Merge pull request #3818 from akohlmey/next_release

Update version strings for upcoming release

.github/CODEOWNERS

@@ -63,9 +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
@@ -149,12 +151,12 @@ tools/vim/*           @hammondkd
 unittest/*            @akohlmey
 
 # cmake
-cmake/*               @junghans @rbberger
+cmake/*               @rbberger
 cmake/Modules/LAMMPSInterfacePlugin.cmake @akohlmey
 cmake/Modules/MPI4WIN.cmake @akohlmey
 cmake/Modules/OpenCLLoader.cmake @akohlmey
-cmake/Modules/Packages/COLVARS.cmake @junghans @rbberger @giacomofiorin
-cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
+cmake/Modules/Packages/COLVARS.cmake @rbberger @giacomofiorin
+cmake/Modules/Packages/KIM.cmake @rbberger @ellio167
 cmake/presets/*.cmake @akohlmey
 
 # python

.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

@@ -36,6 +36,7 @@ jobs:
         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 \
@@ -43,7 +44,7 @@ jobs:
               -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

.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 +55,5 @@ out/RelWithDebInfo
 out/Release
 out/x86
 out/x64
+src/Makefile.package-e
+src/Makefile.package.settings-e

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.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")
@@ -195,8 +202,8 @@ 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 +257,7 @@ set(STANDARD_PACKAGES
   KIM
   KSPACE
   LATBOLTZ
-  LATTE
+  LEPTON
   MACHDYN
   MANIFOLD
   MANYBODY
@@ -433,23 +440,19 @@ 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_ML-POD 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()
@@ -517,7 +520,7 @@ 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()
@@ -534,7 +537,10 @@ 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 ${_FLAG})
+  endif()
 endforeach()
 ########################################################################
 # Basic system tests (standard libraries, headers, functions, types)   #
@@ -562,6 +568,8 @@ RegisterStyles(${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})
@@ -574,8 +582,8 @@ 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})
@@ -602,8 +610,8 @@ 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})
@@ -614,18 +622,11 @@ 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})
@@ -839,9 +840,8 @@ 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(
@@ -854,35 +854,6 @@ 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)
@@ -894,6 +865,23 @@ 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")
@@ -905,6 +893,7 @@ 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}")
@@ -990,6 +979,12 @@ 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/CMakeSettings.json

@@ -72,7 +72,7 @@
       "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 ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe -DBUILD_MPI=off",
       "buildCommandArgs": "",
       "ctestCommandArgs": "",
       "inheritEnvironments": [ "clang_cl_x64" ],
@@ -105,7 +105,7 @@
       "configurationType": "Release",
       "buildRoot": "${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" ],
@@ -305,4 +305,4 @@
       ]
     }
   ]
-}
+}

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/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)

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/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 +60,15 @@ 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()
 
   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"
@@ -65,15 +78,15 @@ 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
@@ -82,11 +95,14 @@ if(GPU_API STREQUAL "CUDA")
 
   # 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 "12.0")
+  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"))
@@ -120,14 +136,14 @@ if(GPU_API STREQUAL "CUDA")
     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
+    # 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()
-    #    # 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 +166,17 @@ 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 +201,7 @@ 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 +210,7 @@ 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 +227,7 @@ 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 +237,26 @@ 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 +270,7 @@ 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 +286,7 @@ 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 +316,22 @@ 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 +343,7 @@ 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 +383,12 @@ 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 +397,8 @@ 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 +414,17 @@ 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 +447,25 @@ 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 ${LAMMPS_LIB_BINARY_DIR}/kokkos)
@@ -89,14 +90,12 @@ else()
   endif()
   add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
 
-
   set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
                           ${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
                           ${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src
                           ${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()
@@ -122,6 +121,11 @@ 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}/grid3d_kokkos.cpp
@@ -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/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

@@ -26,13 +26,15 @@ 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()
 
 if(BUILD_LAMMPS_SHELL)
@@ -50,12 +52,16 @@ 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/)

cmake/presets/all_off.cmake

@@ -43,7 +43,7 @@ set(ALL_PACKAGES
   KOKKOS
   KSPACE
   LATBOLTZ
-  LATTE
+  LEPTON
   MACHDYN
   MANIFOLD
   MANYBODY

cmake/presets/all_on.cmake

@@ -45,7 +45,7 @@ set(ALL_PACKAGES
   KOKKOS
   KSPACE
   LATBOLTZ
-  LATTE
+  LEPTON
   MACHDYN
   MANIFOLD
   MANYBODY

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/mingw-cross.cmake

@@ -35,7 +35,7 @@ set(WIN_PACKAGES
   INTEL
   INTERLAYER
   KSPACE
-  LATTE
+  LEPTON
   MACHDYN
   MANIFOLD
   MANYBODY

cmake/presets/most.cmake

@@ -35,10 +35,12 @@ set(ALL_PACKAGES
   GRANULAR
   INTERLAYER
   KSPACE
+  LEPTON
   MACHDYN
   MANYBODY
   MC
   MEAM
+  MESONT
   MISC
   ML-IAP
   ML-POD

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

@@ -86,18 +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 ;\
 		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
-		python $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
+		env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
+		$(PYTHON) $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
@@ -114,9 +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 ;\
 	)
@@ -131,8 +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 ;\
@@ -146,9 +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 ;\
@@ -167,17 +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 ;\
 		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
-		python utils/check-styles.py -s ../src -d src ;\
+		env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
+		$(PYTHON) utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
@@ -200,22 +202,22 @@ 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 ;\
 	)
 
@@ -224,6 +226,14 @@ char_check :
 
 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
 
@@ -252,7 +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" "22 December 2022" "2022-12-22"
+.TH LAMMPS "1" "15 June 2023" "2023-06-15"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 22 December 2022
+\- Molecular Dynamics Simulator.  Version 15 June 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/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.
 
@@ -28,13 +28,14 @@ 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>`
@@ -42,10 +43,9 @@ This is the list of packages that may require additional steps.
    * :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>`
@@ -125,10 +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
@@ -150,7 +151,9 @@ 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>`_
@@ -177,6 +180,9 @@ 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`.
 
+The GPU library has some multi-thread support using OpenMP.  If LAMMPS is built
+with ``-D BUILD_OMP=on`` this will also be enabled.
+
 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`
@@ -241,10 +247,10 @@ 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
@@ -270,10 +276,13 @@ 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
@@ -284,7 +293,7 @@ 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.
@@ -357,13 +366,13 @@ 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
@@ -375,7 +384,7 @@ 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
@@ -602,6 +611,12 @@ 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
@@ -636,7 +651,7 @@ 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::
 
@@ -668,20 +683,11 @@ 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:
 
@@ -816,60 +822,52 @@ 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``
 
 ----------
 
@@ -961,12 +959,12 @@ 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
@@ -1018,10 +1016,10 @@ 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
@@ -1076,7 +1074,7 @@ 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::
@@ -1107,10 +1105,10 @@ 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++
@@ -1151,13 +1149,13 @@ 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
 
 ----------
 
@@ -1186,10 +1184,10 @@ 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
@@ -1208,17 +1206,17 @@ 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::
 
@@ -1237,10 +1235,10 @@ 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
@@ -1259,21 +1257,20 @@ 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::
@@ -1286,42 +1283,45 @@ 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.
 
 ----------
 
@@ -1336,8 +1336,21 @@ 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
 
@@ -1350,9 +1363,9 @@ 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
@@ -1363,10 +1376,10 @@ 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``
@@ -1406,8 +1419,8 @@ 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.
 
@@ -1434,10 +1447,10 @@ ML-POD package
 
       .. 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
+         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
@@ -1447,10 +1460,10 @@ ML-POD 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-ML-POD``.
 
@@ -1549,10 +1562,10 @@ 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``
@@ -1565,8 +1578,8 @@ 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
@@ -1618,8 +1631,8 @@ 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
@@ -1673,10 +1686,10 @@ 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
@@ -1776,56 +1789,14 @@ 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
@@ -1926,6 +1897,22 @@ 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:
@@ -1980,10 +1967,10 @@ 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
@@ -2132,9 +2119,9 @@ 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>`
@@ -45,6 +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>`

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_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>`
@@ -104,6 +107,7 @@ 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>`
@@ -149,11 +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_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>`
@@ -44,9 +45,6 @@ OPT.
    * :doc:`ave/time <fix_ave_time>`
    * :doc:`aveforce <fix_aveforce>`
    * :doc:`balance <fix_balance>`
-   * :doc:`brownian <fix_brownian>`
-   * :doc:`brownian/asphere <fix_brownian>`
-   * :doc:`brownian/sphere <fix_brownian>`
    * :doc:`bocs <fix_bocs>`
    * :doc:`bond/break <fix_bond_break>`
    * :doc:`bond/create <fix_bond_create>`
@@ -54,6 +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>`
@@ -69,6 +70,7 @@ OPT.
    * :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>`
    * :doc:`electrode/conq (i) <fix_electrode>`
@@ -92,6 +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>`
@@ -101,13 +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>`
@@ -168,7 +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>`
@@ -257,12 +261,13 @@ OPT.
    * :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>`
@@ -270,4 +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>`
@@ -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 +243,7 @@ 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/src/Commands_removed.rst

@@ -38,6 +38,20 @@ 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
 ------------
 
@@ -50,6 +64,27 @@ for some optimizations leading to better performance.  The pair style
 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
 ------------
 

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

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

@@ -1,52 +1,53 @@
 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:
 
@@ -67,14 +68,14 @@ 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``,
@@ -83,7 +84,7 @@ 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*,
@@ -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``
@@ -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
@@ -347,18 +347,19 @@ 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++
 
@@ -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

@@ -28,9 +28,9 @@ 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 sub-domain.  The union of processor
-sub-domains is the global simulation box.  If a grid point is on the
-boundary of two sub-domains, the lower processor owns the grid cell.  A
+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.
 
@@ -62,7 +62,7 @@ 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 sub-domains which
+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.
 
@@ -70,7 +70,7 @@ 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 multi-dimensional array(s) needed to
+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.
 
@@ -115,7 +115,7 @@ which stores *Nvalues* per grid cell.
                                 nyhi_out, nxlo_out, nxhi_out, nvalues,
                                 "data3d_multi");
 
-Note that these multi-dimensional arrays are allocated as contiguous
+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
@@ -160,7 +160,7 @@ cells (the entire allocated grid).
 Grid class constructors
 ^^^^^^^^^^^^^^^^^^^^^^^
 
-The following sub-sections describe the public methods of the Grid3d
+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.
 
@@ -235,7 +235,7 @@ invoked, because they influence its operation.
    void set_zfactor(double factor);
 
 Processors own a grid cell if a point within the grid cell is inside
-the processor's sub-domain.  By default this is the center point of the
+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
@@ -245,9 +245,9 @@ 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 sub-domain between reneighboring.  The
+its particles being outside its subdomain between reneighboring.  The
 *distance* argument of the *set_distance()* method sets the furthest
-distance outside a processor's sub-domain which a particle can move.
+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
@@ -295,7 +295,7 @@ 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 sub-domains are adjacent to the upper
+are assigned to processors whose subdomains are adjacent to the upper
 z boundary of the simulation box.
 
 ----------
@@ -533,7 +533,7 @@ 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 insure more efficient nearest-neighbor-only
+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
@@ -549,13 +549,13 @@ 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 sub-domains.
+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
-sub-domains and migrated atoms (particles) to new owning processors.
+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()*
@@ -564,7 +564,7 @@ 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 sub-domains.  At this point, it can invoke 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.
@@ -753,7 +753,7 @@ their input script syntax, as described on the :doc:`Howto_grid
 * f_ID:gname:dname
 * f_ID:gname:dname[I]
 
-Each grid a command instantiates has a unique *gname*, defined by the
+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.
@@ -784,8 +784,7 @@ 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.  The :doc:`dump grid <dump>` to insure each
-its grid reference arguments are for grids of the same size.
+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
@@ -799,7 +798,7 @@ 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
-multi-dimensional array which stores the requested data.
+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

doc/src/Developer_notes.rst

@@ -11,6 +11,7 @@ Available topics are:
 
 - `Reading and parsing of text and text files`_
 - `Requesting and accessing neighbor lists`_
+- `Choosing between a custom atom style, fix property/atom, and fix STORE/ATOM`_
 - `Fix contributions to instantaneous energy, virial, and cumulative energy`_
 - `KSpace PPPM FFT grids`_
 
@@ -73,6 +74,8 @@ when converting "12.5", while the ValueTokenizer class will throw an
 :cpp:func:`ValueTokenizer::next_int()
 <LAMMPS_NS::ValueTokenizer::next_int>` is called on the same string.
 
+.. _request-neighbor-list:
+
 Requesting and accessing neighbor lists
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -102,7 +105,7 @@ build is then :doc:`processed in parallel <Developer_par_neigh>`.
 The most commonly required neighbor list is a so-called "half" neighbor
 list, where each pair of atoms is listed only once (except when the
 :doc:`newton command setting <newton>` for pair is off; in that case
-pairs straddling sub-domains or periodic boundaries will be listed twice).
+pairs straddling subdomains or periodic boundaries will be listed twice).
 Thus these are the default settings when a neighbor list request is created in:
 
 .. code-block:: c++
@@ -216,6 +219,30 @@ command:
 
    neighbor->add_request(this, "delete_atoms", NeighConst::REQ_FULL);
 
+Choosing between a custom atom style, fix property/atom, and fix STORE/ATOM
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+There are multiple ways to manage per-atom data within LAMMPS.  Often
+the per-atom storage is only used locally and managed by the class that
+uses it.  If the data has to persist between multiple time steps and
+migrate with atoms when they move from sub-domain to sub-domain or
+across periodic boundaries, then using a custom atom style, or :doc:`fix
+property/atom <fix_property_atom>`, or the internal fix STORE/ATOM are
+possible options.
+
+- Using the atom style is usually the most programming effort and mostly
+  needed when the per-atom data is an integral part of the model like a
+  per-atom charge or diameter and thus should be part of the Atoms
+  section of a :doc:`data file <read_data>`.
+
+- Fix property/atom is useful if the data is optional or should be
+  entered by the user, or accessed as a (named) custom property. In this
+  case the fix should be entered as part of the input (and not
+  internally) which allows to enter and store its content with data files.
+
+- Fix STORE/ATOM should be used when the data should be accessed internally
+  only and thus the fix can be created internally.
+
 Fix contributions to instantaneous energy, virial, and cumulative energy
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -361,7 +388,7 @@ allocated as a 1d vector or 3d array.  Either way, the ordering of
 values within contiguous memory x fastest, then y, z slowest.
 
 For the ``3d decomposition`` of the grid, the global grid is
-partitioned into bricks that correspond to the sub-domains of the
+partitioned into bricks that correspond to the subdomains of the
 simulation box that each processor owns.  Often, this is a regular 3d
 array (Px by Py by Pz) of bricks, where P = number of processors =
 Px * Py * Pz.  More generally it can be a tiled decomposition, where

doc/src/Developer_org.rst

@@ -7,7 +7,7 @@ but there are small a number of files in several other languages like C,
 Fortran, Shell script, or Python.
 
