERROR "Compiler must support OpenMP 3.1 or later with Kokkos_ENABLE_OPENMP")
     endif()
   endif()
@@ -48,12 +49,14 @@ 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/3.7.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "84991eca9f066383abe119a5bc7a11c4" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.7.02.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_MD5 "34d7860d548c06a4040236d959c9f99a" CACHE STRING "MD5 checksum of KOKKOS tarball")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
+  GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
+
   ExternalProject_Add(kokkos_build
-    URL     ${KOKKOS_URL}
+    URL     ${KOKKOS_URL} ${KOKKOS_FALLBACK}
     URL_MD5 ${KOKKOS_MD5}
     CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
     BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a <INSTALL_DIR>/lib/libkokkoscontainers.a
@@ -69,13 +72,11 @@ if(DOWNLOAD_KOKKOS)
   set_target_properties(LAMMPS::KOKKOSCONTAINERS PROPERTIES
     IMPORTED_LOCATION "${INSTALL_DIR}/lib/libkokkoscontainers.a")
   target_link_libraries(lammps PRIVATE LAMMPS::KOKKOSCORE LAMMPS::KOKKOSCONTAINERS)
-  target_link_libraries(lmp PRIVATE LAMMPS::KOKKOSCORE LAMMPS::KOKKOSCONTAINERS)
   add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
   add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 3.7.00 REQUIRED CONFIG)
+  find_package(Kokkos 3.7.02 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
-  target_link_libraries(lmp PRIVATE Kokkos::kokkos)
 else()
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
   set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
@@ -87,8 +88,7 @@ else()
   if(CMAKE_REQUEST_PIC)
     set(CMAKE_POSITION_INDEPENDENT_CODE ON)
   endif()
-  add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
-
+  add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR} EXCLUDE_FROM_ALL)
 
   set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
                           ${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
@@ -96,7 +96,6 @@ else()
                           ${LAMMPS_LIB_KOKKOS_BIN_DIR})
   target_include_directories(lammps PRIVATE ${Kokkos_INCLUDE_DIRS})
   target_link_libraries(lammps PRIVATE kokkos)
-  target_link_libraries(lmp PRIVATE kokkos)
   if(BUILD_SHARED_LIBS_WAS_ON)
     set(BUILD_SHARED_LIBS ON)
   endif()
@@ -122,9 +121,14 @@ set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
 
+# fix wall/gran has been refactored in an incompatible way. Use old version of base class for now
+if(PKG_GRANULAR)
+  list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/fix_wall_gran_old.cpp)
+endif()
+
 if(PKG_KSPACE)
   list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/fft3d_kokkos.cpp
-                                 ${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp
+                                 ${KOKKOS_PKG_SOURCES_DIR}/grid3d_kokkos.cpp
                                  ${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
   if(Kokkos_ENABLE_CUDA)
     if(NOT (FFT STREQUAL "KISS"))
@@ -133,8 +137,10 @@ if(PKG_KSPACE)
     endif()
   elseif(Kokkos_ENABLE_HIP)
     if(NOT (FFT STREQUAL "KISS"))
+      include(DetectHIPInstallation)
+      find_package(hipfft REQUIRED)
       target_compile_definitions(lammps PRIVATE -DFFT_HIPFFT)
-      target_link_libraries(lammps PRIVATE hipfft)
+      target_link_libraries(lammps PRIVATE hip::hipfft)
     endif()
   endif()
 endif()
@@ -143,7 +149,24 @@ if(PKG_ML-IAP)
   list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/mliap_data_kokkos.cpp
                                  ${KOKKOS_PKG_SOURCES_DIR}/mliap_descriptor_so3_kokkos.cpp
                                  ${KOKKOS_PKG_SOURCES_DIR}/mliap_model_linear_kokkos.cpp
+                                 ${KOKKOS_PKG_SOURCES_DIR}/mliap_model_python_kokkos.cpp
+                                 ${KOKKOS_PKG_SOURCES_DIR}/mliap_unified_kokkos.cpp
                                  ${KOKKOS_PKG_SOURCES_DIR}/mliap_so3_kokkos.cpp)
+
+  # Add KOKKOS version of ML-IAP Python coupling if non-KOKKOS version is included
+  if(MLIAP_ENABLE_PYTHON AND Cythonize_EXECUTABLE)
+    file(GLOB MLIAP_KOKKOS_CYTHON_SRC ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/KOKKOS/*.pyx)
+    foreach(MLIAP_CYTHON_FILE ${MLIAP_KOKKOS_CYTHON_SRC})
+      get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE)
+      add_custom_command(OUTPUT  ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h
+              COMMAND            ${CMAKE_COMMAND} -E copy_if_different ${MLIAP_CYTHON_FILE} ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
+              COMMAND            ${Cythonize_EXECUTABLE} -3 ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
+              WORKING_DIRECTORY  ${MLIAP_BINARY_DIR}
+              MAIN_DEPENDENCY    ${MLIAP_CYTHON_FILE}
+              COMMENT "Generating C++ sources with cythonize...")
+      list(APPEND KOKKOS_PKG_SOURCES ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp)
+    endforeach()
+  endif()
 endif()
 
 if(PKG_PHONON)

cmake/Modules/Packages/LATTE.cmake

@@ -1,53 +0,0 @@
-enable_language(Fortran)
-
-# using lammps in a super-build setting
-if(TARGET LATTE::latte)
-  target_link_libraries(lammps PRIVATE LATTE::latte)
-  return()
-endif()
-
-find_package(LATTE 1.2.2 CONFIG)
-if(LATTE_FOUND)
-  set(DOWNLOAD_LATTE_DEFAULT OFF)
-else()
-  set(DOWNLOAD_LATTE_DEFAULT ON)
-endif()
-option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
-if(DOWNLOAD_LATTE)
-  message(STATUS "LATTE download requested - we will build our own")
-  set(LATTE_URL "https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz" CACHE STRING "URL for LATTE tarball")
-  set(LATTE_MD5 "820e73a457ced178c08c71389a385de7" CACHE STRING "MD5 checksum of LATTE tarball")
-  mark_as_advanced(LATTE_URL)
-  mark_as_advanced(LATTE_MD5)
-
-  # CMake cannot pass BLAS or LAPACK library variable to external project if they are a list
-  list(LENGTH BLAS_LIBRARIES} NUM_BLAS)
-  list(LENGTH LAPACK_LIBRARIES NUM_LAPACK)
-  if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1) AND NOT USE_INTERNAL_LINALG)
-    message(FATAL_ERROR "Cannot compile downloaded LATTE library due to a technical limitation. "
-                        "Try to configure LAMMPS with '-D USE_INTERNAL_LINALG=on' added as a workaround.")
-  endif()
-
-  include(ExternalProject)
-  ExternalProject_Add(latte_build
-    URL     ${LATTE_URL}
-    URL_MD5 ${LATTE_MD5}
-    SOURCE_SUBDIR cmake
-    CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib
-    -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
-    -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=${CMAKE_Fortran_FLAGS}
-    -DCMAKE_Fortran_FLAGS_${BTYPE}=${CMAKE_Fortran_FLAGS_${BTYPE}} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-    -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM} -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
-    BUILD_BYPRODUCTS <INSTALL_DIR>/lib/liblatte.a
-  )
-  ExternalProject_get_property(latte_build INSTALL_DIR)
-  add_library(LAMMPS::LATTE UNKNOWN IMPORTED)
-  set_target_properties(LAMMPS::LATTE PROPERTIES
-    IMPORTED_LOCATION "${INSTALL_DIR}/lib/liblatte.a"
-    INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
-  target_link_libraries(lammps PRIVATE LAMMPS::LATTE)
-  add_dependencies(LAMMPS::LATTE latte_build)
-else()
-  find_package(LATTE 1.2.2 REQUIRED CONFIG)
-  target_link_libraries(lammps PRIVATE LATTE::latte)
-endif()

cmake/Modules/Packages/LEPTON.cmake

@@ -0,0 +1,35 @@
+# avoid including this file twice
+if(LEPTON_SOURCE_DIR)
+   return()
+endif()
+set(LEPTON_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/lepton)
+
+file(GLOB LEPTON_SOURCES ${CONFIGURE_DEPENDS} ${LEPTON_SOURCE_DIR}/src/[^.]*.cpp)
+
+if((CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "amd64") OR
+   (CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "AMD64") OR
+   (CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "x86_64"))
+   option(LEPTON_ENABLE_JIT "Enable Just-In-Time compiler for Lepton" ON)
+else()
+   option(LEPTON_ENABLE_JIT "Enable Just-In-Time compiler for Lepton" OFF)
+endif()
+
+if(LEPTON_ENABLE_JIT)
+  file(GLOB ASMJIT_SOURCES ${CONFIGURE_DEPENDS} ${LEPTON_SOURCE_DIR}/asmjit/*/[^.]*.cpp)
+endif()
+
+add_library(lepton STATIC ${LEPTON_SOURCES} ${ASMJIT_SOURCES})
+set_target_properties(lepton PROPERTIES OUTPUT_NAME lammps_lepton${LAMMPS_MACHINE})
+target_compile_definitions(lepton PUBLIC LEPTON_BUILDING_STATIC_LIBRARY=1)
+target_include_directories(lepton PUBLIC ${LEPTON_SOURCE_DIR}/include)
+if(CMAKE_SYSTEM_NAME STREQUAL "Linux")
+  find_library(LIB_RT rt QUIET)
+  target_link_libraries(lepton PUBLIC ${LIB_RT})
+endif()
+
+if(LEPTON_ENABLE_JIT)
+  target_compile_definitions(lepton PUBLIC "LEPTON_USE_JIT=1;ASMJIT_BUILD_X86=1;ASMJIT_STATIC=1;ASMJIT_BUILD_RELEASE=1")
+  target_include_directories(lepton PUBLIC ${LEPTON_SOURCE_DIR})
+endif()
+
+target_link_libraries(lammps PRIVATE lepton)

cmake/Modules/Packages/MC.cmake

@@ -0,0 +1,9 @@
+# fix sgcmc may only be installed if also the EAM pair style from MANYBODY is installed
+if(NOT PKG_MANYBODY)
+  get_property(LAMMPS_FIX_HEADERS GLOBAL PROPERTY FIX)
+  list(REMOVE_ITEM LAMMPS_FIX_HEADERS ${LAMMPS_SOURCE_DIR}/MC/fix_sgcmc.h)
+  set_property(GLOBAL PROPERTY FIX "${LAMMPS_FIX_HEADERS}")
+  get_target_property(LAMMPS_SOURCES lammps SOURCES)
+  list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MC/fix_sgcmc.cpp)
+  set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
+endif()

cmake/Modules/Packages/MDI.cmake

@@ -8,10 +8,11 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
 
 if(DOWNLOAD_MDI)
   message(STATUS "MDI download requested - we will build our own")
-  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.12.tar.gz" CACHE STRING "URL for MDI tarball")
-  set(MDI_MD5 "7a222353ae8e03961d5365e6cd48baee" CACHE STRING "MD5 checksum for MDI tarball")
+  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.16.tar.gz" CACHE STRING "URL for MDI tarball")
+  set(MDI_MD5 "407db44e2d79447ab5c1233af1965f65" CACHE STRING "MD5 checksum for MDI tarball")
   mark_as_advanced(MDI_URL)
   mark_as_advanced(MDI_MD5)
+  GetFallbackURL(MDI_URL MDI_FALLBACK)
   enable_language(C)
 
   # only ON/OFF are allowed for "mpi" flag when building MDI library
@@ -63,7 +64,7 @@ if(DOWNLOAD_MDI)
   # support cross-compilation and ninja-build
   include(ExternalProject)
   ExternalProject_Add(mdi_build
-    URL     ${MDI_URL}
+    URL     ${MDI_URL} ${MDI_FALLBACK}
     URL_MD5 ${MDI_MD5}
     PREFIX ${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext
     CMAKE_ARGS

cmake/Modules/Packages/ML-HDNNP.cmake

@@ -6,10 +6,11 @@ else()
 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")
+  set(N2P2_URL "https://github.com/CompPhysVienna/n2p2/archive/v2.2.0.tar.gz" CACHE STRING "URL for n2p2 tarball")
+  set(N2P2_MD5 "a2d9ab7f676b3a74a324fc1eda0a911d" CACHE STRING "MD5 checksum of N2P2 tarball")
   mark_as_advanced(N2P2_URL)
   mark_as_advanced(N2P2_MD5)
+  GetFallbackURL(N2P2_URL N2P2_FALLBACK)
 
   # 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)
@@ -72,7 +73,7 @@ if(DOWNLOAD_N2P2)
   # 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     ${N2P2_URL} ${N2P2_FALLBACK}
     URL_MD5 ${N2P2_MD5}
     UPDATE_COMMAND ""
     CONFIGURE_COMMAND ""

cmake/Modules/Packages/ML-IAP.cmake

@@ -34,7 +34,7 @@ if(MLIAP_ENABLE_PYTHON)
   endif()
 
   set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
-  file(GLOB MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)
+  file(GLOB MLIAP_CYTHON_SRC ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)
   file(MAKE_DIRECTORY ${MLIAP_BINARY_DIR})
   foreach(MLIAP_CYTHON_FILE ${MLIAP_CYTHON_SRC})
     get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE)

cmake/Modules/Packages/ML-PACE.cmake

@@ -1,11 +1,25 @@
-set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2022.10.15.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.01.3.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
 
-set(PACELIB_MD5 "848ad6a6cc79fa82745927001fb1c9b5" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+set(PACELIB_MD5 "4f0b3b5b14456fe9a73b447de3765caa" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
 mark_as_advanced(PACELIB_URL)
 mark_as_advanced(PACELIB_MD5)
+GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)
 
 # download library sources to build folder
-file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5}) #SHOW_PROGRESS
+if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
+  file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
+endif()
+if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
+  message(STATUS "Downloading ${PACELIB_URL}")
+  file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz STATUS DL_STATUS SHOW_PROGRESS)
+  file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
+  if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}"))
+    message(WARNING "Download from primary URL ${PACELIB_URL} failed\nTrying fallback URL ${PACELIB_FALLBACK}")
+    file(DOWNLOAD ${PACELIB_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5} SHOW_PROGRESS)
+  endif()
+else()
+  message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
+endif()
 
 # uncompress downloaded sources
 execute_process(

cmake/Modules/Packages/ML-QUIP.cmake

@@ -16,6 +16,7 @@ if(DOWNLOAD_QUIP)
     set(temp "${temp}DEFINES += -DGETARG_F2003 -DFORTRAN_UNDERSCORE\n")
     set(temp "${temp}F95FLAGS += -fpp -free -fPIC\n")
     set(temp "${temp}F77FLAGS += -fpp -fixed -fPIC\n")
+    set(temp "${temp}F95_PRE_FILENAME_FLAG = -Tf\n")
   elseif(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
     set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${CMAKE_Fortran_FLAGS_${BTYPE}}\n")
     set(temp "${temp}DEFINES += -DGETARG_F2003 -DGETENV_F2003 -DGFORTRAN -DFORTRAN_UNDERSCORE\n")

cmake/Modules/Packages/MSCG.cmake

@@ -7,8 +7,8 @@ else()
 endif()
 option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
 if(DOWNLOAD_MSCG)
-  set(MSCG_URL "https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz" CACHE STRING "URL for MSCG tarball")
-  set(MSCG_MD5 "8c45e269ee13f60b303edd7823866a91" CACHE STRING "MD5 checksum of MSCG tarball")
+  set(MSCG_URL "https://github.com/uchicago-voth/MSCG-release/archive/491270a73539e3f6951e76f7dbe84e258b3ebb45.tar.gz" CACHE STRING "URL for MSCG tarball")
+  set(MSCG_MD5 "7ea50748fba5c3a372e0266bd31d2f11" CACHE STRING "MD5 checksum of MSCG tarball")
   mark_as_advanced(MSCG_URL)
   mark_as_advanced(MSCG_MD5)
 

cmake/Modules/Packages/PLUMED.cmake

@@ -1,105 +1,169 @@
-set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")
-set(PLUMED_MODE_VALUES static shared runtime)
-set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})
-validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
-string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
+# Plumed2 support for PLUMED package
 
-set(PLUMED_LINK_LIBS)
-if(PLUMED_MODE STREQUAL "STATIC")
-  find_package(LAPACK REQUIRED)
-  find_package(BLAS REQUIRED)
-  find_package(GSL REQUIRED)
-  list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} GSL::gsl)
-  find_package(ZLIB QUIET)
-  if(ZLIB_FOUND)
-    list(APPEND PLUMED_LINK_LIBS ZLIB::ZLIB)
-  endif()
-  find_package(FFTW3 QUIET)
-  if(FFTW3_FOUND)
-    list(APPEND PLUMED_LINK_LIBS FFTW3::FFTW3)
-  endif()
+if(BUILD_MPI)
+  set(PLUMED_CONFIG_MPI "--enable-mpi")
+  set(PLUMED_CONFIG_CC  ${CMAKE_MPI_C_COMPILER})
+  set(PLUMED_CONFIG_CXX  ${CMAKE_MPI_CXX_COMPILER})
+  set(PLUMED_CONFIG_CPP "-I ${MPI_CXX_INCLUDE_PATH}")
+  set(PLUMED_CONFIG_LIB "${MPI_CXX_LIBRARIES}")
+  set(PLUMED_CONFIG_DEP "mpi4win_build")
+else()
+  set(PLUMED_CONFIG_MPI "--disable-mpi")
+  set(PLUMED_CONFIG_CC  ${CMAKE_C_COMPILER})
+  set(PLUMED_CONFIG_CXX  ${CMAKE_CXX_COMPILER})
+  set(PLUMED_CONFIG_CPP "")
+  set(PLUMED_CONFIG_LIB "")
+  set(PLUMED_CONFIG_DEP "")
+endif()
+if(BUILD_OMP)
+  set(PLUMED_CONFIG_OMP "--enable-openmp")
+else()
+  set(PLUMED_CONFIG_OMP "--disable-openmp")
 endif()
 
-find_package(PkgConfig QUIET)
-set(DOWNLOAD_PLUMED_DEFAULT ON)
-if(PKG_CONFIG_FOUND)
-  pkg_check_modules(PLUMED QUIET plumed)
-  if(PLUMED_FOUND)
-    set(DOWNLOAD_PLUMED_DEFAULT OFF)
-  endif()
-endif()
+set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.2/plumed-src-2.8.2.tgz"
+  CACHE STRING "URL for PLUMED tarball")
+set(PLUMED_MD5 "599092b6a0aa6fff992612537ad98994" CACHE STRING "MD5 checksum of PLUMED tarball")
 
-option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT})
-if(DOWNLOAD_PLUMED)
-  if(BUILD_MPI)
-    set(PLUMED_CONFIG_MPI "--enable-mpi")
-    set(PLUMED_CONFIG_CC  ${CMAKE_MPI_C_COMPILER})
-    set(PLUMED_CONFIG_CXX  ${CMAKE_MPI_CXX_COMPILER})
+mark_as_advanced(PLUMED_URL)
+mark_as_advanced(PLUMED_MD5)
+GetFallbackURL(PLUMED_URL PLUMED_FALLBACK)
+
+if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (CMAKE_CROSSCOMPILING))
+  if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+    set(CROSS_CONFIGURE mingw64-configure)
+  elseif(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86")
+    set(CROSS_CONFIGURE mingw32-configure)
   else()
-    set(PLUMED_CONFIG_MPI "--disable-mpi")
-    set(PLUMED_CONFIG_CC  ${CMAKE_C_COMPILER})
-    set(PLUMED_CONFIG_CXX  ${CMAKE_CXX_COMPILER})
+    message(FATAL_ERROR "Unsupported target system: ${CMAKE_SYSTEM_NAME}/${CMAKE_SYSTEM_PROCESSOR}")
   endif()
-  if(BUILD_OMP)
-    set(PLUMED_CONFIG_OMP "--enable-openmp")
-  else()
-    set(PLUMED_CONFIG_OMP "--disable-openmp")
-  endif()
-  message(STATUS "PLUMED download requested - we will build our own")
-  if(PLUMED_MODE STREQUAL "STATIC")
-    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX}")
-  elseif(PLUMED_MODE STREQUAL "SHARED")
-    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX};<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
-  elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_PREFIX}")
-  endif()
-
-  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.1/plumed-src-2.8.1.tgz" CACHE STRING "URL for PLUMED tarball")
-  set(PLUMED_MD5 "6bfe72ebdae63dc38a9ca27d9b0e08f8" CACHE STRING "MD5 checksum of PLUMED tarball")
-
-  mark_as_advanced(PLUMED_URL)
-  mark_as_advanced(PLUMED_MD5)
-
+  message(STATUS "Downloading and cross-compiling Plumed2 for ${CMAKE_SYSTEM_NAME}/${CMAKE_SYSTEM_PROCESSOR} with ${CROSS_CONFIGURE}")
   include(ExternalProject)
   ExternalProject_Add(plumed_build
-    URL     ${PLUMED_URL}
+    URL     ${PLUMED_URL} ${PLUMED_FALLBACK}
     URL_MD5 ${PLUMED_MD5}
     BUILD_IN_SOURCE 1
-    CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
+    CONFIGURE_COMMAND ${CROSS_CONFIGURE} --disable-shared --disable-bsymbolic
+                                         --disable-python --enable-cxx=11
+                                         --enable-modules=-adjmat:+crystallization:-dimred:+drr:+eds:-fisst:+funnel:+logmfd:+manyrestraints:+maze:+opes:+multicolvar:-pamm:-piv:+s2cm:-sasa:-ves
+                                         ${PLUMED_CONFIG_OMP}
+                                         ${PLUMED_CONFIG_MPI}
+                                         CXX=${PLUMED_CONFIG_CXX}
+                                         CC=${PLUMED_CONFIG_CC}
+                                         CPPFLAGS=${PLUMED_CONFIG_CPP}
+                                         LIBS=${PLUMED_CONFIG_LIB}
+    INSTALL_COMMAND ""
+    BUILD_BYPRODUCTS "<SOURCE_DIR>/src/lib/install/libplumed.a" "<SOURCE_DIR>/src/lib/install/plumed.exe"
+    DEPENDS "${PLUMED_MPI_CONFIG_DEP}"
+  )
+  ExternalProject_Get_Property(plumed_build SOURCE_DIR)
+  set(PLUMED_BUILD_DIR ${SOURCE_DIR})
+  set(PLUMED_INSTALL_DIR ${PLUMED_BUILD_DIR}/src/lib/install)
+  file(MAKE_DIRECTORY ${PLUMED_BUILD_DIR}/src/include)
+
+  add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
+  add_dependencies(LAMMPS::PLUMED plumed_build)
+  set_target_properties(LAMMPS::PLUMED PROPERTIES
+    IMPORTED_LOCATION "${PLUMED_INSTALL_DIR}/libplumed.a"
+    INTERFACE_LINK_LIBRARIES "-Wl,--image-base -Wl,0x10000000 -lfftw3 -lz  -fstack-protector -lssp -fopenmp"
+    INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_BUILD_DIR}/src/include")
+
+  add_custom_target(plumed_copy ALL ${CMAKE_COMMAND} -E rm -rf ${CMAKE_BINARY_DIR}/plumed.exe ${CMAKE_BINARY_DIR}/plumed_patches
+    COMMAND ${CMAKE_COMMAND} -E copy ${PLUMED_INSTALL_DIR}/plumed.exe ${CMAKE_BINARY_DIR}/plumed.exe
+    COMMAND ${CMAKE_COMMAND} -E copy_directory ${PLUMED_BUILD_DIR}/patches ${CMAKE_BINARY_DIR}/patches
+    BYPRODUCTS ${CMAKE_BINARY_DIR}/plumed.exe ${CMAKE_BINARY_DIR}/patches
+    DEPENDS plumed_build
+    COMMENT "Copying Plumed files"
+  )
+
+else()
+
+  set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")
+  set(PLUMED_MODE_VALUES static shared runtime)
+  set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})
+  validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
+  string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
+
+  set(PLUMED_LINK_LIBS)
+  if(PLUMED_MODE STREQUAL "STATIC")
+    find_package(LAPACK REQUIRED)
+    find_package(BLAS REQUIRED)
+    find_package(GSL REQUIRED)
+    list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} GSL::gsl)
+    find_package(ZLIB QUIET)
+    if(ZLIB_FOUND)
+      list(APPEND PLUMED_LINK_LIBS ZLIB::ZLIB)
+    endif()
+    find_package(FFTW3 QUIET)
+    if(FFTW3_FOUND)
+      list(APPEND PLUMED_LINK_LIBS FFTW3::FFTW3)
+    endif()
+  endif()
+
+  find_package(PkgConfig QUIET)
+  set(DOWNLOAD_PLUMED_DEFAULT ON)
+  if(PKG_CONFIG_FOUND)
+    pkg_check_modules(PLUMED QUIET plumed)
+    if(PLUMED_FOUND)
+      set(DOWNLOAD_PLUMED_DEFAULT OFF)
+    endif()
+  endif()
+
+  option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT})
+  if(DOWNLOAD_PLUMED)
+    message(STATUS "PLUMED download requested - we will build our own")
+    if(PLUMED_MODE STREQUAL "STATIC")
+      set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX}")
+    elseif(PLUMED_MODE STREQUAL "SHARED")
+      set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX};<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+    elseif(PLUMED_MODE STREQUAL "RUNTIME")
+      set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_PREFIX}")
+    endif()
+
+    include(ExternalProject)
+    ExternalProject_Add(plumed_build
+      URL     ${PLUMED_URL} ${PLUMED_FALLBACK}
+      URL_MD5 ${PLUMED_MD5}
+      BUILD_IN_SOURCE 1
+      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
                                              ${CONFIGURE_REQUEST_PIC}
                                              --enable-modules=all
+                                             --enable-cxx=11
+                                             --disable-python
                                              ${PLUMED_CONFIG_MPI}
                                              ${PLUMED_CONFIG_OMP}
                                              CXX=${PLUMED_CONFIG_CXX}
                                              CC=${PLUMED_CONFIG_CC}
-    BUILD_BYPRODUCTS ${PLUMED_BUILD_BYPRODUCTS}
-  )
-  ExternalProject_get_property(plumed_build INSTALL_DIR)
-  add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
-  add_dependencies(LAMMPS::PLUMED plumed_build)
-  if(PLUMED_MODE STREQUAL "STATIC")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
-  elseif(PLUMED_MODE STREQUAL "SHARED")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
-  elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}")
+      BUILD_BYPRODUCTS ${PLUMED_BUILD_BYPRODUCTS}
+    )
+    ExternalProject_get_property(plumed_build INSTALL_DIR)
+    add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
+    add_dependencies(LAMMPS::PLUMED plumed_build)
+    if(PLUMED_MODE STREQUAL "STATIC")
+      set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
+    elseif(PLUMED_MODE STREQUAL "SHARED")
+      set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
+    elseif(PLUMED_MODE STREQUAL "RUNTIME")
+      set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+      set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}")
+    endif()
+    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
+    file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
+  else()
+    find_package(PkgConfig REQUIRED)
+    pkg_check_modules(PLUMED REQUIRED plumed)
+    add_library(LAMMPS::PLUMED INTERFACE IMPORTED)
+    if(PLUMED_MODE STREQUAL "STATIC")
+      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
+    elseif(PLUMED_MODE STREQUAL "SHARED")
+      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
+    elseif(PLUMED_MODE STREQUAL "RUNTIME")
+      set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
+    endif()
+    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_INCLUDE_DIRS}")
   endif()
-  set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
-  file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
-else()
-  find_package(PkgConfig REQUIRED)
-  pkg_check_modules(PLUMED REQUIRED plumed)
-  add_library(LAMMPS::PLUMED INTERFACE IMPORTED)
-  if(PLUMED_MODE STREQUAL "STATIC")
-    include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
-  elseif(PLUMED_MODE STREQUAL "SHARED")
-    include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
-  elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
-    include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
-  endif()
-  set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")
-  set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_INCLUDE_DIRS}")
 endif()
+
 target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)

cmake/Modules/Packages/SCAFACOS.cmake

@@ -18,6 +18,8 @@ if(DOWNLOAD_SCAFACOS)
   set(SCAFACOS_MD5 "bd46d74e3296bd8a444d731bb10c1738" CACHE STRING "MD5 checksum of SCAFACOS tarball")
   mark_as_advanced(SCAFACOS_URL)
   mark_as_advanced(SCAFACOS_MD5)
+  GetFallbackURL(SCAFACOS_URL SCAFACOS_FALLBACK)
+
 
   # version 1.0.1 needs a patch to compile and linke cleanly with GCC 10 and later.
   file(DOWNLOAD ${LAMMPS_THIRDPARTY_URL}/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
@@ -30,7 +32,7 @@ if(DOWNLOAD_SCAFACOS)
 
   include(ExternalProject)
   ExternalProject_Add(scafacos_build
-    URL     ${SCAFACOS_URL}
+    URL     ${SCAFACOS_URL} ${SCAFACOS_FALLBACK}
     URL_MD5 ${SCAFACOS_MD5}
     PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
     CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc

cmake/Modules/StyleHeaderUtils.cmake

@@ -1,5 +1,5 @@
 function(FindStyleHeaders path style_class file_pattern headers)
-    file(GLOB files "${path}/${file_pattern}*.h")
+    file(GLOB files ${CONFIGURE_DEPENDS} "${path}/${file_pattern}*.h")
     get_property(hlist GLOBAL PROPERTY ${headers})
 
     foreach(file_name ${files})
@@ -95,73 +95,76 @@ function(RegisterIntegrateStyle path)
 endfunction(RegisterIntegrateStyle)
 
 function(RegisterStyles search_path)
-    FindStyleHeaders(${search_path} ANGLE_CLASS     angle_     ANGLE     ) # angle     ) # force
-    FindStyleHeaders(${search_path} ATOM_CLASS      atom_vec_  ATOM_VEC  ) # atom      ) # atom      atom_vec_hybrid
-    FindStyleHeaders(${search_path} BODY_CLASS      body_      BODY      ) # body      ) # atom_vec_body
-    FindStyleHeaders(${search_path} BOND_CLASS      bond_      BOND      ) # bond      ) # force
-    FindStyleHeaders(${search_path} COMMAND_CLASS   "[^.]"     COMMAND   ) # command   ) # input
-    FindStyleHeaders(${search_path} COMPUTE_CLASS   compute_   COMPUTE   ) # compute   ) # modify
-    FindStyleHeaders(${search_path} DIHEDRAL_CLASS  dihedral_  DIHEDRAL  ) # dihedral  ) # force
-    FindStyleHeaders(${search_path} DUMP_CLASS      dump_      DUMP      ) # dump      ) # output    write_dump
-    FindStyleHeaders(${search_path} FIX_CLASS       fix_       FIX       ) # fix       ) # modify
-    FindStyleHeaders(${search_path} IMPROPER_CLASS  improper_  IMPROPER  ) # improper  ) # force
-    FindStyleHeaders(${search_path} INTEGRATE_CLASS "[^.]"     INTEGRATE ) # integrate ) # update
-    FindStyleHeaders(${search_path} KSPACE_CLASS    "[^.]"     KSPACE    ) # kspace    ) # force
-    FindStyleHeaders(${search_path} MINIMIZE_CLASS  min_       MINIMIZE  ) # minimize  ) # update
-    FindStyleHeaders(${search_path} NBIN_CLASS      nbin_      NBIN      ) # nbin      ) # neighbor
-    FindStyleHeaders(${search_path} NPAIR_CLASS     npair_     NPAIR     ) # npair     ) # neighbor
-    FindStyleHeaders(${search_path} NSTENCIL_CLASS  nstencil_  NSTENCIL  ) # nstencil  ) # neighbor
-    FindStyleHeaders(${search_path} NTOPO_CLASS     ntopo_     NTOPO     ) # ntopo     ) # neighbor
-    FindStyleHeaders(${search_path} PAIR_CLASS      pair_      PAIR      ) # pair      ) # force
-    FindStyleHeaders(${search_path} READER_CLASS    reader_    READER    ) # reader    ) # read_dump
-    FindStyleHeaders(${search_path} REGION_CLASS    region_    REGION    ) # region    ) # domain
+    FindStyleHeaders(${search_path} ANGLE_CLASS        angle_        ANGLE        ) # angle        ) # force
+    FindStyleHeaders(${search_path} ATOM_CLASS         atom_vec_     ATOM_VEC     ) # atom         ) # atom      atom_vec_hybrid
+    FindStyleHeaders(${search_path} BODY_CLASS         body_         BODY         ) # body         ) # atom_vec_body
+    FindStyleHeaders(${search_path} BOND_CLASS         bond_         BOND         ) # bond         ) # force
+    FindStyleHeaders(${search_path} COMMAND_CLASS      "[^.]"        COMMAND      ) # command      ) # input
+    FindStyleHeaders(${search_path} COMPUTE_CLASS      compute_      COMPUTE      ) # compute      ) # modify
+    FindStyleHeaders(${search_path} DIHEDRAL_CLASS     dihedral_     DIHEDRAL     ) # dihedral     ) # force
+    FindStyleHeaders(${search_path} DUMP_CLASS         dump_         DUMP         ) # dump         ) # output    write_dump
+    FindStyleHeaders(${search_path} FIX_CLASS          fix_          FIX          ) # fix          ) # modify
+    FindStyleHeaders(${search_path} GRAN_SUB_MOD_CLASS gran_sub_mod_ GRAN_SUB_MOD ) # gran_sub_mod ) # granular_model
+    FindStyleHeaders(${search_path} IMPROPER_CLASS     improper_     IMPROPER     ) # improper     ) # force
+    FindStyleHeaders(${search_path} INTEGRATE_CLASS    "[^.]"        INTEGRATE    ) # integrate    ) # update
+    FindStyleHeaders(${search_path} KSPACE_CLASS       "[^.]"        KSPACE       ) # kspace       ) # force
+    FindStyleHeaders(${search_path} MINIMIZE_CLASS     min_          MINIMIZE     ) # minimize     ) # update
+    FindStyleHeaders(${search_path} NBIN_CLASS         nbin_         NBIN         ) # nbin         ) # neighbor
+    FindStyleHeaders(${search_path} NPAIR_CLASS        npair_        NPAIR        ) # npair        ) # neighbor
+    FindStyleHeaders(${search_path} NSTENCIL_CLASS     nstencil_     NSTENCIL     ) # nstencil     ) # neighbor
+    FindStyleHeaders(${search_path} NTOPO_CLASS        ntopo_        NTOPO        ) # ntopo        ) # neighbor
+    FindStyleHeaders(${search_path} PAIR_CLASS         pair_         PAIR         ) # pair         ) # force
+    FindStyleHeaders(${search_path} READER_CLASS       reader_       READER       ) # reader       ) # read_dump
+    FindStyleHeaders(${search_path} REGION_CLASS       region_       REGION       ) # region       ) # domain
 endfunction(RegisterStyles)
 
