Merge branch 'master' of https://github.com/lammps/lammps into lammps-master2

.github/CODEOWNERS

@@ -22,41 +22,42 @@ src/MESSAGE/*         @sjplimp
 src/MLIAP/*           @athomps
 src/SNAP/*            @athomps
 src/SPIN/*            @julient31
-src/USER-BROWNIAN/*   @samueljmcameron
+src/BROWNIAN/*        @samueljmcameron
-src/USER-CGDNA/*      @ohenrich
+src/CG-DNA/*          @ohenrich
-src/USER-CGSDK/*      @akohlmey
+src/CG-SDK/*          @akohlmey
-src/USER-COLVARS/*    @giacomofiorin
+src/COLVARS/*         @giacomofiorin
-src/USER-FEP/*        @agiliopadua
+src/DIELECTRIC/*      @ndtrung81
-src/USER-HDNNP/*      @singraber
+src/FEP/*             @agiliopadua
-src/USER-INTEL/*      @wmbrownintel
+src/ML-HDNNP/*        @singraber
-src/USER-MANIFOLD/*   @Pakketeretet2
+src/INTEL/*           @wmbrownintel
-src/USER-MDI/*        @taylor-a-barnes
+src/MANIFOLD/*        @Pakketeretet2
-src/USER-MEAMC/*      @martok
+src/MDI/*             @taylor-a-barnes
-src/USER-MESONT/*     @iafoss
+src/MEAM/*            @martok
-src/USER-MOFFF/*      @hheenen
+src/MESONT/*          @iafoss
-src/USER-MOLFILE/*    @akohlmey
+src/MOFFF/*           @hheenen
-src/USER-NETCDF/*     @pastewka
+src/MOLFILE/*         @akohlmey
-src/USER-PACE/*       @yury-lysogorskiy
+src/NETCDF/*          @pastewka
-src/USER-PLUMED/*     @gtribello
+src/ML-PACE/*         @yury-lysogorskiy
-src/USER-PHONON/*     @lingtikong
+src/PLUMED/*          @gtribello
-src/USER-PTM/*        @pmla
+src/PHONON/*          @lingtikong
-src/USER-OMP/*        @akohlmey
+src/PTM/*             @pmla
-src/USER-QMMM/*       @akohlmey
+src/OPENMP/*          @akohlmey
-src/USER-REAXC/*      @hasanmetin
+src/QMMM/*            @akohlmey
-src/USER-REACTION/*   @jrgissing
+src/REAXFF/*          @hasanmetin @stanmoore1
-src/USER-SCAFACOS/*   @rhalver
+src/REACTION/*        @jrgissing
-src/USER-TALLY/*      @akohlmey
+src/SCAFACOS/*        @rhalver
-src/USER-UEF/*        @danicholson
+src/TALLY/*           @akohlmey
-src/USER-VTK/*        @rbberger
+src/UEF/*             @danicholson
-
+src/VTK/*             @rbberger
 
 # individual files in packages
 src/GPU/pair_vashishta_gpu.*        @andeplane
 src/KOKKOS/pair_vashishta_kokkos.*  @andeplane
 src/MANYBODY/pair_vashishta_table.* @andeplane
 src/MANYBODY/pair_atm.*             @sergeylishchuk
-src/USER-MISC/*_grem.*              @dstelter92
+src/REPLICA/*_grem.*                @dstelter92
-src/USER-MISC/compute_stress_mop*.* @RomainVermorel
+src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
+src/MISC/*_tracker.*                @jtclemm
 
 # core LAMMPS classes
 src/lammps.*              @sjplimp
@@ -80,6 +81,7 @@ src/kspace.*              @sjplimp
 src/lmptyp.h              @sjplimp
 src/library.*             @sjplimp
 src/main.cpp              @sjplimp
+src/min_*.*               @sjplimp
 src/memory.*              @sjplimp
 src/modify.*              @sjplimp
 src/molecule.*            @sjplimp
@@ -108,7 +110,6 @@ src/thermo.*              @sjplimp
 src/universe.*            @sjplimp
 src/update.*              @sjplimp
 src/variable.*            @sjplimp
-src/verlet.*              @sjplimp
 src/velocity.*            @sjplimp
 src/write_data.*          @sjplimp
 src/write_restart.*       @sjplimp
@@ -121,6 +122,7 @@ src/info.*                @akohlmey @rbberger
 src/timer.*               @akohlmey
 src/min*                  @sjplimp @stanmoore1
 src/utils.*               @akohlmey @rbberger
+src/verlet.*              @sjplimp @stanmoore1
 src/math_eigen_impl.h     @jewettaij
 
 # tools
@@ -137,7 +139,7 @@ unittest/*            @akohlmey @rbberger
 
 # cmake
 cmake/*               @junghans @rbberger
-cmake/Modules/Packages/USER-COLVARS.cmake @junghans @rbberger @giacomofiorin
+cmake/Modules/Packages/COLVARS.cmake @junghans @rbberger @giacomofiorin
 cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
 cmake/presets/*.cmake @akohlmey
 

.github/CONTRIBUTING.md

@@ -74,13 +74,13 @@ Here is a checklist of steps you need to follow to submit a single file or user
 * For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no trailing whitespace, no lines over 80 characters. I/O is done via the C-style stdio library, style class header files should not import any system headers, STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (<name>.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included (<cstdio> instead of <stdio.h>, or <cstring> instead of <string.h>). This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages.
 * Source, style name, and documentation file should follow the following naming convention: style names should be lowercase and words separated by a forward slash; for a new fix style 'foo/bar', the class should be named FixFooBar, the name of the source files should be 'fix_foo_bar.h' and 'fix_foo_bar.cpp' and the corresponding documentation should be in a file 'fix_foo_bar.rst'.
 * If you want your contribution to be added as a user-contributed feature, and it is a single file (actually a `<name>.cpp` and `<name>.h` file) it can be rapidly added to the USER-MISC directory. Include the one-line entry to add to the USER-MISC/README file in that directory, along with the 2 source files. You can do this multiple times if you wish to contribute several individual features.
-* If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this USER-FOO directory.
+* If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this FOO directory.
 * Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code.
-* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). The text files can include mathematical expressions and symbol in ".. math::" sections or ":math:" expressions or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html`, `make pdf` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file.  For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`.
+* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). The text files can include mathematical expressions and symbol in ".. math::" sections or ":math:" expressions or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html`, `make pdf` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file.  For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`.
-* For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/USER for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind
+* For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/PACKAGES for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind
 * For new utility functions or class (i.e. anything that does not depend on a LAMMPS object), new unit tests should be added to the unittest tree.
 * When adding a new LAMMPS style, a .yaml file with a test configuration and reference data should be added for the styles where a suitable tester program already exists (e.g. pair styles, bond styles, etc.).
-* If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the <name>.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide.
+* If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the <name>.cpp source file. See src/EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide.
 
 Finally, as a general rule-of-thumb, the more clear and self-explanatory you make your documentation and README files, and the easier you make it for people to get started, e.g. by providing example scripts, the more likely it is that users will try out your new feature.
 

.gitignore

@@ -12,6 +12,7 @@
 *.sif
 *.dll
 *.pyc
+a.out
 __pycache__
 
 Obj_*
@@ -43,6 +44,8 @@ Thumbs.db
 /build*
 /CMakeCache.txt
 /CMakeFiles/
+/Testing
 /Makefile
+/Testing
 /cmake_install.cmake
 /lmp

.lgtm.yml

@@ -4,7 +4,7 @@ extraction:
       command:
       - "mkdir build"
       - "cd build"
-      - "cmake -G Ninja -C ../cmake/presets/minimal.cmake ../cmake"
+      - "cmake -G Ninja -C ../cmake/presets/most.cmake ../cmake"
     index:
       build_command:
       - "cd build"

bench/POTENTIALS/in.meam

@@ -8,7 +8,7 @@ region		box block 0 20 0 20 0 20
 create_box	1 box
 create_atoms	1 box
 
-pair_style	meam/c
+pair_style	meam
 pair_coeff	* * library.meam Ni4 Ni.meam Ni4
 
 velocity	all create 1600.0 376847 loop geom

bench/POTENTIALS/log.9Oct20.meam.1

@@ -15,7 +15,7 @@ create_atoms	1 box
 Created 32000 atoms
   create_atoms CPU = 0.002 seconds
 
-pair_style	meam/c
+pair_style	meam
 pair_coeff	* * library.meam Ni4 Ni.meam Ni4
 Reading potential file library.meam with DATE: 2012-06-29
 Reading potential file Ni.meam with DATE: 2007-06-11
@@ -38,12 +38,12 @@ Neighbor list info ...
   ghost atom cutoff = 5
   binsize = 2.5, bins = 29 29 29
   2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair meam/c, perpetual
+  (1) pair meam, perpetual
       attributes: full, newton on
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-  (2) pair meam/c, perpetual, half/full from (1)
+  (2) pair meam, perpetual, half/full from (1)
       attributes: half, newton on
       pair build: halffull/newton
       stencil: none

bench/POTENTIALS/log.9Oct20.meam.4

@@ -15,7 +15,7 @@ create_atoms	1 box
 Created 32000 atoms
   create_atoms CPU = 0.001 seconds
 
-pair_style	meam/c
+pair_style	meam
 pair_coeff	* * library.meam Ni4 Ni.meam Ni4
 Reading potential file library.meam with DATE: 2012-06-29
 Reading potential file Ni.meam with DATE: 2007-06-11
@@ -38,12 +38,12 @@ Neighbor list info ...
   ghost atom cutoff = 5
   binsize = 2.5, bins = 29 29 29
   2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair meam/c, perpetual
+  (1) pair meam, perpetual
       attributes: full, newton on
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-  (2) pair meam/c, perpetual, half/full from (1)
+  (2) pair meam, perpetual, half/full from (1)
       attributes: half, newton on
       pair build: halffull/newton
       stencil: none

bench/POTENTIALS/log.9Oct20.reaxc.1

@@ -24,7 +24,7 @@ velocity	all create 300.0 9999
 
 pair_style	reax/c NULL
 pair_coeff      * * ffield.reax C H O N
-WARNING: Changed valency_val to valency_boc for X (src/USER-REAXC/reaxc_ffield.cpp:315)
+WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxc_ffield.cpp:315)
 
 timestep	0.1
 fix		1 all nve

bench/POTENTIALS/log.9Oct20.reaxc.4

@@ -24,7 +24,7 @@ velocity	all create 300.0 9999
 
 pair_style	reax/c NULL
 pair_coeff      * * ffield.reax C H O N
-WARNING: Changed valency_val to valency_boc for X (src/USER-REAXC/reaxc_ffield.cpp:315)
+WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxc_ffield.cpp:315)
 
 timestep	0.1
 fix		1 all nve

cmake/CMakeLists.txt

@@ -77,7 +77,7 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
 include(CheckIncludeFileCXX)
 
 # set required compiler flags and compiler/CPU arch specific optimizations
-if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM"))
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
   if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
     set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
@@ -138,17 +138,92 @@ install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
 
 option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
 
-set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
+set(STANDARD_PACKAGES
-  GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS
+  ADIOS
-  PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
+  ASPHERE
-  USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK
+  ATC
-  USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
+  AWPMD
-  USER-HDNNP USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESONT USER-MGPT USER-MISC
+  BOCS
-  USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
+  BODY
-  USER-RANN USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
+  BROWNIAN
-  USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE USER-BROWNIAN)
+  CG-DNA
+  CG-SDK
+  CLASS2
+  COLLOID
+  COLVARS
+  COMPRESS
+  DIELECTRIC
+  DIFFRACTION
+  DIPOLE
+  DPD-BASIC
+  DPD-MESO
+  DPD-REACT
+  DPD-SMOOTH
+  DRUDE
+  EFF
+  EXTRA-COMPUTE
+  EXTRA-DUMP
+  EXTRA-FIX
+  EXTRA-MOLECULE
+  EXTRA-PAIR
+  FEP
+  GRANULAR
+  H5MD
+  INTERLAYER
+  KIM
+  KSPACE
+  LATBOLTZ
+  LATTE
+  MACHDYN
+  MANIFOLD
+  MANYBODY
+  MC
+  MDI
+  MEAM
+  MESONT
+  MESSAGE
+  MGPT
+  MISC
+  ML-HDNNP
+  ML-IAP
+  ML-PACE
+  ML-QUIP
+  ML-RANN
+  ML-SNAP
+  MOFFF
+  MOLECULE
+  MOLFILE
+  MPIIO
+  MSCG
+  NETCDF
+  ORIENT
+  PERI
+  PHONON
+  PLUGIN
+  PLUMED
+  POEMS
+  PTM
+  PYTHON
+  QEQ
+  QMMM
+  QTB
+  REACTION
+  REAXFF
+  REPLICA
+  RIGID
+  SCAFACOS
+  SHOCK
+  SMTBQ
+  SPH
+  SPIN
+  SRD
+  TALLY
+  UEF
+  VORONOI
+  VTK
+  YAFF)
 
-set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP)
+set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT INTEL OPENMP)
 
 foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
   option(PKG_${PKG} "Build ${PKG} Package" OFF)
@@ -159,7 +234,7 @@ endforeach()
 ######################################################
 target_include_directories(lammps PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}>)
 
-if(PKG_USER-ADIOS)
+if(PKG_ADIOS)
   # The search for ADIOS2 must come before MPI because
   # it includes its own MPI search with the latest FindMPI.cmake
   # script that defines the MPI::MPI_C target
@@ -169,15 +244,16 @@ if(PKG_USER-ADIOS)
 endif()
 
 if(NOT CMAKE_CROSSCOMPILING)
-  set(MPI_CXX_SKIP_MPICXX TRUE)
   find_package(MPI QUIET)
   option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
 else()
-  set(MPI_CXX_SKIP_MPICXX TRUE)
   option(BUILD_MPI "Build MPI version" OFF)
 endif()
 
 if(BUILD_MPI)
+  # do not include the (obsolete) MPI C++ bindings which makes
+  # for leaner object files and avoids namespace conflicts
+  set(MPI_CXX_SKIP_MPICXX TRUE)
   # We use a non-standard procedure to cross-compile with MPI on Windows
   if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
     include(MPI4WIN)
@@ -229,12 +305,16 @@ endif()
 
 # "hard" dependencies between packages resulting
 # in an error instead of skipping over files
-pkg_depends(MLIAP SNAP)
+pkg_depends(ML-IAP ML-SNAP)
 pkg_depends(MPIIO MPI)
-pkg_depends(USER-ATC MANYBODY)
+pkg_depends(ATC MANYBODY)
-pkg_depends(USER-LB MPI)
+pkg_depends(LATBOLTZ MPI)
-pkg_depends(USER-PHONON KSPACE)
+pkg_depends(PHONON KSPACE)
-pkg_depends(USER-SCAFACOS MPI)
+pkg_depends(SCAFACOS MPI)
+pkg_depends(DIELECTRIC KSPACE)
+pkg_depends(DIELECTRIC EXTRA-PAIR)
+pkg_depends(CG-DNA MOLECULE)
+pkg_depends(CG-DNA ASPHERE)
 
 # detect if we may enable OpenMP support by default
 set(BUILD_OMP_DEFAULT OFF)
@@ -256,7 +336,8 @@ if(BUILD_OMP)
   endif()
 
   if(((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
-      (CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR
+      (CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR
+      (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM") OR (CMAKE_CXX_COMPILER_ID STREQUAL "XLClang") OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
@@ -269,7 +350,7 @@ if(BUILD_OMP)
   target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
 endif()
 
-if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
+if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE)
   enable_language(C)
   find_package(LAPACK)
   find_package(BLAS)
@@ -289,6 +370,8 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
   endif()
 endif()
 
+# tweak jpeg library names to avoid linker errors with MinGW cross-compilation
+set(JPEG_NAMES libjpeg libjpeg-62)
 find_package(JPEG QUIET)
 option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND})
 if(WITH_JPEG)
@@ -348,8 +431,8 @@ else()
   set(CUDA_REQUEST_PIC)
 endif()
 
-foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-HDNNP USER-MDI USER-MOLFILE USER-NETCDF USER-PLUMED
+foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
-        USER-QMMM USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE)
+        PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM LATTE MESSAGE MSCG COMPRESS ML-PACE)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
@@ -442,9 +525,8 @@ endforeach()
 ##############################################
 # add lib sources of (simple) enabled packages
 ############################################
-foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT)
+foreach(PKG_LIB POEMS ATC AWPMD H5MD MESONT)
-  if(PKG_${SIMPLE_LIB})
+  if(PKG_${PKG_LIB})
-    string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
     string(TOLOWER "${PKG_LIB}" PKG_LIB)
     if(PKG_LIB STREQUAL "mesont")
       enable_language(Fortran)
@@ -468,13 +550,13 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT)
   endif()
 endforeach()
 
-if(PKG_USER-AWPMD)
+if(PKG_AWPMD)
   target_link_libraries(awpmd PRIVATE ${LAPACK_LIBRARIES})
 endif()
 
-if(PKG_USER-ATC)
+if(PKG_ATC)
   if(LAMMPS_SIZES STREQUAL "BIGBIG")
-    message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG")
+    message(FATAL_ERROR "The ATC Package is not compatible with -DLAMMPS_BIGBIG")
   endif()
   target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES})
   if(BUILD_MPI)
@@ -486,15 +568,15 @@ if(PKG_USER-ATC)
   target_compile_definitions(atc PRIVATE -DLAMMPS_${LAMMPS_SIZES})
 endif()
 
-if(PKG_USER-H5MD)
+if(PKG_H5MD)
-  include(Packages/USER-H5MD)
+  include(Packages/H5MD)
 endif()
 
 ######################################################################
 # packages which selectively include variants based on enabled styles
 # e.g. accelerator packages
 ######################################################################
-foreach(PKG_WITH_INCL CORESHELL QEQ USER-OMP USER-SDPD KOKKOS OPT USER-INTEL GPU)
+foreach(PKG_WITH_INCL CORESHELL QEQ OPENMP DPD-SMOOTH KOKKOS OPT INTEL GPU)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()

cmake/Modules/FindN2P2.cmake

@@ -22,7 +22,7 @@ find_library(N2P2_LIBNNPIF NAMES nnpif HINTS "${N2P2_DIR}/lib")
 #
 # target_compile_definitions(lammps PRIVATE -DN2P2_NO_SF_GROUPS)
 #
-# to "lib/lammps-extra.cmake" which is then included by USER-HDNNP.cmake.
+# to "lib/lammps-extra.cmake" which is then included by ML-HDNNP.cmake.
 find_file(N2P2_CMAKE_EXTRA NAMES lammps-extra.cmake HINTS "${N2P2_DIR}/lib")
 
 find_package_handle_standard_args(N2P2 DEFAULT_MSG

cmake/Modules/LAMMPSUtils.cmake

@@ -67,7 +67,7 @@ endfunction()
 
 macro(pkg_depends PKG1 PKG2)
   if(PKG_${PKG1} AND NOT (PKG_${PKG2} OR BUILD_${PKG2}))
-    message(FATAL_ERROR "${PKG1} package needs LAMMPS to be build with ${PKG2}")
+    message(FATAL_ERROR "The ${PKG1} package needs LAMMPS to be build with the ${PKG2} package")
   endif()
 endmacro()
 

cmake/Modules/OpenCLLoader.cmake

@@ -1,6 +1,6 @@
 message(STATUS "Downloading and building OpenCL loader library")
-set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.05.02.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
+set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.06.30.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
-set(OPENCL_LOADER_MD5 "29180b05056578afda92f0d394c3a373" CACHE STRING "MD5 checksum of OpenCL loader tarball")
+set(OPENCL_LOADER_MD5 "f9e55dd550cfbf77f46507adf7cb8fd2" CACHE STRING "MD5 checksum of OpenCL loader tarball")
 mark_as_advanced(OPENCL_LOADER_URL)
 mark_as_advanced(OPENCL_LOADER_MD5)
 

cmake/Modules/Packages/DPD-SMOOTH.cmake

@@ -1,13 +1,13 @@
 # Fix rigid/meso requires RIGID to be installed
-set(USER-SDPD_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-SDPD)
+set(DPD-SMOOTH_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/DPD-SMOOTH)
 
 get_property(hlist GLOBAL PROPERTY FIX)
 if(NOT PKG_RIGID)
-  list(REMOVE_ITEM hlist ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.h)
+  list(REMOVE_ITEM hlist ${DPD-SMOOTH_SOURCES_DIR}/fix_rigid_meso.h)
   get_target_property(LAMMPS_SOURCES lammps SOURCES)
-  list(REMOVE_ITEM LAMMPS_SOURCES ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.cpp)
+  list(REMOVE_ITEM LAMMPS_SOURCES ${DPD-SMOOTH_SOURCES_DIR}/fix_rigid_meso.cpp)
   set_property(TARGET lammps PROPERTY SOURCES ${LAMMPS_SOURCES})
 endif()
 set_property(GLOBAL PROPERTY FIX "${hlist}")
 