 The core of the code is located in the ``src`` folder and its
-sub-directories.  A sizable number of these files are in the ``src``
+subdirectories.  A sizable number of these files are in the ``src``
 directory itself, but there are plenty of :doc:`packages <Packages>`,
 which can be included or excluded when LAMMPS is built.  See the
 :doc:`Include packages in build <Build_package>` section of the manual
@@ -15,42 +15,42 @@ for more information about that part of the build process.  LAMMPS
 currently supports building with :doc:`conventional makefiles
 <Build_make>` and through :doc:`CMake <Build_cmake>`.  Those procedures
 differ in how packages are enabled or disabled for inclusion into a
-LAMMPS binary so they cannot be mixed.  The source files for each
-package are in all-uppercase sub-directories of the ``src`` folder, for
+LAMMPS binary, so they cannot be mixed.  The source files for each
+package are in all-uppercase subdirectories of the ``src`` folder, for
 example ``src/MOLECULE`` or ``src/EXTRA-MOLECULE``.  The ``src/STUBS``
-sub-directory is not a package but contains a dummy MPI library, that is
+subdirectory is not a package but contains a dummy MPI library, that is
 used when building a serial version of the code. The ``src/MAKE``
-directory and its sub-directories contain makefiles with settings and
+directory and its subdirectories contain makefiles with settings and
 flags for a variety of configuration and machines for the build process
 with traditional makefiles.
 
 The ``lib`` directory contains the source code for several supporting
 libraries or files with configuration settings to use globally installed
-libraries, that are required by some of the optional packages.  They may
+libraries, that are required by some optional packages.  They may
 include python scripts that can transparently download additional source
-code on request.  Each sub-directory, like ``lib/poems`` or ``lib/gpu``,
+code on request.  Each subdirectory, like ``lib/poems`` or ``lib/gpu``,
 contains the source files, some of which are in different languages such
-as Fortran or CUDA. These libraries included in the LAMMPS build,
-if the corresponding package is installed.
+as Fortran or CUDA. These libraries included in the LAMMPS build, if the
+corresponding package is installed.
 
 LAMMPS C++ source files almost always come in pairs, such as
 ``src/run.cpp`` (implementation file) and ``src/run.h`` (header file).
 Each pair of files defines a C++ class, for example the
-:cpp:class:`LAMMPS_NS::Run` class which contains the code invoked by the
-:doc:`run <run>` command in a LAMMPS input script.  As this example
+:cpp:class:`LAMMPS_NS::Run` class, which contains the code invoked by
+the :doc:`run <run>` command in a LAMMPS input script.  As this example
 illustrates, source file and class names often have a one-to-one
 correspondence with a command used in a LAMMPS input script.  Some
 source files and classes do not have a corresponding input script
-command, e.g. ``src/force.cpp`` and the :cpp:class:`LAMMPS_NS::Force`
+command, for example ``src/force.cpp`` and the :cpp:class:`LAMMPS_NS::Force`
 class.  They are discussed in the next section.
 
 The names of all source files are in lower case and may use the
-underscore character '_' to separate words. Outside of bundled libraries
-which may have different conventions, all C and C++ header files have a
-``.h`` extension, all C++ files have a ``.cpp`` extension, and C files a
-``.c`` extension. A small number of C++ classes and utility functions
-are implemented with only a ``.h`` file. Examples are the Pointers and
-Commands classes or the MathVec functions.
+underscore character '_' to separate words. Apart from bundled,
+externally maintained libraries, which may have different conventions,
+all C and C++ header files have a ``.h`` extension, all C++ files have a
+``.cpp`` extension, and C files a ``.c`` extension.  A few C++ classes
+and utility functions are implemented with only a ``.h`` file. Examples
+are the Pointers and Commands classes or the MathVec functions.
 
 Class topology
 --------------
@@ -62,35 +62,36 @@ associated source files in the ``src`` folder, for example the class
 :cpp:class:`LAMMPS_NS::Memory` corresponds to the files ``memory.cpp``
 and ``memory.h``, or the class :cpp:class:`LAMMPS_NS::AtomVec`
 corresponds to the files ``atom_vec.cpp`` and ``atom_vec.h``.  Full
-lines in the figure represent compositing: that is the class at the base
-of the arrow holds a pointer to an instance of the class at the tip.
-Dashed lines instead represent inheritance: the class to the tip of the
-arrow is derived from the class at the base.  Classes with a red boundary
-are not instantiated directly, but they represent the base classes for
-"styles".  Those "styles" make up the bulk of the LAMMPS code and only
-a few representative examples are included in the figure so it remains
-readable.
+lines in the figure represent compositing: that is, the class at the
+base of the arrow holds a pointer to an instance of the class at the
+tip.  Dashed lines instead represent inheritance: the class at the tip
+of the arrow is derived from the class at the base.  Classes with a red
+boundary are not instantiated directly, but they represent the base
+classes for "styles".  Those "styles" make up the bulk of the LAMMPS
+code and only a few representative examples are included in the figure,
+so it remains readable.
 
 .. _class-topology:
 .. figure:: JPG/lammps-classes.png
 
    LAMMPS class topology
 
-   This figure shows some of the relations of the base classes of the
-   LAMMPS simulation package.  Full lines indicate that a class holds an
-   instance of the class it is pointing to; dashed lines point to
-   derived classes that are given as examples of what classes may be
-   instantiated during a LAMMPS run based on the input commands and
-   accessed through the API define by their respective base classes.  At
-   the core is the :cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>` class, which
-   holds pointers to class instances with specific purposes.  Those may
-   hold instances of other classes, sometimes directly, or only
-   temporarily, sometimes as derived classes or derived classes of
-   derived classes, which may also hold instances of other classes.
+      This figure shows relations of base classes of the LAMMPS
+      simulation package.  Full lines indicate that a class holds an
+      instance of the class it is pointing to; dashed lines point to
+      derived classes that are given as examples of what classes may be
+      instantiated during a LAMMPS run based on the input commands and
+      accessed through the API define by their respective base classes.
+      At the core is the :cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>` class,
+      which holds pointers to class instances with specific purposes.
+      Those may hold instances of other classes, sometimes directly, or
+      only temporarily, sometimes as derived classes or derived classes
+      of derived classes, which may also hold instances of other
+      classes.
 
 The :cpp:class:`LAMMPS_NS::LAMMPS` class is the topmost class and
-represents what is generally referred to an "instance" of LAMMPS.  It is
-a composite holding pointers to instances of other core classes
+represents what is generally referred to as an "instance of LAMMPS".  It
+is a composite holding pointers to instances of other core classes
 providing the core functionality of the MD engine in LAMMPS and through
 them abstractions of the required operations.  The constructor of the
 LAMMPS class will instantiate those instances, process the command line
@@ -102,42 +103,44 @@ LAMMPS while passing it the command line flags and input script. It
 deletes the LAMMPS instance after the method reading the input returns
 and shuts down the MPI environment before it exits the executable.
 
-The :cpp:class:`LAMMPS_NS::Pointers` is not shown in the
+The :cpp:class:`LAMMPS_NS::Pointers` class is not shown in the
 :ref:`class-topology` figure for clarity.  It holds references to many
 of the members of the `LAMMPS_NS::LAMMPS`, so that all classes derived
 from :cpp:class:`LAMMPS_NS::Pointers` have direct access to those
-reference.  From the class topology all classes with blue boundary are
+references.  From the class topology all classes with blue boundary are
 referenced in the Pointers class and all classes in the second and third
-columns, that are not listed as derived classes are instead derived from
-:cpp:class:`LAMMPS_NS::Pointers`.  To initialize the pointer references
-in Pointers, a pointer to the LAMMPS class instance needs to be passed
-to the constructor and thus all constructors for classes derived from it
-must do so and pass this pointer to the constructor for Pointers.
+columns, that are not listed as derived classes, are instead derived
+from :cpp:class:`LAMMPS_NS::Pointers`.  To initialize the pointer
+references in Pointers, a pointer to the LAMMPS class instance needs to
+be passed to the constructor. All constructors for classes derived from
+it, must do so and thus pass that pointer to the constructor for
+:cpp:class:`LAMMPS_NS::Pointers`.  The default constructor for
+:cpp:class:`LAMMPS_NS::Pointers` is disabled to enforce this.
 
 Since all storage is supposed to be encapsulated (there are a few
 exceptions), the LAMMPS class can also be instantiated multiple times by
-a calling code.  Outside of the aforementioned exceptions, those LAMMPS
+a calling code.  Outside the aforementioned exceptions, those LAMMPS
 instances can be used alternately.  As of the time of this writing
-(early 2021) LAMMPS is not yet sufficiently thread-safe for concurrent
+(early 2023) LAMMPS is not yet sufficiently thread-safe for concurrent
 execution.  When running in parallel with MPI, care has to be taken,
 that suitable copies of communicators are used to not create conflicts
 between different instances.
 
-The LAMMPS class currently (early 2021) holds instances of 19 classes
-representing the core functionality.  There are a handful of virtual
-parent classes in LAMMPS that define what LAMMPS calls ``styles``.  They
-are shaded red in the :ref:`class-topology` figure.  Each of these are
-parents of a number of child classes that implement the interface
-defined by the parent class.  There are two main categories of these
-``styles``: some may only have one instance active at a time (e.g. atom,
-pair, bond, angle, dihedral, improper, kspace, comm) and there is a
-dedicated pointer variable for each of them in the composite class.
+The LAMMPS class currently holds instances of 19 classes representing
+the core functionality.  There are a handful of virtual parent classes
+in LAMMPS that define what LAMMPS calls ``styles``.  These are shaded
+red in the :ref:`class-topology` figure.  Each of these are parents of a
+number of child classes that implement the interface defined by the
+parent class.  There are two main categories of these ``styles``: some
+may only have one instance active at a time (e.g. atom, pair, bond,
+angle, dihedral, improper, kspace, comm) and there is a dedicated
+pointer variable for each of them in the corresponding composite class.
 Setups that require a mix of different such styles have to use a
-*hybrid* class that takes the place of the one allowed instance and then
-manages and forwards calls to the corresponding sub-styles for the
-designated subset of atoms or data.  The composite class may also have
-lists of class instances, e.g. Modify handles lists of compute and fix
-styles, while Output handles a list of dump class instances.
+*hybrid* class instance that acts as a proxy, and manages and forwards
+calls to the corresponding sub-style class instances for the designated
+subset of atoms or data.  The composite class may also have lists of
+class instances, e.g. ``Modify`` handles lists of compute and fix
+styles, while ``Output`` handles a list of dump class instances.
 
 The exception to this scheme are the ``command`` style classes.  These
 implement specific commands that can be invoked before, after, or in
@@ -146,19 +149,19 @@ command() method called and then, after completion, the class instance
 deleted.  Examples for this are the create_box, create_atoms, minimize,
 run, set, or velocity command styles.
 
-For all those ``styles`` certain naming conventions are employed: for
+For all those ``styles``, certain naming conventions are employed: for
 the fix nve command the class is called FixNVE and the source files are
-``fix_nve.h`` and ``fix_nve.cpp``. Similarly for fix ave/time we have
+``fix_nve.h`` and ``fix_nve.cpp``. Similarly, for fix ave/time we have
 FixAveTime and ``fix_ave_time.h`` and ``fix_ave_time.cpp``.  Style names
 are lower case and without spaces or special characters. A suffix or
 words are appended with a forward slash '/' which denotes a variant of
 the corresponding class without the suffix.  To connect the style name
 and the class name, LAMMPS uses macros like: ``AtomStyle()``,
 ``PairStyle()``, ``BondStyle()``, ``RegionStyle()``, and so on in the
-corresponding header file.  During configuration or compilation files
+corresponding header file.  During configuration or compilation, files
 with the pattern ``style_<name>.h`` are created that consist of a list
 of include statements including all headers of all styles of a given
-type that are currently active (or "installed).
+type that are currently enabled (or "installed").
 
 
 More details on individual classes in the :ref:`class-topology` are as
@@ -172,8 +175,8 @@ follows:
   that one or multiple simulations can be run, on the processors
   allocated for a run, e.g. by the mpirun command.
 
-- The Input class reads and processes input input strings and files,
-  stores variables, and invokes :doc:`commands <Commands_all>`.
+- The Input class reads and processes input (strings and files), stores
+  variables, and invokes :doc:`commands <Commands_all>`.
 
 - Command style classes are derived from the Command class. They provide
   input script commands that perform one-time operations
@@ -192,7 +195,7 @@ follows:
 - The Atom class stores per-atom properties associated with atom styles.
   More precisely, they are allocated and managed by a class derived from
   the AtomVec class, and the Atom class simply stores pointers to them.
-  The classes derived from AtomVec represent the different atom styles
+  The classes derived from AtomVec represent the different atom styles,
   and they are instantiated through the :doc:`atom_style <atom_style>`
   command.
 
@@ -206,18 +209,22 @@ follows:
   class stores a single list (for all atoms).  A NeighRequest class
   instance is created by pair, fix, or compute styles when they need a
   particular kind of neighbor list and use the NeighRequest properties
-  to select the neighbor list settings for the given request. There can
-  be multiple instances of the NeighRequest class and the Neighbor class
-  will try to optimize how they are computed by creating copies or
-  sub-lists where possible.
+  to select the neighbor list settings for the given request.  There can
+  be multiple instances of the NeighRequest class. The Neighbor class
+  will try to optimize how the requests are processed.  Depending on the
+  NeighRequest properties, neighbor lists are constructed from scratch,
+  aliased, or constructed by post-processing an existing list into
+  sub-lists.
 
 - The Comm class performs inter-processor communication, typically of
   ghost atom information.  This usually involves MPI message exchanges
   with 6 neighboring processors in the 3d logical grid of processors
   mapped to the simulation box. There are two :doc:`communication styles
-  <comm_style>` enabling different ways to do the domain decomposition.
-  Sometimes the Irregular class is used, when atoms may migrate to
-  arbitrary processors.
+  <comm_style>`, enabling different ways to perform the domain
+  decomposition.
+
+- The Irregular class is used, when atoms may migrate to arbitrary
+  processors.
 
 - The Domain class stores the simulation box geometry, as well as
   geometric Regions and any user definition of a Lattice.  The latter
@@ -246,7 +253,7 @@ follows:
   file, dump file snapshots, and restart files.  These correspond to the
   :doc:`Thermo <thermo_style>`, :doc:`Dump <dump>`, and
   :doc:`WriteRestart <write_restart>` classes respectively.  The Dump
-  class is a base class with several derived classes implementing
+  class is a base class, with several derived classes implementing
   various dump style variants.
 
 - The Timer class logs timing information, output at the end

doc/src/Developer_par_comm.rst

@@ -1,22 +1,22 @@
 Communication
 ^^^^^^^^^^^^^
 
-Following the partitioning scheme in use all per-atom data is
+Following the selected partitioning scheme, all per-atom data is
 distributed across the MPI processes, which allows LAMMPS to handle very
 large systems provided it uses a correspondingly large number of MPI
 processes.  Since The per-atom data (atom IDs, positions, velocities,
-types, etc.)  To be able to compute the short-range interactions MPI
-processes need not only access to data of atoms they "own" but also
-information about atoms from neighboring sub-domains, in LAMMPS referred
+types, etc.)  To be able to compute the short-range interactions, MPI
+processes need not only access to the data of atoms they "own" but also
+information about atoms from neighboring subdomains, in LAMMPS referred
 to as "ghost" atoms.  These are copies of atoms storing required
 per-atom data for up to the communication cutoff distance. The green
 dashed-line boxes in the :ref:`domain-decomposition` figure illustrate
-the extended ghost-atom sub-domain for one processor.
+the extended ghost-atom subdomain for one processor.
 