 function(RegisterStylesExt search_path extension sources)
-    FindStyleHeadersExt(${search_path} ANGLE_CLASS     ${extension}  ANGLE     ${sources})
-    FindStyleHeadersExt(${search_path} ATOM_CLASS      ${extension}  ATOM_VEC  ${sources})
-    FindStyleHeadersExt(${search_path} BODY_CLASS      ${extension}  BODY      ${sources})
-    FindStyleHeadersExt(${search_path} BOND_CLASS      ${extension}  BOND      ${sources})
-    FindStyleHeadersExt(${search_path} COMMAND_CLASS   ${extension}  COMMAND   ${sources})
-    FindStyleHeadersExt(${search_path} COMPUTE_CLASS   ${extension}  COMPUTE   ${sources})
-    FindStyleHeadersExt(${search_path} DIHEDRAL_CLASS  ${extension}  DIHEDRAL  ${sources})
-    FindStyleHeadersExt(${search_path} DUMP_CLASS      ${extension}  DUMP      ${sources})
-    FindStyleHeadersExt(${search_path} FIX_CLASS       ${extension}  FIX       ${sources})
-    FindStyleHeadersExt(${search_path} IMPROPER_CLASS  ${extension}  IMPROPER  ${sources})
-    FindStyleHeadersExt(${search_path} INTEGRATE_CLASS ${extension}  INTEGRATE ${sources})
-    FindStyleHeadersExt(${search_path} KSPACE_CLASS    ${extension}  KSPACE    ${sources})
-    FindStyleHeadersExt(${search_path} MINIMIZE_CLASS  ${extension}  MINIMIZE  ${sources})
-    FindStyleHeadersExt(${search_path} NBIN_CLASS      ${extension}  NBIN      ${sources})
-    FindStyleHeadersExt(${search_path} NPAIR_CLASS     ${extension}  NPAIR     ${sources})
-    FindStyleHeadersExt(${search_path} NSTENCIL_CLASS  ${extension}  NSTENCIL  ${sources})
-    FindStyleHeadersExt(${search_path} NTOPO_CLASS     ${extension}  NTOPO     ${sources})
-    FindStyleHeadersExt(${search_path} PAIR_CLASS      ${extension}  PAIR      ${sources})
-    FindStyleHeadersExt(${search_path} READER_CLASS    ${extension}  READER    ${sources})
-    FindStyleHeadersExt(${search_path} REGION_CLASS    ${extension}  REGION    ${sources})
+    FindStyleHeadersExt(${search_path} ANGLE_CLASS        ${extension}  ANGLE        ${sources})
+    FindStyleHeadersExt(${search_path} ATOM_CLASS         ${extension}  ATOM_VEC     ${sources})
+    FindStyleHeadersExt(${search_path} BODY_CLASS         ${extension}  BODY         ${sources})
+    FindStyleHeadersExt(${search_path} BOND_CLASS         ${extension}  BOND         ${sources})
+    FindStyleHeadersExt(${search_path} COMMAND_CLASS      ${extension}  COMMAND      ${sources})
+    FindStyleHeadersExt(${search_path} COMPUTE_CLASS      ${extension}  COMPUTE      ${sources})
+    FindStyleHeadersExt(${search_path} DIHEDRAL_CLASS     ${extension}  DIHEDRAL     ${sources})
+    FindStyleHeadersExt(${search_path} DUMP_CLASS         ${extension}  DUMP         ${sources})
+    FindStyleHeadersExt(${search_path} FIX_CLASS          ${extension}  FIX          ${sources})
+    FindStyleHeadersExt(${search_path} GRAN_SUB_MOD_CLASS ${extension}  GRAN_SUB_MOD ${sources})
+    FindStyleHeadersExt(${search_path} IMPROPER_CLASS     ${extension}  IMPROPER     ${sources})
+    FindStyleHeadersExt(${search_path} INTEGRATE_CLASS    ${extension}  INTEGRATE    ${sources})
+    FindStyleHeadersExt(${search_path} KSPACE_CLASS       ${extension}  KSPACE       ${sources})
+    FindStyleHeadersExt(${search_path} MINIMIZE_CLASS     ${extension}  MINIMIZE     ${sources})
+    FindStyleHeadersExt(${search_path} NBIN_CLASS         ${extension}  NBIN         ${sources})
+    FindStyleHeadersExt(${search_path} NPAIR_CLASS        ${extension}  NPAIR        ${sources})
+    FindStyleHeadersExt(${search_path} NSTENCIL_CLASS     ${extension}  NSTENCIL     ${sources})
+    FindStyleHeadersExt(${search_path} NTOPO_CLASS        ${extension}  NTOPO        ${sources})
+    FindStyleHeadersExt(${search_path} PAIR_CLASS         ${extension}  PAIR         ${sources})
+    FindStyleHeadersExt(${search_path} READER_CLASS       ${extension}  READER       ${sources})
+    FindStyleHeadersExt(${search_path} REGION_CLASS       ${extension}  REGION       ${sources})
 endfunction(RegisterStylesExt)
 
 function(GenerateStyleHeaders output_path)
     message(STATUS "Generating style headers...")
-    GenerateStyleHeader(${output_path} ANGLE      angle     ) # force
-    GenerateStyleHeader(${output_path} ATOM_VEC   atom      ) # atom      atom_vec_hybrid
-    GenerateStyleHeader(${output_path} BODY       body      ) # atom_vec_body
-    GenerateStyleHeader(${output_path} BOND       bond      ) # force
-    GenerateStyleHeader(${output_path} COMMAND    command   ) # input
-    GenerateStyleHeader(${output_path} COMPUTE    compute   ) # modify
-    GenerateStyleHeader(${output_path} DIHEDRAL   dihedral  ) # force
-    GenerateStyleHeader(${output_path} DUMP       dump      ) # output    write_dump
-    GenerateStyleHeader(${output_path} FIX        fix       ) # modify
-    GenerateStyleHeader(${output_path} IMPROPER   improper  ) # force
-    GenerateStyleHeader(${output_path} INTEGRATE  integrate ) # update
-    GenerateStyleHeader(${output_path} KSPACE     kspace    ) # force
-    GenerateStyleHeader(${output_path} MINIMIZE   minimize  ) # update
-    GenerateStyleHeader(${output_path} NBIN       nbin      ) # neighbor
-    GenerateStyleHeader(${output_path} NPAIR      npair     ) # neighbor
-    GenerateStyleHeader(${output_path} NSTENCIL   nstencil  ) # neighbor
-    GenerateStyleHeader(${output_path} NTOPO      ntopo     ) # neighbor
-    GenerateStyleHeader(${output_path} PAIR       pair      ) # force
-    GenerateStyleHeader(${output_path} READER     reader    ) # read_dump
-    GenerateStyleHeader(${output_path} REGION     region    ) # domain
+    GenerateStyleHeader(${output_path} ANGLE        angle        ) # force
+    GenerateStyleHeader(${output_path} ATOM_VEC     atom         ) # atom      atom_vec_hybrid
+    GenerateStyleHeader(${output_path} BODY         body         ) # atom_vec_body
+    GenerateStyleHeader(${output_path} BOND         bond         ) # force
+    GenerateStyleHeader(${output_path} COMMAND      command      ) # input
+    GenerateStyleHeader(${output_path} COMPUTE      compute      ) # modify
+    GenerateStyleHeader(${output_path} DIHEDRAL     dihedral     ) # force
+    GenerateStyleHeader(${output_path} DUMP         dump         ) # output    write_dump
+    GenerateStyleHeader(${output_path} FIX          fix          ) # modify
+    GenerateStyleHeader(${output_path} GRAN_SUB_MOD gran_sub_mod ) # granular_model
+    GenerateStyleHeader(${output_path} IMPROPER     improper     ) # force
+    GenerateStyleHeader(${output_path} INTEGRATE    integrate    ) # update
+    GenerateStyleHeader(${output_path} KSPACE       kspace       ) # force
+    GenerateStyleHeader(${output_path} MINIMIZE     minimize     ) # update
+    GenerateStyleHeader(${output_path} NBIN         nbin         ) # neighbor
+    GenerateStyleHeader(${output_path} NPAIR        npair        ) # neighbor
+    GenerateStyleHeader(${output_path} NSTENCIL     nstencil     ) # neighbor
+    GenerateStyleHeader(${output_path} NTOPO        ntopo        ) # neighbor
+    GenerateStyleHeader(${output_path} PAIR         pair         ) # force
+    GenerateStyleHeader(${output_path} READER       reader       ) # read_dump
+    GenerateStyleHeader(${output_path} REGION       region       ) # domain
 endfunction(GenerateStyleHeaders)
 
 function(DetectBuildSystemConflict lammps_src_dir)
@@ -184,7 +187,7 @@ endfunction(DetectBuildSystemConflict)
 
 
 function(FindPackagesHeaders path style_class file_pattern headers)
-    file(GLOB files "${path}/${file_pattern}*.h")
+    file(GLOB files ${CONFIGURE_DEPENDS} "${path}/${file_pattern}*.h")
     get_property(plist GLOBAL PROPERTY ${headers})
 
     foreach(file_name ${files})

cmake/Modules/Testing.cmake

@@ -6,7 +6,7 @@ if(ENABLE_TESTING)
   find_program(VALGRIND_BINARY NAMES valgrind)
   # generate custom suppression file
   file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "\n")
-  file(GLOB VALGRIND_SUPPRESSION_FILES ${LAMMPS_TOOLS_DIR}/valgrind/[^.]*.supp)
+  file(GLOB VALGRIND_SUPPRESSION_FILES ${CONFIGURE_DEPENDS} ${LAMMPS_TOOLS_DIR}/valgrind/[^.]*.supp)
   foreach(SUPP ${VALGRIND_SUPPRESSION_FILES})
     file(READ ${SUPP} SUPPRESSIONS)
     file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "${SUPPRESSIONS}")
@@ -18,29 +18,33 @@ if(ENABLE_TESTING)
 
   # we need to build and link a LOT of tester executables, so it is worth checking if
   # a faster linker is available. requires GNU or Clang compiler, newer CMake.
-  # also only verified with Fedora Linux > 30 and Ubuntu <= 18.04 (Ubuntu 20.04 fails)
+  # also only verified with Fedora Linux > 30 and Ubuntu 18.04 or 22.04+(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))
+      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_DISTRO_VERSION VERSION_GREATER_EQUAL 22.04)))
         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=mold HAVE_MOLD_LINKER_FLAG)
       check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG)
       check_cxx_compiler_flag(-fuse-ld=gold HAVE_GOLD_LINKER_FLAG)
       check_cxx_compiler_flag(-fuse-ld=bfd HAVE_BFD_LINKER_FLAG)
+      find_program(HAVE_MOLD_LINKER_BIN ld.mold)
       find_program(HAVE_LLD_LINKER_BIN lld ld.lld)
       find_program(HAVE_GOLD_LINKER_BIN ld.gold)
       find_program(HAVE_BFD_LINKER_BIN ld.bfd)
-      if(HAVE_LLD_LINKER_FLAG AND HAVE_LLD_LINKER_BIN)
+      if(HAVE_MOLD_LINKER_FLAG AND HAVE_MOLD_LINKER_BIN)
+        set(CMAKE_CUSTOM_LINKER_DEFAULT mold)
+      elseif(HAVE_LLD_LINKER_FLAG AND HAVE_LLD_LINKER_BIN)
         set(CMAKE_CUSTOM_LINKER_DEFAULT lld)
       elseif(HAVE_GOLD_LINKER_FLAG AND HAVE_GOLD_LINKER_BIN)
         set(CMAKE_CUSTOM_LINKER_DEFAULT gold)
       elseif(HAVE_BFD_LINKER_FLAG AND HAVE_BFD_LINKER_BIN)
         set(CMAKE_CUSTOM_LINKER_DEFAULT bfd)
       endif()
-      set(CMAKE_CUSTOM_LINKER_VALUES lld gold bfd default)
-      set(CMAKE_CUSTOM_LINKER ${CMAKE_CUSTOM_LINKER_DEFAULT} CACHE STRING "Choose a custom linker for faster linking (lld, gold, bfd, default)")
+      set(CMAKE_CUSTOM_LINKER_VALUES mold lld gold bfd default)
+      set(CMAKE_CUSTOM_LINKER ${CMAKE_CUSTOM_LINKER_DEFAULT} CACHE STRING "Choose a custom linker for faster linking (mold, lld, gold, bfd, default)")
       validate_option(CMAKE_CUSTOM_LINKER CMAKE_CUSTOM_LINKER_VALUES)
       mark_as_advanced(CMAKE_CUSTOM_LINKER)
       if(NOT "${CMAKE_CUSTOM_LINKER}" STREQUAL "default")

cmake/Modules/Tools.cmake

@@ -26,16 +26,22 @@ if(BUILD_TOOLS)
 
   enable_language(C)
   get_filename_component(MSI2LMP_SOURCE_DIR ${LAMMPS_TOOLS_DIR}/msi2lmp/src ABSOLUTE)
-  file(GLOB MSI2LMP_SOURCES ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
+  file(GLOB MSI2LMP_SOURCES ${CONFIGURE_DEPENDS} ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
   add_executable(msi2lmp ${MSI2LMP_SOURCES})
   if(STANDARD_MATH_LIB)
     target_link_libraries(msi2lmp PRIVATE ${STANDARD_MATH_LIB})
   endif()
   install(TARGETS msi2lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
   install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
+
+  add_subdirectory(${LAMMPS_TOOLS_DIR}/phonon ${CMAKE_BINARY_DIR}/phana_build)
 endif()
 
+find_package(PkgConfig QUIET)
 if(BUILD_LAMMPS_SHELL)
+  if(NOT PkgConfig_FOUND)
+    message(FATAL_ERROR "Must have pkg-config installed for building LAMMPS shell")
+  endif()
   find_package(PkgConfig REQUIRED)
   pkg_check_modules(READLINE IMPORTED_TARGET REQUIRED readline)
   if(NOT LAMMPS_EXCEPTIONS)
@@ -50,15 +56,23 @@ if(BUILD_LAMMPS_SHELL)
 
   add_executable(lammps-shell ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.cpp ${ICON_RC_FILE})
   target_include_directories(lammps-shell PRIVATE ${LAMMPS_TOOLS_DIR}/lammps-shell)
+  target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE)
 
   # workaround for broken readline pkg-config file on 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)
+  if(CMAKE_SYSTEM_NAME STREQUAL "LinuxMUSL")
+    pkg_check_modules(TERMCAP IMPORTED_TARGET REQUIRED termcap)
+    target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::TERMCAP)
+  endif()
   install(TARGETS lammps-shell EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
   install(DIRECTORY ${LAMMPS_TOOLS_DIR}/lammps-shell/icons DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/)
   install(FILES ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.desktop DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/applications/)
 endif()
 
-
+if(BUILD_LAMMPS_GUI)
+  get_filename_component(LAMMPS_GUI_DIR ${LAMMPS_SOURCE_DIR}/../tools/lammps-gui ABSOLUTE)
+  get_filename_component(LAMMPS_GUI_BIN ${CMAKE_BINARY_DIR}/lammps-gui-build ABSOLUTE)
+  add_subdirectory(${LAMMPS_GUI_DIR} ${LAMMPS_GUI_BIN})
+endif()

cmake/packaging/MacOSXBundleInfo.plist.in

@@ -0,0 +1,34 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+	<key>CFBundleDevelopmentRegion</key>
+	<string>en-US</string>
+	<key>CFBundleExecutable</key>
+	<string>${MACOSX_BUNDLE_EXECUTABLE_NAME}</string>
+        <key>CFBundleDisplayName</key>
+        <string>The LAMMPS Molecular Dynamics Software</string>
+	<key>CFBundleIconFile</key>
+	<string>lammps</string>
+	<key>CFBundleIdentifier</key>
+	<string>org.lammps.gui</string>
+	<key>CFBundleInfoDictionaryVersion</key>
+	<string>6.0</string>
+	<key>CFBundleLongVersionString</key>
+	<string>${MACOSX_BUNDLE_LONG_VERSION_STRING}</string>
+	<key>CFBundleName</key>
+	<string>LAMMPS</string>
+	<key>CFBundlePackageType</key>
+	<string>APPL</string>
+	<key>CFBundleShortVersionString</key>
+	<string>${MACOSX_BUNDLE_SHORT_VERSION_STRING}</string>
+	<key>CFBundleSignature</key>
+	<string>????</string>
+	<key>CFBundleVersion</key>
+	<string>${MACOSX_BUNDLE_BUNDLE_VERSION}</string>
+	<key>CSResourcesFileMapped</key>
+	<true/>
+	<key>NSHumanReadableCopyright</key>
+	<string>${MACOSX_BUNDLE_COPYRIGHT}</string>
+</dict>
+</plist>

cmake/packaging/README.macos

@@ -0,0 +1,69 @@
+LAMMPS and LAMMPS GUI universal binaries for macOS (arm64/x86_64)
+=================================================================
+
+This package provides universal binaries of LAMMPS and LAMMPS GUI that should
+run on macOS systems running running macOS version 11 (Big Sur) or newer.  Note
+the binaries are compiled without MPI support and contain a compatible subset
+of the available packages.
+
+The following individual commands are included:
+binary2txt lammps-gui lmp msi2lmp phana stl_bin2txt
+
+After copying the lammps-gui folder into your Applications folder, please follow
+these steps:
+
+1. Open the Terminal app
+
+2. Type the following command and press ENTER:
+
+   open ~/.zprofile
+
+   This will open a text editor for modifying the .zprofile file in your home
+   directory.
+
+3. Add the following lines to the end of the file, save it, and close the editor
+
+   LAMMPS_INSTALL_DIR=/Applications/LAMMPS.app/Contents
+   LAMMPS_POTENTIALS=${LAMMPS_INSTALL_DIR}/share/lammps/potentials
+   LAMMPS_BENCH_DIR=${LAMMPS_INSTALL_DIR}/share/lammps/bench
+   MSI2LMP_LIBRARY=${LAMMPS_INSTALL_DIR}/share/lammps/frc_files
+   PATH=${LAMMPS_INSTALL_DIR}/bin:$PATH
+   export LAMMPS_POTENTIALS LAMMPS_BENCH_DIR PATH
+
+4. In your existing terminal, type the following command make the settings active
+
+   source ~/.zprofile
+
+   Note, you don't have to type this in new terminals, since they will apply
+   the changes from .zprofile automatically.
+
+   Note: the above assumes you use the default shell (zsh) that comes with
+   MacOS. If you customized MacOS to use a different shell, you'll need to modify
+   that shell's init file (.cshrc, .bashrc, etc.) instead with appropiate commands
+   to modify the same environment variables.
+
+5. Try running LAMMPS (which might fail, see step 7)
+
+   lmp -in ${LAMMPS_BENCH_DIR}/in.lj
+
+6. Try running the LAMMPS GUI
+
+   lammps-gui ${LAMMPS_BENCH_DIR}/in.rhodo
+
+   Depending on the size and resolution of your screen, the fonts may
+   be too small to read. This can be adjusted by setting the environment
+   variable QT_FONT_DPI. The default value would be 72, so to increase
+   the fonts by a third one can add to the .zprofile file the line
+
+   export QT_FONT_DPI=96
+
+   and reload as shown above.
+
+7. Give permission to execute the commands (lmp, lammps-gui, msi2lmp, binary2txt, phana, stl_bin2txt)
+
+   MacOS will likely block the initial run of the executables, since they
+   were downloaded from the internet and are missing a known signature from an
+   identified developer. Go to "Settings" and search for "Security settings". It
+   should display a message that an executable like "lmp" was blocked. Press
+   "Open anyway", which might prompt you for your admin credentials. Afterwards
+   "lmp" and the other executables should work as expected.

cmake/packaging/build_linux_tgz.sh

@@ -0,0 +1,77 @@
+#!/bin/bash
+
+APP_NAME=lammps-gui
+DESTDIR=${PWD}/../LAMMPS_GUI
+
+echo "Delete old files, if they exist"
+rm -rf ${DESTDIR} ../LAMMPS-Linux-amd64.tar.gz
+
+echo "Create staging area for deployment and populate"
+DESTDIR=${DESTDIR} cmake --install .  --prefix "/"
+
+echo "Remove debug info"
+for s in ${DESTDIR}/bin/* ${DESTDIR}/lib/liblammps*
+do \
+        test -f $s && strip --strip-debug $s
+done
+
+echo "Remove libc, gcc, and X11 related shared libs"
+rm -f ${DESTDIR}/lib/ld*.so ${DESTDIR}/lib/ld*.so.[0-9]
+rm -f ${DESTDIR}/lib/lib{c,dl,rt,m,pthread}.so.?
+rm -f ${DESTDIR}/lib/lib{c,dl,rt,m,pthread}-[0-9].[0-9]*.so
+rm -f ${DESTDIR}/lib/libX* ${DESTDIR}/lib/libxcb*
+rm -f ${DESTDIR}/lib/libgcc_s*
+rm -f ${DESTDIR}/lib/libstdc++*
+
+# get qt dir
+QTDIR=$(ldd ${DESTDIR}/bin/lammps-gui | grep libQt5Core | sed -e 's/^.*=> *//' -e 's/libQt5Core.so.*$/qt5/')
+cat > ${DESTDIR}/bin/qt.conf <<EOF
+[Paths]
+Plugins = ../qt5plugins
+EOF
+
+# platform plugin
+mkdir -p ${DESTDIR}/qt5plugins/platforms
+cp ${QTDIR}/plugins/platforms/libqxcb.so ${DESTDIR}/qt5plugins/platforms
+
+# get platform plugin dependencies
+QTDEPS=$(LD_LIBRARY_PATH=${DESTDIR}/lib ldd ${QTDIR}/plugins/platforms/libqxcb.so | grep -v ${DESTDIR} | grep libQt5 | sed -e 's/^.*=> *//' -e 's/\(libQt5.*.so.*\) .*$/\1/')
+for dep in ${QTDEPS}
+do \
+    cp ${dep} ${DESTDIR}/lib
+done
+
+echo "Add additional plugins for Qt"
+for dir in styles imageformats
+do \
+    cp -r  ${QTDIR}/plugins/${dir} ${DESTDIR}/qt5plugins/
+done
+
+# get imageplugin dependencies
+for s in ${DESTDIR}/qt5plugins/imageformats/*.so
+do \
+    QTDEPS=$(LD_LIBRARY_PATH=${DESTDIR}/lib ldd $s | grep -v ${DESTDIR} | grep -E '(libQt5|jpeg)' | sed -e 's/^.*=> *//' -e 's/\(lib.*.so.*\) .*$/\1/')
+    for dep in ${QTDEPS}
+    do \
+        cp ${dep} ${DESTDIR}/lib
+    done
+done
+
+echo "Set up wrapper script"
+MYDIR=$(dirname "$0")
+cp ${MYDIR}/linux_wrapper.sh ${DESTDIR}/bin
+for s in ${DESTDIR}/bin/*
+do \
+        EXE=$(basename $s)
+        test ${EXE} = linux_wrapper.sh && continue
+        test ${EXE} = qt.conf && continue
+        ln -s bin/linux_wrapper.sh ${DESTDIR}/${EXE}
+done
+
+pushd ..
+tar -czvvf LAMMPS-Linux-amd64.tar.gz LAMMPS_GUI
+popd
+
+echo "Cleanup dir"
+rm -r ${DESTDIR}
+exit 0

cmake/packaging/build_macos_dmg.sh

@@ -0,0 +1,111 @@
+#!/bin/bash
+
+APP_NAME=lammps-gui
+
+echo "Delete old files, if they exist"
+rm -f ${APP_NAME}.dmg ${APP_NAME}-rw.dmg LAMMPS-macOS-multiarch.dmg
+
+echo "Create initial dmg file with macdeployqt"
+macdeployqt  lammps-gui.app -dmg
+echo "Create writable dmg file"
+hdiutil convert ${APP_NAME}.dmg -format UDRW -o ${APP_NAME}-rw.dmg
+
+echo "Mount writeable DMG file in read-write mode. Keep track of device and volume names"
+DEVICE=$(hdiutil attach -readwrite -noverify ${APP_NAME}-rw.dmg | grep '^/dev/' | sed 1q | awk '{print $1}')
+VOLUME=$(df | grep ${DEVICE} | sed -e 's/^.*\(\/Volumes\/\)/\1/')
+sleep 2
+
+echo "Create link to Application folder and move README and background image files"
+
+pushd "${VOLUME}"
+ln -s /Applications .
+mv  ${APP_NAME}.app/Contents/Resources/README.txt .
+mkdir  .background
+mv ${APP_NAME}.app/Contents/Resources/LAMMPS_DMG_Background.png .background/background.png
+mv ${APP_NAME}.app LAMMPS.app
+cd LAMMPS.app/Contents
+
+echo "Attach icons to LAMMPS console and GUI executables"
+echo "read 'icns' (-16455) \"Resources/lammps.icns\";" > icon.rsrc
+Rez -a icon.rsrc -o bin/lmp
+SetFile -a C bin/lmp
+Rez -a icon.rsrc -o MacOS/lammps-gui
+SetFile -a C MacOS/lammps-gui
+rm icon.rsrc
+popd
+
+echo 'Tell the Finder to resize the window, set the background,'
+echo 'change the icon size, place the icons in the right position, etc.'
+echo '
+    tell application "Finder"
+    tell disk "'${APP_NAME}'"
+
+      -- wait for the image to finish mounting
+      set open_attempts to 0
+      repeat while open_attempts < 4
+        try
+          open
+            delay 1
+            set open_attempts to 5
+          close
+        on error errStr number errorNumber
+          set open_attempts to open_attempts + 1
+          delay 10
+        end try
+      end repeat
+      delay 5
+
+      -- open the image the first time and save a .DS_Store
+      -- just the background and icon setup
+      open
+        set current view of container window to icon view
+        set theViewOptions to the icon view options of container window
+        set background picture of theViewOptions to file ".background:background.png"
+        set arrangement of theViewOptions to not arranged
+        set icon size of theViewOptions to 64
+        delay 5
+      close
+
+      -- next set up the position of the app and Applications symlink
+      -- plus hide all window decorations
+      open
+        update without registering applications
+        tell container window
+          set sidebar width to 0
+          set statusbar visible to false
+          set toolbar visible to false
+          set the bounds to { 100, 40, 868, 640 }
+          set position of item "'LAMMPS'.app" to { 190, 216 }
+          set position of item "Applications" to { 576, 216 }
+          set position of item "README.txt" to { 190, 400 }
+        end tell
+        update without registering applications
+        delay 5
+      close
+
+      -- one last open and close to check the results
+      open
+        delay 5
+      close
+    end tell
+    delay 1
+  end tell
+' | osascript
+
+sync
+
+echo "Unmount modified disk image and convert to compressed read-only image"
+hdiutil detach "${DEVICE}"
+hdiutil convert "${APP_NAME}-rw.dmg" -format UDZO -o "LAMMPS-macOS-multiarch.dmg"
+
+echo "Attach icon to .dmg file"
+echo "read 'icns' (-16455) \"lammps-gui.app/Contents/Resources/lammps.icns\";" > icon.rsrc
+Rez -a icon.rsrc -o LAMMPS-macOS-multiarch.dmg
+SetFile -a C LAMMPS-macOS-multiarch.dmg
+rm icon.rsrc
+
+echo "Delete temporary disk images"
+rm -f "${APP_NAME}-rw.dmg"
+rm -f "${APP_NAME}.dmg"
+
+exit 0

cmake/packaging/build_windows_cross_zip.sh

@@ -0,0 +1,26 @@
+#!/bin/bash -vx
+
+APP_NAME=lammps-gui
+DESTDIR=${PWD}/../LAMMPS_GUI
+
+echo "Delete old files, if they exist"
+rm -rvf ${DESTDIR} LAMMPS-Win10-amd64.zip
+
+echo "Create staging area for deployment and populate"
+DESTDIR=${DESTDIR} cmake --install .  --prefix "/"
+
+echo "Add required dependencies for Qt"
+for dll in Qt5Core.dll Qt5Gui.dll Qt5Widgets.dll
+do \
+    cp /usr/x86_64-w64-mingw32/sys-root/mingw/bin/${dll} ${DESTDIR}/bin/
+done
+for dir in styles platforms imageformats
+do \
+    mkdir -p ${DESTDIR}/${dir}
+    cp -r /usr/x86_64-w64-mingw32/sys-root/mingw/lib/qt5/plugins/${dir}/*.dll ${DESTDIR}/${dir}
+done
+
+pushd ..
+zip -9rv LAMMPS-Win10-amd64.zip LAMMPS_GUI
+popd
+exit 0

cmake/packaging/build_windows_vs.cmake

@@ -0,0 +1,28 @@
+# CMake script to be run post installation to build zipped package
+
+# clean up old zipfile and deployment tree
+file(REMOVE LAMMPS-Win10-amd64.zip)
+file(REMOVE_RECURSE LAMMPS_GUI)
+file(RENAME ${INSTNAME} LAMMPS_GUI)
+
+# move all executables and dlls to main folder and delete bin folder
+file(GLOB BINFILES LIST_DIRECTORIES FALSE LAMMPS_GUI/bin/*.exe LAMMPS_GUI/bin/*.dll)
+foreach(bin ${BINFILES})
+  get_filename_component(exe ${bin} NAME)
+  file(RENAME ${bin} LAMMPS_GUI/${exe})
+endforeach()
+file(REMOVE_RECURSE LAMMPS_GUI/bin)
+
+# create qt.conf so Qt will find its plugins
+file(WRITE LAMMPS_GUI/qt.conf "[Paths]\r\nPlugins = qt5plugins\r\n")
+
+# initialize environment and then run windeployqt to populate folder with missing dependencies and Qt plugins
+file(WRITE qtdeploy.bat "@ECHO OFF\r\nset VSCMD_DEBUG=0\r\nCALL ${VC_INIT} x64\r\nset PATH=${QT5_BIN_DIR};%PATH%\r\nwindeployqt --plugindir LAMMPS_GUI/qt5plugins --release  LAMMPS_GUI/lammps-gui.exe --no-quick-import --no-webkit2 --no-translations --no-system-d3d-compiler --no-angle --no-opengl-sw\r\n")
+execute_process(COMMAND cmd.exe /c qtdeploy.bat COMMAND_ECHO STDERR)
+file(REMOVE qtdeploy.bat)
+
+# create zip archive
+file(WRITE makearchive.ps1 "Compress-Archive -Path LAMMPS_GUI -CompressionLevel Optimal -DestinationPath LAMMPS-Win10-amd64.zip")
+execute_process(COMMAND powershell -ExecutionPolicy Bypass -File makearchive.ps1)
+file(REMOVE makearchive.ps1)
+file(REMOVE_RECURSE LAMMPS_GUI)

cmake/packaging/linux_wrapper.sh

@@ -0,0 +1,15 @@
+#!/bin/sh
+# wrapper for bundled executables
+
+BASEDIR=$(dirname "$0")
+EXENAME=$(basename "$0")
+
+# append to LD_LIBRARY_PATH to prefer local (newer) libs
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${BASEDIR}/lib
+
+# set some environment variables for LAMMPS etc.
+LAMMPS_POTENTIALS=${BASEDIR}/share/lammps/potentials
+MSI2LMP_LIBRARY=${BASEDIR}/share/lammps/frc_files
+export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY
+
+exec "${BASEDIR}/bin/${EXENAME}" "$@"

cmake/packaging/png2iconset.sh

@@ -0,0 +1,30 @@
+#!/bin/sh
+
+if [ $# != 2 ]
+then
+   echo "usage: $0 <pngfile> <iconset name>"
+   exit 1
+fi
+
+png="$1"
+ico="$2"
+
+if [ ! -f ${png} ]
+then
+   echo "PNG Image $1 not found"
+fi
+
+rm -rf ${ico}.iconset
+mkdir ${ico}.iconset
+sips -z   16   16 ${png} --out ${ico}.iconset/icon_16x16.png
+sips -z   32   32 ${png} --out ${ico}.iconset/icon_16x16@2x.png
+sips -z   32   32 ${png} --out ${ico}.iconset/icon_32x32.png
+sips -z   64   64 ${png} --out ${ico}.iconset/icon_32x32@2x.png
+sips -z  128  128 ${png} --out ${ico}.iconset/icon_128x128.png
+sips -z  256  256 ${png} --out ${ico}.iconset/icon_128x128@2x.png
+sips -z  256  256 ${png} --out ${ico}.iconset/icon_256x256.png
+sips -z  512  512 ${png} --out ${ico}.iconset/icon_256x256@2x.png
+sips -z  512  512 ${png} --out ${ico}.iconset/icon_512x512.png
+sips -z 1024 1024 ${png} --out ${ico}.iconset/icon_512x512@2x.png
+iconutil -c icns ${ico}.iconset
+rm -rf ${ico}.iconset

cmake/presets/all_off.cmake

@@ -43,7 +43,7 @@ set(ALL_PACKAGES
   KOKKOS
   KSPACE
   LATBOLTZ
-  LATTE
+  LEPTON
   MACHDYN
   MANIFOLD
   MANYBODY
@@ -56,6 +56,7 @@ set(ALL_PACKAGES
   ML-HDNNP
   ML-IAP
   ML-PACE
+  ML-POD
   ML-QUIP
   ML-RANN
   ML-SNAP

cmake/presets/all_on.cmake

@@ -45,7 +45,7 @@ set(ALL_PACKAGES
   KOKKOS
   KSPACE
   LATBOLTZ
-  LATTE
+  LEPTON
   MACHDYN
   MANIFOLD
   MANYBODY
@@ -58,6 +58,7 @@ set(ALL_PACKAGES
   ML-HDNNP
   ML-IAP
   ML-PACE
+  ML-POD
   ML-QUIP
   ML-RANN
   ML-SNAP

cmake/presets/download.cmake

@@ -1,14 +1,13 @@
 # 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 PLUMED SCAFACOS MACHDYN MESONT MDI ML-PACE)
+set(ALL_PACKAGES KIM MSCG VORONOI PLUMED SCAFACOS MACHDYN MESONT MDI ML-PACE)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)
 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)

cmake/presets/macos-multiarch.cmake

@@ -0,0 +1,14 @@
+# preset that will build portable multi-arch binaries on macOS without MPI
+
+set(CMAKE_OSX_ARCHITECTURES "arm64;x86_64" CACHE STRING "" FORCE)
+set(CMAKE_OSX_DEPLOYMENT_TARGET 11.0 CACHE STRING "" FORCE)
+set(CMAKE_BUILD_TYPE Release CACHE STRING "" FORCE)
+
+set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
+set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+
+set(BUILD_MPI FALSE CACHE BOOL "" FORCE)
+set(BUILD_SHARED_LIBS FALSE CACHE BOOL "" FORCE)
+set(LAMMPS_EXCEPTIONS TRUE CACHE BOOL "" FORCE)

cmake/presets/mingw-cross.cmake

@@ -35,7 +35,7 @@ set(WIN_PACKAGES
   INTEL
   INTERLAYER
   KSPACE
-  LATTE
+  LEPTON
   MACHDYN
   MANIFOLD
   MANYBODY
@@ -47,6 +47,7 @@ set(WIN_PACKAGES
   MISC
   ML-HDNNP
   ML-IAP
+  ML-POD
   ML-RANN
   ML-SNAP
   MOFFF

cmake/presets/most.cmake

@@ -35,12 +35,15 @@ set(ALL_PACKAGES
   GRANULAR
   INTERLAYER
   KSPACE
+  LEPTON
   MACHDYN
   MANYBODY
   MC
   MEAM
+  MESONT
   MISC
   ML-IAP
+  ML-POD
   ML-SNAP
   MOFFF
   MOLECULE

cmake/presets/nolib.cmake

@@ -12,10 +12,9 @@ set(PACKAGES_WITH_LIB
   KIM
   KOKKOS
   LATBOLTZ
-  LATTE
+  LEPTON
   MACHDYN
   MDI
-  MESONT
   ML-HDNNP
   ML-PACE
   ML-QUIP

cmake/presets/windows.cmake

@@ -1,6 +1,7 @@
 set(WIN_PACKAGES
   AMOEBA
   ASPHERE
+  AWPMD
   BOCS
   BODY
   BPM
@@ -20,6 +21,7 @@ set(WIN_PACKAGES
   DPD-SMOOTH
   DRUDE
   EFF
+  ELECTRODE
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -29,12 +31,15 @@ set(WIN_PACKAGES
   GRANULAR
   INTERLAYER
   KSPACE
+  LEPTON
   MANIFOLD
   MANYBODY
   MC
   MEAM
+  MESONT
   MISC
   ML-IAP
+  ML-POD
   ML-SNAP
   MOFFF
   MOLECULE

doc/Makefile

@@ -45,7 +45,7 @@ SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocess
 # 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 html pdf spelling anchor_check style_check char_check xmlgen fasthtml
+.PHONY: help clean-all clean clean-spelling epub mobi html pdf spelling anchor_check style_check char_check role_check xmlgen fasthtml
 