-target_include_directories(lammps PRIVATE ${USER-SDPD_SOURCES_DIR})
+target_include_directories(lammps PRIVATE ${DPD-SMOOTH_SOURCES_DIR})

cmake/Modules/Packages/INTEL.cmake

@@ -3,9 +3,9 @@ if(NOT FOUND_IMMINTRIN)
   message(FATAL_ERROR "immintrin.h header not found, Intel package won't work without it")
 endif()
 
-target_compile_definitions(lammps PRIVATE -DLMP_USER_INTEL)
+target_compile_definitions(lammps PRIVATE -DLMP_INTEL)
 
-set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)")
+set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by INTEL (cpu or knl)")
 set(INTEL_ARCH_VALUES cpu knl)
 set_property(CACHE INTEL_ARCH PROPERTY STRINGS ${INTEL_ARCH_VALUES})
 validate_option(INTEL_ARCH INTEL_ARCH_VALUES)
@@ -40,10 +40,10 @@ endif()
 
 if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
   if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
-    message(FATAL_ERROR "USER-INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
+    message(FATAL_ERROR "INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
   endif()
 else()
-  message(WARNING "USER-INTEL gives best performance with Intel compilers")
+  message(WARNING "INTEL gives best performance with Intel compilers")
 endif()
 
 find_package(TBB_MALLOC QUIET)
@@ -52,7 +52,7 @@ if(TBB_MALLOC_FOUND)
 else()
   target_compile_definitions(lammps PRIVATE -DLMP_INTEL_NO_TBB)
   if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
-    message(WARNING "USER-INTEL with Intel compilers should use TBB malloc libraries")
+    message(WARNING "INTEL with Intel compilers should use TBB malloc libraries")
   endif()
 endif()
 
@@ -65,12 +65,12 @@ else()
 endif()
 
 if((NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "64") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "128") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "256"))
-  message(FATAL_ERROR "USER-INTEL only supports memory alignment of 64, 128 or 256 on this platform")
+  message(FATAL_ERROR "INTEL only supports memory alignment of 64, 128 or 256 on this platform")
 endif()
 
 if(INTEL_ARCH STREQUAL "KNL")
   if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
-    message(FATAL_ERROR "Must use Intel compiler with USER-INTEL for KNL architecture")
+    message(FATAL_ERROR "Must use Intel compiler with INTEL for KNL architecture")
   endif()
   set(CMAKE_EXE_LINKER_FLAGS  "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload")
   set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"")
@@ -91,26 +91,26 @@ else()
 endif()
 
 # collect sources
-set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
+set(INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/INTEL)
-set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/fix_intel.cpp
+set(INTEL_SOURCES ${INTEL_SOURCES_DIR}/fix_intel.cpp
-                       ${USER-INTEL_SOURCES_DIR}/fix_nh_intel.cpp
+                       ${INTEL_SOURCES_DIR}/fix_nh_intel.cpp
-                       ${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp
+                       ${INTEL_SOURCES_DIR}/intel_buffers.cpp
-                       ${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp
+                       ${INTEL_SOURCES_DIR}/nbin_intel.cpp
-                       ${USER-INTEL_SOURCES_DIR}/npair_intel.cpp)
+                       ${INTEL_SOURCES_DIR}/npair_intel.cpp)
 
-set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
+set_property(GLOBAL PROPERTY "INTEL_SOURCES" "${INTEL_SOURCES}")
 
-# detect styles which have a USER-INTEL version
+# detect styles which have a INTEL version
-RegisterStylesExt(${USER-INTEL_SOURCES_DIR} intel USER-INTEL_SOURCES)
+RegisterStylesExt(${INTEL_SOURCES_DIR} intel INTEL_SOURCES)
-RegisterNBinStyle(${USER-INTEL_SOURCES_DIR}/nbin_intel.h)
+RegisterNBinStyle(${INTEL_SOURCES_DIR}/nbin_intel.h)
-RegisterNPairStyle(${USER-INTEL_SOURCES_DIR}/npair_intel.h)
+RegisterNPairStyle(${INTEL_SOURCES_DIR}/npair_intel.h)
-RegisterFixStyle(${USER-INTEL_SOURCES_DIR}/fix_intel.h)
+RegisterFixStyle(${INTEL_SOURCES_DIR}/fix_intel.h)
 
-get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES)
+get_property(INTEL_SOURCES GLOBAL PROPERTY INTEL_SOURCES)
 if(PKG_KSPACE)
-  list(APPEND USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
+  list(APPEND INTEL_SOURCES ${INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
-  RegisterIntegrateStyle(${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
+  RegisterIntegrateStyle(${INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
 endif()
 
-target_sources(lammps PRIVATE ${USER-INTEL_SOURCES})
+target_sources(lammps PRIVATE ${INTEL_SOURCES})
-target_include_directories(lammps PRIVATE ${USER-INTEL_SOURCES_DIR})
+target_include_directories(lammps PRIVATE ${INTEL_SOURCES_DIR})

cmake/Modules/Packages/KOKKOS.cmake

@@ -74,11 +74,12 @@ else()
   target_link_libraries(lammps PRIVATE kokkos)
   target_link_libraries(lmp PRIVATE kokkos)
 endif()
-target_compile_definitions(lammps PRIVATE -DLMP_KOKKOS)
+target_compile_definitions(lammps PUBLIC $<BUILD_INTERFACE:LMP_KOKKOS>)
 
 set(KOKKOS_PKG_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/KOKKOS)
 set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/atom_kokkos.cpp
+                       ${KOKKOS_PKG_SOURCES_DIR}/atom_map_kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp
@@ -116,7 +117,7 @@ RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h)
 RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h)
 RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.h)
 
-if(PKG_USER-DPD)
+if(PKG_DPD-REACT)
   get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
   list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.cpp)
   RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.h)
@@ -126,4 +127,4 @@ endif()
 get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
 
 target_sources(lammps PRIVATE ${KOKKOS_PKG_SOURCES})
-target_include_directories(lammps PRIVATE ${KOKKOS_PKG_SOURCES_DIR})
+target_include_directories(lammps PUBLIC $<BUILD_INTERFACE:${KOKKOS_PKG_SOURCES_DIR}>)

cmake/Modules/Packages/MACHDYN.cmake

@@ -7,8 +7,8 @@ endif()
 option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT})
 if(DOWNLOAD_EIGEN3)
   message(STATUS "Eigen3 download requested - we will build our own")
-  set(EIGEN3_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz" CACHE STRING "URL for Eigen3 tarball")
+  set(EIGEN3_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.9/eigen-3.3.9.tar.gz" CACHE STRING "URL for Eigen3 tarball")
-  set(EIGEN3_MD5 "9e30f67e8531477de4117506fe44669b" CACHE STRING "MD5 checksum of Eigen3 tarball")
+  set(EIGEN3_MD5 "609286804b0f79be622ccf7f9ff2b660" CACHE STRING "MD5 checksum of Eigen3 tarball")
   mark_as_advanced(EIGEN3_URL)
   mark_as_advanced(EIGEN3_MD5)
   include(ExternalProject)
@@ -30,3 +30,8 @@ else()
   endif()
   target_link_libraries(lammps PRIVATE Eigen3::Eigen)
 endif()
+
+# PGI/Nvidia compiler internals collide with vector intrinsics support in Eigen3
+if((CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC"))
+  target_compile_definitions(lammps PRIVATE -DEIGEN_DONT_VECTORIZE)
+endif()

cmake/Modules/Packages/MDI.cmake

@@ -114,5 +114,5 @@ else()
   target_link_libraries(lmp PRIVATE ${mdi_LIBRARY})
 endif()
 
-target_compile_definitions(lammps PRIVATE -DLMP_USER_MDI)
+target_compile_definitions(lammps PRIVATE -DLMP_MDI)
-target_compile_definitions(lmp PRIVATE -DLMP_USER_MDI)
+target_compile_definitions(lmp PRIVATE -DLMP_MDI)

cmake/Modules/Packages/ML-HDNNP.cmake

@@ -16,13 +16,13 @@ if(DOWNLOAD_N2P2)
   if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang"))
     set(N2P2_COMP llvm)
     set(N2P2_CXX_STD "-std=c++11")
-  elseif(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+  elseif((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM"))
     set(N2P2_COMP intel)
     set(N2P2_CXX_STD "-std=c++11")
   elseif(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
     set(N2P2_COMP gnu)
     set(N2P2_CXX_STD "-std=gnu++11")
-  elseif(CMAKE_CXX_COMPILER_ID STREQUAL "PGI")
+  elseif((CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC"))
     set(N2P2_COMP gnu)
     set(N2P2_CXX_STD "--c++11")
   else() # default
@@ -55,6 +55,9 @@ if(DOWNLOAD_N2P2)
     endif()
   endif()
 
+  # prefer GNU make, if available. N2P2 lib seems to need it.
+  find_program(N2P2_MAKE NAMES gmake make)
+
   # override compiler (optimization) flags in n2p2 library to flags used for LAMMPS
   # specifically -march=native can result in problems when compiling on HPC clusters or with a cross compiler
   # this convoluted way gets correct quoting/escaping when configuring the external project
@@ -74,7 +77,7 @@ if(DOWNLOAD_N2P2)
     UPDATE_COMMAND ""
     CONFIGURE_COMMAND ""
     PATCH_COMMAND sed -i -e "s/\\(MPI_\\(P\\|Unp\\)ack(\\)/\\1(void *) /" src/libnnpif/LAMMPS/InterfaceLammps.cpp
-    BUILD_COMMAND make -f makefile libnnpif ${N2P2_BUILD_OPTIONS}
+    BUILD_COMMAND ${N2P2_MAKE} -f makefile libnnpif ${N2P2_BUILD_OPTIONS}
     BUILD_ALWAYS YES
     INSTALL_COMMAND ""
     BUILD_IN_SOURCE 1

cmake/Modules/Packages/ML-IAP.cmake

@@ -1,4 +1,4 @@
-# if PYTHON package is included we may also include Python support in MLIAP
+# if PYTHON package is included we may also include Python support in ML-IAP
 set(MLIAP_ENABLE_PYTHON_DEFAULT OFF)
 if(PKG_PYTHON)
   find_package(Cythonize QUIET)
@@ -7,25 +7,25 @@ if(PKG_PYTHON)
   endif()
 endif()
 
-option(MLIAP_ENABLE_PYTHON "Build MLIAP package with Python support" ${MLIAP_ENABLE_PYTHON_DEFAULT})
+option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_ENABLE_PYTHON_DEFAULT})
 
 if(MLIAP_ENABLE_PYTHON)
   find_package(Cythonize REQUIRED)
   if(NOT PKG_PYTHON)
-    message(FATAL_ERROR "Must enable PYTHON package for including Python support in MLIAP")
+    message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP")
   endif()
   if(CMAKE_VERSION VERSION_LESS 3.12)
     if(PYTHONLIBS_VERSION_STRING VERSION_LESS 3.6)
-      message(FATAL_ERROR "Python support in MLIAP requires Python 3.6 or later")
+      message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
     endif()
   else()
     if(Python_VERSION VERSION_LESS 3.6)
-      message(FATAL_ERROR "Python support in MLIAP requires Python 3.6 or later")
+      message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
     endif()
   endif()
 
   set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
-  set(MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/MLIAP/mliap_model_python_couple.pyx)
+  set(MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/ML-IAP/mliap_model_python_couple.pyx)
   get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_SRC} NAME_WE)
   file(MAKE_DIRECTORY ${MLIAP_BINARY_DIR})
   add_custom_command(OUTPUT  ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h

cmake/Modules/Packages/ML-QUIP.cmake

@@ -0,0 +1,70 @@
+enable_language(Fortran)
+find_package(QUIP QUIET)
+
+if(QUIP_FOUND)
+  set(DOWNLOAD_QUIP_DEFAULT OFF)
+else()
+  set(DOWNLOAD_QUIP_DEFAULT ON)
+endif()
+option(DOWNLOAD_QUIP "Download the QUIP library instead of using an already installed one" ${DOWNLOAD_QUIP_DEFAULT})
+if(DOWNLOAD_QUIP)
+  string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
+  set(temp "F77 = ${CMAKE_Fortran_COMPILER}\nF90 = ${CMAKE_Fortran_COMPILER}\nF95 = ${CMAKE_Fortran_COMPILER}\n")
+  set(temp "${temp}CC=${CMAKE_C_COMPILER}\nCPLUSPLUS=${CMAKE_CXX_COMPILER}\nLINKER=${CMAKE_Fortran_COMPILER}\n")
+  if(CMAKE_Fortran_COMPILER_ID STREQUAL Intel)
+    set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E\nOPTIM=${CMAKE_Fortran_FLAGS_${BTYPE}}\n")
+    set(temp "${temp}DEFINES += -DGETARG_F2003 -DFORTRAN_UNDERSCORE\n")
+    set(temp "${temp}F95FLAGS += -fpp -free -fPIC\n")
+    set(temp "${temp}F77FLAGS += -fpp -fixed -fPIC\n")
+  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 "${temp}DEFINES += -DGETARG_F2003 -DGETENV_F2003 -DGFORTRAN -DFORTRAN_UNDERSCORE\n")
+    set(temp "${temp}F95FLAGS += -x f95-cpp-input -ffree-line-length-none -ffree-form -fno-second-underscore -fPIC\n")
+    set(temp "${temp}F77FLAGS += -x f77-cpp-input -fno-second-underscore -fPIC\n")
+  else()
+    message(FATAL_ERROR "The ${CMAKE_Fortran_COMPILER_ID} Fortran compiler is not (yet) supported for building QUIP")
+  endif()
+  set(temp "${temp}CFLAGS += -fPIC \nCPLUSPLUSFLAGS += -fPIC\nAR_ADD=src\n")
+  set(temp "${temp}MATH_LINKOPTS=")
+  foreach(flag ${BLAS_LIBRARIES})
+    set(temp "${temp} ${flag}")
+  endforeach()
+  foreach(flag ${LAPACK_LIBRARIES})
+    set(temp "${temp} ${flag}")
+  endforeach()
+  set(temp "${temp}\n")
+  set(temp "${temp}PYTHON=python\nPIP=pip\nEXTRA_LINKOPTS=\n")
+  set(temp "${temp}HAVE_CP2K=0\nHAVE_VASP=0\nHAVE_TB=0\nHAVE_PRECON=1\nHAVE_LOTF=0\nHAVE_ONIOM=0\n")
+  set(temp "${temp}HAVE_LOCAL_E_MIX=0\nHAVE_QC=0\nHAVE_GAP=1\nHAVE_DESCRIPTORS_NONCOMMERCIAL=1\n")
+  set(temp "${temp}HAVE_TURBOGAP=0\nHAVE_QR=1\nHAVE_THIRDPARTY=0\nHAVE_FX=0\nHAVE_SCME=0\nHAVE_MTP=0\n")
+  set(temp "${temp}HAVE_MBD=0\nHAVE_TTM_NF=0\nHAVE_CH4=0\nHAVE_NETCDF4=0\nHAVE_MDCORE=0\nHAVE_ASAP=0\n")
+  set(temp "${temp}HAVE_CGAL=0\nHAVE_METIS=0\nHAVE_LMTO_TBE=0\n")
+  file(WRITE ${CMAKE_BINARY_DIR}/quip.config "${temp}")
+
+  message(STATUS "QUIP download via git requested - we will build our own")
+  # QUIP has no releases (except for a tag marking the end of Python 2 support). We use the current "public" branch
+  # The LAMMPS interface wrapper has a compatibility constant that is being checked at runtime.
+  include(ExternalProject)
+  ExternalProject_Add(quip_build
+    GIT_REPOSITORY "https://github.com/libAtoms/QUIP/"
+    GIT_TAG origin/public
+    GIT_SHALLOW YES
+    GIT_PROGRESS YES
+    PATCH_COMMAND cp ${CMAKE_BINARY_DIR}/quip.config <SOURCE_DIR>/arch/Makefile.lammps
+    CONFIGURE_COMMAND env QUIP_ARCH=lammps make config
+    BUILD_COMMAND env QUIP_ARCH=lammps make libquip
+    INSTALL_COMMAND ""
+    BUILD_IN_SOURCE YES
+    BUILD_BYPRODUCTS <SOURCE_DIR>/build/lammps/libquip.a
+  )
+  ExternalProject_get_property(quip_build SOURCE_DIR)
+  add_library(LAMMPS::QUIP UNKNOWN IMPORTED)
+  set_target_properties(LAMMPS::QUIP PROPERTIES
+    IMPORTED_LOCATION "${SOURCE_DIR}/build/lammps/libquip.a"
+    INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
+  target_link_libraries(lammps PRIVATE LAMMPS::QUIP)
+  add_dependencies(LAMMPS::QUIP quip_build)
+else()
+  find_package(QUIP REQUIRED)
+  target_link_libraries(lammps PRIVATE QUIP::QUIP ${LAPACK_LIBRARIES})
+endif()

cmake/Modules/Packages/MOLFILE.cmake

@@ -1,5 +1,7 @@
 set(MOLFILE_INCLUDE_DIR "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
-set(MOLFILE_INCLUDE_DIRS "${MOLFILE_INCLUDE_DIR}")
 add_library(molfile INTERFACE)
-target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
+target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIR})
+if(NOT (CMAKE_SYSTEM_NAME STREQUAL "Windows"))
+  target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
+endif()
 target_link_libraries(lammps PRIVATE molfile)

cmake/Modules/Packages/NETCDF.cmake

@@ -1,4 +1,4 @@
-# USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
+# NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
 # NetCDF library enables dump style "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
 
 # may use NetCDF or PNetCDF with MPI, but must have NetCDF without

cmake/Modules/Packages/OPENMP.cmake

@@ -0,0 +1,40 @@
+  set(OPENMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/OPENMP)
+  set(OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/thr_data.cpp
+                       ${OPENMP_SOURCES_DIR}/thr_omp.cpp
+                       ${OPENMP_SOURCES_DIR}/fix_omp.cpp
+                       ${OPENMP_SOURCES_DIR}/fix_nh_omp.cpp
+                       ${OPENMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp
+                       ${OPENMP_SOURCES_DIR}/domain_omp.cpp)
+  target_compile_definitions(lammps PRIVATE -DLMP_OPENMP)
+  set_property(GLOBAL PROPERTY "OMP_SOURCES" "${OPENMP_SOURCES}")
+
+  # detects styles which have OPENMP version
+  RegisterStylesExt(${OPENMP_SOURCES_DIR} omp OMP_SOURCES)
+  RegisterFixStyle(${OPENMP_SOURCES_DIR}/fix_omp.h)
+
+  get_property(OPENMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
+
+  # manually add package dependent source files from OPENMP that do not provide styles
+
+  if(PKG_ASPHERE)
+    list(APPEND OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp)
+  endif()
+
+  if(PKG_RIGID)
+    list(APPEND OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp)
+  endif()
+
+  if(PKG_REAXFF)
+    list(APPEND OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/reaxff_bond_orders_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_hydrogen_bonds_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_nonbonded_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_bonds_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_init_md_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_torsion_angles_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_forces_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_multi_body_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_valence_angles_omp.cpp)
+  endif()
+
+  target_sources(lammps PRIVATE ${OPENMP_SOURCES})
+  target_include_directories(lammps PRIVATE ${OPENMP_SOURCES_DIR})

cmake/Modules/Packages/PLUMED.cmake

@@ -54,8 +54,8 @@ if(DOWNLOAD_PLUMED)
     set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
   endif()
 