 This approach is also used to implement periodic boundary
 conditions: atoms that lie within the cutoff distance across a periodic
 boundary are also stored as ghost atoms and taken from the periodic
-replication of the sub-domain, which may be the same sub-domain, e.g. if
+replication of the subdomain, which may be the same subdomain, e.g. if
 running in serial.  As a consequence of this, force computation in
 LAMMPS is not subject to minimum image conventions and thus cutoffs may
 be larger than half the simulation domain.
@@ -28,10 +28,10 @@ be larger than half the simulation domain.
    ghost atom communication
 
    This figure shows the ghost atom communication patterns between
-   sub-domains for "brick" (left) and "tiled" communication styles for
+   subdomains for "brick" (left) and "tiled" communication styles for
    2d simulations.  The numbers indicate MPI process ranks.  Here the
-   sub-domains are drawn spatially separated for clarity.  The
-   dashed-line box is the extended sub-domain of processor 0 which
+   subdomains are drawn spatially separated for clarity.  The
+   dashed-line box is the extended subdomain of processor 0 which
    includes its ghost atoms.  The red- and blue-shaded boxes are the
    regions of communicated ghost atoms.
 
@@ -42,7 +42,7 @@ atom communication is performed in two stages for a 2d simulation (three
 in 3d) for both a regular and irregular partitioning of the simulation
 box.  For the regular case (left) atoms are exchanged first in the
 *x*-direction, then in *y*, with four neighbors in the grid of processor
-sub-domains.
+subdomains.
 
 In the *x* stage, processor ranks 1 and 2 send owned atoms in their
 red-shaded regions to rank 0 (and vice versa).  Then in the *y* stage,
@@ -55,11 +55,11 @@ For the irregular case (right) the two stages are similar, but a
 processor can have more than one neighbor in each direction.  In the
 *x* stage, MPI ranks 1,2,3 send owned atoms in their red-shaded regions to
 rank 0 (and vice versa).  These include only atoms between the lower
-and upper *y*-boundary of rank 0's sub-domain.  In the *y* stage, ranks
+and upper *y*-boundary of rank 0's subdomain.  In the *y* stage, ranks
 4,5,6 send atoms in their blue-shaded regions to rank 0.  This may
 include ghost atoms they received in the *x* stage, but only if they
 are needed by rank 0 to fill its extended ghost atom regions in the
-+/-*y* directions (blue rectangles).  Thus in this case, ranks 5 and
++/-*y* directions (blue rectangles).  Thus, in this case, ranks 5 and
 6 do not include ghost atoms they received from each other (in the *x*
 stage) in the atoms they send to rank 0.  The key point is that while
 the pattern of communication is more complex in the irregular
@@ -78,14 +78,14 @@ A "reverse" communication is when computed ghost atom attributes are
 sent back to the processor who owns the atom.  This is used (for
 example) to sum partial forces on ghost atoms to the complete force on
 owned atoms.  The order of the two stages described in the
-:ref:`ghost-atom-comm` figure is inverted and the same lists of atoms
+:ref:`ghost-atom-comm` figure is inverted, and the same lists of atoms
 are used to pack and unpack message buffers with per-atom forces.  When
 a received buffer is unpacked, the ghost forces are summed to owned atom
 forces.  As in forward communication, forces on atoms in the four blue
 corners of the diagrams are sent, received, and summed twice (once at
 each stage) before owning processors have the full force.
 
-These two operations are used many places within LAMMPS aside from
+These two operations are used in many places within LAMMPS aside from
 exchange of coordinates and forces, for example by manybody potentials
 to share intermediate per-atom values, or by rigid-body integrators to
 enable each atom in a body to access body properties.  Here are
@@ -105,16 +105,16 @@ performed in LAMMPS:
   atom pairs when building neighbor lists or computing forces.
 
 - The cutoff distance for exchanging ghost atoms is typically equal to
-  the neighbor cutoff.  But it can also chosen to be longer if needed,
+  the neighbor cutoff.  But it can also set to a larger value if needed,
   e.g. half the diameter of a rigid body composed of multiple atoms or
   over 3x the length of a stretched bond for dihedral interactions.  It
   can also exceed the periodic box size.  For the regular communication
   pattern (left), if the cutoff distance extends beyond a neighbor
-  processor's sub-domain, then multiple exchanges are performed in the
+  processor's subdomain, then multiple exchanges are performed in the
   same direction.  Each exchange is with the same neighbor processor,
   but buffers are packed/unpacked using a different list of atoms. For
-  forward communication, in the first exchange a processor sends only
+  forward communication, in the first exchange, a processor sends only
   owned atoms.  In subsequent exchanges, it sends ghost atoms received
   in previous exchanges.  For the irregular pattern (right) overlaps of
-  a processor's extended ghost-atom sub-domain with all other processors
+  a processor's extended ghost-atom subdomain with all other processors
   in each dimension are detected.

doc/src/Developer_par_long.rst

@@ -20,7 +20,7 @@ e) electric field values from grid points near each atom are interpolated to com
 
 For any of the spatial-decomposition partitioning schemes each processor
 owns the brick-shaped portion of FFT grid points contained within its
-sub-domain.  The two interpolation operations use a stencil of grid
+subdomain.  The two interpolation operations use a stencil of grid
 points surrounding each atom.  To accommodate the stencil size, each
 processor also stores a few layers of ghost grid points surrounding its
 brick.  Forward and reverse communication of grid point values is
@@ -40,31 +40,31 @@ orthogonal boxes.
 
 .. _fft-parallel:
 .. figure:: img/fft-decomp-parallel.png
-   :align: center
 
-   parallel FFT in PPPM
+   Parallel FFT in PPPM
 
-   Stages of a parallel FFT for a simulation domain overlaid
-   with an 8x8x8 3d FFT grid, partitioned across 64 processors.
-   Within each of the 4 diagrams, grid cells of the same color are
-   owned by a single processor; for simplicity only cells owned by 4
-   or 8 of the 64 processors are colored.  The two images on the left
-   illustrate brick-to-pencil communication.  The two images on the
-   right illustrate pencil-to-pencil communication, which in this
-   case transposes the *y* and *z* dimensions of the grid.
+      Stages of a parallel FFT for a simulation domain overlaid with an
+      8x8x8 3d FFT grid, partitioned across 64 processors.  Within each
+      of the 4 diagrams, grid cells of the same color are owned by a
+      single processor; for simplicity, only cells owned by 4 or 8 of
+      the 64 processors are colored.  The two images on the left
+      illustrate brick-to-pencil communication.  The two images on the
+      right illustrate pencil-to-pencil communication, which in this
+      case transposes the *y* and *z* dimensions of the grid.
 
 Parallel 3d FFTs require substantial communication relative to their
 computational cost.  A 3d FFT is implemented by a series of 1d FFTs
-along the *x-*, *y-*, and *z-*\ direction of the FFT grid.  Thus the FFT
-grid cannot be decomposed like atoms into 3 dimensions for parallel
+along the *x-*, *y-*, and *z-*\ direction of the FFT grid.  Thus, the
+FFT grid cannot be decomposed like atoms into 3 dimensions for parallel
 processing of the FFTs but only in 1 (as planes) or 2 (as pencils)
 dimensions and in between the steps the grid needs to be transposed to
 have the FFT grid portion "owned" by each MPI process complete in the
 direction of the 1d FFTs it has to perform. LAMMPS uses the
-pencil-decomposition algorithm as shown in the :ref:`fft-parallel` figure.
+pencil-decomposition algorithm as shown in the :ref:`fft-parallel`
+figure.
 
 Initially (far left), each processor owns a brick of same-color grid
-cells (actually grid points) contained within in its sub-domain.  A
+cells (actually grid points) contained within in its subdomain.  A
 brick-to-pencil communication operation converts this layout to 1d
 pencils in the *x*-dimension (center left).  Again, cells of the same
 color are owned by the same processor.  Each processor can then compute
@@ -97,7 +97,7 @@ across all $P$ processors with a single call to ``MPI_Alltoall()``, but
 this is typically much slower.  However, for the specialized brick and
 pencil tiling illustrated in :ref:`fft-parallel` figure, collective
 communication across the entire MPI communicator is not required.  In
-the example an :math:`8^3` grid with 512 grid cells is partitioned
+the example, an :math:`8^3` grid with 512 grid cells is partitioned
 across 64 processors; each processor owns a 2x2x2 3d brick of grid
 cells.  The initial brick-to-pencil communication (upper left to upper
 right) only requires collective communication within subgroups of 4
@@ -132,7 +132,7 @@ grid/particle operations that LAMMPS supports:
 - The fftMPI library allows each grid dimension to be a multiple of
   small prime factors (2,3,5), and allows any number of processors to
   perform the FFT.  The resulting brick and pencil decompositions are
-  thus not always as well-aligned but the size of subgroups of
+  thus not always as well-aligned, but the size of subgroups of
   processors for the two modes of communication (brick/pencil and
   pencil/pencil) still scale as :math:`O(P^{\frac{1}{3}})` and
   :math:`O(P^{\frac{1}{2}})`.
@@ -143,26 +143,28 @@ grid/particle operations that LAMMPS supports:
   in memory.  This reordering can be done during the packing or
   unpacking of buffers for MPI communication.
 
-- For large systems and particularly a large number of MPI processes,
-  the dominant cost for parallel FFTs is often the communication, not
-  the computation of 1d FFTs, even though the latter scales as :math:`N
-  \log(N)` in the number of grid points *N* per grid direction.  This is
-  due to the fact that only a 2d decomposition into pencils is possible
-  while atom data (and their corresponding short-range force and energy
-  computations) can be decomposed efficiently in 3d.
+- For large systems and particularly many MPI processes, the dominant
+  cost for parallel FFTs is often the communication, not the computation
+  of 1d FFTs, even though the latter scales as :math:`N \log(N)` in the
+  number of grid points *N* per grid direction.  This is due to the fact
+  that only a 2d decomposition into pencils is possible while atom data
+  (and their corresponding short-range force and energy computations)
+  can be decomposed efficiently in 3d.
 
-  This can be addressed by reducing the number of MPI processes involved
-  in the MPI communication by using :doc:`hybrid MPI + OpenMP
-  parallelization <Speed_omp>`.  This will use OpenMP parallelization
-  inside the MPI domains and while that may have a lower parallel
-  efficiency, it reduces the communication overhead.
+  Reducing the number of MPI processes involved in the MPI communication
+  will reduce this kind of overhead.  By using a :doc:`hybrid MPI +
+  OpenMP parallelization <Speed_omp>` it is still possible to use all
+  processes for parallel computation.  It will use OpenMP
+  parallelization inside the MPI domains. While that may have a lower
+  parallel efficiency for some part of the computation, that can be less
+  than the communication overhead in the 3d FFTs.
 
-  As an alternative it is also possible to start a :ref:`multi-partition
+  As an alternative, it is also possible to start a :ref:`multi-partition
   <partition>` calculation and then use the :doc:`verlet/split
   integrator <run_style>` to perform the PPPM computation on a
   dedicated, separate partition of MPI processes.  This uses an integer
-  "1:*p*" mapping of *p* sub-domains of the atom decomposition to one
-  sub-domain of the FFT grid decomposition and where pairwise non-bonded
+  "1:*p*" mapping of *p* subdomains of the atom decomposition to one
+  subdomain of the FFT grid decomposition and where pairwise non-bonded
   and bonded forces and energies are computed on the larger partition
   and the PPPM kspace computation concurrently on the smaller partition.
 
@@ -172,10 +174,10 @@ grid/particle operations that LAMMPS supports:
 
 - LAMMPS implements a ``GridComm`` class which overlays the simulation
   domain with a regular grid, partitions it across processors in a
-  manner consistent with processor sub-domains, and provides methods for
+  manner consistent with processor subdomains, and provides methods for
   forward and reverse communication of owned and ghost grid point
   values.  It is used for PPPM as an FFT grid (as outlined above) and
-  also for the MSM algorithm which uses a cascade of grid sizes from
+  also for the MSM algorithm, which uses a cascade of grid sizes from
   fine to coarse to compute long-range Coulombic forces.  The GridComm
   class is also useful for models where continuum fields interact with
   particles.  For example, the two-temperature model (TTM) defines heat

doc/src/Developer_par_neigh.rst

@@ -3,12 +3,12 @@ Neighbor lists
 
 To compute forces efficiently, each processor creates a Verlet-style
 neighbor list which enumerates all pairs of atoms *i,j* (*i* = owned,
-*j* = owned or ghost) with separation less than the applicable
-neighbor list cutoff distance.  In LAMMPS the neighbor lists are stored
-in a multiple-page data structure; each page is a contiguous chunk of
-memory which stores vectors of neighbor atoms *j* for many *i* atoms.
-This allows pages to be incrementally allocated or deallocated in blocks
-as needed.  Neighbor lists typically consume the most memory of any data
+*j* = owned or ghost) with separation less than the applicable neighbor
+list cutoff distance.  In LAMMPS, the neighbor lists are stored in a
+multiple-page data structure; each page is a contiguous chunk of memory
+which stores vectors of neighbor atoms *j* for many *i* atoms.  This
+allows pages to be incrementally allocated or deallocated in blocks as
+needed.  Neighbor lists typically consume the most memory of any data
 structure in LAMMPS.  The neighbor list is rebuilt (from scratch) once
 every few timesteps, then used repeatedly each step for force or other
 computations.  The neighbor cutoff distance is :math:`R_n = R_f +
@@ -16,20 +16,20 @@ computations.  The neighbor cutoff distance is :math:`R_n = R_f +
 the interatomic potential for computing short-range pairwise or manybody
 forces and :math:`\Delta_s` is a "skin" distance that allows the list to
 be used for multiple steps assuming that atoms do not move very far
-between consecutive time steps.  Typically the code triggers
+between consecutive time steps.  Typically, the code triggers
 reneighboring when any atom has moved half the skin distance since the
 last reneighboring; this and other options of the neighbor list rebuild
 can be adjusted with the :doc:`neigh_modify <neigh_modify>` command.
 
 On steps when reneighboring is performed, atoms which have moved outside
-their owning processor's sub-domain are first migrated to new processors
+their owning processor's subdomain are first migrated to new processors
 via communication.  Periodic boundary conditions are also (only)
 enforced on these steps to ensure each atom is re-assigned to the
 correct processor.  After migration, the atoms owned by each processor
-are stored in a contiguous vector.  Periodically each processor
+are stored in a contiguous vector.  Periodically, each processor
 spatially sorts owned atoms within its vector to reorder it for improved
 cache efficiency in force computations and neighbor list building.  For
-that atoms are spatially binned and then reordered so that atoms in the
+that, atoms are spatially binned and then reordered so that atoms in the
 same bin are adjacent in the vector.  Atom sorting can be disabled or
 its settings modified with the :doc:`atom_modify <atom_modify>` command.
 
@@ -39,12 +39,12 @@ its settings modified with the :doc:`atom_modify <atom_modify>` command.
 
    neighbor list stencils
 
-   A 2d simulation sub-domain (thick black line) and the corresponding
+   A 2d simulation subdomain (thick black line) and the corresponding
    ghost atom cutoff region (dashed blue line) for both orthogonal
    (left) and triclinic (right) domains.  A regular grid of neighbor
    bins (thin lines) overlays the entire simulation domain and need not
-   align with sub-domain boundaries; only the portion overlapping the
-   augmented sub-domain is shown.  In the triclinic case it overlaps the
+   align with subdomain boundaries; only the portion overlapping the
+   augmented subdomain is shown.  In the triclinic case, it overlaps the
    bounding box of the tilted rectangle.  The blue- and red-shaded bins
    represent a stencil of bins searched to find neighbors of a particular
    atom (black dot).
@@ -52,13 +52,13 @@ its settings modified with the :doc:`atom_modify <atom_modify>` command.
 To build a local neighbor list in linear time, the simulation domain is
 overlaid (conceptually) with a regular 3d (or 2d) grid of neighbor bins,
 as shown in the :ref:`neighbor-stencil` figure for 2d models and a
-single MPI processor's sub-domain.  Each processor stores a set of
-neighbor bins which overlap its sub-domain extended by the neighbor
+single MPI processor's subdomain.  Each processor stores a set of
+neighbor bins which overlap its subdomain, extended by the neighbor
 cutoff distance :math:`R_n`.  As illustrated, the bins need not align
 with processor boundaries; an integer number in each dimension is fit to
 the size of the entire simulation box.
 