 # ------------------------------------------
 
@@ -86,17 +86,19 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@(\
-		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build -E $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
-		touch $(RSTDIR)/Fortran.rst ;\
+		touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
 		ln -sf Manual.html html/index.html;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
-		echo "############################################" ;\
+		echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		rst_anchor_check src/*.rst ;\
-		python $(BUILDDIR)/utils/check-packages.py -s ../src -d src ;\
+		$(PYTHON) $(BUILDDIR)/utils/check-packages.py -s ../src -d src ;\
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
-		python $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
+		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
+		env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
+		$(PYTHON) $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
@@ -113,9 +115,9 @@ fasthtml: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@mkdir -p fasthtml
 	@(\
-		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
-		touch $(RSTDIR)/Fortran.rst ;\
+		touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
 		deactivate ;\
 	)
@@ -130,8 +132,8 @@ fasthtml: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 spelling: xmlgen $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives.txt
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@(\
-		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
-		cp $(SPHINXCONFIG)/false_positives.txt $(RSTDIR)/ ; env PYTHONWARNINGS= \
+		. $(VENV)/bin/activate ; \
+		cp $(SPHINXCONFIG)/false_positives.txt $(RSTDIR)/;  env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build -b spelling -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) spelling ;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		deactivate ;\
@@ -145,9 +147,9 @@ epub: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@rm -f LAMMPS.epub
 	@cp src/JPG/*.* epub/JPG
 	@(\
-		. $(VENV)/bin/activate ;\
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build -E $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
-		touch $(RSTDIR)/Fortran.rst ;\
+		touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		deactivate ;\
@@ -166,16 +168,18 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@if [ "$(HAS_PDFLATEX)" == "NO" ] ; then echo "PDFLaTeX or latexmk were not found! Please check README for further instructions" 1>&2; exit 1; fi
 	@(\
-		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build -E $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
-		touch $(RSTDIR)/Fortran.rst ;\
+		touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build  $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
-		echo "############################################" ;\
+		echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		rst_anchor_check src/*.rst ;\
-		python utils/check-packages.py -s ../src -d src ;\
+		$(PYTHON) utils/check-packages.py -s ../src -d src ;\
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
-		python utils/check-styles.py -s ../src -d src ;\
+		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
+		env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
+		$(PYTHON) utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
@@ -198,28 +202,39 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 
 anchor_check : $(ANCHORCHECK)
 	@(\
-		. $(VENV)/bin/activate ;\
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		rst_anchor_check src/*.rst ;\
 		deactivate ;\
 	)
 
 style_check : $(VENV)
 	@(\
-		. $(VENV)/bin/activate ;\
-		python utils/check-styles.py -s ../src -d src ;\
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
+		$(PYTHON) utils/check-styles.py -s ../src -d src ;\
 		deactivate ;\
 	)
 
 package_check : $(VENV)
 	@(\
-		. $(VENV)/bin/activate ;\
-		python utils/check-packages.py -s ../src -d src ;\
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
+		$(PYTHON) utils/check-packages.py -s ../src -d src ;\
 		deactivate ;\
 	)
 
 char_check :
 	@( env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst && exit 1 || : )
 
+role_check :
+	@( env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst && exit 1 || : )
+	@( env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst && exit 1 || : )
+
+link_check : $(VENV) html
+	@(\
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
+		linkchecker -F html --check-extern html/Manual.html ;\
+		deactivate ;\
+	)
+
 xmlgen : doxygen/xml/index.xml
 
 doxygen/Doxyfile: doxygen/Doxyfile.in
@@ -247,7 +262,7 @@ $(MATHJAX):
 
 $(ANCHORCHECK): $(VENV)
 	@( \
-		. $(VENV)/bin/activate; \
+		. $(VENV)/bin/activate; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		pip $(PIP_OPTIONS) install -e utils/converters;\
 		deactivate;\
 	)

doc/README

@@ -40,8 +40,9 @@ environment and local folders.
 Installing prerequisites for the documentation build
 
 To run the HTML documention build toolchain, python 3.x, doxygen, git,
-and virtualenv have to be installed.  Also internet access is initially
-required to download external files and tools.
+and the venv python module have to be installed if not already available.
+Also internet access is initially required to download external files
+and tools.
 
 Building the PDF format manual requires in addition a compatible LaTeX
 installation with support for PDFLaTeX and several add-on LaTeX packages

doc/documentation_conventions.md

@@ -4,45 +4,44 @@ This purpose of this document is to provide a point of reference
 for LAMMPS developers and contributors as to what conventions
 should be used to structure and format files in the LAMMPS manual.
 
-Last change: 2020-04-23
+Last change: 2022-12-30
 
 ## File format and tools
 
-In fall 2019, the LAMMPS documentation file format has changed from
-a home grown minimal markup designed to generate HTML format files
-from a mostly plain text format to using the reStructuredText file
-format.  For a transition period all files in the old .txt format
-were transparently converted to .rst and then processed.  The txt2rst
-tool is still included in the distribution to obtain an initial .rst
-file for integration into the manual.  Since the transition to
-reStructured text as source format, many of the artifacts or the
-translation have been removed though and parts of the documentation
-refactored and expanded to take advantage of the capabilities
-reStructuredText and associated tools.  The conversion from the
-source to the final formats (HTML, PDF, and optionally e-book
-reader formats ePUB and MOBI) is mostly automated and controlled
-by a Makefile in the `doc` folder. This makefile assumes that the
-processing is done on a Unix-like machine and Python 3.5 or later
-and a matching virtualenv module are available.  Additional Python
-packages (like the Sphinx tool and several extensions) are
-transparently installed into a virtual environment over the
-internet using the `pip` package manager.  Further requirements
-and details are discussed in the manual.
+In fall 2019, the LAMMPS documentation file format has changed from a
+home grown markup designed to generate HTML format files only, to
+[reStructuredText](https://docutils.sourceforge.io/rst.html>.  For a
+transition period all files in the old .txt format were transparently
+converted to .rst and then processed.  The `txt2rst tool` is still
+included in the distribution to obtain an initial .rst file for legacy
+integration into the manual.  Since that transition to reStructured
+text, many of the artifacts of the translation have been removed though,
+and parts of the documentation refactored and expanded to take advantage
+of the capabilities reStructuredText and associated tools.  The
+conversion from the source to the final formats (HTML, PDF, and
+optionally e-book reader formats ePUB and MOBI) is mostly automated and
+controlled by a Makefile in the `doc` folder. This makefile assumes that
+the processing is done on a Unix-like machine and Python 3.5 or later
+and a matching venv module are available.  Additional Python
+packages (like the Sphinx tool and several extensions) are transparently
+installed into a virtual environment over the internet using the `pip`
+package manager.  Further requirements and details are discussed in the
+manual.
 
 ## Work in progress
 
 The refactoring and improving of the documentation is an ongoing
 process, so statements in this document may not always be fully
-up-to-date.  If in doubt, contact the LAMMPS developers.
+up-to-date.  When in doubt, contact the LAMMPS developers.
 
 ## General structure
 
-The layout and formatting of added files should follow the example
-of the existing files.  Since those are directly derived from their
-former .txt format versions and the manual has been maintained in
+The layout and formatting of added files should follow the example of
+the existing files.  Since many of those were initially derived from
+their former .txt format versions and the manual has been maintained in
 that format for many years, there is a large degree of consistency
-already, so comparison with similar files should give you a good
-idea what kind of information and sections are needed.
+already, so comparison with similar files should give you a good idea
+what kind of information and sections are needed.
 
 ## Formatting conventions
 
@@ -52,21 +51,27 @@ It seems to be sufficient to have this consistent only within
 any single file and it is not (yet) enforced strictly, but making
 this globally consistent makes it easier to move sections around.
 
-Filenames, folders, paths, (shell) commands, definitions, makefile
+File names, folders, paths, (shell) commands, definitions, makefile
 settings and similar should be formatted as "literals" with
 double backward quotes bracketing the item: \`\`path/to/some/file\`\`
 
 Keywords and options are formatted in italics:  \*option\*
 
 Mathematical expressions, equations, symbols are typeset using
-either a `.. math:`` block or the `:math:` role.
+either a `.. math:` block or the `:math:` role.
 
-Groups of shell commands or LAMMPS input script or C/C++ source
+Groups of shell commands or LAMMPS input script or C/C++/Python source
 code should be typeset into a `.. code-block::` section. A syntax
-highlighting extension for LAMMPS input scripts is provided, so
-`LAMMPS` can be used to indicate the language in the code block
-in addition to `bash`, `c`, or `python`.  When no syntax style
-is indicated, no syntax highlighting is performed.
+highlighting extension for LAMMPS input scripts is provided, so `LAMMPS`
+can be used to indicate the language in the code block in addition to
+`bash`, `c`, `c++`, `console`, `csh`, `diff', `fortran`, `json`, `make`,
+`perl`, `powershell`, `python`, `sh`, or `tcl`, `text`, or `yaml`.  When
+no syntax style is indicated, no syntax highlighting is performed.  When
+typesetting commands executed on the shell, please do not prefix
+commands with a shell prompt and use `bash` highlighting, except when
+the block also shows the output from that command.  In the latter case,
+please use a dollar sign as the shell prompt and `console` for syntax
+highlighting.
 
 As an alternative, e.g. to typeset the syntax of file formats
 a `.. parsed-literal::` block can be used, which allows some
@@ -89,22 +94,30 @@ by `   :class: note`.
 
 ## Required steps when adding a custom style to LAMMPS
 
-When adding a new style (e.g. pair style or a compute or a fix)
-or a new command, it is **required** to include the corresponding
-documentation.  Those are often new files that need to be added.
-In order to be included in the documentation, those new files
-need to be reference in a `.. toctree::` block.  Most of those
-use patterns with wildcards, so the addition will be automatic.
-However, those additions also need to be added to some lists of
-styles or commands.  The `make style\_check` command will perform
-a test and report any missing entries and list the affected files.
-Any references defined with `.. \_refname:` have to be unique
-across all documentation files and this can be checked for with
-`make anchor\_check`.  Finally, a spell-check should be done,
-which is triggered via `make spelling`.  Any offenses need to
-be corrected and false positives should be added to the file
-`utils/sphinx-config/false\_positives.txt`.
+When adding a new style (e.g. pair style or a compute or a fix) or a new
+command, it is **required** to include the **corresponding documentation**
+in [reStructuredText format](https://docutils.sourceforge.io/rst.html).
+Those are often new files that need to be added.  In order to be
+included in the documentation, those new files need to be referenced in a
+`.. toctree::` block.  Most of those use patterns with wild cards, so the
+addition will be automatic.  However, those additions also need to be
+added to some lists of styles or commands.  The `make style\_check`
+command when executed in the `doc` folder will perform a test and report
+any missing entries and list the affected files.  Any references defined
+with `.. \_refname:` have to be unique across all documentation files
+and this can be checked for with `make anchor\_check`.  Finally, a
+spell-check should be done, which is triggered via `make spelling`.  Any
+offenses need to be corrected and false positives should be added to the
+file `utils/sphinx-config/false\_positives.txt`.
 
 ## Required additional steps when adding a new package to LAMMPS
 
-TODO
+When adding a new package, the package must be added to the list of
+packages in the `Packages_list.rst` file.  If additional build instructions
+need to be followed, a corresponding section should be added to the
+`Build_extras.rst` file and linked from the list at the top of the
+file as well as the equivalent list in the `Build_packages.rst` file.
+
+A detailed description of the package and pointers to configuration,
+included commands and examples, external pages, author information and
+more should be added to the `Packages_details.rst` file.

doc/github-development-workflow.md

@@ -1,12 +1,12 @@
 # Outline of the GitHub Development Workflow
 
-This purpose of this document is to provide a point of reference for the
+The purpose of this document is to provide a point of reference for the
 core LAMMPS developers and other LAMMPS contributors to understand the
 choices the LAMMPS developers have agreed on. Git and GitHub provide the
 tools, but do not set policies, so it is up to the developers to come to
 an agreement as to how to define and interpret policies. This document
-is likely to change as our experiences and needs change and we try to
-adapt accordingly. Last change 2021-09-02.
+is likely to change as our experiences and needs change, and we try to
+adapt it accordingly. Last change 2023-02-10.
 
 ## Table of Contents
 
@@ -22,47 +22,50 @@ adapt accordingly. Last change 2021-09-02.
 ## GitHub Merge Management
 
 In the interest of consistency, ONLY ONE of the core LAMMPS developers
-should doing the merging itself.  This is currently
+should do the merging.  This is currently
 [@akohlmey](https://github.com/akohlmey) (Axel Kohlmeyer).  If this
 assignment needs to be changed, it shall be done right after a stable
 release.  If the currently assigned developer cannot merge outstanding
 pull requests in a timely manner, or in other extenuating circumstances,
-other core LAMMPS developers with merge rights can merge pull requests,
-when necessary.
+other core LAMMPS developers with merge permission may merge pull
+requests.
 
 ## Pull Requests
 
-ALL changes to the LAMMPS code and documentation, however trivial, MUST
-be submitted as a pull request to GitHub. All changes to the "develop"
-branch must be made exclusively through merging pull requests. The
-"release" and "stable" branches, respectively are only to be updated
-upon patch or stable releases with fast-forward merges based on the
-associated tags. Pull requests may also be submitted to (long-running)
-feature branches created by LAMMPS developers inside the LAMMPS project,
-if needed. Those are not subject to the merge and review restrictions
-discussed in this document, though, but get managed as needed on a
-case-by-case basis.
+*ALL* changes to the LAMMPS code and documentation, however trivial,
+MUST be submitted as a pull request to GitHub.  All changes to the
+"develop" branch must be made exclusively through merging pull requests.
+The "release" and "stable" branches, respectively, are only to be
+updated upon feature or stable releases based on the associated
+tags.  Updates to the stable release in between stable releases
+(for example, back-ported bug fixes) are first merged into the "maintenance"
+branch and then into the "stable" branch as update releases.
+
+Pull requests may also be submitted to (long-running) feature branches
+created by LAMMPS developers inside the LAMMPS project, if needed. Those
+are not subject to the merge and review restrictions discussed in this
+document, though, but get managed as needed on a case-by-case basis.
 
 ### Pull Request Assignments
 
 Pull requests can be "chaperoned" by one of the LAMMPS core developers.
-This is indicated by who the pull request is assigned to. LAMMPS core
-developers can self-assign or they can decide to assign a pull request
+This is indicated by whom the pull request is assigned to.  LAMMPS core
+developers can self-assign, or they can decide to assign a pull request
 to a different LAMMPS developer. Being assigned to a pull request means,
 that this pull request may need some work and the assignee is tasked to
-determine whether this might be needed or not, and may either implement
-the required changes or ask the submitter of the pull request to implement
-them.  Even though, all LAMMPS developers may have write access to pull
-requests (if enabled by the submitter, which is the default), only the
-submitter or the assignee of a pull request may do so.  During this
-period the `work_in_progress` label may be applied to the pull
-request.  The assignee gets to decide what happens to the pull request
-next, e.g. whether it should be assigned to a different developer for
-additional checks and changes, or is recommended to be merged.  Removing
-the `work_in_progress` label and assigning the pull request to the
-developer tasked with merging signals that a pull request is ready to be
-merged. In addition, a `ready_for_merge` label may also be assigned
-to signal urgency to merge this pull request quickly.
+determine whether this might be needed or not. The assignee may either
+choose to implement required changes or ask the submitter of the pull
+request to implement them.  Even though, all LAMMPS developers may have
+write access to pull requests (if enabled by the submitter, which is the
+default), only the submitter or the assignee of a pull request should do
+so.  During this period, the `work_in_progress` label may be applied to
+the pull request.  The assignee gets to decide what happens to the pull
+request next, e.g. whether it should be assigned to a different
+developer for additional checks and changes, or is recommended to be
+merged.  Removing the `work_in_progress` label and assigning the pull
+request to the developer tasked with merging signals that a pull request
+is ready to be merged. In addition, a `ready_for_merge` label may also
+be assigned to signal urgency to merge this pull request quickly.
 
 ### Pull Request Reviews
 
@@ -70,32 +73,33 @@ People can be assigned to review a pull request in two ways:
 
   * They can be assigned manually to review a pull request
     by the submitter or a LAMMPS developer
-  * They can be automatically assigned, because a developers matches
-    a file pattern in the `.github/CODEOWNERS` file, which associates
-    developers with the code they contributed and maintain.
+  * They can be automatically assigned, because a developer's GitHub
+    handle matches a file pattern in the `.github/CODEOWNERS` file,
+    which associates developers with the code they contributed and
+    maintain.
 
 Reviewers are requested to state their appraisal of the proposed changes
 and either approve or request changes. People may unassign themselves
 from review, if they feel not competent about the changes proposed. At
-least two approvals from LAMMPS developers with write access are required
-before merging in addition to the automated compilation tests.
-Merging counts as implicit approval, so does submission of a pull request
-(by a LAMMPS developer). So the person doing the merge may not also submit
-an approving review. The feature, that reviews from code owners are "hard"
-reviews (i.e. they must all be approved before merging is allowed), is
-currently disabled and it is in the discretion of the merge maintainer to
-assess when a sufficient degree of approval, especially from external
-contributors, has been reached in these cases.  Reviews may be
-(automatically) dismissed, when the reviewed code has been changed,
-and then approval is required a second time.
+least two approvals from LAMMPS developers with write access are
+required before merging, in addition to passing all automated
+compilation and unit tests.  Merging counts as implicit approval, so
+does submission of a pull request (by a LAMMPS developer). So the person
+doing the merge may not also submit an approving review.  The GitHub
+feature, that reviews from code owners are "hard" reviews (i.e. they
+must all approve before merging is allowed), is currently disabled.
+It is in the discretion of the merge maintainer to assess when a
+sufficient degree of approval has been reached, especially from external
+collaborators.  Reviews may be (automatically) dismissed, when the
+reviewed code has been changed. Review may be requested a second time.
 
 ### Pull Request Discussions
 
 All discussions about a pull request should be kept as much as possible
 on the pull request discussion page on GitHub, so that other developers
 can later review the entire discussion after the fact and understand the
-rationale behind choices made.  Exceptions to this policy are technical
-discussions, that are centered on tools or policies themselves
+rationale behind choices that were made.  Exceptions to this policy are
+technical discussions, that are centered on tools or policies themselves
 (git, GitHub, c++) rather than on the content of the pull request.
 
 ## GitHub Issues
@@ -109,39 +113,47 @@ marker in the subject. This is automatically done when using the
 corresponding template for submitting an issue.  Issues may be assigned
 to one or more developers, if they are working on this feature or
 working to resolve an issue.  Issues that have nobody working
-on them at the moment or in the near future, have the label
+on them at the moment, or in the near future, have the label
 `volunteer needed` attached.
 
-When an issue, say `#125` is resolved by a specific pull request,
-the comment for the pull request shall contain the text `closes #125`
-or `fixes #125`, so that the issue is automatically deleted when
-the pull request is merged.  The template for pull requests includes
-a header where connections between pull requests and issues can be listed
-and thus were this comment should be placed.
+When an issue, say `#125` is resolved by a specific pull request, the
+comment for the pull request shall contain the text `closes #125` or
+`fixes #125`, so that the issue is automatically deleted when the pull
+request is merged.  The template for pull requests includes a header
+where connections between pull requests and issues can be listed, and
+thus where this comment should be placed.
 
-## Milestones and Release Planning
+## Release Planning
 
 LAMMPS uses a continuous release development model with incremental
-changes, i.e. significant effort is made - including automated pre-merge
-testing - that the code in the branch "develop" does not get easily
+changes, i.e. significant effort is made -- including automated pre-merge
+testing -- that the code in the branch "develop" does not get easily
 broken.  These tests are run after every update to a pull request.  More
-extensive and time consuming tests (including regression testing) are
-performed after code is merged to the "develop" branch. There are patch
-releases of LAMMPS every 3-5 weeks at a point, when the LAMMPS
-developers feel, that a sufficient amount of changes have happened, and
-the post-merge testing has been successful. These patch releases are
+extensive and time-consuming tests (including regression testing) are
+performed after code is merged to the "develop" branch.  There are feature
+releases of LAMMPS made about every 4-6 weeks at a point, when the LAMMPS
+developers feel, that a sufficient number of changes have been included
+and all post-merge testing has been successful.  These feature releases are
 marked with a `patch_<version date>` tag and the "release" branch
-follows only these versions (and thus is always supposed to be of
-production quality, unlike "develop", which may be temporary broken, in
-the case of larger change sets or unexpected incompatibilities or side
-effects.
+follows only these versions with fast-forward merges.  While "develop" may
+be temporarily broken through issues only detected by the post-merge tests,
+The "release" branch is always supposed to be of production quality.
 
-About 1-2 times each year, there are going to be "stable" releases of
-LAMMPS.  These have seen additional, manual testing and review of
-results from testing with instrumented code and static code analysis.
-Also, the last 1-3 patch releases before a stable release are "release
-candidate" versions which only contain bugfixes and documentation
-updates.  For release planning and the information of code contributors,
-issues and pull requests being actively worked on are assigned a
-"milestone", which corresponds to the next stable release or the stable
-release after that, with a tentative release date.
+About once each year, there is a "stable" release of LAMMPS.  These have
+seen additional, manual testing and review of results from testing with
+instrumented code and static code analysis.  Also, the last few feature
+releases before a stable release are "release candidate" versions which
+only contain bug fixes, feature additions to peripheral functionality,
+and documentation updates.  In between stable releases, bug fixes and
+infrastructure updates are back-ported from the "develop" branch to the
+"maintenance" branch and occasionally merged into "stable" and published
+as update releases.
+
+## Project Management
+
+For release planning and the information of code contributors, issues
+and pull requests are being managed with GitHub Project Boards.  There
+are currently three boards: LAMMPS Feature Requests, LAMMPS Bug Reports,
+and LAMMPS Pull Requests.  Each board is organized in columns where
+submissions are categorized.  Within each column the entries are
+(manually) sorted according their priority.

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "3 November 2022" "2022-11-3"
+.TH LAMMPS "1" "2 August 2023" "2023-08-2"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 3 November 2022
+\- Molecular Dynamics Simulator.  Version 2 August 2023
 
 .SH SYNOPSIS
 .B lmp

doc/msi2lmp.1

@@ -1,11 +1,11 @@
-.TH MSI2LMP "1" "v3.9.9" "2018-11-05"
+.TH MSI2LMP "1" "v3.9.10" "2023-03-10"
 .SH NAME
 .B MSI2LMP
 \- Converter for Materials Studio files to LAMMPS
 
 .SH SYNOPSIS
 .B msi2lmp
-<ROOTNAME> [-class <I|1|II|2|O|0>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift <x> <y> <z>]
+[-help] <ROOTNAME> [-class <I|1|II|2|O|0>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift <x> <y> <z>]
 
 .SH DESCRIPTION
 .PP
@@ -22,6 +22,9 @@ needed between .frc and .car/.mdf files are the atom types.
 
 .SH OPTIONS
 .TP
+\fB\-h\fR, \fB\-help\fR,
+Print detailed help message to the screen and stop.
+.TP
 \fB\<ROOTNAME>\fR
 This has to be the first argument and is a
 .B mandatory

doc/src/2001/basics.html

@@ -63,7 +63,7 @@ In the src directory, there is one top-level Makefile and several
 low-level machine-specific files named Makefile.xxx where xxx = the
 machine name. If a low-level Makefile exists for your platform, you do
 not need to edit the top-level Makefile.  However you should check the
-system-specific section of the low-level Makefile to insure the
+system-specific section of the low-level Makefile to ensure the
 various paths are correct for your environment. If a low-level
 Makefile does not exist for your platform, you will need to add a
 suitable target to the top-level Makefile. You will also need to

doc/src/2001/input_commands.html

@@ -1206,7 +1206,7 @@ this command is not typically needed if the "nonbond style" and "
 an exception to this is if a short cutoff is used initially,
   but a longer cutoff will be used for a subsequent run (in the same
   input script), in this case the "maximum cutoff" command should be
-  used to insure enough memory is allocated for the later run
+  used to ensure enough memory is allocated for the later run
 note that a restart file contains nonbond cutoffs (so it is not necessary
   to use a "nonbond style" command before "read restart"), but LAMMPS
   still needs to know what the maximum cutoff will be before the

doc/src/Bibliography.rst

@@ -203,7 +203,7 @@ Bibliography
    A Caro, DA Crowson, M Caro; Phys Rev Lett, 95, 075702 (2005)
 
 **(CasP)**
-   CasP webpage: https://www.helmholtz-berlin.de/people/gregor-schiwietz/casp_en.html
+   CasP webpage: http://www.casp-program.org/
 
 **(Cawkwell2012)**
    A.\  M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86 (17), 174308 (2012).

doc/src/Build.rst

@@ -6,9 +6,9 @@ either traditional makefiles for use with GNU make (which may require
 manual editing), or using a build environment generated by CMake (Unix
 Makefiles, Ninja, Xcode, Visual Studio, KDevelop, CodeBlocks and more).
 
-As an alternative you can download a package with pre-built executables
-or automated build trees as described on the :doc:`Install <Install>`
-page.
+As an alternative, you can download a package with pre-built executables
+or automated build trees, as described in the :doc:`Install <Install>`
+section of the manual.
 
 .. toctree::
    :maxdepth: 1

doc/src/Build_basics.rst

@@ -44,7 +44,7 @@ standard. A more detailed discussion of that is below.
 
       The executable created by CMake (after running make) is named
       ``lmp`` unless the ``LAMMPS_MACHINE`` option is set.  When setting
-      ``LAMMPS_MACHINE=name`` the executable will be called
+      ``LAMMPS_MACHINE=name``, the executable will be called
       ``lmp_name``.  Using ``BUILD_MPI=no`` will enforce building a
       serial executable using the MPI STUBS library.
 
@@ -60,7 +60,7 @@ standard. A more detailed discussion of that is below.
 
       Any ``make machine`` command will look up the make settings from a
       file ``Makefile.machine`` in the folder ``src/MAKE`` or one of its
-      sub-directories ``MINE``, ``MACHINES``, or ``OPTIONS``, create a
+      subdirectories ``MINE``, ``MACHINES``, or ``OPTIONS``, create a
       folder ``Obj_machine`` with all objects and generated files and an
       executable called ``lmp_machine``\ .  The standard parallel build
       with ``make mpi`` assumes a standard MPI installation with MPI
@@ -107,9 +107,9 @@ MPI and OpenMP support in LAMMPS
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 If you are installing MPI yourself to build a parallel LAMMPS
-executable, we recommend either MPICH or OpenMPI which are regularly
+executable, we recommend either MPICH or OpenMPI, which are regularly
 used and tested with LAMMPS by the LAMMPS developers.  MPICH can be
-downloaded from the `MPICH home page <https://www.mpich.org>`_ and
+downloaded from the `MPICH home page <https://www.mpich.org>`_, and
 OpenMPI can be downloaded correspondingly from the `OpenMPI home page
 <https://www.open-mpi.org>`_.  Other MPI packages should also work.  No
 specific vendor provided and standard compliant MPI library is currently
@@ -128,14 +128,14 @@ and adds vectorization support when compiled with compatible compilers,
 in particular the Intel compilers on top of OpenMP. Also, the ``KOKKOS``
 package can be compiled to include OpenMP threading.
 
-In addition, there are a few commands in LAMMPS that have native OpenMP
-support included as well.  These are commands in the ``MPIIO``,
-``ML-SNAP``, ``DIFFRACTION``, and ``DPD-REACT`` packages.  In addition
-some packages support OpenMP threading indirectly through the libraries
-they interface to: e.g. ``LATTE``, ``KSPACE``, and ``COLVARS``.
-See the :doc:`Packages details <Packages_details>` page for more
-info on these packages and the pages for their respective commands
-for OpenMP threading info.
+In addition, there are a few commands in LAMMPS that have native
+OpenMP support included as well.  These are commands in the ``MPIIO``,
+``ML-SNAP``, ``DIFFRACTION``, and ``DPD-REACT`` packages.
+Furthermore, some packages support OpenMP threading indirectly through
+the libraries they interface to: e.g. ``KSPACE``, and ``COLVARS``.
+See the :doc:`Packages details <Packages_details>` page for more info
+on these packages, and the pages for their respective commands for
+OpenMP threading info.
 
 For CMake, if you use ``BUILD_OMP=yes``, you can use these packages
 and turn on their native OpenMP support and turn on their native OpenMP
@@ -144,9 +144,9 @@ variable before you launch LAMMPS.
 
 For building via conventional make, the ``CCFLAGS`` and ``LINKFLAGS``
 variables in Makefile.machine need to include the compiler flag that
-enables OpenMP. For GNU compilers it is ``-fopenmp``\ .  For (recent) Intel
-compilers it is ``-qopenmp``\ .  If you are using a different compiler,
-please refer to its documentation.
+enables OpenMP. For the GNU compilers or Clang, it is ``-fopenmp``\ .
+For (recent) Intel compilers, it is ``-qopenmp``\ .  If you are using a
+different compiler, please refer to its documentation.
 
 .. _default-none-issues:
 
@@ -174,15 +174,16 @@ Choice of compiler and compile/link options
 The choice of compiler and compiler flags can be important for maximum
 performance.  Vendor provided compilers for a specific hardware can
 produce faster code than open-source compilers like the GNU compilers.
-On the most common x86 hardware most popular C++ compilers are quite
-similar in performance of C/C++ code at high optimization levels.  When
-using the ``INTEL`` package, there is a distinct advantage in using
-the `Intel C++ compiler <intel_>`_ due to much improved vectorization
-through SSE and AVX instructions on compatible hardware as the source
-code includes changes and Intel compiler specific directives to enable
-high degrees of vectorization.  This may change over time as equivalent
-vectorization directives are included into OpenMP standard revisions and
-other compilers adopt them.
+On the most common x86 hardware, the most popular C++ compilers are
+quite similar in their ability to optimize regular C/C++ source code at
+high optimization levels.  When using the ``INTEL`` package, there is a
+distinct advantage in using the `Intel C++ compiler <intel_>`_ due to
+much improved vectorization through SSE and AVX instructions on
+compatible hardware.  The source code in that package conditionally
+includes compiler specific directives to enable these high degrees of
+vectorization.  This may change over time as equivalent vectorization
+directives are included into the OpenMP standard and other compilers
+adopt them.
 
 .. _intel: https://software.intel.com/en-us/intel-compilers
 
@@ -196,7 +197,7 @@ LAMMPS.
    .. tab:: CMake build
 
       By default CMake will use the compiler it finds according to
-      internal preferences and it will add optimization flags
+      internal preferences, and it will add optimization flags
       appropriate to that compiler and any :doc:`accelerator packages
       <Speed_packages>` you have included in the build.  CMake will
       check if the detected or selected compiler is compatible with the
@@ -250,9 +251,9 @@ LAMMPS.
       and `-C ../cmake/presets/pgi.cmake`
       will switch the compiler to the PGI compilers.
 
-      In addition you can set ``CMAKE_TUNE_FLAGS`` to specifically add
-      compiler flags to tune for optimal performance on given hosts. By
-      default this variable is empty.
+      Furthermore, you can set ``CMAKE_TUNE_FLAGS`` to specifically add
+      compiler flags to tune for optimal performance on given hosts.
+      This variable is empty by default.
 
       .. note::
 
@@ -276,7 +277,7 @@ LAMMPS.
 
       Parallel build (see ``src/MAKE/Makefile.mpi``):
 
-      .. code-block:: bash
+      .. code-block:: make
 
          CC =            mpicxx
          CCFLAGS =       -g -O3
@@ -296,7 +297,7 @@ LAMMPS.
 
          If compilation stops with a message like the following:
 
-         .. code-block::
+         .. code-block:: output
 
             g++ -g -O3  -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64    -I../STUBS     -c ../main.cpp
             In file included from ../pointers.h:24:0,
@@ -368,10 +369,10 @@ running LAMMPS from Python via its library interface.
                                       # no default value
 
       The compilation will always produce a LAMMPS library and an
-      executable linked to it.  By default this will be a static library
-      named ``liblammps.a`` and an executable named ``lmp`` Setting
-      ``BUILD_SHARED_LIBS=yes`` will instead produce a shared library
-      called ``liblammps.so`` (or ``liblammps.dylib`` or
+      executable linked to it.  By default, this will be a static
+      library named ``liblammps.a`` and an executable named ``lmp``
+      Setting ``BUILD_SHARED_LIBS=yes`` will instead produce a shared
+      library called ``liblammps.so`` (or ``liblammps.dylib`` or
       ``liblammps.dll`` depending on the platform) If
       ``LAMMPS_MACHINE=name`` is set in addition, the name of the
       generated libraries will be changed to either ``liblammps_name.a``
@@ -429,7 +430,7 @@ You may need to use ``sudo make install`` in place of the last line if
 you do not have write privileges for ``/usr/local/lib`` or use the
 ``--prefix`` configuration option to select an installation folder,
 where you do have write access.  The end result should be the file
-``/usr/local/lib/libmpich.so``.  On many Linux installations the folder
+``/usr/local/lib/libmpich.so``.  On many Linux installations, the folder
 ``${HOME}/.local`` is an alternative to using ``/usr/local`` and does
 not require superuser or sudo access.  In that case the configuration
 step becomes:
@@ -438,9 +439,10 @@ step becomes:
 
   ./configure --enable-shared --prefix=${HOME}/.local
 
-Avoiding to use "sudo" for custom software installation (i.e. from source
-and not through a package manager tool provided by the OS) is generally
-recommended to ensure the integrity of the system software installation.
+Avoiding the use of "sudo" for custom software installation (i.e. from
+source and not through a package manager tool provided by the OS) is
+generally recommended to ensure the integrity of the system software
+installation.
 