-  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.1/plumed-src-2.7.1.tgz" CACHE STRING "URL for PLUMED tarball")
+  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.2/plumed-src-2.7.2.tgz" CACHE STRING "URL for PLUMED tarball")
-  set(PLUMED_MD5 "4eac6a462ec84dfe0cec96c82421b8e8" CACHE STRING "MD5 checksum of PLUMED tarball")
+  set(PLUMED_MD5 "cfa0b4dd90a81c25d3302e8d97bfeaea" CACHE STRING "MD5 checksum of PLUMED tarball")
 
   mark_as_advanced(PLUMED_URL)
   mark_as_advanced(PLUMED_MD5)

cmake/Modules/Packages/QEQ.cmake

@@ -1,18 +1,13 @@
 # Fix qeq/fire requires MANYBODY (i.e. COMB and COMB3) to be installed
 set(QEQ_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/QEQ)
-file(GLOB QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix*.h)
-file(GLOB QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix*.cpp)
 
+get_property(hlist GLOBAL PROPERTY FIX)
 if(NOT PKG_MANYBODY)
-  list(REMOVE_ITEM QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix_qeq_fire.h)
+  list(REMOVE_ITEM hlist ${QEQ_SOURCES_DIR}/fix_qeq_fire.h)
-  list(REMOVE_ITEM QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix_qeq_fire.cpp)
+  get_target_property(LAMMPS_SOURCES lammps SOURCES)
+  list(REMOVE_ITEM LAMMPS_SOURCES ${QEQ_SOURCES_DIR}/fix_qeq_fire.cpp)
+  set_property(TARGET lammps PROPERTY SOURCES ${LAMMPS_SOURCES})
 endif()
-set_property(GLOBAL PROPERTY "QEQ_SOURCES" "${QEQ_SOURCES}")
+set_property(GLOBAL PROPERTY FIX "${hlist}")
 
-foreach(MY_HEADER ${QEQ_HEADERS})
-  AddStyleHeader(${MY_HEADER} FIX)
-endforeach()
-
-get_property(QEQ_SOURCES GLOBAL PROPERTY QEQ_SOURCES)
-target_sources(lammps PRIVATE ${QEQ_SOURCES})
 target_include_directories(lammps PRIVATE ${QEQ_SOURCES_DIR})

cmake/Modules/Packages/USER-OMP.cmake

@@ -1,40 +0,0 @@
-  set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP)
-  set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
-                       ${USER-OMP_SOURCES_DIR}/thr_omp.cpp
-                       ${USER-OMP_SOURCES_DIR}/fix_omp.cpp
-                       ${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp
-                       ${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp
-                       ${USER-OMP_SOURCES_DIR}/domain_omp.cpp)
-  target_compile_definitions(lammps PRIVATE -DLMP_USER_OMP)
-  set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}")
-
-  # detects styles which have USER-OMP version
-  RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
-  RegisterFixStyle(${USER-OMP_SOURCES_DIR}/fix_omp.h)
-
-  get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
-
-  # manually add package dependent source files from USER-OMP that do not provide styles
-
-  if(PKG_ASPHERE)
-    list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp)
-  endif()
-
-  if(PKG_RIGID)
-    list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp)
-  endif()
-
-  if(PKG_USER-REAXC)
-    list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp
-                                 ${USER-OMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp
-                                 ${USER-OMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp
-                                 ${USER-OMP_SOURCES_DIR}/reaxc_bonds_omp.cpp
-                                 ${USER-OMP_SOURCES_DIR}/reaxc_init_md_omp.cpp
-                                 ${USER-OMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp
-                                 ${USER-OMP_SOURCES_DIR}/reaxc_forces_omp.cpp
-                                 ${USER-OMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp
-                                 ${USER-OMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp)
-  endif()
-
-  target_sources(lammps PRIVATE ${USER-OMP_SOURCES})
-  target_include_directories(lammps PRIVATE ${USER-OMP_SOURCES_DIR})

cmake/Modules/Packages/USER-QUIP.cmake

@@ -1,3 +0,0 @@
-enable_language(Fortran)
-find_package(QUIP REQUIRED)
-target_link_libraries(lammps PRIVATE QUIP::QUIP ${LAPACK_LIBRARIES})

cmake/presets/all_off.cmake

@@ -1,17 +1,96 @@
-# preset that turns on all existing packages off. can be used to reset
+# Preset that turns on all existing packages off. Can be used to reset
 # an existing package selection without losing any other settings
 
-set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
+set(ALL_PACKAGES
-  GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE
+  ADIOS
-  MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
+  ASPHERE
-  SRD VORONOI
+  ATC
-  USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK
+  AWPMD
-  USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
+  BOCS
-  USER-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD
+  BODY
-  USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
+  BROWNIAN
-  USER-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN
+  CG-DNA
-  USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
+  CG-SDK
-  USER-TALLY USER-UEF USER-VTK USER-YAFF)
+  CLASS2
+  COLLOID
+  COLVARS
+  COMPRESS
+  CORESHELL
+  DIELECTRIC
+  DIFFRACTION
+  DIPOLE
+  DPD-BASIC
+  DPD-MESO
+  DPD-REACT
+  DPD-SMOOTH
+  DRUDE
+  EFF
+  EXTRA-COMPUTE
+  EXTRA-DUMP
+  EXTRA-FIX
+  EXTRA-MOLECULE
+  EXTRA-PAIR
+  FEP
+  GPU
+  GRANULAR
+  H5MD
+  INTEL
+  INTERLAYER
+  KIM
+  KOKKOS
+  KSPACE
+  LATBOLTZ
+  LATTE
+  MACHDYN
+  MANIFOLD
+  MANYBODY
+  MC
+  MDI
+  MEAM
+  MESONT
+  MESSAGE
+  MGPT
+  MISC
+  ML-HDNNP
+  ML-IAP
+  ML-PACE
+  ML-QUIP
+  ML-RANN
+  ML-SNAP
+  MOFFF
+  MOLECULE
+  MOLFILE
+  MPIIO
+  MSCG
+  NETCDF
+  OPENMP
+  OPT
+  ORIENT
+  PERI
+  PHONON
+  PLUGIN
+  PLUMED
+  POEMS
+  PTM
+  PYTHON
+  QEQ
+  QMMM
+  QTB
+  REACTION
+  REAXFF
+  REPLICA
+  RIGID
+  SCAFACOS
+  SHOCK
+  SMTBQ
+  SPH
+  SPIN
+  SRD
+  TALLY
+  UEF
+  VORONOI
+  VTK
+  YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

cmake/presets/all_on.cmake

@@ -1,19 +1,98 @@
-# preset that turns on all existing packages. using the combination
+# Preset that turns on all existing packages. Using the combination
-# this preset followed by the nolib.cmake preset should configure a
+# of this preset followed by the nolib.cmake preset should configure
-# LAMMPS binary, with as many packages included, that can be compiled
+# a LAMMPS binary, with as many packages included, that can be compiled
 # with just a working C++ compiler and an MPI library.
 
-set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
+set(ALL_PACKAGES
-  GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE
+  ADIOS
-  MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
+  ASPHERE
-  SRD VORONOI
+  ATC
-  USER-ADIOS USER-ATC USER-AWPMD USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK
+  AWPMD
-  USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
+  BOCS
-  USER-HDNNP USER-INTEL USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD
+  BODY
-  USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
+  BROWNIAN
-  USER-PACE USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-RANN
+  CG-DNA
-  USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
+  CG-SDK
-  USER-TALLY USER-UEF USER-VTK USER-YAFF)
+  CLASS2
+  COLLOID
+  COLVARS
+  COMPRESS
+  CORESHELL
+  DIELECTRIC
+  DIFFRACTION
+  DIPOLE
+  DPD-BASIC
+  DPD-MESO
+  DPD-REACT
+  DPD-SMOOTH
+  DRUDE
+  EFF
+  EXTRA-COMPUTE
+  EXTRA-DUMP
+  EXTRA-FIX
+  EXTRA-MOLECULE
+  EXTRA-PAIR
+  FEP
+  GPU
+  GRANULAR
+  H5MD
+  INTEL
+  INTERLAYER
+  KIM
+  KOKKOS
+  KSPACE
+  LATBOLTZ
+  LATTE
+  MACHDYN
+  MANIFOLD
+  MANYBODY
+  MC
+  MDI
+  MEAM
+  MESONT
+  MESSAGE
+  MGPT
+  MISC
+  ML-HDNNP
+  ML-IAP
+  ML-PACE
+  ML-QUIP
+  ML-RANN
+  ML-SNAP
+  MOFFF
+  MOLECULE
+  MOLFILE
+  MPIIO
+  MSCG
+  NETCDF
+  OPENMP
+  OPT
+  ORIENT
+  PERI
+  PHONON
+  PLUGIN
+  PLUMED
+  POEMS
+  PTM
+  PYTHON
+  QEQ
+  QMMM
+  QTB
+  REACTION
+  REAXFF
+  REPLICA
+  RIGID
+  SCAFACOS
+  SHOCK
+  SMTBQ
+  SPH
+  SPIN
+  SRD
+  TALLY
+  UEF
+  VORONOI
+  VTK
+  YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)

cmake/presets/clang.cmake

@@ -1,13 +1,18 @@
 # preset that will enable clang/clang++ with support for MPI and OpenMP (on Linux boxes)
 
+# prefer flang over gfortran, if available
+find_program(CLANG_FORTRAN NAMES flang gfortran f95)
+set(ENV{OMPI_FC} ${CLANG_FORTRAN})
+
 set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_COMPILER ${CLANG_FORTRAN} CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g -std=f95" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f95" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f95" CACHE STRING "" FORCE)
 set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
 set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
 set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)

cmake/presets/download.cmake

@@ -1,7 +1,7 @@
 # Preset that turns on packages with automatic downloads of sources or potentials.
 # Compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time.
 
-set(ALL_PACKAGES KIM LATTE MSCG VORONOI USER-PLUMED USER-SCAFACOS USER-SMD USER-MESONT USER-MDI USER-PACE)
+set(ALL_PACKAGES KIM LATTE MSCG VORONOI PLUMED SCAFACOS MACHDYN MESONT MDI ML-PACE)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)

cmake/presets/gcc.cmake

@@ -2,10 +2,22 @@
 
 set(CMAKE_CXX_COMPILER "g++" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
-set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_COMPILER "gfortran" CACHE STRING "" FORCE)
-set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_DEBUG "-Wall -g" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
 set(MPI_CXX "g++" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
+set(MPI_C "gcc" CACHE STRING "" FORCE)
+set(MPI_C_COMPILER "mpicc" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_DEBUG "-Wall -g" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(MPI_Fortran "gfortran" CACHE STRING "" FORCE)
+set(MPI_Fortran_COMPILER "mpifort" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -g" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
 unset(HAVE_OMP_H_INCLUDE CACHE)
 
 set(OpenMP_C "gcc" CACHE STRING "" FORCE)

cmake/presets/mingw-cross.cmake

@@ -1,13 +1,76 @@
-set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
+set(WIN_PACKAGES
-                 GRANULAR KSPACE LATTE MANYBODY MC MISC MLIAP MOLECULE OPT
+  ASPHERE
-                 PERI POEMS QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
+  ATC
-                 USER-ATC USER-AWPMD USER-BOCS USER-BROWNIAN USER-CGDNA USER-CGSDK
+  AWPMD
-                 USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
+  BOCS
-                 USER-HDNNP USER-INTEL USER-MANIFOLD USER-MDI USER-MEAMC USER-MESODPD
+  BODY
-                 USER-MESONT USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP
+  BROWNIAN
-                 USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC
+  CG-DNA
-                 USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
+  CG-SDK
-                 USER-YAFF)
+  CLASS2
+  COLLOID
+  COLVARS
+  COMPRESS
+  CORESHELL
+  DIELECTRIC
+  DIFFRACTION
+  DIPOLE
+  DPD-BASIC
+  DPD-MESO
+  DPD-REACT
+  DPD-SMOOTH
+  DRUDE
+  EFF
+  EXTRA-COMPUTE
+  EXTRA-DUMP
+  EXTRA-FIX
+  EXTRA-MOLECULE
+  EXTRA-PAIR
+  FEP
+  GPU
+  GRANULAR
+  INTEL
+  INTERLAYER
+  KSPACE
+  LATTE
+  MACHDYN
+  MANIFOLD
+  MANYBODY
+  MC
+  MDI
+  MEAM
+  MESONT
+  MGPT
+  MISC
+  ML-HDNNP
+  ML-IAP
+  ML-SNAP
+  ML-RANN
+  MOFFF
+  MOLECULE
+  MOLFILE
+  OPENMP
+  OPT
+  ORIENT
+  PERI
+  PHONON
+  POEMS
+  PTM
+  QEQ
+  QTB
+  REACTION
+  REAXFF
+  REPLICA
+  RIGID
+  SHOCK
+  SMTBQ
+  SPH
+  SPIN
+  SRD
+  TALLY
+  UEF
+  VORONOI
+  YAFF)
 
 foreach(PKG ${WIN_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)
@@ -16,7 +79,7 @@ endforeach()
 # these two packages require a full MPI implementation
 if(BUILD_MPI)
   set(PKG_MPIIO ON CACHE BOOL "" FORCE)
-  set(PKG_USER-LB ON CACHE BOOL "" FORCE)
+  set(PKG_LATBOLTZ ON CACHE BOOL "" FORCE)
 endif()
 
 set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)

cmake/presets/most.cmake

@@ -2,13 +2,65 @@
 # external libraries. Compared to all_on.cmake some more unusual packages
 # are removed. The resulting binary should be able to run most inputs.
 
-set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
+set(ALL_PACKAGES
-        GRANULAR KSPACE MANYBODY MC MISC MLIAP MOLECULE OPT PERI
+  ASPHERE
-        PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
+  BOCS
-        USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
+  BODY
-        USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC
+  BROWNIAN
-        USER-MESODPD USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
+  CG-DNA
-        USER-REAXC USER-SDPD USER-SPH USER-SMD USER-UEF USER-YAFF)
+  CG-SDK
+  CLASS2
+  COLLOID
+  COLVARS
+  COMPRESS
+  CORESHELL
+  DIELECTRIC
+  DIFFRACTION
+  DIPOLE
+  DPD-BASIC
+  DPD-MESO
+  DPD-REACT
+  DPD-SMOOTH
+  DRUDE
+  EFF
+  EXTRA-COMPUTE
+  EXTRA-FIX
+  EXTRA-MOLECULE
+  EXTRA-PAIR
+  FEP
+  GRANULAR
+  INTERLAYER
+  KSPACE
+  MACHDYN
+  MANYBODY
+  MC
+  MEAM
+  MISC
+  ML-IAP
+  ML-SNAP
+  MOFFF
+  MOLECULE
+  OPENMP
+  OPT
+  ORIENT
+  PERI
+  PHONON
+  PLUGIN
+  POEMS
+  PYTHON
+  QEQ
+  REACTION
+  REAXFF
+  REPLICA
+  RIGID
+  SHOCK
+  SPH
+  SPIN
+  SRD
+  TALLY
+  UEF
+  VORONOI
+  YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)

cmake/presets/nolib.cmake

@@ -1,11 +1,34 @@
 # preset that turns off all packages that require some form of external
 # library or special compiler (fortran or cuda) or equivalent.
 
-set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MESSAGE MPIIO MSCG
+set(PACKAGES_WITH_LIB
-  PYTHON VORONOI
+  ADIOS
-  USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-HDNNP USER-LB USER-MOLFILE
+  ATC
-  USER-MESONT USER-MDI USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP
+  AWPMD
-  USER-SCAFACOS USER-SMD USER-VTK)
+  COMPRESS
+  GPU
+  H5MD
+  KIM
+  KOKKOS
+  LATBOLTZ
+  LATTE
+  MACHDYN
+  MDI
+  MESONT
+  MESSAGE
+  ML-HDNNP
+  ML-PACE
+  ML-QUIP
+  MOLFILE
+  MPIIO
+  MSCG
+  NETCDF
+  PLUMED
+  PYTHON
+  QMMM
+  SCAFACOS
+  VORONOI
+  VTK)
 
 foreach(PKG ${PACKAGES_WITH_LIB})
   set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

cmake/presets/pedantic.cmake

@@ -0,0 +1,26 @@
+# preset that will restore gcc/g++ with support for MPI and OpenMP (on Linux boxes)
+
+set(CMAKE_CXX_COMPILER "g++" CACHE STRING "" FORCE)
+set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_COMPILER "gfortran" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -Werror=vla -Wno-maybe-uninitialized -g" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -Werror=vla -Wno-maybe-uninitialized -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELEASE "-Wall -O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(MPI_CXX "g++" CACHE STRING "" FORCE)
+set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
+set(MPI_C "gcc" CACHE STRING "" FORCE)
+set(MPI_C_COMPILER "mpicc" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -Wno-maybe-uninitialized -g" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -Wno-maybe-uninitialized -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELEASE "-Wall -O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(MPI_Fortran "gfortran" CACHE STRING "" FORCE)
+set(MPI_Fortran_COMPILER "mpifort" CACHE STRING "" FORCE)
+unset(HAVE_OMP_H_INCLUDE CACHE)
+
+set(OpenMP_C "gcc" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_C_LIB_NAMES "gomp" CACHE STRING "" FORCE)
+set(OpenMP_CXX "g++" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_CXX_LIB_NAMES "gomp" CACHE STRING "" FORCE)
+set(OpenMP_omp_LIBRARY "libgomp.so" CACHE PATH "" FORCE)

doc/Makefile

@@ -230,7 +230,7 @@ $(VENV):
 	)
 
 $(MATHJAX):
-	@git clone -b 3.1.4 -c advice.detachedHead=0 --depth 1 git://github.com/mathjax/MathJax.git $@
+	@git clone -b 3.2.0 -c advice.detachedHead=0 --depth 1 git://github.com/mathjax/MathJax.git $@
 
 $(ANCHORCHECK): $(VENV)
 	@( \

doc/include-file-conventions.md

@@ -122,7 +122,7 @@ recorded compilation commands information when typing `make iwyu`.
 A lot of code predates the application of the rules in this document
 and the rules themselves are a moving target.  So there are going to be
 significant chunks of code that do not fully comply.  This applies
-for example to the USER-REAXC, or the USER-ATC package.  The LAMMPS
+for example to the REAXFF, or the ATC package.  The LAMMPS
 developers are dedicated to make an effort to improve the compliance
 and welcome volunteers wanting to help with the process.
 

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "27 May 2021" "2021-05-27"
+.TH LAMMPS "30 July 2021" "2021-07-30"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.
@@ -135,7 +135,7 @@ For example "-pk gpu 2" is the same as "package gpu 2" in the input
 script. The possible styles and options are discussed in the
 .B LAMMPS
 manual for the "package" command. This switch can be used multiple
-times, e.g. to set options for the USER-INTEL and USER-OMP packages
+times, e.g. to set options for the INTEL and OPENMP packages
 when used together. Along with the "-sf" or "-suffix" switch, this
 is a convenient mechanism for invoking accelerator packages and their
 options without having to edit an input script.

doc/src/Bibliography.rst

@@ -191,7 +191,7 @@ Bibliography
    A.\  Calhoun, M. Pavese, G. Voth, Chem Phys Letters, 262, 415 (1996).
 
 **(Campana)**
-   C.\  Campana and M. H. Muser, *Practical Green's function approach to the simulation of elastic semi-infinite solids*\ , `Phys. Rev. B [74], 075420 (2006) <https://doi.org/10.1103/PhysRevB.74.075420>`_
+   C.\  Campana and M. H. Muser, *Practical Green's function approach to the simulation of elastic semi-infinite solids*, `Phys. Rev. B [74], 075420 (2006) <https://doi.org/10.1103/PhysRevB.74.075420>`_
 
 **(Cao1)**
    J.\  Cao and B. Berne, J Chem Phys, 99, 2902 (1993).
@@ -767,7 +767,7 @@ Bibliography
    Morris, Fox, Zhu, J Comp Physics, 136, 214-226 (1997).
 
