Merge branch 'clean-master2' of github.com:julient31/lammps into STT2

cmake/CMakeLists.txt

@@ -124,7 +124,7 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
   USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
   USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
   USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
-  USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF)
+  USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE)
 
 set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP)
 
@@ -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)
@@ -387,7 +388,7 @@ else()
 endif()
 
 foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM
-        USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS)
+        USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL}) 
   endif()
@@ -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}")

cmake/Modules/LAMMPSUtils.cmake

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

cmake/Modules/Packages/USER-PACE.cmake

@@ -0,0 +1,26 @@
+
+set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.4.9.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+set(PACELIB_MD5 "4db54962fbd6adcf8c18d46e1798ceb5" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+mark_as_advanced(PACELIB_URL)
+mark_as_advanced(PACELIB_MD5)
+
+# download library sources to build folder
+file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz SHOW_PROGRESS EXPECTED_HASH MD5=${PACELIB_MD5})
+
+# uncompress downloaded sources
+execute_process(
+  COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
+  COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
+  WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+)
+
+
+file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE)
+file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE/*.cpp)
+list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp)
+
+add_library(pace STATIC ${PACE_EVALUATOR_SOURCES})
+set_target_properties(pace PROPERTIES OUTPUT_NAME pace${LAMMPS_MACHINE})
+target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR})
+target_link_libraries(lammps PRIVATE pace)
+

cmake/Modules/Packages/USER-PLUMED.cmake

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

cmake/Modules/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.
+  # we need to build and link a LOT of tester executables, so it is worth checking if
-  # only verified with GNU and Clang compilers and new CMake
+  # a faster linker is available. requires GNU or Clang compiler, newer CMake.
-  if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
+  # also only verified with Fedora Linux > 30 and Ubuntu <= 18.04 (Ubuntu 20.04 fails)
-    if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
+  if((CMAKE_SYSTEM_NAME STREQUAL Linux) AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
-        OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
+      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)

doc/graphviz/lammps-classes.dot

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

doc/src/Build_extras.rst

@@ -52,6 +52,7 @@ This is the list of packages that may require additional steps.
    * :ref:`USER-MESONT <user-mesont>`
    * :ref:`USER-MOLFILE <user-molfile>`
    * :ref:`USER-NETCDF <user-netcdf>`
+   * :ref:`USER-PACE <user-pace>`
    * :ref:`USER-PLUMED <user-plumed>`
    * :ref:`USER-OMP <user-omp>`
    * :ref:`USER-QMMM <user-qmmm>`
@@ -1247,6 +1248,46 @@ be built for the most part with all major versions of the C++ language.
 
 ----------
 
+.. _user-pace:
+
+USER-PACE package
+-----------------------------
+
+This package requires a library that can be downloaded and built
+in lib/pace or somewhere else, which must be done before building
+LAMMPS with this package. The code for the library can be found
+at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps-user-pace/>`_
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      By default the library will be downloaded from the git repository
+      and built automatically when the USER-PACE package is enabled with
+      ``-D PKG_USER-PACE=yes``.  The location for the sources may be
+      customized by setting the variable ``PACELIB_URL`` when
+      configuring with CMake (e.g. to use a local archive on machines
+      without internet access).  Since CMake checks the validity of the
+      archive with ``md5sum`` you may also need to set ``PACELIB_MD5``
+      if you provide a different library version than what is downloaded
+      automatically.
+
+
+   .. tab:: Traditional make
+
+      You can download and build the USER-PACE library
+      in one step from the ``lammps/src`` dir, using these commands,
+      which invoke the ``lib/pace/Install.py`` script.
+
+      .. code-block:: bash
+
+         $ make lib-pace                          # print help message
+         $ make lib-pace args="-b"                # download and build the default version in lib/pace
+
+      You should not need to edit the ``lib/pace/Makefile.lammps`` file.
+
+----------
+
 .. _user-plumed:
 
 USER-PLUMED package

doc/src/Build_package.rst

@@ -30,17 +30,17 @@ steps, as explained on the :doc:`Build extras <Build_extras>` page.
 These links take you to the extra instructions for those select
 packages:
 
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
 | :ref:`COMPRESS <compress>`           | :ref:`GPU <gpu>`               | :ref:`KIM <kim>`                   | :ref:`KOKKOS <kokkos>`       | :ref:`LATTE <latte>`           | :ref:`MESSAGE <message>`             |
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
 | :ref:`MSCG <mscg>`                   | :ref:`OPT <opt>`               | :ref:`POEMS <poems>`               | :ref:`PYTHON <python>`       | :ref:`VORONOI <voronoi>`       | :ref:`USER-ADIOS <user-adios>`       |
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
 | :ref:`USER-ATC <user-atc>`           | :ref:`USER-AWPMD <user-awpmd>` | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>` | :ref:`USER-INTEL <user-intel>` | :ref:`USER-MOLFILE <user-molfile>`   |
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
-| :ref:`USER-NETCDF <user-netcdf>` | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>`         | :ref:`USER-QMMM <user-qmmm>` | :ref:`USER-QUIP <user-quip>`   | :ref:`USER-SCAFACOS <user-scafacos>` |
+| :ref:`USER-NETCDF <user-netcdf>`     | :ref:`USER-PACE <user-pace>`   | :ref:`USER-PLUMED <user-plumed>`   | :ref:`USER-OMP <user-omp>`   | :ref:`USER-QMMM <user-qmmm>`   | :ref:`USER-QUIP <user-quip>`         |
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
-| :ref:`USER-SMD <user-smd>`       | :ref:`USER-VTK <user-vtk>`       |                                    |                              |                                |                                      |
+| :ref:`USER-SCAFACOS <user-scafacos>` | :ref:`USER-SMD <user-smd>`     | :ref:`USER-VTK <user-vtk>`         |                              |                                |                                      |
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
 
 The mechanism for including packages is simple but different for CMake
 versus make.

doc/src/Commands_fix.rst

@@ -46,6 +46,7 @@ OPT.
    * :doc:`bond/react <fix_bond_react>`
    * :doc:`bond/swap <fix_bond_swap>`
    * :doc:`box/relax <fix_box_relax>`
+   * :doc:`charge/regulation <fix_charge_regulation>`
    * :doc:`client/md <fix_client_md>`
    * :doc:`cmap <fix_cmap>`
    * :doc:`colvars <fix_colvars>`

doc/src/Commands_pair.rst

@@ -216,6 +216,7 @@ OPT.
    * :doc:`oxrna2/stk <pair_oxrna2>`
    * :doc:`oxrna2/xstk <pair_oxrna2>`
    * :doc:`oxrna2/coaxstk <pair_oxrna2>`
+   * :doc:`pace <pair_pace>`
    * :doc:`peri/eps <pair_peri>`
    * :doc:`peri/lps (o) <pair_peri>`
    * :doc:`peri/pmb (o) <pair_peri>`

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
+are implemented with only a ``.h`` file. Examples are the Pointers and
-or the MathVec functions.
+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
+- Command style classes are derived from the Command class. They provide
-  the Pointers class. They provide input script commands that perform
+  input script commands that perform one-time operations
-  one-time operations before/after/between simulations or which invoke a
+  before/after/between simulations or which invoke a simulation.  They
-  simulation.  They are instantiated from within the Input class,
+  are usually instantiated from within the Input class, its ``command``
-  invoked, then immediately destructed.
+  method invoked, and then immediately destructed.
 
 - The Finish class is instantiated to print statistics to the screen
   after a simulation is performed, by commands like run and minimize.

doc/src/Developer_plugins.rst

@@ -59,31 +59,25 @@ Members of ``lammpsplugin_t``
    * - author
      - String with the name and email of the author
    * - creator.v1
-     - Pointer to factory function for pair, bond, angle, dihedral, or improper styles
+     - Pointer to factory function for pair, bond, angle, dihedral, improper or command styles
    * - creator.v2
      - Pointer to factory function for compute, fix, or region styles
-   * - creator.v3
-     - Pointer to factory function for command styles
    * - handle
      - Pointer to the open DSO file handle
 
 Only one of the three alternate creator entries can be used at a time
-and which of those is determined by the style of plugin. The "creator.v1"
+and which of those is determined by the style of plugin. The
-element is for factory functions of supported styles computing forces (i.e.
+"creator.v1" element is for factory functions of supported styles
-pair, bond, angle, dihedral, or improper styles) and the function takes
+computing forces (i.e.  command, pair, bond, angle, dihedral, or
-as single argument the pointer to the LAMMPS instance. The factory function
+improper styles) and the function takes as single argument the pointer
-is cast to the ``lammpsplugin_factory1`` type before assignment.  The
+to the LAMMPS instance. The factory function is cast to the
-"creator.v2" element is for factory functions creating an instance of
+``lammpsplugin_factory1`` type before assignment.  The "creator.v2"
-a fix, compute, or region style and takes three arguments: a pointer to
+element is for factory functions creating an instance of a fix, compute,
-the LAMMPS instance, an integer with the length of the argument list and
+or region style and takes three arguments: a pointer to the LAMMPS
-a ``char **`` pointer to the list of arguments. The factory function pointer
+instance, an integer with the length of the argument list and a ``char
-needs to be cast to the ``lammpsplugin_factory2`` type before assignment.
+**`` pointer to the list of arguments. The factory function pointer
-The "creator.v3" element takes the same arguments as "creator.v3" but is
+needs to be cast to the ``lammpsplugin_factory2`` type before
-specific to creating command styles: the factory function has to instantiate
+assignment.
-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.
 
 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
+be assigned to the *creator.v1* member of the plugin struct and cast to
-``lammpsplugin_factory1`` pointer type.  It returns a
+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.
+This function may be declared static to avoid clashes with other
-The name of the derived class, ``PairMorse2``, must be unique inside
+plugins.  The name of the derived class, ``PairMorse2``, however must be
-the entire LAMMPS executable.
+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);
+     return new Hello(lmp);
-     hello.command(argc,argv);
    }
 
    extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
@@ -216,9 +209,9 @@ file as the plugin interface code:
      plugin.version = LAMMPS_VERSION;
      plugin.style   = "command";
      plugin.name    = "hello";
-     plugin.info    = "Hello world command v1.0";
+     plugin.info    = "Hello world command v1.1";
      plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
-     plugin.creator.v3 = (lammpsplugin_factory3 *) &hellocreator;
+     plugin.creator.v1 = (lammpsplugin_factory1 *) &hellocreator;
      plugin.handle  = handle;
      (*register_plugin)(&plugin,lmp);
    }

doc/src/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
+torque can be an external magnetic field (Zeeman interaction), and an
-uniaxial magnetic anisotropy.
+uniaxial or cubic magnetic anisotropy.
 
 A Langevin thermostat can be applied to those magnetic spins using
 :doc:`fix langevin/spin <fix_langevin_spin>`. Typically, this thermostat

doc/src/Modify_command.rst

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

doc/src/Packages_details.rst

@@ -90,6 +90,7 @@ page gives those details.
    * :ref:`USER-MOLFILE <PKG-USER-MOLFILE>`
    * :ref:`USER-NETCDF <PKG-USER-NETCDF>`
    * :ref:`USER-OMP <PKG-USER-OMP>`
+   * :ref:`USER-PACE <PKG-USER-PACE>`
    * :ref:`USER-PHONON <PKG-USER-PHONON>`
    * :ref:`USER-PLUMED <PKG-USER-PLUMED>`
    * :ref:`USER-PTM <PKG-USER-PTM>`
@@ -585,7 +586,7 @@ MC package
 Several fixes and a pair style that have Monte Carlo (MC) or MC-like
 attributes.  These include fixes for creating, breaking, and swapping
 bonds, for performing atomic swaps, and performing grand-canonical MC
-(GCMC) in conjunction with dynamics.
+(GCMC) or similar processes in conjunction with dynamics.
 
