Merge remote-tracking branch 'origin/master' into collected_small_changes

2021-04-17 11:05:23 -04:00 · 2021-04-17 11:05:23 -04:00 · 025489ec2c
parent e5877d8aa9 288c0a8023
commit 025489ec2c
188 changed files with 2269 additions and 676 deletions
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@ -269,6 +269,7 @@ endif()
 set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool")
 mark_as_advanced(ENABLE_IWYU)
 if(ENABLE_IWYU)
+  set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
  find_program(IWYU_EXE NAMES include-what-you-use iwyu)
  find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py)
  if (IWYU_EXE AND IWYU_TOOL)
@ -730,7 +731,7 @@ get_target_property(DEFINES lammps COMPILE_DEFINITIONS)
 include(FeatureSummary)
 feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND)
 message(STATUS "<<< Build configuration >>>
-   Operating System: ${CMAKE_SYSTEM_NAME}
+   Operating System: ${CMAKE_SYSTEM_NAME} ${CMAKE_LINUX_DISTRO} ${CMAKE_DISTRO_VERSION}
   Build type:       ${CMAKE_BUILD_TYPE}
   Install path:     ${CMAKE_INSTALL_PREFIX}
   Generator:        ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}")
--- a/cmake/Modules/LAMMPSUtils.cmake
+++ b/cmake/Modules/LAMMPSUtils.cmake
@ -104,3 +104,13 @@ function(FetchPotentials pkgfolder potfolder)
    endforeach()
  endif()
 endfunction(FetchPotentials)
+
+# set CMAKE_LINUX_DISTRO and CMAKE_DISTRO_VERSION on Linux
+if((CMAKE_SYSTEM_NAME STREQUAL Linux) AND (EXISTS /etc/os-release))
+  file(STRINGS /etc/os-release distro REGEX "^NAME=")
+  string(REGEX REPLACE "NAME=\"?([^\"]*)\"?" "\\1" distro "${distro}")
+  file(STRINGS /etc/os-release disversion REGEX "^VERSION_ID=")
+  string(REGEX REPLACE "VERSION_ID=\"?([^\"]*)\"?" "\\1" disversion "${disversion}")
+  set(CMAKE_LINUX_DISTRO ${distro})
+  set(CMAKE_DISTRO_VERSION ${disversion})
+endif()
--- a/cmake/Modules/Packages/USER-PLUMED.cmake
+++ b/cmake/Modules/Packages/USER-PLUMED.cmake
@ -54,8 +54,9 @@ if(DOWNLOAD_PLUMED)
    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
  endif()

-  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.0/plumed-src-2.7.0.tgz" CACHE STRING "URL for PLUMED tarball")
-  set(PLUMED_MD5 "95f29dd0c067577f11972ff90dfc7d12" CACHE STRING "MD5 checksum of PLUMED tarball")
+  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.1/plumed-src-2.7.1.tgz" CACHE STRING "URL for PLUMED tarball")
+  set(PLUMED_MD5 "4eac6a462ec84dfe0cec96c82421b8e8" CACHE STRING "MD5 checksum of PLUMED tarball")
+
  mark_as_advanced(PLUMED_URL)
  mark_as_advanced(PLUMED_MD5)

--- a/cmake/Modules/Testing.cmake
+++ b/cmake/Modules/Testing.cmake
@ -16,11 +16,14 @@ if(ENABLE_TESTING)
  set(MEMORYCHECK_COMMAND "${VALGRIND_BINARY}" CACHE FILEPATH "Memory Check Command")
  set(MEMORYCHECK_COMMAND_OPTIONS "${VALGRIND_DEFAULT_OPTIONS}" CACHE STRING "Memory Check Command Options")

-  # check if a faster linker is available.
-  # only verified with GNU and Clang compilers and new CMake
-  if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
-    if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
-        OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
+  # we need to build and link a LOT of tester executables, so it is worth checking if
+  # a faster linker is available. requires GNU or Clang compiler, newer CMake.
+  # also only verified with Fedora Linux > 30 and Ubuntu <= 18.04 (Ubuntu 20.04 fails)
+  if((CMAKE_SYSTEM_NAME STREQUAL Linux) AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
+      AND ((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
+        OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")))
+    if (((CMAKE_LINUX_DISTRO STREQUAL Ubuntu) AND (CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04))
+        OR ((CMAKE_LINUX_DISTRO STREQUAL Fedora) AND (CMAKE_DISTRO_VERSION VERSION_GREATER 30)))
      include(CheckCXXCompilerFlag)
      set(CMAKE_CUSTOM_LINKER_DEFAULT default)
      check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG)
--- a/doc/graphviz/lammps-classes.dot
+++ b/doc/graphviz/lammps-classes.dot
@ -18,8 +18,8 @@ digraph lammps {
    Up [shape=box label="Update" color=blue]
    Un [shape=box label="Universe" color=blue]
    Ti [shape=box label="Timer" color=blue]
-    Lt [label="Lattice"]
    Rg [label="Region" color=red]
+    Lt [label="Lattice"]
    Rb [shape=box label="RegionBlock"]
    Rs [shape=box label="RegionSphere"]
    Av [label="AtomVec" color=red]
@ -34,6 +34,7 @@ digraph lammps {
    Du [label="Dump" color=red]
    Fi [label="Fix" color=red]
    Cp [label="Compute" color=red]
+    Cm [label="Command" color=red]
    Th [label="Thermo"]
    Va [label="Variable"]
    Ew [shape=box label="Ewald"]
@ -71,16 +72,19 @@ digraph lammps {
    Dg [shape=box label="DumpCFG"]
    Ve [shape=box label="Verlet"]
    Rr [shape=box label="Respa"]
+    Ru [shape=box label="Run"]
+    Se [shape=box label="Set"]
    Pt [shape=box label="PPPMTIP4P"]
    Vs [shape=box label="VerletSplit"]
    Ro [shape=box label="RespaOMP"]
    Mc [shape=box label="MinCG"]
    Mf [shape=box label="MinFire"]
    La -> {At Ci Co Do Er Fo Gr In Me Mo Ne Ou Ti Up Un} [penwidth=2]
-    Do -> {Lt Rg} [penwidth=2]
+    Do -> {Rg Lt} [penwidth=2]
    Rg -> {Rb Rs} [style=dashed penwidth=2]
    Co -> {Cb Ct} [style=dashed penwidth=2]
-    In -> Va [penwidth=2]
+    In -> {Va Cm} [penwidth=2]
+    Cm -> {Ru Se} [style=dashed penwidth=2]
    Mo -> {Fi Cp} [penwidth=2]
    Fo -> {Pa Bo An Di Im Ks} [penwidth=2]
    Ks -> {Ew Pp} [style=dashed penwidth=2]
--- a/doc/src/Build_extras.rst
+++ b/doc/src/Build_extras.rst
@ -1253,8 +1253,8 @@ be built for the most part with all major versions of the C++ language.
 USER-PACE package
 -----------------------------

-This package requires a library that can be downloaded and built 
-in lib/pace or somewhere else, which must be done before building 
+This package requires a library that can be downloaded and built
+in lib/pace or somewhere else, which must be done before building
 LAMMPS with this package. The code for the library can be found
 at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps-user-pace/>`_

@ -1276,8 +1276,8 @@ 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
-      in one step from the ``lammps/src`` dir, using these commands, 
-      which invoke the ``lib/pace/Install.py`` script. 
+      in one step from the ``lammps/src`` dir, using these commands,
+      which invoke the ``lib/pace/Install.py`` script.

      .. code-block:: bash

--- a/doc/src/Developer_org.rst
+++ b/doc/src/Developer_org.rst
@ -49,8 +49,8 @@ underscore character '_' to separate words. Outside of bundled libraries
 which may have different conventions, all C and C++ header files have a
 ``.h`` extension, all C++ files have a ``.cpp`` extension, and C files a
 ``.c`` extension. A small number of C++ classes and utility functions
-are implemented with only a ``.h`` file. Examples are the Pointer class
-or the MathVec functions.
+are implemented with only a ``.h`` file. Examples are the Pointers and
+Commands classes or the MathVec functions.

 Class topology
 --------------
@ -144,7 +144,7 @@ implement specific commands that can be invoked before, after, or in
 between runs.  For these an instance of the class is created, its
 command() method called and then, after completion, the class instance
 deleted.  Examples for this are the create_box, create_atoms, minimize,
-run, or velocity command styles.
+run, set, or velocity command styles.

 For all those ``styles`` certain naming conventions are employed: for
 the fix nve command the class is called FixNVE and the source files are
@ -175,11 +175,11 @@ follows:
 - The Input class reads and processes input input strings and files,
  stores variables, and invokes :doc:`commands <Commands_all>`.

- As discussed above, command style classes are directly derived from
-  the Pointers class. They provide input script commands that perform
-  one-time operations before/after/between simulations or which invoke a
-  simulation.  They are instantiated from within the Input class,
-  invoked, then immediately destructed.
+- Command style classes are derived from the Command class. They provide
+  input script commands that perform one-time operations
+  before/after/between simulations or which invoke a simulation.  They
+  are usually instantiated from within the Input class, its ``command``
+  method invoked, and then immediately destructed.

 - The Finish class is instantiated to print statistics to the screen
  after a simulation is performed, by commands like run and minimize.
--- a/doc/src/Developer_plugins.rst
+++ b/doc/src/Developer_plugins.rst
@ -59,31 +59,25 @@ Members of ``lammpsplugin_t``
   * - author
     - String with the name and email of the author
   * - creator.v1
-     - Pointer to factory function for pair, bond, angle, dihedral, or improper styles
+     - Pointer to factory function for pair, bond, angle, dihedral, improper or command styles
   * - creator.v2
     - Pointer to factory function for compute, fix, or region styles
-   * - creator.v3
-     - Pointer to factory function for command styles
   * - handle
     - Pointer to the open DSO file handle

 Only one of the three alternate creator entries can be used at a time
-and which of those is determined by the style of plugin. The "creator.v1"
-element is for factory functions of supported styles computing forces (i.e.
-pair, bond, angle, dihedral, or improper styles) and the function takes
-as single argument the pointer to the LAMMPS instance. The factory function
-is cast to the ``lammpsplugin_factory1`` type before assignment.  The
-"creator.v2" element is for factory functions creating an instance of
-a fix, compute, or region style and takes three arguments: a pointer to
-the LAMMPS instance, an integer with the length of the argument list and
-a ``char **`` pointer to the list of arguments. The factory function pointer
-needs to be cast to the ``lammpsplugin_factory2`` type before assignment.
-The "creator.v3" element takes the same arguments as "creator.v3" but is
-specific to creating command styles: the factory function has to instantiate
-the command style locally passing the LAMMPS pointer as argument and then
-call its "command" member function with the number and list of arguments.
-The factory function pointer needs to be cast to the
-``lammpsplugin_factory3`` type before assignment.
+and which of those is determined by the style of plugin. The
+"creator.v1" element is for factory functions of supported styles
+computing forces (i.e.  command, pair, bond, angle, dihedral, or
+improper styles) and the function takes as single argument the pointer
+to the LAMMPS instance. The factory function is cast to the
+``lammpsplugin_factory1`` type before assignment.  The "creator.v2"
+element is for factory functions creating an instance of a fix, compute,
+or region style and takes three arguments: a pointer to the LAMMPS
+instance, an integer with the length of the argument list and a ``char
+**`` pointer to the list of arguments. The factory function pointer
+needs to be cast to the ``lammpsplugin_factory2`` type before
+assignment.

 Pair style example
 ^^^^^^^^^^^^^^^^^^
@ -123,12 +117,12 @@ function would look like this:

 The factory function in this example is called ``morse2creator()``.  It
 receives a pointer to the LAMMPS class as only argument and thus has to
-be assigned to the *creator.v1* member of the plugin struct and cast to the
-``lammpsplugin_factory1`` pointer type.  It returns a
+be assigned to the *creator.v1* member of the plugin struct and cast to
+the ``lammpsplugin_factory1`` function pointer type.  It returns a
 pointer to the allocated class instance derived from the ``Pair`` class.
-This function may be declared static to avoid clashes with other plugins.
-The name of the derived class, ``PairMorse2``, must be unique inside
-the entire LAMMPS executable.
+This function may be declared static to avoid clashes with other
+plugins.  The name of the derived class, ``PairMorse2``, however must be
+unique inside the entire LAMMPS executable.