 **(Moustafa)**
-   Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, *Very fast averaging of thermal properties of crystals by molecular simulation*\ , `Phys. Rev. E [92], 043303 (2015) <https://link.aps.org/doi/10.1103/PhysRevE.92.043303>`_
+   Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, *Very fast averaging of thermal properties of crystals by molecular simulation*, `Phys. Rev. E [92], 043303 (2015) <https://link.aps.org/doi/10.1103/PhysRevE.92.043303>`_
 
 **(Muller-Plathe1)**
    Muller-Plathe, J Chem Phys, 106, 6082 (1997).

doc/src/Build_basics.rst

@@ -90,7 +90,7 @@ standard. A more detailed discussion of that is below.
       directory, or ``make`` from the ``src/STUBS`` dir.  If the build
       fails, you may need to edit the ``STUBS/Makefile`` for your
       platform.  The stubs library does not provide MPI/IO functions
-      required by some LAMMPS packages, e.g. ``MPIIO`` or ``USER-LB``,
+      required by some LAMMPS packages, e.g. ``MPIIO`` or ``LATBOLTZ``,
       and thus is not compatible with those packages.
 
       .. note::
@@ -120,19 +120,19 @@ self-installed MPICH or OpenMPI, so you should study the provided
 documentation to find out how to build and link with it.
 
 The majority of OpenMP (threading) support in LAMMPS is provided by the
-``USER-OMP`` package; see the :doc:`Speed_omp`
+``OPENMP`` package; see the :doc:`Speed_omp`
-page for details. The ``USER-INTEL`` package also includes OpenMP
+page for details. The ``INTEL`` package also includes OpenMP
-threading (it is compatible with ``USER-OMP`` and will usually fall
+threading (it is compatible with ``OPENMP`` and will usually fall
-back on styles from that package, if a ``USER-INTEL`` does not exist)
+back on styles from that package, if a ``INTEL`` does not exist)
 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``,
-``SNAP``, ``USER-DIFFRACTION``, and ``USER-DPD`` packages.  In addition
+``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 ``USER-COLVARS``.
+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.
@@ -176,7 +176,7 @@ 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 ``USER-INTEL`` package, there is a distinct advantage in using
+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
@@ -325,9 +325,9 @@ LAMMPS.
          .. code-block:: bash
 
             Makefile.opt                   # OPT package
-            Makefile.omp                   # USER-OMP package
+            Makefile.omp                   # OPENMP package
-            Makefile.intel_cpu             # USER-INTEL package for CPUs
+            Makefile.intel_cpu             # INTEL package for CPUs
-            Makefile.intel_coprocessor     # USER-INTEL package for KNLs
+            Makefile.intel_coprocessor     # INTEL package for KNLs
             Makefile.gpu                   # GPU package
             Makefile.kokkos_cuda_mpi       # KOKKOS package for GPUs
             Makefile.kokkos_omp            # KOKKOS package for CPUs (OpenMP)

doc/src/Build_cmake.rst

@@ -140,7 +140,7 @@ can be used several times in one command.
 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/minimal.cmake``).  This step would only be needed
+(``-C ../cmake/presets/basic.cmake``).  This step would only be needed
 once, as the settings from the preset files are stored in the
 ``CMakeCache.txt`` file. It is also possible to customize the build
 by adding one or more *-D* flags to the CMake command line.

doc/src/Build_development.rst

@@ -310,7 +310,7 @@ and working.
      parameter needs to be adjusted. Typically a value around 1.0e-13
      can be used, but it may need to be as large as 1.0e-8 in some
      cases.
-   - The tests for pair styles from OPT, USER-OMP and USER-INTEL are
+   - The tests for pair styles from OPT, OPENMP and INTEL are
      performed with automatically rescaled epsilon to account for
      additional loss of precision from code optimizations and different
      summation orders.
@@ -345,7 +345,7 @@ and compared.  If the fix is a thermostat and thus the internal property
 ``t_target`` can be extracted, then this is compared to the reference
 data.  The tests are repeated with the respa run style.
 
-If the fix has a multi-threaded version in the USER-OMP package, then
+If the fix has a multi-threaded version in the OPENMP package, then
 the entire set of tests is repeated for that version as well.
 
 For this to work, some additional conditions have to be met by the

doc/src/Build_extras.rst

@@ -31,37 +31,37 @@ This is the list of packages that may require additional steps.
 .. table_from_list::
    :columns: 6
 
+   * :ref:`ADIOS <adios>`
+   * :ref:`ATC <atc>`
+   * :ref:`AWPMD <awpmd>`
+   * :ref:`COLVARS <colvars>`
    * :ref:`COMPRESS <compress>`
    * :ref:`GPU <gpu>`
+   * :ref:`H5MD <h5md>`
+   * :ref:`INTEL <intel>`
    * :ref:`KIM <kim>`
    * :ref:`KOKKOS <kokkos>`
    * :ref:`LATTE <latte>`
+   * :ref:`MACHDYN <machdyn>`
+   * :ref:`MDI <mdi>`
+   * :ref:`MESONT <mesont>`
    * :ref:`MESSAGE <message>`
-   * :ref:`MLIAP <mliap>`
+   * :ref:`ML-HDNNP <ml-hdnnp>`
+   * :ref:`ML-IAP <mliap>`
+   * :ref:`ML-PACE <ml-pace>`
+   * :ref:`ML-QUIP <ml-quip>`
+   * :ref:`MOLFILE <molfile>`
    * :ref:`MSCG <mscg>`
+   * :ref:`NETCDF <netcdf>`
+   * :ref:`OPENMP <openmp>`
    * :ref:`OPT <opt>`
+   * :ref:`PLUMED <plumed>`
    * :ref:`POEMS <poems>`
    * :ref:`PYTHON <python>`
+   * :ref:`QMMM <qmmm>`
+   * :ref:`SCAFACOS <scafacos>`
    * :ref:`VORONOI <voronoi>`
-   * :ref:`USER-ADIOS <user-adios>`
+   * :ref:`VTK <vtk>`
-   * :ref:`USER-ATC <user-atc>`
-   * :ref:`USER-AWPMD <user-awpmd>`
-   * :ref:`USER-COLVARS <user-colvars>`
-   * :ref:`USER-H5MD <user-h5md>`
-   * :ref:`USER-HDNNP <user-hdnnp>`
-   * :ref:`USER-INTEL <user-intel>`
-   * :ref:`USER-MDI <user-mdi>`
-   * :ref:`USER-MESONT <user-mesont>`
-   * :ref:`USER-MOLFILE <user-molfile>`
-   * :ref:`USER-NETCDF <user-netcdf>`
-   * :ref:`USER-PACE <user-pace>`
-   * :ref:`USER-PLUMED <user-plumed>`
-   * :ref:`USER-OMP <user-omp>`
-   * :ref:`USER-QMMM <user-qmmm>`
-   * :ref:`USER-QUIP <user-quip>`
-   * :ref:`USER-SCAFACOS <user-scafacos>`
-   * :ref:`USER-SMD <user-smd>`
-   * :ref:`USER-VTK <user-vtk>`
 
 ----------
 
@@ -74,7 +74,8 @@ To build with this package you must have the `zlib compression library
 <https://zlib.net>`_ available on your system to build dump styles with
 a '/gz' suffix.  There are also styles using the
 `Zstandard <https://facebook.github.io/zstd/>`_ library which have a
-'/zstd' suffix.
+'/zstd' suffix.  The zstd library version must be at least 1.4.  Older
+versions use an incompatible API and thus LAMMPS will fail to compile.
 
 .. tabs::
 
@@ -622,7 +623,7 @@ This list was last updated for version 3.4.1 of the Kokkos library.
 
          mkdir build-kokkos-cuda
          cd build-kokkos-cuda
-         cmake -C ../cmake/presets/minimal.cmake -C ../cmake/presets/kokkos-cuda.cmake ../cmake
+         cmake -C ../cmake/presets/basic.cmake -C ../cmake/presets/kokkos-cuda.cmake ../cmake
          cmake --build .
 
    .. tab:: Basic traditional make settings:
@@ -811,16 +812,17 @@ be installed on your system.
 
 .. _mliap:
 
-MLIAP package
+ML-IAP package
 ---------------------------
 
-Building the MLIAP package requires including the :ref:`SNAP <PKG-SNAP>`
+Building the ML-IAP package requires including the :ref:`ML-SNAP
-package.  There will be an error message if this requirement is not satisfied.
+<PKG-ML-SNAP>` package.  There will be an error message if this requirement
-Using the *mliappy* model also requires enabling Python support, which
+is not satisfied.  Using the *mliappy* model also requires enabling
-in turn requires the :ref:`PYTHON <PKG-PYTHON>`
+Python support, which in turn requires to include the :ref:`PYTHON
-package **and** requires you have the `cython <https://cython.org>`_ software
+<PKG-PYTHON>` package **and** requires to have the `cython
-installed and with it a working ``cythonize`` command.  This feature requires
+<https://cython.org>`_ software installed and with it a working
-compiling LAMMPS with Python version 3.6 or later.
+``cythonize`` command.  This feature requires compiling LAMMPS with
+Python version 3.6 or later.
 
 .. tabs::
 
@@ -834,9 +836,9 @@ compiling LAMMPS with Python version 3.6 or later.
       suitable Python version and the ``cythonize`` command and choose
       the default accordingly.  During the build procedure the provided
       .pyx file(s) will be automatically translated to C++ code and compiled.
-      Please do **not** run ``cythonize`` manually in the ``src/MLIAP`` folder,
+      Please do **not** run ``cythonize`` manually in the ``src/ML-IAP`` folder,
       as that can lead to compilation errors if Python support is not enabled.
-      If you did by accident, please remove the generated .cpp and .h files.
+      If you did it by accident, please remove the generated .cpp and .h files.
 
    .. tab:: Traditional make
 
@@ -845,15 +847,16 @@ compiling LAMMPS with Python version 3.6 or later.
       the ``cythonize`` command in case the corresponding .pyx file(s) were
       modified.  You may need to modify ``lib/python/Makefile.lammps``
       if the LAMMPS build fails.
-      To manually enforce building MLIAP with Python support enabled,
+
-      you can add
+      To enable building the ML-IAP package with Python support enabled,
-      ``-DMLIAP_PYTHON`` to the ``LMP_INC`` variable in your machine makefile.
+      you need to add ``-DMLIAP_PYTHON`` to the ``LMP_INC`` variable in
-      You may have to manually run the ``cythonize`` command on .pyx file(s)
+      your machine makefile.  You may have to manually run the
-      in the ``src`` folder, if this is not automatically done during
+      ``cythonize`` command on .pyx file(s) in the ``src`` folder, if
-      installing the MLIAP package.  Please do **not** run ``cythonize``
+      this is not automatically done during installing the ML-IAP
-      in the ``src/MLIAP`` folder, as that can lead to compilation errors
+      package.  Please do **not** run ``cythonize`` in the ``src/ML-IAP``
-      if Python support is not enabled.
+      folder, as that can lead to compilation errors if Python support
-      If you did by accident, please remove the generated .cpp and .h files.
+      is not enabled.  If you did this by accident, please remove the
+      generated .cpp and .h files.
 
 ----------
 
@@ -1054,12 +1057,12 @@ binary package provided by your operating system.
 
 ----------
 
-.. _user-adios:
+.. _adios:
 
-USER-ADIOS package
+ADIOS package
 -----------------------------------
 
-The USER-ADIOS package requires the `ADIOS I/O library
+The ADIOS package requires the `ADIOS I/O library
 <https://github.com/ornladios/ADIOS2>`_, version 2.3.1 or newer. Make
 sure that you have ADIOS built either with or without MPI to match if
 you build LAMMPS with or without MPI.  ADIOS compilation settings for
@@ -1075,38 +1078,38 @@ systems.
       .. code-block:: bash
 
          -D ADIOS2_DIR=path        # path is where ADIOS 2.x is installed
-         -D PKG_USER-ADIOS=yes
+         -D PKG_ADIOS=yes
 
    .. tab:: Traditional make
 
-      Turn on the USER-ADIOS package before building LAMMPS. If the
+      Turn on the ADIOS package before building LAMMPS. If the
       ADIOS 2.x software is installed in PATH, there is nothing else to
       do:
 
       .. code-block:: bash
 
-         $ make yes-user-adios
+         $ make yes-adios
 
       otherwise, set ADIOS2_DIR environment variable when turning on the package:
 
       .. code-block:: bash
 
-         $ ADIOS2_DIR=path make yes-user-adios   # path is where ADIOS 2.x is installed
+         $ ADIOS2_DIR=path make yes-adios   # path is where ADIOS 2.x is installed
 
 ----------
 
-.. _user-atc:
+.. _atc:
 
-USER-ATC package
+ATC package
 -------------------------------
 
-The USER-ATC package requires the MANYBODY package also be installed.
+The ATC package requires the MANYBODY package also be installed.
 
 .. tabs::
 
    .. tab:: CMake build
 
-      No additional settings are needed besides ``-D PKG_USER-ATC=yes``
+      No additional settings are needed besides ``-D PKG_ATC=yes``
       and ``-D PKG_MANYBODY=yes``.
 
    .. tab:: Traditional make
@@ -1149,16 +1152,16 @@ The USER-ATC package requires the MANYBODY package also be installed.
 
 ----------
 
-.. _user-awpmd:
+.. _awpmd:
 
-USER-AWPMD package
+AWPMD package
 ------------------
 
 .. tabs::
 
    .. tab:: CMake build
 
-      No additional settings are needed besides ``-D PKG_USER-AQPMD=yes``.
+      No additional settings are needed besides ``-D PKG_AQPMD=yes``.
 
    .. tab:: Traditional make
 
@@ -1200,9 +1203,9 @@ USER-AWPMD package
 
 ----------
 
-.. _user-colvars:
+.. _colvars:
 
-USER-COLVARS package
+COLVARS package
 ---------------------------------------
 
 This package includes the `Colvars library
@@ -1216,7 +1219,7 @@ be built for the most part with all major versions of the C++ language.
 
       This is the recommended build procedure for using Colvars in
       LAMMPS. No additional settings are normally needed besides
-      ``-D PKG_USER-COLVARS=yes``.
+      ``-D PKG_COLVARS=yes``.
 
    .. tab:: Traditional make
 
@@ -1259,9 +1262,9 @@ be built for the most part with all major versions of the C++ language.
 
 ----------
 
-.. _user-pace:
+.. _ml-pace:
 
-USER-PACE package
+ML-PACE package
 -----------------------------
 
 This package requires a library that can be downloaded and built
@@ -1274,8 +1277,8 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
    .. tab:: CMake build
 
       By default the library will be downloaded from the git repository
-      and built automatically when the USER-PACE package is enabled with
+      and built automatically when the ML-PACE package is enabled with
-      ``-D PKG_USER-PACE=yes``.  The location for the sources may be
+      ``-D PKG_ML-PACE=yes``.  The location for the sources may be
       customized by setting the variable ``PACELIB_URL`` when
       configuring with CMake (e.g. to use a local archive on machines
       without internet access).  Since CMake checks the validity of the
@@ -1286,7 +1289,7 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
 
    .. tab:: Traditional make
 
-      You can download and build the USER-PACE library
+      You can download and build the ML-PACE library
       in one step from the ``lammps/src`` dir, using these commands,
       which invoke the ``lib/pace/Install.py`` script.
 
@@ -1299,9 +1302,9 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
 
 ----------
 
-.. _user-plumed:
+.. _plumed:
 
-USER-PLUMED package
+PLUMED package
 -------------------------------------
 
 .. _plumedinstall: https://plumed.github.io/doc-master/user-doc/html/_installation.html
@@ -1309,7 +1312,7 @@ USER-PLUMED package
 Before building LAMMPS with this package, you must first build PLUMED.
 PLUMED can be built as part of the LAMMPS build or installed separately
 from LAMMPS using the generic `PLUMED installation instructions <plumedinstall_>`_.
-The USER-PLUMED package has been tested to work with Plumed versions
+The PLUMED package has been tested to work with Plumed versions
 2.4.x, 2.5.x, and 2.6.x and will error out, when trying to run calculations
 with a different version of the Plumed kernel.
 
@@ -1345,7 +1348,7 @@ LAMMPS build.
 
    .. tab:: CMake build
 
-      When the ``-D PKG_USER-PLUMED=yes`` flag is included in the cmake
+      When the ``-D PKG_PLUMED=yes`` flag is included in the cmake
       command you must ensure that GSL is installed in locations that
       are specified in your environment.  There are then two additional
       variables that control the manner in which PLUMED is obtained and
@@ -1378,7 +1381,7 @@ LAMMPS build.
 
    .. tab:: Traditional make
 
-      PLUMED needs to be installed before the USER-PLUMED package is
+      PLUMED needs to be installed before the PLUMED package is
       installed so that LAMMPS can find the right settings when
       compiling and linking the LAMMPS executable.  You can either
       download and build PLUMED inside the LAMMPS plumed library folder
@@ -1403,12 +1406,12 @@ LAMMPS build.
       build to use. A new file ``lib/plumed/Makefile.lammps`` is also
       created with settings suitable for LAMMPS to compile and link
       PLUMED using the desired linkage mode. After this step is
-      completed, you can install the USER-PLUMED package and compile
+      completed, you can install the PLUMED package and compile
       LAMMPS in the usual manner:
 
       .. code-block:: bash
 
-         $ make yes-user-plumed
+         $ make yes-plumed
          $ make machine
 
       Once this compilation completes you should be able to run LAMMPS
@@ -1423,15 +1426,15 @@ LAMMPS build.
 
       If you want to change the linkage mode, you have to re-run "make
       lib-plumed" with the desired settings **and** do a re-install if
-      the USER-PLUMED package with "make yes-user-plumed" to update the
+      the PLUMED package with "make yes-plumed" to update the
       required makefile settings with the changes in the lib/plumed
       folder.
 
 ----------
 
-.. _user-h5md:
+.. _h5md:
 
-USER-H5MD package
+H5MD package
 ---------------------------------
 
 To build with this package you must have the HDF5 software package
@@ -1442,7 +1445,7 @@ the HDF5 library.
 
    .. tab:: CMake build
 
-      No additional settings are needed besides ``-D PKG_USER-H5MD=yes``.
+      No additional settings are needed besides ``-D PKG_H5MD=yes``.
 
       This should auto-detect the H5MD library on your system.  Several
       advanced CMake H5MD options exist if you need to specify where it
@@ -1474,13 +1477,13 @@ the HDF5 library.
 
 ----------
 
-.. _user-hdnnp:
+.. _ml-hdnnp:
 
-USER-HDNNP package
+ML-HDNNP package
----------------------------------
+----------------
 
-To build with the USER-HDNNP package it is required to download and build the
+To build with the ML-HDNNP package it is required to download and build the
-external `n2p2 <https://github.com/CompPhysVienna/n2p2>`__ library ``v2.1.4``
+external `n2p2 <https://github.com/CompPhysVienna/n2p2>`_ library ``v2.1.4``
 (or higher). The LAMMPS build process offers an automatic download and
 compilation of *n2p2* or allows you to choose the installation directory of
 *n2p2* manually. Please see the boxes below for the CMake and traditional build
@@ -1490,7 +1493,7 @@ In case of a manual installation of *n2p2* you only need to build the *n2p2* cor
 library ``libnnp`` and interface library ``libnnpif``. When using GCC it should
 suffice to execute ``make libnnpif`` in the *n2p2* ``src`` directory. For more
 details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
-<https://compphysvienna.github.io/n2p2/topics/build.html>`__.
+<https://compphysvienna.github.io/n2p2/topics/build.html>`_.
 
 .. tabs::
 
@@ -1528,24 +1531,24 @@ details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
 
 ----------
 
-.. _user-intel:
+.. _intel:
 
-USER-INTEL package
+INTEL package
 -----------------------------------
 
 To build with this package, you must choose which hardware you want to
 build for, either x86 CPUs or Intel KNLs in offload mode.  You should
-also typically :ref:`install the USER-OMP package <user-omp>`, as it can be
+also typically :ref:`install the OPENMP package <openmp>`, as it can be
-used in tandem with the USER-INTEL package to good effect, as explained
+used in tandem with the INTEL package to good effect, as explained
 on the :doc:`Speed_intel` page.
 