 **Supporting info:**
 
@@ -593,8 +594,12 @@ bonds, for performing atomic swaps, and performing grand-canonical MC
 * :doc:`fix atom/swap <fix_atom_swap>`
 * :doc:`fix bond/break <fix_bond_break>`
 * :doc:`fix bond/create <fix_bond_create>`
+* :doc:`fix bond/create/angle <fix_bond_create>`
 * :doc:`fix bond/swap <fix_bond_swap>`
+* :doc:`fix charge/regulation <fix_charge_regulation>`
 * :doc:`fix gcmc <fix_gcmc>`
+* :doc:`fix tfmc <fix_tfmc>`
+* :doc:`fix widom <fix_widom>`
 * :doc:`pair_style dsmc <pair_dsmc>`
 * https://lammps.sandia.gov/movies.html#gcmc
 
@@ -1349,6 +1354,46 @@ This package has :ref:`specific installation instructions <user-colvars>` on the
 
 ----------
 
+.. _PKG-USER-PACE:
+
+USER-PACE package
+-------------------
+
+**Contents:**
+
+A pair style for the Atomic Cluster Expansion potential (ACE).
+ACE is a methodology for deriving a highly accurate classical potential
+fit to a large archive of quantum mechanical (DFT) data. The USER-PACE
+package provides an efficient implementation for running simulations
+with ACE potentials.
+
+**Authors:**
+
+This package was written by Yury Lysogorskiy^1,
+Cas van der Oord^2, Anton Bochkarev^1,
+Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
+Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1.
+
+ ^1: Ruhr-University Bochum, Bochum, Germany
+
+ ^2: University of Cambridge, Cambridge, United Kingdom
+
+ ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
+
+ ^4: University of British Columbia, Vancouver, BC, Canada
+
+**Install:**
+
+This package has :ref:`specific installation instructions <user-pace>` on the :doc:`Build extras <Build_extras>` page.
+
+**Supporting info:**
+
+* src/USER-PACE: filenames -> commands
+* :doc:`pair_style pace <pair_pace>`
+* examples/USER/pace
+
+----------
+
 .. _PKG-USER-PLUMED:
 
 USER-PLUMED package

doc/src/Packages_user.rst

@@ -81,6 +81,8 @@ package:
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-OMP <PKG-USER-OMP>`                 | OpenMP-enabled styles                                           | :doc:`Speed omp <Speed_omp>`                                                  | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
+| :ref:`USER-PACE <PKG-USER-PACE>`               | Fast implementation of Atomic Cluster Expansion (ACE) potential | :doc:`pair pace <pair_pace>`                                                  | USER/pace                                            | ext     |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-PHONON <PKG-USER-PHONON>`           | phonon dynamical matrix                                         | :doc:`fix phonon <fix_phonon>`                                                | USER/phonon                                          | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-PLUMED <PKG-USER-PLUMED>`           | :ref:`PLUMED <PLUMED>` free energy library                      | :doc:`fix plumed <fix_plumed>`                                                | USER/plumed                                          | ext     |

doc/src/atom_style.rst

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

doc/src/dump_modify.rst

@@ -308,8 +308,8 @@ performed with dump style *xtc*\ .
 
 ----------
 
-The *format* keyword can be used to change the default numeric format
+The *format* keyword can be used to change the default numeric format output
-output by the text-based dump styles: *atom*\ , *custom*\ , *cfg*\ , and
+by the text-based dump styles: *atom*\ , *local*\ , *custom*\ , *cfg*\ , and
 *xyz* styles, and their MPIIO variants. Only the *line* or *none*
 options can be used with the *atom* and *xyz* styles.
 
@@ -362,7 +362,7 @@ settings, reverting all values to their default format.
 
    compute     1 all property/local batom1 batom2
    dump        1 all local 100 tmp.bonds index c_1[1] c_1[2]
-   dump_modify 1 format "%d %0.0f %0.0f"
+   dump_modify 1 format line "%d %0.0f %0.0f"
 
 will output the two atom IDs for atoms in each bond as integers.  If
 the dump_modify command were omitted, they would appear as

doc/src/fix.rst

@@ -189,6 +189,7 @@ accelerated styles exist.
 * :doc:`bond/react <fix_bond_react>` - apply topology changes to model reactions
 * :doc:`bond/swap <fix_bond_swap>` - Monte Carlo bond swapping
 * :doc:`box/relax <fix_box_relax>` - relax box size during energy minimization
+* :doc:`charge/regulation <fix_charge_regulation>` - Monte Carlo sampling of charge regulation
 * :doc:`client/md <fix_client_md>` - MD client for client/server simulations
 * :doc:`cmap <fix_cmap>` - enables CMAP cross-terms of the CHARMM force field
 * :doc:`colvars <fix_colvars>` - interface to the collective variables "Colvars" library

doc/src/fix_charge_regulation.rst

@@ -0,0 +1,276 @@
+
+.. index:: fix charge/regulation
+
+fix charge/regulation command
+=============================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+    fix ID group-ID charge/regulation cation_type anion_type keyword value(s)
+
+* ID, group-ID are documented in fix command
+* charge/regulation = style name of this fix command
+* cation_type = atom type of free cations
+* anion_type = atom type of free anions
+
+* zero or more keyword/value pairs may be appended
+
+  .. parsed-literal::
+
+     keyword = *pH*, *pKa*, *pKb*, *pIp*, *pIm*, *pKs*, *acid_type*, *base_type*, *lunit_nm*, *temp*, *tempfixid*, *nevery*, *nmc*, *xrd*, *seed*, *tag*, *group*, *onlysalt*, *pmcmoves*
+     *pH* value = pH of the solution
+     *pKa* value = acid dissociation constant
+     *pKb* value = base dissociation constant
+     *pIp* value = chemical potential of free cations
+     *pIm* value = chemical potential of free anions
+     *pKs* value = solution self-dissociation constant
+     *acid_type* = atom type of acid groups
+     *base_type*  = atom type of base groups
+     *lunit_nm* value = unit length used by LAMMPS (# in the units of nanometers)
+     *temp* value = temperature
+     *tempfixid* value = fix ID of temperature thermostat
+     *nevery* value = invoke this fix every nevery steps
+     *nmc* value = number of charge regulation MC moves to attempt every nevery steps
+     *xrd* value = cutoff distance for acid/base reaction
+     *seed* value = random # seed (positive integer)
+     *tag* value = yes or no (yes: The code assign unique tags to inserted ions; no: The tag of all inserted ions is "0")
+     *group* value = group-ID, inserted ions are assigned to group group-ID. Can be used multiple times to assign inserted ions to multiple groups.
+     *onlysalt* values = flag charge_cation charge_anion.
+        flag = yes or no (yes: the fix performs only ion insertion/deletion, no: perform acid/base dissociation and ion insertion/deletion)
+        charge_cation, charge_anion = value of cation/anion charge, must be an integer (only specify if flag = yes)
+     *pmcmoves* values = pmcA pmcB pmcI -  MC move fractions for acid ionization (pmcA), base ionization (pmcB) and free ion exchange (pmcI)
+
+Examples
+""""""""
+.. code-block:: LAMMPS
+
+    fix chareg all charge/regulation 1 2 acid_type 3 base_type 4 pKa 5 pKb 7 lb 1.0 nevery 200 nexchange 200 seed 123 tempfixid fT
+
+    fix chareg all charge/regulation 1 2 pIp 3 pIm 3 onlysalt yes 2 -1 seed 123 tag yes temp 1.0
+
+Description
+"""""""""""
+
+This fix performs Monte Carlo (MC) sampling of charge regulation and
+exchange of ions with a reservoir as discussed in :ref:`(Curk1) <Curk1>`
+and :ref:`(Curk2) <Curk2>`.  The implemented method is largely analogous
+to the grand-reaction ensemble method in :ref:`(Landsgesell)
+<Landsgesell>`.  The implementation is parallelized, compatible with
+existing LAMMPS functionalities, and applicable to any system utilizing
+discrete, ionizable groups or surface sites.
+
+Specifically, the fix implements the following three types of MC moves,
+which discretely change the charge state of individual particles and
+insert ions into the systems: :math:`\mathrm{A} \rightleftharpoons
+\mathrm{A}^-+\mathrm{X}^+`, :math:`\mathrm{B} \rightleftharpoons
+\mathrm{B}^++\mathrm{X}^-`, and :math:`\emptyset \rightleftharpoons
+Z^-\mathrm{X}^{Z^+}+Z^+\mathrm{X}^{-Z^-}`.  In the former two types of
+reactions, Monte Carlo moves alter the charge value of specific atoms
+(:math:`\mathrm{A}`, :math:`\mathrm{B}`) and simultaneously insert a
+counterion to preserve the charge neutrality of the system, modeling the
+dissociation/association process.  The last type of reaction performs
+grand canonical MC exchange of ion pairs with a (fictitious) reservoir.
+
+In our implementation "acid" refers to particles that can attain charge
+:math:`q=\{0,-1\}` and "base" to particles with :math:`q=\{0,1\}`,
+whereas the MC exchange of free ions allows any integer charge values of
+:math:`{Z^+}` and :math:`{Z^-}`.
+
+Here we provide several practical examples for modeling charge
+regulation effects in solvated systems.  An acid ionization reaction
+(:math:`\mathrm{A} \rightleftharpoons \mathrm{A}^-+\mathrm{H}^+`) can be
+defined via a single line in the input file
+
+.. code-block:: LAMMPS
+
+    fix acid_reaction all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 5.0 pIp 7.0 pIm 7.0
+
+where the fix attempts to charge :math:`\mathrm{A}` (discharge
+:math:`\mathrm{A}^-`) to :math:`\mathrm{A}^-` (:math:`\mathrm{A}`) and
+insert (delete) a proton (atom type 2). Besides, the fix implements
+self-ionization reaction of water :math:`\emptyset \rightleftharpoons
+\mathrm{H}^++\mathrm{OH}^-`.  However, this approach is highly
+inefficient at :math:`\mathrm{pH} \approx 7` when the concentration of
+both protons and hydroxyl ions is low, resulting in a relatively low
+acceptance rate of MC moves.
+
+A more efficient way is to allow salt ions to participate in ionization
+reactions, which can be easily achieved via
+
+.. code-block:: LAMMPS
+
+    fix acid_reaction all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 5.0 pIp 2.0 pIm 2.0
+
+where particles of atom type 4 and 5 are the salt cations and anions,
+both at chemical potential pI=2.0, see :ref:`(Curk1) <Curk1>` and
+:ref:`(Landsgesell) <Landsgesell>` for more details.
+
+
+ Similarly, we could have simultaneously added a base ionization reaction
+ (:math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{OH}^-`)
+
+.. code-block:: LAMMPS
+
+    fix base_reaction all charge/regulation 2 3 base_type 6 pH 7.0 pKb 6.0 pIp 7.0 pIm 7.0
+
+where the fix will attempt to charge :math:`\mathrm{B}` (discharge
+:math:`\mathrm{B}^+`) to :math:`\mathrm{B}^+` (:math:`\mathrm{B}`) and
+insert (delete) a hydroxyl ion :math:`\mathrm{OH}^-` of atom type 3.  If
+neither the acid or the base type is specified, for example,
+
+.. code-block:: LAMMPS
+
+    fix salt_reaction all charge/regulation 4 5 pIp 2.0 pIm 2.0
+
+the fix simply inserts or deletes an ion pair of a free cation (atom
+type 4) and a free anion (atom type 5) as done in a conventional
+grand-canonical MC simulation.
+
+
+The fix is compatible with LAMMPS sub-packages such as *molecule* or
+*rigid*. That said, the acid and base particles can be part of larger
+molecules or rigid bodies. Free ions that are inserted to or deleted
+from the system must be defined as single particles (no bonded
+interactions allowed) and cannot be part of larger molecules or rigid
+bodies. If *molecule* package is used, all inserted ions have a molecule
+ID equal to zero.
+
+Note that LAMMPS implicitly assumes a constant number of particles
+(degrees of freedom). Since using this fix alters the total number of
+particles during the simulation, any thermostat used by LAMMPS, such as
+NVT or Langevin, must use a dynamic calculation of system
+temperature. This can be achieved by specifying a dynamic temperature
+compute (e.g. dtemp) and using it with the desired thermostat, e.g. a
+Langevin thermostat:
+
+.. code-block:: LAMMPS
+
+    compute dtemp all temp
+    compute_modify dtemp dynamic yes
+    fix fT all langevin 1.0 1.0 1.0 123
+    fix_modify fT temp dtemp
+
+The chemical potential units (e.g. pH) are in the standard log10
+representation assuming reference concentration :math:`\rho_0 =
+\mathrm{mol}/\mathrm{l}`.  Therefore, to perform the internal unit
+conversion, the length (in nanometers) of the LAMMPS unit length must be
+specified via *lunit_nm* (default is set to the Bjerrum length in water
+at room temperature *lunit_nm* = 0.71nm). For example, in the dilute
+ideal solution limit, the concentration of free ions will be
+:math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`.
+
+The temperature used in MC acceptance probability is set by *temp*. This
+temperature should be the same as the temperature set by the molecular
+dynamics thermostat. For most purposes, it is probably best to use
+*tempfixid* keyword which dynamically sets the temperature equal to the
+chosen MD thermostat temperature, in the example above we assumed the
+thermostat fix-ID is *fT*. The inserted particles attain a random
+velocity corresponding to the specified temperature. Using *tempfixid*
+overrides any fixed temperature set by *temp*.
+
+The *xrd* keyword can be used to restrict the inserted/deleted
+counterions to a specific radial distance from an acid or base particle
+that is currently participating in a reaction. This can be used to
+simulate more realist reaction dynamics. If *xrd* = 0 or *xrd* > *L* /
+2, where *L* is the smallest box dimension, the radial restriction is
+automatically turned off and free ion can be inserted or deleted
+anywhere in the simulation box.
+
+If the *tag yes* is used, every inserted atom gets a unique tag ID,
+otherwise, the tag of every inserted atom is set to 0. *tag yes* might
+cause an integer overflow in very long simulations since the tags are
+unique to every particle and thus increase with every successful
+particle insertion.
+
+The *pmcmoves* keyword sets the relative probability of attempting the
+three types of MC moves (reactions): acid charging, base charging, and
+ion pair exchange.  The fix only attempts to perform particle charging
+MC moves if *acid_type* or *base_type* is defined. Otherwise fix only
+performs free ion insertion/deletion. For example, if *acid_type* is not
+defined, *pmcA* is automatically set to 0. The vector *pmcmoves* is
+automatically normalized, for example, if set to *pmcmoves* 0 0.33 0.33,
+the vector would be normalized to [0,0.5,0.5].
+
+The *only_salt* option can be used to perform multivalent
+grand-canonical ion-exchange moves. If *only_salt yes* is used, no
+charge exchange is performed, only ion insertion/deletion (*pmcmoves* is
+set to [0,0,1]), but ions can be multivalent. In the example above, an
+MC move would consist of three ion insertion/deletion to preserve the
+charge neutrality of the system.
+
+The *group* keyword can be used to add inserted particles to a specific
+group-ID. All inserted particles are automatically added to group *all*.
+
+
+Output
+""""""
+
+This fix computes a global vector of length 8, which can be accessed by
+various output commands. The vector values are the following global
+quantities:
+
+* 1 = cumulative MC attempts
+* 2 = cumulative MC successes
+* 3 = current # of neutral acid atoms
+* 4 = current # of -1 charged acid atoms
+* 5 = current # of neutral base atoms
+* 6 = current # of +1 charged base atoms
+* 7 = current # of free cations
+* 8 = current # of free anions
+
+
+Restrictions
+""""""""""""
+
+This fix is part of the MC package. It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package
+<Build_package>` doc page for more info.
+
+The :doc:`atom_style <atom_style>`, used must contain the charge
+property, for example, the style could be *charge* or *full*. Only
+usable for 3D simulations. Atoms specified as free ions cannot be part
+of rigid bodies or molecules and cannot have bonding interactions. The
+scheme is limited to integer charges, any atoms with non-integer charges
+will not be considered by the fix.
+
+All interaction potentials used must be continuous, otherwise the MD
+integration and the particle exchange MC moves do not correspond to the
+same equilibrium ensemble. For example, if an lj/cut pair style is used,
+the LJ potential must be shifted so that it vanishes at the cutoff. This
+can be easily achieved using the :doc:`pair_modify <pair_modify>`
+command, i.e., by using: *pair_modify shift yes*.
+
+.. note::
+
+   Region restrictions are not yet implemented.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix gcmc <fix_gcmc>`,
+:doc:`fix atom/swap <fix_atom_swap>`
+
+Default
+"""""""
+
+pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs = 14.0;
+acid_type = -1; base_type = -1; lunit_nm = 0.71; temp = 1.0; nevery =
+100; nmc = 100; xrd = 0; seed = 0; tag = no; onlysalt = no, pmcmoves =
+[1/3, 1/3, 1/3], group-ID = all
+
+----------
+
+.. _Curk1:
+
+**(Curk1)** T. Curk, J. Yuan, and E. Luijten, "Coarse-grained simulation of charge regulation using LAMMPS", preprint (2021).
+
+.. _Curk2:
+
+**(Curk2)** T. Curk and E. Luijten, "Charge-regulation effects in nanoparticle self-assembly", PRL (2021)
+
+.. _Landsgesell:
+
+**(Landsgesell)** J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Kosovan, and C. Holm, "Grand-reaction method for simulations of ionization equilibria coupled to ion partitioning", Macromolecules 53, 3007-3020 (2020).