 Fix style example
 ^^^^^^^^^^^^^^^^^
@ -169,9 +163,9 @@ Below is an example for that:

 Command style example
 ^^^^^^^^^^^^^^^^^^^^^
-For command styles there is a third variant of factory function as
+Command styles also use the first variant of factory function as
 demonstrated in the following example, which also shows that the
-implementation of the plugin class may also be within the same
+implementation of the plugin class may be within the same source
 file as the plugin interface code:

 .. code-block:: C++
@ -180,15 +174,15 @@ file as the plugin interface code:

   #include "comm.h"
   #include "error.h"
-   #include "pointers.h"
+   #include "command.h"
   #include "version.h"

   #include <cstring>

   namespace LAMMPS_NS {
-     class Hello : protected Pointers {
+     class Hello : public Command {
      public:
-       Hello(class LAMMPS *lmp) : Pointers(lmp) {};
+       Hello(class LAMMPS *lmp) : Command(lmp) {};
       void command(int, char **);
     };
   }
@ -202,10 +196,9 @@ file as the plugin interface code:
        utils::logmesg(lmp,fmt::format("Hello, {}!\n",argv[0]));
   }

-   static void hellocreator(LAMMPS *lmp, int argc, char **argv)
+   static void hellocreator(LAMMPS *lmp)
   {
-     Hello hello(lmp);
-     hello.command(argc,argv);
+     return new Hello(lmp);
   }

   extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
@ -216,9 +209,9 @@ file as the plugin interface code:
     plugin.version = LAMMPS_VERSION;
     plugin.style   = "command";
     plugin.name    = "hello";
-     plugin.info    = "Hello world command v1.0";
+     plugin.info    = "Hello world command v1.1";
     plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
-     plugin.creator.v3 = (lammpsplugin_factory3 *) &hellocreator;
+     plugin.creator.v1 = (lammpsplugin_factory1 *) &hellocreator;
     plugin.handle  = handle;
     (*register_plugin)(&plugin,lmp);
   }
--- a/doc/src/Howto_spins.rst
+++ b/doc/src/Howto_spins.rst
@ -21,8 +21,8 @@ orientations and their associated inter-atomic distances.

 The command :doc:`fix precession/spin <fix_precession_spin>` allows to
 apply a constant magnetic torque on all the spins in the system. This
-torque can be an external magnetic field (Zeeman interaction), or an
-uniaxial magnetic anisotropy.
+torque can be an external magnetic field (Zeeman interaction), and an
+uniaxial or cubic magnetic anisotropy.

 A Langevin thermostat can be applied to those magnetic spins using
 :doc:`fix langevin/spin <fix_langevin_spin>`. Typically, this thermostat
--- a/doc/src/JPG/lammps-classes.png
+++ b/doc/src/JPG/lammps-classes.png
--- a/doc/src/Modify_command.rst
+++ b/doc/src/Modify_command.rst
@ -1,14 +1,15 @@
 Input script command style
 ==========================

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

 The single method your new class must define is as follows:

--- a/doc/src/atom_style.rst
+++ b/doc/src/atom_style.rst
@ -27,7 +27,7 @@ Syntax
           template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command
         *hybrid* args = list of one or more sub-styles, each with their args

-* accelerated styles (with same args) = *angle/kk* or *atomic/kk* or *bond/kk* or *charge/kk* or *full/kk* or *molecular/kk*
+* accelerated styles (with same args) = *angle/kk* or *atomic/kk* or *bond/kk* or *charge/kk* or *full/kk* or *molecular/kk* or *spin/kk*

 Examples
 """"""""
--- a/doc/src/fix_qeq.rst
+++ b/doc/src/fix_qeq.rst
@ -56,27 +56,28 @@ Examples
 Description
 """""""""""

-Perform the charge equilibration (QEq) method as described in :ref:`(Rappe and Goddard) <Rappe1>` and formulated in :ref:`(Nakano) <Nakano1>` (also known
-as the matrix inversion method) and in :ref:`(Rick and Stuart) <Rick1>` (also
-known as the extended Lagrangian method) based on the
-electronegativity equilization principle.
+Perform the charge equilibration (QEq) method as described in
+:ref:`(Rappe and Goddard) <Rappe1>` and formulated in :ref:`(Nakano)
+<Nakano1>` (also known as the matrix inversion method) and in
+:ref:`(Rick and Stuart) <Rick1>` (also known as the extended Lagrangian
+method) based on the electronegativity equilization principle.

 These fixes can be used with any :doc:`pair style <pair_style>` in
 LAMMPS, so long as per-atom charges are defined.  The most typical
 use-case is in conjunction with a :doc:`pair style <pair_style>` that
 performs charge equilibration periodically (e.g. every timestep), such
-as the ReaxFF or Streitz-Mintmire potential.
-But these fixes can also be used with
-potentials that normally assume per-atom charges are fixed, e.g. a
-:doc:`Buckingham <pair_buck>` or :doc:`LJ/Coulombic <pair_lj>` potential.
+as the ReaxFF or Streitz-Mintmire potential.  But these fixes can also
+be used with potentials that normally assume per-atom charges are fixed,
+e.g. a :doc:`Buckingham <pair_buck>` or :doc:`LJ/Coulombic <pair_lj>`
+potential.

-Because the charge equilibration calculation is effectively
-independent of the pair style, these fixes can also be used to perform
-a one-time assignment of charges to atoms.  For example, you could
-define the QEq fix, perform a zero-timestep run via the :doc:`run <run>`
-command without any pair style defined which would set per-atom
-charges (based on the current atom configuration), then remove the fix
-via the :doc:`unfix <unfix>` command before performing further dynamics.
+Because the charge equilibration calculation is effectively independent
+of the pair style, these fixes can also be used to perform a one-time
+assignment of charges to atoms.  For example, you could define the QEq
+fix, perform a zero-timestep run via the :doc:`run <run>` command
+without any pair style defined which would set per-atom charges (based
+on the current atom configuration), then remove the fix via the
+:doc:`unfix <unfix>` command before performing further dynamics.

 .. note::

@ -87,11 +88,14 @@ via the :doc:`unfix <unfix>` command before performing further dynamics.

 .. note::

-   The :doc:`fix qeq/comb <fix_qeq_comb>` command must still be used
-   to perform charge equilibration with the :doc:`COMB potential <pair_comb>`.  The :doc:`fix qeq/reax <fix_qeq_reax>`
-   command can be used to perform charge equilibration with the :doc:`ReaxFF force field <pair_reaxc>`, although fix qeq/shielded yields the
-   same results as fix qeq/reax if *Nevery*\ , *cutoff*\ , and *tolerance*
-   are the same.  Eventually the fix qeq/reax command will be deprecated.
+   The :doc:`fix qeq/comb <fix_qeq_comb>` command must still be used to
+   perform charge equilibration with the :doc:`COMB potential
+   <pair_comb>`.  The :doc:`fix qeq/reax <fix_qeq_reax>` command can be
+   used to perform charge equilibration with the :doc:`ReaxFF force
+   field <pair_reaxc>`, although fix qeq/shielded yields the same
+   results as fix qeq/reax if *Nevery*\ , *cutoff*\ , and *tolerance*
+   are the same.  Eventually the fix qeq/reax command will be
+   deprecated.

 The QEq method minimizes the electrostatic energy of the system (or
 equalizes the derivative of energy with respect to charge of all the
@ -134,55 +138,57 @@ usually a good number.
 The *qeq/shielded* style describes partial charges on atoms also as
 point charges, but uses a shielded Coulomb potential to describe the
 interaction between a pair of charged particles.  Interaction through
-the shielded Coulomb is given by equation (13) of the :ref:`ReaxFF force field <vanDuin>` paper.  The shielding accounts for charge overlap
+the shielded Coulomb is given by equation (13) of the :ref:`ReaxFF force
+field <vanDuin>` paper.  The shielding accounts for charge overlap
 between charged particles at small separation.  This style is the same
-as :doc:`fix qeq/reax <fix_qeq_reax>`, and can be used with :doc:`pair_style reax/c <pair_reaxc>`.  Only the *chi*\ , *eta*\ , and *gamma*
-parameters from the *qfile* file are used. When using the string
-*reax/c* as filename, these parameters are extracted directly from
-an active *reax/c* pair style.  This style solves partial
-charges on atoms via the matrix inversion method.  A tolerance of
-1.0e-6 is usually a good number.
+as :doc:`fix qeq/reax <fix_qeq_reax>`, and can be used with
+:doc:`pair_style reax/c <pair_reaxc>`.  Only the *chi*\ , *eta*\ , and
+*gamma* parameters from the *qfile* file are used. When using the string
+*reax/c* as filename, these parameters are extracted directly from an
+active *reax/c* pair style.  This style solves partial charges on atoms
+via the matrix inversion method.  A tolerance of 1.0e-6 is usually a
+good number.

 The *qeq/slater* style describes partial charges on atoms as spherical
 charge densities centered around atoms via the Slater 1\ *s* orbital, so
-that the interaction between a pair of charged particles is the
-product of two Slater 1\ *s* orbitals.  The expression for the Slater
-1\ *s* orbital is given under equation (6) of the
-:ref:`Streitz-Mintmire <Streitz1>` paper.  Only the *chi*\ , *eta*\ , *zeta*\ , and
-*qcore* parameters from the *qfile* file are used. When using the string
+that the interaction between a pair of charged particles is the product
+of two Slater 1\ *s* orbitals.  The expression for the Slater 1\ *s*
+orbital is given under equation (6) of the :ref:`Streitz-Mintmire
+<Streitz1>` paper.  Only the *chi*\ , *eta*\ , *zeta*\ , and *qcore*
+parameters from the *qfile* file are used. When using the string
 *coul/streitz* as filename, these parameters are extracted directly from
-an active *coul/streitz* pair style.  This style solves
-partial charges on atoms via the matrix inversion method.  A tolerance
-of 1.0e-6 is usually a good number.  Keyword *alpha* can be used to
-change the Slater type orbital exponent.
+an active *coul/streitz* pair style.  This style solves partial charges
+on atoms via the matrix inversion method.  A tolerance of 1.0e-6 is
+usually a good number.  Keyword *alpha* can be used to change the Slater
+type orbital exponent.

 The *qeq/dynamic* style describes partial charges on atoms as point
-charges that interact through 1/r, but the extended Lagrangian method
-is used to solve partial charges on atoms.  Only the *chi* and *eta*
+charges that interact through 1/r, but the extended Lagrangian method is
+used to solve partial charges on atoms.  Only the *chi* and *eta*
 parameters from the *qfile* file are used.  Note that Coulomb
-catastrophe can occur if repulsion between the pair of charged
-particles is too weak.  A tolerance of 1.0e-3 is usually a good
-number.  Keyword *qdamp* can be used to change the damping factor, while
-keyword *qstep* can be used to change the time step size.
+catastrophe can occur if repulsion between the pair of charged particles
+is too weak.  A tolerance of 1.0e-3 is usually a good number.  Keyword
+*qdamp* can be used to change the damping factor, while keyword *qstep*
+can be used to change the time step size.

-The :ref:`\ *qeq/fire*\ <Shan>` style describes the same charge model and charge
-solver as the *qeq/dynamic* style, but employs a FIRE minimization
-algorithm to solve for equilibrium charges.
-Keyword *qdamp* can be used to change the damping factor, while
-keyword *qstep* can be used to change the time step size.
+The :ref:`\ *qeq/fire*\ <Shan>` style describes the same charge model
+and charge solver as the *qeq/dynamic* style, but employs a FIRE
+minimization algorithm to solve for equilibrium charges.  Keyword
+*qdamp* can be used to change the damping factor, while keyword *qstep*
+can be used to change the time step size.

 Note that *qeq/point*\ , *qeq/shielded*\ , and *qeq/slater* describe
 different charge models, whereas the matrix inversion method and the
 extended Lagrangian method (\ *qeq/dynamic* and *qeq/fire*\ ) are
 different solvers.

-Note that *qeq/point*\ , *qeq/dynamic* and *qeq/fire* styles all describe
-charges as point charges that interact through 1/r relationship, but
-solve partial charges on atoms using different solvers.  These three
-styles should yield comparable results if
-the QEq parameters and *Nevery*\ , *cutoff*\ , and *tolerance* are the
-same.  Style *qeq/point* is typically faster, *qeq/dynamic* scales
-better on larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ .
+Note that *qeq/point*\ , *qeq/dynamic* and *qeq/fire* styles all
+describe charges as point charges that interact through 1/r
+relationship, but solve partial charges on atoms using different
+solvers.  These three styles should yield comparable results if the QEq
+parameters and *Nevery*\ , *cutoff*\ , and *tolerance* are the same.
+Style *qeq/point* is typically faster, *qeq/dynamic* scales better on
+larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ .

 .. note::

@ -200,9 +206,11 @@ better on larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ .
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""

-No information about these fixes is written to :doc:`binary restart files <restart>`.  No global scalar or vector or per-atom
-quantities are stored by these fixes for access by various :doc:`output commands <Howto_output>`.  No parameter of these fixes can be used
-with the *start/stop* keywords of the :doc:`run <run>` command.
+No information about these fixes is written to :doc:`binary restart
+files <restart>`.  No global scalar or vector or per-atom quantities are
+stored by these fixes for access by various :doc:`output commands
+<Howto_output>`.  No parameter of these fixes can be used with the
+*start/stop* keywords of the :doc:`run <run>` command.

 Thexe fixes are invoked during :doc:`energy minimization <minimize>`.

@ -210,7 +218,8 @@ Restrictions
 """"""""""""

 These fixes are part of the QEQ package.  They are only enabled if
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` doc page for more info.