 When using Intel compilers version 16.0 or later is required.  You can
 also use the GNU or Clang compilers and they will provide performance
-improvements over regular styles and USER-OMP styles, but less so than
+improvements over regular styles and OPENMP styles, but less so than
 with the Intel compilers.  Please also note, that some compilers have
 been found to apply memory alignment constraints incompletely or
 incorrectly and thus can cause segmentation faults in otherwise correct
-code when using features from the USER-INTEL package.
+code when using features from the INTEL package.
 
 
 .. tabs::
@@ -1562,7 +1565,7 @@ code when using features from the USER-INTEL package.
       Choose which hardware to compile for in Makefile.machine via the
       following settings.  See ``src/MAKE/OPTIONS/Makefile.intel_cpu*``
       and ``Makefile.knl`` files for examples. and
-      ``src/USER-INTEL/README`` for additional information.
+      ``src/INTEL/README`` for additional information.
 
       For CPUs:
 
@@ -1598,9 +1601,9 @@ TBB and MKL.
 
 ----------
 
-.. _user-mdi:
+.. _mdi:
 
-USER-MDI package
+MDI package
 -----------------------------
 
 .. tabs::
@@ -1627,9 +1630,9 @@ USER-MDI package
 
 ----------
 
-.. _user-mesont:
+.. _mesont:
 
-USER-MESONT package
+MESONT package
 -------------------------
 
 This package includes a library written in Fortran 90 in the
@@ -1642,7 +1645,7 @@ they will be downloaded the first time this package is installed.
 
    .. tab:: CMake build
 
-      No additional settings are needed besides ``-D PKG_USER-MESONT=yes``
+      No additional settings are needed besides ``-D PKG_MESONT=yes``
 
    .. tab:: Traditional make
 
@@ -1669,9 +1672,9 @@ they will be downloaded the first time this package is installed.
 
 ----------
 
-.. _user-molfile:
+.. _molfile:
 
-USER-MOLFILE package
+MOLFILE package
 ---------------------------------------
 
 .. tabs::
@@ -1681,9 +1684,9 @@ USER-MOLFILE package
       .. code-block:: bash
 
          -D MOLFILE_INCLUDE_DIR=path   # (optional) path where VMD molfile plugin headers are installed
-         -D PKG_USER-MOLFILE=yes
+         -D PKG_MOLFILE=yes
 
-      Using ``-D PKG_USER-MOLFILE=yes`` enables the package, and setting
+      Using ``-D PKG_MOLFILE=yes`` enables the package, and setting
       ``-D MOLFILE_INCLUDE_DIR`` allows to provide a custom location for
       the molfile plugin header files. These should match the ABI of the
       plugin files used, and thus one typically sets them to include
@@ -1707,9 +1710,9 @@ USER-MOLFILE package
 
 ----------
 
-.. _user-netcdf:
+.. _netcdf:
 
-USER-NETCDF package
+NETCDF package
 -------------------------------------
 
 To build with this package you must have the NetCDF library installed
@@ -1719,7 +1722,7 @@ on your system.
 
    .. tab:: CMake build
 
-      No additional settings are needed besides ``-D PKG_USER-NETCDF=yes``.
+      No additional settings are needed besides ``-D PKG_NETCDF=yes``.
 
       This should auto-detect the NETCDF library if it is installed on
       your system at standard locations.  Several advanced CMake NETCDF
@@ -1738,9 +1741,9 @@ on your system.
 
 ----------
 
-.. _user-omp:
+.. _openmp:
 
-USER-OMP package
+OPENMP package
 -------------------------------
 
 .. tabs::
@@ -1748,13 +1751,13 @@ USER-OMP package
    .. tab:: CMake build
 
       No additional settings are required besides ``-D
-      PKG_USER-OMP=yes``.  If CMake detects OpenMP compiler support, the
+      PKG_OPENMP=yes``.  If CMake detects OpenMP compiler support, the
-      USER-OMP code will be compiled with multi-threading support
+      OPENMP code will be compiled with multi-threading support
       enabled, otherwise as optimized serial code.
 
    .. tab:: Traditional make
 
-      To enable multi-threading support in the USER-OMP package (and
+      To enable multi-threading support in the OPENMP package (and
       other styles supporting OpenMP) the following compile and link
       flags must be added to your Makefile.machine file.  See
       ``src/MAKE/OPTIONS/Makefile.omp`` for an example.
@@ -1771,12 +1774,12 @@ USER-OMP package
 
 ----------
 
-.. _user-qmmm:
+.. _qmmm:
 
-USER-QMMM package
+QMMM package
 ---------------------------------
 
-For using LAMMPS to do QM/MM simulations via the USER-QMMM package you
+For using LAMMPS to do QM/MM simulations via the QMMM package you
 need to build LAMMPS as a library.  A LAMMPS executable with :doc:`fix
 qmmm <fix_qmmm>` included can be built, but will not be able to do a
 QM/MM simulation on as such.  You must also build a QM code - currently
@@ -1799,11 +1802,11 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
       libqmmm.a) are not included in the static LAMMPS library and
       (currently) not installed, while their code is included in the
       shared LAMMPS library.  Thus a typical command line to configure
-      building LAMMPS for USER-QMMM would be:
+      building LAMMPS for QMMM would be:
 
       .. code-block:: bash
 
-         cmake -C ../cmake/presets/minimal.cmake -D PKG_USER-QMMM=yes \
+         cmake -C ../cmake/presets/basic.cmake -D PKG_QMMM=yes \
              -D BUILD_LIB=yes -DBUILD_SHARED_LIBS=yes ../cmake
 
       After completing the LAMMPS build and also configuring and
@@ -1846,16 +1849,16 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
 
 ----------
 
-.. _user-quip:
+.. _ml-quip:
 
-USER-QUIP package
+ML-QUIP package
 ---------------------------------
 
 To build with this package, you must download and build the QUIP
 library.  It can be obtained from GitHub.  For support of GAP
 potentials, additional files with specific licensing conditions need
-to be downloaded and configured.  See step 1 and step 1.1 in the
+to be downloaded and configured.  The automatic download will from
-``lib/quip/README`` file for details on how to do this.
+within CMake will download the non-commercial use version.
 
 .. tabs::
 
@@ -1863,11 +1866,14 @@ to be downloaded and configured.  See step 1 and step 1.1 in the
 
       .. code-block:: bash
 
+         -D DOWNLOAD_QUIP=value   # download OpenKIM API v2 for build, value = no (default) or yes
          -D QUIP_LIBRARY=path     # path to libquip.a (only needed if a custom location)
 
-      CMake will **not** download and build the QUIP library.  But once you have
+      CMake will try to download and build the QUIP library from GitHub, if it is not
-      done that, a CMake build of LAMMPS with ``-D PKG_USER-QUIP=yes`` should
+      found on the local machine. This requires to have git installed. It will use the same compilers
-      work.  Set the ``QUIP_LIBRARY`` variable if CMake cannot find the QUIP library.
+      and flags as used for compiling LAMMPS.  Currently this is only supported for the GNU and the
+      Intel compilers. Set the ``QUIP_LIBRARY`` variable if you want to use a previously compiled
+      and installed QUIP library and CMake cannot find it.
 
    .. tab:: Traditional make
 
@@ -1881,9 +1887,9 @@ to be downloaded and configured.  See step 1 and step 1.1 in the
 
 ----------
 
-.. _user-scafacos:
+.. _scafacos:
 
-USER-SCAFACOS package
+SCAFACOS package
 -----------------------------------------
 
 To build with this package, you must download and build the
@@ -1928,9 +1934,9 @@ To build with this package, you must download and build the
 
 ----------
 
-.. _user-smd:
+.. _machdyn:
 
-USER-SMD package
+MACHDYN package
 -------------------------------
 
 To build with this package, you must download the Eigen3 library.
@@ -1972,9 +1978,9 @@ Eigen3 is a template library, so you do not need to build it.
 
 ----------
 
-.. _user-vtk:
+.. _vtk:
 
-USER-VTK package
+VTK package
 -------------------------------
 
 To build with this package you must have the VTK library installed on
@@ -1984,7 +1990,7 @@ your system.
 
    .. tab:: CMake build
 
-      No additional settings are needed besides ``-D PKG_USER-VTK=yes``.
+      No additional settings are needed besides ``-D PKG_VTK=yes``.
 
       This should auto-detect the VTK library if it is installed on your
       system at standard locations.  Several advanced VTK options exist

doc/src/Build_make.rst

@@ -117,10 +117,10 @@ settings may become outdated:
 
    make mac             # build serial LAMMPS on a Mac
    make mac_mpi         # build parallel LAMMPS on a Mac
-   make intel_cpu       # build with the USER-INTEL package optimized for CPUs
+   make intel_cpu       # build with the INTEL package optimized for CPUs
-   make knl             # build with the USER-INTEL package optimized for KNLs
+   make knl             # build with the INTEL package optimized for KNLs
    make opt             # build with the OPT package optimized for CPUs
-   make omp             # build with the USER-OMP package optimized for OpenMP
+   make omp             # build with the OPENMP package optimized for OpenMP
    make kokkos_omp      # build with the KOKKOS package for OpenMP
    make kokkos_cuda_mpi # build with the KOKKOS package for GPUs
    make kokkos_phi      # build with the KOKKOS package for KNLs

doc/src/Build_manual.rst

@@ -204,9 +204,9 @@ be multiple tests run automatically:
 
   .. parsed-literal::
 
-     Found 33 standard and 41 user packages
+     Found 88 packages
-     Standard package NEWPACKAGE missing in Packages_standard.rst
+     Package NEWPACKAGE missing in Packages_list.rst
-     Standard package NEWPACKAGE missing in Packages_details.rst
+     Package NEWPACKAGE missing in Packages_details.rst
 
 - A test that only standard, printable ASCII text characters are used.
   This runs the command ``env LC_ALL=C grep -n '[^ -~]' src/*.rst`` and

doc/src/Build_package.rst

@@ -30,17 +30,37 @@ steps, as explained on the :doc:`Build extras <Build_extras>` page.
 These links take you to the extra instructions for those select
 packages:
 
-+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
+.. table_from_list::
-| :ref:`COMPRESS <compress>`           | :ref:`GPU <gpu>`                     | :ref:`KIM <kim>`                   | :ref:`KOKKOS <kokkos>`           | :ref:`LATTE <latte>`           | :ref:`MESSAGE <message>`       |
+   :columns: 6
-+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
+
-| :ref:`MSCG <mscg>`                   | :ref:`OPT <opt>`                     | :ref:`POEMS <poems>`               | :ref:`PYTHON <python>`           | :ref:`VORONOI <voronoi>`       | :ref:`USER-ADIOS <user-adios>` |
+   * :ref:`ADIOS <adios>`
-+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
+   * :ref:`ATC <atc>`
-| :ref:`USER-ATC <user-atc>`           | :ref:`USER-AWPMD <user-awpmd>`       | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>`     | :ref:`USER-HDNNP <user-hdnnp>` | :ref:`USER-INTEL <user-intel>` |
+   * :ref:`AWPMD <awpmd>`
-+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
+   * :ref:`COLVARS <colvars>`
-| :ref:`USER-MOLFILE <user-molfile>`   | :ref:`USER-NETCDF <user-netcdf>`     | :ref:`USER-PACE <user-pace>`       | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>`     | :ref:`USER-QMMM <user-qmmm>`   |
+   * :ref:`COMPRESS <compress>`
-+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
+   * :ref:`GPU <gpu>`
-| :ref:`USER-QUIP <user-quip>`         | :ref:`USER-SCAFACOS <user-scafacos>` | :ref:`USER-SMD <user-smd>`         | :ref:`USER-VTK <user-vtk>`       |                                |                                |
+   * :ref:`H5MD <h5md>`
-+--------------------------------------+--------------------------------------+------------------------------------+----------------------------------+--------------------------------+--------------------------------+
+   * :ref:`INTEL <intel>`
+   * :ref:`KIM <kim>`
+   * :ref:`KOKKOS <kokkos>`
+   * :ref:`LATTE <latte>`
+   * :ref:`MACHDYN <machdyn>`
+   * :ref:`MESSAGE <message>`
+   * :ref:`ML-HDNNP <ml-hdnnp>`
+   * :ref:`ML-PACE <ml-pace>`
+   * :ref:`ML-QUIP <ml-quip>`
+   * :ref:`MOLFILE <molfile>`
+   * :ref:`MSCG <mscg>`
+   * :ref:`NETCDF <netcdf>`
+   * :ref:`OPENMP <openmp>`
+   * :ref:`OPT <opt>`
+   * :ref:`PLUMED <plumed>`
+   * :ref:`POEMS <poems>`
+   * :ref:`PYTHON <python>`
+   * :ref:`QMMM <qmmm>`
+   * :ref:`SCAFACOS <scafacos>`
+   * :ref:`VORONOI <voronoi>`
+   * :ref:`VTK <vtk>`
 
 The mechanism for including packages is simple but different for CMake
 versus make.
@@ -58,14 +78,10 @@ versus make.
       .. code-block:: csh
 
          -D PKG_MANYBODY=yes
-         -D PKG_USER-INTEL=yes
+         -D PKG_INTEL=yes
 
-      All standard and user packages are included the same way.  Note
+      All packages are included the same way.  See the shortcut section
-      that USER packages have a hyphen between USER and the rest of the
+      below for how to install many packages at once with CMake.
-      package name, not an underscore.
-
-      See the shortcut section below for how to install many packages at
-      once with CMake.
 
       .. note::
 
@@ -89,12 +105,10 @@ versus make.
       .. code-block:: bash
 
          make no-rigid
-         make yes-user-intel
+         make yes-intel
 
-      All standard and user packages are included the same way.
+      All packages are included the same way.  See the shortcut section
-
+      below for how to install many packages at once with make.
-      See the shortcut section below for how to install many packages at
-      once with make.
 
       .. note::
 
@@ -126,7 +140,7 @@ other files dependent on that package are also excluded.
 
 .. note::
 
-   By default no package is installed.  Prior to August 2018, however,
+   By default no packages are installed.  Prior to August 2018, however,
    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
@@ -153,7 +167,7 @@ one of them as a starting point and customize it to your needs.
 
 .. code-block:: bash
 
-    cmake -C ../cmake/presets/minimal.cmake  [OPTIONS] ../cmake  # enable just a few core packages
+    cmake -C ../cmake/presets/basic.cmake    [OPTIONS] ../cmake  # enable just a few core packages
     cmake -C ../cmake/presets/most.cmake     [OPTIONS] ../cmake  # enable most packages
     cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake  # enable packages which download sources or potential files
     cmake -C ../cmake/presets/nolib.cmake    [OPTIONS] ../cmake  # disable packages that do require extra libraries or tools
@@ -208,10 +222,10 @@ These commands install/un-install sets of packages:
 
     make yes-all                        # install all packages
     make no-all                         # uninstall all packages
-    make yes-standard or make yes-std   # install standard packages
+    make yes-basic                      # install a few commonly used packages'
-    make no-standard or make no-std     # uninstall standard packages
+    make no-basic                       # remove a few commonly used packages'
-    make yes-user                       # install user packages
+    make yes-most                       # install most packages w/o libs'
-    make no-user                        # uninstall user packages
+    make no-most                        # remove most packages w/o libs'
     make yes-lib                        # install packages that require extra libraries
     make no-lib                         # uninstall packages that require extra libraries
     make yes-ext                        # install packages that require external libraries
@@ -225,15 +239,14 @@ package`` will list all the these commands.
    Installing or un-installing 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.
-   src/KSPACE, src/USER-ATC), so that the files are included or excluded
+   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
 need to use these commands unless you are editing LAMMPS files or are
-:doc:`installing a patch <Install_patch>` downloaded from the LAMMPS web
+updating LAMMPS via git.
-site.
 
 Type ``make package-status`` or ``make ps`` to show which packages are
 currently installed.  For those that are installed, it will list any
@@ -245,10 +258,10 @@ 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.
+files from the package sub-directories if the package is installed.  It
-It should be used after a :doc:`patch has been applied <Install_patch>`,
+should be used after the checkout has been :doc:`updated or changed
-since patches only update the files in the package sub-directory, but
+withy git <Install_git>`, this will only update the files in the package
-not the src files.
+sub-directories, but not the copies in the src folder.
 
 Type ``make package-overwrite`` to overwrite files in the package
 sub-directories with src files.

doc/src/Build_settings.rst

@@ -64,7 +64,7 @@ LAMMPS can use them if they are available on your system.
       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 USER-OMP is used.  If CMake cannot detect
+      packages like KOKKOS or OPENMP is used.  If CMake cannot detect
       the FFT library, you can set these variables to assist:
 
       .. code-block:: bash
@@ -242,8 +242,8 @@ does not support 64-bit integers or incurs performance penalties when
 using them.
 
 These are limits for the core of the LAMMPS code, specific features or
-some styles may impose additional limits.  The :ref:`USER-ATC
+some styles may impose additional limits.  The :ref:`ATC
-<PKG-USER-ATC>` package cannot be compiled with the "bigbig" setting.
+<PKG-ATC>` package cannot be compiled with the "bigbig" setting.
 Also, there are limitations when using the library interface where some
 functions with known issues have been replaced by dummy calls printing a
 corresponding error message rather than crashing randomly or corrupting

doc/src/Commands_bond.rst

@@ -18,7 +18,7 @@ Bond_style potentials
 
 All LAMMPS :doc:`bond_style <bond_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
@@ -57,7 +57,7 @@ Angle_style potentials
 
 All LAMMPS :doc:`angle_style <angle_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
@@ -99,7 +99,7 @@ Dihedral_style potentials
 
 All LAMMPS :doc:`dihedral_style <dihedral_style>` commands.  Some styles
 have accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
@@ -135,7 +135,7 @@ Improper_style potentials
 
 All LAMMPS :doc:`improper_style <improper_style>` commands.  Some styles
 have accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::

doc/src/Commands_category.rst

@@ -2,7 +2,7 @@ Commands by category
 ====================
 
 This page lists most of the LAMMPS commands, grouped by category.  The
-:doc:`General commands <Commands_all>` doc page lists all general commands
+:doc:`General commands <Commands_all>` page lists all general commands
 alphabetically.  Style options for entries like fix, compute, pair etc.
 have their own pages where they are listed alphabetically.
 

doc/src/Commands_compute.rst

@@ -16,8 +16,8 @@ Compute commands
 
 An alphabetic list of all LAMMPS :doc:`compute <compute>` commands.
 Some styles have accelerated versions.  This is indicated by
-additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
+additional letters in parenthesis: g = GPU, i = INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
+KOKKOS, o = OPENMP, t = OPT.
 
 .. table_from_list::
    :columns: 5
@@ -47,17 +47,20 @@ KOKKOS, o = USER-OMP, t = OPT.
    * :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:`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:`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/atom <compute_erotate_sphere_atom>`
    * :doc:`event/displace <compute_event_displace>`
+   * :doc:`fabric <compute_fabric>`
    * :doc:`fep <compute_fep>`
    * :doc:`force/tally <compute_tally>`
    * :doc:`fragment/atom <compute_cluster_atom>`
@@ -69,6 +72,7 @@ KOKKOS, o = USER-OMP, t = OPT.
    * :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>`
    * :doc:`heat/flux <compute_heat_flux>`
    * :doc:`heat/flux/tally <compute_tally>`
+   * :doc:`heat/flux/virial/tally <compute_tally>`
    * :doc:`hexorder/atom <compute_hexorder_atom>`
    * :doc:`hma <compute_hma>`
    * :doc:`improper <compute_improper>`

doc/src/Commands_fix.rst

@@ -16,7 +16,7 @@ Fix commands
 
 An alphabetic list of all LAMMPS :doc:`fix <fix>` commands.  Some styles
 have accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
@@ -157,11 +157,15 @@ OPT.
    * :doc:`orient/fcc <fix_orient>`
    * :doc:`orient/eco <fix_orient_eco>`
    * :doc:`pafi <fix_pafi>`
+   * :doc:`pair/tracker <fix_pair_tracker>`
    * :doc:`phonon <fix_phonon>`
    * :doc:`pimd <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`
    * :doc:`plumed <fix_plumed>`
    * :doc:`poems <fix_poems>`
+   * :doc:`polarize/bem/gmres <fix_polarize>`
+   * :doc:`polarize/bem/icc <fix_polarize>`
+   * :doc:`polarize/functional <fix_polarize>`
    * :doc:`pour <fix_pour>`
    * :doc:`precession/spin <fix_precession_spin>`
    * :doc:`press/berendsen <fix_press_berendsen>`
@@ -175,14 +179,14 @@ OPT.
    * :doc:`qeq/dynamic <fix_qeq>`
    * :doc:`qeq/fire <fix_qeq>`
    * :doc:`qeq/point <fix_qeq>`
-   * :doc:`qeq/reax (ko) <fix_qeq_reax>`
+   * :doc:`qeq/reaxff (ko) <fix_qeq_reaxff>`
    * :doc:`qeq/shielded <fix_qeq>`
    * :doc:`qeq/slater <fix_qeq>`
    * :doc:`qmmm <fix_qmmm>`
    * :doc:`qtb <fix_qtb>`
    * :doc:`rattle <fix_shake>`
-   * :doc:`reax/c/bonds (k) <fix_reaxc_bonds>`
+   * :doc:`reaxff/bonds (k) <fix_reaxff_bonds>`
-   * :doc:`reax/c/species (k) <fix_reaxc_species>`
+   * :doc:`reaxff/species (k) <fix_reaxff_species>`
    * :doc:`recenter <fix_recenter>`
    * :doc:`restrain <fix_restrain>`
    * :doc:`rhok <fix_rhok>`

doc/src/Commands_input.rst

@@ -50,6 +50,6 @@ values are not desired, the :doc:`processors <processors>` and
 tell LAMMPS how to map processors to the simulation box.
 