-Most often LAMMPS builds what it calls a "half" neighbor list where
+Most often, LAMMPS builds what is called a "half" neighbor list where
 each *i,j* neighbor pair is stored only once, with either atom *i* or
 *j* as the central atom.  The build can be done efficiently by using a
 pre-computed "stencil" of bins around a central origin bin which
@@ -67,18 +67,18 @@ is simply a list of integer offsets in *x,y,z* of nearby bins
 surrounding the origin bin which are close enough to contain any
 neighbor atom *j* within a distance :math:`R_n` from any atom *i* in the
 origin bin.  Note that for a half neighbor list, the stencil can be
-asymmetric since each atom only need store half its nearby neighbors.
+asymmetric, since each atom only need store half its nearby neighbors.
 
 These stencils are illustrated in the figure for a half list and a bin
 size of :math:`\frac{1}{2} R_n`.  There are 13 red+blue stencil bins in
 2d (for the orthogonal case, 15 for triclinic).  In 3d there would be
 63, 13 in the plane of bins that contain the origin bin and 25 in each
 of the two planes above it in the *z* direction (75 for triclinic).  The
-reason the triclinic stencil has extra bins is because the bins tile the
-bounding box of the entire triclinic domain and thus are not periodic
-with respect to the simulation box itself.  The stencil and logic for
-determining which *i,j* pairs to include in the neighbor list are
-altered slightly to account for this.
+triclinic stencil has extra bins because the bins tile the bounding box
+of the entire triclinic domain, and thus are not periodic with respect
+to the simulation box itself.  The stencil and logic for determining
+which *i,j* pairs to include in the neighbor list are altered slightly
+to account for this.
 
 To build a neighbor list, a processor first loops over its "owned" plus
 "ghost" atoms and assigns each to a neighbor bin.  This uses an integer
@@ -95,7 +95,7 @@ supports:
   been found to be optimal for many typical cases.  Smaller bins incur
   additional overhead to loop over; larger bins require more distance
   calculations.  Note that for smaller bin sizes, the 2d stencil in the
-  figure would be more semi-circular in shape (hemispherical in 3d),
+  figure would be of a more semicircular shape (hemispherical in 3d),
   with bins near the corners of the square eliminated due to their
   distance from the origin bin.
 
@@ -111,8 +111,8 @@ supports:
   symmetric stencil.  It also includes lists with partial enumeration of
   ghost atom neighbors.  The full and ghost-atom lists are used by
   various manybody interatomic potentials.  Lists may also use different
-  criteria for inclusion of a pair interaction.  Typically this simply
-  depends only on the distance between two atoms and the cutoff
+  criteria for inclusion of a pairwise interaction.  Typically, this
+  simply depends only on the distance between two atoms and the cutoff
   distance.  But for finite-size coarse-grained particles with
   individual diameters (e.g. polydisperse granular particles), it can
   also depend on the diameters of the two particles.
@@ -121,11 +121,11 @@ supports:
   of the master neighbor list for the full system need to be generated,
   one for each sub-style, which contains only the *i,j* pairs needed to
   compute interactions between subsets of atoms for the corresponding
-  potential.  This means not all *i* or *j* atoms owned by a processor
+  potential.  This means, not all *i* or *j* atoms owned by a processor
   are included in a particular sub-list.
 
 - Some models use different cutoff lengths for pairwise interactions
-  between different kinds of particles which are stored in a single
+  between different kinds of particles, which are stored in a single
   neighbor list.  One example is a solvated colloidal system with large
   colloidal particles where colloid/colloid, colloid/solvent, and
   solvent/solvent interaction cutoffs can be dramatically different.
@@ -144,7 +144,7 @@ supports:
 
 - For small and sparse systems and as a fallback method, LAMMPS also
   supports neighbor list construction without binning by using a full
-  :math:`O(N^2)` loop over all *i,j* atom pairs in a sub-domain when
+  :math:`O(N^2)` loop over all *i,j* atom pairs in a subdomain when
   using the :doc:`neighbor nsq <neighbor>` command.
 
 - Dependent on the "pair" setting of the :doc:`newton <newton>` command,
@@ -153,7 +153,7 @@ supports:
   For the newton pair *on* setting the atom *j* is only added to the
   list if its *z* coordinate is larger, or if equal the *y* coordinate
   is larger, and that is equal, too, the *x* coordinate is larger.  For
-  homogeneously dense systems that will result in picking neighbors from
+  homogeneously dense systems, that will result in picking neighbors from
   a same size sector in always the same direction relative to the
-  "owned" atom and thus it should lead to similar length neighbor lists
-  and thus reduce the chance of a load imbalance.
+  "owned" atom, and thus it should lead to similar length neighbor lists
+  and reduce the chance of a load imbalance.

doc/src/Developer_par_openmp.rst

@@ -6,7 +6,7 @@ thread parallelism to predominantly distribute loops over local data
 and thus follow an orthogonal parallelization strategy to the
 decomposition into spatial domains used by the :doc:`MPI partitioning
 <Developer_par_part>`.  For clarity, this section discusses only the
-implementation in the OPENMP package as it is the simplest. The INTEL
+implementation in the OPENMP package, as it is the simplest. The INTEL
 and KOKKOS package offer additional options and are more complex since
 they support more features and different hardware like co-processors
 or GPUs.
@@ -14,7 +14,7 @@ or GPUs.
 One of the key decisions when implementing the OPENMP package was to
 keep the changes to the source code small, so that it would be easier to
 maintain the code and keep it in sync with the non-threaded standard
-implementation.  this is achieved by a) making the OPENMP version a
+implementation.  This is achieved by a) making the OPENMP version a
 derived class from the regular version (e.g. ``PairLJCutOMP`` from
 ``PairLJCut``) and overriding only methods that are multi-threaded or
 need to be modified to support multi-threading (similar to what was done
@@ -26,13 +26,13 @@ into three separate classes ``ThrOMP``, ``ThrData``, and ``FixOMP``.
 available in the corresponding base class (e.g. ``Pair`` for
 ``PairLJCutOMP``) like multi-thread aware variants of the "tally"
 functions. Those functions are made available through multiple
-inheritance so those new functions have to have unique names to avoid
+inheritance, so those new functions have to have unique names to avoid
 ambiguities; typically ``_thr`` is appended to the name of the function.
-``ThrData`` is a classes that manages per-thread data structures.
-It is used instead of extending the corresponding storage to per-thread
-arrays to avoid slowdowns due to "false sharing" when multiple threads
-update adjacent elements in an array and thus force the CPU cache lines
-to be reset and re-fetched.  ``FixOMP`` finally manages the "multi-thread
+``ThrData`` is a class that manages per-thread data structures.  It is
+used instead of extending the corresponding storage to per-thread arrays
+to avoid slowdowns due to "false sharing" when multiple threads update
+adjacent elements in an array and thus force the CPU cache lines to be
+reset and re-fetched.  ``FixOMP`` finally manages the "multi-thread
 state" like settings and access to per-thread storage, it is activated
 by the :doc:`package omp <package>` command.
 
@@ -46,24 +46,24 @@ involve multiple atoms and thus there are race conditions when multiple
 threads want to update per-atom data of the same atoms.  Five possible
 strategies have been considered to avoid this:
 
-1) restructure the code so that there is no overlapping access possible
+1. Restructure the code so that there is no overlapping access possible
    when computing in parallel, e.g. by breaking lists into multiple
    parts and synchronizing threads in between.
-2) have each thread be "responsible" for a specific group of atoms and
+2. Have each thread be "responsible" for a specific group of atoms and
    compute these interactions multiple times, once on each thread that
-   is responsible for a given atom and then have each thread only update
+   is responsible for a given atom, and then have each thread only update
    the properties of this atom.
-3) use mutexes around functions and regions of code where the data race
-   could happen
-4) use atomic operations when updating per-atom properties
-5) use replicated per-thread data structures to accumulate data without
+3. Use mutexes around functions and regions of code where the data race
+   could happen.
+4. Use atomic operations when updating per-atom properties.
+5. Use replicated per-thread data structures to accumulate data without
    conflicts and then use a reduction to combine those results into the
    data structures used by the regular style.
 
 Option 5 was chosen for the OPENMP package because it would retain the
-performance for the case of 1 thread and the code would be more
+performance for the case of a single thread and the code would be more
 maintainable.  Option 1 would require extensive code changes,
-particularly to the neighbor list code; options 2 would have incurred a
+particularly to the neighbor list code; option 2 would have incurred a
 2x or more performance penalty for the serial case; option 3 causes
 significant overhead and would enforce serialization of operations in
 inner loops and thus defeat the purpose of multi-threading; option 4
@@ -80,7 +80,7 @@ equivalent to the number of CPU cores per CPU socket on high-end
 supercomputers.
 
 Thus arrays like the force array are dimensioned to the number of atoms
-times the number of threads when enabling OpenMP support and inside the
+times the number of threads when enabling OpenMP support, and inside the
 compute functions a pointer to a different chunk is obtained by each thread.
 Similarly, accumulators like potential energy or virial are kept in
 per-thread instances of the ``ThrData`` class and then only reduced and
@@ -91,7 +91,7 @@ Loop scheduling
 """""""""""""""
 
 Multi-thread parallelization is applied by distributing (outer) loops
-statically across threads.  Typically this would be the loop over local
+statically across threads.  Typically, this would be the loop over local
 atoms *i* when processing *i,j* pairs of atoms from a neighbor list.
 The design of the neighbor list code results in atoms having a similar
 number of neighbors for homogeneous systems and thus load imbalances

doc/src/Developer_par_part.rst

@@ -7,39 +7,39 @@ distributed-memory parallelism is set with the :doc:`comm_style command
 
 .. _domain-decomposition:
 .. figure:: img/domain-decomp.png
-   :align: center
 
-   domain decomposition
+   Domain decomposition schemes
 
-   This figure shows the different kinds of domain decomposition used
-   for MPI parallelization: "brick" on the left with an orthogonal
-   (left) and a triclinic (middle) simulation domain, and a "tiled"
-   decomposition (right).  The black lines show the division into
-   sub-domains and the contained atoms are "owned" by the corresponding
-   MPI process. The green dashed lines indicate how sub-domains are
-   extended with "ghost" atoms up to the communication cutoff distance.
+      This figure shows the different kinds of domain decomposition used
+      for MPI parallelization: "brick" on the left with an orthogonal
+      (left) and a triclinic (middle) simulation domain, and a "tiled"
+      decomposition (right).  The black lines show the division into
+      subdomains, and the contained atoms are "owned" by the
+      corresponding MPI process. The green dashed lines indicate how
+      subdomains are extended with "ghost" atoms up to the communication
+      cutoff distance.
 
-The LAMMPS simulation box is a 3d or 2d volume, which can be orthogonal
-or triclinic in shape, as illustrated in the :ref:`domain-decomposition`
-figure for the 2d case.  Orthogonal means the box edges are aligned with
-the *x*, *y*, *z* Cartesian axes, and the box faces are thus all
-rectangular.  Triclinic allows for a more general parallelepiped shape
-in which edges are aligned with three arbitrary vectors and the box
-faces are parallelograms.  In each dimension box faces can be periodic,
-or non-periodic with fixed or shrink-wrapped boundaries.  In the fixed
-case, atoms which move outside the face are deleted; shrink-wrapped
-means the position of the box face adjusts continuously to enclose all
-the atoms.
+The LAMMPS simulation box is a 3d or 2d volume, which can be of
+orthogonal or triclinic shape, as illustrated in the
+:ref:`domain-decomposition` figure for the 2d case.  Orthogonal means
+the box edges are aligned with the *x*, *y*, *z* Cartesian axes, and the
+box faces are thus all rectangular.  Triclinic allows for a more general
+parallelepiped shape in which edges are aligned with three arbitrary
+vectors and the box faces are parallelograms.  In each dimension, box
+faces can be periodic, or non-periodic with fixed or shrink-wrapped
+boundaries.  In the fixed case, atoms which move outside the face are
+deleted; shrink-wrapped means the position of the box face adjusts
+continuously to enclose all the atoms.
 
 For distributed-memory MPI parallelism, the simulation box is spatially
-decomposed (partitioned) into non-overlapping sub-domains which fill the
+decomposed (partitioned) into non-overlapping subdomains which fill the
 box. The default partitioning, "brick", is most suitable when atom
 density is roughly uniform, as shown in the left-side images of the
-:ref:`domain-decomposition` figure.  The sub-domains comprise a regular
-grid and all sub-domains are identical in size and shape.  Both the
+:ref:`domain-decomposition` figure.  The subdomains comprise a regular
+grid, and all subdomains are identical in size and shape.  Both the
 orthogonal and triclinic boxes can deform continuously during a
 simulation, e.g. to compress a solid or shear a liquid, in which case
-the processor sub-domains likewise deform.
+the processor subdomains likewise deform.
 
 
 For models with non-uniform density, the number of particles per
@@ -50,14 +50,14 @@ load.  For such models, LAMMPS supports multiple strategies to reduce
 the load imbalance:
 
 - The processor grid decomposition is by default based on the simulation
-  cell volume and tries to optimize the volume to surface ratio for the sub-domains.
+  cell volume and tries to optimize the volume to surface ratio for the subdomains.
   This can be changed with the :doc:`processors command <processors>`.
-- The parallel planes defining the size of the sub-domains can be shifted
+- The parallel planes defining the size of the subdomains can be shifted
   with the :doc:`balance command <balance>`. Which can be done in addition
   to choosing a more optimal processor grid.
 - The recursive bisectioning algorithm in combination with the "tiled"
   communication style can produce a partitioning with equal numbers of
-  particles in each sub-domain.
+  particles in each subdomain.
 
 
 .. |decomp1| image:: img/decomp-regular.png
@@ -76,14 +76,14 @@ the load imbalance:
 
 The pictures above demonstrate different decompositions for a 2d system
 with 12 MPI ranks.  The atom colors indicate the load imbalance of each
-sub-domain with green being optimal and red the least optimal.
+subdomain, with green being optimal and red the least optimal.
 