 Related commands
 """"""""""""""""
--- a/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py
+++ b/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py
@ -6,7 +6,7 @@ import matplotlib.pyplot as plt
 import mpmath as mp

 hbar=0.658212           # Planck's constant (eV.fs/rad)
-# J0=0.05                 # per-neighbor exchange interaction (eV)
+J0=0.05                 # per-neighbor exchange interaction (eV)

 # exchange interaction parameters
 J1 = 11.254 # in eV 
--- a/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh
+++ b/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh
@ -3,9 +3,15 @@
 # clean old res
 rm res_*.dat

-# compute Lammps 
+# test standard Lammps 
 ./../../../../src/lmp_serial \
  -in test-spin-precession.in 
+
+# test spin/kk with Kokkos Lammps
+# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \
+#   -k on -sf kk -in test-spin-precession.in
+
+# extract data from Lammps run
 in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')"
 en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')"
 in="$(echo "$in+1" | bc -l)"
--- a/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in
+++ b/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in
@ -2,8 +2,10 @@
 
 units           metal
 atom_style      spin
+# atom_style      spin/kk
 atom_modify     map array
 boundary        f f f 
+shell           echo "test1"

 atom_modify 	map array 
 lattice 	sc 3.0
--- a/examples/SPIN/test_problems/validation_damped_precession/run-test-prec.sh
+++ b/examples/SPIN/test_problems/validation_damped_precession/run-test-prec.sh
@ -3,9 +3,15 @@
 # clean old res
 rm res_*.dat

-# compute Lammps 
+# test standard Lammps 
 ./../../../../src/lmp_serial \
  -in test-spin-precession.in 
+
+# test spin/kk with Kokkos Lammps
+# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \
+#   -k on -sf kk -in test-spin-precession.in
+
+# extract data from Lammps run
 in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')"
 en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')"
 in="$(echo "$in+1" | bc -l)"
--- a/examples/SPIN/test_problems/validation_damped_precession/test-spin-precession.in
+++ b/examples/SPIN/test_problems/validation_damped_precession/test-spin-precession.in
@ -2,6 +2,7 @@
 
 units           metal
 atom_style      spin
+# atom_style      spin/kk
 atom_modify     map array
 boundary        f f f

--- a/examples/SPIN/test_problems/validation_langevin_precession/run-test-prec.sh
+++ b/examples/SPIN/test_problems/validation_langevin_precession/run-test-prec.sh
@ -12,7 +12,14 @@ do
  temp="$(echo "$tempi+$i*($tempf-$tempi)/$N" | bc -l)"
  sed s/temperature/${temp}/g test-prec-spin.template > \
    test-prec-spin.in
+  
+  # test standard Lammps 
  ./../../../../src/lmp_serial -in test-prec-spin.in 
+
+  # test spin/kk with Kokkos Lammps
+  # mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \
+  #   -k on -sf kk -in test-prec-spin.in
+  
  Hz="$(tail -n 1 average_spin | awk -F " " '{print $3}')"
  sz="$(tail -n 1 average_spin | awk -F " " '{print $5}')"
  en="$(tail -n 1 average_spin | awk -F " " '{print $6}')"
--- a/examples/SPIN/test_problems/validation_langevin_precession/test-prec-spin.template
+++ b/examples/SPIN/test_problems/validation_langevin_precession/test-prec-spin.template
@ -2,6 +2,7 @@
 
 units           metal
 atom_style      spin
+# atom_style      spin/kk
 atom_modify     map array
 boundary        p p p

--- a/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve
+++ b/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve
@ -3,6 +3,7 @@
 clear 
 units 		metal
 atom_style 	spin
+# atom_style 	spin/kk

 dimension 	3
 boundary 	p p p
@ -46,4 +47,8 @@ variable 	tmag      equal c_out_mag[6]
 thermo_style    custom step time v_tmag temp v_emag ke pe etotal
 thermo          200

+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 10 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
 run 		100000
+# run 		1
--- a/examples/SPIN/test_problems/validation_nve/run-test-nve.sh
+++ b/examples/SPIN/test_problems/validation_nve/run-test-nve.sh
@ -3,9 +3,14 @@
 # clean old res
 rm res_*.dat

-# compute Lammps 
-./../../../../src/lmp_serial \
-  -in in.spin.iron-nve 
+# test standard Lammps 
+../../../../src/lmp_serial -in in.spin.iron-nve 
+
+# test spin/kk with Kokkos Lammps
+# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \
+#   -k on -sf kk -in in.spin.iron-nve
+
+# extract data from Lammps run
 in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')"
 en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')"
 in="$(echo "$in+1" | bc -l)"
--- a/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice
+++ b/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice
@ -3,6 +3,7 @@
 clear 
 units 		metal
 atom_style 	spin
+# atom_style 	spin/kk

 dimension 	3
 boundary 	p p p
--- a/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin
+++ b/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin
@ -3,6 +3,7 @@
 clear 
 units 		metal
 atom_style 	spin
+# atom_style 	spin/kk

 dimension 	3
 boundary 	p p p
--- a/examples/SPIN/test_problems/validation_nvt/run-test-nvt.sh
+++ b/examples/SPIN/test_problems/validation_nvt/run-test-nvt.sh
@ -3,16 +3,32 @@
 # clean old res
 rm res_*.dat

-# compute NVT Spin -> Lattice 
+### compute NVT Spin -> Lattice 
+
+# test standard Lammps 
 ./../../../../src/lmp_serial -in in.spin.nvt_spin 
+
+# test spin/kk with Kokkos Lammps
+# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \
+#   -k on -sf kk -in in.spin.nvt_spin
+
+# extract data from Lammps run
 in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')"
 en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')"
 in="$(echo "$in+1" | bc -l)"
 en="$(echo "$en-$in" | bc -l)"
 tail -n +$in log.lammps | head -n $en > res_nvt_spin.dat

-# compute NVT Lattice -> Spin
+### compute NVT Lattice -> Spin
+
+# test standard Lammps 
 ./../../../../src/lmp_serial -in in.spin.nvt_lattice 
+
+# test spin/kk with Kokkos Lammps
+# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \
+#   -k on -sf kk -in in.spin.nvt_lattice
+
+# extract data from Lammps run
 in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')"
 en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')"
 in="$(echo "$in+1" | bc -l)"
--- a/examples/plugins/helloplugin.cpp
+++ b/examples/plugins/helloplugin.cpp
@ -2,16 +2,16 @@
 #include "lammpsplugin.h"

 #include "comm.h"
+#include "command.h"
 #include "error.h"
-#include "pointers.h"
 #include "version.h"

 #include <cstring>

 namespace LAMMPS_NS {
-  class Hello : protected Pointers {
+  class Hello : public Command {
    public:
-      Hello(class LAMMPS *lmp) : Pointers(lmp) {};
+      Hello(class LAMMPS *lmp) : Command(lmp) {};
      void command(int, char **);
  };
 }
@ -25,10 +25,9 @@ void Hello::command(int argc, char **argv)
     utils::logmesg(lmp,fmt::format("Hello, {}!\n",argv[0]));
 }

-static void hellocreator(LAMMPS *lmp, int argc, char **argv)
+static Command *hellocreator(LAMMPS *lmp)
 {
-    Hello hello(lmp);
-    hello.command(argc,argv);
+    return new Hello(lmp);
 }

 extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
@ -39,9 +38,9 @@ extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
  plugin.version = LAMMPS_VERSION;
  plugin.style   = "command";
  plugin.name    = "hello";
-  plugin.info    = "Hello world command v1.0";
+  plugin.info    = "Hello world command v1.1";
  plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
-  plugin.creator.v3 = (lammpsplugin_factory3 *) &hellocreator;
+  plugin.creator.v1 = (lammpsplugin_factory1 *) &hellocreator;
  plugin.handle  = handle;
  (*register_plugin)(&plugin,lmp);
 }
--- a/lib/plumed/Install.py
+++ b/lib/plumed/Install.py
@ -17,7 +17,7 @@ parser = ArgumentParser(prog='Install.py',

 # settings

-version = "2.7.0"
+version = "2.7.1"
 mode = "static"

 # help message
@ -47,9 +47,12 @@ checksums = { \
        '2.5.2' : 'bd2f18346c788eb54e1e52f4f6acf41a', \
        '2.5.3' : 'de30d6e7c2dcc0973298e24a6da24286', \
        '2.5.4' : 'f31b7d16a4be2e30aa7d5c19c3d37853', \
+        '2.5.7' : '1ca36226fdb8110b1009aa61d615d4e5', \
        '2.6.0' : '204d2edae58d9b10ba3ad460cad64191', \
        '2.6.1' : '89a9a450fc6025299fe16af235957163', \
+        '2.6.3' : 'a9f8028fd74528c2024781ea1fdefeee', \
        '2.7.0' : '95f29dd0c067577f11972ff90dfc7d12', \
+        '2.7.1' : '4eac6a462ec84dfe0cec96c82421b8e8', \
        }

 # parse and process arguments
--- a/python/install.py
+++ b/python/install.py
@ -10,7 +10,7 @@ build target in the conventional and CMake based build systems
 # copy LAMMPS shared library and lammps package to system dirs

 from __future__ import print_function
-import sys,os,shutil
+import sys,os,shutil,time
 from argparse import ArgumentParser

 parser = ArgumentParser(prog='install.py',
@ -80,13 +80,15 @@ if args.dir:

  sys.exit()

-# extract version string from header
+# extract LAMMPS version string from header
+# and convert to python packaging compatible version
 def get_lammps_version(header):
    with open(header, 'r') as f:
        line = f.readline()
        start_pos = line.find('"')+1
        end_pos = line.find('"', start_pos)
-        return "".join(line[start_pos:end_pos].split())
+        t = time.strptime("".join(line[start_pos:end_pos].split()), "%d%b%Y")
+        return "{}.{}.{}".format(t.tm_year,t.tm_mon,t.tm_mday)

 verstr = get_lammps_version(args.version)

--- a/python/lammps/init.py
+++ b/python/lammps/init.py
@ -13,10 +13,16 @@ from .core import *
 from .data import *
 from .pylammps import *

-# convert module string version to numeric version
+# convert installed module string version to numeric version
 def get_version_number():
    import time
+    from os.path import join
    from sys import version_info
+
+    # must report 0 when inside LAMMPS source tree
+    if __file__.find(join('python', 'lammps', '__init__.py')) > 0:
+        return 0
+
    vstring = None
    if version_info.major == 3 and version_info.minor >= 8:
        from importlib.metadata import version
@ -32,7 +38,7 @@ def get_version_number():
    if not vstring:
        return 0

-    t = time.strptime(vstring, "%d%b%Y")
+    t = time.strptime(vstring, "%Y.%m.%d")
    return t.tm_year*10000 + t.tm_mon*100 + t.tm_mday

 __version__ = get_version_number()
--- a/python/setup.py
+++ b/python/setup.py
@ -1,7 +1,8 @@
 # this only installs the LAMMPS python package
 # it assumes the LAMMPS shared library is already installed
 from distutils.core import setup
-import os
+from sys import version_info
+import os,time

 LAMMPS_PYTHON_DIR = os.path.dirname(os.path.realpath(__file__))
 LAMMPS_DIR = os.path.dirname(LAMMPS_PYTHON_DIR)
@ -12,7 +13,13 @@ def get_lammps_version():
        line = f.readline()
        start_pos = line.find('"')+1
        end_pos = line.find('"', start_pos)
-        return "".join(line[start_pos:end_pos].split())
+        t = time.strptime("".join(line[start_pos:end_pos].split()), "%d%b%Y")
+        return "{}.{}.{}".format(t.tm_year,t.tm_mon,t.tm_mday)
+
+if version_info.major >= 3:
+    pkgs = ['lammps', 'lammps.mliap']
+else:
+    pkgs = ['lammps']

 setup(
    name = "lammps",
@ -22,5 +29,5 @@ setup(
    url = "https://lammps.sandia.gov",
    description = "LAMMPS Molecular Dynamics Python package",
    license = "GPL",
-    packages=["lammps","lammps.mliap"],
+    packages=pkgs,
 )
--- a/src/COMPRESS/gz_file_writer.cpp
+++ b/src/COMPRESS/gz_file_writer.cpp
@ -67,7 +67,7 @@ size_t GzFileWriter::write(const void * buffer, size_t length)
 void GzFileWriter::flush()
 {
  if (!isopen()) return;
-  
+
  gzflush(gzFp, Z_SYNC_FLUSH);
 }

--- a/src/KIM/kim_command.h
+++ b/src/KIM/kim_command.h
@ -62,13 +62,13 @@ CommandStyle(kim,KimCommand)
 #ifndef LMP_KIM_COMMAND_H
 #define LMP_KIM_COMMAND_H

-#include "pointers.h"
+#include "command.h"

 namespace LAMMPS_NS {

-class KimCommand : protected Pointers {
+class KimCommand : public Command {
 public:
-  KimCommand(class LAMMPS *lmp) : Pointers(lmp) {};
+  KimCommand(class LAMMPS *lmp) : Command(lmp) {};
  void command(int, char **);
 };