 Many input script errors are detected by LAMMPS and an ERROR or
-WARNING message is printed.  The :doc:`Errors <Errors>` doc page gives
+WARNING message is printed.  The :doc:`Errors <Errors>` page gives
 more information on what errors mean.  The documentation for each
 command lists restrictions on how the command can be used.

doc/src/Commands_kspace.rst

@@ -16,7 +16,7 @@ KSpace solvers
 
 All LAMMPS :doc:`kspace_style <kspace_style>` solvers.  Some styles have
 accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
@@ -28,12 +28,16 @@ OPT.
    * :doc:`ewald/dipole/spin <kspace_style>`
    * :doc:`msm (o) <kspace_style>`
    * :doc:`msm/cg (o) <kspace_style>`
+   * :doc:`msm/dielectric <kspace_style>`
    * :doc:`pppm (giko) <kspace_style>`
    * :doc:`pppm/cg (o) <kspace_style>`
    * :doc:`pppm/dipole <kspace_style>`
    * :doc:`pppm/dipole/spin <kspace_style>`
+   * :doc:`pppm/dielectric <kspace_style>`
    * :doc:`pppm/disp (io) <kspace_style>`
    * :doc:`pppm/disp/tip4p (o) <kspace_style>`
+   * :doc:`pppm/disp/dielectric <kspace_style>`
    * :doc:`pppm/stagger <kspace_style>`
    * :doc:`pppm/tip4p (o) <kspace_style>`
+   * :doc:`pppm/dielectric <kspace_style>`
    * :doc:`scafacos <kspace_style>`

doc/src/Commands_pair.rst

@@ -16,7 +16,7 @@ Pair_style potentials
 
 All LAMMPS :doc:`pair_style <pair_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
@@ -29,7 +29,7 @@ OPT.
    * :doc:`hybrid/scaled <pair_hybrid>`
    * :doc:`kim <pair_kim>`
    * :doc:`list <pair_list>`
-   *
+   * :doc:`tracker <pair_tracker>`
    *
    *
    *
@@ -69,13 +69,16 @@ OPT.
    * :doc:`comb3 <pair_comb>`
    * :doc:`cosine/squared <pair_cosine_squared>`
    * :doc:`coul/cut (gko) <pair_coul>`
+   * :doc:`coul/cut/dielectric <pair_dielectric>`
    * :doc:`coul/cut/global (o) <pair_coul>`
    * :doc:`coul/cut/soft (o) <pair_fep_soft>`
    * :doc:`coul/debye (gko) <pair_coul>`
    * :doc:`coul/diel (o) <pair_coul_diel>`
    * :doc:`coul/dsf (gko) <pair_coul>`
+   * :doc:`coul/exclude <pair_coul>`
    * :doc:`coul/long (gko) <pair_coul>`
    * :doc:`coul/long/cs (g) <pair_cs>`
+   * :doc:`coul/long/dielectric <pair_dielectric>`
    * :doc:`coul/long/soft (o) <pair_fep_soft>`
    * :doc:`coul/msm (o) <pair_coul>`
    * :doc:`coul/slater/cut <pair_coul_slater>`
@@ -143,13 +146,17 @@ OPT.
    * :doc:`lj/cubic (go) <pair_lj_cubic>`
    * :doc:`lj/cut (gikot) <pair_lj>`
    * :doc:`lj/cut/coul/cut (gko) <pair_lj_cut_coul>`
+   * :doc:`lj/cut/coul/cut/dielectric (o) <pair_dielectric>`
    * :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>`
    * :doc:`lj/cut/coul/debye (gko) <pair_lj_cut_coul>`
+   * :doc:`lj/cut/coul/debye/dielectric <pair_dielectric>`
    * :doc:`lj/cut/coul/dsf (gko) <pair_lj_cut_coul>`
    * :doc:`lj/cut/coul/long (gikot) <pair_lj_cut_coul>`
    * :doc:`lj/cut/coul/long/cs <pair_cs>`
+   * :doc:`lj/cut/coul/long/dielectric (o) <pair_dielectric>`
    * :doc:`lj/cut/coul/long/soft (o) <pair_fep_soft>`
    * :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/long (g) <pair_dipole>`
@@ -164,6 +171,7 @@ OPT.
    * :doc:`lj/gromacs (gko) <pair_gromacs>`
    * :doc:`lj/gromacs/coul/gromacs (ko) <pair_gromacs>`
    * :doc:`lj/long/coul/long (iot) <pair_lj_long>`
+   * :doc:`lj/long/coul/long/dielectric <pair_dielectric>`
    * :doc:`lj/long/dipole/long <pair_dipole>`
    * :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
    * :doc:`lj/mdf <pair_mdf>`
@@ -183,7 +191,7 @@ OPT.
    * :doc:`lubricateU/poly <pair_lubricateU>`
    * :doc:`mdpd <pair_mesodpd>`
    * :doc:`mdpd/rhosum <pair_mesodpd>`
-   * :doc:`meam/c <pair_meamc>`
+   * :doc:`meam <pair_meam>`
    * :doc:`meam/spline (o) <pair_meam_spline>`
    * :doc:`meam/sw/spline <pair_meam_sw_spline>`
    * :doc:`mesocnt <pair_mesocnt>`
@@ -228,7 +236,7 @@ OPT.
    * :doc:`python <pair_python>`
    * :doc:`quip <pair_quip>`
    * :doc:`rann <pair_rann>`
-   * :doc:`reax/c (ko) <pair_reaxc>`
+   * :doc:`reaxff (ko) <pair_reaxff>`
    * :doc:`rebo (io) <pair_airebo>`
    * :doc:`resquared (go) <pair_resquared>`
    * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`

doc/src/Commands_parse.rst

@@ -47,7 +47,7 @@ LAMMPS:
    named "x" followed by an "x" character.
 
    How the variable is converted to a text string depends on what style
-   of variable it is; see the :doc:`variable <variable>` doc page for
+   of variable it is; see the :doc:`variable <variable>` page for
    details.  It can be a variable that stores multiple text strings, and
    return one of them.  The returned text string can be multiple "words"
    (space separated) which will then be interpreted as multiple

doc/src/Commands_removed.rst

@@ -25,23 +25,20 @@ The reset_ids command has been renamed to :doc:`reset_atom_ids <reset_atom_ids>`
 MEAM package
 ------------
 
-The MEAM package has been removed since it was superseded by the
+The MEAM package in Fortran has been replaced by a C++ implementation.
-:ref:`USER-MEAMC package <PKG-USER-MEAMC>`. The code in
+The code in the :ref:`MEAM package <PKG-MEAM>` is a translation of the
-the USER-MEAMC package is a translation of the Fortran code of MEAM into C++,
+Fortran code of MEAM into C++, which removes several restrictions
-which removes several restrictions (e.g. there can be multiple instances
+(e.g. there can be multiple instances in hybrid pair styles) and allows
-in hybrid pair styles) and allows for some optimizations leading
+for some optimizations leading to better performance.  The pair style
-to better performance.  The new pair style :doc:`meam/c <pair_meamc>` has
+:doc:`meam <pair_meam>` has the exact same syntax.
-the exact same syntax as the old "meam" pair style and thus pair style
-meam is an alias to the new style and backward
-compatibility of old inputs is preserved.
 
 REAX package
 ------------
 
 The REAX package has been removed since it was superseded by the
-:ref:`USER-REAXC package <PKG-USER-REAXC>`.  The USER-REAXC
+:ref:`REAXFF package <PKG-REAXFF>`.  The REAXFF
 package has been tested to yield equivalent results to the REAX package,
-offers better performance, supports OpenMP multi-threading via USER-OMP,
+offers better performance, supports OpenMP multi-threading via OPENMP,
 and GPU and threading parallelization through KOKKOS.  The new pair styles
 are not syntax compatible with the removed reax pair style, so input
 files will have to be adapted.

doc/src/Developer_org.rst

@@ -17,7 +17,7 @@ currently supports building with :doc:`conventional makefiles
 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
-example ``src/MOLECULE`` or ``src/USER-MISC``.  The ``src/STUBS``
+example ``src/MOLECULE`` or ``src/EXTRA-MOLECULE``.  The ``src/STUBS``
 sub-directory 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

doc/src/Developer_unittest.rst

@@ -404,8 +404,8 @@ noise). Then it will restart from the previously generated restart and
 compare with the reference and also start from the data file.  A final
 check will use multi-cutoff r-RESPA (if supported by the pair style) at
 a 1:1 split and compare to the Verlet results.  These sets of tests are
-run with multiple test fixtures for accelerated styles (OPT, USER-OMP,
+run with multiple test fixtures for accelerated styles (OPT, OPENMP,
-USER-INTEL) and for the latter two with 4 OpenMP threads enabled.  For
+INTEL) and for the latter two with 4 OpenMP threads enabled.  For
 these tests the relative error (epsilon) is lowered by a common factor
 due to the additional numerical noise, but the tests are still comparing
 to the same reference data.

doc/src/Developer_utils.rst

@@ -334,10 +334,11 @@ arguments of commands in LAMMPS are parsed and to make abstractions of
 repetitive tasks.
 
 The :cpp:class:`LAMMPS_NS::ArgInfo` class provides an abstraction
-for parsing references to compute or fix styles or variables. These
+for parsing references to compute or fix styles, variables or custom
-would start with a "c\_", "f\_", "v\_" followed by the ID or name of
+integer or double properties handled by :doc:`fix property/atom <fix_property_atom>`.
-than instance and may be postfixed with one or two array indices
+These would start with a "c\_", "f\_", "v\_", "d\_", "d2\_", "i\_", or "i2\_"
-"[<number>]" with numbers > 0.
+followed by the ID or name of than instance and may be postfixed with
+one or two array indices "[<number>]" with numbers > 0.
 
 A typical code segment would look like this:
 

doc/src/Developer_write.rst

@@ -59,7 +59,7 @@ of each timestep. First of all, implement a constructor:
    }
 
 In the constructor you should parse your fix arguments which are
-specified in the script. All fixes have pretty the same syntax:
+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

doc/src/Errors.rst

@@ -1,11 +1,11 @@
 Errors
 ******
 
-These doc pages describe the errors you can encounter when using
+These doc pages describe many of the error and warning message you can
-LAMMPS.  The common problems include conceptual issues.  The messages
+encounter when using LAMMPS.  The common problems include conceptual
-and warnings doc pages give complete lists of all the messages the
+issues.  The messages and warnings doc pages give complete lists of all
-code may generate (except those generated by USER packages), with
+the messages the code may generate, with additional details for many of
-additional details for many of them.
+them.
 
 .. toctree::
    :maxdepth: 1

doc/src/Errors_bugs.rst

@@ -17,8 +17,9 @@ the steps outlined below:
    if your issue has already been reported and if it is still open.
  * Check the `GitHub Pull Requests page <https://github.com/lammps/lammps/pulls>`_
    to see if there is already a fix for your bug pending.
- * Check the `mailing list archives <https://www.lammps.org/mail.html>`_
+ * Check the `mailing list archives <https://www.lammps.org/mail.html>`_ or
-   to see if the issue has been discussed before.
+   the `LAMMPS forum <https://www.lammps.org/forum.html>`_ to see if the
+   issue has been discussed before.
 
 If none of these steps yields any useful information, please file a new
 bug report on the `GitHub Issue page <https://github.com/lammps/lammps/issues>`_.

doc/src/Errors_messages.rst

@@ -14,10 +14,6 @@ For example, a message like this:
 means that line #78 in the file src/velocity.cpp generated the error.
 Looking in the source code may help you figure out what went wrong.
 
-Note that error messages from :doc:`user-contributed packages <Packages_user>` are not listed here.  If such an error
-occurs and is not self-explanatory, you will need to look in the source
-code or contact the author of the package.
-
 Doc page with :doc:`WARNING messages <Errors_warnings>`
 
 ----------
@@ -574,10 +570,10 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    See the region prism command for details.
 
 *Can only use -plog with multiple partitions*
-   Self-explanatory.  See doc page discussion of command-line switches.
+   Self-explanatory.  See page discussion of command-line switches.
 
 *Can only use -pscreen with multiple partitions*
-   Self-explanatory.  See doc page discussion of command-line switches.
+   Self-explanatory.  See page discussion of command-line switches.
 
 *Can only use Kokkos supported regions with Kokkos package*
    Self-explanatory.
@@ -1158,7 +1154,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    Self-explanatory.
 
 *Cannot use -reorder after -partition*
-   Self-explanatory.  See doc page discussion of command-line switches.
+   Self-explanatory.  See page discussion of command-line switches.
 
 *Cannot use Ewald with 2d simulation*
    The kspace style ewald cannot be used in 2d simulations.  You can use
@@ -2351,14 +2347,14 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
 *Compute used in variable between runs is not current*
    Computes cannot be invoked by a variable in between runs.  Thus they
    must have been evaluated on the last timestep of the previous run in
-   order for their value(s) to be accessed.  See the doc page for the
+   order for their value(s) to be accessed.  See the page for the
    variable command for more info.
 
 *Compute used in variable thermo keyword between runs is not current*
    Some thermo keywords rely on a compute to calculate their value(s).
    Computes cannot be invoked by a variable in between runs.  Thus they
    must have been evaluated on the last timestep of the previous run in
-   order for their value(s) to be accessed.  See the doc page for the
+   order for their value(s) to be accessed.  See the page for the
    variable command for more info.
 
 *Compute vcm/chunk does not use chunk/atom compute*
@@ -3130,7 +3126,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
 *Energy was not tallied on needed timestep*
    You are using a thermo keyword that requires potentials to
    have tallied energy, but they did not on this timestep.  See the
-   variable doc page for ideas on how to make this work.
+   variable page for ideas on how to make this work.
 
 *Epsilon or sigma reference not set by pair style in PPPMDisp*
    Self-explanatory.
@@ -4539,10 +4535,10 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    particles.
 
 *Incorrect # of floating-point values in Bodies section of data file*
-   See doc page for body style.
+   See page for body style.
 
 *Incorrect # of integer values in Bodies section of data file*
-   See doc page for body style.
+   See page for body style.
 
 *Incorrect %s format in data file*
    A section of the data file being read by fix property/atom does
@@ -4577,7 +4573,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    The number of fields per line is not what expected.
 
 *Incorrect bonus data format in data file*
-   See the read_data doc page for a description of how various kinds of
+   See the read_data page for a description of how various kinds of
    bonus data must be formatted for certain atom styles.
 
 *Incorrect boundaries with slab Ewald*
@@ -4645,7 +4641,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    Incorrect number of words per line in the potential file.
 
 *Incorrect integer value in Bodies section of data file*
-   See doc page for body style.
+   See page for body style.
 
 *Incorrect multiplicity arg for dihedral coefficients*
    Self-explanatory.  Check the input script or data file.
@@ -5914,7 +5910,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    other.
 
 *Must set number of threads via package omp command*
-   Because you are using the USER-OMP package, set the number of threads
+   Because you are using the OPENMP package, set the number of threads
    via its settings, not by the pair_style snap nthreads setting.
 
 *Must shrink-wrap piston boundary*
@@ -6015,7 +6011,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    Self-explanatory.
 
 *Needed bonus data not in data file*
-   Some atom styles require bonus data.  See the read_data doc page for
+   Some atom styles require bonus data.  See the read_data page for
    details.
 
 *Needed molecular topology not in data file*
@@ -6217,7 +6213,7 @@ keyword to allow for additional bonds to be formed
 
 *One or more atom IDs is too big*
    The limit on atom IDs is set by the SMALLBIG, BIGBIG, SMALLSMALL
-   setting in your LAMMPS build.  See the :doc:`Build settings <Build_settings>` doc page for more info.
+   setting in your LAMMPS build.  See the :doc:`Build settings <Build_settings>` page for more info.
 
 *One or more atom IDs is zero*
    Either all atoms IDs must be zero or none of them.
@@ -6359,16 +6355,16 @@ keyword to allow for additional bonds to be formed
    The GPU package must be installed via "make yes-gpu" before LAMMPS is
    built.
 
-*Package intel command without USER-INTEL package installed*
+*Package intel command without INTEL package installed*
-   The USER-INTEL package must be installed via "make yes-user-intel"
+   The INTEL package must be installed via "make yes-intel"
    before LAMMPS is built.
 
 *Package kokkos command without KOKKOS package enabled*
    The KOKKOS package must be installed via "make yes-kokkos" before
    LAMMPS is built, and the "-k on" must be used to enable the package.
 
-*Package omp command without USER-OMP package installed*
+*Package omp command without OPENMP package installed*
-   The USER-OMP package must be installed via "make yes-user-omp" before
+   The OPENMP package must be installed via "make yes-openmp" before
    LAMMPS is built.
 
 *Pair body requires atom style body*
@@ -6612,7 +6608,7 @@ keyword to allow for additional bonds to be formed
 
 *Pair style bop requires comm ghost cutoff at least 3x larger than %g*
    Use the communicate ghost command to set this.  See the pair bop
-   doc page for more details.
+   page for more details.
 
 *Pair style born/coul/long requires atom attribute q*
    An atom style that defines this attribute must be used.
@@ -6932,7 +6928,7 @@ keyword to allow for additional bonds to be formed
 *Per-atom energy was not tallied on needed timestep*
    You are using a thermo keyword that requires potentials to
    have tallied energy, but they did not on this timestep.  See the
-   variable doc page for ideas on how to make this work.
+   variable page for ideas on how to make this work.
 
 *Per-atom fix in equal-style variable formula*
    Equal-style variables cannot use per-atom quantities.
@@ -6940,7 +6936,7 @@ keyword to allow for additional bonds to be formed
 *Per-atom virial was not tallied on needed timestep*
    You are using a thermo keyword that requires potentials to have
    tallied the virial, but they did not on this timestep.  See the
-   variable doc page for ideas on how to make this work.
+   variable page for ideas on how to make this work.
 
 *Per-processor system is too big*
    The number of owned atoms plus ghost atoms on a single
@@ -8079,13 +8075,13 @@ keyword to allow for additional bonds to be formed
 *Using suffix gpu without GPU package installed*
    Self-explanatory.
 
-*Using suffix intel without USER-INTEL package installed*
+*Using suffix intel without INTEL package installed*
    Self-explanatory.
 
 *Using suffix kk without KOKKOS package enabled*
    Self-explanatory.
 
-*Using suffix omp without USER-OMP package installed*
+*Using suffix omp without OPENMP package installed*
    Self-explanatory.
 
 *Using update dipole flag requires atom attribute mu*
@@ -8427,7 +8423,7 @@ keyword to allow for additional bonds to be formed
 *Virial was not tallied on needed timestep*
    You are using a thermo keyword that requires potentials to
    have tallied the virial, but they did not on this timestep.  See the
-   variable doc page for ideas on how to make this work.
+   variable page for ideas on how to make this work.
 