-Due to the vacuum in the system, the default decomposition is unbalanced
-with several MPI ranks without atoms (left). By forcing a 1x12x1
-processor grid, every MPI rank does computations now, but number of
-atoms per sub-domain is still uneven and the thin slice shape increases
-the amount of communication between sub-domains (center left). With a
-2x6x1 processor grid and shifting the sub-domain divisions, the load
-imbalance is further reduced and the amount of communication required
-between sub-domains is less (center right).  And using the recursive
-bisectioning leads to further improved decomposition (right).
+Due to the vacuum in the system, the default decomposition is
+unbalanced, with several MPI ranks without atoms (left). By forcing a
+1x12x1 processor grid, every MPI rank does computations now, but the
+number of atoms per subdomain is still uneven, and the thin slice shape
+increases the amount of communication between subdomains (center
+left). With a 2x6x1 processor grid and shifting the subdomain divisions,
+the load imbalance is further reduced and the amount of communication
+required between subdomains is less (center right).  And using the
+recursive bisectioning leads to further improved decomposition (right).

doc/src/Developer_parallel.rst

@@ -3,11 +3,11 @@ Parallel algorithms
 
 LAMMPS is designed to enable running simulations in parallel using the
 MPI parallel communication standard with distributed data via domain
-decomposition.  The parallelization aims to be efficient result in good
-strong scaling (= good speedup for the same system) and good weak
-scaling (= the computational cost of enlarging the system is
+decomposition.  The parallelization aims to be efficient, and resulting
+in good strong scaling (= good speedup for the same system) and good
+weak scaling (= the computational cost of enlarging the system is
 proportional to the system size).  Additional parallelization using GPUs
-or OpenMP can also be applied within the sub-domain assigned to an MPI
+or OpenMP can also be applied within the subdomain assigned to an MPI
 process.  For clarity, most of the following illustrations show the 2d
 simulation case. The underlying algorithms in those cases, however,
 apply to both 2d and 3d cases equally well.

doc/src/Developer_unittest.rst

@@ -489,7 +489,7 @@ to update the YAML files. Running a command like
 
 .. code-block:: bash
 
-   $ test_pair_style mol-pair-lennard_mdf.yaml -g new.yaml
+   test_pair_style mol-pair-lennard_mdf.yaml -g new.yaml
 
 will read the settings from the ``mol-pair-lennard_mdf.yaml`` file and then compute
 the reference data and write a new file with to ``new.yaml``.  If this step fails,
@@ -500,13 +500,13 @@ It is also possible to do an update in place with:
 
 .. code-block:: bash
 
-   $ test_pair_style mol-pair-lennard_mdf.yaml -u
+   test_pair_style mol-pair-lennard_mdf.yaml -u
 
 And one can finally run the full set of tests with:
 
 .. code-block:: bash
 
-   $ test_pair_style mol-pair-lennard_mdf.yaml
+   test_pair_style mol-pair-lennard_mdf.yaml
 
 This will just print a summary of the groups of tests.  When using the "-v" flag
 the test will also keep any LAMMPS output and when using the "-s" flag, there

doc/src/Developer_updating.rst

@@ -24,6 +24,7 @@ Available topics in mostly chronological order are:
 - `Use of "override" instead of "virtual"`_
 - `Simplified and more compact neighbor list requests`_
 - `Split of fix STORE into fix STORE/GLOBAL and fix STORE/PERATOM`_
+- `Rename of fix STORE/PERATOM to fix STORE/ATOM and change of arguments`_
 - `Use Output::get_dump_by_id() instead of Output::find_dump()`_
 - `Refactored grid communication using Grid3d/Grid2d classes instead of GridComm`_
 
@@ -385,6 +386,34 @@ New:
 
 This change is **required** or else the code will not compile.
 
+Rename of fix STORE/PERATOM to fix STORE/ATOM and change of arguments
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 28Mar2023
+
+The available functionality of the internal fix to store per-atom
+properties was expanded to enable storing data with ghost atoms and to
+support binary restart files.  With those changes, the fix was renamed
+to fix STORE/ATOM and the number and order of (required) arguments has
+changed.
+
+Old syntax: ``ID group-ID STORE/PERATOM rflag n1 n2 [n3]``
+
+- *rflag* = 0/1, *no*/*yes* store per-atom values in restart file
+- :math:`n1 = 1, n2 = 1, \mathrm{no}\;n3 \to` per-atom vector, single value per atom
+- :math:`n1 = 1, n2 > 1, \mathrm{no}\;n3 \to` per-atom array, *n2* values per atom
+- :math:`n1 = 1, n2 > 0, n3 > 0 \to` per-atom tensor, *n2* x *n3* values per atom
+
+New syntax:  ``ID group-ID STORE/ATOM n1 n2 gflag rflag``
+
+- :math:`n1 = 1, n2 = 0 \to` per-atom vector, single value per atom
+- :math:`n1 > 1, n2 = 0 \to` per-atom array, *n1* values per atom
+- :math:`n1 > 0, n2 > 0 \to` per-atom tensor, *n1* x *n2* values per atom
+- *gflag* = 0/1, *no*/*yes* communicate per-atom values with ghost atoms
+- *rflag* = 0/1, *no*/*yes* store per-atom values in restart file
+
+Since this is an internal fix, there is no user visible change.
+
 Use Output::get_dump_by_id() instead of Output::find_dump()
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

doc/src/Developer_utils.rst

@@ -643,11 +643,13 @@ Tohoku University (under MIT license)
 
 ---------------------------
 
+.. _communication_buffer_coding_with_ubuf:
+
 Communication buffer coding with *ubuf*
 ---------------------------------------
 
 LAMMPS uses communication buffers where it collects data from various
-class instances and then exchanges the data with neighboring sub-domains.
+class instances and then exchanges the data with neighboring subdomains.
 For simplicity those buffers are defined as ``double`` buffers and
 used for doubles and integer numbers. This presents a unique problem
 when 64-bit integers are used.  While the storage needed for a ``double``

doc/src/Developer_write.rst

@@ -6,250 +6,9 @@ be extended by writing new classes that derive from existing
 parent classes in LAMMPS.  Here, some specific coding
 details are provided for writing code for LAMMPS.
 
-Writing a new fix style
-^^^^^^^^^^^^^^^^^^^^^^^
 
-Writing fixes is a flexible way of extending LAMMPS.  Users can
-implement many things using fixes:
-
-- changing particles attributes (positions, velocities, forces, etc.). Examples: FixNVE, FixFreeze.
-- reading/writing data. Example: FixRestart.
-- adding or modifying properties due to geometry. Example: FixWall.
-- interacting with other subsystems or external code: Examples: FixTTM, FixExternal, FixLATTE
-- saving information for analysis or future use (previous positions,
-  for instance). Examples: Fix AveTime, FixStoreState.
-
-
-All fixes are derived from the Fix base class and must have a
-constructor with the signature: ``FixPrintVel(class LAMMPS *, int, char **)``.
-
-Every fix must be registered in LAMMPS by writing the following lines
-of code in the header before include guards:
-
-.. code-block:: c++
-
-   #ifdef FIX_CLASS
-   // clang-format off
-   FixStyle(print/vel,FixPrintVel);
-   // clang-format on
-   #else
-   /* the definition of the FixPrintVel class comes here */
-   ...
-   #endif
-
-Where ``print/vel`` is the style name of your fix in the input script and
-``FixPrintVel`` is the name of the class. The header file would be called
-``fix_print_vel.h`` and the implementation file ``fix_print_vel.cpp``.
-These conventions allow LAMMPS to automatically integrate it into the
-executable when compiling and associate your new fix class with the designated
-keyword when it parses the input script.
-
-Let's write a simple fix which will print the average velocity at the end
-of each timestep. First of all, implement a constructor:
-
-.. code-block:: c++
-
-   FixPrintVel::FixPrintVel(LAMMPS *lmp, int narg, char **arg)
-   : Fix(lmp, narg, arg)
-   {
-     if (narg < 4)
-       error->all(FLERR,"Illegal fix print/vel command");
-
-     nevery = utils::inumeric(FLERR,arg[3],false,lmp);
-     if (nevery <= 0)
-       error->all(FLERR,"Illegal fix print/vel command");
-   }
-
-In the constructor you should parse your fix arguments which are
-specified in the script. All fixes have pretty much the same syntax:
-``fix <fix-ID> <fix group> <fix name> <fix arguments ...>``. The
-first 3 parameters are parsed by Fix base class constructor, while
-``<fix arguments>`` should be parsed by you. In our case, we need to
-specify how often we want to print an average velocity. For instance,
-once in 50 timesteps: ``fix 1 print/vel 50``. There is a special variable
-in the Fix class called ``nevery`` which specifies how often the method
-``end_of_step()`` is called. Thus all we need to do is just set it up.
-
-The next method we need to implement is ``setmask()``:
-
-.. code-block:: c++
-
-   int FixPrintVel::setmask()
-   {
-     int mask = 0;
-     mask |= FixConst::END_OF_STEP;
-     return mask;
-   }
-
-Here the user specifies which methods of your fix should be called
-during execution. The constant ``END_OF_STEP`` corresponds to the
-``end_of_step()`` method. The most important available methods that
-are called during a timestep and the order in which they are called
-are shown in the previous section.
-
-.. code-block:: c++
-
-   void FixPrintVel::end_of_step()
-   {
-     // for add3, scale3
-     using namespace MathExtra;
-
-     double** v = atom->v;
-     int nlocal = atom->nlocal;
-     double localAvgVel[4]; // 4th element for particles count
-     memset(localAvgVel, 0, 4 * sizeof(double));
-     for (int particleInd = 0; particleInd < nlocal; ++particleInd) {
-       add3(localAvgVel, v[particleInd], localAvgVel);
-     }
-     localAvgVel[3] = nlocal;
-     double globalAvgVel[4];
-     memset(globalAvgVel, 0, 4 * sizeof(double));
-     MPI_Allreduce(localAvgVel, globalAvgVel, 4, MPI_DOUBLE, MPI_SUM, world);
-     scale3(1.0 / globalAvgVel[3], globalAvgVel);
-     if ((comm->me == 0) && screen) {
-       fmt::print(screen,"{}, {}, {}\n",
-                  globalAvgVel[0], globalAvgVel[1], globalAvgVel[2]);
-     }
-   }
-
-In the code above, we use MathExtra routines defined in
-``math_extra.h``.  There are bunch of math functions to work with
-arrays of doubles as with math vectors.  It is also important to note
-that LAMMPS code should always assume to be run in parallel and that
-atom data is thus distributed across the MPI ranks.  Thus you can
-only process data from local atoms directly and need to use MPI library
-calls to combine or exchange data.  For serial execution, LAMMPS
-comes bundled with the MPI STUBS library that contains the MPI library
-function calls in dummy versions that only work for a single MPI rank.
-
-In this code we use an instance of Atom class. This object is stored
-in the Pointers class (see ``pointers.h``) which is the base class of
-the Fix base class. This object contains references to various class
-instances (the original instances are created and held by the LAMMPS
-class) with all global information about the simulation system.
-Data from the Pointers class is available to all classes inherited from
-it using protected inheritance. Hence when you write you own class,
-which is going to use LAMMPS data, don't forget to inherit from Pointers
-or pass an Pointer to it to all functions that need access. When writing
-fixes we inherit from class Fix which is inherited from Pointers so
-there is no need to inherit from it directly.
-
-The code above computes average velocity for all particles in the
-simulation.  Yet you have one unused parameter in fix call from the
-script: ``group_name``.  This parameter specifies the group of atoms
-used in the fix. So we should compute average for all particles in the
-simulation only if ``group_name == "all"``, but it can be any group.
-The group membership information of an atom is contained in the *mask*
-property of and atom and the bit corresponding to a given group is
-stored in the groupbit variable which is defined in Fix base class:
-
-.. code-block:: c++
-
-   for (int i = 0; i < nlocal; ++i) {
-     if (atom->mask[i] & groupbit) {
-     // Do all job here
-     }
-   }
-
-Class Atom encapsulates atoms positions, velocities, forces, etc. User
-can access them using particle index. Note, that particle indexes are
-usually changed every few timesteps because of neighbor list rebuilds
-and spatial sorting (to improve cache efficiency).
-
-Let us consider another Fix example: We want to have a fix which stores
-atoms position from previous time step in your fix. The local atoms
-indexes may not be valid on the next iteration. In order to handle
-this situation there are several methods which should be implemented:
-
-- ``double memory_usage()``: return how much memory the fix uses (optional)
-- ``void grow_arrays(int)``: do reallocation of the per particle arrays in your fix
-- ``void copy_arrays(int i, int j, int delflag)``: copy i-th per-particle
-  information to j-th. Used when atom sorting is performed. if delflag is set
-  and atom j owns a body, move the body information to atom i.
-- ``void set_arrays(int i)``: sets i-th particle related information to zero
-
-Note, that if your class implements these methods, it must call add calls of
-add_callback and delete_callback to constructor and destructor. Since we want
-to store positions of atoms from previous timestep, we need to add
-``double** xold`` to the header file. Than add allocation code
-to the constructor:
-
-.. code-block:: c++
-
-   FixSavePos::FixSavePos(LAMMPS *lmp, int narg, char **arg), xold(nullptr)
-   {
-   //...
-     memory->create(xold, atom->nmax, 3, "FixSavePos:x");
-     atom->add_callback(0);
-   }
-
-   FixSavePos::~FixSavePos() {
-     atom->delete_callback(id, 0);
-     memory->destroy(xold);
-   }
-
-Implement the aforementioned methods:
-
-.. code-block:: c++
-
-   double FixSavePos::memory_usage()
-   {
-     int nmax = atom->nmax;
-     double bytes = 0.0;
-     bytes += nmax * 3 * sizeof(double);
-     return bytes;
-   }
-
-   void FixSavePos::grow_arrays(int nmax)
-   {
-     memory->grow(xold, nmax, 3, "FixSavePos:xold");
-   }
-
-   void FixSavePos::copy_arrays(int i, int j, int delflag)
-   {
-     memcpy(xold[j], xold[i], sizeof(double) * 3);
-   }
-
-   void FixSavePos::set_arrays(int i)
-   {
-     memset(xold[i], 0, sizeof(double) * 3);
-   }
-
-   int FixSavePos::pack_exchange(int i, double *buf)
-   {
-     int m = 0;
-     buf[m++] = xold[i][0];
-     buf[m++] = xold[i][1];
-     buf[m++] = xold[i][2];
-
-     return m;
-   }
-
-   int FixSavePos::unpack_exchange(int nlocal, double *buf)
-   {
-     int m = 0;
-     xold[nlocal][0] = buf[m++];
-     xold[nlocal][1] = buf[m++];
-     xold[nlocal][2] = buf[m++];
-
-     return m;
-   }
-
-Now, a little bit about memory allocation. We use the Memory class which
-is just a bunch of template functions for allocating 1D and 2D
-arrays. So you need to add include ``memory.h`` to have access to them.
-
-Finally, if you need to write/read some global information used in
-your fix to the restart file, you might do it by setting flag
-``restart_global = 1`` in the constructor and implementing methods void
-``write_restart(FILE *fp)`` and ``void restart(char *buf)``.
-If, in addition, you want to write the per-atom property to restart
-files additional settings and functions are needed:
-
-- a fix flag indicating this needs to be set ``restart_peratom = 1;``
-- ``atom->add_callback()`` and ``atom->delete_callback()`` must be called
-  a second time with the final argument set to 1 instead of 0 (indicating
-  restart processing instead of per-atom data memory management).
-- the functions ``void pack_restart(int i, double *buf)`` and
-  ``void unpack_restart(int nlocal, int nth)`` need to be implemented
+.. toctree::
+   :maxdepth: 1
 