--- a/src/KOKKOS/Install.sh
+++ b/src/KOKKOS/Install.sh
@ -63,6 +63,8 @@ action atom_vec_bond_kokkos.cpp atom_vec_bond.cpp
 action atom_vec_bond_kokkos.h atom_vec_bond.h
 action atom_vec_charge_kokkos.cpp
 action atom_vec_charge_kokkos.h
+action atom_vec_spin_kokkos.cpp
+action atom_vec_spin_kokkos.h
 action atom_vec_dpd_kokkos.cpp atom_vec_dpd.cpp
 action atom_vec_dpd_kokkos.h atom_vec_dpd.h
 action atom_vec_full_kokkos.cpp atom_vec_full.cpp
--- a/src/KOKKOS/atom_kokkos.cpp
+++ b/src/KOKKOS/atom_kokkos.cpp
@ -76,6 +76,12 @@ AtomKokkos::~AtomKokkos()
  memoryKK->destroy_kokkos(k_improper_atom3, improper_atom3);
  memoryKK->destroy_kokkos(k_improper_atom4, improper_atom4);

+  // SPIN package
+
+  memoryKK->destroy_kokkos(k_sp, sp);
+  memoryKK->destroy_kokkos(k_fm, fm);
+  memoryKK->destroy_kokkos(k_fm_long, fm_long);
+
  // USER-DPD package
  memoryKK->destroy_kokkos(k_uCond,uCond);
  memoryKK->destroy_kokkos(k_uMech,uMech);
--- a/src/KOKKOS/atom_kokkos.h
+++ b/src/KOKKOS/atom_kokkos.h
@ -54,6 +54,11 @@ class AtomKokkos : public Atom {

  DAT::tdual_float_2d k_dvector;

+  // SPIN package
+
+  DAT::tdual_float_1d_4 k_sp;
+  DAT::tdual_f_array k_fm;
+  DAT::tdual_f_array k_fm_long;

 // USER-DPD package
  DAT::tdual_efloat_1d k_uCond, k_uMech, k_uChem, k_uCG, k_uCGnew,
--- a/src/KOKKOS/atom_vec_spin_kokkos.cpp
+++ b/src/KOKKOS/atom_vec_spin_kokkos.cpp
--- a/src/KOKKOS/atom_vec_spin_kokkos.h
+++ b/src/KOKKOS/atom_vec_spin_kokkos.h
@ -0,0 +1,132 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef ATOM_CLASS
+
+AtomStyle(spin/kk,AtomVecSpinKokkos)
+AtomStyle(spin/kk/device,AtomVecSpinKokkos)
+AtomStyle(spin/kk/host,AtomVecSpinKokkos)
+
+#else
+
+#ifndef LMP_ATOM_VEC_SPIN_KOKKOS_H
+#define LMP_ATOM_VEC_SPIN_KOKKOS_H
+
+#include "atom_vec_kokkos.h"
+#include "kokkos_type.h"
+
+namespace LAMMPS_NS {
+
+class AtomVecSpinKokkos : public AtomVecKokkos {
+ public:
+  AtomVecSpinKokkos(class LAMMPS *);
+  void grow(int);
+  void copy(int, int, int);
+  int pack_border(int, int *, double *, int, int *);
+  int pack_border_vel(int, int *, double *, int, int *);
+  int pack_border_hybrid(int, int *, double *);
+  void unpack_border(int, int, double *);
+  void unpack_border_vel(int, int, double *);
+  int unpack_border_hybrid(int, int, double *);
+  int pack_exchange(int, double *);
+  int unpack_exchange(double *);
+  int size_restart();
+  int pack_restart(int, double *);
+  int unpack_restart(double *);
+  void create_atom(int, double *);
+  void data_atom(double *, imageint, char **);
+  int data_atom_hybrid(int, char **);
+  void pack_data(double **);
+  int pack_data_hybrid(int, double *);
+  void write_data(FILE *, int, double **);
+  int write_data_hybrid(FILE *, double *);
+  double memory_usage();
+
+  // clear magnetic and mechanic forces
+
+  void force_clear(int, size_t);
+
+  void grow_pointers();
+  // input lists to be checked
+  int pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist,
+                         DAT::tdual_xfloat_2d buf,int iswap,
+                         int pbc_flag, int *pbc, ExecutionSpace space);
+  void unpack_border_kokkos(const int &n, const int &nfirst,
+                            const DAT::tdual_xfloat_2d &buf,
+                            ExecutionSpace space);
+  int pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &buf,
+                           DAT::tdual_int_1d k_sendlist,
+                           DAT::tdual_int_1d k_copylist,
+                           ExecutionSpace space, int dim,
+                           X_FLOAT lo, X_FLOAT hi);
+  int unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf, int nrecv,
+                             int nlocal, int dim, X_FLOAT lo, X_FLOAT hi,
+                             ExecutionSpace space);
+
+  void sync(ExecutionSpace space, unsigned int mask);
+  void modified(ExecutionSpace space, unsigned int mask);
+  void sync_overlapping_device(ExecutionSpace space, unsigned int mask);
+
+ protected:
+  tagint *tag;
+  int *type,*mask;
+  imageint *image;
+  double **x,**v,**f;           // lattice quantities
+
+                                // spin quantities
+  double **sp;                  // sp[i][0-2] direction of the spin i
+                                // sp[i][3] atomic magnetic moment of the spin i
+  double **fm;                  // fm[i][0-2] direction of magnetic precession
+  double **fm_long;             // storage of long-range spin prec. components
+
+  DAT::t_tagint_1d d_tag;
+  HAT::t_tagint_1d h_tag;
+
+  DAT::t_int_1d d_type, d_mask;
+  HAT::t_int_1d h_type, h_mask;
+
+  DAT::t_imageint_1d d_image;
+  HAT::t_imageint_1d h_image;
+
+  DAT::t_x_array d_x;
+  DAT::t_v_array d_v;
+  DAT::t_f_array d_f;
+
+  DAT::t_sp_array d_sp;
+  DAT::t_fm_array d_fm;
+  DAT::t_fm_long_array d_fm_long;
+
+  HAT::t_sp_array h_sp;
+  HAT::t_fm_array h_fm;
+  HAT::t_fm_long_array h_fm_long;
+
+  DAT::tdual_int_1d k_count;
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Per-processor system is too big
+
+The number of owned atoms plus ghost atoms on a single
+processor must fit in 32-bit integer.
+
+E: Invalid atom type in Atoms section of data file
+
+Atom types must range from 1 to specified # of types.
+
+*/
--- a/src/KOKKOS/kokkos_type.h
+++ b/src/KOKKOS/kokkos_type.h
@ -769,6 +769,36 @@ typedef tdual_virial_array::t_dev_um t_virial_array_um;
 typedef tdual_virial_array::t_dev_const_um t_virial_array_const_um;
 typedef tdual_virial_array::t_dev_const_randomread t_virial_array_randomread;

+// Spin Types
+
+//3d SP_FLOAT array n*4
+#ifdef LMP_KOKKOS_NO_LEGACY
+typedef Kokkos::DualView<X_FLOAT*[4], Kokkos::LayoutLeft, LMPDeviceType> tdual_float_1d_4;
+#else
+typedef Kokkos::DualView<X_FLOAT*[4], Kokkos::LayoutRight, LMPDeviceType> tdual_float_1d_4;
+#endif
+typedef tdual_float_1d_4::t_dev t_sp_array;
+typedef tdual_float_1d_4::t_dev_const t_sp_array_const;
+typedef tdual_float_1d_4::t_dev_um t_sp_array_um;
+typedef tdual_float_1d_4::t_dev_const_um t_sp_array_const_um;
+typedef tdual_float_1d_4::t_dev_const_randomread t_sp_array_randomread;
+
+//3d FM_FLOAT array n*3
+
+typedef tdual_f_array::t_dev t_fm_array;
+typedef tdual_f_array::t_dev_const t_fm_array_const;
+typedef tdual_f_array::t_dev_um t_fm_array_um;
+typedef tdual_f_array::t_dev_const_um t_fm_array_const_um;
+typedef tdual_f_array::t_dev_const_randomread t_fm_array_randomread;
+
+//3d FML_FLOAT array n*3
+
+typedef tdual_f_array::t_dev t_fm_long_array;
+typedef tdual_f_array::t_dev_const t_fm_long_array_const;
+typedef tdual_f_array::t_dev_um t_fm_long_array_um;
+typedef tdual_f_array::t_dev_const_um t_fm_long_array_const_um;
+typedef tdual_f_array::t_dev_const_randomread t_fm_long_array_randomread;
+
 //Energy Types
 //1d E_FLOAT array n

@ -1005,6 +1035,28 @@ typedef tdual_virial_array::t_host_um t_virial_array_um;
 typedef tdual_virial_array::t_host_const_um t_virial_array_const_um;
 typedef tdual_virial_array::t_host_const_randomread t_virial_array_randomread;

+// Spin types
+
+//2d X_FLOAT array n*4
+typedef tdual_float_1d_4::t_host t_sp_array;
+typedef tdual_float_1d_4::t_host_const t_sp_array_const;
+typedef tdual_float_1d_4::t_host_um t_sp_array_um;
+typedef tdual_float_1d_4::t_host_const_um t_sp_array_const_um;
+typedef tdual_float_1d_4::t_host_const_randomread t_sp_array_randomread;
+
+//2d F_FLOAT array n*3
+typedef tdual_f_array::t_host t_fm_array;
+typedef tdual_f_array::t_host_const t_fm_array_const;
+typedef tdual_f_array::t_host_um t_fm_array_um;
+typedef tdual_f_array::t_host_const_um t_fm_array_const_um;
+typedef tdual_f_array::t_host_const_randomread t_fm_array_randomread;
+
+//2d F_FLOAT array n*3
+typedef tdual_f_array::t_host t_fm_long_array;
+typedef tdual_f_array::t_host_const t_fm_long_array_const;
+typedef tdual_f_array::t_host_um t_fm_long_array_um;
+typedef tdual_f_array::t_host_const_um t_fm_long_array_const_um;
+typedef tdual_f_array::t_host_const_randomread t_fm_long_array_randomread;


 //Energy Types
--- a/src/KOKKOS/verlet_kokkos.cpp
+++ b/src/KOKKOS/verlet_kokkos.cpp
@ -595,6 +595,15 @@ void VerletKokkos::force_clear()
      atomKK->modified(Device,TORQUE_MASK);
    }

+    // reset SPIN forces
+
+    if (extraflag) {
+      Kokkos::parallel_for(nall, Zero<typename ArrayTypes<LMPDeviceType>::t_fm_array>(atomKK->k_fm.view<LMPDeviceType>()));
+      atomKK->modified(Device,FM_MASK);
+      Kokkos::parallel_for(nall, Zero<typename ArrayTypes<LMPDeviceType>::t_fm_array>(atomKK->k_fm_long.view<LMPDeviceType>()));
+      atomKK->modified(Device,FML_MASK);
+    }
+
  // neighbor includegroup flag is set
  // clear force only on initial nfirst particles
  // if either newton flag is set, also include ghosts
@ -608,6 +617,15 @@ void VerletKokkos::force_clear()
      atomKK->modified(Device,TORQUE_MASK);
    }

+    // reset SPIN forces
+
+    if (extraflag) {
+      Kokkos::parallel_for(atomKK->nfirst, Zero<typename ArrayTypes<LMPDeviceType>::t_fm_array>(atomKK->k_fm.view<LMPDeviceType>()));
+      atomKK->modified(Device,FM_MASK);
+      Kokkos::parallel_for(atomKK->nfirst, Zero<typename ArrayTypes<LMPDeviceType>::t_fm_array>(atomKK->k_fm_long.view<LMPDeviceType>()));
+      atomKK->modified(Device,FML_MASK);
+    }
+
    if (force->newton) {
      auto range = Kokkos::RangePolicy<LMPDeviceType>(atomKK->nlocal, atomKK->nlocal + atomKK->nghost);
      Kokkos::parallel_for(range, Zero<typename ArrayTypes<LMPDeviceType>::t_f_array>(atomKK->k_f.view<LMPDeviceType>()));
@ -617,6 +635,15 @@ void VerletKokkos::force_clear()
        Kokkos::parallel_for(range, Zero<typename ArrayTypes<LMPDeviceType>::t_f_array>(atomKK->k_torque.view<LMPDeviceType>()));
        atomKK->modified(Device,TORQUE_MASK);
      }
+
+      // reset SPIN forces
+
+      if (extraflag) {
+        Kokkos::parallel_for(range, Zero<typename ArrayTypes<LMPDeviceType>::t_fm_array>(atomKK->k_fm.view<LMPDeviceType>()));
+        atomKK->modified(Device,FM_MASK);
+        Kokkos::parallel_for(range, Zero<typename ArrayTypes<LMPDeviceType>::t_fm_array>(atomKK->k_fm_long.view<LMPDeviceType>()));
+        atomKK->modified(Device,FML_MASK);
+      }
    }
  }
 }
--- a/src/MANYBODY/fix_qeq_comb.cpp
+++ b/src/MANYBODY/fix_qeq_comb.cpp
@ -17,21 +17,21 @@

 #include "fix_qeq_comb.h"

-#include <cmath>
-#include <cstring>
-#include "pair_comb.h"
-#include "pair_comb3.h"
-#include "neigh_list.h"
 #include "atom.h"
 #include "comm.h"
+#include "error.h"
 #include "force.h"
 #include "group.h"
+#include "memory.h"
+#include "neigh_list.h"
 #include "respa.h"
 #include "update.h"
-#include "memory.h"
-#include "error.h"