 ----------
 
@@ -514,11 +516,11 @@ using CMake or Make.
 Install LAMMPS after a build
 ------------------------------------------
 
-After building LAMMPS, you may wish to copy the LAMMPS executable of
-library, along with other LAMMPS files (library header, doc files) to
-a globally visible place on your system, for others to access.  Note
-that you may need super-user privileges (e.g. sudo) if the directory
-you want to copy files to is protected.
+After building LAMMPS, you may wish to copy the LAMMPS executable or
+library, along with other LAMMPS files (library header, doc files), to a
+globally visible place on your system, for others to access.  Note that
+you may need super-user privileges (e.g. sudo) if the directory you want
+to copy files to is protected.
 
 .. tabs::
 
@@ -536,7 +538,7 @@ you want to copy files to is protected.
       environment variable, if you are installing LAMMPS into a non-system
       location and/or are linking to libraries in a non-system location that
       depend on such runtime path settings.
-      As an alternative you may set the CMake variable ``LAMMPS_INSTALL_RPATH``
+      As an alternative, you may set the CMake variable ``LAMMPS_INSTALL_RPATH``
       to ``on`` and then the runtime paths for any linked shared libraries
       and the library installation folder for the LAMMPS library will be
       embedded and thus the requirement to set environment variables is avoided.

doc/src/Build_cmake.rst

@@ -9,10 +9,10 @@ page.
 
 The following text assumes some familiarity with CMake and focuses on
 using the command line tool ``cmake`` and what settings are supported
-for building LAMMPS.  A more detailed tutorial on how to use ``cmake``
-itself, the text mode or graphical user interface, change the generated
-output files for different build tools and development environments is
-on a :doc:`separate page <Howto_cmake>`.
+for building LAMMPS.  A more detailed tutorial on how to use CMake
+itself, the text mode or graphical user interface, to change the
+generated output files for different build tools and development
+environments is on a :doc:`separate page <Howto_cmake>`.
 
 .. note::
 
@@ -22,12 +22,12 @@ on a :doc:`separate page <Howto_cmake>`.
 .. warning::
 
    You must not mix the :doc:`traditional make based <Build_make>`
-   LAMMPS build procedure with using CMake.  Thus no packages may be
+   LAMMPS build procedure with using CMake.  No packages may be
    installed or a build been previously attempted in the LAMMPS source
    directory by using ``make <machine>``.  CMake will detect if this is
    the case and generate an error.  To remove conflicting files from the
    ``src`` you can use the command ``make no-all purge`` which will
-   un-install all packages and delete all auto-generated files.
+   uninstall all packages and delete all auto-generated files.
 
 
 Advantages of using CMake
@@ -44,9 +44,9 @@ software or for people that want to modify or extend LAMMPS.
   and adapt the LAMMPS default build configuration accordingly.
 - CMake can generate files for different build tools and integrated
   development environments (IDE).
-- CMake supports customization of settings with a text mode or graphical
-  user interface. No knowledge of file formats or and complex command
-  line syntax required.
+- CMake supports customization of settings with a command line, text
+  mode, or graphical user interface.  No knowledge of file formats or
+  complex command line syntax is required.
 - All enabled components are compiled in a single build operation.
 - Automated dependency tracking for all files and configuration options.
 - Support for true out-of-source compilation. Multiple configurations
@@ -55,23 +55,23 @@ software or for people that want to modify or extend LAMMPS.
   source tree.
 - Simplified packaging of LAMMPS for Linux distributions, environment
   modules, or automated build tools like `Homebrew <https://brew.sh/>`_.
-- Integration of automated regression testing (the LAMMPS side for that
-  is still under development).
+- Integration of automated unit and regression testing (the LAMMPS side
+  of this is still under active development).
 
 .. _cmake_build:
 
 Getting started
 ^^^^^^^^^^^^^^^
 
-Building LAMMPS with CMake is a two-step process.  First you use CMake
-to generate a build environment in a new directory.  For that purpose
-you can use either the command-line utility ``cmake`` (or ``cmake3``),
-the text-mode UI utility ``ccmake`` (or ``ccmake3``) or the graphical
-utility ``cmake-gui``, or use them interchangeably.  The second step is
-then the compilation and linking of all objects, libraries, and
-executables. Here is a minimal example using the command line version of
-CMake to build LAMMPS with no add-on packages enabled and no
-customization:
+Building LAMMPS with CMake is a two-step process.  In the first step,
+you use CMake to generate a build environment in a new directory.  For
+that purpose you can use either the command-line utility ``cmake`` (or
+``cmake3``), the text-mode UI utility ``ccmake`` (or ``ccmake3``) or the
+graphical utility ``cmake-gui``, or use them interchangeably.  The
+second step is then the compilation and linking of all objects,
+libraries, and executables using the selected build tool.  Here is a
+minimal example using the command line version of CMake to build LAMMPS
+with no add-on packages enabled and no customization:
 
 .. code-block:: bash
 
@@ -96,17 +96,17 @@ Compilation can take a long time, since LAMMPS is a large project with
 many features. If your machine has multiple CPU cores (most do these
 days), you can speed this up by compiling sources in parallel with
 ``make -j N`` (with N being the maximum number of concurrently executed
-tasks).  Also installation of the `ccache <https://ccache.dev/>`_ (=
-Compiler Cache) software may speed up repeated compilation even more,
-e.g. during code development.
+tasks).  Installation of the `ccache <https://ccache.dev/>`_ (= Compiler
+Cache) software may speed up repeated compilation even more, e.g. during
+code development, especially when repeatedly switching between branches.
 
 After the initial build, whenever you edit LAMMPS source files, enable
 or disable packages, change compiler flags or build options, you must
 re-compile and relink the LAMMPS executable with ``cmake --build .`` (or
 ``make``).  If the compilation fails for some reason, try running
 ``cmake .`` and then compile again. The included dependency tracking
-should make certain that only the necessary subset of files are
-re-compiled.  You can also delete compiled objects, libraries and
+should make certain that only the necessary subset of files is
+re-compiled.  You can also delete compiled objects, libraries, and
 executables with ``cmake --build . --target clean`` (or ``make clean``).
 
 After compilation, you may optionally install the LAMMPS executable into
@@ -132,12 +132,12 @@ file called ``CMakeLists.txt`` (for LAMMPS it is located in the
 ``CMakeCache.txt``, which is generated at the end of the CMake
 configuration step.  The cache file contains all current CMake settings.
 
-To modify settings, enable or disable features, you need to set *variables*
-with either the *-D* command line flag (``-D VARIABLE1_NAME=value``) or
-change them in the text mode of graphical user interface.  The *-D* flag
-can be used several times in one command.
+To modify settings, enable or disable features, you need to set
+*variables* with either the *-D* command line flag (``-D
+VARIABLE1_NAME=value``) or change them in the text mode of the graphical
+user interface.  The *-D* flag can be used several times in one command.
 
-For your convenience we provide :ref:`CMake presets <cmake_presets>`
+For your convenience, we provide :ref:`CMake presets <cmake_presets>`
 that combine multiple settings to enable optional LAMMPS packages or use
 a different compiler tool chain.  Those are loaded with the *-C* flag
 (``-C ../cmake/presets/basic.cmake``).  This step would only be needed
@@ -155,22 +155,23 @@ specific CMake version is given when running ``cmake --help``.
 Multi-configuration build systems
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Throughout this manual it is mostly assumed that LAMMPS is being built
+Throughout this manual, it is mostly assumed that LAMMPS is being built
 on a Unix-like operating system with "make" as the underlying "builder",
-since this is the most common case.  In this case the build "configuration"
-is chose using ``-D CMAKE_BUILD_TYPE=<configuration>`` with ``<configuration>``
-being one of "Release", "Debug", "RelWithDebInfo", or "MinSizeRel".
-Some build tools, however, can also use or even require to have a so-called
-multi-configuration build system setup.  For those the built type (or
-configuration) is chosen at compile time using the same build files. E.g.
-with:
+since this is the most common case.  In this case the build
+"configuration" is chose using ``-D CMAKE_BUILD_TYPE=<configuration>``
+with ``<configuration>`` being one of "Release", "Debug",
+"RelWithDebInfo", or "MinSizeRel".  Some build tools, however, can also
+use or even require having a so-called multi-configuration build system
+setup.  For a multi-configuration build, the built type (or
+configuration) is selected at compile time using the same build
+files. E.g.  with:
 
 .. code-block:: bash
 
    cmake --build build-multi --config Release
 
 In that case the resulting binaries are not in the build folder directly
-but in sub-directories corresponding to the build type (i.e. Release in
+but in subdirectories corresponding to the build type (i.e. Release in
 the example from above).  Similarly, for running unit tests the
 configuration is selected with the *-C* flag:
 
@@ -184,7 +185,7 @@ particular applicable to compiling packages that require additional libraries
 that would be downloaded and compiled by CMake.  The "windows" preset file
 tries to keep track of which packages can be compiled natively with the
 MSVC compilers out-of-the box.  Not all of those external libraries are
-portable to Windows either.
+portable to Windows, either.
 
 
 Installing CMake

doc/src/Build_development.rst

@@ -46,7 +46,7 @@ It can be enabled for all C++ code with the following CMake flag
 
 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.
+significantly more time-consuming than the compilation itself.
 
 ----------
 
@@ -154,32 +154,48 @@ for implementing the tests.
    framework are more strict than for the main part of LAMMPS.  For
    example the default GNU C++ and Fortran compilers of RHEL/CentOS 7.x
    (version 4.8.x) are not sufficient.  The CMake configuration will try
-   to detect compatible versions and either skip incompatible tests or
-   stop with an error.
+   to detect incompatible versions and either skip incompatible tests or
+   stop with an error.  Also the number of tests will depend on
+   installed LAMMPS packages, development environment, operating system,
+   and configuration settings.
 
 After compilation is complete, the unit testing is started in the build
 folder using the ``ctest`` command, which is part of the CMake software.
-The output of this command will be looking something like this::
+The output of this command will be looking something like this:
 
-   [...]$ ctest
-   Test project /home/akohlmey/compile/lammps/build-testing
-         Start  1: MolPairStyle:hybrid-overlay
-   1/109 Test  #1: MolPairStyle:hybrid-overlay .........   Passed    0.02 sec
-         Start  2: MolPairStyle:hybrid
-   2/109 Test  #2: MolPairStyle:hybrid .................   Passed    0.01 sec
-         Start  3: MolPairStyle:lj_class2
-    [...]
-         Start 107: PotentialFileReader
- 107/109 Test #107: PotentialFileReader ................   Passed    0.04 sec
-         Start 108: EIMPotentialFileReader
- 108/109 Test #108: EIMPotentialFileReader .............   Passed    0.03 sec
-         Start 109: TestSimpleCommands
- 109/109 Test #109: TestSimpleCommands .................   Passed    0.02 sec
+.. code-block:: console
 
-   100% tests passed, 0 tests failed out of 26
+    $ ctest
+    Test project /home/akohlmey/compile/lammps/build-testing
+         Start   1: RunLammps
+   1/563 Test   #1: RunLammps ..........................................   Passed    0.28 sec
+         Start   2: HelpMessage
+   2/563 Test   #2: HelpMessage ........................................   Passed    0.06 sec
+         Start   3: InvalidFlag
+   3/563 Test   #3: InvalidFlag ........................................   Passed    0.06 sec
+         Start   4: Tokenizer
+   4/563 Test   #4: Tokenizer ..........................................   Passed    0.05 sec
+         Start   5: MemPool
+   5/563 Test   #5: MemPool ............................................   Passed    0.05 sec
+         Start   6: ArgUtils
+   6/563 Test   #6: ArgUtils ...........................................   Passed    0.05 sec
+       [...]
+         Start 561: ImproperStyle:zero
+ 561/563 Test #561: ImproperStyle:zero .................................   Passed    0.07 sec
+         Start 562: TestMliapPyUnified
+ 562/563 Test #562: TestMliapPyUnified .................................   Passed    0.16 sec
+         Start 563: TestPairList
+ 563/563 Test #563: TestPairList .......................................   Passed    0.06 sec
 
-   Total Test time (real) =  25.57 sec
+ 100% tests passed, 0 tests failed out of 563
 
+ Label Time Summary:
+ generated    =   0.85 sec*proc (3 tests)
+ noWindows    =   4.16 sec*proc (2 tests)
+ slow         =  78.33 sec*proc (67 tests)
+ unstable     =  28.23 sec*proc (34 tests)
+
+ Total Test time (real) = 132.34 sec
 
 The ``ctest`` command has many options, the most important ones are:
 
@@ -210,11 +226,13 @@ Fortran) and testing different aspects of the LAMMPS software and its features.
 The tests will adapt to the compilation settings of LAMMPS, so that tests
 will be skipped if prerequisite features are not available in LAMMPS.
 
-.. note::
+.. admonition:: Work in Progress
+   :class: note
 
    The unit test framework was added in spring 2020 and is under active
    development.  The coverage is not complete and will be expanded over
-   time.
+   time.  Preference is given to parts of the code base that are easy to
+   test or commonly used.
 
 Tests for styles of the same kind of style (e.g. pair styles or bond
 styles) are performed with the same test executable using different
@@ -248,9 +266,9 @@ the CMake option ``-D BUILD_MPI=off`` can significantly speed up testing,
 since this will skip the MPI initialization for each test run.
 Below is an example command and output:
 
-.. parsed-literal::
+.. code-block:: console
 
-   [tests]$ test_pair_style mol-pair-lj_cut.yaml
+   $ test_pair_style mol-pair-lj_cut.yaml
    [==========] Running 6 tests from 1 test suite.
    [----------] Global test environment set-up.
    [----------] 6 tests from PairStyle
@@ -505,6 +523,8 @@ The following options are available.
 These should help to make source and documentation files conforming
 to some the coding style preferences of the LAMMPS developers.
 
+.. _clang-format:
+
 Clang-format support
 --------------------
 
@@ -530,7 +550,7 @@ commands like the following:
 
 .. code-block:: bash
 
-   $ clang-format -i some_file.cpp
+   clang-format -i some_file.cpp
 
 
 The following target are available for both, GNU make and CMake:
@@ -539,3 +559,19 @@ The following target are available for both, GNU make and CMake:
 
    make format-src       # apply clang-format to all files in src and the package folders
    make format-tests     # apply clang-format to all files in the unittest tree
+
+----------
+
+.. _gh-cli:
+
+GitHub command line interface
+-----------------------------
+
+GitHub is developing a `tool for the command line
+<https://cli.github.com>`_ that interacts with the GitHub website via a
+command called ``gh``.  This can be extremely convenient when working
+with a Git repository hosted on GitHub (like LAMMPS).  It is thus highly
+recommended to install it when doing LAMMPS development.
+
+The capabilities of the ``gh`` command is continually expanding, so
+please see the documentation at https://cli.github.com/manual/

doc/src/Build_extras.rst

@@ -12,11 +12,11 @@ in addition to
      - Traditional make
    * - .. code-block:: bash
 
-          $ cmake -D PKG_NAME=yes
+          cmake -D PKG_NAME=yes
 
-     - .. code-block:: bash
+     - .. code-block:: console
 
-          $ make yes-name
+          make yes-name
 
 as described on the :doc:`Build_package <Build_package>` page.
 
@@ -28,26 +28,28 @@ You may need to tell LAMMPS where it is found on your system.
 
 This is the list of packages that may require additional steps.
 
+.. this list must be kept in sync with its counterpart in Build_package.rst
 .. table_from_list::
    :columns: 6
 
    * :ref:`ADIOS <adios>`
    * :ref:`ATC <atc>`
    * :ref:`AWPMD <awpmd>`
-   * :ref:`COLVARS <colvars>`
+   * :ref:`COLVARS <colvar>`
    * :ref:`COMPRESS <compress>`
+   * :ref:`ELECTRODE <electrode>`
    * :ref:`GPU <gpu>`
    * :ref:`H5MD <h5md>`
    * :ref:`INTEL <intel>`
    * :ref:`KIM <kim>`
    * :ref:`KOKKOS <kokkos>`
-   * :ref:`LATTE <latte>`
+   * :ref:`LEPTON <lepton>`
    * :ref:`MACHDYN <machdyn>`
    * :ref:`MDI <mdi>`
-   * :ref:`MESONT <mesont>`
    * :ref:`ML-HDNNP <ml-hdnnp>`
    * :ref:`ML-IAP <mliap>`
    * :ref:`ML-PACE <ml-pace>`
+   * :ref:`ML-POD <ml-pod>`
    * :ref:`ML-QUIP <ml-quip>`
    * :ref:`MOLFILE <molfile>`
    * :ref:`MSCG <mscg>`
@@ -123,10 +125,11 @@ CMake build
    -D GPU_API=value             # value = opencl (default) or cuda or hip
    -D GPU_PREC=value            # precision setting
                                 # value = double or mixed (default) or single
-   -D HIP_PATH                  # path to HIP installation. Must be set if GPU_API=HIP
    -D GPU_ARCH=value            # primary GPU hardware choice for GPU_API=cuda
-                                # value = sm_XX, see below
-                                # default is sm_50
+                                # value = sm_XX (see below, default is sm_50)
+   -D GPU_DEBUG=value           # enable debug code in the GPU package library, mostly useful for developers
+                                # value = yes or no (default)
+   -D HIP_PATH=value            # value = path to HIP installation. Must be set if GPU_API=HIP
    -D HIP_ARCH=value            # primary GPU hardware choice for GPU_API=hip
                                 # value depends on selected HIP_PLATFORM
                                 # default is 'gfx906' for HIP_PLATFORM=amd and 'sm_50' for HIP_PLATFORM=nvcc
@@ -137,6 +140,8 @@ CMake build
                                 # value = yes or no (default)
    -D CUDA_MPS_SUPPORT=value    # enables some tweaks required to run with active nvidia-cuda-mps daemon
                                 # value = yes or no (default)
+   -D CUDA_BUILD_MULTIARCH=value  # enables building CUDA kernels for all supported GPU architectures
+                                  # value = yes (default) or no
    -D USE_STATIC_OPENCL_LOADER=value  # downloads/includes OpenCL ICD loader library, no local OpenCL headers/libs needed
                                       # value = yes (default) or no
 
@@ -148,43 +153,56 @@ CMake build
 * sm_60 or sm_61 for Pascal (supported since CUDA 8)
 * sm_70 for Volta (supported since CUDA 9)
 * sm_75 for Turing (supported since CUDA 10)
-* sm_80 for Ampere (supported since CUDA 11)
+* sm_80 or sm_86 for Ampere (supported since CUDA 11, sm_86 since CUDA 11.1)
+* sm_89 for Lovelace (supported since CUDA 11.8)
+* sm_90 for Hopper (supported since CUDA 12.0)
 
 A more detailed list can be found, for example,
 at `Wikipedia's CUDA article <https://en.wikipedia.org/wiki/CUDA#GPUs_supported>`_
 
-CMake can detect which version of the CUDA toolkit is used and thus will try
-to include support for **all** major GPU architectures supported by this toolkit.
-Thus the GPU_ARCH setting is merely an optimization, to have code for
-the preferred GPU architecture directly included rather than having to wait
-for the JIT compiler of the CUDA driver to translate it.
+CMake can detect which version of the CUDA toolkit is used and thus will
+try to include support for **all** major GPU architectures supported by
+this toolkit.  Thus the GPU_ARCH setting is merely an optimization, to
+have code for the preferred GPU architecture directly included rather
+than having to wait for the JIT compiler of the CUDA driver to translate
+it.  This behavior can be turned off (e.g. to speed up compilation) by
+setting :code:`CUDA_ENABLE_MULTIARCH` to :code:`no`.
 
-When compiling for CUDA or HIP with CUDA, version 8.0 or later of the CUDA toolkit
-is required and a GPU architecture of Kepler or later, which must *also* be
-supported by the CUDA toolkit in use **and** the CUDA driver in use.
-When compiling for OpenCL, OpenCL version 1.2 or later is required and the
-GPU must be supported by the GPU driver and OpenCL runtime bundled with the driver.
+When compiling for CUDA or HIP with CUDA, version 8.0 or later of the
+CUDA toolkit is required and a GPU architecture of Kepler or later,
+which must *also* be supported by the CUDA toolkit in use **and** the
+CUDA driver in use.  When compiling for OpenCL, OpenCL version 1.2 or
+later is required and the GPU must be supported by the GPU driver and
+OpenCL runtime bundled with the driver.
 
-When building with CMake, you **must NOT** build the GPU library in ``lib/gpu``
-using the traditional build procedure. CMake will detect files generated by that
-process and will terminate with an error and a suggestion for how to remove them.
+When building with CMake, you **must NOT** build the GPU library in
+``lib/gpu`` using the traditional build procedure. CMake will detect
+files generated by that process and will terminate with an error and a
+suggestion for how to remove them.
 
-If you are compiling for OpenCL, the default setting is to download, build, and
-link with a static OpenCL ICD loader library and standard OpenCL headers.  This
-way no local OpenCL development headers or library needs to be present and only
-OpenCL compatible drivers need to be installed to use OpenCL.  If this is not
-desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
+If you are compiling for OpenCL, the default setting is to download,
+build, and link with a static OpenCL ICD loader library and standard
+OpenCL headers.  This way no local OpenCL development headers or library
+needs to be present and only OpenCL compatible drivers need to be
+installed to use OpenCL.  If this is not desired, you can set
+:code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
 
-If you are compiling with HIP, note that before running CMake you will have to
-set appropriate environment variables. Some variables such as
-:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc`
-and the linker to work correctly.
+The GPU library has some multi-thread support using OpenMP.  If LAMMPS
+is built with ``-D BUILD_OMP=on`` this will also be enabled.
 
-Using CHIP-SPV implementation of HIP is now supported. It allows one to run HIP
-code on Intel GPUs via the OpenCL or Level Zero backends. To use CHIP-SPV, you must
-set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake command line as CHIP-SPV does not
-yet support hipCUB. The use of HIP for Intel GPUs is still experimental so you
-should only use this option in preparations to run on Aurora system at ANL.
+If you are compiling with HIP, note that before running CMake you will
+have to set appropriate environment variables. Some variables such as
+:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are
+necessary for :code:`hipcc` and the linker to work correctly.
+
+.. versionadded:: 3Aug2022
+
+Using the CHIP-SPV implementation of HIP is supported. It allows one to
+run HIP code on Intel GPUs via the OpenCL or Level Zero backends. To use
+CHIP-SPV, you must set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake
+command line as CHIP-SPV does not yet support hipCUB. As of Summer 2022,
+the use of HIP for Intel GPUs is experimental. You should only use this
+option in preparations to run on Aurora system at Argonne.
 
 .. code:: bash
 
@@ -239,10 +257,10 @@ script with the specified args:
 
 .. code-block:: bash
 
-  $ make lib-gpu               # print help message
-  $ make lib-gpu args="-b"     # build GPU library with default Makefile.linux
-  $ make lib-gpu args="-m xk7 -p single -o xk7.single"  # create new Makefile.xk7.single, altered for single-precision
-  $ make lib-gpu args="-m mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi
+  make lib-gpu               # print help message
+  make lib-gpu args="-b"     # build GPU library with default Makefile.linux
+  make lib-gpu args="-m xk7 -p single -o xk7.single"  # create new Makefile.xk7.single, altered for single-precision
+  make lib-gpu args="-m mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi
 
 Note that this procedure starts with a Makefile.machine in lib/gpu, as
 specified by the "-m" switch.  For your convenience, machine makefiles
@@ -268,10 +286,13 @@ To enable GPU binning via CUDA performance primitives set the Makefile variable
 most modern GPUs.
 
 To support the CUDA multiprocessor server you can set the define
-``-DCUDA_PROXY``.  Please note that in this case you must **not** use
+``-DCUDA_MPS_SUPPORT``.  Please note that in this case you must **not** use
 the CUDA performance primitives and thus set the variable ``CUDPP_OPT``
 to empty.
 
+The GPU library has some multi-thread support using OpenMP.  You need to add
+the compiler flag that enables OpenMP to the ``CUDR_OPTS`` Makefile variable.
+
 If the library build is successful, 3 files should be created:
 ``lib/gpu/libgpu.a``\ , ``lib/gpu/nvc_get_devices``\ , and
 ``lib/gpu/Makefile.lammps``\ .  The latter has settings that enable LAMMPS
@@ -282,7 +303,7 @@ your machine are not correct, the LAMMPS build will fail, and
 .. note::
 
    If you re-build the GPU library in ``lib/gpu``, you should always
-   un-install the GPU package in ``lammps/src``, then re-install it and
+   uninstall the GPU package in ``lammps/src``, then re-install it and
    re-build LAMMPS.  This is because the compilation of files in the GPU
    package uses the library settings from the ``lib/gpu/Makefile.machine``
    used to build the GPU library.
@@ -355,13 +376,13 @@ minutes to hours) to build.  Of course you only need to do that once.)
 
       .. code-block:: bash
 
-         $ make lib-kim              # print help message
-         $ make lib-kim args="-b "   # (re-)install KIM API lib with only example models
-         $ make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001"  # ditto plus one model
-         $ make lib-kim args="-b -a everything"     # install KIM API lib with all models
-         $ make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002"       # add one model or model driver
-         $ make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
-         $ make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver
+         make lib-kim              # print help message
+         make lib-kim args="-b "   # (re-)install KIM API lib with only example models
+         make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001"  # ditto plus one model
+         make lib-kim args="-b -a everything"     # install KIM API lib with all models
+         make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002"       # add one model or model driver
+         make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
+         make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver
 
       When using the "-b " option, the KIM library is built using its native
       cmake build system.  The ``lib/kim/Install.py`` script supports a
@@ -373,7 +394,7 @@ minutes to hours) to build.  Of course you only need to do that once.)
 
       .. code-block:: bash
 
-         $ CMAKE=cmake3 CXX=g++-11 CC=gcc-11 FC=gfortran-11 make lib-kim args="-b "  # (re-)install KIM API lib using cmake3 and gnu v11 compilers with only example models
+         CMAKE=cmake3 CXX=g++-11 CC=gcc-11 FC=gfortran-11 make lib-kim args="-b "  # (re-)install KIM API lib using cmake3 and gnu v11 compilers with only example models
 
       Settings for debugging OpenKIM web queries discussed below need to
       be applied by adding them to the ``LMP_INC`` variable through
@@ -600,6 +621,12 @@ They must be specified in uppercase.
    *  - AMPERE86
       - GPU
       - NVIDIA Ampere generation CC 8.6 GPU
+   *  - ADA89
+      - GPU
+      - NVIDIA Ada Lovelace generation CC 8.9 GPU
+   *  - HOPPER90
+      - GPU
+      - NVIDIA Hopper generation CC 9.0 GPU
    *  - VEGA900
       - GPU
       - AMD GPU MI25 GFX900
@@ -634,7 +661,7 @@ They must be specified in uppercase.
       - GPU
       - Intel GPU Ponte Vecchio
 
-This list was last updated for version 3.7.0 of the Kokkos library.
+This list was last updated for version 3.7.1 of the Kokkos library.
 
 .. tabs::
 
@@ -666,20 +693,11 @@ This list was last updated for version 3.7.0 of the Kokkos library.
          -D Kokkos_ARCH_GPUARCH=yes    # GPUARCH = GPU from list above
          -D Kokkos_ENABLE_CUDA=yes
          -D Kokkos_ENABLE_OPENMP=yes
-         -D CMAKE_CXX_COMPILER=wrapper # wrapper = full path to Cuda nvcc wrapper
 
       This will also enable executing FFTs on the GPU, either via the
       internal KISSFFT library, or - by preference - with the cuFFT
       library bundled with the CUDA toolkit, depending on whether CMake
-      can identify its location.  The *wrapper* value for
-      ``CMAKE_CXX_COMPILER`` variable is the path to the CUDA nvcc
-      compiler wrapper provided in the Kokkos library:
-      ``lib/kokkos/bin/nvcc_wrapper``\ .  The setting should include the
-      full path name to the wrapper, e.g.
-
-      .. code-block:: bash
-
-         -D CMAKE_CXX_COMPILER=${HOME}/lammps/lib/kokkos/bin/nvcc_wrapper
+      can identify its location.
 
       For AMD or NVIDIA GPUs using HIP, set these variables:
 
@@ -814,60 +832,52 @@ will thus always enable it.
 
 ----------
 
-.. _latte:
+.. _lepton:
 
-LATTE package
--------------------------
+LEPTON package
+--------------
 
-To build with this package, you must download and build the LATTE
-library.
+To build with this package, you must build the Lepton library which is
+included in the LAMMPS source distribution in the ``lib/lepton`` folder.
 
 .. tabs::
 
    .. tab:: CMake build
 
-      .. code-block:: bash
+      This is the recommended build procedure for using Lepton in
+      LAMMPS. No additional settings are normally needed besides
+      ``-D PKG_LEPTON=yes``.
 
-         -D DOWNLOAD_LATTE=value      # download LATTE for build, value = no (default) or yes
-         -D LATTE_LIBRARY=path        # LATTE library file (only needed if a custom location)
-         -D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
-                                      #   value = no (default) or yes
-
-      If ``DOWNLOAD_LATTE`` is set, the LATTE library will be downloaded
-      and built inside the CMake build directory.  If the LATTE library
-      is already on your system (in a location CMake cannot find it),
-      ``LATTE_LIBRARY`` is the filename (plus path) of the LATTE library
-      file, not the directory the library file is in.
-
-      The LATTE library requires LAPACK (and BLAS) and CMake can identify
-      their locations and pass that info to the LATTE build script. But
-      on some systems this triggers a (current) limitation of CMake and
-      the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
-      those cases to use the bundled linear algebra library and work around
-      the limitation.
+      On x86 hardware the Lepton library will also include a just-in-time
+      compiler for faster execution.  This is auto detected but can
+      be explicitly disabled by setting ``-D LEPTON_ENABLE_JIT=no``
+      (or enabled by setting it to yes).
 
    .. tab:: Traditional make
 
-      You can download and build the LATTE library manually if you
-      prefer; follow the instructions in ``lib/latte/README``\ .  You
-      can also do it in one step from the ``lammps/src`` dir, using a
-      command like these, which simply invokes the
-      ``lib/latte/Install.py`` script with the specified args:
+      Before building LAMMPS, one must build the Lepton library in lib/lepton.
+
+      This can be done manually in the same folder by using or adapting
+      one of the provided Makefiles: for example, ``Makefile.serial`` for
+      the GNU C++ compiler, or ``Makefile.mpi`` for the MPI compiler wrapper.
+      The Lepton library is written in C++-11 and thus the C++ compiler
+      may need to be instructed to enable support for that.
+
+      In general, it is safer to use build setting consistent with the
+      rest of LAMMPS.  This is best carried out from the LAMMPS src
+      directory using a command like these, which simply invokes the
+      ``lib/lepton/Install.py`` script with the specified args:
 
       .. code-block:: bash
 
-         $ make lib-latte                          # print help message
-         $ make lib-latte args="-b"                # download and build in lib/latte/LATTE-master
-         $ make lib-latte args="-p $HOME/latte"    # use existing LATTE installation in $HOME/latte
-         $ make lib-latte args="-b -m gfortran"    # download and build in lib/latte and
-                                                   #   copy Makefile.lammps.gfortran to Makefile.lammps
+         make lib-lepton                      # print help message
+         make lib-lepton args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")
+         make lib-lepton args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
 
-      Note that 3 symbolic (soft) links, ``includelink`` and ``liblink``
-      and ``filelink.o``, are created in ``lib/latte`` to point to
-      required folders and files in the LATTE home directory.  When
-      LAMMPS itself is built it will use these links.  You should also
-      check that the ``Makefile.lammps`` file you create is appropriate
-      for the compiler you use on your system to build LATTE.
+      The "machine" argument of the "-m" flag is used to find a
+      Makefile.machine to use as build recipe.
+
+      The build should produce a ``build`` folder and the library ``lib/lepton/liblmplepton.a``
 
 ----------
 
@@ -959,12 +969,12 @@ more details.
 
       .. code-block:: bash
 
-         $ make lib-mscg             # print help message
-         $ make lib-mscg args="-b -m serial"   # download and build in lib/mscg/MSCG-release-master
-                                               # with the settings compatible with "make serial"
-         $ make lib-mscg args="-b -m mpi"      # download and build in lib/mscg/MSCG-release-master
-                                               # with the settings compatible with "make mpi"
-         $ make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release
+         make lib-mscg             # print help message
+         make lib-mscg args="-b -m serial"   # download and build in lib/mscg/MSCG-release-master
+                                             # with the settings compatible with "make serial"
+         make lib-mscg args="-b -m mpi"      # download and build in lib/mscg/MSCG-release-master
+                                             # with the settings compatible with "make mpi"
+         make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release
 
       Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``,
       will be created in ``lib/mscg`` to point to the MS-CG
@@ -1016,10 +1026,10 @@ POEMS package
 
       .. code-block:: bash
 
-         $ make lib-poems                   # print help message
-         $ make lib-poems args="-m serial"  # build with GNU g++ compiler (settings as with "make serial")
-         $ make lib-poems args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
-         $ make lib-poems args="-m icc"     # build with Intel icc compiler
+         make lib-poems                   # print help message
+         make lib-poems args="-m serial"  # build with GNU g++ compiler (settings as with "make serial")
+         make lib-poems args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
+         make lib-poems args="-m icc"     # build with Intel icc compiler
 
       The build should produce two files: ``lib/poems/libpoems.a`` and
       ``lib/poems/Makefile.lammps``.  The latter is copied from an
@@ -1074,7 +1084,7 @@ VORONOI package
 -----------------------------
 
 To build with this package, you must download and build the
-`Voro++ library <https://math.lbl.gov/voro++>`_ or install a
+`Voro++ library <https://math.lbl.gov/voro++/>`_ or install a
 binary package provided by your operating system.
 
 .. tabs::
@@ -1105,10 +1115,10 @@ binary package provided by your operating system.
 
       .. code-block:: bash
 
-         $ make lib-voronoi                          # print help message
-         $ make lib-voronoi args="-b"                # download and build the default version in lib/voronoi/voro++-<version>
-         $ make lib-voronoi args="-p $HOME/voro++"   # use existing Voro++ installation in $HOME/voro++
-         $ make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6
+         make lib-voronoi                          # print help message
+         make lib-voronoi args="-b"                # download and build the default version in lib/voronoi/voro++-<version>
+         make lib-voronoi args="-p $HOME/voro++"   # use existing Voro++ installation in $HOME/voro++
+         make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6
 
       Note that 2 symbolic (soft) links, ``includelink`` and
       ``liblink``, are created in lib/voronoi to point to the Voro++
@@ -1149,13 +1159,13 @@ systems.
 