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
+Perform the charge equilibration (QEq) method as described in
-as the matrix inversion method) and in :ref:`(Rick and Stuart) <Rick1>` (also
+:ref:`(Rappe and Goddard) <Rappe1>` and formulated in :ref:`(Nakano)
-known as the extended Lagrangian method) based on the
+<Nakano1>` (also known as the matrix inversion method) and in
-electronegativity equilization principle.
+: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.
+as the ReaxFF or Streitz-Mintmire potential.  But these fixes can also
-But these fixes can also be used with
+be used with potentials that normally assume per-atom charges are fixed,
-potentials that normally assume per-atom charges are fixed, e.g. a
+e.g. a :doc:`Buckingham <pair_buck>` or :doc:`LJ/Coulombic <pair_lj>`
-:doc:`Buckingham <pair_buck>` or :doc:`LJ/Coulombic <pair_lj>` potential.
+potential.
 
-Because the charge equilibration calculation is effectively
+Because the charge equilibration calculation is effectively independent
-independent of the pair style, these fixes can also be used to perform
+of the pair style, these fixes can also be used to perform a one-time
-a one-time assignment of charges to atoms.  For example, you could
+assignment of charges to atoms.  For example, you could define the QEq
-define the QEq fix, perform a zero-timestep run via the :doc:`run <run>`
+fix, perform a zero-timestep run via the :doc:`run <run>` command
-command without any pair style defined which would set per-atom
+without any pair style defined which would set per-atom charges (based
-charges (based on the current atom configuration), then remove the fix
+on the current atom configuration), then remove the fix via the
-via the :doc:`unfix <unfix>` command before performing further dynamics.
+: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
+   The :doc:`fix qeq/comb <fix_qeq_comb>` command must still be used to
-   to perform charge equilibration with the :doc:`COMB potential <pair_comb>`.  The :doc:`fix qeq/reax <fix_qeq_reax>`
+   perform charge equilibration with the :doc:`COMB potential
-   command can be used to perform charge equilibration with the :doc:`ReaxFF force field <pair_reaxc>`, although fix qeq/shielded yields the
+   <pair_comb>`.  The :doc:`fix qeq/reax <fix_qeq_reax>` command can be
-   same results as fix qeq/reax if *Nevery*\ , *cutoff*\ , and *tolerance*
+   used to perform charge equilibration with the :doc:`ReaxFF force
-   are the same.  Eventually the fix qeq/reax command will be deprecated.
+   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*
+as :doc:`fix qeq/reax <fix_qeq_reax>`, and can be used with
-parameters from the *qfile* file are used. When using the string
+:doc:`pair_style reax/c <pair_reaxc>`.  Only the *chi*\ , *eta*\ , and
-*reax/c* as filename, these parameters are extracted directly from
+*gamma* parameters from the *qfile* file are used. When using the string
-an active *reax/c* pair style.  This style solves partial
+*reax/c* as filename, these parameters are extracted directly from an
-charges on atoms via the matrix inversion method.  A tolerance of
+active *reax/c* pair style.  This style solves partial charges on atoms
-1.0e-6 is usually a good number.
+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
+that the interaction between a pair of charged particles is the product
-product of two Slater 1\ *s* orbitals.  The expression for the Slater
+of two Slater 1\ *s* orbitals.  The expression for the Slater 1\ *s*
-1\ *s* orbital is given under equation (6) of the
+orbital is given under equation (6) of the :ref:`Streitz-Mintmire
-:ref:`Streitz-Mintmire <Streitz1>` paper.  Only the *chi*\ , *eta*\ , *zeta*\ , and
+<Streitz1>` paper.  Only the *chi*\ , *eta*\ , *zeta*\ , and *qcore*
-*qcore* parameters from the *qfile* file are used. When using the string
+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
+an active *coul/streitz* pair style.  This style solves partial charges
-partial charges on atoms via the matrix inversion method.  A tolerance
+on atoms via the matrix inversion method.  A tolerance of 1.0e-6 is
-of 1.0e-6 is usually a good number.  Keyword *alpha* can be used to
+usually a good number.  Keyword *alpha* can be used to change the Slater
-change the Slater type orbital exponent.
+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
+charges that interact through 1/r, but the extended Lagrangian method is
-is used to solve partial charges on atoms.  Only the *chi* and *eta*
+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
+catastrophe can occur if repulsion between the pair of charged particles
-particles is too weak.  A tolerance of 1.0e-3 is usually a good
+is too weak.  A tolerance of 1.0e-3 is usually a good number.  Keyword
-number.  Keyword *qdamp* can be used to change the damping factor, while
+*qdamp* can be used to change the damping factor, while keyword *qstep*
-keyword *qstep* can be used to change the time step size.
+can be used to change the time step size.
 
-The :ref:`\ *qeq/fire*\ <Shan>` style describes the same charge model and charge
+The :ref:`\ *qeq/fire*\ <Shan>` style describes the same charge model
-solver as the *qeq/dynamic* style, but employs a FIRE minimization
+and charge solver as the *qeq/dynamic* style, but employs a FIRE
-algorithm to solve for equilibrium charges.
+minimization algorithm to solve for equilibrium charges.  Keyword
-Keyword *qdamp* can be used to change the damping factor, while
+*qdamp* can be used to change the damping factor, while keyword *qstep*
-keyword *qstep* can be used to change the time step size.
+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
+Note that *qeq/point*\ , *qeq/dynamic* and *qeq/fire* styles all
-charges as point charges that interact through 1/r relationship, but
+describe charges as point charges that interact through 1/r
-solve partial charges on atoms using different solvers.  These three
+relationship, but solve partial charges on atoms using different
-styles should yield comparable results if
+solvers.  These three styles should yield comparable results if the QEq
-the QEq parameters and *Nevery*\ , *cutoff*\ , and *tolerance* are the
+parameters and *Nevery*\ , *cutoff*\ , and *tolerance* are the same.
-same.  Style *qeq/point* is typically faster, *qeq/dynamic* scales
+Style *qeq/point* is typically faster, *qeq/dynamic* scales better on
-better on larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ .
+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
+No information about these fixes is written to :doc:`binary restart
-quantities are stored by these fixes for access by various :doc:`output commands <Howto_output>`.  No parameter of these fixes can be used
+files <restart>`.  No global scalar or vector or per-atom quantities are
-with the *start/stop* keywords of the :doc:`run <run>` command.
+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
 """"""""""""""""