+#include <cmath>
+#include <cstring>

+#include "pair_comb.h"
+#include "pair_comb3.h"

 using namespace LAMMPS_NS;
 using namespace FixConst;
@ -85,9 +85,6 @@ FixQEQComb::FixQEQComb(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
  int nlocal = atom->nlocal;
  for (int i = 0; i < nlocal; i++) qf[i] = 0.0;

-  comb = nullptr;
-  comb3 = nullptr;
-
  comm_forward = 1;
 }

@ -119,8 +116,9 @@ void FixQEQComb::init()
  if (!atom->q_flag)
    error->all(FLERR,"Fix qeq/comb requires atom attribute q");

-  comb = (PairComb *) force->pair_match("^comb",0);
  comb3 = (PairComb3 *) force->pair_match("^comb3",0);
+  if (!comb3) comb = (PairComb *) force->pair_match("^comb",0);
+
  if (comb == nullptr && comb3 == nullptr)
    error->all(FLERR,"Must use pair_style comb or comb3 with fix qeq/comb");

@ -204,14 +202,17 @@ void FixQEQComb::post_force(int /*vflag*/)
  double *q = atom->q;
  int *mask = atom->mask;

- if (comb) {
+  if (comb) {
    inum = comb->list->inum;
    ilist = comb->list->ilist;
-  }
-  if (comb3) {
+  } else if (comb3) {
    inum = comb3->list->inum;
    ilist = comb3->list->ilist;
+  } else {
+    inum = 0;
+    ilist = nullptr;
  }
+
  for (ii = 0; ii < inum; ii++) {
    i = ilist[ii];
    q1[i] = q2[i] = qf[i] = 0.0;
@ -227,8 +228,9 @@ void FixQEQComb::post_force(int /*vflag*/)
    }

    comm->forward_comm_fix(this);
+    enegtot = 0.0;
    if (comb) enegtot = comb->yasu_char(qf,igroup);
-    if (comb3) enegtot = comb3->combqeq(qf,igroup);
+    else if (comb3) enegtot = comb3->combqeq(qf,igroup);

    enegtot /= ngroup;
    enegchk = enegmax = 0.0;
--- a/src/MC/fix_charge_regulation.cpp
+++ b/src/MC/fix_charge_regulation.cpp
@ -147,7 +147,7 @@ int FixChargeRegulation::setmask() {

 void FixChargeRegulation::init() {

-  triclinic = domain->triclinic; 
+  triclinic = domain->triclinic;
  int ipe = modify->find_compute("thermo_pe");
  c_pe = modify->compute[ipe];

@ -187,14 +187,7 @@ void FixChargeRegulation::init() {
    // neighbor list exclusion setup
    // turn off interactions between group all and the exclusion group

-    int narg = 4;
-    char **arg = new char*[narg];;
-    arg[0] = (char *) "exclude";
-    arg[1] = (char *) "group";
-    arg[2] = (char *) group_id.c_str();
-    arg[3] = (char *) "all";
-    neighbor->modify_params(narg,arg);
-    delete [] arg;
+    neighbor->modify_params(fmt::format("exclude group {} all",group_id));
  }

  // check that no deletable atoms are in atom->firstgroup
@ -356,7 +349,7 @@ void FixChargeRegulation::forward_acid() {

  double energy_before = energy_stored;
  double factor;
-  double *dummyp = nullptr;
+  double dummyp[3];
  double pos[3];
  pos[0] = 0;
  pos[1] = 0;
@ -415,7 +408,7 @@ void FixChargeRegulation::backward_acid() {
  double energy_before = energy_stored;
  double factor;
  int mask_tmp;
-  double *dummyp = nullptr;
+  double dummyp[3];
  double pos[3];
  pos[0] = 0;
  pos[1] = 0;
@ -488,7 +481,7 @@ void FixChargeRegulation::forward_base() {

  double energy_before = energy_stored;
  double factor;
-  double *dummyp = nullptr;
+  double dummyp[3];
  double pos[3];
  pos[0] = 0;
  pos[1] = 0;
@ -546,7 +539,7 @@ void FixChargeRegulation::backward_base() {

  double energy_before = energy_stored;
  double factor;
-  double *dummyp = nullptr;
+  double dummyp[3];
  int mask_tmp;
  double pos[3];
  pos[0] = 0;
@ -619,7 +612,7 @@ void FixChargeRegulation::forward_ions() {

  double energy_before = energy_stored;
  double factor;
-  double *dummyp = nullptr;
+  double dummyp[3];
  int m1 = -1, m2 = -1;
  factor = volume_rx * volume_rx * c10pI_plus * c10pI_minus /
           ((1 + ncation) * (1 + nanion));
@ -654,7 +647,7 @@ void FixChargeRegulation::backward_ions() {
  double energy_before = energy_stored;
  double factor;
  int mask1_tmp = 0, mask2_tmp = 0;
-  double *dummyp = nullptr;
+  double dummyp[3];
  int m1 = -1, m2 = -1;

  m1 = get_random_particle(cation_type, +1, 0, dummyp);
@ -733,7 +726,7 @@ void FixChargeRegulation::forward_ions_multival() {

  double energy_before = energy_stored;
  double factor = 1;
-  double *dummyp = nullptr;
+  double dummyp[3];
  int mm[salt_charge_ratio + 1];// particle ID array for all ions to be inserted

  if (salt_charge[0] <= -salt_charge[1]) {
@ -787,7 +780,7 @@ void FixChargeRegulation::backward_ions_multival() {

  double energy_before = energy_stored;
  double factor = 1;
-  double *dummyp = nullptr;  // dummy pointer
+  double dummyp[3];  // dummy particle
  int mm[salt_charge_ratio + 1];  // particle ID array for all deleted ions
  double qq[salt_charge_ratio + 1];  // charge array for all deleted ions
  int mask_tmp[salt_charge_ratio + 1];  // temporary mask array
--- a/src/MC/fix_gcmc.cpp
+++ b/src/MC/fix_gcmc.cpp
@ -580,14 +580,7 @@ void FixGCMC::init()
    // neighbor list exclusion setup
    // turn off interactions between group all and the exclusion group

-    int narg = 4;
-    char **arg = new char*[narg];;
-    arg[0] = (char *) "exclude";
-    arg[1] = (char *) "group";
-    arg[2] = (char *) group_id.c_str();
-    arg[3] = (char *) "all";
-    neighbor->modify_params(narg,arg);
-    delete [] arg;
+    neighbor->modify_params(fmt::format("exclude group {} all",group_id));
  }

  // create a new group for temporary use with selected molecules
--- a/src/MC/fix_widom.cpp
+++ b/src/MC/fix_widom.cpp
@ -342,14 +342,7 @@ void FixWidom::init()
    // neighbor list exclusion setup
    // turn off interactions between group all and the exclusion group

-    int narg = 4;
-    char **arg = new char*[narg];;
-    arg[0] = (char *) "exclude";
-    arg[1] = (char *) "group";
-    arg[2] = (char *) group_id.c_str();
-    arg[3] = (char *) "all";
-    neighbor->modify_params(narg,arg);
-    delete [] arg;
+    neighbor->modify_params(fmt::format("exclude group {} all",group_id));
  }

  // create a new group for temporary use with selected molecules
--- a/src/MESSAGE/message.h
+++ b/src/MESSAGE/message.h
@ -20,13 +20,13 @@ CommandStyle(message,Message)
 #ifndef LMP_MESSAGE_H
 #define LMP_MESSAGE_H

-#include "pointers.h"
+#include "command.h"

 namespace LAMMPS_NS {

-class Message : protected Pointers {
+class Message : public Command {
 public:
-  Message(class LAMMPS *lmp) : Pointers(lmp) {};
+  Message(class LAMMPS *lmp) : Command(lmp) {};
  void command(int, char **);

 private:
--- a/src/MESSAGE/server.h
+++ b/src/MESSAGE/server.h
@ -20,13 +20,13 @@ CommandStyle(server,Server)
 #ifndef LMP_SERVER_H
 #define LMP_SERVER_H

-#include "pointers.h"
+#include "command.h"

 namespace LAMMPS_NS {

-class Server : protected Pointers {
+class Server : public Command {
 public:
-  Server(class LAMMPS *lmp) : Pointers(lmp) {};
+  Server(class LAMMPS *lmp) : Command(lmp) {};
  void command(int, char **);
 };

--- a/src/PLUGIN/plugin.cpp
+++ b/src/PLUGIN/plugin.cpp
@ -41,7 +41,7 @@ namespace LAMMPS_NS

 /* ---------------------------------------------------------------------- */

-  Plugin::Plugin(LAMMPS *lmp) : Pointers(lmp) {}
+  Plugin::Plugin(LAMMPS *lmp) : Command(lmp) {}

 /* ---------------------------------------------------------------------- */

@ -257,7 +257,7 @@ namespace LAMMPS_NS
                                                "style {} from plugin",
                                                plugin->name));
      }
-      (*command_map)[plugin->name] = (Input::CommandCreator)plugin->creator.v3;
+      (*command_map)[plugin->name] = (Input::CommandCreator)plugin->creator.v1;

    } else {
      utils::logmesg(lmp,fmt::format("Loading plugin for {} styles not "
--- a/src/PLUGIN/plugin.h
+++ b/src/PLUGIN/plugin.h
@ -21,12 +21,12 @@ CommandStyle(plugin,Plugin)
 #define LMP_PLUGIN_H

 #include "lammpsplugin.h"
-#include "pointers.h"
+#include "command.h"

 namespace LAMMPS_NS
 {

-  class Plugin : protected Pointers {
+  class Plugin : public Command {
  public:
    Plugin(class LAMMPS *);
    void command(int, char **);
--- a/src/PYTHON/fix_python_invoke.cpp
+++ b/src/PYTHON/fix_python_invoke.cpp
@ -93,7 +93,7 @@ void FixPythonInvoke::end_of_step()
 {
  PyUtils::GIL lock;

-  PyObject * result = PyObject_CallFunction((PyObject*)pFunc, "O", (PyObject*)lmpPtr);
+  PyObject * result = PyObject_CallFunction((PyObject*)pFunc, (char *)"O", (PyObject*)lmpPtr);

  if (!result) {
    PyUtils::Print_Errors();
@ -110,8 +110,9 @@ void FixPythonInvoke::post_force(int vflag)
  if (update->ntimestep % nevery != 0) return;

  PyUtils::GIL lock;
+  char fmt[] = "Oi";

-  PyObject * result = PyObject_CallFunction((PyObject*)pFunc, "Oi", (PyObject*)lmpPtr, vflag);
+  PyObject * result = PyObject_CallFunction((PyObject*)pFunc, fmt, (PyObject*)lmpPtr, vflag);

  if (!result) {
    PyUtils::Print_Errors();
--- a/src/PYTHON/fix_python_move.cpp
+++ b/src/PYTHON/fix_python_move.cpp
@ -75,7 +75,7 @@ FixPythonMove::FixPythonMove(LAMMPS *lmp, int narg, char **arg) :
  }

  PyObject *ptr = PY_VOID_POINTER(lmp);
-  PyObject *py_move_obj = PyObject_CallFunction(py_move_type, "O", ptr);
+  PyObject *py_move_obj = PyObject_CallFunction(py_move_type, (char *)"O", ptr);
  Py_CLEAR(ptr);

  if (!py_move_obj) {
@ -112,7 +112,7 @@ int FixPythonMove::setmask()
 void FixPythonMove::init()
 {
  PyUtils::GIL lock;
-  PyObject * result = PyObject_CallMethod((PyObject *)py_move, "init", nullptr);
+  PyObject * result = PyObject_CallMethod((PyObject *)py_move, (char *)"init", nullptr);

  if (!result) {
    PyUtils::Print_Errors();
@ -126,7 +126,7 @@ void FixPythonMove::init()
 void FixPythonMove::initial_integrate(int vflag)
 {
  PyUtils::GIL lock;
-  PyObject * result = PyObject_CallMethod((PyObject*)py_move, "initial_integrate", "i", vflag);
+  PyObject * result = PyObject_CallMethod((PyObject*)py_move, (char *)"initial_integrate", (char *)"i", vflag);

  if (!result) {
    PyUtils::Print_Errors();
@ -140,7 +140,7 @@ void FixPythonMove::initial_integrate(int vflag)
 void FixPythonMove::final_integrate()
 {
  PyUtils::GIL lock;
-  PyObject * result = PyObject_CallMethod((PyObject*)py_move, "final_integrate", nullptr);
+  PyObject * result = PyObject_CallMethod((PyObject*)py_move, (char *)"final_integrate", nullptr);

  if (!result) {
    PyUtils::Print_Errors();
@ -154,7 +154,7 @@ void FixPythonMove::final_integrate()
 void FixPythonMove::initial_integrate_respa(int vflag, int ilevel, int iloop)
 {
  PyUtils::GIL lock;
-  PyObject * result = PyObject_CallMethod((PyObject*)py_move, "initial_integrate_respa", "iii", vflag, ilevel, iloop);
+  PyObject * result = PyObject_CallMethod((PyObject*)py_move, (char *)"initial_integrate_respa", (char *)"iii", vflag, ilevel, iloop);

  if (!result) {
    PyUtils::Print_Errors();
@ -168,7 +168,7 @@ void FixPythonMove::initial_integrate_respa(int vflag, int ilevel, int iloop)
 void FixPythonMove::final_integrate_respa(int ilevel, int iloop)
 {
  PyUtils::GIL lock;
-  PyObject * result = PyObject_CallMethod((PyObject*)py_move, "final_integrate_respa", "ii", ilevel, iloop);
+  PyObject * result = PyObject_CallMethod((PyObject*)py_move, (char *)"final_integrate_respa", (char *)"ii", ilevel, iloop);

  if (!result) {
    PyUtils::Print_Errors();
@ -182,7 +182,7 @@ void FixPythonMove::final_integrate_respa(int ilevel, int iloop)
 void FixPythonMove::reset_dt()
 {
  PyUtils::GIL lock;
-  PyObject * result = PyObject_CallMethod((PyObject*)py_move, "reset_dt", nullptr);
+  PyObject * result = PyObject_CallMethod((PyObject*)py_move, (char *)"reset_dt", nullptr);

  if (!result) {
    PyUtils::Print_Errors();
--- a/src/PYTHON/pair_python.cpp
+++ b/src/PYTHON/pair_python.cpp
@ -288,7 +288,7 @@ void PairPython::coeff(int narg, char **arg)

  py_potential = (void *) py_pair_instance;