       .. code-block:: bash
 
-         $ make yes-adios
+         make yes-adios
 
       otherwise, set ADIOS2_DIR environment variable when turning on the package:
 
       .. code-block:: bash
 
-         $ ADIOS2_DIR=path make yes-adios   # path is where ADIOS 2.x is installed
+         ADIOS2_DIR=path make yes-adios   # path is where ADIOS 2.x is installed
 
 ----------
 
@@ -1184,10 +1194,10 @@ The ATC package requires the MANYBODY package also be installed.
 
       .. code-block:: bash
 
-         $ make lib-atc                      # print help message
-         $ make lib-atc args="-m serial"     # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-         $ make lib-atc args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
-         $ make lib-atc args="-m icc"        # build with Intel icc compiler
+         make lib-atc                      # print help message
+         make lib-atc args="-m serial"     # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+         make lib-atc args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
+         make lib-atc args="-m icc"        # build with Intel icc compiler
 
       The build should produce two files: ``lib/atc/libatc.a`` and
       ``lib/atc/Makefile.lammps``.  The latter is copied from an
@@ -1206,17 +1216,17 @@ The ATC package requires the MANYBODY package also be installed.
 
       .. code-block:: bash
 
-         $ make lib-linalg                     # print help message
-         $ make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
-         $ make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
-         $ make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler
+         make lib-linalg                   # print help message
+         make lib-linalg args="-m serial"  # build with GNU C++ compiler (settings as with "make serial")
+         make lib-linalg args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
+         make lib-linalg args="-m g++"     # build with GNU Fortran compiler
 
 ----------
 
 .. _awpmd:
 
 AWPMD package
-------------------
+-------------
 
 .. tabs::
 
@@ -1235,10 +1245,10 @@ AWPMD package
 
       .. code-block:: bash
 
-         $ make lib-awpmd                   # print help message
-         $ make lib-awpmd args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-         $ make lib-awpmd args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
-         $ make lib-awpmd args="-m icc"     # build with Intel icc compiler
+         make lib-awpmd                   # print help message
+         make lib-awpmd args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+         make lib-awpmd args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
+         make lib-awpmd args="-m icc"     # build with Intel icc compiler
 
       The build should produce two files: ``lib/awpmd/libawpmd.a`` and
       ``lib/awpmd/Makefile.lammps``.  The latter is copied from an
@@ -1257,21 +1267,20 @@ AWPMD package
 
       .. code-block:: bash
 
-         $ make lib-linalg                     # print help message
-         $ make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
-         $ make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
-         $ make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler
+         make lib-linalg                   # print help message
+         make lib-linalg args="-m serial"  # build with GNU C++ compiler (settings as with "make serial")
+         make lib-linalg args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
+         make lib-linalg args="-m g++"     # build with GNU C++ compiler
 
 ----------
 
-.. _colvars:
+.. _colvar:
 
 COLVARS package
----------------------------------------
+---------------
 
-This package includes the `Colvars library
-<https://colvars.github.io/>`_ into the LAMMPS distribution, which can
-be built for the most part with all major versions of the C++ language.
+This package enables the use of the `Colvars <https://colvars.github.io/>`_
+module included in the LAMMPS source distribution.
 
 
 .. tabs::
@@ -1284,42 +1293,45 @@ be built for the most part with all major versions of the C++ language.
 
    .. tab:: Traditional make
 
-      Before building LAMMPS, one must build the Colvars library in lib/colvars.
+      As with other libraries distributed with LAMMPS, the Colvars library
+      needs to be built before building the LAMMPS program with the COLVARS
+      package enabled.
 
-      This can be done manually in the same folder by using or adapting
-      one of the provided Makefiles: for example, ``Makefile.g++`` for
-      the GNU C++ compiler.  C++11 compatibility may need to be enabled
-      for some older compilers (as is done in the example makefile).
-
-      In general, it is safer to use build setting consistent with the
-      rest of LAMMPS.  This is best carried out from the LAMMPS src
-      directory using a command like these, which simply invokes the
-      ``lib/colvars/Install.py`` script with the specified args:
+      From the LAMMPS ``src`` directory, this is most easily and safely done
+      via one of the following commands, which implicitly rely on the
+      ``lib/colvars/Install.py`` script with optional arguments:
 
       .. code-block:: bash
 
-         $ make lib-colvars                      # print help message
-         $ make lib-colvars args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")
-         $ make lib-colvars args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
-         $ make lib-colvars args="-m g++-debug"  # build with GNU g++ compiler and colvars debugging enabled
+         make lib-colvars                      # print help message
+         make lib-colvars args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")
+         make lib-colvars args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
+         make lib-colvars args="-m g++-debug"  # build with GNU g++ compiler and colvars debugging enabled
 
       The "machine" argument of the "-m" flag is used to find a
-      Makefile.machine to use as build recipe.  If it does not already
-      exist in ``lib/colvars``, it will be auto-generated by using
-      compiler flags consistent with those parsed from the core LAMMPS
-      makefiles.
+      ``Makefile.machine`` file to use as build recipe.  If such recipe does
+      not already exist in ``lib/colvars``, suitable settings will be
+      auto-generated consistent with those used in the core LAMMPS makefiles.
+
+
+      .. versionchanged:: 8Feb2023
+
+      Please note that Colvars uses the Lepton library, which is now
+      included with the LEPTON package; if you use anything other than
+      the ``make lib-colvars`` command, please make sure to :ref:`build
+      Lepton beforehand <lepton>`.
 
       Optional flags may be specified as environment variables:
 
       .. code-block:: bash
 
-         $ COLVARS_DEBUG=yes make lib-colvars args="-m machine"  # Build with debug code (much slower)
-         $ COLVARS_LEPTON=no make lib-colvars args="-m machine"  # Build without Lepton (included otherwise)
+         COLVARS_DEBUG=yes make lib-colvars args="-m machine"  # Build with debug code (much slower)
+         COLVARS_LEPTON=no make lib-colvars args="-m machine"  # Build without Lepton (included otherwise)
 
-      The build should produce two files: the library ``lib/colvars/libcolvars.a``
-      (which also includes Lepton objects if enabled) and the specification file
-      ``lib/colvars/Makefile.lammps``.  The latter is auto-generated, and normally does
-      not need to be edited.
+      The build should produce two files: the library
+      ``lib/colvars/libcolvars.a`` and the specification file
+      ``lib/colvars/Makefile.lammps``.  The latter is auto-generated,
+      and normally does not need to be edited.
 
 ----------
 
@@ -1334,8 +1346,21 @@ This package depends on the KSPACE package.
 
    .. tab:: CMake build
 
-      No additional settings are needed besides ``-D PKG_KSPACE=yes`` and
-      ``-D PKG_ELECTRODE=yes``.
+      .. code-block:: bash
+
+         -D PKG_ELECTRODE=yes          # enable the package itself
+         -D PKG_KSPACE=yes             # the ELECTRODE package requires KSPACE
+         -D USE_INTERNAL_LINALG=value  #
+
+      Features in the ELECTRODE package are dependent on code in the
+      KSPACE package so the latter one *must* be enabled.
+
+      The ELECTRODE package also requires LAPACK (and BLAS) and CMake
+      can identify their locations and pass that info to the ELECTRODE
+      build script.  But on some systems this may cause problems when
+      linking or the dependency is not desired.  Try enabling
+      ``USE_INTERNAL_LINALG`` in those cases to use the bundled linear
+      algebra library and work around the limitation.
 
    .. tab:: Traditional make
 
@@ -1348,9 +1373,9 @@ This package depends on the KSPACE package.
 
       .. code-block:: bash
 
-         $ make lib-electrode                   # print help message
-         $ make lib-electrode args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-         $ make lib-electrode args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
+         make lib-electrode                   # print help message
+         make lib-electrode args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+         make lib-electrode args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
 
 
       Note that the ``Makefile.lammps`` file has settings for the BLAS
@@ -1361,10 +1386,10 @@ This package depends on the KSPACE package.
 
       .. code-block:: bash
 
-         $ make lib-linalg                     # print help message
-         $ make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
-         $ make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
-         $ make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler
+         make lib-linalg                   # print help message
+         make lib-linalg args="-m serial"  # build with GNU C++ compiler (settings as with "make serial")
+         make lib-linalg args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
+         make lib-linalg args="-m g++"     # build with GNU C++ compiler
 
       The package itself is activated with ``make yes-KSPACE`` and
       ``make yes-ELECTRODE``
@@ -1404,13 +1429,56 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
 
       .. code-block:: bash
 
-         $ make lib-pace                          # print help message
-         $ make lib-pace args="-b"                # download and build the default version in lib/pace
+         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.
 
 ----------
 
+.. _ml-pod:
+
+ML-POD package
+-----------------------------
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      No additional settings are needed besides ``-D PKG_ML-POD=yes``.
+
+   .. tab:: Traditional make
+
+      Before building LAMMPS, you must configure the ML-POD support
+      settings in ``lib/mlpod``.  You can do this manually, if you
+      prefer, or do it in one step from the ``lammps/src`` dir, using a
+      command like the following, which simply invoke the
+      ``lib/mlpod/Install.py`` script with the specified args:
+
+      .. code-block:: bash
+
+         make lib-mlpod                   # print help message
+         make lib-mlpod args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+         make lib-mlpod args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
+         make lib-mlpod args="-m mpi -e linalg"   # same as above but use the bundled linalg lib
+
+      Note that the ``Makefile.lammps`` file has settings to use the BLAS
+      and LAPACK linear algebra libraries.  These can either exist on
+      your system, or you can use the files provided in ``lib/linalg``.
+      In the latter case you also need to build the library in
+      ``lib/linalg`` with a command like these:
+
+      .. code-block:: bash
+
+         make lib-linalg                   # print help message
+         make lib-linalg args="-m serial"  # build with GNU C++ compiler (settings as with "make serial")
+         make lib-linalg args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
+         make lib-linalg args="-m g++"     # build with GNU C++ compiler
+
+      The package itself is activated with ``make yes-ML-POD``.
+
+----------
+
 .. _plumed:
 
 PLUMED package
@@ -1504,10 +1572,10 @@ LAMMPS build.
 
       .. code-block:: bash
 
-         $ make lib-plumed                         # print help message
-         $ make lib-plumed args="-b"               # download and build PLUMED in lib/plumed/plumed2
-         $ make lib-plumed args="-p $HOME/.local"  # use existing PLUMED installation in $HOME/.local
-         $ make lib-plumed args="-p /usr/local -m shared"  # use existing PLUMED installation in
+         make lib-plumed                         # print help message
+         make lib-plumed args="-b"               # download and build PLUMED in lib/plumed/plumed2
+         make lib-plumed args="-p $HOME/.local"  # use existing PLUMED installation in $HOME/.local
+         make lib-plumed args="-p /usr/local -m shared"  # use existing PLUMED installation in
                                                            # /usr/local and use shared linkage mode
 
       Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``
@@ -1520,8 +1588,8 @@ LAMMPS build.
 
       .. code-block:: bash
 
-         $ make yes-plumed
-         $ make machine
+         make yes-plumed
+         make machine
 
       Once this compilation completes you should be able to run LAMMPS
       in the usual way.  For shared linkage mode, libplumed.so must be
@@ -1573,8 +1641,8 @@ the HDF5 library.
 
       .. code-block:: bash
 
-         $ make lib-h5md                     # print help message
-         $ make lib-h5md args="-m h5cc"      # build with h5cc compiler
+         make lib-h5md                     # print help message
+         make lib-h5md args="-m h5cc"      # build with h5cc compiler
 
       The build should produce two files: ``lib/h5md/libch5md.a`` and
       ``lib/h5md/Makefile.lammps``.  The latter is copied from an
@@ -1628,10 +1696,10 @@ details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
 
       .. 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
+         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
@@ -1731,56 +1799,14 @@ MDI package
 
       .. code-block:: bash
 
-         $ python Install.py -m gcc       # build using gcc compiler
-         $ python Install.py -m icc       # build using icc compiler
+         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``\ .
 
 ----------
 
-.. _mesont:
-
-MESONT package
--------------------------
-
-This package includes a library written in Fortran 90 in the
-``lib/mesont`` folder, so a working Fortran 90 compiler is required to
-compile it.  Also, the files with the force field data for running the
-bundled examples are not included in the source distribution. Instead
-they will be downloaded the first time this package is installed.
-
-.. tabs::
-
-   .. tab:: CMake build
-
-      No additional settings are needed besides ``-D PKG_MESONT=yes``
-
-   .. tab:: Traditional make
-
-      Before building LAMMPS, you must build the *mesont* library in
-      ``lib/mesont``\ .  You can also do it in one step from the
-      ``lammps/src`` dir, using a command like these, which simply
-      invokes the ``lib/mesont/Install.py`` script with the specified
-      args:
-
-      .. code-block:: bash
-
-         $ make lib-mesont                    # print help message
-         $ make lib-mesont args="-m gfortran" # build with GNU g++ compiler (settings as with "make serial")
-         $ make lib-mesont args="-m ifort"    # build with Intel icc compiler
-
-      The build should produce two files: ``lib/mesont/libmesont.a`` and
-      ``lib/mesont/Makefile.lammps``\ .  The latter is copied from an
-      existing ``Makefile.lammps.\*`` and has settings needed to build
-      LAMMPS with the *mesont* library (though typically the settings
-      contain only the Fortran runtime library).  If necessary, you can
-      edit/create a new ``lib/mesont/Makefile.machine`` file for your
-      system, which should define an ``EXTRAMAKE`` variable to specify a
-      corresponding ``Makefile.lammps.machine`` file.
-
-----------
-
 .. _molfile:
 
 MOLFILE package
@@ -1881,6 +1907,22 @@ OPENMP package
       For other platforms and compilers, please consult the
       documentation about OpenMP support for your compiler.
 
+.. admonition:: Adding OpenMP support on macOS
+   :class: note
+
+   Apple offers the `Xcode package and IDE
+   <https://developer.apple.com/xcode/>`_ for compiling software on
+   macOS, so you have likely installed it to compile LAMMPS.  Their
+   compiler is based on `Clang <https://clang.llvm.org/>`_, but while it
+   is capable of processing OpenMP directives, the necessary header
+   files and OpenMP runtime library are missing.  The `R developers
+   <https://www.r-project.org/>`_ have figured out a way to build those
+   in a compatible fashion. One can download them from
+   `https://mac.r-project.org/openmp/
+   <https://mac.r-project.org/openmp/>`_.  Simply adding those files as
+   instructed enables the Xcode C++ compiler to compile LAMMPS with ``-D
+   BUILD_OMP=yes``.
+
 ----------
 
 .. _qmmm:
@@ -1935,10 +1977,10 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
 
       .. code-block:: bash
 
-         $ make lib-qmmm                      # print help message
-         $ make lib-qmmm args="-m serial"     # build with GNU Fortran compiler (settings as in "make serial")
-         $ make lib-qmmm args="-m mpi"        # build with default MPI compiler (settings as in "make mpi")
-         $ make lib-qmmm args="-m gfortran"   # build with GNU Fortran compiler
+         make lib-qmmm                      # print help message
+         make lib-qmmm args="-m serial"     # build with GNU Fortran compiler (settings as in "make serial")
+         make lib-qmmm args="-m mpi"        # build with default MPI compiler (settings as in "make mpi")
+         make lib-qmmm args="-m gfortran"   # build with GNU Fortran compiler
 
       The build should produce two files: ``lib/qmmm/libqmmm.a`` and
       ``lib/qmmm/Makefile.lammps``.  The latter is copied from an
@@ -2087,9 +2129,9 @@ Eigen3 is a template library, so you do not need to build it.
 
       .. code-block:: bash
 
-         $ make lib-smd                         # print help message
-         $ make lib-smd args="-b"               # download to lib/smd/eigen3
-         $ make lib-smd args="-p /usr/include/eigen3"    # use existing Eigen installation in /usr/include/eigen3
+         make lib-smd                         # print help message
+         make lib-smd args="-b"               # download to lib/smd/eigen3
+         make lib-smd args="-p /usr/include/eigen3"    # use existing Eigen installation in /usr/include/eigen3
 
       Note that a symbolic (soft) link named ``includelink`` is created
       in ``lib/smd`` to point to the Eigen dir.  When LAMMPS builds it

doc/src/Build_link.rst

@@ -1,33 +1,32 @@
 Link LAMMPS as a library to another code
 ========================================
 
-LAMMPS is designed as a library of C++ objects that can be
-integrated into other applications including Python scripts.
-The files ``src/library.cpp`` and ``src/library.h`` define a
-C-style API for using LAMMPS as a library.  See the
-:doc:`Howto_library` page
-for a description of the interface and how to use it for your needs.
+LAMMPS is designed as a library of C++ objects that can be integrated
+into other applications, including Python scripts.  The files
+``src/library.cpp`` and ``src/library.h`` define a C-style API for using
+LAMMPS as a library.  See the :doc:`Howto_library` page for a
+description of the interface and how to use it for your needs.
 
-The :doc:`Build_basics` page explains how to build
-LAMMPS as either a shared or static library.  This results in a file
-in the compilation folder called ``liblammps.a`` or ``liblammps_<name>.a``
-in case of building a static library.  In case of a shared library
-the name is the same only that the suffix is going to be either ``.so``
-or ``.dylib`` or ``.dll`` instead of ``.a`` depending on the OS.
-In some cases the ``.so`` file may be a symbolic link to a file with
-the suffix ``.so.0`` (or some other number).
+The :doc:`Build_basics` page explains how to build LAMMPS as either a
+shared or static library.  This results in a file in the compilation
+folder called ``liblammps.a`` or ``liblammps_<name>.a`` in case of
+building a static library.  In case of a shared library, the name is the
+same only that the suffix is going to be either ``.so`` or ``.dylib`` or
+``.dll`` instead of ``.a`` depending on the OS.  In some cases, the
+``.so`` file may be a symbolic link to a file with the suffix ``.so.0``
+(or some other number).
 
 .. note::
 
    Care should be taken to use the same MPI library for the calling code
-   and the LAMMPS library unless LAMMPS is to be compiled without (real)
-   MPI support using the include STUBS MPI library.
+   and the LAMMPS library, unless LAMMPS is to be compiled without (real)
+   MPI support using the included STUBS MPI library.
 
 Link with LAMMPS as a static library
 ------------------------------------
 
 The calling application can link to LAMMPS as a static library with
-compilation and link commands as in the examples shown below.  These
+compilation and link commands, as in the examples shown below.  These
 are examples for a code written in C in the file ``caller.c``.
 The benefit of linking to a static library is, that the resulting
 executable is independent of that library since all required
@@ -142,10 +141,10 @@ Link with LAMMPS as a shared library
 When linking to LAMMPS built as a shared library, the situation becomes
 much simpler, as all dependent libraries and objects are either included
 in the shared library or registered as a dependent library in the shared
-library file.  Thus those libraries need not to be specified when
-linking the calling executable.  Only the *-I* flags are needed.  So the
-example case from above of the serial version static LAMMPS library with
-the POEMS package installed becomes:
+library file.  Thus, those libraries need not be specified when linking
+the calling executable.  Only the *-I* flags are needed.  So the example
+case from above of the serial version static LAMMPS library with the
+POEMS package installed becomes:
 
 .. tabs::
 
@@ -209,7 +208,7 @@ You can verify whether all required shared libraries are found with the
 
 .. code-block:: bash
 
-   $ LD_LIBRARY_PATH=/home/user/lammps/src ldd caller
+   LD_LIBRARY_PATH=/home/user/lammps/src ldd caller
         linux-vdso.so.1 (0x00007ffe729e0000)
         liblammps.so => /home/user/lammps/src/liblammps.so (0x00007fc91bb9e000)
         libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fc91b984000)
@@ -222,7 +221,7 @@ If a required library is missing, you would get a 'not found' entry:
 
 .. code-block:: bash
 
-   $  ldd caller
+   ldd caller
         linux-vdso.so.1 (0x00007ffd672fe000)
         liblammps.so => not found
         libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fb7c7e86000)

doc/src/Build_make.rst

@@ -20,21 +20,22 @@ with :doc:`CMake <Build_cmake>`.  The makefiles of the traditional
 make based build process and the scripts they are calling expect a few
 additional tools to be available and functioning.
 
-  * a working C/C++ compiler toolchain supporting the C++11 standard; on
-    Linux these are often the GNU compilers. Some older compilers
+  * A working C/C++ compiler toolchain supporting the C++11 standard; on
+    Linux, these are often the GNU compilers. Some older compiler versions
     require adding flags like ``-std=c++11`` to enable the C++11 mode.
-  * a Bourne shell compatible "Unix" shell program (often this is ``bash``)
-  * a few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname``
-  * python (optional, required for ``make lib-<pkg>`` in the src folder).
-    python scripts are currently tested with python 2.7 and 3.6. The procedure
-    for :doc:`building the documentation <Build_manual>` requires python 3.5 or later.
+  * A Bourne shell compatible "Unix" shell program (frequently this is ``bash``)
+  * A few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname``
+  * Python (optional, required for ``make lib-<pkg>`` in the src
+    folder).  Python scripts are currently tested with python 2.7 and
+    3.6 to 3.11. The procedure for :doc:`building the documentation
+    <Build_manual>` *requires* Python 3.5 or later.
 
 Getting started
 ^^^^^^^^^^^^^^^
 
 To include LAMMPS packages (i.e. optional commands and styles) you must
 enable (or "install") them first, as discussed on the :doc:`Build
-package <Build_package>` page.  If a packages requires (provided or
+package <Build_package>` page.  If a package requires (provided or
 external) libraries, you must configure and build those libraries
 **before** building LAMMPS itself and especially **before** enabling
 such a package with ``make yes-<package>``.  :doc:`Building LAMMPS with
@@ -56,36 +57,36 @@ Compilation can take a long time, since LAMMPS is a large project with
 many features. If your machine has multiple CPU cores (most do these
 days), you can speed this up by compiling sources in parallel with
 ``make -j N`` (with N being the maximum number of concurrently executed
-tasks).  Also installation of the `ccache <https://ccache.dev/>`_ (=
-Compiler Cache) software may speed up repeated compilation even more,
-e.g. during code development.
+tasks).  Installation of the `ccache <https://ccache.dev/>`_ (= Compiler
+Cache) software may speed up repeated compilation even more, e.g. during
+code development, especially when repeatedly switching between branches.
 
 After the initial build, whenever you edit LAMMPS source files, or add
 or remove new files to the source directory (e.g. by installing or
 uninstalling packages), you must re-compile and relink the LAMMPS
 executable with the same ``make <machine>`` command.  The makefile's
-dependency tracking should insure that only the necessary subset of
-files are re-compiled.  If you change settings in the makefile, you have
-to recompile *everything*.  To delete all objects you can use ``make
+dependency tracking should ensure that only the necessary subset of
+files is re-compiled.  If you change settings in the makefile, you have
+to recompile *everything*.  To delete all objects, you can use ``make
 clean-<machine>``.
 
 .. note::
 
    Before the actual compilation starts, LAMMPS will perform several
-   steps to collect information from the configuration and setup that
-   is then embedded into the executable.  When you build LAMMPS for
-   the first time, it will also compile a tool to quickly assemble
-   a list of dependencies, that are required for the make program to
-   correctly detect which parts need to be recompiled after changes
-   were made to the sources.
+   steps to collect information from the configuration and setup that is
+   then embedded into the executable.  When you build LAMMPS for the
+   first time, it will also compile a tool to quickly determine a list
+   of dependencies.  Those are required for the make program to
+   correctly detect, which files need to be recompiled or relinked
+   after changes were made to the sources.
 
 Customized builds and alternate makefiles
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The ``src/MAKE`` directory tree contains the ``Makefile.<machine>``
 files included in the LAMMPS distribution.  Typing ``make example`` uses
-``Makefile.example`` from one of those folders, if available.  Thus the
-``make serial`` and ``make mpi`` lines above use
+``Makefile.example`` from one of those folders, if available.  The
+``make serial`` and ``make mpi`` lines above, for example, use
 ``src/MAKE/Makefile.serial`` and ``src/MAKE/Makefile.mpi``,
 respectively.  Other makefiles are in these directories:
 
@@ -106,17 +107,18 @@ a new name, please edit the first line with the description and machine
 name, so you will not confuse yourself, when looking at the machine
 summary.
 
-Makefiles you may wish to try include these (some require a package
-first be installed).  Many of these include specific compiler flags
-for optimized performance.  Please note, however, that some of these
-customized machine Makefile are contributed by users.  Since both
-compilers, OS configurations, and LAMMPS itself keep changing, their
-settings may become outdated:
+Makefiles you may wish to try out, include those listed below (some
+require a package first be installed).  Many of these include specific
+compiler flags for optimized performance.  Please note, however, that
+some of these customized machine Makefile are contributed by users, and
+thus may have modifications specific to the systems of those users.
+Since compilers, OS configurations, and LAMMPS itself keep changing,
+their settings may become outdated, too:
 
 .. code-block:: bash
 
-   make mac             # build serial LAMMPS on a Mac
-   make mac_mpi         # build parallel LAMMPS on a Mac
+   make mac             # build serial LAMMPS on macOS
+   make mac_mpi         # build parallel LAMMPS on macOS
    make intel_cpu       # build with the INTEL package optimized for CPUs
    make knl             # build with the INTEL package optimized for KNLs
    make opt             # build with the OPT package optimized for CPUs

doc/src/Build_manual.rst

@@ -2,7 +2,7 @@ Build the LAMMPS documentation
 ==============================
 
 Depending on how you obtained LAMMPS and whether you have built the
-manual yourself, this directory has a number of sub-directories and
+manual yourself, this directory has a number of subdirectories and
 files. Here is a list with descriptions:
 
 .. code-block:: bash
@@ -33,7 +33,7 @@ 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, that is the state
+A current version of the manual (latest feature release, that is the state
 of the *release* branch) is is available online at:
 `https://docs.lammps.org/ <https://docs.lammps.org/>`_.
 A version of the manual corresponding to the ongoing development (that is
@@ -48,15 +48,15 @@ Build using GNU make
 
 The LAMMPS manual is written in `reStructuredText <rst_>`_ format which
 can be translated to different output format using the `Sphinx
-<https://sphinx-doc.org>`_ document generator tool.  It also
+<https://www.sphinx-doc.org/>`_ document generator tool.  It also
 incorporates programmer documentation extracted from the LAMMPS C++
-sources through the `Doxygen <https://doxygen.nl>`_ program.  Currently
+sources through the `Doxygen <https://doxygen.nl/>`_ program.  Currently
 the translation to HTML, PDF (via LaTeX), ePUB (for many e-book readers)
 and MOBI (for Amazon Kindle readers) are supported.  For that to work a
-Python 3 interpreter, the ``doxygen`` tools and internet access to
-download additional files and tools are required.  This download is
-usually only required once or after the documentation folder is returned
-to a pristine state with ``make clean-all``.
+Python interpreter version 3.8 or later, the ``doxygen`` tools and
+internet access to download additional files and tools are required.
+This download is usually only required once or after the documentation
+folder is returned to a pristine state with ``make clean-all``.
 
 For the documentation build a python virtual environment is set up in
 the folder ``doc/docenv`` and various python packages are installed into
@@ -87,6 +87,7 @@ folder.  The following ``make`` commands are available:
    make anchor_check  # check for duplicate anchor labels
    make style_check   # check for complete and consistent style lists
    make package_check # check for complete and consistent package lists
+   make link_check    # check for broken or outdated URLs
    make spelling      # spell-check the manual
 
 ----------
@@ -125,38 +126,29 @@ common setups:
 
       .. code-block:: bash
 
-         sudo apt-get install python-virtualenv git doxygen
+         sudo apt-get install git doxygen
 
    .. tab:: RHEL or CentOS (Version 7.x)
 
       .. code-block:: bash
 
-         sudo yum install python3-virtualenv git doxygen
+         sudo yum install git doxygen
 
    .. tab:: Fedora or RHEL/CentOS (8.x or later)
 
       .. code-block:: bash
 
-         sudo dnf install python3-virtualenv git doxygen
+         sudo dnf install git doxygen
 
-   .. tab:: MacOS X
+   .. tab:: macOS
 
       *Python 3*
 
-      Download the latest Python 3 MacOS X package from
+      If Python 3 is not available on your macOS system, you can
+      download the latest Python 3 macOS package from
       `https://www.python.org <https://www.python.org>`_ and install it.
       This will install both Python 3 and pip3.
 
-      *virtualenv*
-
-      Once Python 3 is installed, open a Terminal and type
-
-      .. code-block:: bash
-
-         pip3 install virtualenv
-
-      This will install virtualenv from the Python Package Index.
-
 Prerequisites for PDF
 ---------------------
 

doc/src/Build_package.rst

@@ -4,13 +4,14 @@ Include packages in build
 In LAMMPS, a package is a group of files that enable a specific set of
 features.  For example, force fields for molecular systems or
 rigid-body constraints are in packages.  In the src directory, each
-package is a sub-directory with the package name in capital letters.
+package is a subdirectory with the package name in capital letters.
 
 An overview of packages is given on the :doc:`Packages <Packages>` doc
-page.  Brief overviews of each package are on the :doc:`Packages details <Packages_details>` page.
+page.  Brief overviews of each package are on the :doc:`Packages details
+<Packages_details>` page.
 
 When building LAMMPS, you can choose to include or exclude each
-package.  In general there is no need to include a package if you
+package.  Generally, there is no need to include a package if you
 never plan to use its features.
 
 If you get a run-time error that a LAMMPS command or style is
@@ -30,23 +31,28 @@ steps, as explained on the :doc:`Build extras <Build_extras>` page.
 These links take you to the extra instructions for those select
 packages:
 
+.. this list must be kept in sync with its counterpart in Build_extras.rst
 .. table_from_list::
    :columns: 6
 
    * :ref:`ADIOS <adios>`
    * :ref:`ATC <atc>`
    * :ref:`AWPMD <awpmd>`
-   * :ref:`COLVARS <colvars>`
+   * :ref:`COLVARS <colvar>`
    * :ref:`COMPRESS <compress>`
+   * :ref:`ELECTRODE <electrode>`
    * :ref:`GPU <gpu>`
    * :ref:`H5MD <h5md>`
    * :ref:`INTEL <intel>`
    * :ref:`KIM <kim>`
    * :ref:`KOKKOS <kokkos>`
-   * :ref:`LATTE <latte>`
+   * :ref:`LEPTON <lepton>`
    * :ref:`MACHDYN <machdyn>`
+   * :ref:`MDI <mdi>`
    * :ref:`ML-HDNNP <ml-hdnnp>`
+   * :ref:`ML-IAP <mliap>`
    * :ref:`ML-PACE <ml-pace>`
+   * :ref:`ML-POD <ml-pod>`
    * :ref:`ML-QUIP <ml-quip>`
    * :ref:`MOLFILE <molfile>`
    * :ref:`MSCG <mscg>`
@@ -87,7 +93,7 @@ versus make.
          If you switch between building with CMake and make builds, no
          packages in the src directory can be installed when you invoke
          ``cmake``.  CMake will give an error if that is not the case,
-         indicating how you can un-install all packages in the src dir.
+         indicating how you can uninstall all packages in the src dir.
 
    .. tab:: Traditional make
 
@@ -96,7 +102,7 @@ versus make.
          cd lammps/src
          make ps                    # check which packages are currently installed
          make yes-name              # install a package with name
-         make no-name               # un-install a package with name
+         make no-name               # uninstall a package with name
          make mpi                   # build LAMMPS with whatever packages are now installed
 
       Examples:
@@ -112,13 +118,13 @@ versus make.
       .. note::
 
          You must always re-build LAMMPS (via make) after installing or
-         un-installing a package, for the action to take effect. The
+         uninstalling a package, for the action to take effect. The
          included dependency tracking will make certain only files that
          are required to be rebuilt are recompiled.
 
       .. note::
 
-         You cannot install or un-install packages and build LAMMPS in a
+         You cannot install or uninstall packages and build LAMMPS in a
          single make command with multiple targets, e.g. ``make
          yes-colloid mpi``.  This is because the make procedure creates
          a list of source files that will be out-of-date for the build
@@ -143,7 +149,7 @@ other files dependent on that package are also excluded.
    if you downloaded a tarball, 3 packages (KSPACE, MANYBODY, MOLECULE)
    were pre-installed via the traditional make procedure in the ``src``
    directory.  That is no longer the case, so that CMake will build
-   as-is without needing to un-install those packages.
+   as-is without needing to uninstall those packages.
 
 ----------
 
@@ -160,9 +166,9 @@ control flow constructs for more complex operations.
 
 LAMMPS includes several of these files to define configuration
 "presets", similar to the options that exist for the Make based
-system. Using these files you can enable/disable portions of the
-available packages in LAMMPS. If you need a custom preset you can take
-one of them as a starting point and customize it to your needs.
+system. Using these files, you can enable/disable portions of the
+available packages in LAMMPS. If you need a custom preset, you can
+make a copy of one of them and modify it to suit your needs.
 
 .. code-block:: bash
 
@@ -176,7 +182,7 @@ one of them as a starting point and customize it to your needs.
     cmake -C ../cmake/presets/pgi.cmake      [OPTIONS] ../cmake  # change settings to use the PGI compilers by default
     cmake -C ../cmake/presets/all_on.cmake   [OPTIONS] ../cmake  # enable all packages
     cmake -C ../cmake/presets/all_off.cmake  [OPTIONS] ../cmake  # disable all packages
-    mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake  #  compile with MinGW cross compilers
+    mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake  #  compile with MinGW cross-compilers
 
 Presets that have names starting with "windows" are specifically for
 compiling LAMMPS :doc:`natively on Windows <Build_windows>` and
@@ -220,7 +226,7 @@ The following commands are useful for managing package source files
 and their installation when building LAMMPS via traditional make.
 Just type ``make`` in lammps/src to see a one-line summary.
 
-These commands install/un-install sets of packages:
+These commands install/uninstall sets of packages:
 
 .. code-block:: bash
 
@@ -236,40 +242,40 @@ These commands install/un-install sets of packages:
     make yes-ext                        # install packages that require external libraries
     make no-ext                         # uninstall packages that require external libraries
 
-which install/un-install various sets of packages.  Typing ``make
+which install/uninstall various sets of packages.  Typing ``make
 package`` will list all the these commands.
 
 .. note::
 
-   Installing or un-installing a package for the make based build process
+   Installing or uninstalling a package for the make based build process
    works by simply copying files back and forth between the main source
-   directory src and the sub-directories with the package name (e.g.
+   directory src and the subdirectories with the package name (e.g.
    src/KSPACE, src/ATC), so that the files are included or excluded
    when LAMMPS is built.  Only source files in the src folder will be
    compiled.
 
 The following make commands help manage files that exist in both the
-src directory and in package sub-directories.  You do not normally
+src directory and in package subdirectories.  You do not normally
 need to use these commands unless you are editing LAMMPS files or are
 updating LAMMPS via git.
 
 Type ``make package-status`` or ``make ps`` to show which packages are
 currently installed.  For those that are installed, it will list any
 files that are different in the src directory and package
-sub-directory.
+subdirectory.
 