+   Developer_write_pair
+   Developer_write_fix

doc/src/Developer_write_fix.rst

@@ -0,0 +1,245 @@
+Writing a new fix style
+^^^^^^^^^^^^^^^^^^^^^^^
+
+Writing fix styles is a flexible way of extending LAMMPS.  Users can
+implement many things using fixes.  Some fix styles are only used
+internally to support compute styles or pair styles:
+
+- change particles attributes (positions, velocities, forces, etc.). Examples: ``FixNVE``, ``FixFreeze``.
+- read or write data.  Example: ``FixRestart``.
+- adding or modifying properties due to geometry. Example: ``FixWall``.
+- interacting with other subsystems or external code: Examples: ``FixTTM``, ``FixExternal``, ``FixMDI``
+- saving information for analysis or future use (previous positions,
+  for instance). Examples: ``FixAveTime``, ``FixStoreState``.
+
+All fixes are derived from the ``Fix`` base class and must have a
+constructor with the signature: ``FixPrintVel(class LAMMPS *, int, char **)``.
+
+Every fix must be registered in LAMMPS by writing the following lines
+of code in the header before include guards:
+
+.. code-block:: c++
+
+   #ifdef FIX_CLASS
+   // clang-format off
+   FixStyle(print/vel,FixPrintVel);
+   // clang-format on
+   #else
+   /* the definition of the FixPrintVel class comes here */
+   ...
+   #endif
+
+Where ``print/vel`` is the style name of your fix in the input script and
+``FixPrintVel`` is the name of the class. The header file would be called
+``fix_print_vel.h`` and the implementation file ``fix_print_vel.cpp``.
+These conventions allow LAMMPS to automatically integrate it into the
+executable when compiling and associate your new fix class with the designated
+keyword when it parses the input script.
+
+Let's write a simple fix which will print the average velocity at the end
+of each timestep. First of all, implement a constructor:
+
+.. code-block:: c++
+
+   FixPrintVel::FixPrintVel(LAMMPS *lmp, int narg, char **arg)
+   : Fix(lmp, narg, arg)
+   {
+     if (narg < 4) utils::missing_cmd_args(FLERR, "fix print/vel", error);
+
+     nevery = utils::inumeric(FLERR,arg[3],false,lmp);
+     if (nevery <= 0)
+       error->all(FLERR,"Illegal fix print/vel nevery value: {}", nevery);
+   }
+
+In the constructor you should parse the fix arguments which are
+specified in the script.  All fixes have pretty much the same syntax:
+``fix <fix-ID> <fix group> <fix name> <fix arguments ...>``. The first 3
+parameters are parsed by Fix base class constructor, while ``<fix
+arguments>`` should be parsed by you.  In our case, we need to specify
+how often we want to print an average velocity. For instance, once in 50
+timesteps: ``fix 1 print/vel 50``. There is a special variable in the
+Fix class called ``nevery`` which specifies how often the method
+``end_of_step()`` is called.  Thus all we need to do is just set it up.
+
+The next method we need to implement is ``setmask()``:
+
+.. code-block:: c++
+
+   int FixPrintVel::setmask()
+   {
+     int mask = 0;
+     mask |= FixConst::END_OF_STEP;
+     return mask;
+   }
+
+Here the we specify which methods of the fix should be called during
+:doc:`execution of a timestep <Developer_flow>`.  The constant
+``END_OF_STEP`` corresponds to the ``end_of_step()`` method. The most
+important available methods that are called during a timestep.
+
+.. code-block:: c++
+
+   void FixPrintVel::end_of_step()
+   {
+     // for add3, scale3
+     using namespace MathExtra;
+
+     double** v = atom->v;
+     int nlocal = atom->nlocal;
+     double localAvgVel[4]; // 4th element for particles count
+     memset(localAvgVel, 0, 4 * sizeof(double));
+     for (int particleInd = 0; particleInd < nlocal; ++particleInd) {
+       add3(localAvgVel, v[particleInd], localAvgVel);
+     }
+     localAvgVel[3] = nlocal;
+     double globalAvgVel[4];
+     memset(globalAvgVel, 0, 4 * sizeof(double));
+     MPI_Allreduce(localAvgVel, globalAvgVel, 4, MPI_DOUBLE, MPI_SUM, world);
+     scale3(1.0 / globalAvgVel[3], globalAvgVel);
+     if ((comm->me == 0) && screen) {
+       fmt::print(screen,"{}, {}, {}\n",
+                  globalAvgVel[0], globalAvgVel[1], globalAvgVel[2]);
+     }
+   }
+
+In the code above, we use MathExtra routines defined in
+``math_extra.h``.  There are bunch of math functions to work with
+arrays of doubles as with math vectors.  It is also important to note
+that LAMMPS code should always assume to be run in parallel and that
+atom data is thus distributed across the MPI ranks.  Thus you can
+only process data from local atoms directly and need to use MPI library
+calls to combine or exchange data.  For serial execution, LAMMPS
+comes bundled with the MPI STUBS library that contains the MPI library
+function calls in dummy versions that only work for a single MPI rank.
+
+In this code we use an instance of Atom class. This object is stored
+in the Pointers class (see ``pointers.h``) which is the base class of
+the Fix base class. This object contains references to various class
+instances (the original instances are created and held by the LAMMPS
+class) with all global information about the simulation system.
+Data from the Pointers class is available to all classes inherited from
+it using protected inheritance. Hence when you write you own class,
+which is going to use LAMMPS data, don't forget to inherit from Pointers
+or pass a Pointer to it to all functions that need access. When writing
+fixes we inherit from class Fix which is inherited from Pointers so
+there is no need to inherit from it directly.
+
+The code above computes average velocity for all particles in the
+simulation.  Yet you have one unused parameter in fix call from the
+script: ``group_name``.  This parameter specifies the group of atoms
+used in the fix. So we should compute average for all particles in the
+simulation only if ``group_name == "all"``, but it can be any group.
+The group membership information of an atom is contained in the *mask*
+property of an atom and the bit corresponding to a given group is
+stored in the groupbit variable which is defined in Fix base class:
+
+.. code-block:: c++
+
+   for (int i = 0; i < nlocal; ++i) {
+     if (atom->mask[i] & groupbit) {
+     // Do all job here
+     }
+   }
+
+Class Atom encapsulates atoms positions, velocities, forces, etc. Users
+can access them using particle index. Note, that particle indexes are
+usually changed every few timesteps because of neighbor list rebuilds
+and spatial sorting (to improve cache efficiency).
+
+Let us consider another Fix example: We want to have a fix which stores
+atoms position from the previous time step in your fix. The local atoms
+indexes may not be valid on the next iteration. In order to handle
+this situation there are several methods which should be implemented:
+
+- ``double memory_usage()``: return how much memory the fix uses (optional)
+- ``void grow_arrays(int)``: do reallocation of the per-particle arrays in your fix
+- ``void copy_arrays(int i, int j, int delflag)``: copy i-th per-particle
+  information to j-th. Used when atom sorting is performed. if delflag is set
+  and atom j owns a body, move the body information to atom i.
+- ``void set_arrays(int i)``: sets i-th particle related information to zero
+
+Note, that if your class implements these methods, it must add calls of
+add_callback and delete_callback to the constructor and destructor. Since we want
+to store positions of atoms from the previous timestep, we need to add
+``double** xold`` to the header file. Than add allocation code
+to the constructor:
+
+.. code-block:: c++
+
+   FixSavePos::FixSavePos(LAMMPS *lmp, int narg, char **arg), xold(nullptr)
+   {
+   //...
+     memory->create(xold, atom->nmax, 3, "FixSavePos:x");
+     atom->add_callback(0);
+   }
+
+   FixSavePos::~FixSavePos() {
+     atom->delete_callback(id, 0);
+     memory->destroy(xold);
+   }
+
+Implement the aforementioned methods:
+
+.. code-block:: c++
+
+   double FixSavePos::memory_usage()
+   {
+     int nmax = atom->nmax;
+     double bytes = 0.0;
+     bytes += nmax * 3 * sizeof(double);
+     return bytes;
+   }
+
+   void FixSavePos::grow_arrays(int nmax)
+   {
+     memory->grow(xold, nmax, 3, "FixSavePos:xold");
+   }
+
+   void FixSavePos::copy_arrays(int i, int j, int delflag)
+   {
+     memcpy(xold[j], xold[i], sizeof(double) * 3);
+   }
+
+   void FixSavePos::set_arrays(int i)
+   {
+     memset(xold[i], 0, sizeof(double) * 3);
+   }
+
+   int FixSavePos::pack_exchange(int i, double *buf)
+   {
+     int m = 0;
+     buf[m++] = xold[i][0];
+     buf[m++] = xold[i][1];
+     buf[m++] = xold[i][2];
+
+     return m;
+   }
+
+   int FixSavePos::unpack_exchange(int nlocal, double *buf)
+   {
+     int m = 0;
+     xold[nlocal][0] = buf[m++];
+     xold[nlocal][1] = buf[m++];
+     xold[nlocal][2] = buf[m++];
+
+     return m;
+   }
+
+Now, a little bit about memory allocation. We use the Memory class which
+is just a bunch of template functions for allocating 1D and 2D
+arrays. So you need to add include ``memory.h`` to have access to them.
+
+Finally, if you need to write/read some global information used in
+your fix to the restart file, you might do it by setting flag
+``restart_global = 1`` in the constructor and implementing methods void
+``write_restart(FILE *fp)`` and ``void restart(char *buf)``.
+If, in addition, you want to write the per-atom property to restart
+files additional settings and functions are needed:
+
+- a fix flag indicating this needs to be set ``restart_peratom = 1;``
+- ``atom->add_callback()`` and ``atom->delete_callback()`` must be called
+  a second time with the final argument set to 1 instead of 0 (indicating
+  restart processing instead of per-atom data memory management).
+- the functions ``void pack_restart(int i, double *buf)`` and
+  ``void unpack_restart(int nlocal, int nth)`` need to be implemented
+

doc/src/Errors_common.rst

@@ -113,7 +113,7 @@ LAMMPS output, something is wrong with your simulation.  If you
 suspect this is happening, it is a good idea to print out
 thermodynamic info frequently (e.g. every timestep) via the
 :doc:`thermo <thermo>` so you can monitor what is happening.
-Visualizing the atom movement is also a good idea to insure your model
+Visualizing the atom movement is also a good idea to ensure your model
 is behaving as you expect.
 
 In parallel, one way LAMMPS can hang is due to how different MPI

doc/src/Errors_debug.rst

@@ -40,7 +40,7 @@ We use it to show how to identify the origin of a segmentation fault.
 
 After recompiling LAMMPS and running the input you should get something like this:
 
-.. code-block::
+.. code-block:: console
 
    $ ./lmp -in in.melt
    LAMMPS (19 Mar 2020)
@@ -75,7 +75,7 @@ Using the GDB debugger to get a stack trace
 There are two options to use the GDB debugger for identifying the origin
 of the segmentation fault or similar crash. The GDB debugger has many
 more features and options, as can be seen for example its `online
-documentation <https://sourceware.org/gdb/current/onlinedocs/gdb/>`_.
+documentation <https://www.sourceware.org/gdb/documentation/>`_.
 
 Run LAMMPS from within the debugger
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -90,8 +90,9 @@ it.  When it reaches the code causing the segmentation fault, it will
 stop with a message why it stopped, print the current line of code, and
 drop back to the GDB prompt.
 
-.. code-block::
+.. code-block:: console
 
+   (gdb) run
    [...]
    Setting up Verlet run ...
      Unit style    : lj
@@ -106,7 +107,7 @@ drop back to the GDB prompt.
 Now typing the command "where" will show the stack of functions starting from
 the current function back to "main()".
 
-.. code-block::
+.. code-block:: console
 
    (gdb) where
    #0  0x00000000006653ab in LAMMPS_NS::PairLJCut::compute (this=0x829740, eflag=1, vflag=<optimized out>) at /home/akohlmey/compile/lammps/src/pair_lj_cut.cpp:139
@@ -124,7 +125,7 @@ You can also print the value of variables and see if there is anything
 unexpected.  Segmentation faults, for example, commonly happen when a
 pointer variable is not assigned and still initialized to NULL.
 
-.. code-block::
+.. code-block:: console
 
    (gdb) print x
    $1 = (double **) 0x7ffff7ca1010
@@ -153,7 +154,7 @@ utility to the current folder. Example: ``coredumpctl -o core dump lmp``.
 Now you can launch the debugger to load the executable, its debug info
 and the core dump and drop you to a prompt like before.
 
-.. code-block::
+.. code-block:: console
 
    $ gdb lmp core
    Reading symbols from lmp...
@@ -186,7 +187,7 @@ recommended to redirect the valgrind output to a file (e.g. with
 process ID) so that the messages of the multiple valgrind instances to
 the console are not mixed.
 
-.. code-block::
+.. code-block:: console
 
    $ valgrind ./lmp -in in.melt
    ==1933642== Memcheck, a memory error detector

doc/src/Errors_messages.rst

@@ -5635,7 +5635,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    Lost atoms are checked for each time thermo output is done.  See the
    thermo_modify lost command for options.  Lost atoms usually indicate
    bad dynamics, e.g. atoms have been blown far out of the simulation
-   box, or moved further than one processor's sub-domain away before
+   box, or moved further than one processor's subdomain away before
    reneighboring.
 
 *MEAM library error %d*
@@ -6092,7 +6092,7 @@ keyword to allow for additional bonds to be formed
    after a read_data, read_restart, or create_box command.
 
 *Next command must list all universe and uloop variables*
-   This is to insure they stay in sync.
+   This is to ensure they stay in sync.
 
 *No Kspace style defined for compute group/group*
    Self-explanatory.
@@ -6266,14 +6266,14 @@ keyword to allow for additional bonds to be formed
    One or more atoms are attempting to map their charge to a MSM grid point
    that is not owned by a processor.  This is likely for one of two
    reasons, both of them bad.  First, it may mean that an atom near the
-   boundary of a processor's sub-domain has moved more than 1/2 the
+   boundary of a processor's subdomain has moved more than 1/2 the
    :doc:`neighbor skin distance <neighbor>` without neighbor lists being
    rebuilt and atoms being migrated to new processors.  This also means
    you may be missing pairwise interactions that need to be computed.
    The solution is to change the re-neighboring criteria via the
    :doc:`neigh_modify <neigh_modify>` command.  The safest settings are
    "delay 0 every 1 check yes".  Second, it may mean that an atom has
-   moved far outside a processor's sub-domain or even the entire
+   moved far outside a processor's subdomain or even the entire
    simulation box. This indicates bad physics, e.g. due to highly
    overlapping atoms, too large a timestep, etc.
 
@@ -6281,14 +6281,14 @@ keyword to allow for additional bonds to be formed
    One or more atoms are attempting to map their charge to a PPPM grid
    point that is not owned by a processor.  This is likely for one of two
    reasons, both of them bad.  First, it may mean that an atom near the
-   boundary of a processor's sub-domain has moved more than 1/2 the
+   boundary of a processor's subdomain has moved more than 1/2 the
    :doc:`neighbor skin distance <neighbor>` without neighbor lists being
    rebuilt and atoms being migrated to new processors.  This also means
    you may be missing pairwise interactions that need to be computed.
    The solution is to change the re-neighboring criteria via the
    :doc:`neigh_modify <neigh_modify>` command.  The safest settings are
    "delay 0 every 1 check yes".  Second, it may mean that an atom has
-   moved far outside a processor's sub-domain or even the entire
+   moved far outside a processor's subdomain or even the entire
    simulation box. This indicates bad physics, e.g. due to highly
    overlapping atoms, too large a timestep, etc.
 
@@ -6296,14 +6296,14 @@ keyword to allow for additional bonds to be formed
    One or more atoms are attempting to map their charge to a PPPM grid
    point that is not owned by a processor.  This is likely for one of two
    reasons, both of them bad.  First, it may mean that an atom near the
-   boundary of a processor's sub-domain has moved more than 1/2 the
+   boundary of a processor's subdomain has moved more than 1/2 the
    :doc:`neighbor skin distance <neighbor>` without neighbor lists being
    rebuilt and atoms being migrated to new processors.  This also means
    you may be missing pairwise interactions that need to be computed.
    The solution is to change the re-neighboring criteria via the
    :doc:`neigh_modify <neigh_modify>` command.  The safest settings are
    "delay 0 every 1 check yes".  Second, it may mean that an atom has
-   moved far outside a processor's sub-domain or even the entire
+   moved far outside a processor's subdomain or even the entire
    simulation box. This indicates bad physics, e.g. due to highly
    overlapping atoms, too large a timestep, etc.
 
@@ -7231,7 +7231,7 @@ keyword to allow for additional bonds to be formed
 
 *Replacing a fix, but new style != old style*
    A fix ID can be used a second time, but only if the style matches the
-   previous fix.  In this case it is assumed you with to reset a fix's
+   previous fix.  In this case it is assumed you want to reset a fix's
    parameters.  This error may mean you are mistakenly re-using a fix ID
    when you do not intend to.
 