-  PyObject *py_value = PyObject_CallMethod(py_pair_instance, "check_units", "s", update->unit_style);
+  PyObject *py_value = PyObject_CallMethod(py_pair_instance, (char *)"check_units", (char *)"s", update->unit_style);
  if (!py_value) {
    PyUtils::Print_Errors();
    error->all(FLERR,"Calling 'check_units' function failed");
@ -306,7 +306,7 @@ void PairPython::coeff(int narg, char **arg)
    } else skip_types[i] = 0;
    const int type = i;
    const char * name = arg[2+i];
-    py_value = PyObject_CallMethod(py_pair_instance, "map_coeff", "si", name, type);
+    py_value = PyObject_CallMethod(py_pair_instance, (char *)"map_coeff", (char *)"si", name, type);
    if (!py_value) {
      PyUtils::Print_Errors();
      error->all(FLERR,"Calling 'map_coeff' function failed");
--- a/src/QEQ/fix_qeq.cpp
+++ b/src/QEQ/fix_qeq.cpp
@ -18,16 +18,16 @@

 #include "fix_qeq.h"

-#include <cmath>
-#include <cstring>
 #include "atom.h"
 #include "comm.h"
-#include "neigh_list.h"
-#include "update.h"
+#include "error.h"
 #include "force.h"
 #include "memory.h"
-#include "error.h"
+#include "neigh_list.h"
+#include "update.h"

+#include <cmath>
+#include <cstring>

 using namespace LAMMPS_NS;
 using namespace FixConst;
@ -386,13 +386,11 @@ int FixQEq::CG( double *b, double *x )
    vector_sum( d, 1., p, beta, d, inum );
  }

-  if (loop >= maxiter && comm->me == 0) {
-    char str[128];
-    sprintf(str,"Fix qeq CG convergence failed (%g) after %d iterations "
-            "at " BIGINT_FORMAT " step",sqrt(sig_new)/b_norm,loop,update->ntimestep);
-    error->warning(FLERR,str);
-  }
-
+  if ((comm->me == 0) && (loop >= maxiter))
+    error->warning(FLERR,fmt::format("Fix qeq CG convergence failed ({}) "
+                                     "after {} iterations at step {}",
+                                     sqrt(sig_new)/b_norm,loop,
+                                     update->ntimestep));
  return loop;
 }

@ -708,11 +706,9 @@ void FixQEq::read_file(char *file)
  FILE *fp;
  if (comm->me == 0) {
    fp = utils::open_potential(file,lmp,nullptr);
-    if (fp == nullptr) {
-      char str[128];
-      snprintf(str,128,"Cannot open fix qeq parameter file %s",file);
-      error->one(FLERR,str);
-    }
+    if (fp == nullptr)
+      error->one(FLERR,fmt::format("Cannot open fix qeq parameter file {}: {}",
+                                   file,utils::getsyserror()));
  }

  // read each line out of file, skipping blank lines or leading '#'
--- a/src/QEQ/fix_qeq_dynamic.cpp
+++ b/src/QEQ/fix_qeq_dynamic.cpp
@ -17,20 +17,20 @@

 #include "fix_qeq_dynamic.h"

-#include <cmath>
-
-#include <cstring>
 #include "atom.h"
 #include "comm.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
+#include "error.h"
 #include "force.h"
 #include "group.h"
 #include "kspace.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "respa.h"
-#include "error.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>

 using namespace LAMMPS_NS;

@ -154,14 +154,9 @@ void FixQEqDynamic::pre_force(int /*vflag*/)
    }
  }

-  if (comm->me == 0) {
-    if (iloop == maxiter) {
-      char str[128];
-      sprintf(str,"Charges did not converge at step " BIGINT_FORMAT
-                  ": %lg",update->ntimestep,enegchk);
-      error->warning(FLERR,str);
-    }
-  }
+  if ((comm->me == 0) && (iloop >= maxiter))
+      error->warning(FLERR,fmt::format("Charges did not converge at step "
+                                       "{}: {}",update->ntimestep,enegchk));

  if (force->kspace) force->kspace->qsum_qsq();
 }
--- a/src/QEQ/fix_qeq_fire.cpp
+++ b/src/QEQ/fix_qeq_fire.cpp
@ -17,22 +17,22 @@

 #include "fix_qeq_fire.h"

-#include <cmath>
-
-#include <cstring>
 #include "atom.h"
 #include "comm.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
+#include "error.h"
 #include "force.h"
 #include "group.h"
+#include "kspace.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "pair_comb.h"
 #include "pair_comb3.h"
-#include "kspace.h"
 #include "respa.h"
-#include "error.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>

 using namespace LAMMPS_NS;
 using namespace FixConst;
@ -47,7 +47,7 @@ using namespace FixConst;
 /* ---------------------------------------------------------------------- */

 FixQEqFire::FixQEqFire(LAMMPS *lmp, int narg, char **arg) :
-  FixQEq(lmp, narg, arg)
+  FixQEq(lmp, narg, arg), comb(nullptr), comb3(nullptr)
 {
  qdamp = 0.20;
  qstep = 0.20;
@ -65,9 +65,6 @@ FixQEqFire::FixQEqFire(LAMMPS *lmp, int narg, char **arg) :
      iarg += 2;
    } else error->all(FLERR,"Illegal fix qeq/fire command");
  }
-
-  comb = nullptr;
-  comb3 = nullptr;
 }

 /* ---------------------------------------------------------------------- */
@ -94,9 +91,8 @@ void FixQEqFire::init()
  if (utils::strmatch(update->integrate_style,"^respa"))
    nlevels_respa = ((Respa *) update->integrate)->nlevels;

-  comb = (PairComb *) force->pair_match("comb",1);
-  comb3 = (PairComb3 *) force->pair_match("comb3",1);
-
+  comb3 = (PairComb3 *) force->pair_match("^comb3",0);
+  if (!comb3) comb = (PairComb *) force->pair_match("^comb",0);
 }

 /* ---------------------------------------------------------------------- */
@ -218,14 +214,9 @@ void FixQEqFire::pre_force(int /*vflag*/)
    if (enegchk < tolerance) break;
  }

-  if (comm->me == 0) {
-    if (iloop == maxiter) {
-      char str[128];
-      sprintf(str,"Charges did not converge at step " BIGINT_FORMAT
-                  ": %lg",update->ntimestep,enegchk);
-      error->warning(FLERR,str);
-    }
-  }
+  if ((comm->me == 0) && (iloop >= maxiter))
+    error->warning(FLERR,fmt::format("Charges did not converge at step "
+                                     "{}: {}",update->ntimestep,enegchk));

  if (force->kspace) force->kspace->qsum_qsq();
 }
--- a/src/QEQ/fix_qeq_point.cpp
+++ b/src/QEQ/fix_qeq_point.cpp
@ -16,20 +16,22 @@
 ------------------------------------------------------------------------- */

 #include "fix_qeq_point.h"
-#include <cmath>
-#include <cstring>
+
 #include "atom.h"
 #include "comm.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
+#include "error.h"
 #include "force.h"
 #include "group.h"
 #include "kspace.h"
-#include "respa.h"
 #include "memory.h"
-#include "error.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+#include "respa.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>

 using namespace LAMMPS_NS;

@ -158,13 +160,9 @@ void FixQEqPoint::compute_H()
    }
  }

-  if (m_fill >= H.m) {
-    char str[128];
-    sprintf(str,"H matrix size has been exceeded: m_fill=%d H.m=%d\n",
-             m_fill, H.m );
-    error->warning(FLERR,str);
-    error->all(FLERR,"Fix qeq/point has insufficient QEq matrix size");
-  }
+  if (m_fill >= H.m)
+    error->all(FLERR,fmt::format("Fix qeq/point has insufficient H matrix "
+                                 "size: m_fill={} H.m={}\n",m_fill, H.m));
 }

 /* ---------------------------------------------------------------------- */
--- a/src/QEQ/fix_qeq_shielded.cpp
+++ b/src/QEQ/fix_qeq_shielded.cpp
@ -16,21 +16,23 @@
 ------------------------------------------------------------------------- */

 #include "fix_qeq_shielded.h"
-#include <cmath>
-#include <cstring>
+
 #include "atom.h"
 #include "comm.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
+#include "error.h"
 #include "force.h"
 #include "group.h"
-#include "pair.h"
 #include "kspace.h"
-#include "respa.h"
 #include "memory.h"
-#include "error.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+#include "pair.h"
+#include "respa.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>

 using namespace LAMMPS_NS;

@ -223,13 +225,9 @@ void FixQEqShielded::compute_H()
    }
  }

-  if (m_fill >= H.m) {
-    char str[128];
-    sprintf(str,"H matrix size has been exceeded: m_fill=%d H.m=%d\n",
-             m_fill, H.m );
-    error->warning(FLERR,str);
-    error->all(FLERR,"Fix qeq/shielded has insufficient QEq matrix size");
-  }
+  if (m_fill >= H.m)
+    error->all(FLERR,fmt::format("Fix qeq/shielded has insufficient H matrix "
+                                 "size: m_fill={} H.m={}\n",m_fill,H.m));
 }

 /* ---------------------------------------------------------------------- */
@ -247,7 +245,7 @@ double FixQEqShielded::calculate_H( double r, double gamma )
  Taper = Taper * r + Tap[0];

  denom = r * r * r + gamma;
-  denom = pow(denom,0.3333333333333);
+  denom = pow(denom,1.0/3.0);

  return Taper * EV_TO_KCAL_PER_MOL / denom;
 }
--- a/src/QEQ/fix_qeq_slater.cpp
+++ b/src/QEQ/fix_qeq_slater.cpp
@ -16,22 +16,23 @@
 ------------------------------------------------------------------------- */

 #include "fix_qeq_slater.h"
-#include <cmath>

-#include <cstring>
 #include "atom.h"
 #include "comm.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
+#include "error.h"
 #include "force.h"
 #include "group.h"
-#include "pair.h"
 #include "kspace.h"
-#include "respa.h"
 #include "math_const.h"
-#include "error.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+#include "pair.h"
+#include "respa.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>

 using namespace LAMMPS_NS;
 using namespace MathConst;
@ -207,14 +208,9 @@ void FixQEqSlater::compute_H()
    chizj[i] = zjtmp;
  }

-  if (m_fill >= H.m) {
-    char str[128];
-    sprintf(str,"H matrix size has been exceeded: m_fill=%d H.m=%d\n",
-             m_fill, H.m );
-    error->warning(FLERR,str);
-    error->all(FLERR,"Fix qeq/slater has insufficient QEq matrix size");
-  }
-
+  if (m_fill >= H.m)
+    error->all(FLERR,fmt::format(FLERR,"Fix qeq/slater has insufficient H "
+                                 "matrix size:m_fill={} H.m={}\n",m_fill,H.m));
 }

 /* ---------------------------------------------------------------------- */
--- a/src/REPLICA/hyper.cpp
+++ b/src/REPLICA/hyper.cpp
@ -38,7 +38,7 @@ enum{NOHYPER,GLOBAL,LOCAL};

 /* ---------------------------------------------------------------------- */

-Hyper::Hyper(LAMMPS *lmp) : Pointers(lmp), dumplist(nullptr) {}
+Hyper::Hyper(LAMMPS *lmp) : Command(lmp), dumplist(nullptr) {}

 /* ----------------------------------------------------------------------
   perform hyperdynamics simulation
--- a/src/REPLICA/hyper.h
+++ b/src/REPLICA/hyper.h
@ -20,11 +20,11 @@ CommandStyle(hyper,Hyper)
 #ifndef LMP_HYPER_H
 #define LMP_HYPER_H

-#include "pointers.h"
+#include "command.h"

 namespace LAMMPS_NS {

-class Hyper : protected Pointers {
+class Hyper : public Command {
 public:
  Hyper(class LAMMPS *);
  ~Hyper() {}
--- a/src/REPLICA/neb.cpp
+++ b/src/REPLICA/neb.cpp
@ -42,7 +42,7 @@ using namespace MathConst;