 Type ``make package-installed`` or ``make pi`` to show which packages are
 currently installed, without listing the status of packages that are
 not installed.
 
 Type ``make package-update`` or ``make pu`` to overwrite src files with
-files from the package sub-directories if the package is installed.  It
+files from the package subdirectories if the package is installed.  It
 should be used after the checkout has been :doc:`updated or changed
-withy git <Install_git>`, this will only update the files in the package
-sub-directories, but not the copies in the src folder.
+with git <Install_git>`, this will only update the files in the package
+subdirectories, but not the copies in the src folder.
 
 Type ``make package-overwrite`` to overwrite files in the package
-sub-directories with src files.
+subdirectories with src files.
 
 Type ``make package-diff`` to list all differences between pairs of
 files in both the source directory and the package directory.

doc/src/Build_settings.rst

@@ -1,8 +1,8 @@
 Optional build settings
 =======================
 
-LAMMPS can be built with several optional settings.  Each sub-section
-explain how to do this for building both with CMake and make.
+LAMMPS can be built with several optional settings.  Each subsection
+explains how to do this for building both with CMake and make.
 
 * `C++11 standard compliance`_ when building all of LAMMPS
 * `FFT library`_ for use with the :doc:`kspace_style pppm <kspace_style>` command
@@ -41,7 +41,7 @@ FFT library
 When the KSPACE package is included in a LAMMPS build, the
 :doc:`kspace_style pppm <kspace_style>` command performs 3d FFTs which
 require use of an FFT library to compute 1d FFTs.  The KISS FFT
-library is included with LAMMPS but other libraries can be faster.
+library is included with LAMMPS, but other libraries can be faster.
 LAMMPS can use them if they are available on your system.
 
 .. tabs::
@@ -63,9 +63,9 @@ LAMMPS can use them if they are available on your system.
       Usually these settings are all that is needed.  If FFTW3 is
       selected, then CMake will try to detect, if threaded FFTW
       libraries are available and enable them by default.  This setting
-      is independent of whether OpenMP threads are enabled and a
-      packages like KOKKOS or OPENMP is used.  If CMake cannot detect
-      the FFT library, you can set these variables to assist:
+      is independent of whether OpenMP threads are enabled and a package
+      like KOKKOS or OPENMP is used.  If CMake cannot detect the FFT
+      library, you can set these variables to assist:
 
       .. code-block:: bash
 
@@ -141,18 +141,18 @@ The Intel MKL math library is part of the Intel compiler suite.  It
 can be used with the Intel or GNU compiler (see the ``FFT_LIB`` setting
 above).
 
-Performing 3d FFTs in parallel can be time consuming due to data
-access and required communication.  This cost can be reduced by
-performing single-precision FFTs instead of double precision.  Single
-precision means the real and imaginary parts of a complex datum are
-4-byte floats.  Double precision means they are 8-byte doubles.  Note
-that Fourier transform and related PPPM operations are somewhat less
-sensitive to floating point truncation errors and thus the resulting
-error is less than the difference in precision. Using the ``-DFFT_SINGLE``
-setting trades off a little accuracy for reduced memory use and
-parallel communication costs for transposing 3d FFT data.
+Performing 3d FFTs in parallel can be time-consuming due to data access
+and required communication.  This cost can be reduced by performing
+single-precision FFTs instead of double precision.  Single precision
+means the real and imaginary parts of a complex datum are 4-byte floats.
+Double precision means they are 8-byte doubles.  Note that Fourier
+transform and related PPPM operations are somewhat less sensitive to
+floating point truncation errors, and thus the resulting error is
+generally less than the difference in precision. Using the
+``-DFFT_SINGLE`` setting trades off a little accuracy for reduced memory
+use and parallel communication costs for transposing 3d FFT data.
 
-When using ``-DFFT_SINGLE`` with FFTW3 you may need to build the FFTW
+When using ``-DFFT_SINGLE`` with FFTW3, you may need to build the FFTW
 library a second time with support for single-precision.
 
 For FFTW3, do the following, which should produce the additional
@@ -177,11 +177,11 @@ ARRAY mode.
 Size of LAMMPS integer types and size limits
 --------------------------------------------
 
-LAMMPS has a few integer data types which can be defined as either
-4-byte (= 32-bit) or 8-byte (= 64-bit) integers at compile time.
-This has an impact on the size of a system that can be simulated
-or how large counters can become before "rolling over".
-The default setting of "smallbig" is almost always adequate.
+LAMMPS uses a few custom integer data types, which can be defined as
+either 4-byte (= 32-bit) or 8-byte (= 64-bit) integers at compile time.
+This has an impact on the size of a system that can be simulated, or how
+large counters can become before "rolling over".  The default setting of
+"smallbig" is almost always adequate.
 
 .. tabs::
 
@@ -254,7 +254,7 @@ topology information, though IDs are enabled by default.  The
 :doc:`atom_modify id no <atom_modify>` command will turn them off.  Atom
 IDs are required for molecular systems with bond topology (bonds,
 angles, dihedrals, etc).  Similarly, some force or compute or fix styles
-require atom IDs.  Thus if you model a molecular system or use one of
+require atom IDs.  Thus, if you model a molecular system or use one of
 those styles with more than 2 billion atoms, you need the "bigbig"
 setting.
 
@@ -264,7 +264,7 @@ systems and 500 million for systems with bonds (the additional
 restriction is due to using the 2 upper bits of the local atom index
 in neighbor lists for storing special bonds info).
 
-Image flags store 3 values per atom in a single integer which count the
+Image flags store 3 values per atom in a single integer, which count the
 number of times an atom has moved through the periodic box in each
 dimension.  See the :doc:`dump <dump>` manual page for a discussion.  If
 an atom moves through the periodic box more than this limit, the value
@@ -285,7 +285,7 @@ Output of JPG, PNG, and movie files
 --------------------------------------------------
 
 The :doc:`dump image <dump_image>` command has options to output JPEG or
-PNG image files.  Likewise the :doc:`dump movie <dump_image>` command
+PNG image files.  Likewise, the :doc:`dump movie <dump_image>` command
 outputs movie files in a variety of movie formats.  Using these options
 requires the following settings:
 
@@ -354,7 +354,7 @@ Read or write compressed files
 If this option is enabled, large files can be read or written with
 compression by ``gzip`` or similar tools by several LAMMPS commands,
 including :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and
-:doc:`dump <dump>`.  Currently supported compression tools are:
+:doc:`dump <dump>`.  Supported compression tools are currently
 ``gzip``, ``bzip2``, ``zstd``, and ``lzma``.
 
 .. tabs::
@@ -394,7 +394,7 @@ Memory allocation alignment
 ---------------------------------------
 
 This setting enables the use of the "posix_memalign()" call instead of
-"malloc()" when LAMMPS allocates large chunks or memory.  Vector
+"malloc()" when LAMMPS allocates large chunks of memory.  Vector
 instructions on CPUs may become more efficient, if dynamically allocated
 memory is aligned on larger-than-default byte boundaries.  On most
 current operating systems, the "malloc()" implementation returns
@@ -496,7 +496,7 @@ Trigger selected floating-point exceptions
 ------------------------------------------
 
 Many kinds of CPUs have the capability to detect when a calculation
-results in an invalid math operation like a division by zero or calling
+results in an invalid math operation, like a division by zero or calling
 the square root with a negative argument.  The default behavior on
 most operating systems is to continue and have values for ``NaN`` (= not
 a number) or ``Inf`` (= infinity).  This allows software to detect and

doc/src/Commands_all.rst

@@ -24,6 +24,7 @@ table above.
 
    * :doc:`angle_coeff <angle_coeff>`
    * :doc:`angle_style <angle_style>`
+   * :doc:`angle_write <angle_write>`
    * :doc:`atom_modify <atom_modify>`
    * :doc:`atom_style <atom_style>`
    * :doc:`balance <balance>`
@@ -31,7 +32,6 @@ table above.
    * :doc:`bond_style <bond_style>`
    * :doc:`bond_write <bond_write>`
    * :doc:`boundary <boundary>`
-   * :doc:`box <box>`
    * :doc:`change_box <change_box>`
    * :doc:`clear <clear>`
    * :doc:`comm_modify <comm_modify>`
@@ -46,6 +46,7 @@ table above.
    * :doc:`dielectric <dielectric>`
    * :doc:`dihedral_coeff <dihedral_coeff>`
    * :doc:`dihedral_style <dihedral_style>`
+   * :doc:`dihedral_write <dihedral_write>`
    * :doc:`dimension <dimension>`
    * :doc:`displace_atoms <displace_atoms>`
    * :doc:`dump <dump>`
@@ -90,8 +91,7 @@ table above.
    * :doc:`region <region>`
    * :doc:`replicate <replicate>`
    * :doc:`rerun <rerun>`
-   * :doc:`reset_atom_ids <reset_atom_ids>`
-   * :doc:`reset_mol_ids <reset_mol_ids>`
+   * :doc:`reset_atoms <reset_atoms>`
    * :doc:`reset_timestep <reset_timestep>`
    * :doc:`restart <restart>`
    * :doc:`run <run>`
@@ -127,6 +127,7 @@ additional letter in parenthesis: k = KOKKOS.
    * :doc:`group2ndx <group2ndx>`
    * :doc:`hyper <hyper>`
    * :doc:`kim <kim_commands>`
+   * :doc:`fitpod <fitpod_command>`
    * :doc:`mdi <mdi>`
    * :doc:`ndx2group <group2ndx>`
    * :doc:`neb <neb>`

doc/src/Commands_bond.rst

@@ -42,8 +42,10 @@ OPT.
    * :doc:`gaussian <bond_gaussian>`
    * :doc:`gromos (o) <bond_gromos>`
    * :doc:`harmonic (iko) <bond_harmonic>`
+   * :doc:`harmonic/restrain <bond_harmonic_restrain>`
    * :doc:`harmonic/shift (o) <bond_harmonic_shift>`
    * :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>`
+   * :doc:`lepton (o) <bond_lepton>`
    * :doc:`mesocnt <bond_mesocnt>`
    * :doc:`mm3 <bond_mm3>`
    * :doc:`morse (o) <bond_morse>`
@@ -93,6 +95,7 @@ OPT.
    * :doc:`fourier/simple (o) <angle_fourier_simple>`
    * :doc:`gaussian <angle_gaussian>`
    * :doc:`harmonic (iko) <angle_harmonic>`
+   * :doc:`lepton (o) <angle_lepton>`
    * :doc:`mesocnt <angle_mesocnt>`
    * :doc:`mm3 <angle_mm3>`
    * :doc:`quartic (o) <angle_quartic>`
@@ -127,6 +130,7 @@ OPT.
    * :doc:`fourier (io) <dihedral_fourier>`
    * :doc:`harmonic (iko) <dihedral_harmonic>`
    * :doc:`helix (o) <dihedral_helix>`
+   * :doc:`lepton (o) <dihedral_lepton>`
    * :doc:`multi/harmonic (o) <dihedral_multi_harmonic>`
    * :doc:`nharmonic (o) <dihedral_nharmonic>`
    * :doc:`opls (iko) <dihedral_opls>`

doc/src/Commands_category.rst

@@ -25,7 +25,6 @@ Setup simulation box:
    :columns: 4
 
    * :doc:`boundary <boundary>`
-   * :doc:`box <box>`
    * :doc:`change_box <change_box>`
    * :doc:`create_box <create_box>`
    * :doc:`dimension <dimension>`

doc/src/Commands_compute.rst

@@ -46,21 +46,25 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`com/chunk <compute_com_chunk>`
    * :doc:`contact/atom <compute_contact_atom>`
    * :doc:`coord/atom (k) <compute_coord_atom>`
+   * :doc:`count/type <compute_count_type>`
    * :doc:`damage/atom <compute_damage_atom>`
    * :doc:`dihedral <compute_dihedral>`
    * :doc:`dihedral/local <compute_dihedral_local>`
    * :doc:`dilatation/atom <compute_dilatation_atom>`
    * :doc:`dipole <compute_dipole>`
    * :doc:`dipole/chunk <compute_dipole_chunk>`
+   * :doc:`dipole/tip4p <compute_dipole>`
+   * :doc:`dipole/tip4p/chunk <compute_dipole_chunk>`
    * :doc:`displace/atom <compute_displace_atom>`
    * :doc:`dpd <compute_dpd>`
    * :doc:`dpd/atom <compute_dpd_atom>`
    * :doc:`edpd/temp/atom <compute_edpd_temp_atom>`
    * :doc:`efield/atom <compute_efield_atom>`
+   * :doc:`efield/wolf/atom <compute_efield_wolf_atom>`
    * :doc:`entropy/atom <compute_entropy_atom>`
    * :doc:`erotate/asphere <compute_erotate_asphere>`
    * :doc:`erotate/rigid <compute_erotate_rigid>`
-   * :doc:`erotate/sphere <compute_erotate_sphere>`
+   * :doc:`erotate/sphere (k) <compute_erotate_sphere>`
    * :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>`
    * :doc:`event/displace <compute_event_displace>`
    * :doc:`fabric <compute_fabric>`
@@ -87,7 +91,6 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`ke/atom/eff <compute_ke_atom_eff>`
    * :doc:`ke/eff <compute_ke_eff>`
    * :doc:`ke/rigid <compute_ke_rigid>`
-   * :doc:`mesont <compute_mesont>`
    * :doc:`mliap <compute_mliap>`
    * :doc:`momentum <compute_momentum>`
    * :doc:`msd <compute_msd>`
@@ -104,9 +107,11 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`pe/tally <compute_tally>`
    * :doc:`plasticity/atom <compute_plasticity_atom>`
    * :doc:`pressure <compute_pressure>`
+   * :doc:`pressure/alchemy <compute_pressure_alchemy>`
    * :doc:`pressure/uef <compute_pressure_uef>`
    * :doc:`property/atom <compute_property_atom>`
    * :doc:`property/chunk <compute_property_chunk>`
+   * :doc:`property/grid <compute_property_grid>`
    * :doc:`property/local <compute_property_local>`
    * :doc:`ptm/atom <compute_ptm_atom>`
    * :doc:`rdf <compute_rdf>`
@@ -148,11 +153,11 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`sph/t/atom <compute_sph_t_atom>`
    * :doc:`spin <compute_spin>`
    * :doc:`stress/atom <compute_stress_atom>`
-   * :doc:`stress/cartesian <compute_stress_profile>`
-   * :doc:`stress/cylinder <compute_stress_profile>`
+   * :doc:`stress/cartesian <compute_stress_cartesian>`
+   * :doc:`stress/cylinder <compute_stress_curvilinear>`
    * :doc:`stress/mop <compute_stress_mop>`
    * :doc:`stress/mop/profile <compute_stress_mop>`
-   * :doc:`stress/spherical <compute_stress_profile>`
+   * :doc:`stress/spherical <compute_stress_curvilinear>`
    * :doc:`stress/tally <compute_tally>`
    * :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>`
    * :doc:`temp (k) <compute_temp>`

doc/src/Commands_dump.rst

@@ -36,7 +36,8 @@ An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
    * :doc:`custom/mpiio <dump>`
    * :doc:`custom/zstd <dump>`
    * :doc:`dcd <dump>`
-   * :doc:`deprecated <dump>`
+   * :doc:`grid <dump>`
+   * :doc:`grid/vtk <dump>`
    * :doc:`h5md <dump_h5md>`
    * :doc:`image <dump_image>`
    * :doc:`local <dump>`

doc/src/Commands_fix.rst

@@ -29,6 +29,7 @@ OPT.
    * :doc:`adapt/fep <fix_adapt_fep>`
    * :doc:`addforce <fix_addforce>`
    * :doc:`addtorque <fix_addtorque>`
+   * :doc:`alchemy <fix_alchemy>`
    * :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>`
    * :doc:`amoeba/pitorsion <fix_amoeba_pitorsion>`
    * :doc:`append/atoms <fix_append_atoms>`
@@ -38,14 +39,12 @@ OPT.
    * :doc:`ave/chunk <fix_ave_chunk>`
    * :doc:`ave/correlate <fix_ave_correlate>`
    * :doc:`ave/correlate/long <fix_ave_correlate_long>`
+   * :doc:`ave/grid <fix_ave_grid>`
    * :doc:`ave/histo <fix_ave_histo>`
    * :doc:`ave/histo/weight <fix_ave_histo>`
    * :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>`
@@ -53,6 +52,9 @@ OPT.
    * :doc:`bond/react <fix_bond_react>`
    * :doc:`bond/swap <fix_bond_swap>`
    * :doc:`box/relax <fix_box_relax>`
+   * :doc:`brownian <fix_brownian>`
+   * :doc:`brownian/asphere <fix_brownian>`
+   * :doc:`brownian/sphere <fix_brownian>`
    * :doc:`charge/regulation <fix_charge_regulation>`
    * :doc:`cmap <fix_cmap>`
    * :doc:`colvars <fix_colvars>`
@@ -65,13 +67,14 @@ OPT.
    * :doc:`drude <fix_drude>`
    * :doc:`drude/transform/direct <fix_drude_transform>`
    * :doc:`drude/transform/inverse <fix_drude_transform>`
-   * :doc:`dt/reset <fix_dt_reset>`
+   * :doc:`dt/reset (k) <fix_dt_reset>`
    * :doc:`edpd/source <fix_dpd_source>`
    * :doc:`efield <fix_efield>`
+   * :doc:`efield/tip4p <fix_efield>`
    * :doc:`ehex <fix_ehex>`
-   * :doc:`electrode/conp (i) <fix_electrode_conp>`
-   * :doc:`electrode/conq (i) <fix_electrode_conp>`
-   * :doc:`electrode/thermo (i) <fix_electrode_conp>`
+   * :doc:`electrode/conp (i) <fix_electrode>`
+   * :doc:`electrode/conq (i) <fix_electrode>`
+   * :doc:`electrode/thermo (i) <fix_electrode>`
    * :doc:`electron/stopping <fix_electron_stopping>`
    * :doc:`electron/stopping/fit <fix_electron_stopping>`
    * :doc:`enforce2d (k) <fix_enforce2d>`
@@ -91,6 +94,7 @@ OPT.
    * :doc:`grem <fix_grem>`
    * :doc:`halt <fix_halt>`
    * :doc:`heat <fix_heat>`
+   * :doc:`heat/flow <fix_heat_flow>`
    * :doc:`hyper/global <fix_hyper_global>`
    * :doc:`hyper/local <fix_hyper_local>`
    * :doc:`imd <fix_imd>`
@@ -100,13 +104,13 @@ OPT.
    * :doc:`langevin/drude <fix_langevin_drude>`
    * :doc:`langevin/eff <fix_langevin_eff>`
    * :doc:`langevin/spin <fix_langevin_spin>`
-   * :doc:`latte <fix_latte>`
    * :doc:`lb/fluid <fix_lb_fluid>`
    * :doc:`lb/momentum <fix_lb_momentum>`
    * :doc:`lb/viscous <fix_lb_viscous>`
    * :doc:`lineforce <fix_lineforce>`
    * :doc:`manifoldforce <fix_manifoldforce>`
    * :doc:`mdi/qm <fix_mdi_qm>`
+   * :doc:`mdi/qmmm <fix_mdi_qmmm>`
    * :doc:`meso/move <fix_meso_move>`
    * :doc:`mol/swap <fix_mol_swap>`
    * :doc:`momentum (k) <fix_momentum>`
@@ -167,7 +171,8 @@ OPT.
    * :doc:`pafi <fix_pafi>`
    * :doc:`pair <fix_pair>`
    * :doc:`phonon <fix_phonon>`
-   * :doc:`pimd <fix_pimd>`
+   * :doc:`pimd/langevin <fix_pimd>`
+   * :doc:`pimd/nvt <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`
    * :doc:`plumed <fix_plumed>`
    * :doc:`poems <fix_poems>`
@@ -213,6 +218,7 @@ OPT.
    * :doc:`saed/vtk <fix_saed_vtk>`
    * :doc:`setforce (k) <fix_setforce>`
    * :doc:`setforce/spin <fix_setforce>`
+   * :doc:`sgcmc <fix_sgcmc>`
    * :doc:`shake (k) <fix_shake>`
    * :doc:`shardlow (k) <fix_shardlow>`
    * :doc:`smd <fix_smd>`
@@ -249,18 +255,19 @@ OPT.
    * :doc:`tune/kspace <fix_tune_kspace>`
    * :doc:`vector <fix_vector>`
    * :doc:`viscosity <fix_viscosity>`
-   * :doc:`viscous <fix_viscous>`
+   * :doc:`viscous (k) <fix_viscous>`
    * :doc:`viscous/sphere <fix_viscous_sphere>`
    * :doc:`wall/body/polygon <fix_wall_body_polygon>`
    * :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>`
    * :doc:`wall/colloid <fix_wall>`
    * :doc:`wall/ees <fix_wall_ees>`
-   * :doc:`wall/gran <fix_wall_gran>`
+   * :doc:`wall/gran (k) <fix_wall_gran>`
    * :doc:`wall/gran/region <fix_wall_gran_region>`
    * :doc:`wall/harmonic <fix_wall>`
    * :doc:`wall/lj1043 <fix_wall>`
    * :doc:`wall/lj126 <fix_wall>`
    * :doc:`wall/lj93 (k) <fix_wall>`
+   * :doc:`wall/lepton <fix_wall>`
    * :doc:`wall/morse <fix_wall>`
    * :doc:`wall/piston <fix_wall_piston>`
    * :doc:`wall/reflect (k) <fix_wall_reflect>`
@@ -268,4 +275,5 @@ OPT.
    * :doc:`wall/region <fix_wall_region>`
    * :doc:`wall/region/ees <fix_wall_ees>`
    * :doc:`wall/srd <fix_wall_srd>`
+   * :doc:`wall/table <fix_wall>`
    * :doc:`widom <fix_widom>`

doc/src/Commands_pair.rst

@@ -37,9 +37,10 @@ OPT.
    *
    * :doc:`adp (ko) <pair_adp>`
    * :doc:`agni (o) <pair_agni>`
+   * :doc:`aip/water/2dm (t) <pair_aip_water_2dm>`
    * :doc:`airebo (io) <pair_airebo>`
    * :doc:`airebo/morse (io) <pair_airebo>`
-   * :doc:`amoeba <pair_amoeba>`
+   * :doc:`amoeba (g) <pair_amoeba>`
    * :doc:`atm <pair_atm>`
    * :doc:`awpmd/cut <pair_awpmd>`
    * :doc:`beck (go) <pair_beck>`
@@ -55,6 +56,7 @@ OPT.
    * :doc:`born/coul/msm (o) <pair_born>`
    * :doc:`born/coul/wolf (go) <pair_born>`
    * :doc:`born/coul/wolf/cs (g) <pair_cs>`
+   * :doc:`born/gauss <pair_born_gauss>`
    * :doc:`bpm/spring <pair_bpm_spring>`
    * :doc:`brownian (o) <pair_brownian>`
    * :doc:`brownian/poly (o) <pair_brownian>`
@@ -93,8 +95,8 @@ OPT.
    * :doc:`coul/wolf/cs <pair_cs>`
    * :doc:`dpd (giko) <pair_dpd>`
    * :doc:`dpd/fdt <pair_dpd_fdt>`
-   * :doc:`dpd/ext (k) <pair_dpd_ext>`
-   * :doc:`dpd/ext/tstat (k) <pair_dpd_ext>`
+   * :doc:`dpd/ext (ko) <pair_dpd_ext>`
+   * :doc:`dpd/ext/tstat (ko) <pair_dpd_ext>`
    * :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
    * :doc:`dpd/tstat (gko) <pair_dpd>`
    * :doc:`dsmc <pair_dsmc>`
@@ -126,7 +128,7 @@ OPT.
    * :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
    * :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
    * :doc:`hdnnp <pair_hdnnp>`
-   * :doc:`hippo <pair_amoeba>`
+   * :doc:`hippo (g) <pair_amoeba>`
    * :doc:`ilp/graphene/hbn (t) <pair_ilp_graphene_hbn>`
    * :doc:`ilp/tmd (t) <pair_ilp_tmd>`
    * :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
@@ -134,6 +136,9 @@ OPT.
    * :doc:`lcbop <pair_lcbop>`
    * :doc:`lebedeva/z <pair_lebedeva_z>`
    * :doc:`lennard/mdf <pair_mdf>`
+   * :doc:`lepton (o) <pair_lepton>`
+   * :doc:`lepton/coul (o) <pair_lepton>`
+   * :doc:`lepton/sphere (o) <pair_lepton>`
    * :doc:`line/lj <pair_line_lj>`
    * :doc:`lj/charmm/coul/charmm (giko) <pair_charmm>`
    * :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`
@@ -164,16 +169,18 @@ OPT.
    * :doc:`lj/cut/coul/msm (go) <pair_lj_cut_coul>`
    * :doc:`lj/cut/coul/msm/dielectric <pair_dielectric>`
    * :doc:`lj/cut/coul/wolf (o) <pair_lj_cut_coul>`
-   * :doc:`lj/cut/dipole/cut (go) <pair_dipole>`
+   * :doc:`lj/cut/dipole/cut (gko) <pair_dipole>`
    * :doc:`lj/cut/dipole/long (g) <pair_dipole>`
    * :doc:`lj/cut/dipole/sf (go) <pair_dipole>`
    * :doc:`lj/cut/soft (o) <pair_fep_soft>`
+   * :doc:`lj/cut/sphere (o) <pair_lj_cut_sphere>`
    * :doc:`lj/cut/thole/long (o) <pair_thole>`
    * :doc:`lj/cut/tip4p/cut (o) <pair_lj_cut_tip4p>`
    * :doc:`lj/cut/tip4p/long (got) <pair_lj_cut_tip4p>`
    * :doc:`lj/cut/tip4p/long/soft (o) <pair_fep_soft>`
    * :doc:`lj/expand (gko) <pair_lj_expand>`
-   * :doc:`lj/expand/coul/long (g) <pair_lj_expand>`
+   * :doc:`lj/expand/coul/long (gk) <pair_lj_expand>`
+   * :doc:`lj/expand/sphere (o) <pair_lj_expand_sphere>`
    * :doc:`lj/gromacs (gko) <pair_gromacs>`
    * :doc:`lj/gromacs/coul/gromacs (ko) <pair_gromacs>`
    * :doc:`lj/long/coul/long (iot) <pair_lj_long>`
@@ -198,11 +205,11 @@ OPT.
    * :doc:`mdpd <pair_mesodpd>`
    * :doc:`mdpd/rhosum <pair_mesodpd>`
    * :doc:`meam (k) <pair_meam>`
+   * :doc:`meam/ms (k) <pair_meam>`
    * :doc:`meam/spline (o) <pair_meam_spline>`
    * :doc:`meam/sw/spline <pair_meam_sw_spline>`
    * :doc:`mesocnt <pair_mesocnt>`
    * :doc:`mesocnt/viscous <pair_mesocnt>`
-   * :doc:`mesont/tpm <pair_mesont_tpm>`
    * :doc:`mgpt <pair_mgpt>`
    * :doc:`mie/cut (g) <pair_mie>`
    * :doc:`mliap (k) <pair_mliap>`
@@ -236,7 +243,8 @@ OPT.
    * :doc:`oxrna2/xstk <pair_oxrna2>`
    * :doc:`oxrna2/coaxstk <pair_oxrna2>`
    * :doc:`pace (k) <pair_pace>`
-   * :doc:`pace/extrapolation <pair_pace>`
+   * :doc:`pace/extrapolation (k) <pair_pace>`
+   * :doc:`pod <pair_pod>`
    * :doc:`peri/eps <pair_peri>`
    * :doc:`peri/lps (o) <pair_peri>`
    * :doc:`peri/pmb (o) <pair_peri>`

doc/src/Commands_removed.rst

@@ -2,14 +2,17 @@ Removed commands and packages
 =============================
 
 This page lists LAMMPS commands and packages that have been removed from
-the distribution and provides suggestions for alternatives or replacements.
-LAMMPS has special dummy styles implemented, that will stop LAMMPS and
-print a suitable error message in most cases, when a style/command is used
-that has been removed.
+the distribution and provides suggestions for alternatives or
+replacements.  LAMMPS has special dummy styles implemented, that will
+stop LAMMPS and print a suitable error message in most cases, when a
+style/command is used that has been removed or will replace the command
+with the direct alternative (if available) and print a warning.
 
 Fix ave/spatial and fix ave/spatial/sphere
 ------------------------------------------
 
+.. deprecated:: 11Dec2015
+
 The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS
 since they were superseded by the more general and extensible "chunk
 infrastructure".  Here the system is partitioned in one of many possible
@@ -17,10 +20,37 @@ ways through the :doc:`compute chunk/atom <compute_chunk_atom>` command
 and then averaging is done using :doc:`fix ave/chunk <fix_ave_chunk>`.
 Please refer to the :doc:`chunk HOWTO <Howto_chunk>` section for an overview.
 
-Reset_ids command
------------------
+Box command
+-----------
 
-The reset_ids command has been renamed to :doc:`reset_atom_ids <reset_atom_ids>`.
+.. deprecated:: 22Dec2022
+
+The *box* command has been removed and the LAMMPS code changed so it won't
+be needed.  If present, LAMMPS will ignore the command and print a warning.
+
+Reset_ids, reset_atom_ids, reset_mol_ids commands
+-------------------------------------------------
+
+.. deprecated:: 22Dec2022
+
+The *reset_ids*, *reset_atom_ids*, and *reset_mol_ids* commands have
+been folded into the :doc:`reset_atoms <reset_atoms>` command.  If
+present, LAMMPS will replace the commands accordingly and print a
+warning.
+
+LATTE package
+-------------
+
+.. deprecated:: 15Jun2023
+
+The LATTE package with the fix latte command was removed from LAMMPS.
+This functionality has been superseded by :doc:`fix mdi/qm <fix_mdi_qm>`
+and :doc:`fix mdi/qmmm <fix_mdi_qmmm>` from the :ref:`MDI package
+<PKG-MDI>`.  These fixes are compatible with several quantum software
+packages, including LATTE.  See the ``examples/QUANTUM`` dir and the
+:doc:`MDI coupling HOWTO <Howto_mdi>` page.  MDI supports running LAMMPS
+with LATTE as a plugin library (similar to the way fix latte worked), as
+well as on a different set of MPI processors.
 
 MEAM package
 ------------
@@ -30,18 +60,42 @@ The code in the :ref:`MEAM package <PKG-MEAM>` is a translation of the
 Fortran code of MEAM into C++, which removes several restrictions
 (e.g. there can be multiple instances in hybrid pair styles) and allows
 for some optimizations leading to better performance.  The pair style
-:doc:`meam <pair_meam>` has the exact same syntax.
+:doc:`meam <pair_meam>` has the exact same syntax.  For a transition
+period the C++ version of MEAM was called USER-MEAMC so it could
+coexist with the Fortran version.
+
+Minimize style fire/old
+-----------------------
+
+.. deprecated:: 8Feb2023
+
+Minimize style *fire/old* has been removed. Its functionality can be
+reproduced with *fire* with specific options. Please see the
+:doc:`min_modify command <min_modify>` documentation for details.
+
+Pair style mesont/tpm, compute style mesont, atom style mesont
+--------------------------------------------------------------
+
+.. deprecated:: 8Feb2023
+
+Pair style *mesont/tpm*, compute style *mesont*, and atom style
+*mesont* have been removed from the :ref:`MESONT package <PKG-MESONT>`.
+The same functionality is available through
+:doc:`pair style mesocnt <pair_mesocnt>`,
+:doc:`bond style mesocnt <bond_mesocnt>` and
+:doc:`angle style mesocnt <angle_mesocnt>`.
 
 REAX package
 ------------
 
 The REAX package has been removed since it was superseded by the
-:ref:`REAXFF package <PKG-REAXFF>`.  The REAXFF
-package has been tested to yield equivalent results to the REAX package,
-offers better performance, supports OpenMP multi-threading via OPENMP,
-and GPU and threading parallelization through KOKKOS.  The new pair styles
-are not syntax compatible with the removed reax pair style, so input
-files will have to be adapted.
+:ref:`REAXFF package <PKG-REAXFF>`.  The REAXFF package has been tested
+to yield equivalent results to the REAX package, offers better
+performance, supports OpenMP multi-threading via OPENMP, and GPU and
+threading parallelization through KOKKOS.  The new pair styles are not
+syntax compatible with the removed reax pair style, so input files will
+have to be adapted.  The REAXFF package was originally called
+USER-REAXC.
 