doc/src/pair_pace.rst

@@ -0,0 +1,114 @@
+.. index:: pair_style pace
+
+pair_style pace command
+========================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style pace ... keyword values ...
+
+* an optional keyword may be appended
+* keyword = *product* or *recursive*
+
+  .. parsed-literal::
+
+       *product* = use product algorithm for basis functions
+       *recursive* = use recursive algorithm for basis functions
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style pace
+   pair_style pace product
+   pair_coeff * * Cu-PBE-core-rep.ace Cu
+
+Description
+"""""""""""
+
+Pair style *pace* computes interactions using the Atomic Cluster
+Expansion (ACE), which is a general expansion of the atomic energy in
+multi-body basis functions. :ref:`(Drautz) <Drautz20191>`.
+The *pace* pair style
+provides an efficient implementation that
+is described in this paper :ref:`(Lysogorskiy) <Lysogorskiy20211>`.
+
+In ACE, the total energy is decomposed into a sum over
+atomic energies. The energy of atom *i* is expressed as a
+linear or non-linear function of one or more density functions.
+By projecting the
+density onto a local atomic base, the lowest order contributions
+to the energy can be expressed as a set of scalar polynomials in
+basis function contributions summed over neighbor atoms.
+
+Only a single pair_coeff command is used with the *pace* style which
+specifies an ACE coefficient file followed by N additional arguments
+specifying the mapping of ACE elements to LAMMPS atom types,
+where N is the number of LAMMPS atom types:
+
+* ACE coefficient file
+* N element names = mapping of ACE elements to atom types
+
+Only a single pair_coeff command is used with the *pace* style which
+specifies an ACE file that fully defines the potential.
+Note that unlike for other potentials, cutoffs are
+not set in the pair_style or pair_coeff command; they are specified in
+the ACE file.
+
+The pair_style *pace* command may be followed by an optional keyword
+*product* or *recursive*, which determines which of two algorithms
+is used for the calculation of basis functions and derivatives.
+The default is *recursive*.
+
+See the :doc:`pair_coeff <pair_coeff>` doc page for alternate ways
+to specify the path for the ACE coefficient file.
+
+Mixing, shift, table, tail correction, restart, rRESPA info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+For atom type pairs I,J and I != J, where types I and J correspond to
+two different element types, mixing is performed by LAMMPS with
+user-specifiable parameters as described above.  You never need to
+specify a pair_coeff command with I != J arguments for this style.
+
+This pair style does not support the :doc:`pair_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files.  Thus, you
+need to re-specify the pair_style and pair_coeff commands in an input
+script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run_style respa <run_style>` command.  It does not support the
+*inner*\ , *middle*\ , *outer* keywords.
+
+----------
+
+Restrictions
+""""""""""""
+
+This pair style is part of the USER-PACE package.  It is only enabled if LAMMPS
+was built with that package.
+See the :doc:`Build package <Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair_style snap  <pair_snap>`
+
+Default
+"""""""
+
+recursive
+
+.. _Drautz20191:
+
+**(Drautz)** Drautz, Phys Rev B, 99, 014104 (2019).
+
+.. _Lysogorskiy20211:
+
+**(Lysogorskiy)** Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, TBD (2021).

doc/src/pair_style.rst

@@ -99,7 +99,7 @@ accelerated styles exist.
 * :doc:`zero <pair_zero>` - neighbor list but no interactions
 
 * :doc:`adp <pair_adp>` - angular dependent potential (ADP) of Mishin
-* :doc:`agni <pair_agni>` - machine learned potential mapping atomic environment to forces
+* :doc:`agni <pair_agni>` - AGNI machine-learning potential
 * :doc:`airebo <pair_airebo>` - AIREBO potential of Stuart
 * :doc:`airebo/morse <pair_airebo>` - AIREBO with Morse instead of LJ
 * :doc:`atm <pair_atm>` - Axilrod-Teller-Muto potential
@@ -280,6 +280,7 @@ accelerated styles exist.
 * :doc:`oxrna2/hbond <pair_oxrna2>` -
 * :doc:`oxrna2/stk <pair_oxrna2>` -
 * :doc:`oxrna2/xstk <pair_oxrna2>` -
+* :doc:`pace <pair_pace>` - Atomic Cluster Expansion (ACE) machine-learning potential
 * :doc:`peri/eps <pair_peri>` - peridynamic EPS potential
 * :doc:`peri/lps <pair_peri>` - peridynamic LPS potential
 * :doc:`peri/pmb <pair_peri>` - peridynamic PMB potential
@@ -297,7 +298,7 @@ accelerated styles exist.
 * :doc:`smd/ulsph <pair_smd_ulsph>` -
 * :doc:`smtbq <pair_smtbq>` -
 * :doc:`mliap <pair_mliap>` - Multiple styles of machine-learning potential
-* :doc:`snap <pair_snap>` - SNAP quantum-accurate potential
+* :doc:`snap <pair_snap>` - SNAP machine-learning potential
 * :doc:`soft <pair_soft>` - Soft (cosine) potential
 * :doc:`sph/heatconduction <pair_sph_heatconduction>` -
 * :doc:`sph/idealgas <pair_sph_idealgas>` -

doc/utils/sphinx-config/false_positives.txt

@@ -261,6 +261,7 @@ bitmask
 bitrate
 bitrates
 Bitzek
+Bjerrum
 Blaise
 blanchedalmond
 blocksize
@@ -268,6 +269,7 @@ blueviolet
 bn
 bni
 bo
+Bochkarev
 Bochum
 bocs
 bodyflag
@@ -343,6 +345,7 @@ Cao
 Capolungo
 Caro
 cartesian
+Cas
 CasP
 Caswell
 Cates
@@ -502,6 +505,8 @@ coulgauss
 coulombic
 Coulombic
 Coulombics
+counterion
+counterions
 Courant
 covalent
 covalently
@@ -730,6 +735,7 @@ DRUDE
 dsf
 dsmc
 dt
+dtemp
 dtgrow
 dtheta
 dtshrink
@@ -878,6 +884,7 @@ equilibrates
 equilibrating
 equilibration
 Equilibria
+equilibria
 equilization
 equipartitioning
 Ercolessi
@@ -1069,6 +1076,7 @@ fuer
 fx
 fy
 fz
+Gabor
 Gahler
 gainsboro
 Galindo
@@ -1193,6 +1201,7 @@ Halperin
 Halver
 Hamaker
 Hamel
+Hammerschmidt
 haptic
 Hara
 Harpertown
@@ -1212,6 +1221,7 @@ hbnewflag
 hbond
 hcp
 heatconduction
+Hebbeker
 Hebenstreit
 Hecht
 Heenen
@@ -1279,6 +1289,7 @@ hy
 hydrophobicity
 hydrostatic
 hydrostatically
+hydroxyl
 Hynninen
 Hyoungki
 hyperdynamics
@@ -1369,6 +1380,7 @@ ints
 inv
 invariants
 inversed
+ionizable
 ionocovalent
 iostreams
 iparam
@@ -1548,6 +1560,7 @@ Koning
 Kooser
 Korn
 Koskinen
+Kosovan
 Koster
 Kosztin
 Kp
@@ -1594,6 +1607,7 @@ Lamoureux
 Lanczos
 Lande
 Landron
+Landsgesell
 langevin
 Langevin
 Langston
@@ -1731,10 +1745,13 @@ lpsapi
 lrt
 lsfftw
 ltbbmalloc
+Lua
 lubricateU
 lucy
-Lua
 Luding
+Luijten
+lunit
+Lunkad
 Lussetti
 Lustig
 lval
@@ -1743,6 +1760,7 @@ lx
 ly
 Lybrand
 lyon
+Lysogorskiy
 Lyulin
 lz
 Maaravi
@@ -1801,8 +1819,10 @@ Materias
 mathbf
 mathjax
 matlab
+Matous
 matplotlib
 Matsubara
+Matteo
 Mattice
 Mattox
 Mattson
@@ -1863,6 +1883,7 @@ MEMALIGN
 membered
 memcheck
 Mendelev
+Menon
 mer
 Meremianin
 Mersenne
@@ -1986,6 +2007,7 @@ mpiio
 mpirun
 mplayer
 mps
+Mrovec
 Mryglod
 mscg
 MSCG
@@ -2020,6 +2042,7 @@ multiscale
 multisectioning
 multithreading
 Multithreading
+multivalent
 Mundy
 Murdick
 Murtola
@@ -2065,6 +2088,7 @@ Nanoletters
 nanomechanics
 nanometer
 nanometers
+nanoparticle
 nanoparticles
 Nanotube
 nanotube
@@ -2174,6 +2198,7 @@ nm
 Nm
 Nmax
 nmax
+nmc
 Nmin
 nmin
 Nmols
@@ -2308,9 +2333,11 @@ OMP
 oneAPI
 onelevel
 oneway
+onlysalt
 onn
 ons
 OO
+Oord
 opencl
 openKIM
 openmp
@@ -2331,6 +2358,7 @@ Orsi
 ortho
 orthonormal
 orthorhombic
+Ortner
 oso
 Otype
 Ouldridge
@@ -2390,6 +2418,8 @@ pbc
 pc
 pchain
 Pchain
+pcmoves
+pmcmoves
 Pdamp
 pdb
 pdf
@@ -2434,6 +2464,7 @@ phosphide
 Phs
 Physica
 physik
+pI
 Piaggi
 picocoulomb
 picocoulombs
@@ -2445,7 +2476,9 @@ pid
 piecewise
 Pieniazek
 Pieter
+pIm
 pimd
+pIp
 Piola
 Pisarev
 Pishevar
@@ -2460,6 +2493,9 @@ ploop
 PloS
 plt
 plumedfile
+pKa
+pKb
+pKs
 pmb
 Pmolrotate
 Pmoltrans
@@ -2620,6 +2656,7 @@ radians
 Rafferty
 rahman
 Rahman
+Ralf
 Raman
 ramped
 ramping
@@ -2727,6 +2764,7 @@ Rij
 RIj
 Rik
 Rin
+Rinaldi
 Rino
 RiRj
 Risi
@@ -2786,6 +2824,7 @@ rst
 rstyle
 Rubensson
 Rubia
+Rud
 Rudd
 Rudra
 Rudranarayan
@@ -2815,6 +2854,7 @@ Sandia
 sandybrown
 sanitizer
 Sanyal
+Sarath
 sc
 scafacos
 SCAFACOS

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)"

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

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)"

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
 

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}')"

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
 

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

examples/SPIN/test_problems/validation_nve/run-test-nve.sh

@@ -3,9 +3,14 @@
 # clean old res
 rm res_*.dat
 
-# compute Lammps 
+# test standard Lammps 
-./../../../../src/lmp_serial \
+../../../../src/lmp_serial -in in.spin.iron-nve 
-  -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)"

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

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

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)"

examples/USER/misc/charge_regulation/README

@@ -0,0 +1,36 @@
+This directory has two input scripts that illustrates how to use fix
+charge_regulation in LAMMPS to perform coarse-grained molecular dynamics
+(MD) simulations with incorporation of charge regulation effects. The
+charge regulation is implemented via Monte Carlo (MC) sampling following
+the reaction ensemble MC approach, producing a MC/MD hybrid tool for
+modeling charge regulation in solvated systems.
+
+The script `in.chreg-acid` sets up a simple weak acid electrolyte
+(pH=7,pKa=6,pI=3). Four different types of MC moves are implemented:
+acid protonation & de-protonation, and monovalent ion pair insertion and
+deletion. Note here we have grouped all free monovalent ions into a
+single type, a physically natural choice on the level of coarse-grained
+primitive electrolyte models, which increases the calculation
+performance but has no effects on thermodynamic observables. The
+variables such as pH, pKa, pI, and lb at the top of the input script can
+be adjusted to play with various simulation parameters. The cumulative
+MC attempted moves and cumulative number of accepted moves, as well as,
+current number of neutral and charged acid particles, neutral and
+charged base particles (in this example always 0), and the current
+number of free cations and anions in the system are printed in the
+output.
+
+The script `in.chreg-polymer` sets up a weak poly-electrolyte chain of
+N=80 beads. Each bead is a weak acid with pKa=5 and solution has pH=7
+and monovalent salt chemical potential pI=3. In this example, we choose
+to treat salt ions, protons, and hydroxyl ions separately, which results
+in 5 types of MC moves: acid [type 1] protonation & de-protonation (with
+protons [type 4] insertion & deletion), acid [type 1] protonation &
+de-protonation (with salt cation [type 2] insertion & deletion), water
+self-ionization (insertion and deletion of proton [type4] and hydroxyl
+ion [type 5] pair), insertion and deletion of monovalent salt pair [type
+2 and type 3] , insertion and deletion of a proton [type4] and salt
+anion [type 3].  The current number of neutral and charged acid
+particles, the current number of free salt cations and anions, and the
+current number of protons and hydroxyl ions are printed in the output.
+