@@ -7337,7 +7337,7 @@ keyword to allow for additional bonds to be formed
 *Rigid body atoms %d %d missing on proc %d at step %ld*
    This means that an atom cannot find the atom that owns the rigid body
    it is part of, or vice versa.  The solution is to use the communicate
-   cutoff command to insure ghost atoms are acquired from far enough away
+   cutoff command to ensure ghost atoms are acquired from far enough away
    to encompass the max distance printed when the fix rigid/small command
    was invoked.
 

doc/src/Errors_warnings.rst

@@ -109,9 +109,9 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
 *Communication cutoff is shorter than a bond length based estimate. This may lead to errors.*
    Since LAMMPS stores topology data with individual atoms, all atoms
    comprising a bond, angle, dihedral or improper must be present on any
-   sub-domain that "owns" the atom with the information, either as a
+   subdomain that "owns" the atom with the information, either as a
    local or a ghost atom. The communication cutoff is what determines up
-   to what distance from a sub-domain boundary ghost atoms are created.
+   to what distance from a subdomain boundary ghost atoms are created.
    The communication cutoff is by default the largest non-bonded cutoff
    plus the neighbor skin distance, but for short or non-bonded cutoffs
    and/or long bonds, this may not be sufficient. This warning indicates
@@ -351,7 +351,7 @@ This will most likely cause errors in kinetic fluctuations.
    Self-explanatory.
 
 *Kspace_modify slab param < 2.0 may cause unphysical behavior*
-   The kspace_modify slab parameter should be larger to insure periodic
+   The kspace_modify slab parameter should be larger to ensure periodic
    grids padded with empty space do not overlap.
 
 *Less insertions than requested*
@@ -398,7 +398,7 @@ This will most likely cause errors in kinetic fluctuations.
    Lost atoms are checked for each time thermo output is done.  See the
    thermo_modify lost command for options.  Lost atoms usually indicate
    bad dynamics, e.g. atoms have been blown far out of the simulation
-   box, or moved further than one processor's sub-domain away before
+   box, or moved further than one processor's subdomain away before
    reneighboring.
 
 *MSM mesh too small, increasing to 2 points in each direction*
@@ -491,7 +491,7 @@ This will most likely cause errors in kinetic fluctuations.
 *Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies*
    This is because excluding specific pair interactions also excludes
    them from long-range interactions which may not be the desired effect.
-   The special_bonds command handles this consistently by insuring
+   The special_bonds command handles this consistently by ensuring
    excluded (or weighted) 1-2, 1-3, 1-4 interactions are treated
    consistently by both the short-range pair style and the long-range
    solver.  This is not done for exclusions of charged atom pairs via the
@@ -545,7 +545,7 @@ This will most likely cause errors in kinetic fluctuations.
    If there are other fixes that act immediately after the initial stage
    of time integration within a timestep (i.e. after atoms move), then
    the command that sets up the dynamic group should appear after those
-   fixes.  This will insure that dynamic group assignments are made
+   fixes.  This will ensure that dynamic group assignments are made
    after all atoms have moved.
 
 *One or more respa levels compute no forces*
@@ -582,13 +582,13 @@ This will most likely cause errors in kinetic fluctuations.
    needed.  The requested volume fraction may be too high, or other atoms
    may be in the insertion region.
 
-*Proc sub-domain size < neighbor skin, could lead to lost atoms*
+*Proc subdomain size < neighbor skin, could lead to lost atoms*
    The decomposition of the physical domain (likely due to load
-   balancing) has led to a processor's sub-domain being smaller than the
+   balancing) has led to a processor's subdomain being smaller than the
    neighbor skin in one or more dimensions.  Since reneighboring is
    triggered by atoms moving the skin distance, this may lead to lost
    atoms, if an atom moves all the way across a neighboring processor's
-   sub-domain before reneighboring is triggered.
+   subdomain before reneighboring is triggered.
 
 *Reducing PPPM order b/c stencil extends beyond nearest neighbor processor*
    This may lead to a larger grid than desired.  See the kspace_modify overlap

doc/src/Examples.rst

@@ -1,7 +1,7 @@
 Example scripts
 ===============
 
-The LAMMPS distribution includes an examples sub-directory with many
+The LAMMPS distribution includes an examples subdirectory with many
 sample problems.  Many are 2d models that run quickly and are
 straightforward to visualize, requiring at most a couple of minutes to
 run on a desktop machine.  Each problem has an input script (in.\*) and
@@ -29,7 +29,7 @@ be quickly post-processed into a movie using commands described on the
 Animations of many of the examples can be viewed on the Movies section
 of the `LAMMPS website <https://www.lammps.org/movies.html>`_.
 
-There are two kinds of sub-directories in the examples folder.  Lower
+There are two kinds of subdirectories in the examples folder.  Lower
 case named directories contain one or a few simple, quick-to-run
 problems.  Upper case named directories contain up to several complex
 scripts that illustrate a particular kind of simulation method or
@@ -94,8 +94,6 @@ Lowercase directories
 +-------------+------------------------------------------------------------------+
 | kim         | use of potentials from the `OpenKIM Repository <openkim_>`_      |
 +-------------+------------------------------------------------------------------+
-| latte       | examples for using fix latte for DFTB via the LATTE library      |
-+-------------+------------------------------------------------------------------+
 | mdi         | use of the MDI package and MolSSI MDI code coupling library      |
 +-------------+------------------------------------------------------------------+
 | meam        | MEAM test for SiC and shear (same as shear examples)             |
@@ -221,10 +219,10 @@ Uppercase directories
 Nearly all of these directories have README files which give more
 details on how to understand and use their contents.
 
-The PACKAGES directory has a large number of sub-directories which
+The PACKAGES directory has a large number of subdirectories which
 correspond by name to specific packages.  They contain scripts that
 illustrate how to use the command(s) provided in those packages.  Many
-of the sub-directories have their own README files which give further
+of the subdirectories have their own README files which give further
 instructions.  See the :doc:`Packages_details <Packages_details>` doc
 page for more info on specific packages.
 

doc/src/Fortran.rst

@@ -5,46 +5,67 @@ The :f:mod:`LIBLAMMPS` module provides an interface to call LAMMPS from
 Fortran.  It is based on the LAMMPS C library interface and requires a
 fully Fortran 2003-compatible compiler to be compiled.  It is designed
 to be self-contained and not require any support functions written in C,
-C++, or Fortran other than those in the C library interface and the module
-itself.
+C++, or Fortran other than those in the C library interface and the
+LAMMPS Fortran module itself.
 
 While C libraries have a defined binary interface (ABI) and can thus be
-used from multiple compiler versions from different vendors as long
-as they are compatible with the hosting operating system, the same is
-not true for Fortran programs.  Thus, the LAMMPS Fortran module needs to be
+used from multiple compiler versions from different vendors as long as
+they are compatible with the hosting operating system, the same is not
+true for Fortran programs.  Thus, the LAMMPS Fortran module needs to be
 compiled alongside the code using it from the source code in
-``fortran/lammps.f90``.  When linking, you also need to
-:doc:`link to the LAMMPS library <Build_link>`.  A typical command line
-for a simple program using the Fortran interface would be:
+``fortran/lammps.f90`` *and* with the same compiler used to build the
+rest of the Fortran code that interfaces to LAMMPS.  When linking, you
+also need to :doc:`link to the LAMMPS library <Build_link>`.  A typical
+command line for a simple program using the Fortran interface would be:
 
 .. code-block:: bash
 
    mpifort -o testlib.x lammps.f90 testlib.f90 -L. -llammps
 
 Please note that the MPI compiler wrapper is only required when the
-calling the library from an MPI-parallelized program.  Otherwise, using
-the plain Fortran compiler (gfortran, ifort, flang, etc.) will suffice.
-It may be necessary to link to additional libraries, depending on how
-LAMMPS was configured and whether the LAMMPS library :doc:`was compiled
-as a static or dynamic library <Build_link>`.
+calling the library *from* an MPI-parallelized program.  Otherwise,
+using the plain Fortran compiler (gfortran, ifort, flang, etc.) will
+suffice, since there are no direct references to MPI library features,
+definitions and subroutine calls; MPI communicators are referred to by
+their integer index representation as required by the Fortran MPI
+interface.  It may be necessary to link to additional libraries,
+depending on how LAMMPS was configured and whether the LAMMPS library
+:doc:`was compiled as a static or dynamic library <Build_link>`.
 
 If the LAMMPS library itself has been compiled with MPI support, the
-resulting executable will still be able to run LAMMPS in parallel with
-``mpirun``, ``mpiexec``, or equivalent.  Please also note that the order
-of the source files matters: the ``lammps.f90`` file needs to be
-compiled first, since it provides the :f:mod:`LIBLAMMPS` module that is
-imported by the Fortran code that uses the interface.  A working example
-can be found together with equivalent examples in C and C++ in the
-``examples/COUPLE/simple`` folder of the LAMMPS distribution.
+resulting executable will be able to run LAMMPS in parallel with
+``mpirun``, ``mpiexec``, or equivalent.  This may be either on the
+"world" communicator or a sub-communicator created by the calling
+Fortran code.  If, on the other hand, the LAMMPS library has been
+compiled **without** MPI support, each LAMMPS instance will run
+independently using just one processor.
 
-.. versionadded:: 9Oct2020
+Please also note that the order of the source files matters: the
+``lammps.f90`` file needs to be compiled first, since it provides the
+:f:mod:`LIBLAMMPS` module that would need to be imported by the calling
+Fortran code in order to uses the Fortran interface.
+A working example can be found together with equivalent examples in C and
+C++ in the ``examples/COUPLE/simple`` folder of the LAMMPS distribution.
+
+.. admonition:: Fortran compiler compatibility
+   :class: note
+
+   A fully Fortran 2003 compatible Fortran compiler is required.
+   This means that currently only GNU Fortran 9 and later are
+   compatible and thus the default compilers of Red Hat or CentOS 7
+   and Ubuntu 18.04 LTS and not compatible.  Either newer compilers
+   need to be installed or the Linux updated.
+
+.. versionchanged:: 8Feb2023
 
 .. note::
 
-   A contributed Fortran interface that more closely resembles the C library
-   interface is available in the ``examples/COUPLE/fortran2`` folder.  Please
-   see the ``README`` file in that folder for more information about it and how
-   to contact its author and maintainer.
+   A contributed Fortran interface is available in the
+   ``examples/COUPLE/fortran2`` folder.  However, since the completion
+   of the :f:mod:`LIBLAMMPS` module, this interface is now deprecated,
+   no longer actively maintained and will likely be removed in the
+   future.  Please see the ``README`` file in that folder for more
+   information about it and how to contact its author and maintainer.
 
 ----------
 
@@ -182,40 +203,62 @@ Below is an example demonstrating some of the possible uses.
 
 .. code-block:: fortran
 
-  PROGRAM testprop
-    USE LIBLAMMPS
-    USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int64_t
-    USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT
-    TYPE(lammps) :: lmp
-    INTEGER(KIND=c_int64_t), POINTER :: natoms
-    REAL(KIND=c_double), POINTER :: dt
-    INTEGER(KIND=c_int64_t), POINTER :: ntimestep
-    REAL(KIND=c_double) :: pe, ke
+   PROGRAM testprop
+     USE LIBLAMMPS
+     USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int64_t, c_int
+     USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT
+     TYPE(lammps) :: lmp
+     INTEGER(KIND=c_int64_t), POINTER :: natoms, ntimestep, bval
+     REAL(KIND=c_double), POINTER :: dt, dval
+     INTEGER(KIND=c_int), POINTER :: nfield, typ, ival
+     INTEGER(KIND=c_int) :: i
+     CHARACTER(LEN=11) :: key
+     REAL(KIND=c_double) :: pe, ke
 
-    lmp = lammps()
-    CALL lmp%file('in.sysinit')
-    natoms = lmp%extract_global('natoms')
-    WRITE(OUTPUT_UNIT,'(A,I0,A)') 'Running a simulation with ', natoms, ' atoms'
-    WRITE(OUTPUT_UNIT,'(I0,A,I0,A,I0,A)') lmp%extract_setting('nlocal'), &
-        ' local and ', lmp%extract_setting('nghost'), ' ghost atoms. ', &
-        lmp%extract_setting('ntypes'), ' atom types'
+     lmp = lammps()
+     CALL lmp%file('in.sysinit')
+     natoms = lmp%extract_global('natoms')
+     WRITE(OUTPUT_UNIT,'(A,I0,A)') 'Running a simulation with ', natoms, ' atoms'
+     WRITE(OUTPUT_UNIT,'(I0,A,I0,A,I0,A)') lmp%extract_setting('nlocal'), &
+         ' local and ', lmp%extract_setting('nghost'), ' ghost atoms. ', &
+         lmp%extract_setting('ntypes'), ' atom types'
 
-    CALL lmp%command('run 2 post no')
-    dt = lmp%extract_global('dt')
-    ntimestep = lmp%extract_global('ntimestep')
-    WRITE(OUTPUT_UNIT,'(A,I0,A,F4.1,A)') 'At step: ', ntimestep, &
-        '  Changing timestep from', dt, ' to 0.5'
-    dt = 0.5_c_double
-    CALL lmp%command('run 2 post no')
+     CALL lmp%command('run 2 post no')
 
-    WRITE(OUTPUT_UNIT,'(A,I0)') 'At step: ', ntimestep
-    pe = lmp%get_thermo('pe')
-    ke = lmp%get_thermo('ke')
-    PRINT*, 'PE = ', pe
-    PRINT*, 'KE = ', ke
+     ntimestep = lmp%last_thermo('step', 0)
+     nfield = lmp%last_thermo('num', 0)
+     WRITE(OUTPUT_UNIT,'(A,I0,A,I0)') 'Last thermo output on step: ', ntimestep, &
+         ',  number of fields: ', nfield
+     DO i=1, nfield
+         key = lmp%last_thermo('keyword',i)
+         typ = lmp%last_thermo('type',i)
+         IF (typ == lmp%dtype%i32) THEN
+             ival = lmp%last_thermo('data',i)
+             WRITE(OUTPUT_UNIT,*) key, ':', ival
+         ELSE IF (typ == lmp%dtype%i64) THEN
+             bval = lmp%last_thermo('data',i)
+             WRITE(OUTPUT_UNIT,*) key, ':', bval
+         ELSE IF (typ == lmp%dtype%r64) THEN
+             dval = lmp%last_thermo('data',i)
+             WRITE(OUTPUT_UNIT,*) key, ':', dval
+         END IF
+     END DO
 
-    CALL lmp%close(.TRUE.)
-  END PROGRAM testprop
+     dt = lmp%extract_global('dt')
+     ntimestep = lmp%extract_global('ntimestep')
+     WRITE(OUTPUT_UNIT,'(A,I0,A,F4.1,A)') 'At step: ', ntimestep, &
+         '  Changing timestep from', dt, ' to 0.5'
+     dt = 0.5_c_double
+     CALL lmp%command('run 2 post no')
+
+     WRITE(OUTPUT_UNIT,'(A,I0)') 'At step: ', ntimestep
+     pe = lmp%get_thermo('pe')
+     ke = lmp%get_thermo('ke')
+     WRITE(OUTPUT_UNIT,*) 'PE = ', pe
+     WRITE(OUTPUT_UNIT,*) 'KE = ', ke
+
+     CALL lmp%close(.TRUE.)
+   END PROGRAM testprop
 