 USER-CUDA package
 -----------------
@@ -60,5 +114,6 @@ restart2data tool
 The functionality of the restart2data tool has been folded into the
 LAMMPS executable directly instead of having a separate tool.  A
 combination of the commands :doc:`read_restart <read_restart>` and
-:doc:`write_data <write_data>` can be used to the same effect.  For added
-convenience this conversion can also be triggered by :doc:`command line flags <Run_options>`
+:doc:`write_data <write_data>` can be used to the same effect.  For
+added convenience this conversion can also be triggered by
+:doc:`command line flags <Run_options>`

doc/src/Developer.rst

@@ -13,6 +13,7 @@ of time and requests from the LAMMPS user community.
    Developer_org
    Developer_code_design
    Developer_parallel
+   Developer_atom
    Developer_comm_ops
    Developer_flow
    Developer_write
@@ -23,3 +24,4 @@ of time and requests from the LAMMPS user community.
    Classes
    Developer_platform
    Developer_utils
+   Developer_grid

doc/src/Developer_atom.rst

@@ -0,0 +1,88 @@
+Accessing per-atom data
+-----------------------
+
+This page discusses how per-atom data is managed in LAMMPS, how it can
+be accessed, what communication patters apply, and some of the utility
+functions that exist for a variety of purposes.
+
+
+Owned and ghost atoms
+^^^^^^^^^^^^^^^^^^^^^
+
+As described on the :doc:`parallel partitioning algorithms
+<Developer_par_part>` page, LAMMPS uses a domain decomposition of the
+simulation domain, either in a *brick* or *tiled* manner.  Each MPI
+process *owns* exactly one subdomain and the atoms within it. To compute
+forces for tuples of atoms that are spread across sub-domain boundaries,
+also a "halo" of *ghost* atoms are maintained within a the communication
+cutoff distance of its subdomain.
+
+The total number of atoms is stored in `Atom::natoms` (within any
+typical class this can be referred to at `atom->natoms`. The number of
+*owned* (or "local" atoms) are stored in `Atom::nlocal`; the number of
+*ghost* atoms is stored in `Atom::nghost`.  The sum of `Atom::nlocal`
+over all MPI processes should be `Atom::natoms`. This is by default
+regularly checked by the Thermo class, and if the sum does not match,
+LAMMPS stops with a "lost atoms" error.  For convenience also the
+property `Atom::nmax` is available, this is the maximum of
+`Atom::nlocal + Atom::nghost` across all MPI processes.
+
+Per-atom properties are either managed by the atom style, or individual
+classes.  or as custom arrays by the individual classes. If only access
+to *owned* atoms is needed, they are usually allocated to be of size
+`Atom::nlocal`, otherwise of size `Atom::nmax`. Please note that not all
+per-atom properties are available or updated on *ghost* atoms. For
+example, per-atom velocities are only updated with :doc:`comm_modify vel
+yes <comm_modify>`.
+
+
+Atom indexing
+^^^^^^^^^^^^^
+
+When referring to individual atoms, they may be indexed by their local
+*index*, their index in their `Atom::x` array. This is densely populated
+containing first all *owned* atoms (index < `Atom::nlocal`) and then all
+*ghost* atoms.  The order of atoms in these arrays can change due to
+atoms migrating between between subdomains, atoms being added or
+deleted, or atoms being sorted for better cache efficiency.  Atoms are
+globally uniquely identified by their *atom ID*. There may be multiple
+atoms with the same atom ID present, but only one of them may be an
+*owned* atom.
+
+To find the local *index* of an atom, when the *atom ID* is known, the
+`Atom::map()` function may be used. It will return the local atom index
+or -1. If the returned value is between 0 (inclusive) and `Atom::nlocal`
+(exclusive) it is an *owned* or "local" atom; for larger values the atom
+is present as a ghost atom; for a value of -1, the atom is not present
+on the current subdomain at all.
+
+If multiple atoms with the same tag exist in the same subdomain, they
+can be found via the `Atom::sametag` array. It points to the next atom
+index with the same tag or -1 if there are no more atoms with the same
+tag.  The list will be exhaustive when starting with an index of an
+*owned* atom, since the atom IDs are unique, so there can only be one
+such atom.  Example code to count atoms with same atom ID in subdomain:
+
+.. code-block:: c++
+
+   for (int i = 0; i < atom->nlocal; ++i) {
+     int count = 0;
+     while (sametag[i] >= 0) {
+       i = sametag[i];
+       ++count;
+     }
+     printf("Atom ID: %ld is present %d times\n", atom->tag[i], count);
+   }
+
+Atom class versus AtomVec classes
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The `Atom` class contains all kinds of flags and counters about atoms in
+the system and that includes pointers to **all** per-atom properties
+available for atoms.  However, only a subset of these pointers are
+non-NULL and which those are depends on the atom style.  For each atom
+style there is a corresponding `AtomVecXXX` class derived from the
+`AtomVec` base class, where the XXX indicates the atom style.  This
+`AtomVecXXX` class will update the counters and per-atom pointers if
+atoms are added or removed to the system or migrate between subdomains.
+

doc/src/Developer_code_design.rst

@@ -1,56 +1,57 @@
 Code design
 -----------
 
-This section explains some of the code design choices in LAMMPS with
-the goal of helping developers write new code similar to the existing
-code.  Please see the section on :doc:`Requirements for contributed
-code <Modify_style>` for more specific recommendations and guidelines.
-While that section is organized more in the form of a checklist for
-code contributors, the focus here is on overall code design strategy,
-choices made between possible alternatives, and discussing some
-relevant C++ programming language constructs.
+This section explains some code design choices in LAMMPS with the goal
+of helping developers write new code similar to the existing code.
+Please see the section on :doc:`Requirements for contributed code
+<Modify_style>` for more specific recommendations and guidelines.  While
+that section is organized more in the form of a checklist for code
+contributors, the focus here is on overall code design strategy, choices
+made between possible alternatives, and discussing some relevant C++
+programming language constructs.
 
 Historically, the basic design philosophy of the LAMMPS C++ code was a
 "C with classes" style.  The motivation was to make it easy to modify
-LAMMPS for people without significant training in C++ programming.
-Data structures and code constructs were used that resemble the
-previous implementation(s) in Fortran.  A contributing factor to this
-choice also was that at the time, C++ compilers were often not mature
-and some of the advanced features contained bugs or did not function
-as the standard required.  There were also disagreements between
-compiler vendors as to how to interpret the C++ standard documents.
+LAMMPS for people without significant training in C++ programming.  Data
+structures and code constructs were used that resemble the previous
+implementation(s) in Fortran.  A contributing factor to this choice was
+that at the time, C++ compilers were often not mature and some advanced
+features contained bugs or did not function as the standard required.
+There were also disagreements between compiler vendors as to how to
+interpret the C++ standard documents.
 
-However, C++ compilers have now advanced significantly.  In 2020 we
-decided to to require the C++11 standard as the minimum C++ language
-standard for LAMMPS.  Since then we have begun to also replace some of
-the C-style constructs with equivalent C++ functionality, either from
-the C++ standard library or as custom classes or functions, in order
-to improve readability of the code and to increase code reuse through
-abstraction of commonly used functionality.
+However, C++ compilers and the C++ programming language have advanced
+significantly.  In 2020, the LAMMPS developers decided to require the
+C++11 standard as the minimum C++ language standard for LAMMPS.  Since
+then, we have begun to replace C-style constructs with equivalent C++
+functionality.  This was taken either from the C++ standard library or
+implemented as custom classes or functions.  The goal is to improve
+readability of the code and to increase code reuse through abstraction
+of commonly used functionality.
 
 .. note::
 
-   Please note that as of spring 2022 there is still a sizable chunk
-   of legacy code in LAMMPS that has not yet been refactored to
-   reflect these style conventions in full.  LAMMPS has a large code
-   base and many different contributors and there also is a hierarchy
-   of precedence in which the code is adapted.  Highest priority has
-   been the code in the ``src`` folder, followed by code in packages
-   in order of their popularity and complexity (simpler code is
-   adapted sooner), followed by code in the ``lib`` folder.  Source
-   code that is downloaded from external packages or libraries during
-   compilation is not subject to the conventions discussed here.
+   Please note that as of spring 2023 there is still a sizable chunk of
+   legacy code in LAMMPS that has not yet been refactored to reflect
+   these style conventions in full.  LAMMPS has a large code base and
+   many contributors.  There is also a hierarchy of precedence in which
+   the code is adapted.  Highest priority has been the code in the
+   ``src`` folder, followed by code in packages in order of their
+   popularity and complexity (simpler code gets adapted sooner), followed
+   by code in the ``lib`` folder.  Source code that is downloaded from
+   external packages or libraries during compilation is not subject to
+   the conventions discussed here.
 
-Object oriented code
+Object-oriented code
 ^^^^^^^^^^^^^^^^^^^^
 
-LAMMPS is designed to be an object oriented code.  Each simulation is
+LAMMPS is designed to be an object-oriented code.  Each simulation is
 represented by an instance of the LAMMPS class.  When running in
-parallel each MPI process creates such an instance.  This can be seen
+parallel, each MPI process creates such an instance.  This can be seen
 in the ``main.cpp`` file where the core steps of running a LAMMPS
 simulation are the following 3 lines of code:
 
-.. code-block:: C++
+.. code-block:: c++
 
     LAMMPS *lammps = new LAMMPS(argc, argv, lammps_comm);
     lammps->input->file();
@@ -67,29 +68,29 @@ other special features.
 The basic LAMMPS class hierarchy which is created by the LAMMPS class
 constructor is shown in :ref:`class-topology`.  When input commands
 are processed, additional class instances are created, or deleted, or
-replaced.  Likewise specific member functions of specific classes are
+replaced.  Likewise, specific member functions of specific classes are
 called to trigger actions such creating atoms, computing forces,
 computing properties, time-propagating the system, or writing output.
 
 Compositing and Inheritance
 ===========================
 
-LAMMPS makes extensive use of the object oriented programming (OOP)
+LAMMPS makes extensive use of the object-oriented programming (OOP)
 principles of *compositing* and *inheritance*. Classes like the
 ``LAMMPS`` class are a **composite** containing pointers to instances
 of other classes like ``Atom``, ``Comm``, ``Force``, ``Neighbor``,
-``Modify``, and so on.  Each of these classes implement certain
+``Modify``, and so on.  Each of these classes implements certain
 functionality by storing and manipulating data related to the
 simulation and providing member functions that trigger certain
 actions.  Some of those classes like ``Force`` are themselves
 composites, containing instances of classes describing different force
-interactions.  Similarly the ``Modify`` class contains a list of
+interactions.  Similarly, the ``Modify`` class contains a list of
 ``Fix`` and ``Compute`` classes.  If the input commands that
 correspond to these classes include the word *style*, then LAMMPS
 stores only a single instance of that class.  E.g. *atom_style*,
-*comm_style*, *pair_style*, *bond_style*.  It the input command does
-not include the word *style*, there can be many instances of that
-class defined.  E.g. *region*, *fix*, *compute*, *dump*.
+*comm_style*, *pair_style*, *bond_style*.  If the input command does
+**not** include the word *style*, then there may be many instances of
+that class defined, for example *region*, *fix*, *compute*, *dump*.
 
 **Inheritance** enables creation of *derived* classes that can share
 common functionality in their base class while providing a consistent
@@ -100,19 +101,18 @@ derived class variant was instantiated.  In LAMMPS these derived
 classes are often referred to as "styles", e.g.  pair styles, fix
 styles, atom styles and so on.
 
-This is the origin of the flexibility of LAMMPS.  For example pair
+This is the origin of the flexibility of LAMMPS.  For example, pair
 styles implement a variety of different non-bonded interatomic
 potentials functions.  All details for the implementation of a
 potential are stored and executed in a single class.
 
 As mentioned above, there can be multiple instances of classes derived
 from the ``Fix`` or ``Compute`` base classes.  They represent a
-different facet of LAMMPS flexibility as they provide methods which
-can be called at different points in time within a timestep, as
-explained in `Developer_flow`.  This allows the input script to tailor
-how a specific simulation is run, what diagnostic computations are
-performed, and how the output of those computations is further
-processed or output.
+different facet of LAMMPS' flexibility, as they provide methods which
+can be called at different points within a timestep, as explained in
+`Developer_flow`.  This allows the input script to tailor how a specific
+simulation is run, what diagnostic computations are performed, and how
+the output of those computations is further processed or output.
 
 Additional code sharing is possible by creating derived classes from the
 derived classes (e.g., to implement an accelerated version of a pair
@@ -164,15 +164,15 @@ The difference in behavior of the ``normal()`` and the ``poly()`` member
 functions is which of the two member functions is called when executing
 `base1->call()` versus `base2->call()`.  Without polymorphism, a
 function within the base class can only call member functions within the
-same scope, that is ``Base::call()`` will always call
-``Base::normal()``.  But for the `base2->call()` case the call of the
+same scope: that is, ``Base::call()`` will always call
+``Base::normal()``.  But for the `base2->call()` case, the call of the
 virtual member function will be dispatched to ``Derived::poly()``
-instead.  This mechanism means that functions are called within the
-scope of the class type that was used to *create* the class instance are
-invoked; even if they are assigned to a pointer using the type of a base
-class.  This is the desired behavior and this way LAMMPS can even use
-styles that are loaded at runtime from a shared object file with the
-:doc:`plugin command <plugin>`.
+instead.  This mechanism results in calling functions that are within
+the scope of the class that was used to *create* the instance, even if
+they are assigned to a pointer for their base class.  This is the
+desired behavior, and this way LAMMPS can even use styles that are loaded
+at runtime from a shared object file with the :doc:`plugin command
+<plugin>`.
 
 A special case of virtual functions are so-called pure functions.  These
 are virtual functions that are initialized to 0 in the class declaration
@@ -189,12 +189,12 @@ This has the effect that an instance of the base class cannot be
 created and that derived classes **must** implement these functions.
 Many of the functions listed with the various class styles in the
 section :doc:`Modify` are pure functions.  The motivation for this is
-to define the interface or API of the functions but defer their
+to define the interface or API of the functions, but defer their
 implementation to the derived classes.
 
 However, there are downsides to this. For example, calls to virtual
-functions from within a constructor, will not be in the scope of the
-derived class and thus it is good practice to either avoid calling them
+functions from within a constructor, will *not* be in the scope of the
+derived class, and thus it is good practice to either avoid calling them
 or to provide an explicit scope such as ``Base::poly()`` or
 ``Derived::poly()``.  Furthermore, any destructors in classes containing
 virtual functions should be declared virtual too, so they will be
@@ -208,8 +208,8 @@ dispatch.
    that are intended to replace a virtual or pure function use the
    ``override`` property keyword.  For the same reason, the use of
    overloads or default arguments for virtual functions should be
-   avoided as they lead to confusion over which function is supposed to
-   override which and which arguments need to be declared.
+   avoided, as they lead to confusion over which function is supposed to
+   override which, and which arguments need to be declared.
 
 Style Factories
 ===============
@@ -219,10 +219,10 @@ uses a programming pattern called `Factory`.  Those are functions that
 create an instance of a specific derived class, say ``PairLJCut`` and
 return a pointer to the type of the common base class of that style,
 ``Pair`` in this case.  To associate the factory function with the
-style keyword, an ``std::map`` class is used with function pointers
+style keyword, a ``std::map`` class is used with function pointers
 indexed by their keyword (for example "lj/cut" for ``PairLJCut`` and
 "morse" for ``PairMorse``).  A couple of typedefs help keep the code
-readable and a template function is used to implement the actual
+readable, and a template function is used to implement the actual
 factory functions for the individual classes.  Below is an example
 of such a factory function from the ``Force`` class as declared in
 ``force.h`` and implemented in ``force.cpp``.  The file ``style_pair.h``
@@ -232,7 +232,7 @@ macro ``PairStyle()`` will associate the style name "lj/cut"
 with a factory function creating an instance of the ``PairLJCut``
 class.
 
-.. code-block:: C++
+.. code-block:: c++
 
    // from force.h
    typedef Pair *(*PairCreator)(LAMMPS *);
@@ -279,26 +279,26 @@ from and writing to files and console instead of C++ "iostreams".
 This is mainly motivated by better performance, better control over
 formatting, and less effort to achieve specific formatting.
 
-Since mixing "stdio" and "iostreams" can lead to unexpected
-behavior. use of the latter is strongly discouraged.  Also output to
-the screen should not use the predefined ``stdout`` FILE pointer, but
-rather the ``screen`` and ``logfile`` FILE pointers managed by the
-LAMMPS class.  Furthermore, output should generally only be done by
-MPI rank 0 (``comm->me == 0``).  Output that is sent to both
-``screen`` and ``logfile`` should use the :cpp:func:`utils::logmesg()
-convenience function <LAMMPS_NS::utils::logmesg>`.
+Since mixing "stdio" and "iostreams" can lead to unexpected behavior,
+use of the latter is strongly discouraged.  Output to the screen should
+*not* use the predefined ``stdout`` FILE pointer, but rather the
+``screen`` and ``logfile`` FILE pointers managed by the LAMMPS class.
+Furthermore, output should generally only be done by MPI rank 0
+(``comm->me == 0``).  Output that is sent to both ``screen`` and
+``logfile`` should use the :cpp:func:`utils::logmesg() convenience
+function <LAMMPS_NS::utils::logmesg>`.
 
-We also discourage the use of stringstreams because the bundled {fmt}
-library and the customized tokenizer classes can provide the same
-functionality in a cleaner way with better performance.  This also
-helps maintain a consistent programming syntax with code from many
-different contributors.
+We discourage the use of stringstreams because the bundled {fmt} library
+and the customized tokenizer classes provide the same functionality in a
+cleaner way with better performance.  This also helps maintain a
+consistent programming syntax with code from many different
+contributors.
 
 Formatting with the {fmt} library
 ===================================
 
 The LAMMPS source code includes a copy of the `{fmt} library
-<https://fmt.dev>`_ which is preferred over formatting with the
+<https://fmt.dev>`_, which is preferred over formatting with the
 "printf()" family of functions.  The primary reason is that it allows
 a typesafe default format for any type of supported data.  This is
 particularly useful for formatting integers of a given size (32-bit or
@@ -313,17 +313,16 @@ been included into the C++20 language standard, so changes to adopt it
 are future-proof.
 
 Formatted strings are frequently created by calling the
-``fmt::format()`` function which will return a string as a
-``std::string`` class instance.  In contrast to the ``%`` placeholder
-in ``printf()``, the {fmt} library uses ``{}`` to embed format
-descriptors.  In the simplest case, no additional characters are
-needed as {fmt} will choose the default format based on the data type
-of the argument.  Otherwise the ``fmt::print()`` function may be
-used instead of ``printf()`` or ``fprintf()``.  In addition, several
-LAMMPS output functions, that originally accepted a single string as
-argument have been overloaded to accept a format string with optional
-arguments as well (e.g., ``Error::all()``, ``Error::one()``,
-``utils::logmesg()``).
+``fmt::format()`` function, which will return a string as a
+``std::string`` class instance.  In contrast to the ``%`` placeholder in
+``printf()``, the {fmt} library uses ``{}`` to embed format descriptors.
+In the simplest case, no additional characters are needed, as {fmt} will
+choose the default format based on the data type of the argument.
+Otherwise, the ``fmt::print()`` function may be used instead of
+``printf()`` or ``fprintf()``.  In addition, several LAMMPS output
+functions, that originally accepted a single string as argument have
+been overloaded to accept a format string with optional arguments as
+well (e.g., ``Error::all()``, ``Error::one()``, ``utils::logmesg()``).
 
 Summary of the {fmt} format syntax
 ==================================
@@ -332,10 +331,11 @@ The syntax of the format string is "{[<argument id>][:<format spec>]}",
 where either the argument id or the format spec (separated by a colon
 ':') is optional.  The argument id is usually a number starting from 0
 that is the index to the arguments following the format string.  By
-default these are assigned in order (i.e. 0, 1, 2, 3, 4 etc.).  The most
-common case for using argument id would be to use the same argument in
-multiple places in the format string without having to provide it as an
-argument multiple times. In LAMMPS the argument id is rarely used.
+default, these are assigned in order (i.e. 0, 1, 2, 3, 4 etc.).  The
+most common case for using argument id would be to use the same argument
+in multiple places in the format string without having to provide it as
+an argument multiple times. The argument id is rarely used in the LAMMPS
+source code.
 
 More common is the use of a format specifier, which starts with a colon.
 This may optionally be followed by a fill character (default is ' '). If
@@ -347,20 +347,21 @@ width, which may be followed by a dot '.' and a precision for floating
 point numbers.  The final character in the format string would be an
 indicator for the "presentation", i.e. 'd' for decimal presentation of
 integers, 'x' for hexadecimal, 'o' for octal, 'c' for character etc.
-This mostly follows the "printf()" scheme but without requiring an
+This mostly follows the "printf()" scheme, but without requiring an
 additional length parameter to distinguish between different integer
 widths.  The {fmt} library will detect those and adapt the formatting
 accordingly.  For floating point numbers there are correspondingly, 'g'
 for generic presentation, 'e' for exponential presentation, and 'f' for
 fixed point presentation.
 
-Thus "{:8}" would represent *any* type argument using at least 8
-characters; "{:<8}" would do this as left aligned, "{:^8}" as centered,
-"{:>8}" as right aligned.  If a specific presentation is selected, the
-argument type must be compatible or else the {fmt} formatting code will
-throw an exception. Some format string examples are given below:
+The format string "{:8}" would thus represent *any* type argument and be
+replaced by at least 8 characters; "{:<8}" would do this as left
+aligned, "{:^8}" as centered, "{:>8}" as right aligned.  If a specific
+presentation is selected, the argument type must be compatible or else
+the {fmt} formatting code will throw an exception.  Some format string
+examples are given below:
 
-.. code-block:: C
+.. code-block:: c++
 
    auto mesg = fmt::format("  CPU time: {:4d}:{:02d}:{:02d}\n", cpuh, cpum, cpus);
    mesg = fmt::format("{:<8s}| {:<10.5g} | {:<10.5g} | {:<10.5g} |{:6.1f} |{:6.2f}\n",
@@ -392,12 +393,12 @@ documentation <https://fmt.dev/latest/syntax.html>`_ website.
 Memory management
 ^^^^^^^^^^^^^^^^^
 
-Dynamical allocation of small data and objects can be done with the
-the C++ commands "new" and "delete/delete[].  Large data should use
-the member functions of the ``Memory`` class, most commonly,
-``Memory::create()``, ``Memory::grow()``, and ``Memory::destroy()``,
-which provide variants for vectors, 2d arrays, 3d arrays, etc.
-These can also be used for small data.
+Dynamical allocation of small data and objects can be done with the C++
+commands "new" and "delete/delete[]".  Large data should use the member
+functions of the ``Memory`` class, most commonly, ``Memory::create()``,
+``Memory::grow()``, and ``Memory::destroy()``, which provide variants
+for vectors, 2d arrays, 3d arrays, etc.  These can also be used for
+small data.
 
 The use of ``malloc()``, ``calloc()``, ``realloc()`` and ``free()``
 directly is strongly discouraged.  To simplify adapting legacy code
@@ -408,26 +409,24 @@ perform additional error checks for safety.
 Use of these custom memory allocation functions is motivated by the
 following considerations:
 
-- memory allocation failures on *any* MPI rank during a parallel run
-  will trigger an immediate abort of the entire parallel calculation
-  instead of stalling it
-- a failing "new" will trigger an exception which is also captured by
-  LAMMPS and triggers a global abort
-- allocation of multi-dimensional arrays will be done in a C compatible
-  fashion but so that the storage of the actual data is stored in one
-  large contiguous block.  Thus when MPI communication is needed,
+- Memory allocation failures on *any* MPI rank during a parallel run
+  will trigger an immediate abort of the entire parallel calculation.
+- A failing "new" will trigger an exception, which is also captured by
+  LAMMPS and triggers a global abort.
+- Allocation of multidimensional arrays will be done in a C compatible
+  fashion, but such that the storage of the actual data is stored in one
+  large contiguous block.  Thus, when MPI communication is needed,
   the data can be communicated directly (similar to Fortran arrays).
-- the "destroy()" and "sfree()" functions may safely be called on NULL
-  pointers
-- the "destroy()" functions will nullify the pointer variables making
-  "use after free" errors easy to detect
-- it is possible to use a larger than default memory alignment (not on
+- The "destroy()" and "sfree()" functions may safely be called on NULL
+  pointers.
+- The "destroy()" functions will nullify the pointer variables, thus
+  making "use after free" errors easy to detect.
+- It is possible to use a larger than default memory alignment (not on
   all operating systems, since the allocated storage pointers must be
-  compatible with ``free()`` for technical reasons)
+  compatible with ``free()`` for technical reasons).
 
-In the practical implementation of code this means that any pointer
-variables that are class members should be initialized to a
-``nullptr`` value in their respective constructors.  That way it is
-safe to call ``Memory::destroy()`` or ``delete[]`` on them before
-*any* allocation outside the constructor.  This helps prevent memory
-leaks.
+In the practical implementation of code this means, that any pointer
+variables, that are class members should be initialized to a ``nullptr``
+value in their respective constructors.  That way, it is safe to call
+``Memory::destroy()`` or ``delete[]`` on them before *any* allocation
+outside the constructor.  This helps prevent memory leaks.

doc/src/Developer_comm_ops.rst

@@ -14,8 +14,8 @@ Owned and ghost atoms
 As described on the :doc:`parallel partitioning algorithms
 <Developer_par_part>` page, LAMMPS spatially decomposes the simulation
 domain, either in a *brick* or *tiled* manner.  Each processor (MPI
-task) owns atoms within its sub-domain and additionally stores ghost
-atoms within a cutoff distance of its sub-domain.
+task) owns atoms within its subdomain and additionally stores ghost
+atoms within a cutoff distance of its subdomain.
 
 Forward and reverse communication
 =================================
@@ -28,7 +28,7 @@ The need to do this communication arises when data from the owned atoms
 is updated (e.g. their positions) and this updated information needs to
 be **copied** to the corresponding ghost atoms.
 
-And second, *reverse communication* which sends ghost atom information
+And second, *reverse communication*, which sends ghost atom information
 from each processor to the owning processor to **accumulate** (sum)
 the values with the corresponding owned atoms.  The need for this
 arises when data is computed and also stored with ghost atoms
@@ -58,7 +58,7 @@ embedded-atom method (EAM) which compute intermediate values in the
 first part of the compute() function that need to be stored by both
 owned and ghost atoms for the second part of the force computation.
 The *Comm* class methods perform the MPI communication for buffers of
-per-atom data.  They "call back" to the *Pair* class so it can *pack*
+per-atom data.  They "call back" to the *Pair* class, so it can *pack*
 or *unpack* the buffer with data the *Pair* class owns.  There are 4
 such methods that the *Pair* class must define, assuming it uses both
 forward and reverse communication:
@@ -70,22 +70,22 @@ forward and reverse communication:
 
 The arguments to these methods include the buffer and a list of atoms
 to pack or unpack.  The *Pair* class also must set the *comm_forward*
-and *comm_reverse* variables which store the number of values stored
+and *comm_reverse* variables, which store the number of values stored
 in the communication buffers for each operation.  This means, if
 desired, it can choose to store multiple per-atom values in the
 buffer, and they will be communicated together to minimize
 communication overhead.  The communication buffers are defined vectors
 containing ``double`` values.  To correctly store integers that may be
 64-bit (bigint, tagint, imageint) in the buffer, you need to use the
-`ubuf union <Communication buffer coding with ubuf>`_ construct.
+:ref:`ubuf union <communication_buffer_coding_with_ubuf>` construct.
 
 The *Fix*, *Compute*, and *Dump* classes can also invoke the same kind
 of forward and reverse communication operations using the same *Comm*
-class methods.  Likewise the same pack/unpack methods and
+class methods.  Likewise, the same pack/unpack methods and
 comm_forward/comm_reverse variables must be defined by the calling
 *Fix*, *Compute*, or *Dump* class.
 
-For *Fix* classes there is an optional second argument to the
+For *Fix* classes, there is an optional second argument to the
 *forward_comm()* and *reverse_comm()* call which can be used when the
 fix performs multiple modes of communication, with different numbers
 of values per atom.  The fix should set the *comm_forward* and
@@ -150,7 +150,7 @@ latter case, when the *ring* operation is complete, each processor can
 examine its original buffer to extract modified values.
 
 Note that the *ring* operation is similar to an MPI_Alltoall()
-operation where every processor effectively sends and receives data to
+operation, where every processor effectively sends and receives data to
 every other processor.  The difference is that the *ring* operation
 does it one step at a time, so the total volume of data does not need
 to be stored by every processor.  However, the *ring* operation is
@@ -184,8 +184,8 @@ The *exchange_data()* method triggers the communication to be
 performed.  Each processor provides the vector of *N* datums to send,
 and the size of each datum.  All datums must be the same size.
 
-The *create_atom()* and *exchange_atom()* methods are similar except
-that the size of each datum can be different.  Typically this is used
+The *create_atom()* and *exchange_atom()* methods are similar, except
+that the size of each datum can be different.  Typically, this is used
 to communicate atoms, each with a variable amount of per-atom data, to
 other processors.
 

doc/src/Developer_flow.rst

@@ -45,9 +45,9 @@ other methods in the class.
   zero before each timestep, so that forces (torques, etc) can be
   accumulated.
 
-Now for the ``Verlet::run()`` method.  Its basic structure in hi-level pseudo
-code is shown below.  In the actual code in ``src/verlet.cpp`` some of
-these operations are conditionally invoked.
+Now for the ``Verlet::run()`` method.  Its basic structure in hi-level
+pseudocode is shown below.  In the actual code in ``src/verlet.cpp``
+some of these operations are conditionally invoked.
 
 .. code-block:: python
 
@@ -105,17 +105,17 @@ need it.  These flags are passed to the various methods that compute
 particle interactions, so that they either compute and tally the
 corresponding data or can skip the extra calculations if the energy and
 virial are not needed.  See the comments for the ``Integrate::ev_set()``
-method which document the flag values.
+method, which document the flag values.
 
 At various points of the timestep, fixes are invoked,
 e.g. ``fix->initial_integrate()``.  In the code, this is actually done
-via the Modify class which stores all the Fix objects and lists of which
+via the Modify class, which stores all the Fix objects and lists of which
 should be invoked at what point in the timestep.  Fixes are the LAMMPS
 mechanism for tailoring the operations of a timestep for a particular
 simulation.  As described elsewhere, each fix has one or more methods,
 each of which is invoked at a specific stage of the timestep, as show in
-the timestep pseudo-code.  All the active fixes defined in an input
-script, that are flagged to have an ``initial_integrate()`` method are
+the timestep pseudocode.  All the active fixes defined in an input
+script, that are flagged to have an ``initial_integrate()`` method, are
 invoked at the beginning of each timestep.  Examples are :doc:`fix nve
 <fix_nve>` or :doc:`fix nvt or fix npt <fix_nh>` which perform the
 start-of-timestep velocity-Verlet integration operations to update
@@ -131,15 +131,15 @@ can be changed using the :doc:`neigh_modify every/delay/check
 <neigh_modify>` command.  If not, coordinates of ghost atoms are
 acquired by each processor via the ``forward_comm()`` method of the Comm
 class.  If neighbor lists need to be built, several operations within
-the inner if clause of the pseudo-code are first invoked.  The
+the inner if clause of the pseudocode are first invoked.  The
 ``pre_exchange()`` method of any defined fixes is invoked first.
-Typically this inserts or deletes particles from the system.
+Typically, this inserts or deletes particles from the system.
 
 Periodic boundary conditions are then applied by the Domain class via
 its ``pbc()`` method to remap particles that have moved outside the
 simulation box back into the box.  Note that this is not done every
 timestep, but only when neighbor lists are rebuilt.  This is so that
-each processor's sub-domain will have consistent (nearby) atom
+each processor's subdomain will have consistent (nearby) atom
 coordinates for its owned and ghost atoms.  It is also why dumped atom
 coordinates may be slightly outside the simulation box if not dumped
 on a step where the neighbor lists are rebuilt.
@@ -148,15 +148,15 @@ The box boundaries are then reset (if needed) via the ``reset_box()``
 method of the Domain class, e.g. if box boundaries are shrink-wrapped to
 current particle coordinates.  A change in the box size or shape
 requires internal information for communicating ghost atoms (Comm class)
-and neighbor list bins (Neighbor class) be updated.  The ``setup()``
+and neighbor list bins (Neighbor class) to be updated.  The ``setup()``
 method of the Comm class and ``setup_bins()`` method of the Neighbor
 class perform the update.
 
 The code is now ready to migrate atoms that have left a processor's
-geometric sub-domain to new processors.  The ``exchange()`` method of
+geometric subdomain to new processors.  The ``exchange()`` method of
 the Comm class performs this operation.  The ``borders()`` method of the
 Comm class then identifies ghost atoms surrounding each processor's
-sub-domain and communicates ghost atom information to neighboring
+subdomain and communicates ghost atom information to neighboring
 processors.  It does this by looping over all the atoms owned by a
 processor to make lists of those to send to each neighbor processor.  On
 subsequent timesteps, the lists are used by the ``Comm::forward_comm()``
@@ -217,20 +217,21 @@ file, and restart files.  See the :doc:`thermo_style <thermo_style>`,
 :doc:`dump <dump>`, and :doc:`restart <restart>` commands for more
 details.
 
-The the flow of control during energy minimization iterations is
-similar to that of a molecular dynamics timestep.  Forces are computed,
-neighbor lists are built as needed, atoms migrate to new processors, and
-atom coordinates and forces are communicated to neighboring processors.
-The only difference is what Fix class operations are invoked when.  Only
-a subset of LAMMPS fixes are useful during energy minimization, as
+The flow of control during energy minimization iterations is similar to
+that of a molecular dynamics timestep.  Forces are computed, neighbor
+lists are built as needed, atoms migrate to new processors, and atom
+coordinates and forces are communicated to neighboring processors.  The
+only difference is what Fix class operations are invoked when.  Only a
+subset of LAMMPS fixes are useful during energy minimization, as
 explained in their individual doc pages.  The relevant Fix class methods
-are ``min_pre_exchange()``, ``min_pre_force()``, and ``min_post_force()``.
-Each fix is invoked at the appropriate place within the minimization
-iteration.  For example, the ``min_post_force()`` method is analogous to
-the ``post_force()`` method for dynamics; it is used to alter or constrain
-forces on each atom, which affects the minimization procedure.
+are ``min_pre_exchange()``, ``min_pre_force()``, and
+``min_post_force()``.  Each fix is invoked at the appropriate place
+within the minimization iteration.  For example, the
+``min_post_force()`` method is analogous to the ``post_force()`` method
+for dynamics; it is used to alter or constrain forces on each atom,
+which affects the minimization procedure.
 