 *Voro++ error: narea and neigh have a different size*
    This error is returned by the Voro++ library.

doc/src/Errors_warnings.rst

@@ -14,10 +14,6 @@ generated.  For example, a message like this:
 means that line #187 in the file src/domain.cpp generated the error.
 Looking in the source code may help you figure out what went wrong.
 
-Note that warning messages from :doc:`user-contributed packages <Packages_user>` are not listed here.  If such a warning
-occurs and is not self-explanatory, you will need to look in the source
-code or contact the author of the package.
-
 Doc page with :doc:`ERROR messages <Errors_messages>`
 
 ----------
@@ -217,7 +213,7 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    in unexpected behavior.
 
 *Fix bond/swap will ignore defined angles*
-   See the doc page for fix bond/swap for more info on this
+   See the page for fix bond/swap for more info on this
    restriction.
 
 *Fix deposit near setting < possible overlap separation %g*
@@ -518,7 +514,7 @@ This will most likely cause errors in kinetic fluctuations.
    will integrate the body motion, but it would be more efficient to use
    fix rigid.
 
-*Not using real units with pair reax*
+*Not using real units with pair reaxff*
    This is most likely an error, unless you have created your own ReaxFF
    parameter file in a different set of units.
 
@@ -529,7 +525,7 @@ This will most likely cause errors in kinetic fluctuations.
 
 *OMP_NUM_THREADS environment is not set.*
    This environment variable must be set appropriately to use the
-   USER-OMP package.
+   OPENMP package.
 
 *One or more atoms are time integrated more than once*
    This is probably an error since you typically do not want to
@@ -809,5 +805,3 @@ This will most likely cause errors in kinetic fluctuations.
 *Using pair tail corrections with pair_modify compute no*
    The tail corrections will thus not be computed.
 
-*pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c*
-   Self-explanatory.

doc/src/Examples.rst

@@ -150,6 +150,8 @@ Lowercase directories
 +-------------+------------------------------------------------------------------+
 | threebody   | regression test input for a variety of manybody potentials       |
 +-------------+------------------------------------------------------------------+
+| tracker     | track interactions in LJ melt                                    |
++-------------+------------------------------------------------------------------+
 | vashishta   | use of the Vashishta potential                                   |
 +-------------+------------------------------------------------------------------+
 | voronoi     | Voronoi tesselation via compute voronoi/atom command             |
@@ -172,10 +174,10 @@ web site.
 If you uncomment the :doc:`dump image <dump_image>` line(s) in the input
 script a series of JPG images will be produced by the run (assuming
 you built LAMMPS with JPG support; see the
-:doc:`Build_settings <Build_settings>` doc page for details).  These can
+:doc:`Build_settings <Build_settings>` page for details).  These can
 be viewed individually or turned into a movie or animated by tools
 like ImageMagick or QuickTime or various Windows-based tools.  See the
-:doc:`dump image <dump_image>` doc page for more details.  E.g. this
+:doc:`dump image <dump_image>` page for more details.  E.g. this
 Imagemagick command would create a GIF file suitable for viewing in a
 browser.
 
@@ -205,23 +207,23 @@ Uppercase directories
 +------------+--------------------------------------------------------------------------------------------------+
 | MC         | using LAMMPS in a Monte Carlo mode to relax the energy of a system                               |
 +------------+--------------------------------------------------------------------------------------------------+
+| PACKAGES   | examples for specific packages and contributed commands                                          |
++------------+--------------------------------------------------------------------------------------------------+
 | SPIN       | examples for features of the SPIN package                                                        |
 +------------+--------------------------------------------------------------------------------------------------+
 | UNITS      | examples that run the same simulation in lj, real, metal units                                   |
 +------------+--------------------------------------------------------------------------------------------------+
-| USER       | examples for USER packages and USER-contributed commands                                         |
-+------------+--------------------------------------------------------------------------------------------------+
 | VISCOSITY  | compute viscosity via several methods                                                            |
 +------------+--------------------------------------------------------------------------------------------------+
 
 Nearly all of these directories have README files which give more
 details on how to understand and use their contents.
 
-The USER directory has a large number of sub-directories which
+The PACKAGES directory has a large number of sub-directories which
-correspond by name to a USER package.  They contain scripts that
+correspond by name to specific packages.  They contain scripts that
-illustrate how to use the command(s) provided in that package.  Many
+illustrate how to use the command(s) provided in those packages.  Many
 of the sub-directories have their own README files which give further
 instructions.  See the :doc:`Packages_details <Packages_details>` doc
-page for more info on specific USER packages.
+page for more info on specific packages.
 
 .. _openkim: https://openkim.org

doc/src/Howto_barostat.rst

@@ -50,7 +50,7 @@ a temperature or pressure compute to a barostatting fix.
 
 Thermodynamic output, which can be setup via the
 :doc:`thermo_style <thermo_style>` command, often includes pressure
-values.  As explained on the doc page for the
+values.  As explained on the page for the
 :doc:`thermo_style <thermo_style>` command, the default pressure is
 setup by the thermo command itself.  It is NOT the pressure associated
 with any barostatting fix you have defined or with any compute you

doc/src/Howto_bioFF.rst

@@ -49,7 +49,7 @@ command's documentation for the formula it computes.
 COMPASS is a general force field for atomistic simulation of common
 organic molecules, inorganic small molecules, and polymers which was
 developed using ab initio and empirical parameterization techniques.
-See the :doc:`Tools <Tools>` doc page for the msi2lmp tool for creating
+See the :doc:`Tools <Tools>` page for the msi2lmp tool for creating
 LAMMPS template input and data files from BIOVIA's Materials Studio
 files.  Please note that the msi2lmp tool is very old and largely
 unmaintained, so it does not support all features of Materials Studio

doc/src/Howto_body.rst

@@ -10,7 +10,7 @@ deformable objects, etc.  Note that other kinds of finite-size
 spherical and aspherical particles are also supported by LAMMPS, such
 as spheres, ellipsoids, line segments, and triangles, but they are
 simpler entities than body particles.  See the :doc:`Howto spherical
-<Howto_spherical>` doc page for a general overview of all these
+<Howto_spherical>` page for a general overview of all these
 particle types.
 
 Body particles are used via the :doc:`atom_style body <atom_style>`
@@ -170,14 +170,14 @@ with this body style to compute body/body and body/non-body interactions.
 The *rounded/polygon* body style represents body particles as a 2d
 polygon with a variable number of N vertices.  This style can only be
 used for 2d models; see the :doc:`boundary <boundary>` command.  See the
-"pair_style body/rounded/polygon" doc page for a diagram of two
+"pair_style body/rounded/polygon" page for a diagram of two
 squares with rounded circles at the vertices.  Special cases for N = 1
 (circle) and N = 2 (rod with rounded ends) can also be specified.
 
 One use of this body style is for 2d discrete element models, as
 described in :ref:`Fraige <body-Fraige>`.
 
-Similar to body style *nparticle*\ , the atom_style body command for
+Similar to body style *nparticle*, the atom_style body command for
 this body style takes two additional arguments:
 
 .. parsed-literal::
@@ -284,7 +284,7 @@ The *rounded/polyhedron* body style represents body particles as a 3d
 polyhedron with a variable number of N vertices, E edges and F faces.
 This style can only be used for 3d models; see the
 :doc:`boundary <boundary>` command.  See the "pair_style
-body/rounded/polygon" doc page for a diagram of a two 2d squares with
+body/rounded/polygon" page for a diagram of a two 2d squares with
 rounded circles at the vertices.  A 3d cube with rounded spheres at
 the 8 vertices and 12 rounded edges would be similar.  Special cases
 for N = 1 (sphere) and N = 2 (rod with rounded ends) can also be
@@ -293,7 +293,7 @@ specified.
 This body style is for 3d discrete element models, as described in
 :ref:`Wang <body-Wang>`.
 
-Similar to body style *rounded/polygon*\ , the atom_style body command
+Similar to body style *rounded/polygon*, the atom_style body command
 for this body style takes two additional arguments:
 
 .. parsed-literal::

doc/src/Howto_chunk.rst

@@ -51,7 +51,7 @@ scales the floating point value to spread it across multiple integers.
 Spatial bins can be of various kinds, e.g. 1d bins = slabs, 2d bins =
 pencils, 3d bins = boxes, spherical bins, cylindrical bins.
 
-This compute also calculates the number of chunks *Nchunk*\ , which is
+This compute also calculates the number of chunks *Nchunk*, which is
 used by other commands to tally per-chunk data.  *Nchunk* can be a
 static value or change over time (e.g. the number of clusters).  The
 chunk ID for an individual atom can also be static (e.g. a molecule

doc/src/Howto_client_server.rst

@@ -119,7 +119,7 @@ server code.  Another code could be substituted for either.
 
 The examples below show launching both codes from the same window (or
 batch script), using the "&" character to launch the first code in the
-background.  For all modes except *mpi/one*\ , you could also launch the
+background.  For all modes except *mpi/one*, you could also launch the
 codes in separate windows on your desktop machine.  It does not
 matter whether you launch the client or server first.
 
@@ -132,7 +132,7 @@ mpirun, even if one or both of them runs on a single processor.  This
 is so that MPI can figure out how to connect both MPI processes
 together to exchange MPI messages between them.
 
-For message exchange in *file*\ , *zmq*\ , or *mpi/two* modes:
+For message exchange in *file*, *zmq*, or *mpi/two* modes:
 
 .. code-block:: bash
 

doc/src/Howto_cmake.rst

@@ -362,7 +362,7 @@ have to be enabled to be included into a LAMMPS executable.  Packages
 are enabled through setting variables of the kind ``PKG_<NAME>`` to
 ``on`` and disabled by setting them to ``off`` (or using ``yes``,
 ``no``, ``1``, ``0`` correspondingly).  ``<NAME>`` has to be replaced by
-the name of the package, e.g. ``MOLECULE`` or ``USER-MISC``.
+the name of the package, e.g. ``MOLECULE`` or ``EXTRA-PAIR``.
 
 
 Using presets
@@ -382,9 +382,9 @@ change some variables later with additional *-D* flags.  A few examples:
 
 .. code-block:: bash
 
-   cmake -C ../cmake/presets/minimal.cmake -D PKG_MISC=on ../cmake
+   cmake -C ../cmake/presets/basic.cmake -D PKG_MISC=on ../cmake
    cmake -C ../cmake/presets/clang.cmake -C ../cmake/presets/most.cmake ../cmake
-   cmake -C ../cmake/presets/minimal.cmake -D BUILD_MPI=off ../cmake
+   cmake -C ../cmake/presets/basic.cmake -D BUILD_MPI=off ../cmake
 
 The first command will install the packages ``KSPACE``, ``MANYBODY``,
 ``MOLECULE``, ``RIGID`` and ``MISC``; the first four from the preset
@@ -400,7 +400,7 @@ It is also possible to do this incrementally.
 
 .. code-block:: bash
 
-   cmake -C ../cmake/presets/minimal.cmake ../cmake
+   cmake -C ../cmake/presets/basic.cmake ../cmake
    cmake -D PKG_MISC=on .
 
 will achieve the same final configuration as in the first example above.

doc/src/Howto_coreshell.rst

@@ -5,7 +5,7 @@ The adiabatic core-shell model by :ref:`Mitchell and Fincham <MitchellFincham>`
 to a system.  In order to mimic the electron shell of an ion, a
 satellite particle is attached to it. This way the ions are split into
 a core and a shell where the latter is meant to react to the
-electrostatic environment inducing polarizability.  See the :doc:`Howto polarizable <Howto_polarizable>` doc page for a discussion of all
+electrostatic environment inducing polarizability.  See the :doc:`Howto polarizable <Howto_polarizable>` page for a discussion of all
 the polarizable models available in LAMMPS.
 
 Technically, shells are attached to the cores by a spring force f =
@@ -78,7 +78,7 @@ satellite particle if desired.
 Since the core/shell model permits distances of r = 0.0 between the
 core and shell, a pair style with a "cs" suffix needs to be used to
 implement a valid long-range Coulombic correction.  Several such pair
-styles are provided in the CORESHELL package.  See :doc:`this doc page <pair_cs>` for details.  All of the core/shell enabled pair
+styles are provided in the CORESHELL package.  See :doc:`this page <pair_cs>` for details.  All of the core/shell enabled pair
 styles require the use of a long-range Coulombic solver, as specified
 by the :doc:`kspace_style <kspace_style>` command.  Either the PPPM or
 Ewald solvers can be used.

doc/src/Howto_couple.rst

@@ -42,7 +42,7 @@ context of your application.
    stand-alone code could communicate with LAMMPS through files that the
    command writes and reads.
 
-   See the :doc:`Modify command <Modify_command>` doc page for info on how
+   See the :doc:`Modify command <Modify_command>` page for info on how
    to add a new command to LAMMPS.
 
 .. spacer

doc/src/Howto_drude2.rst

@@ -2,14 +2,14 @@ Tutorial for Thermalized Drude oscillators in LAMMPS
 ====================================================
 
 This tutorial explains how to use Drude oscillators in LAMMPS to
-simulate polarizable systems using the USER-DRUDE package. As an
+simulate polarizable systems using the DRUDE package. As an
 illustration, the input files for a simulation of 250 phenol molecules
 are documented. First of all, LAMMPS has to be compiled with the
-USER-DRUDE package activated. Then, the data file and input scripts
+DRUDE package activated. Then, the data file and input scripts
 have to be modified to include the Drude dipoles and how to handle
 them.
 
-Example input scripts available: examples/USER/drude
+Example input scripts available: examples/PACKAGES/drude
 
 ----------
 
@@ -82,7 +82,7 @@ The data file is similar to a standard LAMMPS data file for
 to their DC should appear in the data file as normal atoms and bonds.
 
 You can use the *polarizer* tool (Python script distributed with the
-USER-DRUDE package) to convert a non-polarizable data file (here
+DRUDE package) to convert a non-polarizable data file (here
 *data.102494.lmp*\ ) to a polarizable data file (\ *data-p.lmp*\ )
 
 .. code-block:: bash
@@ -91,7 +91,7 @@ USER-DRUDE package) to convert a non-polarizable data file (here
 
 This will automatically insert the new atoms and bonds.
 The masses and charges of DCs and DPs are computed
-from *phenol.dff*\ , as well as the DC-DP bond constants.  The file
+from *phenol.dff*, as well as the DC-DP bond constants.  The file
 *phenol.dff* contains the polarizabilities of the atom types
 and the mass of the Drude particles, for instance:
 
@@ -106,7 +106,7 @@ and the mass of the Drude particles, for instance:
 
 The hydrogen atoms are absent from this file, so they will be treated
 as non-polarizable atoms.  In the non-polarizable data file
-*data.102494.lmp*\ , atom names corresponding to the atom type numbers
+*data.102494.lmp*, atom names corresponding to the atom type numbers
 have to be specified as comments at the end of lines of the *Masses*
 section.  You probably need to edit it to add these names. It should
 look like
@@ -125,7 +125,7 @@ look like
 
 **Basic input file**
 
-The atom style should be set to (or derive from) *full*\ , so that you
+The atom style should be set to (or derive from) *full*, so that you
 can define atomic charges and molecular bonds, angles, dihedrals...
 
 The *polarizer* tool also outputs certain lines related to the input
@@ -143,7 +143,7 @@ and N for non-polarizable atoms.  Here the atom types 1 to 3 (C and O
 atoms) are DC, atom types 4 and 5 (H atoms) are non-polarizable and
 the atom types 6 to 8 are the newly created DPs.
 
-By recognizing the fix *drude*\ , LAMMPS will find and store matching
+By recognizing the fix *drude*, LAMMPS will find and store matching
 DC-DP pairs and will treat DP as equivalent to their DC in the
 *special bonds* relations.  It may be necessary to extend the space
 for storing such special relations.  In this case extra space should
@@ -340,11 +340,11 @@ For the *thole* pair style the coefficients are
 The special neighbors have charge-charge and charge-dipole
 interactions screened by the *coul* factors of the *special_bonds*
 command (0.0, 0.0, and 0.5 in the example above).  Without using the
-pair_style *thole*\ , dipole-dipole interactions are screened by the
+pair_style *thole*, dipole-dipole interactions are screened by the
-same factor.  By using the pair_style *thole*\ , dipole-dipole
+same factor.  By using the pair_style *thole*, dipole-dipole
 interactions are screened by Thole's function, whatever their special
 relationship (except within each DC-DP pair of course).  Consider for
-example 1-2 neighbors: using the pair_style *thole*\ , their dipoles
+example 1-2 neighbors: using the pair_style *thole*, their dipoles
 will see each other (despite the *coul* factor being 0.) and the
 interactions between these dipoles will be damped by Thole's function.
 
@@ -384,7 +384,7 @@ For our phenol example, the groups would be defined as
    group CORES  type 1 2 3     # DCs
    group DRUDES type 6 7 8     # DPs
 
-Note that with the fixes *drude/transform*\ , it is not required to
+Note that with the fixes *drude/transform*, it is not required to
 specify *comm_modify vel yes* because the fixes do it anyway (several
 times and for the forces also).
 

doc/src/Howto_github.rst

@@ -140,8 +140,8 @@ After everything is done, add the files to the branch and commit them:
    flag) will automatically include **all** modified **and** new files
    and that is rarely the behavior you want.  It can easily lead to
    accidentally adding unrelated and unwanted changes into the
-   repository.  Instead it is preferable to explicitly use *git add*\ ,
+   repository.  Instead it is preferable to explicitly use *git add*,
-   *git rm*\ , *git mv* for adding, removing, renaming individual files,
+   *git rm*, *git mv* for adding, removing, renaming individual files,
    respectively, and then *git commit* to finalize the commit.
    Carefully check all pending changes with *git status* before
    committing them.  If you find doing this on the command line too

doc/src/Howto_granular.rst

@@ -17,6 +17,11 @@ This compute
 * :doc:`compute erotate/sphere <compute_erotate_sphere>`
 
 calculates rotational kinetic energy which can be :doc:`output with thermodynamic info <Howto_output>`.
+The compute
+
+* :doc:`compute fabric <compute_fabric>`
+
+calculates various versions of the fabric tensor for granular and non-granular pair styles.
 
 Use one of these 4 pair potentials, which compute forces and torques
 between interacting pairs of particles:

doc/src/Howto_kappa.rst

@@ -4,7 +4,7 @@ Calculate thermal conductivity
 The thermal conductivity kappa of a material can be measured in at
 least 4 ways using various options in LAMMPS.  See the examples/KAPPA
 directory for scripts that implement the 4 methods discussed here for
-a simple Lennard-Jones fluid model.  Also, see the :doc:`Howto viscosity <Howto_viscosity>` doc page for an analogous discussion
+a simple Lennard-Jones fluid model.  Also, see the :doc:`Howto viscosity <Howto_viscosity>` page for an analogous discussion
 for viscosity.
 
 The thermal conductivity tensor kappa is a measure of the propensity
@@ -58,7 +58,7 @@ between hot and cold regions of the simulation box.
 The :doc:`compute heat/flux <compute_heat_flux>` command can calculate
 the needed heat flux and describes how to implement the Green_Kubo
 formalism using additional LAMMPS commands, such as the :doc:`fix ave/correlate <fix_ave_correlate>` command to calculate the needed
-auto-correlation.  See the doc page for the :doc:`compute heat/flux <compute_heat_flux>` command for an example input script
+auto-correlation.  See the page for the :doc:`compute heat/flux <compute_heat_flux>` command for an example input script
 that calculates the thermal conductivity of solid Ar via the GK
 formalism.
 

doc/src/Howto_manifold.rst

@@ -3,13 +3,13 @@ Manifolds (surfaces)
 
 **Overview:**
 
-This doc page is not about a LAMMPS input script command, but about
+This page is not about a LAMMPS input script command, but about
 manifolds, which are generalized surfaces, as defined and used by the
-USER-MANIFOLD package, to track particle motion on the manifolds.  See
+MANIFOLD package, to track particle motion on the manifolds.  See
-the src/USER-MANIFOLD/README file for more details about the package
+the src/MANIFOLD/README file for more details about the package
 and its commands.
 