 ---------------
 
@@ -241,6 +284,8 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
    :ftype style: type(lammps_style)
    :f type: derived type to access lammps type constants
    :ftype type: type(lammps_type)
+   :f dtype: derived type to access lammps data type constants
+   :ftype dtype: type(lammps_dtype)
    :f close: :f:subr:`close`
    :ftype close: subroutine
    :f subroutine error: :f:subr:`error`
@@ -257,6 +302,8 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
    :ftype get_natoms: function
    :f get_thermo: :f:func:`get_thermo`
    :ftype get_thermo: function
+   :f last_thermo: :f:func:`last_thermo`
+   :ftype last_thermo: function
    :f extract_box: :f:subr:`extract_box`
    :ftype extract_box: subroutine
    :f reset_box: :f:subr:`reset_box`
@@ -291,6 +338,12 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
    :ftype scatter_atoms_subset: subroutine
    :f gather_bonds: :f:subr:`gather_bonds`
    :ftype gather_bonds: subroutine
+   :f gather_angles: :f:subr:`gather_angles`
+   :ftype gather_angles: subroutine
+   :f gather_dihedrals: :f:subr:`gather_dihedrals`
+   :ftype gather_dihedrals: subroutine
+   :f gather_impropers: :f:subr:`gather_impropers`
+   :ftype gather_impropers: subroutine
    :f gather: :f:subr:`gather`
    :ftype gather: subroutine
    :f gather_concat: :f:subr:`gather_concat`
@@ -560,6 +613,96 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
 --------
 
+.. f:function:: last_thermo(what, index)
+
+   This function will call :cpp:func:`lammps_last_thermo` and returns
+   either a string or a pointer to a cached copy of LAMMPS last thermodynamic
+   output, depending on the data requested through *what*.  Note that *index*
+   uses 1-based indexing to access thermo output columns.
+
+   .. versionadded:: 15Jun2023
+
+   Note that this function actually does not return a value, but rather
+   associates the pointer on the left side of the assignment to point to
+   internal LAMMPS data (with the exception of string data, which are
+   copied and returned as ordinary Fortran strings).  Pointers must be
+   of the correct data type to point to said data (typically
+   ``INTEGER(c_int)``, ``INTEGER(c_int64_t)``, or ``REAL(c_double)``).
+   The pointer being associated with LAMMPS data is type-checked at
+   run-time via an overloaded assignment operator.  The pointers
+   returned by this function point to temporary, read-only data that may
+   be overwritten at any time, so their target values need to be copied
+   to local storage if they are supposed to persist.
+
+   For example,
+
+   .. code-block:: fortran
+
+      PROGRAM thermo
+        USE LIBLAMMPS
+        USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int64_t, c_int
+        TYPE(lammps) :: lmp
+        INTEGER(KIND=c_int64_t), POINTER :: ntimestep, bval
+        REAL(KIND=c_double), POINTER :: dval
+        INTEGER(KIND=c_int), POINTER :: nfield, typ, ival
+        INTEGER(KIND=c_int) :: i
+        CHARACTER(LEN=11) :: key
+
+        lmp = lammps()
+        CALL lmp%file('in.sysinit')
+
+        ntimestep = lmp%last_thermo('step', 0)
+        nfield = lmp%last_thermo('num', 0)
+        PRINT*, 'Last thermo output on step: ', ntimestep, '  Number of fields: ', nfield
+        DO i=1, nfield
+            key = lmp%last_thermo('keyword',i)
+            typ = lmp%last_thermo('type',i)
+            IF (typ == lmp%dtype%i32) THEN
+                ival = lmp%last_thermo('data',i)
+                PRINT*, key, ':', ival
+            ELSE IF (typ == lmp%dtype%i64) THEN
+                bval = lmp%last_thermo('data',i)
+                PRINT*, key, ':', bval
+            ELSE IF (typ == lmp%dtype%r64) THEN
+                dval = lmp%last_thermo('data',i)
+                PRINT*, key, ':', dval
+            END IF
+        END DO
+        CALL lmp%close(.TRUE.)
+      END PROGRAM thermo
+
+   would extract the last timestep where thermo output was done and the number
+   of columns it printed.  Then it loops over the columns to print out column
+   header keywords and the corresponding data.
+
+   .. note::
+
+      If :f:func:`last_thermo` returns a string, the string must have a length
+      greater than or equal to the length of the string (not including the
+      terminal ``NULL`` character) that LAMMPS returns. If the variable's
+      length is too short, the string will be truncated.  As usual in Fortran,
+      strings are padded with spaces at the end.  If you use an allocatable
+      string, the string **must be allocated** prior to calling this function.
+
+   :p character(len=\*) what: string with the name of the thermo keyword
+   :p integer(c_int) index: 1-based column index
+   :to: :cpp:func:`lammps_last_thermo`
+   :r pointer [polymorphic]: pointer to LAMMPS data. The left-hand side of the
+    assignment should be either a string (if expecting string data) or a
+    C-compatible pointer (e.g., ``INTEGER(c_int), POINTER :: nlocal``) to the
+    extracted property.
+
+   .. warning::
+
+       Modifying the data in the location pointed to by the returned pointer
+       may lead to inconsistent internal data and thus may cause failures,
+       crashes, or bogus simulations.  In general, it is much better
+       to use a LAMMPS input command that sets or changes these parameters.
+       Using an input command will take care of all side effects and necessary
+       updates of settings derived from such settings.
+
+--------
+
 .. f:subroutine:: extract_box([boxlo][, boxhi][, xy][, yz][, xz][, pflags][, boxflag])
 
    This subroutine will call :cpp:func:`lammps_extract_box`. All
@@ -737,13 +880,14 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
    .. note::
 
-      If :f:func:`extract_global` returns a string, the string must have length
-      greater than or equal to the length of the string (not including the
-      terminal ``NULL`` character) that LAMMPS returns. If the variable's
-      length is too short, the string will be truncated. As usual in Fortran,
-      strings are padded with spaces at the end. If you use an allocatable
-      string, the string **must be allocated** prior to calling this function,
-      but you can automatically reallocate it to the correct length after the
+      If :f:func:`extract_global` returns a string, the string must have
+      a length greater than or equal to the length of the string (not
+      including the terminal ``NULL`` character) that LAMMPS returns. If
+      the variable's length is too short, the string will be
+      truncated. As usual in Fortran, strings are padded with spaces at
+      the end. If you use an allocatable string, the string **must be
+      allocated** prior to calling this function, but you can
+      automatically reallocate it to the correct length after the
       function returns, viz.,
 
       .. code-block :: fortran
@@ -1520,6 +1664,51 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
 --------
 
+.. f:subroutine:: gather_angles(data)
+
+   Gather type and constituent atom information for all angles.
+
+   .. versionadded:: 8Feb2023
+
+   This function copies the list of all angles into an allocatable array.
+   The array will be filled with (angle type, angle atom 1, angle atom 2, angle atom 3)
+   for each angle. The array is allocated to the right length (i.e., four times the
+   number of angles). The array *data* must be of the same type as the LAMMPS
+   ``tagint`` type, which is equivalent to either ``INTEGER(c_int)`` or
+   ``INTEGER(c_int64_t)``, depending on whether ``-DLAMMPS_BIGBIG`` was used
+   when LAMMPS was built. If the supplied array does not match, an error will
+   result at run-time.
+
+   An example of how to use this routine is below:
+
+   .. code-block:: fortran
+
+      PROGRAM angles
+        USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
+        USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT
+        USE LIBLAMMPS
+        IMPLICIT NONE
+        INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET :: angles
+        INTEGER(c_int), DIMENSION(:,:), POINTER :: angles_array
+        TYPE(lammps) :: lmp
+        INTEGER :: i
+        ! other commands to initialize LAMMPS, create angles, etc.
+        CALL lmp%gather_angles(angles)
+        angles_array(1:4, 1:SIZE(angles)/4) => angles
+        DO i = 1, SIZE(angles)/4
+          WRITE(OUTPUT_UNIT,'(A,1X,I4,A,I4,1X,I4,1X,I4)') 'angle', angles_array(1,i), &
+            '; type = ', angles_array(2,i), angles_array(3,i), angles_array(4,i)
+        END DO
+      END PROGRAM angles
+
+   :p data: array into which to copy the result. \*The ``KIND`` parameter is
+    either ``c_int`` or, if LAMMPS was compiled with ``-DLAMMPS_BIGBIG``,
+    kind ``c_int64_t``.
+   :ptype data: integer(kind=\*),allocatable
+   :to: :cpp:func:`lammps_gather_angles`
+
+--------
+
 .. f:subroutine:: gather(self, name, count, data)
 
    Gather the named per-atom, per-atom fix, per-atom compute, or fix
@@ -1562,6 +1751,98 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
 --------
 
+.. f:subroutine:: gather_dihedrals(data)
+
+   Gather type and constituent atom information for all dihedrals.
+
+   .. versionadded:: 8Feb2023
+
+   This function copies the list of all dihedrals into an allocatable array.
+   The array will be filled with (dihedral type, dihedral atom 1, dihedral atom 2,
+   dihedral atom 3, dihedral atom 4) for each dihedral. The array is allocated to
+   the right length (i.e., five times the number of dihedrals).
+   The array *data* must be of the same type as the LAMMPS
+   ``tagint`` type, which is equivalent to either ``INTEGER(c_int)`` or
+   ``INTEGER(c_int64_t)``, depending on whether ``-DLAMMPS_BIGBIG`` was used
+   when LAMMPS was built. If the supplied array does not match, an error will
+   result at run-time.
+
+   An example of how to use this routine is below:
+
+   .. code-block:: fortran
+
+      PROGRAM dihedrals
+        USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
+        USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT
+        USE LIBLAMMPS
+        IMPLICIT NONE
+        INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET :: dihedrals
+        INTEGER(c_int), DIMENSION(:,:), POINTER :: dihedrals_array
+        TYPE(lammps) :: lmp
+        INTEGER :: i
+        ! other commands to initialize LAMMPS, create dihedrals, etc.
+        CALL lmp%gather_dihedrals(dihedrals)
+        dihedrals_array(1:5, 1:SIZE(dihedrals)/5) => dihedrals
+        DO i = 1, SIZE(dihedrals)/5
+          WRITE(OUTPUT_UNIT,'(A,1X,I4,A,I4,1X,I4,1X,I4,1X,I4)') 'dihedral', dihedrals_array(1,i), &
+            '; type = ', dihedrals_array(2,i), dihedrals_array(3,i), dihedrals_array(4,i), dihedrals_array(5,i)
+        END DO
+      END PROGRAM dihedrals
+
+   :p data: array into which to copy the result. \*The ``KIND`` parameter is
+    either ``c_int`` or, if LAMMPS was compiled with ``-DLAMMPS_BIGBIG``,
+    kind ``c_int64_t``.
+   :ptype data: integer(kind=\*),allocatable
+   :to: :cpp:func:`lammps_gather_dihedrals`
+
+--------
+
+.. f:subroutine:: gather_impropers(data)
+
+   Gather type and constituent atom information for all impropers.
+
+   .. versionadded:: 8Feb2023
+
+   This function copies the list of all impropers into an allocatable array.
+   The array will be filled with (improper type, improper atom 1, improper atom 2,
+   improper atom 3, improper atom 4) for each improper. The array is allocated to
+   the right length (i.e., five times the number of impropers).
+   The array *data* must be of the same type as the LAMMPS
+   ``tagint`` type, which is equivalent to either ``INTEGER(c_int)`` or
+   ``INTEGER(c_int64_t)``, depending on whether ``-DLAMMPS_BIGBIG`` was used
+   when LAMMPS was built. If the supplied array does not match, an error will
+   result at run-time.
+
+   An example of how to use this routine is below:
+
+   .. code-block:: fortran
+
+      PROGRAM impropers
+        USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int
+        USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT
+        USE LIBLAMMPS
+        IMPLICIT NONE
+        INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET :: impropers
+        INTEGER(c_int), DIMENSION(:,:), POINTER :: impropers_array
+        TYPE(lammps) :: lmp
+        INTEGER :: i
+        ! other commands to initialize LAMMPS, create impropers, etc.
+        CALL lmp%gather_impropers(impropers)
+        impropers_array(1:5, 1:SIZE(impropers)/5) => impropers
+        DO i = 1, SIZE(impropers)/5
+          WRITE(OUTPUT_UNIT,'(A,1X,I4,A,I4,1X,I4,1X,I4,1X,I4)') 'improper', impropers_array(1,i), &
+            '; type = ', impropers_array(2,i), impropers_array(3,i), impropers_array(4,i), impropers_array(5,i)
+        END DO
+      END PROGRAM impropers
+
+   :p data: array into which to copy the result. \*The ``KIND`` parameter is
+    either ``c_int`` or, if LAMMPS was compiled with ``-DLAMMPS_BIGBIG``,
+    kind ``c_int64_t``.
+   :ptype data: integer(kind=\*),allocatable
+   :to: :cpp:func:`lammps_gather_impropers`
+
+--------
+
 .. f:subroutine:: gather_concat(self, name, count, data)
 
    Gather the named per-atom, per-atom fix, per-atom compute, or fix
@@ -1991,7 +2272,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
    The LAMMPS :doc:`dump style movie <dump_image>` supports generating movies
    from images on-the-fly via creating a pipe to the
-   `ffmpeg <https://ffmpeg.org/ffmpeg/>`_ program.
+   `ffmpeg <https://ffmpeg.org/>`_ program.
    This function checks whether this feature was
    :ref:`enabled at compile time <graphics>`.
    It does **not** check whether the ``ffmpeg`` itself is installed and usable.
@@ -2391,7 +2672,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    mode. The function should have Fortran language bindings with the following
    interface, which depends on how LAMMPS was compiled:
 
-   .. code-block:: Fortran
+   .. code-block:: fortran
 
       ABSTRACT INTERFACE
         SUBROUTINE external_callback(caller, timestep, ids, x, fexternal)
@@ -2450,7 +2731,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
       with ``-DLAMMPS_SMALLBIG``) that applies something akin to Hooke's Law
       (with each atom having a different *k* value) is shown below.
 
-      .. code-block:: Fortran
+      .. code-block:: fortran
 
          MODULE stuff
            USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double, c_int64_t

doc/src/Howto.rst

@@ -4,10 +4,10 @@ Howto discussions
 These doc pages describe how to perform various tasks with LAMMPS,
 both for users and developers.  The
 `glossary <https://www.lammps.org/glossary.html>`_ website page also lists MD
-terminology with links to corresponding LAMMPS manual pages.  The
-example input scripts included in the examples directory of the LAMMPS
-distribution and highlighted on the :doc:`Examples <Examples>` doc page
-also show how to setup and run various kinds of simulations.
+terminology, with links to corresponding LAMMPS manual pages.  The
+example input scripts included in the ``examples`` directory of the LAMMPS
+source code distribution and highlighted on the :doc:`Examples` page
+also show how to set up and run various kinds of simulations.
 
 General howto
 =============
@@ -23,7 +23,6 @@ General howto
    Howto_library
    Howto_couple
    Howto_mdi
-   Howto_bpm
    Howto_broken_bonds
 
 Settings howto
@@ -70,6 +69,7 @@ Force fields howto
    Howto_amoeba
    Howto_tip3p
    Howto_tip4p
+   Howto_tip5p
    Howto_spc
 
 Packages howto
@@ -82,6 +82,7 @@ Packages howto
    Howto_spherical
    Howto_granular
    Howto_body
+   Howto_bpm
    Howto_polarizable
    Howto_coreshell
    Howto_drude

doc/src/Howto_2d.rst

@@ -22,7 +22,7 @@ atom in the file, assign a z coordinate so it falls inside the
 z-boundaries of the box - e.g. 0.0.
 
 Use the :doc:`fix enforce2d <fix_enforce2d>` command as the last
-defined fix to insure that the z-components of velocities and forces
+defined fix to ensure that the z-components of velocities and forces
 are zeroed out every timestep.  The reason to make it the last fix is
 so that any forces induced by other fixes will be zeroed out.