-After all iterations are completed there is a ``cleanup`` step which
+After all iterations are completed, there is a ``cleanup`` step which
 calls the ``post_run()`` method of fixes to perform operations only required
-at the end of a calculations (like freeing temporary storage or creating
+at the end of a calculation (like freeing temporary storage or creating
 final outputs).

doc/src/Developer_grid.rst

@@ -0,0 +1,845 @@
+Use of distributed grids within style classes
+---------------------------------------------
+
+.. versionadded:: 22Dec2022
+
+The LAMMPS source code includes two classes which facilitate the
+creation and use of distributed grids.  These are the Grid2d and
+Grid3d classes in the src/grid2d.cpp.h and src/grid3d.cpp.h files
+respectively.  As the names imply, they are used for 2d or 3d
+simulations, as defined by the :doc:`dimension <dimension>` command.
+
+The :doc:`Howto_grid <Howto_grid>` page gives an overview of how
+distributed grids are defined from a user perspective, lists LAMMPS
+commands which use them, and explains how grid cell data is referenced
+from an input script.  Please read that page first as it motivates the
+coding details discussed here.
+
+This doc page is for users who wish to write new styles (input script
+commands) which use distributed grids.  There are a variety of
+material models and analysis methods which use atoms (or
+coarse-grained particles) and grids in tandem.
+
+A *distributed* grid means each processor owns a subset of the grid
+cells.  In LAMMPS, the subset for each processor will be a sub-block
+of grid cells with low and high index bounds in each dimension of the
+grid.  The union of the sub-blocks across all processors is the global
+grid.
+
+More specifically, a grid point is defined for each cell (by default
+the center point), and a processor owns a grid cell if its point is
+within the processor's spatial subdomain.  The union of processor
+subdomains is the global simulation box.  If a grid point is on the
+boundary of two subdomains, the lower processor owns the grid cell.  A
+processor may also store copies of ghost cells which surround its
+owned cells.
+
+----------
+
+Style commands
+^^^^^^^^^^^^^^
+
+Style commands which can define and use distributed grids include the
+:doc:`compute <compute>`, :doc:`fix <fix>`, :doc:`pair <pair_style>`,
+and :doc:`kspace <kspace_style>` styles.  If you wish grid cell data
+to persist across timesteps, then use a fix.  If you wish grid cell
+data to be accessible by other commands, then use a fix or compute.
+Currently in LAMMPS, the :doc:`pair_style amoeba <pair_amoeba>`,
+:doc:`kspace_style pppm <kspace_style>`, and :doc:`kspace_style msm
+<kspace_style>` commands use distributed grids but do not require
+either of these capabilities; they thus create and use distributed
+grids internally.  Note that a pair style which needs grid cell data
+to persist could be coded to work in tandem with a fix style which
+provides that capability.
+
+The *size* of a grid is specified by the number of grid cells in each
+dimension of the simulation domain.  In any dimension the size can be
+any value >= 1.  Thus a 10x10x1 grid for a 3d simulation is
+effectively a 2d grid, where each grid cell spans the entire
+z-dimension.  A 1x100x1 grid for a 3d simulation is effectively a 1d
+grid, where grid cells are a series of thin xz slabs in the
+y-dimension.  It is even possible to define a 1x1x1 3d grid, though it
+may be inefficient to use it in a computational sense.
+
+Note that the choice of grid size is independent of the number of
+processors or their layout in a grid of processor subdomains which
+overlays the simulations domain.  Depending on the distributed grid
+size, a single processor may own many 1000s or no grid cells.
+
+A command can define multiple grids, each of a different size.  Each
+grid is an instantiation of the Grid2d or Grid3d class.
+
+The command also defines what data it will store for each grid it
+creates and it allocates the multidimensional array(s) needed to
+store the data.  No grid cell data is stored within the Grid2d or
+Grid3d classes.
+
+If a single value per grid cell is needed, the data array will have
+the same dimension as the grid, i.e. a 2d array for a 2d grid,
+likewise for 3d.  If multiple values per grid cell are needed, the
+data array will have one more dimension than the grid, i.e. a 3d array
+for a 2d grid, or 4d array for a 3d grid.  A command can choose to
+define multiple data arrays for each grid it defines.
+
+----------
+
+Grid data allocation and access
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The simplest way for a command to allocate and access grid cell data
+is to use the *create_offset()* methods provided by the Memory class.
+Arguments for these methods can be values returned by the
+*setup_grid()* method (described below), which define the extent of
+the grid cells (owned+ghost) the processor owns.  These 4 methods
+allocate memory for 2d (first two) and 3d (second two) grid data.  The
+two methods that end in "_offset" allocate an array which stores a single
+value per grid cell.  The two that end in "_last" allocate an array
+which stores *Nvalues* per grid cell.
+
+.. code-block:: c++
+
+   // single value per cell for a 2d grid = 2d array
+   memory->create2d_offset(data2d_one, nylo_out, nyhi_out,
+                           nxlo_out, nxhi_out, "data2d_one");
+
+   // nvalues per cell for a 2d grid = 3d array
+   memory->create3d_offset_last(data2d_multi, nylo_out, nyhi_out,
+                                nxlo_out, nxhi_out, nvalues, "data2d_multi");
+
+   // single value per cell for a 3d grid = 3d array
+   memory->create3d_offset(data3d_one, nzlo_out, nzhi_out, nylo_out,
+                           nyhi_out, nxlo_out, nxhi_out, "data3d_one");
+
+   // nvalues per cell for a 3d grid = 4d array
+   memory->create4d_offset_last(data3d_multi, nzlo_out, nzhi_out, nylo_out,
+                                nyhi_out, nxlo_out, nxhi_out, nvalues,
+                                "data3d_multi");
+
+Note that these multidimensional arrays are allocated as contiguous
+chunks of memory where the x-index of the grid varies fastest, then y,
+and the z-index slowest.  For multiple values per grid cell, the
+Nvalues are contiguous, so their index varies even faster than the
+x-index.
+
+The key point is that the "offset" methods create arrays which are
+indexed by the range of indices which are the bounds of the sub-block
+of the global grid owned by this processor.  This means loops like
+these can be written in the caller code to loop over owned grid cells,
+where the "i" loop bounds are the range of owned grid cells for the
+processor.  These are the bounds returned by the *setup_grid()*
+method:
+
+.. code-block:: c++
+
+    for (int iy = iylo; iy <= iyhi; iy++)
+      for (int ix = ixlo; ix <= ixhi; ix++)
+        data2d_one[iy][ix] = 0.0;
+
+    for (int iy = iylo; iy <= iyhi; iy++)
+      for (int ix = ixlo; ix <= ixhi; ix++)
+        for (int m = 0; m < nvalues; m++)
+          data2d_multi[iy][ix][m] = 0.0;
+
+    for (int iz = izlo; iz <= izhi; iz++)
+      for (int iy = iylo; iy <= iyhi; iy++)
+        for (int ix = ixlo; ix <= ixhi; ix++)
+          data3d_one[iz][iy][ix] = 0.0;
+
+    for (int iz = izlo; iz <= izhi; iz++)
+      for (int iy = iylo; iy <= iyhi; iy++)
+        for (int ix = ixlo; ix <= ixhi; ix++)
+           for (int m = 0; m < nvalues; m++)
+              data3d_multi[iz][iy][ix][m] = 0.0;
+
+Simply replacing the "i" bounds with "o" bounds, also returned by the
+*setup_grid()* method, would alter this code to loop over owned+ghost
+cells (the entire allocated grid).
+
+----------
+
+Grid class constructors
+^^^^^^^^^^^^^^^^^^^^^^^
+
+The following subsections describe the public methods of the Grid3d
+class which a style command can invoke.  The Grid2d methods are
+similar; simply remove arguments which refer to the z-dimension.
+
+There are 2 constructors which can be used.  They differ in the extra
+i/o xyz lo/hi arguments:
+
+.. code-block:: c++
+
+   Grid3d(class LAMMPS *lmp, MPI_Comm gcomm, int gnx, int gny, int gnz)
+   Grid3d(class LAMMPS *lmp, MPI_Comm gcomm, int gnx, int gny, int gnz,
+          int ixlo, int ixhi, int iylo, int iyhi, int izlo, int izhi,
+          int oxlo, int oxhi, int oylo, int oyhi, int ozlo, int ozhi)
+
+Both constructors take the LAMMPS instance pointer and a communicator
+over which the grid will be distributed.  Typically this is the
+*world* communicator the LAMMPS instance is using.  The
+:doc:`kspace_style msm <kspace_style>` command creates a series of
+grids, each of different size, which are partitioned across different
+sub-communicators of processors.  Both constructors are also passed
+the global grid size: *gnx* by *gny* by *gnz*.
+
+The first constructor is used when the caller wants the Grid class to
+partition the global grid across processors; the Grid class defines
+which grid cells each processor owns and also which it stores as ghost
+cells.  A subsequent call to *setup_grid()*, discussed below, returns
+this info to the caller.
+
+The second constructor allows the caller to define the extent of owned
+and ghost cells, and pass them to the Grid class.  The 6 arguments
+which start with "i" are the inclusive lower and upper index bounds of
+the owned (inner) grid cells this processor owns in each of the 3
+dimensions within the global grid.  Owned grid cells are indexed from
+0 to N-1 in each dimension.
+
+The 6 arguments which start with "o" are the inclusive bounds of the
+owned+ghost (outer) grid cells it stores.  If the ghost cells are on
+the other side of a periodic boundary, then these indices may be < 0
+or >= N in any dimension, so that oxlo <= ixlo and ixhi >= ixhi is
+always the case.
+
+For example, if Nx = 100, then a processor might pass ixlo=50,
+ixhi=60, oxlo=48, oxhi=62 to the Grid class.  Or ixlo=0, ixhi=10,
+oxlo=-2, oxhi=13.  If a processor owns no grid cells in a dimension,
+then the ihi value should be specified as one less than the ilo value.
+
+Note that the only reason to use the second constructor is if the
+logic for assigning ghost cells is too complex for the Grid class to
+compute, using the various set() methods described next.  Currently
+only the kspace_style pppm/electrode and kspace_style msm commands use
+the second constructor.
+
+----------
+
+Grid class set methods
+^^^^^^^^^^^^^^^^^^^^^^
+
+The following methods affect how the Grid class computes which owned
+and ghost cells are assigned to each processor.  *Set_shift_grid()* is
+the only method which influences owned cell assignment; all the rest
+influence ghost cell assignment.  These methods are only used with the
+first constructor; they are ignored if the second constructor is used.
+These methods must be called before the *setup_grid()* method is
+invoked, because they influence its operation.
+
+.. code-block:: c++
+
+   void set_shift_grid(double shift);
+   void set_distance(double distance);
+   void set_stencil_atom(int lo, int hi);
+   void set_shift_atom(double shift_lo, double shift_hi);
+   void set_stencil_grid(int lo, int hi);
+   void set_zfactor(double factor);
+
+Processors own a grid cell if a point within the grid cell is inside
+the processor's subdomain.  By default this is the center point of the
+grid cell.  The *set_shift_grid()* method can change this.  The *shift*
+argument is a value from 0.0 to 1.0 (inclusive) which is the offset of
+the point within the grid cell in each dimension.  The default is 0.5
+for the center of the cell.  A value of 0.0 is the lower left corner
+point; a value of 1.0 is the upper right corner point.  There is
+typically no need to change the default as it is optimal for
+minimizing the number of ghost cells needed.
+
+If a processor maps its particles to grid cells, it needs to allow for
+its particles being outside its subdomain between reneighboring.  The
+*distance* argument of the *set_distance()* method sets the furthest
+distance outside a processor's subdomain which a particle can move.
+Typically this is half the neighbor skin distance, assuming
+reneighboring is done appropriately.  This distance is used in
+determining how many ghost cells a processor needs to store to enable
+its particles to be mapped to grid cells.  The default value is 0.0.
+
+Some commands, like the :doc:`kspace_style pppm <kspace_style>`
+command, map values (charge in the case of PPPM) to a stencil of grid
+cells beyond the grid cell the particle is in.  The stencil extent may
+be different in the low and high directions.  The *set_stencil_atom()*
+method defines the maximum values of those 2 extents, assumed to be
+the same in each of the 3 dimensions.  Both the lo and hi values are
+specified as positive integers.  The default values are both 0.
+
+Some commands, like the :doc:`kspace_style pppm <kspace_style>`
+command, shift the position of an atom when mapping it to a grid cell,
+based on the size of the stencil used to map values to the grid
+(charge in the case of PPPM).  The lo and hi arguments of the
+*set_shift_atom()* method are the minimum shift in the low direction
+and the maximum shift in the high direction, assumed to be the same in
+each of the 3 dimensions.  The shifts should be fractions of a grid
+cell size with values between 0.0 and 1.0 inclusive.  The default
+values are both 0.0.  See the src/pppm.cpp file for examples of these
+lo/hi values for regular and staggered grids.
+
+Some methods like the :doc:`fix ttm/grid <fix_ttm>` command, perform
+finite difference kinds of operations on the grid, to diffuse electron
+heat in the case of the two-temperature model (TTM).  This operation
+uses ghost grid values beyond the owned grid values the processor
+updates.  The *set_stencil_grid()* method defines the extent of this
+stencil in both directions, assumed to be the same in each of the 3
+dimensions.  Both the lo and hi values are specified as positive
+integers.  The default values are both 0.
+
+The kspace_style pppm commands allow a grid to be defined which
+overlays a volume which extends beyond the simulation box in the z
+dimension.  This is for the purpose of modeling a 2d-periodic slab
+(non-periodic in z) as if it were a larger 3d periodic system,
+extended (with empty space) in the z dimension.  The
+:doc:`kspace_modify slab <kspace_modify>` command is used to specify
+the ratio of the larger volume to the simulation volume; a volume
+ratio of ~3 is typical.  For this kind of model, the PPPM caller sets
+the global grid size *gnz* ~3x larger than it would be otherwise.
+This same ratio is passed by the PPPM caller as the *factor* argument
+to the Grid class via the *set_zfactor()* method (*set_yfactor()* for
+2d grids).  The Grid class will then assign ownership of the 1/3 of
+grid cells that overlay the simulation box to the processors which
+also overlay the simulation box.  The remaining 2/3 of the grid cells
+are assigned to processors whose subdomains are adjacent to the upper
+z boundary of the simulation box.
+
+----------
+
+Grid class setup_grid method
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The *setup_grid()* method is called after the first constructor
+(above) to partition the grid across processors, which determines
+which grid cells each processor owns.  It also calculates how many
+ghost grid cells in each dimension and each direction each processor
+needs to store.
+
+Note that this method is NOT called if the second constructor above is
+used.  In that case, the caller assigns owned and ghost cells to each
+processor.
+
+Also note that this method must be invoked after any *set_*()* methods have
+been used, since they can influence the assignment of owned and ghost
+cells.
+
+.. code-block:: c++
+
+   void setup_grid(int &ixlo, int &ixhi, int &iylo, int &iyhi, int &izlo, int &izhi,
+                   int &oxlo, int &oxhi, int &oylo, int &oyhi, int &ozlo, int &ozhi)
+
+The 6 return arguments which start with "i" are the inclusive lower
+and upper index bounds of the owned (inner) grid cells this processor
+owns in each of the 3 dimensions within the global grid.  Owned grid
+cells are indexed from 0 to N-1 in each dimension.
+
+The 6 return arguments which start with "o" are the inclusive bounds of
+the owned+ghost cells it owns.  If the ghost cells are on the other
+side of a periodic boundary, then these indices may be < 0 or >= N in
+any dimension, so that oxlo <= ixlo and ixhi >= ixhi is always the
+case.
+
+----------
+
+More grid class set methods
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The following 2 methods can be used to override settings made by the
+constructors above.  If used, they must be called called before the
+*setup_comm()* method is invoked, since it uses the settings that
+these methods override.  In LAMMPS these methods are called by by the
+:doc:`kspace_style msm <kspace_style>` command for the grids it
+instantiates using the 2nd constructor above.
+
+.. code-block:: c++
+
+   void set_proc_neighs(int pxlo, int pxhi, int pylo, int pyhi, int pzlo, int pzhi)
+   void set_caller_grid(int fxlo, int fxhi, int fylo, int fyhi, int fzlo, int fzhi)
+
+The *set_proc_neighs()* method sets the processor IDs of the 6
+neighboring processors for each processor.  Normally these would match
+the processor grid neighbors which LAMMPS creates to overlay the
+simulation box (the default).  However, MSM excludes non-participating
+processors from coarse grid communication when less processors are
+used.  This method allows MSM to override the default values.
+
+The *set_caller_grid()* method species the size of the data arrays the
+caller allocates.  Normally these would match the extent of the ghost
+grid cells (the default).  However the MSM caller allocates a larger
+data array (more ghost cells) for its finest-level grid, for use in
+other operations besides owned/ghost cell communication.  This method
+allows MSM to override the default values.
+
+
+----------
+
+Grid class get methods
+^^^^^^^^^^^^^^^^^^^^^^
+
+The following methods allow the caller to query the settings for a
+specific grid, whether it created the grid or another command created
+it.
+
+.. code-block:: c++
+
+   void get_size(int &nxgrid, int &nygrid, int &nzgrid);
+   void get_bounds_owned(int &xlo, int &xhi, int &ylo, int &yhi, int &zlo, int &zhi)
+   void get_bounds_ghost(int &xlo, int &xhi, int &ylo, int &yhi, int &zlo, int &zhi)
+
+The *get_size()* method returns the size of the global grid in each dimension.
+
+The *get_bounds_owned()* method return the inclusive index bounds of
+the grid cells this processor owns.  The values range from 0 to N-1 in
+each dimension.  These values are the same as the "i" values returned
+by *setup_grid()*.
+
+The *get_bounds_ghost()* method return the inclusive index bounds of
+the owned+ghost grid cells this processor stores.  The owned cell
+indices range from 0 to N-1, so these indices may be less than 0 or
+greater than or equal to N in each dimension.  These values are the
+same as the "o" values returned by *setup_grid()*.
+
+----------
+
+Grid class owned/ghost communication
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If needed by the command, the following methods setup and perform
+communication of grid data to/from neighboring processors.  The
+*forward_comm()* method sends owned grid cell data to the
+corresponding ghost grid cells on other processors.  The
+*reverse_comm()* method sends ghost grid cell data to the
+corresponding owned grid cells on another processor.  The caller can
+choose to sum ghost grid cell data to the owned grid cell or simply
+copy it.
+
+.. code-block:: c++
+
+   void setup_comm(int &nbuf1, int &nbuf2)
+   void forward_comm(int caller, void *ptr, int which, int nper, int nbyte,
+                     void *buf1, void *buf2, MPI_Datatype datatype);
+   void reverse_comm(int caller, void *ptr, int which, int nper, int nbyte,
+                     void *buf1, void *buf2, MPI_Datatype datatype)
+   int ghost_adjacent();
+
+The *setup_comm()* method must be called one time before performing
+*forward* or *reverse* communication (multiple times if needed).  It
+returns two integers, which should be used to allocate two buffers.
+The *nbuf1* and *nbuf2* values are the number of grid cells whose data
+will be stored in two buffers by the Grid class when *forward* or
+*reverse* communication is performed.  The caller should thus allocate
+them to a size large enough to hold all the data used in any single
+forward or reverse communication operation it performs.  Note that the
+caller may allocate and communicate multiple data arrays for a grid it
+instantiates.  This size includes the bytes needed for the data type
+of the grid data it stores, e.g. double precision values.
+
+The *forward_comm()* and *reverse_comm()* methods send grid cell data
+from owned to ghost cells, or ghost to owned cells, respectively, as
+described above.  The *caller* argument should be one of these values
+-- Grid3d::COMPUTE, Grid3d::FIX, Grid3d::KSPACE, Grid3d::PAIR --
+depending on the style of the caller class.  The *ptr* argument is the
+"this" pointer to the caller class.  These 2 arguments are used to
+call back to pack()/unpack() functions in the caller class, as
+explained below.
+
+The *which* argument is a flag the caller can set which is passed to
+the caller's pack()/unpack() methods.  This allows a single callback
+method to pack/unpack data for several different flavors of
+forward/reverse communication, e.g. operating on different grids or
+grid data.
+
+The *nper* argument is the number of values per grid cell to be
+communicated.  The *nbyte* argument is the number of bytes per value,
+e.g. 8 for double-precision values.  The *buf1* and *buf2* arguments
+are the two allocated buffers described above.  So long as they are
+allocated for the maximum size communication, they can be re-used for
+any *forward_comm()/reverse_comm()* call.  The *datatype* argument is
+the MPI_Datatype setting, which should match the buffer allocation and
+the *nbyte* argument.  E.g. MPI_DOUBLE for buffers storing double
+precision values.
+
+To use the *forward_grid()* method, the caller must provide two
+callback functions; likewise for use of the *reverse_grid()* methods.
+These are the 4 functions, their arguments are all the same.
+
+.. code-block:: c++
+
+   void pack_forward_grid(int which, void *vbuf, int nlist, int *list);
+   void unpack_forward_grid(int which, void *vbuf, int nlist, int *list);
+   void pack_reverse_grid(int which, void *vbuf, int nlist, int *list);
+   void unpack_reverse_grid(int which, void *vbuf, int nlist, int *list);
+
+The *which* argument is set to the *which* value of the
+*forward_comm()* or *reverse_comm()* calls.  It allows the pack/unpack
+function to select what data values to pack/unpack.  *Vbuf* is the
+buffer to pack/unpack the data to/from.  It is a void pointer so that
+the caller can cast it to whatever data type it chooses, e.g. double
+precision values.  *Nlist* is the number of grid cells to pack/unpack
+and *list* is a vector (nlist in length) of offsets to where the data
+for each grid cell resides in the caller's data arrays, which is best
+illustrated with an example from the src/EXTRA-FIX/fix_ttm_grid.cpp
+class which stores the scalar electron temperature for 3d system in a
+3d grid (one value per grid cell):
+
+.. code-block:: c++
+
+   void FixTTMGrid::pack_forward_grid(int /*which*/, void *vbuf, int nlist, int *list)
+   {
+     auto buf = (double *) vbuf;
+     double *src = &T_electron[nzlo_out][nylo_out][nxlo_out];
+     for (int i = 0; i < nlist; i++) buf[i] = src[list[i]];
+   }
+
+In this case, the *which* argument is not used, *vbuf* points to a
+buffer of doubles, and the electron temperature is stored by the
+FixTTMGrid class in a 3d array of owned+ghost cells called T_electron.
+That array is allocated by the *memory->create_3d_offset()* method
+described above so that the first grid cell it stores is indexed as
+T_electron[nzlo_out][nylo_out][nxlo_out].  The *nlist* values in
+*list* are integer offsets from that first grid cell.  Setting *src*
+to the address of the first cell allows those offsets to be used to
+access the temperatures to pack into the buffer.
+
+Here is a similar portion of code from the src/fix_ave_grid.cpp class
+which can store two kinds of data, a scalar count of atoms in a grid
+cell, and one or more grid-cell-averaged atom properties.  The code
+from its *unpack_reverse_grid()* function for 2d grids and multiple
+per-atom properties per grid cell (*nvalues*) is shown here:
+
+.. code-block:: c++
+
+   void FixAveGrid::unpack_reverse_grid(int /*which*/, void *vbuf, int nlist, int *list)
+   {
+     auto buf = (double *) vbuf;
+     double *count,*data,*values;
+     count = &count2d[nylo_out][nxlo_out];
+     data = &array2d[nylo_out][nxlo_out][0];
+     m = 0;
+     for (i = 0; i < nlist; i++) {
+       count[list[i]] += buf[m++];
+       values = &data[nvalues*list[i]];
+       for (j = 0; j < nvalues; j++)
+        values[j] += buf[m++];
+     }
+   }
+
+Both the count and the multiple values per grid cell are communicated
+in *vbuf*.  Note that *data* is now a pointer to the first value in
+the first grid cell.  And *values* points to where the first value in
+*data* is for an offset of grid cells, calculated by multiplying
+*nvalues* by *list[i]*.  Finally, because this is reverse
+communication, the communicated buffer values are summed to the caller
+values.
+
+The *ghost_adjacent()* method returns a 1 if every processor can
+perform the necessary owned/ghost communication with only its nearest
+neighbor processors (4 in 2d, 6 in 3d).  It returns a 0 if any
+processor's ghost cells extend further than nearest neighbor
+processors.
+
+This can be checked by callers who have the option to change the
+global grid size to ensure more efficient nearest-neighbor-only
+communication if they wish.  In this case, they instantiate a grid of
+a given size (resolution), then invoke *setup_comm()* followed by
+*ghost_adjacent()*.  If the ghost cells are not adjacent, they destroy
+the grid instance and start over with a higher-resolution grid.
+Several of the :doc:`kspace_style pppm <kspace_style>` command
+variants have this option.
+
+----------
+
+Grid class remap methods for load balancing
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The following methods are used when a load-balancing operation,
+triggered by the :doc:`balance <balance>` or :doc:`fix balance
+<fix_balance>` commands, changes the partitioning of the simulation
+domain into processor subdomains.
+
+In order to work with load-balancing, any style command (compute, fix,
+pair, or kspace style) which allocates a grid and stores per-grid data
+should define a *reset_grid()* method; it takes no arguments.  It will
+be called by the two balance commands after they have reset processor
+subdomains and migrated atoms (particles) to new owning processors.
+The *reset_grid()* method will typically perform some or all of the
+following operations.  See the src/fix_ave_grid.cpp and
+src/EXTRA_FIX/fix_ttm_grid.cpp files for examples of *reset_grid()*
+methods, as well as the *pack_remap_grid()* and *unpack_remap_grid()*
+functions.
+
+First, the *reset_grid()* method can instantiate new grid(s) of the
+same global size, then call *setup_grid()* to partition them via the
+new processor subdomains.  At this point, it can invoke the
+*identical()* method which compares the owned and ghost grid cell
+index bounds between two grids, the old grid passed as a pointer
+argument, and the new grid whose *identical()* method is being called.
+It returns 1 if the indices match on all processors, otherwise 0.  If
+they all match, then the new grids can be deleted; the command can
+continue to use the old grids.
+
+If not, then the command should allocate new grid data array(s) which
+depend on the new partitioning.  If the command does not need to
+persist its grid data from the old partitioning to the new one, then
+the command can simply delete the old data array(s) and grid
+instance(s).  It can then return.
+
+If the grid data does need to persist, then the data for each grid
+needs to be "remapped" from the old grid partitioning to the new grid
+partitioning.  The *setup_remap()* and *remap()* methods are used for
+that purpose.
+
+.. code-block:: c++
+
+   int identical(Grid3d *old);
+   void setup_remap(Grid3d *old, int &nremap_buf1, int &nremap_buf2)
+   void remap(int caller, void *ptr, int which, int nper, int nbyte,
+              void *buf1, void *buf2, MPI_Datatype datatype)
+
+The arguments to these methods are identical to those for
+the *setup_comm()* and *forward_comm()* or *reverse_comm()* methods.
+However the returned *nremap_buf1* and *nremap2_buf* values will be
+different than the *nbuf1* and *nbuf2* values.  They should be used to
+allocate two different remap buffers, separate from the owned/ghost
+communication buffers.
+
+To use the *remap()* method, the caller must provide two
+callback functions:
+
+.. code-block:: c++
+
+   void pack_remap_grid(int which, void *vbuf, int nlist, int *list);
+   void unpack_remap_grid(int which, void *vbuf, int list, int *list);
+
+Their arguments are identical to those for the *pack_forward_grid()*
+and *unpack_forward_grid()* callback functions (or the reverse
+variants) discussed above.  Normally, both these methods pack/unpack
+all the data arrays for a given grid.  The *which* argument of the
+*remap()* method sets the *which* value for the pack/unpack functions.
+If the command instantiates multiple grids (of different sizes), it
+can be used within the pack/unpack methods to select which grid's data
+is being remapped.
+
+Note that the *pack_remap_grid()* function must copy values from the
+OLD grid data arrays into the *vbuf* buffer. The *unpack_remap_grid()*
+function must copy values from the *vbuf* buffer into the NEW grid
+data arrays.
+
+After the remap operation for grid cell data has been performed, the
+*reset_grid()* method can deallocate the two remap buffers it created,
+and can then exit.
+
+----------
+
+Grid class I/O methods
+^^^^^^^^^^^^^^^^^^^^^^
+
+There are two I/O methods in the Grid classes which can be used to
+read and write grid cell data to files.  The caller can decide on the
+precise format of each file, e.g. whether header lines are prepended
+or comment lines are allowed.  Fundamentally, the file should contain
+one line per grid cell for the entire global grid.  Each line should
+contain identifying info as to which grid cell it is, e.g. a unique
+grid cell ID or the ix,iy,iz indices of the cell within a 3d grid.
+The line should also contain one or more data values which are stored
+within the grid data arrays created by the command
+
+For grid cell IDs, the LAMMPS convention is that the IDs run from 1 to
+N, where N = Nx * Ny for 2d grids and N = Nx * Ny * Nz for 3d grids.
+The x-index of the grid cell varies fastest, then y, and the z-index
+varies slowest.  So for a 10x10x10 grid the cell IDs from 901-1000
+would be in the top xy layer of the z dimension.
+
+The *read_file()* method does something simple.  It reads a chunk of
+consecutive lines from the file and passes them back to the caller to
+process.  The caller provides a *unpack_read_grid()* function for this
+purpose.  The function checks the grid cell ID or indices and only
+stores grid cell data for the grid cells it owns.
+
+The *write_file()* method does something slightly more complex.  Each
+processor packs the data for its owned grid cells into a buffer.  The
+caller provides a *pack_write_grid()* function for this purpose.  The
+*write_file()* method then loops over all processors and each sends
+its buffer one at a time to processor 0, along with the 3d (or 2d)
+index bounds of its grid cell data within the global grid.  Processor
+0 calls back to the *unpack_write_grid()* function provided by the
+caller with the buffer.  The function writes one line per grid cell to
+the file.
+
+See the src/EXTRA_FIX/fix_ttm_grid.cpp file for examples of now both
+these methods are used to read/write electron temperature values
+from/to a file, as well as for implementations of the the pack/unpack
+functions described below.
+
+Here are the details of the two I/O methods and the 3 callback
+functions.  See the src/fix_ave_grid.cpp file for examples of all of
+them.
+
+.. code-block:: c++
+
+   void read_file(int caller, void *ptr, FILE *fp, int nchunk, int maxline)
+   void write_file(int caller, void *ptr, int which,
+                   int nper, int nbyte, MPI_Datatype datatype
+
+The *caller* argument in both methods should be one of these values --
+Grid3d::COMPUTE, Grid3d::FIX, Grid3d::KSPACE, Grid3d::PAIR --
+depending on the style of the caller class.  The *ptr* argument in
+both methods is the "this" pointer to the caller class.  These 2
+arguments are used to call back to pack()/unpack() functions in the
+caller class, as explained below.
+
+For the *read_file()* method, the *fp* argument is a file pointer to
+the file to be read from, opened on processor 0 by the caller.
+*Nchunk* is the number of lines to read per chunk, and *maxline* is
+the maximum number of characters per line.  The Grid class will
+allocate a buffer for storing chunks of lines based on these values.
+
+For the *write_file()* method, the *which* argument is a flag the
+caller can set which is passed back to the caller's pack()/unpack()
+methods.  If the command instantiates multiple grids (of different
+sizes), this flag can be used within the pack/unpack methods to select
+which grid's data is being written out (presumably to different
+files).  the *nper* argument is the number of values per grid cell to
+be written out.  The *nbyte* argument is the number of bytes per
+value, e.g. 8 for double-precision values.  The *datatype* argument is
+the MPI_Datatype setting, which should match the *nbyte* argument.
+E.g. MPI_DOUBLE for double precision values.
+
+To use the *read_grid()* method, the caller must provide one callback
+function.  To use the *write_grid()* method, it provides two callback
+functions:
+
+.. code-block:: c++
+
+   int unpack_read_grid(int nlines, char *buffer)
+   void pack_write_grid(int which, void *vbuf)
+   void unpack_write_grid(int which, void *vbuf, int *bounds)
+
+For *unpack_read_grid()* the *nlines* argument is the number of lines
+of character data read from the file and contained in *buffer*.  The
+lines each include a newline character at the end.  When the function
+processes the lines, it may choose to skip some of them (header or
+comment lines).  It returns an integer count of the number of grid
+cell lines it processed.  This enables the Grid class *read_file()*
+method to know when it has read the correct number of lines.
+
+For *pack_write_grid()* and *unpack_write_grid()*, the *vbuf* argument
+is the buffer to pack/unpack data to/from.  It is a void pointer so
+that the caller can cast it to whatever data type it chooses,
+e.g. double precision values.  the *which* argument is set to the
+*which* value of the *write_file()* method.  It allows the caller to
+choose which grid data to operate on.
+
+For *unpack_write_grid()*, the *bounds* argument is a vector of 4 or 6
+integer grid indices (4 for 2d, 6 for 3d).  They are the
+xlo,xhi,ylo,yhi,zlo,zhi index bounds of the portion of the global grid
+which the *vbuf* holds owned grid cell data values for.  The caller
+should loop over the values in *vbuf* with a double loop (2d) or
+triple loop (3d), similar to the code snippets listed above.  The
+x-index varies fastest, then y, and the z-index slowest.  If there are
+multiple values per grid cell, the index for those values varies
+fastest of all.  The caller can add the x,y,z indices of the grid cell
+(or the corresponding grid cell ID) to the data value(s) written as
+one line to the output file.
+
+----------
+
+Style class grid access methods
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+A style command can enable its grid cell data to be accessible from
+other commands.  For example :doc:`fix ave/grid <fix_ave_grid>` or
+:doc:`dump grid <dump>` or :doc:`dump grid/vtk <dump>`.  Those
+commands access the grid cell data by using a *grid reference* in
+their input script syntax, as described on the :doc:`Howto_grid
+<Howto_grid>` doc page.  They look like this:
+
+* c_ID:gname:dname
+* c_ID:gname:dname[I]
+* f_ID:gname:dname
+* f_ID:gname:dname[I]
+
+Each grid command instantiates has a unique *gname*, defined by the
+command.  Likewise each grid cell data structure (scalar or vector)
+associated with a grid has a unique *dname*, also defined by the
+command.
+
+To provide access to its grid cell data, a style command needs to
+implement the following 4 methods:
+
+.. code-block:: c++
+
+   int get_grid_by_name(const std::string &name, int &dim);
+   void *get_grid_by_index(int index);
+   int get_griddata_by_name(int igrid, const std::string &name, int &ncol);
+   void *get_griddata_by_index(int index);
+
+Currently only computes and fixes can implement these methods.  If it
+does so, the compute of fix should also set the variable
+*pergrid_flag* to 1.  See any of the compute or fix commands which set
+"pergrid_flag = 1" for examples of how these 4 functions can be
+implemented.
+
+The *get_grid_by_name()* method takes a grid name as input and returns
+two values.  The *dim* argument is returned as 2 or 3 for the
+dimensionality of the grid.  The function return is a grid index from
+0 to G-1 where *G* is the number of grids the command instantiates.  A
+value of -1 is returned if the grid name is not recognized.
+
+The *get_grid_by_index()* method is called after the
+*get_grid_by_name()* method, using the grid index it returned as its
+argument.  This method will return a pointer to the Grid2d or Grid3d
+class.  The caller can use this to query grid attributes, such as the
+global size of the grid, to ensure it is of the expected size.
+
+The *get_griddata_by_name()* method takes a grid index *igrid* and a
+data name as input.  It returns two values.  The *ncol* argument is
+returned as a 0 if the grid data is a single value (scalar) per grid
+cell, or an integer M > 0 if there are M values (vector) per grid
+cell.  Note that even if M = 1, it is still a 1-length vector, not a
+scalar.  The function return is a data index from 0 to D-1 where *D*
+is the number of data sets associated with that grid by the command.
+A value of -1 is returned if the data name is not recognized.
+
+The *get_griddata_by_index()* method is called after the
+*get_griddata_by_name()* method, using the data index it returned as
+its argument.  This method will return a pointer to the
+multidimensional array which stores the requested data.
+
+As in the discussion above of the Memory class *create_offset()*
+methods, the dimensionality of the array associated with the returned
+pointer depends on whether it is a 2d or 3d grid and whether there is
+a single or multiple values stored for each grid cell:
+
+* single value per cell for a 2d grid = 2d array pointer
+* multiple values per cell for a 2d grid = 3d array pointer
+* single value per cell for a 3d grid = 3d array pointer
+* multiple values per cell for a 3d grid = 4d array pointer
+
+The caller will typically access the data by casting the void pointer
+to the corresponding array pointer and using nested loops in x,y,z
+between owned or ghost index bounds returned by the
+*get_bounds_owned()* or *get_bounds_ghost()* methods to index into the
+array.  Example code snippets with this logic were listed above,
+
+----------
+
+Final notes
+^^^^^^^^^^^
+
+Finally, here are some additional issues to pay attention to for
+writing any style command which uses distributed grids via the Grid2d
+or Grid3d class.
+
+The command destructor should delete all instances of the Grid class,
+any buffers it allocated for forward/reverse or remap communication,
+and any data arrays it allocated to store grid cell data.
+
+If a command is intended to work for either 2d or 3d simulations, then
+it should have logic to instantiate either 2d or 3d grids and their
+associated data arrays, depending on the dimension of the simulation
+box.  The :doc:`fix ave/grid <fix_ave_grid>` command is an example of
+such a command.
+
+When a command maps its particles to the grid and updates grid cell
+values, it should check that it is not updating or accessing a grid
+cell value outside the range of its owned+ghost cells, and generate an
+error message if that is the case.  This could happen, for example, if
+a particle has moved further than half the neighbor skin distance,
+because the neighbor list update criterion are not adequate to prevent
+it from happening.  See the src/KSPACE/pppm.cpp file and its
+*particle_map()* method for an example of this kind of error check.