-Below is a list of currently supported manifolds by the USER-MANIFOLD
+Below is a list of currently supported manifolds by the MANIFOLD
 package, their parameters and a short description of them.  The
 parameters listed here are in the same order as they should be passed
 to the relevant fixes.

doc/src/Howto_mdi.rst

@@ -3,7 +3,7 @@ Using LAMMPS with the MDI library for code coupling
 
 .. note::
 
-  This Howto doc page will eventually replace the
+  This Howto page will eventually replace the
   :doc:`Howto client/server <Howto_client_server>` doc page.
 
 Client/server coupling of two codes is where one code is the "client"
@@ -120,7 +120,7 @@ input script will continue.  After finishing execution of the input
 script, the instance of LAMMPS will be destroyed.
 
 LAMMPS supports the full set of MD-appropriate engine commands defined
-by the MDI library.  See the :doc:`mdi/engine <mdi_engine>` doc page for
+by the MDI library.  See the :doc:`mdi/engine <mdi_engine>` page for
 a list of these.
 
 If those commands are not sufficient for a user-developed driver to use

doc/src/Howto_output.rst

@@ -268,7 +268,7 @@ Computes that generate values to output
 Every :doc:`compute <compute>` in LAMMPS produces either global or
 per-atom or local values.  The values can be scalars or vectors or
 arrays of data.  These values can be output using the other commands
-described in this section.  The doc page for each compute command
+described in this section.  The page for each compute command
 describes what it produces.  Computes that produce per-atom or local
 values have the word "atom" or "local" in their style name.  Computes
 without the word "atom" or "local" produce global values.
@@ -281,7 +281,7 @@ Fixes that generate values to output
 Some :doc:`fixes <fix>` in LAMMPS produces either global or per-atom or
 local values which can be accessed by other commands.  The values can
 be scalars or vectors or arrays of data.  These values can be output
-using the other commands described in this section.  The doc page for
+using the other commands described in this section.  The page for
 each fix command tells whether it produces any output quantities and
 describes them.
 

doc/src/Howto_polarizable.rst

@@ -10,7 +10,7 @@ systems can be simulated in LAMMPS using three methods:
 * the adiabatic core-shell method, implemented in the
   :doc:`CORESHELL <Howto_coreshell>` package,
 * the thermalized Drude dipole method, implemented in the
-  :doc:`USER-DRUDE <Howto_drude>` package.
+  :doc:`DRUDE <Howto_drude>` package.
 
 The fluctuating charge method calculates instantaneous charges on
 interacting atoms based on the electronegativity equalization

doc/src/Howto_replica.rst

@@ -8,34 +8,33 @@ periodically.
 
 These are the relevant commands:
 
-* :doc:`neb <neb>` for nudged elastic band calculations
+* :doc:`hyper <hyper>` for bond boost hyperdynamics (HD)
+* :doc:`neb <neb>` for nudged elastic band calculations (NEB)
 * :doc:`neb_spin <neb_spin>` for magnetic nudged elastic band calculations
-* :doc:`prd <prd>` for parallel replica dynamics
+* :doc:`prd <prd>` for parallel replica dynamics (PRD)
-* :doc:`tad <tad>` for temperature accelerated dynamics
+* :doc:`tad <tad>` for temperature accelerated dynamics (TAD)
-* :doc:`temper <temper>` for parallel tempering
+* :doc:`temper <temper>` for parallel tempering with fixed volume
+* :doc:`temper/npt <temper_npt>` for parallel tempering extended for NPT
+* :doc:`temper/grem <temper_grem>` for parallel tempering with generalized replica exchange (gREM)
 * :doc:`fix pimd <fix_pimd>` for path-integral molecular dynamics (PIMD)
 
-NEB is a method for finding transition states and barrier energies.
+NEB is a method for finding transition states and barrier potential energies.
-PRD and TAD are methods for performing accelerated dynamics to find
+HD, PRD, and TAD are methods for performing accelerated dynamics to find and
-and perform infrequent events.  Parallel tempering or replica exchange
+perform infrequent events.  Parallel tempering or replica exchange runs
-runs different replicas at a series of temperature to facilitate
+different replicas at a series of temperature to facilitate rare-event
-rare-event sampling.
+sampling.  PIMD runs different replicas whose individual particles in different
+replicas are coupled together by springs to model a system of ring-polymers which
+can represent the quantum nature of atom cores.
 
 These commands can only be used if LAMMPS was built with the REPLICA
-package.  See the :doc:`Build package <Build_package>` doc page for more
+package.  See the :doc:`Build package <Build_package>` page for more
-info.
-
-PIMD runs different replicas whose individual particles are coupled
-together by springs to model a system or ring-polymers.
-
-This commands can only be used if LAMMPS was built with the USER-MISC
-package.  See the :doc:`Build package <Build_package>` doc page for more
 info.
 
 In all these cases, you must run with one or more processors per
 replica.  The processors assigned to each replica are determined at
-run-time by using the :doc:`-partition command-line switch <Run_options>` to launch LAMMPS on multiple partitions,
+run-time by using the :doc:`-partition command-line switch
-which in this context are the same as replicas.  E.g.  these commands:
+<Run_options>` to launch LAMMPS on multiple partitions, which in this
+context are the same as replicas.  E.g.  these commands:
 
 .. code-block:: bash
 
@@ -46,9 +45,11 @@ would each run 8 replicas, on either 16 or 8 processors.  Note the use
 of the :doc:`-in command-line switch <Run_options>` to specify the input
 script which is required when running in multi-replica mode.
 
-Also note that with MPI installed on a machine (e.g. your desktop),
+Also note that with MPI installed on a machine (e.g. your desktop), you
-you can run on more (virtual) processors than you have physical
+can run on more (virtual) processors than you have physical processors.
-processors.  Thus the above commands could be run on a
+Thus the above commands could be run on a single-processor (or
-single-processor (or few-processor) desktop so that you can run
+few-processor) desktop so that you can run a multi-replica simulation on
-a multi-replica simulation on more replicas than you have
+more replicas than you have physical processors. This is useful for
-physical processors.
+testing and debugging, since with most modern processors and MPI
+libraries the efficiency of a calculation can severely diminish when
+oversubscribing processors.

doc/src/Howto_thermostat.rst

@@ -28,7 +28,7 @@ can be invoked via the *dpd/tstat* pair style:
 :doc:`Fix nvt <fix_nh>` only thermostats the translational velocity of
 particles.  :doc:`Fix nvt/sllod <fix_nvt_sllod>` also does this, except
 that it subtracts out a velocity bias due to a deforming box and
-integrates the SLLOD equations of motion.  See the :doc:`Howto nemd <Howto_nemd>` doc page for further details.  :doc:`Fix nvt/sphere <fix_nvt_sphere>` and :doc:`fix nvt/asphere <fix_nvt_asphere>` thermostat not only translation
+integrates the SLLOD equations of motion.  See the :doc:`Howto nemd <Howto_nemd>` page for further details.  :doc:`Fix nvt/sphere <fix_nvt_sphere>` and :doc:`fix nvt/asphere <fix_nvt_asphere>` thermostat not only translation
 velocities but also rotational velocities for spherical and aspherical
 particles.
 
@@ -88,7 +88,7 @@ Below is a list of some custom temperature computes that can be used like that:
 
 Thermodynamic output, which can be setup via the
 :doc:`thermo_style <thermo_style>` command, often includes temperature
-values.  As explained on the doc page for the
+values.  As explained on the page for the
 :doc:`thermo_style <thermo_style>` command, the default temperature is
 setup by the thermo command itself.  It is NOT the temperature
 associated with any thermostatting fix you have defined or with any

doc/src/Howto_triclinic.rst

@@ -23,21 +23,21 @@ origin given by **a** = (xhi-xlo,0,0); **b** = (xy,yhi-ylo,0); **c** =
 and are called "tilt factors" because they are the amount of
 displacement applied to faces of an originally orthogonal box to
 transform it into the parallelepiped.  In LAMMPS the triclinic
-simulation box edge vectors **a**\ , **b**\ , and **c** cannot be arbitrary
+simulation box edge vectors **a**, **b**, and **c** cannot be arbitrary
 vectors.  As indicated, **a** must lie on the positive x axis.  **b** must
 lie in the xy plane, with strictly positive y component. **c** may have
 any orientation with strictly positive z component.  The requirement
-that **a**\ , **b**\ , and **c** have strictly positive x, y, and z components,
+that **a**, **b**, and **c** have strictly positive x, y, and z components,
-respectively, ensures that **a**\ , **b**\ , and **c** form a complete
+respectively, ensures that **a**, **b**, and **c** form a complete
 right-handed basis.  These restrictions impose no loss of generality,
 since it is possible to rotate/invert any set of 3 crystal basis
 vectors so that they conform to the restrictions.
 
-For example, assume that the 3 vectors **A**\ ,\ **B**\ ,\ **C** are the edge
+For example, assume that the 3 vectors **A**,\ **B**,\ **C** are the edge
 vectors of a general parallelepiped, where there is no restriction on
-**A**\ ,\ **B**\ ,\ **C** other than they form a complete right-handed basis i.e.
+**A**,\ **B**,\ **C** other than they form a complete right-handed basis i.e.
-**A** x **B** . **C** > 0.  The equivalent LAMMPS **a**\ ,\ **b**\ ,\ **c** are a linear
+**A** x **B** . **C** > 0.  The equivalent LAMMPS **a**,\ **b**,\ **c** are a linear
-rotation of **A**\ , **B**\ , and **C** and can be computed as follows:
+rotation of **A**, **B**, and **C** and can be computed as follows:
 
 .. math::
 
@@ -57,9 +57,9 @@ rotation of **A**\ , **B**\ , and **C** and can be computed as follows:
 where A = \| **A** \| indicates the scalar length of **A**\ . The hat symbol (\^)
 indicates the corresponding unit vector. :math:`\beta` and :math:`\gamma` are angles
 between the vectors described below. Note that by construction,
-**a**\ , **b**\ , and **c** have strictly positive x, y, and z components, respectively.
+**a**, **b**, and **c** have strictly positive x, y, and z components, respectively.
 If it should happen that
-**A**\ , **B**\ , and **C** form a left-handed basis, then the above equations
+**A**, **B**, and **C** form a left-handed basis, then the above equations
 are not valid for **c**\ . In this case, it is necessary
 to first apply an inversion. This can be achieved
 by interchanging two basis vectors or by changing the sign of one of them.
@@ -95,7 +95,7 @@ for details.
 The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the
 time the simulation box is created.  This happens in one of 3 ways.
 If the :doc:`create_box <create_box>` command is used with a region of
-style *prism*\ , then a triclinic box is setup.  See the
+style *prism*, then a triclinic box is setup.  See the
 :doc:`region <region>` command for details.  If the
 :doc:`read_data <read_data>` command is used to define the simulation
 box, and the header of the data file contains a line with the "xy xz
@@ -135,7 +135,7 @@ example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
 ... are geometrically all equivalent.  If the box tilt exceeds this
 limit during a dynamics run (e.g. via the :doc:`fix deform <fix_deform>`
 command), then the box is "flipped" to an equivalent shape with a tilt
-factor within the bounds, so the run can continue.  See the :doc:`fix deform <fix_deform>` doc page for further details.
+factor within the bounds, so the run can continue.  See the :doc:`fix deform <fix_deform>` page for further details.
 
 One exception to this rule is if the first dimension in the tilt
 factor (x for xy) is non-periodic.  In that case, the limits on the
@@ -160,10 +160,10 @@ For extreme values of tilt, LAMMPS may also lose atoms and generate an
 error.
 
 Triclinic crystal structures are often defined using three lattice
-constants *a*\ , *b*\ , and *c*\ , and three angles :math:`\alpha`,
+constants *a*, *b*, and *c*, and three angles :math:`\alpha`,
 :math:`\beta`, and :math:`\gamma`. Note that in this nomenclature,
 the a, b, and c lattice constants are the scalar lengths of the edge
-vectors **a**\ , **b**\ , and **c** defined above.  The relationship
+vectors **a**, **b**, and **c** defined above.  The relationship
 between these 6 quantities (a, b, c, :math:`\alpha`, :math:`\beta`,
 :math:`\gamma`) and the LAMMPS box sizes (lx,ly,lz) =
 (xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) is as follows:
@@ -188,10 +188,10 @@ The inverse relationship can be written as follows:
   {\rm yz}   = & \frac{b*c \cos{\alpha} - {\rm xy}*{\rm xz}}{\rm ly} \\
   {\rm lz}^2 = & c^2 - {\rm xz}^2 - {\rm yz}^2 \\
 
-The values of *a*\ , *b*\ , *c* , :math:`\alpha` , :math:`\beta`, and
+The values of *a*, *b*, *c*, :math:`\alpha` , :math:`\beta`, and
 :math:`\gamma` can be printed out or accessed by computes using the
 :doc:`thermo_style custom <thermo_style>` keywords
-*cella*\ , *cellb*\ , *cellc*\ , *cellalpha*\ , *cellbeta*\ , *cellgamma*\ ,
+*cella*, *cellb*, *cellc*, *cellalpha*, *cellbeta*, *cellgamma*,
 respectively.
 
 As discussed on the :doc:`dump <dump>` command doc page, when the BOX

doc/src/Howto_viscosity.rst

@@ -42,7 +42,7 @@ command, which determines grad(Vstream) in the equation above.
 E.g. the derivative in the y-direction of the Vx component of fluid
 motion or grad(Vstream) = dVx/dy.  The Pxy off-diagonal component of
 the pressure or stress tensor, as calculated by the :doc:`compute pressure <compute_pressure>` command, can also be monitored, which
-is the J term in the equation above.  See the :doc:`Howto nemd <Howto_nemd>` doc page for details on NEMD simulations.
+is the J term in the equation above.  See the :doc:`Howto nemd <Howto_nemd>` page for details on NEMD simulations.
 
 The third method is to perform a reverse non-equilibrium MD simulation
 using the :doc:`fix viscosity <fix_viscosity>` command which implements

doc/src/Howto_viz.rst

@@ -13,7 +13,7 @@ by several popular visualization tools. The :doc:`dump image <dump_image>` and :
 output internally rendered images and convert a sequence of them to a
 movie during the MD run.  Several programs included with LAMMPS as
 auxiliary tools can convert between LAMMPS format files and other
-formats.  See the :doc:`Tools <Tools>` doc page for details.
+formats.  See the :doc:`Tools <Tools>` page for details.
 
 A Python-based toolkit distributed by our group can read native LAMMPS
 dump files, including custom dump files with additional columns of
@@ -25,7 +25,7 @@ RasMol visualization programs.  Pizza.py has tools that do interactive
 3d OpenGL visualization and one that creates SVG images of dump file
 snapshots.
 
-.. _pizza: https://pizza.sandia.gov
+.. _pizza: https://lammps.github.io/pizza
 
 .. _ensight: https://www.ansys.com/products/fluids/ansys-ensight
 

doc/src/Howto_walls.rst

@@ -53,7 +53,7 @@ granular particles; all the other commands create smooth walls.
 * :doc:`fix wall/region <fix_wall_region>` - use region surface as wall
 * :doc:`fix wall/gran <fix_wall_gran>` - flat or curved walls with :doc:`pair_style granular <pair_gran>` potential
 
-The *lj93*\ , *lj126*\ , *colloid*\ , *harmonic*\ , and *morse* styles all
+The *lj93*, *lj126*, *colloid*, *harmonic*, and *morse* styles all
 allow the flat walls to move with a constant velocity, or oscillate in
 time.  The :doc:`fix wall/region <fix_wall_region>` command offers the
 most generality, since the region surface is treated as a wall, and

doc/src/Howto_wsl.rst

@@ -208,7 +208,7 @@ Presets are a way to specify a collection of CMake options using a file.
 
 .. code-block:: bash
 
-   cmake ../cmake/presets/minimal.cmake ../cmake
+   cmake ../cmake/presets/basic.cmake ../cmake
 
 This command configures the build and generates the necessary Makefiles. To compile the binary, run the make command.
 

doc/src/Install.rst

@@ -18,7 +18,6 @@ need the source code.
 
    Install_tarball
    Install_git
-   Install_patch
 
 These are the files and sub-directories in the LAMMPS distribution:
 
@@ -27,6 +26,8 @@ These are the files and sub-directories in the LAMMPS distribution:
 +------------+-------------------------------------------+
 | LICENSE    | GNU General Public License (GPL)          |
 +------------+-------------------------------------------+
+| SECURITY.md| Security Policy for the LAMMPS package    |
++------------+-------------------------------------------+
 | bench      | benchmark problems                        |
 +------------+-------------------------------------------+
 | cmake      | CMake build files                         |

doc/src/Install_git.rst

@@ -120,8 +120,11 @@ changed.  How to do this depends on the build system you are using.
          $ make package-update    # sync package files with src files
          $ make foo               # re-build for your machine (mpi, serial, etc)
 
-      Just as described on the :doc:`Apply patch <Install_patch>` page,
+      to enforce consistency of the source between the src folder
-      after a patch has been installed.
+      and package directories.  This is OK to do even if you don't
+      use any packages. The "make purge" command removes any deprecated
+      src files if they were removed by the patch from a package
+      sub-directory.
 
       .. warning::
 

doc/src/Install_patch.rst

@@ -1,96 +0,0 @@
-Applying patches
-----------------
-
-It is easy to stay current with the most recent LAMMPS patch releases
-if you use git to track the LAMMPS development.  Instructions for
-how to stay current are on the
-:doc:`Download the LAMMPS source with git <Install_git>` page.
-
-If you prefer to download a tarball, as described on the
-:doc:`tarball download <Install_tarball>` page, you can stay current by
-downloading "patch files" when new patch releases are made.  A link to
-a patch file is posted on the
-`bug fixes and new feature page <https://www.lammps.org/bug.html>`_
-of the LAMMPS website, along
-with a list of changed files and details about what is in the new patch
-release.  This page explains how to apply the patch file to your local
-LAMMPS directory.
-
-.. note::
-
-   You should not apply patch files to a local git checkout of
-   LAMMPS, only to an unpacked tarball.  Use git commands to
-   update such a version of the LAMMPS source code.
-
-Here are the steps to apply a patch file.  Note that if your version
-of LAMMPS is several patch releases behind, you need to apply all the
-intervening patch files in succession to bring your version of LAMMPS
-up to date.
-
-* Download the patch file.  You may have to shift-click in your browser
-  to download the file instead of display it.  Patch files have names
-  like patch.12Dec16.
-* Put the patch file in your top-level LAMMPS directory, where the
-  LICENSE and README files are.
-* Apply the patch by typing the following command from your top-level
-  LAMMPS directory, where the redirected file is the name of the patch
-  file.
-
-  .. code-block:: bash
-
-     $ patch -bp1 < patch.12Dec16
-
-* A list of updated files print out to the screen.  The -b switch
-  creates backup files of your originals (e.g. src/force.cpp.orig), so
-  you can manually undo the patch if something goes wrong.
-
-* Once you have updated your local files you need to re-build LAMMPS.
-  If you are applying several patches successively, you only need to
-  do the rebuild once at the end. How to do it depends on the build
-  system you are using.
-
-  .. tabs::
-
-     .. tab:: CMake build
-
-        Change to your build folder and type:
-
-        .. code-block:: bash
-
-           cmake . --build
-
-        CMake should auto-detect whether it needs to re-run the CMake
-        configuration step and otherwise redo the build for all files
-        that have been changed or files that depend on changed files.
-        In case some build options have been changed or renamed, you
-        may have to update those by running:
-
-        .. code-block:: bash
-
-           cmake .
-
-        and then rebuild.
-
-     .. tab:: Traditional make
-
-        Switch to the src directory and type:
-
-        .. code-block:: bash
-
-           $ make purge             # remove any deprecated src files
-           $ make package-update    # sync package files with src files
-           $ make foo               # re-build for your machine (mpi, serial, etc)
-
-        to enforce consistency of the source between the src folder
-        and package directories.  This is OK to do even if you don't
-        use any packages. The "make purge" command removes any deprecated
-        src files if they were removed by the patch from a package
-        sub-directory.
-
-        .. warning::
-
-           If you wish to edit/change a src file that is from a package,
-           you should edit the version of the file inside the package
-           sub-directory with src, then re-install the package.  The
-           version in the source directory is merely a copy and will be
-           wiped out if you type "make package-update".