examples/USER/misc/charge_regulation/data.chreg-acid

@@ -0,0 +1,235 @@
+LAMMPS data file generated by get_input.py
+
+219 atoms
+3 atom types
+-2.5000000000000000e+01 2.5000000000000000e+01 xlo xhi
+-2.5000000000000000e+01 2.5000000000000000e+01 ylo yhi
+-2.5000000000000000e+01 2.5000000000000000e+01 zlo zhi
+
+Masses
+
+1 1
+2 1 
+3 1 
+
+Atoms
+
+1 1 0 2.5983275747497636 -8.368052973860795 20.001288664343484
+2 1 -1 -18.182868728594865 -8.079792367885453 8.253737231981816
+3 1 -1 -17.437350808966414 8.120411567445771 10.747650340639332
+4 1 -1 6.502476583291578 -23.497326620756837 19.948223080086798
+5 1 -1 -22.528179279677296 -18.783433570718127 -17.964657736688018
+6 1 -1 -9.713496019164342 18.97235576760402 -19.495620818582825
+7 1 -1 -12.831976006720659 0.12265736526942561 -21.679396938423718
+8 1 -1 20.909063679212295 -2.16535062758771 0.46197866620165584
+9 1 -1 23.86211981166997 24.024928465132284 10.534067202515907
+10 1 -1 -0.5289298325031275 23.820222457999776 -2.657199543669442
+11 1 -1 9.57021229491361 11.973871502198485 3.4206509716759186
+12 1 -1 -10.201559985782705 7.557482594092384 12.07004973873643
+13 1 -1 4.898458045226889 2.0169997859717945 -20.765285372762087
+14 1 -1 -24.086606883730077 4.424991619615298 -4.204294764756856
+15 1 -1 3.6837161829600795 -4.763233144818308 -12.75873457519811
+16 1 -1 -12.217842496816345 -17.720229208905618 -13.556354139556914
+17 1 -1 -21.456229140133704 -7.423996317612119 -6.94398044071275
+18 1 -1 13.697298849253912 8.503639732052164 8.085487457359058
+19 1 -1 -5.764222710061347 11.49890485049034 -5.1113880296575935
+20 1 -1 3.9944161041544426 16.928204188257893 -14.875635895409372
+21 1 -1 4.509525276444776 16.63590711792657 -22.21846494992397
+22 1 -1 22.115374932704306 -18.97293932558108 -23.982486000144267
+23 1 -1 14.169061011408473 -16.69837647199978 13.779039228068108
+24 1 -1 17.186846147657228 8.827459489898189 23.055435051390333
+25 1 -1 2.9822901981431045 -16.83687718528342 -21.278623587083484
+26 1 -1 16.657554689423897 -1.6217275605348647 -11.315859420404218
+27 1 -1 19.215533149393543 -15.512634977936068 7.2701088767584565
+28 1 -1 -8.886744157248422 -24.09644410100167 4.013016013803799
+29 1 -1 20.99918340066754 4.4716257356730225 0.3847245765737597
+30 1 -1 1.3442294253060716 5.601341425720583 -14.918594492786674
+31 1 -1 -6.962977050326831 20.470183675946515 -16.37885865567279
+32 1 -1 -9.98531733187143 9.52233798117566 -24.979630708193724
+33 1 -1 -17.327989778292306 5.761352103841766 5.720220488689204
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examples/USER/misc/charge_regulation/data.chreg-acid-real

@@ -0,0 +1,235 @@
+LAMMPS data file generated by get_input.py
+
+219 atoms
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+-180 180 ylo yhi
+-180 180 zlo zhi
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+78 1 -1 -21.80051132 76.35556687 53.9496888
+79 1 -1 36.00388293 84.74463507 124.0379428
+80 1 -1 8.341344194 -176.0991953 -90.11296078
+81 1 -1 13.79742378 -101.263178 81.37760753
+82 1 -1 -150.1706978 153.3081009 125.261789
+83 1 -1 -176.434078 -91.73850736 -13.91415701
+84 1 -1 19.14212656 -8.014482902 53.93954558
+85 1 -1 -133.3111329 174.2862517 104.1616036
+86 1 -1 141.4028288 71.58712061 62.57853826
+87 1 -1 -55.41310448 84.69012271 -53.69230074
+88 1 -1 7.57030387 -82.51421069 121.7019339
+89 1 -1 6.593627122 170.3286085 -47.07783075
+90 1 -1 167.9772199 -52.51603119 -77.32359634
+91 1 -1 9.68753279 2.580696533 63.63273049
+92 1 -1 -157.900078 -78.41001295 -74.97298362
+93 1 -1 157.7779932 -77.61759639 83.11626672
+94 1 -1 8.735687555 -51.63741526 149.2886008
+95 1 -1 166.3370649 158.0395191 2.108272744
+96 1 -1 -136.2080224 -0.233620925 170.1641304
+97 1 -1 54.59763504 77.34086464 -34.97254442
+98 1 -1 -53.93524806 -102.0122253 -46.27109402
+99 1 -1 -148.8398471 -62.976886 79.28200649
+100 1 -1 -134.367229 -153.7685306 -62.89913905
+101 2 1 85.68701047 47.45902631 136.9309939
+102 2 1 -168.7218611 -136.4862888 34.82926874
+103 2 1 -85.14342147 -27.50852705 22.44064244
+104 2 1 -125.9841936 -166.432033 69.22175254
+105 2 1 78.40196016 32.48784706 134.5355212
+106 2 1 -158.7356866 172.6075363 -168.6081077
+107 2 1 -97.70696089 125.0552693 152.541151
+108 2 1 47.42532862 117.2059839 -26.2001494
+109 2 1 58.97843054 49.16794046 -45.70255405
+110 2 1 -113.2077086 -147.4896474 -109.0593944
+111 2 1 133.7818478 137.2370883 -74.12887346
+112 2 1 -151.8619681 -55.72321046 39.00697883
+113 2 1 -101.5491513 -113.5421107 -135.9492067
+114 2 1 -105.4410412 63.66017268 62.00391546
+115 2 1 -84.37716183 -35.78408568 -7.089644848
+116 2 1 140.387382 -75.00992841 -159.2710691
+117 2 1 157.3753205 145.1311104 -98.29723102
+118 2 1 -126.8885841 157.4914592 -47.04455377
+119 2 1 52.06885202 -100.2669325 38.59257737
+120 2 1 -54.06789629 137.7750035 -116.8953091
+121 2 1 -29.14739431 94.50860741 -51.527097
+122 2 1 -145.9322739 154.5384232 112.3421798
+123 2 1 -32.24342538 -22.90490626 -133.4101075
+124 2 1 155.0953371 97.30799449 -13.02231424
+125 2 1 -109.6079033 -42.89844953 -51.80376701
+126 2 1 -150.2770445 -55.20818421 147.7312972
+127 2 1 -26.96028917 151.3053234 51.82429115
+128 2 1 -42.51040448 55.12547194 -10.01649745
+129 2 1 -154.7332138 -166.4922488 75.56066422
+130 2 1 179.3252381 50.98353603 -103.842222
+131 2 1 -87.64561442 -167.4026399 -37.04977996
+132 2 1 -141.7543098 32.23109989 44.99445113
+133 2 1 121.3596596 -6.092779973 129.6856923
+134 2 1 124.4836766 -86.35531223 85.50625099
+135 2 1 140.6305506 -165.9843021 -35.3966949
+136 2 1 -89.51258901 36.2123163 54.25434215
+137 2 1 107.5306105 58.22419926 141.7457531
+138 2 1 -51.03564423 -166.277591 119.3103596
+139 2 1 106.3738063 153.673561 100.7747233
+140 2 1 -105.1662471 -49.88388187 -163.5658795
+141 2 1 -123.4063552 104.6405545 -157.1806703
+142 2 1 30.68517662 111.7365757 -128.0988407
+143 2 1 -70.66650991 -36.87088431 101.1920697
+144 2 1 59.85584345 28.56015074 -148.8751279
+145 2 1 76.34296857 -18.88899045 11.99663247
+146 2 1 -127.898772 9.029786744 -155.2067979
+147 2 1 -61.47407783 106.6906337 -32.24644961
+148 2 1 -41.82882356 105.2048819 95.67134776
+149 2 1 64.70518204 -125.5606981 -130.2221179
+150 2 1 -95.86998176 64.01110464 -62.69889224
+151 2 1 -3.893149866 -170.4938796 -173.9425756
+152 2 1 -142.5571999 -115.9852755 -42.33527796
+153 2 1 -170.1094774 67.22933296 -69.41406448
+154 2 1 -135.7002446 -117.3853245 -77.66219554
+155 2 1 97.68794466 -176.3481416 64.0577303
+156 2 1 98.30084322 -179.1048324 157.6098802
+157 2 1 -61.74657154 71.45180441 36.21267022
+158 2 1 148.9924395 8.130617629 2.580809806
+159 2 1 -7.179797893 131.8852645 48.92705878
+160 2 1 166.7210737 111.3028256 122.5151765
+161 2 1 160.4061661 105.4292149 147.9164951
+162 2 1 70.35573238 -156.217711 -37.86968306
+163 2 1 37.82167168 128.9612675 113.5371453
+164 2 1 -149.4650805 40.2544478 -89.16446826
+165 2 1 23.15794976 -35.62998186 -128.5225995
+166 2 1 148.5909499 65.59167763 44.47571026
+167 2 1 38.20567747 91.06090259 167.2556933
+168 2 1 -173.8935359 124.3001041 -123.4154022
+169 2 1 -113.0780192 -112.7185827 -75.51909042
+170 2 1 -47.52814398 -162.0232543 -40.84518679
+171 2 1 164.6580923 96.26106544 -67.52475023
+172 2 1 -166.687599 -28.28821753 -80.04284273
+173 2 1 9.786487166 -133.5748603 -110.4924395
+174 2 1 73.69685916 -130.6229707 -12.1566579
+175 2 1 90.69039384 -12.53964183 -156.8650452
+176 2 1 -1.065055548 123.2458955 9.207883208
+177 2 1 175.3144942 -62.38332615 89.50309521
+178 2 1 -135.5554643 -135.3786299 -12.22599884
+179 2 1 -65.15130962 -12.87802388 -85.25728639
+180 2 1 -161.9760397 -159.2069523 72.10033228
+181 2 1 -116.5200037 9.430944126 5.8294178
+182 2 1 -28.85454266 -176.0245493 -141.7245957
+183 2 1 63.2968571 -114.4145268 -168.891953
+184 2 1 -61.61686575 -158.2947391 162.9099557
+185 2 1 51.43661765 119.3411567 4.253266919
+186 2 1 50.78017633 47.93871152 129.5527454
+187 2 1 151.0842128 -27.15258927 -161.0800505
+188 2 1 -63.76595621 -118.2333675 -55.31381078
+189 2 1 -103.5498203 -55.20725862 -73.28180307
+190 2 1 -165.1300235 72.52455317 27.04945294
+191 2 1 68.10471264 124.0704131 -0.252243467
+192 2 1 79.29794618 142.8637277 -42.01908928
+193 2 1 167.6806551 20.41616629 -147.6924841
+194 2 1 -135.8036012 64.48710622 102.1923975
+195 2 1 98.55703781 -115.0070794 78.85760695
+196 2 1 15.16187488 19.73322691 -170.7866955
+197 2 1 151.0729333 50.92372407 -173.3272023
+198 2 1 42.92899709 -139.8564977 161.7836767
+199 2 1 -123.3797296 144.2768906 93.18435951
+200 2 1 83.46684339 160.4439871 16.84583748
+201 2 1 -9.982765467 138.2373541 -55.3263136
+202 2 1 -161.6023131 -141.5797686 -64.66795638
+203 2 1 2.63144963 -54.92560391 117.5540027
+204 2 1 -70.31638318 175.5673808 -103.3383852
+205 2 1 -4.543770763 -40.50287551 98.39515078
+206 2 1 19.2926167 -2.671035153 112.1413205
+207 2 1 76.93260202 177.3949067 -126.2787212
+208 2 1 131.8183006 132.4167597 131.6586696
+209 2 1 -82.9844547 -85.47123292 92.81285561
+210 3 -1 115.4743016 -5.981969165 65.81311346
+211 3 -1 -86.91538943 171.1823129 -45.00079
+212 3 -1 174.0893311 141.4009485 159.8631805
+213 3 -1 164.8739505 64.21237704 -8.113691614
+214 3 -1 -75.49748308 40.97887837 158.0779944
+215 3 -1 45.16399203 72.25791157 159.9861897
+216 3 -1 105.7676225 -56.05853127 3.624467826
+217 3 -1 166.8523536 -151.4993186 -151.6124408
+218 3 -1 -43.30886503 46.05330597 155.3934201
+219 3 -1 -5.592027058 2.85325065 11.39381158