 /* ---------------------------------------------------------------------- */

-NEB::NEB(LAMMPS *lmp) : Pointers(lmp), all(nullptr), rdist(nullptr) {}
+NEB::NEB(LAMMPS *lmp) : Command(lmp), all(nullptr), rdist(nullptr) {}

 /* ----------------------------------------------------------------------
   internal NEB constructor, called from TAD
@ -50,7 +50,7 @@ NEB::NEB(LAMMPS *lmp) : Pointers(lmp), all(nullptr), rdist(nullptr) {}

 NEB::NEB(LAMMPS *lmp, double etol_in, double ftol_in, int n1steps_in,
         int n2steps_in, int nevery_in, double *buf_init, double *buf_final)
-  : Pointers(lmp), all(nullptr), rdist(nullptr)
+  : Command(lmp), all(nullptr), rdist(nullptr)
 {
  double delx,dely,delz;

--- a/src/REPLICA/neb.h
+++ b/src/REPLICA/neb.h
@ -20,11 +20,11 @@ CommandStyle(neb,NEB)
 #ifndef LMP_NEB_H
 #define LMP_NEB_H

-#include "pointers.h"
+#include "command.h"

 namespace LAMMPS_NS {

-class NEB : protected Pointers {
+class NEB : public Command {
 public:
  NEB(class LAMMPS *);
  NEB(class LAMMPS *, double, double, int, int, int, double *, double *);
--- a/src/REPLICA/prd.cpp
+++ b/src/REPLICA/prd.cpp
@ -46,7 +46,7 @@ enum{SINGLE_PROC_DIRECT,SINGLE_PROC_MAP,MULTI_PROC};

 /* ---------------------------------------------------------------------- */

-PRD::PRD(LAMMPS *lmp) : Pointers(lmp) {}
+PRD::PRD(LAMMPS *lmp) : Command(lmp) {}

 /* ----------------------------------------------------------------------
   perform PRD simulation on one or more replicas
--- a/src/REPLICA/prd.h
+++ b/src/REPLICA/prd.h
@ -20,11 +20,11 @@ CommandStyle(prd,PRD)
 #ifndef LMP_PRD_H
 #define LMP_PRD_H

-#include "pointers.h"
+#include "command.h"

 namespace LAMMPS_NS {

-class PRD : protected Pointers {
+class PRD : public Command {
 public:
  PRD(class LAMMPS *);
  ~PRD() {}
--- a/src/REPLICA/tad.cpp
+++ b/src/REPLICA/tad.cpp
@ -43,7 +43,7 @@ using namespace LAMMPS_NS;

 /* ---------------------------------------------------------------------- */

-TAD::TAD(LAMMPS *lmp) : Pointers(lmp) {}
+TAD::TAD(LAMMPS *lmp) : Command(lmp) {}

 /* ---------------------------------------------------------------------- */

--- a/src/REPLICA/tad.h
+++ b/src/REPLICA/tad.h
@ -20,11 +20,11 @@ CommandStyle(tad,TAD)
 #ifndef LMP_TAD_H
 #define LMP_TAD_H

-#include "pointers.h"
+#include "command.h"

 namespace LAMMPS_NS {

-class TAD : protected Pointers {
+class TAD : public Command {
 public:
  TAD(class LAMMPS *);
  ~TAD();
--- a/src/REPLICA/temper.cpp
+++ b/src/REPLICA/temper.cpp
@ -40,7 +40,7 @@ using namespace LAMMPS_NS;

 /* ---------------------------------------------------------------------- */

-Temper::Temper(LAMMPS *lmp) : Pointers(lmp) {}
+Temper::Temper(LAMMPS *lmp) : Command(lmp) {}

 /* ---------------------------------------------------------------------- */

--- a/src/REPLICA/temper.h
+++ b/src/REPLICA/temper.h
@ -20,11 +20,11 @@ CommandStyle(temper,Temper)
 #ifndef LMP_TEMPER_H
 #define LMP_TEMPER_H

-#include "pointers.h"
+#include "command.h"

 namespace LAMMPS_NS {

-class Temper : protected Pointers {
+class Temper : public Command {
 public:
  Temper(class LAMMPS *);
  ~Temper();
--- a/src/SPIN/fix_nve_spin.cpp
+++ b/src/SPIN/fix_nve_spin.cpp
@ -507,11 +507,23 @@ void FixNVESpin::sectoring()
 {
  int sec[3];
  double sublo[3],subhi[3];
-  double* sublotmp = domain->sublo;
-  double* subhitmp = domain->subhi;
-  for (int dim = 0 ; dim < 3 ; dim++) {
-    sublo[dim]=sublotmp[dim];
-    subhi[dim]=subhitmp[dim];
+
+  if (domain->triclinic == 1){
+     double* sublotmp = domain->sublo_lamda;
+     double* subhitmp = domain->subhi_lamda;
+     for (int dim = 0 ; dim < 3 ; dim++) {
+       sublo[dim]=sublotmp[dim]*domain->boxhi[dim];
+       subhi[dim]=subhitmp[dim]*domain->boxhi[dim];
+     }
+  }
+
+  else {
+     double* sublotmp = domain->sublo;
+     double* subhitmp = domain->subhi;
+     for (int dim = 0 ; dim < 3 ; dim++) {
+       sublo[dim]=sublotmp[dim];
+       subhi[dim]=subhitmp[dim];
+     }
  }

  const double rsx = subhi[0] - sublo[0];
--- a/src/SPIN/neb_spin.cpp
+++ b/src/SPIN/neb_spin.cpp
@ -67,7 +67,7 @@ static const char cite_neb_spin[] =

 /* ---------------------------------------------------------------------- */

-NEBSpin::NEBSpin(LAMMPS *lmp) : Pointers(lmp) {
+NEBSpin::NEBSpin(LAMMPS *lmp) : Command(lmp) {
  if (lmp->citeme) lmp->citeme->add(cite_neb_spin);
 }

--- a/src/SPIN/neb_spin.h
+++ b/src/SPIN/neb_spin.h
@ -20,11 +20,11 @@ CommandStyle(neb/spin,NEBSpin)
 #ifndef LMP_NEB_SPIN_H
 #define LMP_NEB_SPIN_H

-#include "pointers.h"
+#include "command.h"

 namespace LAMMPS_NS {

-class NEBSpin : protected Pointers {
+class NEBSpin : public Command {
 public:
  NEBSpin(class LAMMPS *);
  ~NEBSpin();
--- a/src/SPIN/pair_spin_exchange_biquadratic.cpp
+++ b/src/SPIN/pair_spin_exchange_biquadratic.cpp
@ -393,7 +393,7 @@ void PairSpinExchangeBiquadratic::compute_exchange(int i, int j, double rsq,
  jtype = type[j];

  r2j = rsq/J3[itype][jtype]/J3[itype][jtype];
-  r2k = rsq/J3[itype][jtype]/J3[itype][jtype];
+  r2k = rsq/K3[itype][jtype]/K3[itype][jtype];

  Jex = 4.0*J1_mag[itype][jtype]*r2j;
  Jex *= (1.0-J2[itype][jtype]*r2j);
--- a/src/USER-COLVARS/group_ndx.h
+++ b/src/USER-COLVARS/group_ndx.h
@ -22,13 +22,13 @@ CommandStyle(group2ndx,Group2Ndx)
 #ifndef LMP_GROUP_NDX_H
 #define LMP_GROUP_NDX_H

-#include "pointers.h"
+#include "command.h"

 namespace LAMMPS_NS {

-class Group2Ndx : protected Pointers {
+class Group2Ndx : public Command {
 public:
-  Group2Ndx(class LAMMPS *lmp) : Pointers(lmp) {};
+  Group2Ndx(class LAMMPS *lmp) : Command(lmp) {};
  void command(int, char **);
 private:
  void write_group(FILE *, int);
--- a/src/USER-COLVARS/ndx_group.h
+++ b/src/USER-COLVARS/ndx_group.h
@ -22,15 +22,16 @@ CommandStyle(ndx2group,Ndx2Group)
 #ifndef LMP_NDX_GROUP_H
 #define LMP_NDX_GROUP_H

-#include "pointers.h"
+#include "command.h"
 #include <vector>

 namespace LAMMPS_NS {

-class Ndx2Group : protected Pointers {
+class Ndx2Group : public Command {
 public:
-  Ndx2Group(class LAMMPS *lmp) : Pointers(lmp) {};
+  Ndx2Group(class LAMMPS *lmp) : Command(lmp) {};
  void command(int, char **);
+ private:
  void create(const std::string &, const std::vector<tagint> &);
 };

--- a/src/USER-MISC/fix_srp.cpp
+++ b/src/USER-MISC/fix_srp.cpp
@ -128,20 +128,10 @@ void FixSRP::init()
  // bond particles do not interact with other types
  // type bptype only interacts with itself

-  char* arg1[4];
-  arg1[0] = (char *) "exclude";
-  arg1[1] = (char *) "type";
-  char c0[20];
-  char c1[20];
-
  for (int z = 1; z < atom->ntypes; z++) {
    if (z == bptype)
      continue;
-    sprintf(c0, "%d", z);
-    arg1[2] = c0;
-    sprintf(c1, "%d", bptype);
-    arg1[3] = c1;
-    neighbor->modify_params(4, arg1);
+    neighbor->modify_params(fmt::format("exclude type {} {}",z,bptype));
  }
 }

--- a/src/USER-MISC/temper_grem.cpp
+++ b/src/USER-MISC/temper_grem.cpp
@ -40,7 +40,7 @@ using namespace LAMMPS_NS;

 /* ---------------------------------------------------------------------- */

-TemperGrem::TemperGrem(LAMMPS *lmp) : Pointers(lmp) {}
+TemperGrem::TemperGrem(LAMMPS *lmp) : Command(lmp) {}

 /* ---------------------------------------------------------------------- */

--- a/src/USER-MISC/temper_grem.h
+++ b/src/USER-MISC/temper_grem.h
@ -20,11 +20,11 @@ CommandStyle(temper/grem,TemperGrem)
 #ifndef LMP_TEMPER_GREM_H
 #define LMP_TEMPER_GREM_H

-#include "pointers.h"
+#include "command.h"

 namespace LAMMPS_NS {

-class TemperGrem : protected Pointers {
+class TemperGrem : public Command {
 public:
  TemperGrem(class LAMMPS *);
  ~TemperGrem();
--- a/src/USER-MISC/temper_npt.cpp
+++ b/src/USER-MISC/temper_npt.cpp
@ -42,7 +42,7 @@ using namespace LAMMPS_NS;

 /* ---------------------------------------------------------------------- */

-TemperNPT::TemperNPT(LAMMPS *lmp) : Pointers(lmp) {}
+TemperNPT::TemperNPT(LAMMPS *lmp) : Command(lmp) {}

 /* ---------------------------------------------------------------------- */

--- a/src/USER-MISC/temper_npt.h
+++ b/src/USER-MISC/temper_npt.h
@ -21,11 +21,11 @@ CommandStyle(temper/npt,TemperNPT)
 #ifndef LMP_TEMPERNPT_H
 #define LMP_TEMPERNPT_H

-#include "pointers.h"
+#include "command.h"

 namespace LAMMPS_NS {

-class TemperNPT : protected Pointers {
+class TemperNPT : public Command {
 public:
  TemperNPT(class LAMMPS *);
  ~TemperNPT();
--- a/src/USER-PACE/README
+++ b/src/USER-PACE/README
@ -1,23 +1,23 @@
-The USER-PACE package provides the pace pair style, 
-an efficient implementation of the Atomic Cluster Expansion 
+The USER-PACE package provides the pace pair style,
+an efficient implementation of the Atomic Cluster Expansion
 potential (ACE).

-ACE is a methodology for deriving a highly accurate classical 
-potential fit to a large archive of quantum mechanical (DFT) data. 
+ACE is a methodology for deriving a highly accurate classical
+potential fit to a large archive of quantum mechanical (DFT) data.
 This package was written by Yury Lysogorskiy and others
-at ICAMS, the Interdisciplinary Centre for Advanced Materials Simulation, 
+at ICAMS, the Interdisciplinary Centre for Advanced Materials Simulation,
 Ruhr University Bochum, Germany (http://www.icams.de).

-This package requires a library that can be downloaded and built 
-in lib/pace or somewhere else, which must be done before building 
-LAMMPS with this package. Details of the download, build, and 
-install process for this package using traditional make (not CMake) 
+This package requires a library that can be downloaded and built
+in lib/pace or somewhere else, which must be done before building
+LAMMPS with this package. Details of the download, build, and
+install process for this package using traditional make (not CMake)
 are given in the lib/pace/README file, and scripts are
 provided to help automate the process.  Also see the LAMMPS manual for
 general information on building LAMMPS with external libraries
 using either traditional make or CMake.