examples/USER/misc/charge_regulation/data.chreg-polymer

@@ -0,0 +1,264 @@
+##A Weak PE Chain of N=80
+
+160 atoms
+79 bonds
+
+5 atom types
+1 bond types
+
+-50 50 xlo xhi
+-50 50 ylo yhi
+-50 50 zlo zhi
+
+Masses
+
+1 1.0
+2 1.0
+3 1.0
+4 1.0
+5 1.0
+
+Atoms
+# atom_id molecule_id atom_type charge x y z 
+1 1 1 -1 0 0 -48.37753795169063
+2 1 1 -1 0 0 -47.255075903381254
+3 1 1 -1 0 0 -46.13261385507188
+4 1 1 -1 0 0 -45.01015180676251
+5 1 1 -1 0 0 -43.887689758453135
+6 1 1 -1 0 0 -42.76522771014376
+7 1 1 -1 0 0 -41.64276566183439
+8 1 1 -1 0 0 -40.520303613525016
+9 1 1 -1 0 0 -39.39784156521564
+10 1 1 -1 0 0 -38.27537951690627
+11 1 1 -1 0 0 -37.1529174685969
+12 1 1 -1 0 0 -36.030455420287524
+13 1 1 -1 0 0 -34.90799337197815
+14 1 1 -1 0 0 -33.78553132366878
+15 1 1 -1 0 0 -32.663069275359405
+16 1 1 -1 0 0 -31.54060722705003
+17 1 1 -1 0 0 -30.41814517874066
+18 1 1 -1 0 0 -29.295683130431286
+19 1 1 -1 0 0 -28.173221082121913
+20 1 1 -1 0 0 -27.05075903381254
+21 1 1 -1 0 0 -25.928296985503167
+22 1 1 -1 0 0 -24.805834937193794
+23 1 1 -1 0 0 -23.68337288888442
+24 1 1 -1 0 0 -22.560910840575048
+25 1 1 -1 0 0 -21.438448792265675
+26 1 1 -1 0 0 -20.3159867439563
+27 1 1 -1 0 0 -19.19352469564693
+28 1 1 -1 0 0 -18.071062647337556
+29 1 1 -1 0 0 -16.948600599028183
+30 1 1 -1 0 0 -15.82613855071881
+31 1 1 -1 0 0 -14.703676502409436
+32 1 1 -1 0 0 -13.581214454100063
+33 1 1 -1 0 0 -12.45875240579069
+34 1 1 -1 0 0 -11.336290357481317
+35 1 1 -1 0 0 -10.213828309171944
+36 1 1 -1 0 0 -9.091366260862571
+37 1 1 -1 0 0 -7.968904212553198
+38 1 1 -1 0 0 -6.846442164243825
+39 1 1 -1 0 0 -5.723980115934452
+40 1 1 -1 0 0 -4.601518067625079
+41 1 1 -1 0 0 -3.4790560193157063
+42 1 1 -1 0 0 -2.3565939710063333
+43 1 1 -1 0 0 -1.2341319226969603
+44 1 1 -1 0 0 -0.11166987438758724
+45 1 1 -1 0 0 1.0107921739217858
+46 1 1 -1 0 0 2.133254222231159
+47 1 1 -1 0 0 3.255716270540532
+48 1 1 -1 0 0 4.378178318849905
+49 1 1 -1 0 0 5.500640367159278
+50 1 1 -1 0 0 6.623102415468651
+51 1 1 -1 0 0 7.745564463778024
+52 1 1 -1 0 0 8.868026512087397
+53 1 1 -1 0 0 9.99048856039677
+54 1 1 -1 0 0 11.112950608706143
+55 1 1 -1 0 0 12.235412657015516
+56 1 1 -1 0 0 13.357874705324889
+57 1 1 -1 0 0 14.480336753634262
+58 1 1 -1 0 0 15.602798801943635
+59 1 1 -1 0 0 16.725260850253008
+60 1 1 -1 0 0 17.84772289856238
+61 1 1 -1 0 0 18.970184946871754
+62 1 1 -1 0 0 20.092646995181127
+63 1 1 -1 0 0 21.2151090434905
+64 1 1 -1 0 0 22.337571091799873
+65 1 1 -1 0 0 23.460033140109246
+66 1 1 -1 0 0 24.58249518841862
+67 1 1 -1 0 0 25.704957236727992
+68 1 1 -1 0 0 26.827419285037365
+69 1 1 -1 0 0 27.949881333346738
+70 1 1 -1 0 0 29.07234338165611
+71 1 1 -1 0 0 30.194805429965484
+72 1 1 -1 0 0 31.317267478274857
+73 1 1 -1 0 0 32.43972952658423
+74 1 1 -1 0 0 33.5621915748936
+75 1 1 -1 0 0 34.684653623202976
+76 1 1 -1 0 0 35.80711567151235
+77 1 1 -1 0 0 36.92957771982172
+78 1 1 -1 0 0 38.052039768131095
+79 1 1 -1 0 0 39.17450181644047
+80 1 1 -1 0 0 40.29696386474984
+81 0 2 1 -27.886422274724097 27.72001798427955 38.68169635811057
+82 0 2 1 29.812255760623188 17.871838747003693 -29.094648426460257
+83 0 2 1 -13.23881351410531 13.28123966828678 -24.422176415560116
+84 0 2 1 4.9465650593939685 -37.7521903558826 -15.115417767729575
+85 0 2 1 34.82527943387106 29.457664434004897 -25.565595338061254
+86 0 2 1 46.35660570786446 -7.161776614070412 -20.2471250527001
+87 0 2 1 39.20854546781531 34.96815569014278 13.893531822586723
+88 0 2 1 -7.797240698180197 0.07861219105048889 48.686453603015224
+89 0 2 1 43.92391845355516 -39.42362941705827 22.448930565867585
+90 0 2 1 -40.371744364329984 -17.743039071967246 -15.08153047835009
+91 0 2 1 -21.573165497710058 -0.5844447399891948 -45.73596994149077
+92 0 2 1 -19.882394451769102 -7.392447895357577 30.733607063808876
+93 0 2 1 -17.393031309514107 26.882975097407467 -47.64059480000892
+94 0 2 1 25.652222561671735 1.0229206994719107 -14.959030208952043
+95 0 2 1 26.075045766879313 19.902341017250052 46.70284805469666
+96 0 2 1 39.91980369168496 0.753749460187592 -26.203575929573407
+97 0 2 1 13.777613371273958 7.112171629839359 -33.5270487721399
+98 0 2 1 18.944534687271826 20.090215089875286 -34.381335468790574
+99 0 2 1 -23.801856387842435 -42.275962146864586 -8.322936238250279
+100 0 2 1 -31.386991395893826 29.83894468611787 8.937114269513422
+101 0 2 1 -41.07090001085809 49.59339931450579 6.666864232174753
+102 0 2 1 -46.58911504232167 -32.46068937927039 19.40424197066872
+103 0 2 1 -39.94659416571965 -36.28203465180086 5.841020764632312
+104 0 2 1 -26.027467090120137 -41.05522015175137 -1.1145958296128313
+105 0 2 1 37.09602855959457 23.76087951027276 45.09142423198867
+106 0 2 1 -27.78138413517528 -48.97344929918942 45.91491289356401
+107 0 2 1 4.468912883622387 -5.217782298407556 6.381420595433383
+108 0 2 1 36.758686966564525 48.425582881586166 -25.909273336802997
+109 0 2 1 -27.045102667146036 -19.713951008254117 4.339232870380627
+110 0 2 1 -5.984280016624311 -49.45311479123866 36.35727783065221
+111 0 2 1 27.833389147163018 -47.80144978082761 -47.71458334276804
+112 0 2 1 -23.628507668044364 -30.353876765128685 36.174277933133254
+113 0 2 1 -40.93360714431151 40.1336490864843 -27.035347797435495
+114 0 2 1 6.3523980881104976 -28.636485436097082 -10.671354350535445
+115 0 2 1 42.765716958607086 -32.85779663523676 -1.9682360265562124
+116 0 2 1 -33.68069757415453 16.800769050458484 -6.273374390373085
+117 0 2 1 13.909148568042937 4.921040289518388 12.111069913598996
+118 0 2 1 6.728324076730296 -48.44092815223126 -35.92436883370601
+119 0 2 1 -18.121173967321912 -15.76903395165283 2.2495451015454933
+120 0 2 1 -11.75253233489407 -45.82569982175387 -12.477142440015896
+121 0 2 1 1.9713864197144133 17.961034900064007 32.97992150691711
+122 0 2 1 -3.993384770632943 -47.63120435620297 27.75490859098018
+123 0 2 1 -0.32208279553454844 -47.30616152402566 -22.751109302380367
+124 0 2 1 -0.135777029397957 23.88599790464609 -31.87440560354473
+125 0 2 1 -6.123924906817393 -2.038519565120424 45.4809181974626
+126 0 2 1 -29.622588299895046 42.40404115712096 6.640479709229595
+127 0 2 1 -11.694512971272673 19.983258641775762 -38.152427411711145
+128 0 2 1 -20.93721440637313 39.46397829322392 -45.52708262202337
+129 0 2 1 34.13340147809369 36.14268504987945 -23.978137043267044
+130 0 2 1 -37.422309952611485 29.181841318883087 27.55677757161692
+131 0 2 1 30.11314373799594 18.721794400471353 1.5553303682670574
+132 0 2 1 -7.3563467211571805 46.84253369205935 -39.84708490437832
+133 0 2 1 -3.695927445484358 2.494403998274727 -7.634369981832755
+134 0 2 1 44.09701173592077 17.717328437831043 31.54108326477207
+135 0 2 1 48.070189931616795 10.601166369398662 -28.28574863896286
+136 0 2 1 -7.044858382811761 -42.080663380241766 -1.4369925734636553
+137 0 2 1 -12.485032488076918 23.87106169116919 6.178803347562642
+138 0 2 1 -15.613232443702309 10.103630885941392 -20.447182948810916
+139 0 2 1 28.610332347774147 37.08335835592116 -19.90280831362493
+140 0 2 1 25.853920233242505 -27.768648181803655 24.971357611943475
+141 0 2 1 9.256159541363296 -23.562096053197934 -4.722701100419371
+142 0 2 1 39.96929397877305 -11.88228547846326 -28.70638149104603
+143 0 2 1 -37.98545134633291 -23.50528193202669 -10.939982626098441
+144 0 2 1 25.40017763114089 -47.49220127581256 15.1783064865064
+145 0 2 1 28.073596076651768 3.6631266774864386 31.54355751177208
+146 0 2 1 -19.596457173068703 46.79824882013442 -12.302655772327597
+147 0 2 1 -36.46192411958321 -2.785830672302666 -25.1901381125736
+148 0 2 1 -27.377389198969894 11.295792272951147 39.32842550184691
+149 0 2 1 32.24967019136358 -20.517755791016402 31.20590722085157
+150 0 2 1 47.70698618147787 9.75462874031868 -28.267447889542563
+151 0 2 1 17.157803106328345 -27.48141290657965 7.7670687016760525
+152 0 2 1 15.089833959419678 5.342811012118396 27.35336620165029
+153 0 2 1 9.836963929211372 -11.047378229392443 -20.960811370690678
+154 0 2 1 44.66600586278604 14.949733274456321 -29.328965994323575
+155 0 2 1 -21.006260382140685 8.492712712433658 -46.31580169190271
+156 0 2 1 -29.970979487850748 -36.46250489415931 26.914372830947457
+157 0 2 1 -1.0821372755756329 -8.453379951300242 -19.95665062432509
+158 0 2 1 -24.033653425909772 -39.51330620205049 20.067656167683793
+159 0 2 1 27.747287624384626 -21.904990435351312 -10.819345241055956
+160 0 2 1 -40.86737066410612 -25.609300376714796 -21.128139356809783
+
+Bonds
+ # bond_id bond_type atom1_id atom2_id
+1 1 1 2
+2 1 2 3
+3 1 3 4
+4 1 4 5
+5 1 5 6
+6 1 6 7
+7 1 7 8
+8 1 8 9
+9 1 9 10
+10 1 10 11
+11 1 11 12
+12 1 12 13
+13 1 13 14
+14 1 14 15
+15 1 15 16
+16 1 16 17
+17 1 17 18
+18 1 18 19
+19 1 19 20
+20 1 20 21
+21 1 21 22
+22 1 22 23
+23 1 23 24
+24 1 24 25
+25 1 25 26
+26 1 26 27
+27 1 27 28
+28 1 28 29
+29 1 29 30
+30 1 30 31
+31 1 31 32
+32 1 32 33
+33 1 33 34
+34 1 34 35
+35 1 35 36
+36 1 36 37
+37 1 37 38
+38 1 38 39
+39 1 39 40
+40 1 40 41
+41 1 41 42
+42 1 42 43
+43 1 43 44
+44 1 44 45
+45 1 45 46
+46 1 46 47
+47 1 47 48
+48 1 48 49
+49 1 49 50
+50 1 50 51
+51 1 51 52
+52 1 52 53
+53 1 53 54
+54 1 54 55
+55 1 55 56
+56 1 56 57
+57 1 57 58
+58 1 58 59
+59 1 59 60
+60 1 60 61
+61 1 61 62
+62 1 62 63
+63 1 63 64
+64 1 64 65
+65 1 65 66
+66 1 66 67
+67 1 67 68
+68 1 68 69
+69 1 69 70
+70 1 70 71
+71 1 71 72
+72 1 72 73
+73 1 73 74
+74 1 74 75
+75 1 75 76
+76 1 76 77
+77 1 77 78
+78 1 78 79
+79 1 79 80