-More information about the USER-PACE implementation of ACE 
+More information about the USER-PACE implementation of ACE
 is available here:

 https://github.com/ICAMS/lammps-user-pace
--- a/src/USER-PHONON/dynamical_matrix.cpp
+++ b/src/USER-PHONON/dynamical_matrix.cpp
@ -32,7 +32,7 @@ enum{REGULAR,ESKM};

 /* ---------------------------------------------------------------------- */

-DynamicalMatrix::DynamicalMatrix(LAMMPS *lmp) : Pointers(lmp), fp(nullptr)
+DynamicalMatrix::DynamicalMatrix(LAMMPS *lmp) : Command(lmp), fp(nullptr)
 {
    external_force_clear = 1;
 }
--- a/src/USER-PHONON/dynamical_matrix.h
+++ b/src/USER-PHONON/dynamical_matrix.h
@ -11,62 +11,62 @@ CommandStyle(dynamical_matrix,DynamicalMatrix)
 #ifndef LMP_DYNAMICAL_MATRIX_H
 #define LMP_DYNAMICAL_MATRIX_H

-#include "pointers.h"
+#include "command.h"

 namespace LAMMPS_NS {

-    class DynamicalMatrix : protected Pointers {
-    public:
-        DynamicalMatrix(class LAMMPS *);
-        virtual ~DynamicalMatrix();
-        void command(int, char **);
-        void setup();
+class DynamicalMatrix : public Command {
+ public:
+  DynamicalMatrix(class LAMMPS *);
+  virtual ~DynamicalMatrix();
+  void command(int, char **);
+  void setup();

-    protected:
-        int eflag,vflag;            // flags for energy/virial computation
-        int external_force_clear;   // clear forces locally or externally
+ protected:
+  int eflag,vflag;            // flags for energy/virial computation
+  int external_force_clear;   // clear forces locally or externally


-        int triclinic;              // 0 if domain is orthog, 1 if triclinic
-        int pairflag;
+  int triclinic;              // 0 if domain is orthog, 1 if triclinic
+  int pairflag;

-        int pair_compute_flag;            // 0 if pair->compute is skipped
-        int kspace_compute_flag;          // 0 if kspace->compute is skipped
+  int pair_compute_flag;            // 0 if pair->compute is skipped
+  int kspace_compute_flag;          // 0 if kspace->compute is skipped

-        int nvec;                   // local atomic dof = length of xvec
+  int nvec;                   // local atomic dof = length of xvec

-        void update_force();
-        void force_clear();
-        virtual void openfile(const char* filename);
+  void update_force();
+  void force_clear();
+  virtual void openfile(const char* filename);

-    private:
-        void options(int, char **);
-        void calculateMatrix();
-        void dynmat_clear(double **dynmat);
-        void create_groupmap();
-        void writeMatrix(double **dynmat);
-        void convert_units(const char *style);
-        void displace_atom(int local_idx, int direction, int magnitude);
+ private:
+  void options(int, char **);
+  void calculateMatrix();
+  void dynmat_clear(double **dynmat);
+  void create_groupmap();
+  void writeMatrix(double **dynmat);
+  void convert_units(const char *style);
+  void displace_atom(int local_idx, int direction, int magnitude);

-        double conversion;
-        double conv_energy;
-        double conv_distance;
-        double conv_mass;
-        double del;
-        int igroup,groupbit;
-        bigint gcount;             // number of atoms in group
-        bigint dynlen;             // rank of dynamical matrix
-        int scaleflag;
-        int me;
-        bigint *groupmap;
+  double conversion;
+  double conv_energy;
+  double conv_distance;
+  double conv_mass;
+  double del;
+  int igroup,groupbit;
+  bigint gcount;             // number of atoms in group
+  bigint dynlen;             // rank of dynamical matrix
+  int scaleflag;
+  int me;
+  bigint *groupmap;

-        int compressed;            // 1 if dump file is written compressed, 0 no
-        int binaryflag;            // 1 if dump file is written binary, 0 no
-        int file_opened;           // 1 if openfile method has been called, 0 no
-        int file_flag;             // 1 custom file name, 0 dynmat.dat
+  int compressed;            // 1 if dump file is written compressed, 0 no
+  int binaryflag;            // 1 if dump file is written binary, 0 no
+  int file_opened;           // 1 if openfile method has been called, 0 no
+  int file_flag;             // 1 custom file name, 0 dynmat.dat

-        FILE *fp;
-    };
+  FILE *fp;
+};
 }


--- a/src/USER-PHONON/third_order.cpp
+++ b/src/USER-PHONON/third_order.cpp
@ -32,7 +32,7 @@ enum{REGULAR,BALLISTICO};

 /* ---------------------------------------------------------------------- */

-ThirdOrder::ThirdOrder(LAMMPS *lmp) : Pointers(lmp), fp(nullptr)
+ThirdOrder::ThirdOrder(LAMMPS *lmp) : Command(lmp), fp(nullptr)
 {
  external_force_clear = 1;
 }
--- a/src/USER-PHONON/third_order.h
+++ b/src/USER-PHONON/third_order.h
@ -12,11 +12,11 @@ CommandStyle(third_order,ThirdOrder)
 #ifndef LMP_THIRD_ORDER_H
 #define LMP_THIRD_ORDER_H

-#include "pointers.h"
+#include "command.h"

 namespace LAMMPS_NS {

-  class ThirdOrder : protected Pointers {
+  class ThirdOrder : public Command {
   public:
    ThirdOrder(class LAMMPS *);
    virtual ~ThirdOrder();
--- a/src/balance.cpp
+++ b/src/balance.cpp
@ -51,7 +51,7 @@ enum{X,Y,Z};

 /* ---------------------------------------------------------------------- */

-Balance::Balance(LAMMPS *lmp) : Pointers(lmp)
+Balance::Balance(LAMMPS *lmp) : Command(lmp)
 {
  MPI_Comm_rank(world,&me);
  MPI_Comm_size(world,&nprocs);
--- a/src/balance.h
+++ b/src/balance.h
@ -20,11 +20,11 @@ CommandStyle(balance,Balance)
 #ifndef LMP_BALANCE_H
 #define LMP_BALANCE_H

-#include "pointers.h"
+#include "command.h"

 namespace LAMMPS_NS {

-class Balance : protected Pointers {
+class Balance : public Command {
 public:
  class RCB *rcb;
  class FixStore *fixstore;       // per-atom weights stored in FixStore
--- a/src/body.cpp
+++ b/src/body.cpp
@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */

 #include "body.h"
-#include <cstring>

 using namespace LAMMPS_NS;

--- a/src/change_box.cpp
+++ b/src/change_box.cpp
@ -35,7 +35,7 @@ enum{X=0,Y,Z,YZ,XZ,XY};

 /* ---------------------------------------------------------------------- */

-ChangeBox::ChangeBox(LAMMPS *lmp) : Pointers(lmp) {}
+ChangeBox::ChangeBox(LAMMPS *lmp) : Command(lmp) {}

 /* ---------------------------------------------------------------------- */

--- a/src/change_box.h
+++ b/src/change_box.h
@ -20,11 +20,11 @@ CommandStyle(change_box,ChangeBox)
 #ifndef LMP_CHANGE_BOX_H
 #define LMP_CHANGE_BOX_H

-#include "pointers.h"
+#include "command.h"

 namespace LAMMPS_NS {

-class ChangeBox : protected Pointers {
+class ChangeBox : public Command {
 public:
  ChangeBox(class LAMMPS *);
  void command(int, char **);
--- a/src/command.h
+++ b/src/command.h
@ -0,0 +1,29 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifndef LMP_COMMAND_H
+#define LMP_COMMAND_H
+
+#include "pointers.h"
+
+namespace LAMMPS_NS {
+
+class Command : protected Pointers {
+ public:
+  Command(class LAMMPS *lmp) : Pointers(lmp) {};
+  virtual void command(int, char **) = 0;
+};
+
+}
+
+#endif
--- a/src/compute.cpp
+++ b/src/compute.cpp
@ -22,7 +22,6 @@
 #include "modify.h"

 #include <cstring>
-#include <cctype>

 using namespace LAMMPS_NS;

--- a/src/compute_chunk_spread_atom.cpp
+++ b/src/compute_chunk_spread_atom.cpp
@ -23,6 +23,8 @@
 #include "modify.h"
 #include "update.h"

+#include <cstring>
+
 using namespace LAMMPS_NS;

 /* ---------------------------------------------------------------------- */
--- a/src/compute_reduce.cpp
+++ b/src/compute_reduce.cpp
@ -25,6 +25,8 @@
 #include "update.h"
 #include "variable.h"

+#include <cstring>
+
 using namespace LAMMPS_NS;

 #define BIG 1.0e20
--- a/src/compute_temp_region.cpp
+++ b/src/compute_temp_region.cpp
@ -13,15 +13,14 @@

 #include "compute_temp_region.h"

-#include <cstring>
 #include "atom.h"
-#include "update.h"
-#include "force.h"
 #include "domain.h"
-#include "region.h"
+#include "error.h"
+#include "force.h"
 #include "group.h"
 #include "memory.h"
-#include "error.h"
+#include "region.h"
+#include "update.h"

 using namespace LAMMPS_NS;

--- a/src/create_atoms.cpp
+++ b/src/create_atoms.cpp
@ -52,7 +52,7 @@ enum{NONE,RATIO,SUBSET};

 /* ---------------------------------------------------------------------- */

-CreateAtoms::CreateAtoms(LAMMPS *lmp) : Pointers(lmp), basistype(nullptr) {}
+CreateAtoms::CreateAtoms(LAMMPS *lmp) : Command(lmp), basistype(nullptr) {}

 /* ---------------------------------------------------------------------- */

--- a/src/create_atoms.h
+++ b/src/create_atoms.h
@ -20,11 +20,11 @@ CommandStyle(create_atoms,CreateAtoms)
 #ifndef LMP_CREATE_ATOMS_H
 #define LMP_CREATE_ATOMS_H

-#include "pointers.h"
+#include "command.h"

 namespace LAMMPS_NS {

-class CreateAtoms : protected Pointers {
+class CreateAtoms : public Command {
 public:
  CreateAtoms(class LAMMPS *);
  void command(int, char **);
--- a/src/create_bonds.cpp
+++ b/src/create_bonds.cpp
@ -38,7 +38,7 @@ enum{MANY,SBOND,SANGLE,SDIHEDRAL,SIMPROPER};

 /* ---------------------------------------------------------------------- */

-CreateBonds::CreateBonds(LAMMPS *lmp) : Pointers(lmp) {}
+CreateBonds::CreateBonds(LAMMPS *lmp) : Command(lmp) {}

 /* ---------------------------------------------------------------------- */

--- a/src/create_bonds.h
+++ b/src/create_bonds.h
@ -20,11 +20,11 @@ CommandStyle(create_bonds,CreateBonds)
 #ifndef LMP_CREATE_BONDS_H
 #define LMP_CREATE_BONDS_H

-#include "pointers.h"
+#include "command.h"

 namespace LAMMPS_NS {

-class CreateBonds : protected Pointers {
+class CreateBonds : public Command {
 public:
  CreateBonds(class LAMMPS *);
  void command(int, char **);
--- a/src/create_box.cpp
+++ b/src/create_box.cpp
@ -12,22 +12,24 @@
 ------------------------------------------------------------------------- */

 #include "create_box.h"
-#include <cstring>
+
 #include "atom.h"
 #include "atom_vec.h"
+#include "comm.h"
 #include "domain.h"
+#include "error.h"
+#include "force.h"
 #include "region.h"
 #include "region_prism.h"
-#include "force.h"
-#include "comm.h"
 #include "update.h"
-#include "error.h"
+
+#include <cstring>

 using namespace LAMMPS_NS;

 /* ---------------------------------------------------------------------- */

-CreateBox::CreateBox(LAMMPS *lmp) : Pointers(lmp) {}
+CreateBox::CreateBox(LAMMPS *lmp) : Command(lmp) {}

 /* ---------------------------------------------------------------------- */

--- a/src/create_box.h
+++ b/src/create_box.h
@ -20,11 +20,11 @@ CommandStyle(create_box,CreateBox)
 #ifndef LMP_CREATE_BOX_H
 #define LMP_CREATE_BOX_H

-#include "pointers.h"
+#include "command.h"

 namespace LAMMPS_NS {

-class CreateBox : protected Pointers {
+class CreateBox : public Command {
 public:
  CreateBox(class LAMMPS *);
  void command(int, char **);
--- a/src/delete_atoms.cpp
+++ b/src/delete_atoms.cpp
@ -41,7 +41,7 @@ using namespace LAMMPS_NS;

 /* ---------------------------------------------------------------------- */

-DeleteAtoms::DeleteAtoms(LAMMPS *lmp) : Pointers(lmp) {}
+DeleteAtoms::DeleteAtoms(LAMMPS *lmp) : Command(lmp) {}

 /* ---------------------------------------------------------------------- */

--- a/src/delete_atoms.h
+++ b/src/delete_atoms.h
@ -20,12 +20,12 @@ CommandStyle(delete_atoms,DeleteAtoms)
 #ifndef LMP_DELETE_ATOMS_H
 #define LMP_DELETE_ATOMS_H

-#include "pointers.h"
+#include "command.h"
 #include <map>

 namespace LAMMPS_NS {

-class DeleteAtoms : protected Pointers {
+class DeleteAtoms : public Command {
 public:
  DeleteAtoms(class LAMMPS *);
  void command(int, char **);
--- a/Show More
+++ b/Show More