examples/USER/misc/charge_regulation/in.chreg-acid

@@ -0,0 +1,36 @@
+# Charge regulation lammps for simple weak electrolyte
+
+units           lj
+atom_style      charge
+neighbor        3.0 bin
+read_data       data.chreg-acid
+
+variable        cut_long equal 12.5
+variable        nevery equal 100
+variable        nmc equal 100
+variable        pH equal 7.0
+variable        pKa equal 6.0
+variable        pIm equal 3.0
+variable        pIp equal 3.0
+
+variable        cut_lj equal 2^(1.0/6.0)
+variable        lunit_nm equal 0.72 # in the units of nm
+velocity        all create 1.0 8008 loop geom
+
+pair_style      lj/cut/coul/long ${cut_lj} ${cut_long}
+pair_coeff      * *  1.0 1.0
+kspace_style    ewald 1.0e-3
+pair_modify     shift yes
+
+#########  VERLET INTEGRATION WITH LANGEVIN THERMOSTAT  ###########
+fix             fnve all nve
+compute         dtemp all temp
+compute_modify  dtemp dynamic yes
+fix             fT all langevin 1.0 1.0 1.0 123
+fix_modify      fT temp dtemp
+
+fix chareg      all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+thermo          100
+thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
+timestep        0.005
+run             2000

examples/USER/misc/charge_regulation/in.chreg-acid-real

@@ -0,0 +1,44 @@
+# Charge regulation lammps for simple weak electrolyte
+
+units           real
+atom_style      charge
+neighbor        10.0 bin
+read_data       data.chreg-acid-real
+
+#real units
+variable 	sigma equal 7.2	              # particle diameter 0.72 nm	    	
+variable	temperature equal 298         # temperature 298 K
+variable        kb index 0.0019872067         # kB in Kcal/mol/K
+variable 	epsilon equal ${kb}*${temperature}
+variable	tunit   equal 	2000          # time unit is 2000 fs    
+variable	timestep equal 0.005*${tunit}
+
+variable        cut_long equal 12.5*${sigma}
+variable        nevery equal 100
+variable        nmc equal 100
+variable        pH equal 7.0
+variable        pKa equal 6.0
+variable        pIm equal 3.0
+variable        pIp equal 3.0
+
+variable        cut_lj equal 2^(1.0/6.0)*${sigma}
+velocity        all create ${temperature} 8008 loop geom
+
+pair_style      lj/cut/coul/long ${cut_lj} ${cut_long}
+pair_coeff      * *  ${epsilon} ${sigma}
+kspace_style    pppm 1.0e-3
+dielectric	78
+pair_modify     shift yes
+
+#########  VERLET INTEGRATION WITH LANGEVIN THERMOSTAT  ###########
+fix             fnve all nve
+compute         dtemp all temp
+compute_modify  dtemp dynamic yes
+fix             fT all langevin $(v_temperature) $(v_temperature) $(v_tunit) 123
+fix_modify      fT temp dtemp
+
+fix chareg      all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+thermo          100
+thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
+timestep        ${timestep}
+run             2000

examples/USER/misc/charge_regulation/in.chreg-polymer

@@ -0,0 +1,33 @@
+# Charge regulation lammps for a polymer chain
+units           lj
+atom_style      full
+neighbor        3.0 bin
+read_data       data.chreg-polymer
+
+bond_style      harmonic
+bond_coeff      1 100 1.122462 # K R0
+velocity        all create 1.0 8008 loop geom
+
+pair_style      lj/cut/coul/long 1.122462 20
+pair_coeff      * *  1.0 1.0 1.122462 # charges
+kspace_style    pppm 1.0e-3
+pair_modify     shift yes
+dielectric      1.0
+
+#########  VERLET INTEGRATION WITH LANGEVIN THERMOSTAT  ###########
+fix             fnve all nve
+compute         dtemp all temp
+compute_modify  dtemp dynamic yes
+fix             fT all langevin 1.0 1.0 1.0 123
+fix_modify      fT temp dtemp
+
+fix chareg1 all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 seed 2345
+fix chareg2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 seed 2345
+fix chareg3 all charge/regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 seed 2345
+
+thermo          100
+#               print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions
+thermo_style    custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8]
+
+timestep        0.005
+run             2000

examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.1

@@ -0,0 +1,125 @@
+LAMMPS (10 Feb 2021)
+  using 1 OpenMP thread(s) per MPI task
+# Charge regulation lammps for simple weak electrolyte
+
+units           lj
+atom_style      charge
+neighbor        3.0 bin
+read_data       data.chreg-acid
+Reading data file ...
+  orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  219 atoms
+  read_data CPU = 0.003 seconds
+
+variable        cut_long equal 12.5
+variable        nevery equal 100
+variable        nmc equal 100
+variable        pH equal 7.0
+variable        pKa equal 6.0
+variable        pIm equal 3.0
+variable        pIp equal 3.0
+
+variable        cut_lj equal 2^(1.0/6.0)
+variable        lunit_nm equal 0.72 # in the units of nm
+velocity        all create 1.0 8008 loop geom
+
+pair_style      lj/cut/coul/long ${cut_lj} ${cut_long}
+pair_style      lj/cut/coul/long 1.12246204830937 ${cut_long}
+pair_style      lj/cut/coul/long 1.12246204830937 12.5
+pair_coeff      * *  1.0 1.0
+kspace_style    ewald 1.0e-3
+pair_modify     shift yes
+
+#########  VERLET INTEGRATION WITH LANGEVIN THERMOSTAT  ###########
+fix             fnve all nve
+compute         dtemp all temp
+compute_modify  dtemp dynamic yes
+fix             fT all langevin 1.0 1.0 1.0 123
+fix_modify      fT temp dtemp
+
+fix chareg      all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery 100 nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery 100 nmc 100 seed 2345 tempfixid fT
+thermo          100
+thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
+timestep        0.005
+run             2000
+Ewald initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
+  G vector (1/distance) = 0.14221027
+  estimated absolute RMS force accuracy = 0.0010128126
+  estimated relative force accuracy = 0.0010128126
+  KSpace vectors: actual max1d max3d = 257 5 665
+                  kxmax kymax kzmax  = 5 5 5
+0 atoms in group FixChargeRegulation:exclusion_group:chareg
+WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 15.5
+  ghost atom cutoff = 15.5
+  binsize = 7.75, bins = 7 7 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.91 | 11.91 | 11.91 Mbytes
+Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] 
+       0 -0.049662059            1            0            0            1           99            0            0          109           10 
+     100 -0.053672881   0.99159291          100           71           16           84            0            0           92            8 
+     200 -0.053383027   0.90935145          200          156           26           74            0            0           85           11 
+     300 -0.040471335   0.97937429          300          240           21           79            0            0           87            8 
+     400 -0.036188123    1.0837424          400          319           14           86            0            0           92            6 
+     500 -0.057294925    1.0507526          500          407           10           90            0            0           98            8 
+     600 -0.056009748    1.0669354          600          487           15           85            0            0           92            7 
+     700 -0.069686562   0.99202496          700          567           14           86            0            0           96           10 
+     800 -0.054695624    1.0592933          800          647           25           75            0            0           82            7 
+     900 -0.058693653   0.97870458          900          728           27           73            0            0           83           10 
+    1000 -0.062352957    1.0008923         1000          805           24           76            0            0           84            8 
+    1100 -0.065011926   0.91691048         1100          886           22           78            0            0           87            9 
+    1200 -0.080463686   0.98879304         1200          963           23           77            0            0           88           11 
+    1300 -0.062146141    1.0566033         1300         1047           21           79            0            0           88            9 
+    1400 -0.046980246    1.0847512         1400         1129           17           83            0            0           94           11 
+    1500 -0.042935292    1.0075805         1500         1203           24           76            0            0           86           10 
+    1600 -0.056075891   0.94173489         1600         1277           23           77            0            0           90           13 
+    1700 -0.042279161    1.1126317         1700         1355           28           72            0            0           82           10 
+    1800 -0.036842528    1.0255327         1800         1436           24           76            0            0           83            7 
+    1900 -0.038816022   0.93883373         1900         1511           23           77            0            0           86            9 
+    2000 -0.047008287   0.98904085         2000         1592           26           74            0            0           81            7 
+Loop time of 11.6365 on 1 procs for 2000 steps with 188 atoms
+
+Performance: 74249.079 tau/day, 171.873 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.24337    | 0.24337    | 0.24337    |   0.0 |  2.09
+Kspace  | 4.6009     | 4.6009     | 4.6009     |   0.0 | 39.54
+Neigh   | 0.023451   | 0.023451   | 0.023451   |   0.0 |  0.20
+Comm    | 0.027729   | 0.027729   | 0.027729   |   0.0 |  0.24
+Output  | 0.0007813  | 0.0007813  | 0.0007813  |   0.0 |  0.01
+Modify  | 6.7345     | 6.7345     | 6.7345     |   0.0 | 57.87
+Other   |            | 0.005713   |            |       |  0.05
+
+Nlocal:        188.000 ave         188 max         188 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        597.000 ave         597 max         597 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:        2196.00 ave        2196 max        2196 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2196
+Ave neighs/atom = 11.680851
+Neighbor list builds = 2059
+Dangerous builds = 0
+Total wall time: 0:00:11

examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.4

@@ -0,0 +1,125 @@
+LAMMPS (10 Feb 2021)
+  using 1 OpenMP thread(s) per MPI task
+# Charge regulation lammps for simple weak electrolyte
+
+units           lj
+atom_style      charge
+neighbor        3.0 bin
+read_data       data.chreg-acid
+Reading data file ...
+  orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  219 atoms
+  read_data CPU = 0.003 seconds
+
+variable        cut_long equal 12.5
+variable        nevery equal 100
+variable        nmc equal 100
+variable        pH equal 7.0
+variable        pKa equal 6.0
+variable        pIm equal 3.0
+variable        pIp equal 3.0
+
+variable        cut_lj equal 2^(1.0/6.0)
+variable        lunit_nm equal 0.72 # in the units of nm
+velocity        all create 1.0 8008 loop geom
+
+pair_style      lj/cut/coul/long ${cut_lj} ${cut_long}
+pair_style      lj/cut/coul/long 1.12246204830937 ${cut_long}
+pair_style      lj/cut/coul/long 1.12246204830937 12.5
+pair_coeff      * *  1.0 1.0
+kspace_style    ewald 1.0e-3
+pair_modify     shift yes
+
+#########  VERLET INTEGRATION WITH LANGEVIN THERMOSTAT  ###########
+fix             fnve all nve
+compute         dtemp all temp
+compute_modify  dtemp dynamic yes
+fix             fT all langevin 1.0 1.0 1.0 123
+fix_modify      fT temp dtemp
+
+fix chareg      all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery 100 nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery 100 nmc 100 seed 2345 tempfixid fT
+thermo          100
+thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
+timestep        0.005
+run             2000
+Ewald initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
+  G vector (1/distance) = 0.14221027
+  estimated absolute RMS force accuracy = 0.0010128126
+  estimated relative force accuracy = 0.0010128126
+  KSpace vectors: actual max1d max3d = 257 5 665
+                  kxmax kymax kzmax  = 5 5 5
+0 atoms in group FixChargeRegulation:exclusion_group:chareg
+WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 15.5
+  ghost atom cutoff = 15.5
+  binsize = 7.75, bins = 7 7 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.89 | 11.89 | 11.89 Mbytes
+Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] 
+       0 -0.049662059            1            0            0            1           99            0            0          109           10 
+     100  -0.06196414    1.0156327          100           72           15           85            0            0           93            8 
+     200 -0.053901683   0.95128403          200          160           24           76            0            0           87           11 
+     300 -0.043852423   0.98035058          300          246           22           78            0            0           85            7 
+     400 -0.048370798    1.0909844          400          324           16           84            0            0           91            7 
+     500 -0.042546472     1.026849          500          410           13           87            0            0           95            8 
+     600  -0.06133022   0.97805065          600          494           14           86            0            0           93            7 
+     700 -0.053815853    1.0641005          700          572           17           83            0            0           91            8 
+     800 -0.059974814    1.0192348          800          650           23           77            0            0           83            6 
+     900 -0.051808132    1.0773288          900          728           25           75            0            0           85           10 
+    1000 -0.050390995    1.0236954         1000          804           28           72            0            0           81            9 
+    1100 -0.069766444     1.030965         1100          890           25           75            0            0           85           10 
+    1200 -0.074580231    1.0490058         1200          963           21           79            0            0           88            9 
+    1300 -0.060169443   0.93456607         1300         1043           22           78            0            0           86            8 
+    1400  -0.05120764    1.0374062         1400         1127           19           81            0            0           92           11 
+    1500 -0.027644416   0.99804782         1500         1204           24           76            0            0           85            9 
+    1600 -0.038599195   0.99015524         1600         1283           22           78            0            0           90           12 
+    1700 -0.050222686    1.1444379         1700         1365           27           73            0            0           84           11 
+    1800 -0.049338003    1.1188048         1800         1449           22           78            0            0           84            6 
+    1900  -0.04533154   0.99894341         1900         1527           22           78            0            0           86            8 
+    2000 -0.058837311   0.95302017         2000         1608           26           74            0            0           81            7 
+Loop time of 3.98119 on 4 procs for 2000 steps with 188 atoms
+
+Performance: 217020.495 tau/day, 502.362 timesteps/s
+96.2% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.050626   | 0.061127   | 0.071318   |   3.4 |  1.54
+Kspace  | 1.1987     | 1.2504     | 1.288      |   3.1 | 31.41
+Neigh   | 0.0056982  | 0.0063858  | 0.0069821  |   0.7 |  0.16
+Comm    | 0.068302   | 0.11638    | 0.17922    |  12.8 |  2.92
+Output  | 0.00055408 | 0.00092399 | 0.0020106  |   0.0 |  0.02
+Modify  | 2.5399     | 2.5406     | 2.5417     |   0.0 | 63.81
+Other   |            | 0.005394   |            |       |  0.14
+
+Nlocal:        47.0000 ave          55 max          42 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+Nghost:        328.250 ave         335 max         317 min
+Histogram: 1 0 0 0 0 1 0 0 0 2
+Neighs:        547.000 ave         659 max         466 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 2188
+Ave neighs/atom = 11.638298
+Neighbor list builds = 2057
+Dangerous builds = 0
+Total wall time: 0:00:04

examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.1

@@ -0,0 +1,131 @@
+LAMMPS (10 Feb 2021)
+  using 1 OpenMP thread(s) per MPI task
+# Charge regulation lammps for a polymer chain
+units           lj
+atom_style      full
+neighbor        3.0 bin
+read_data       data.chreg-polymer
+Reading data file ...
+  orthogonal box = (-50.000000 -50.000000 -50.000000) to (50.000000 50.000000 50.000000)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  160 atoms
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  79 bonds
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     2 = max # of 1-3 neighbors
+     4 = max # of 1-4 neighbors
+     6 = max # of special neighbors
+  special bonds CPU = 0.001 seconds
+  read_data CPU = 0.009 seconds
+
+bond_style      harmonic
+bond_coeff      1 100 1.122462 # K R0
+velocity        all create 1.0 8008 loop geom
+
+pair_style      lj/cut/coul/long 1.122462 20
+pair_coeff      * *  1.0 1.0 1.122462 # charges
+kspace_style    pppm 1.0e-3
+pair_modify     shift yes
+dielectric      1.0
+
+#########  VERLET INTEGRATION WITH LANGEVIN THERMOSTAT  ###########
+fix             fnve all nve
+compute         dtemp all temp
+compute_modify  dtemp dynamic yes
+fix             fT all langevin 1.0 1.0 1.0 123
+fix_modify      fT temp dtemp
+
+fix chareg1 all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 seed 2345
+fix chareg2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 seed 2345
+fix chareg3 all charge/regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 seed 2345
+
+thermo          100
+#               print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions
+thermo_style    custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8]
+
+timestep        0.005
+run             2000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
+  G vector (1/distance) = 0.077106934
+  grid = 8 8 8
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00074388331
+  estimated relative force accuracy = 0.00074388331
+  using double precision FFTW3
+  3d grid and FFT values/proc = 2197 512
+0 atoms in group FixChargeRegulation:exclusion_group:chareg1
+0 atoms in group FixChargeRegulation:exclusion_group:chareg2
+0 atoms in group FixChargeRegulation:exclusion_group:chareg3
+WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 23
+  ghost atom cutoff = 23
+  binsize = 11.5, bins = 9 9 9
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.962 | 6.962 | 6.962 Mbytes
+Step PotEng c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] 
+       0   0.50528297            1            0           80           80            0            0            0 
+     100   0.61185377   0.95892928           13           67           74            7            0            0 
+     200   0.54355177    1.1282424           19           61           76           15            0            0 
+     300    0.4519957    1.0764688           20           60           85           26            1            0 
+     400   0.41479389   0.99212685           24           56           92           36            0            0 
+     500   0.37382446   0.99776674           28           52           98           46            0            0 
+     600   0.34785337    1.1115081           28           52          109           57            0            0 
+     700   0.34637618    1.0332262           28           52          120           68            0            0 
+     800   0.21020932    1.1264036           29           51          125           74            0            0 
+     900   0.21246108    1.1168609           30           50          131           81            0            0 
+    1000   0.20997475    1.1201478           32           48          132           84            0            0 
+    1100    0.1984165    1.0209092           31           49          144           95            0            0 
+    1200    0.2061932   0.95880059           35           45          151          106            0            0 
+    1300   0.17220376     0.980077           36           44          156          112            0            0 
+    1400   0.15671143   0.93535342           37           43          161          118            0            0 
+    1500   0.16174665    0.9495928           36           44          168          124            0            0 
+    1600   0.11062965   0.94072924           40           40          164          124            0            0 
+    1700   0.13002563   0.95010828           38           42          167          125            0            0 
+    1800   0.14527814   0.93555342           37           43          172          129            0            0 
+    1900   0.17627465   0.96682495           32           48          176          128            0            0 
+    2000   0.16497265   0.95226954           33           47          180          133            0            0 
+Loop time of 7.45499 on 1 procs for 2000 steps with 393 atoms
+
+Performance: 115895.577 tau/day, 268.277 timesteps/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.45607    | 0.45607    | 0.45607    |   0.0 |  6.12
+Bond    | 0.0062385  | 0.0062385  | 0.0062385  |   0.0 |  0.08
+Kspace  | 2.3257     | 2.3257     | 2.3257     |   0.0 | 31.20
+Neigh   | 0.067103   | 0.067103   | 0.067103   |   0.0 |  0.90
+Comm    | 0.02577    | 0.02577    | 0.02577    |   0.0 |  0.35
+Output  | 0.00087047 | 0.00087047 | 0.00087047 |   0.0 |  0.01
+Modify  | 4.5664     | 4.5664     | 4.5664     |   0.0 | 61.25
+Other   |            | 0.006848   |            |       |  0.09
+
+Nlocal:        393.000 ave         393 max         393 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        749.000 ave         749 max         749 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:        5359.00 ave        5359 max        5359 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 5359
+Ave neighs/atom = 13.636132
+Ave special neighs/atom = 1.1908397
+Neighbor list builds = 1489
+Dangerous builds = 0
+Total wall time: 0:00:07

examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.4

@@ -0,0 +1,131 @@
+LAMMPS (10 Feb 2021)
+  using 1 OpenMP thread(s) per MPI task
+# Charge regulation lammps for a polymer chain
+units           lj
+atom_style      full
+neighbor        3.0 bin
+read_data       data.chreg-polymer
+Reading data file ...
+  orthogonal box = (-50.000000 -50.000000 -50.000000) to (50.000000 50.000000 50.000000)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  160 atoms
+  scanning bonds ...
+  1 = max bonds/atom
+  reading bonds ...
+  79 bonds
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     2 = max # of 1-2 neighbors
+     2 = max # of 1-3 neighbors
+     4 = max # of 1-4 neighbors
+     6 = max # of special neighbors
+  special bonds CPU = 0.001 seconds
+  read_data CPU = 0.016 seconds
+
+bond_style      harmonic
+bond_coeff      1 100 1.122462 # K R0
+velocity        all create 1.0 8008 loop geom
+
+pair_style      lj/cut/coul/long 1.122462 20
+pair_coeff      * *  1.0 1.0 1.122462 # charges
+kspace_style    pppm 1.0e-3
+pair_modify     shift yes
+dielectric      1.0
+
+#########  VERLET INTEGRATION WITH LANGEVIN THERMOSTAT  ###########
+fix             fnve all nve
+compute         dtemp all temp
+compute_modify  dtemp dynamic yes
+fix             fT all langevin 1.0 1.0 1.0 123
+fix_modify      fT temp dtemp
+
+fix chareg1 all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 seed 2345
+fix chareg2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 seed 2345
+fix chareg3 all charge/regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 seed 2345
+
+thermo          100
+#               print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions
+thermo_style    custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8]
+
+timestep        0.005
+run             2000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:339)
+  G vector (1/distance) = 0.077106934
+  grid = 8 8 8
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00074388331
+  estimated relative force accuracy = 0.00074388331
+  using double precision FFTW3
+  3d grid and FFT values/proc = 1053 128
+0 atoms in group FixChargeRegulation:exclusion_group:chareg1
+0 atoms in group FixChargeRegulation:exclusion_group:chareg2
+0 atoms in group FixChargeRegulation:exclusion_group:chareg3
+WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 23
+  ghost atom cutoff = 23
+  binsize = 11.5, bins = 9 9 9
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.878 | 6.935 | 6.992 Mbytes
+Step PotEng c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] 
+       0   0.50528297            1            0           80           80            0            0            0 
+     100   0.60223729   0.89547569           13           67           75            8            0            0 
+     200   0.65253636   0.87662399           18           62           78           16            0            0 
+     300   0.51550501    1.0542131           22           58           84           27            1            0 
+     400   0.43566766   0.94557633           26           54           90           36            0            0 
+     500   0.36269507    1.0386276           31           49           94           45            0            0 
+     600   0.32430641   0.99903033           27           53          111           58            0            0 
+     700   0.30255299   0.91225991           28           52          121           69            0            0 
+     800   0.27189951    0.9747089           28           52          127           75            0            0 
+     900   0.25495247    1.0747821           28           52          135           83            0            0 
+    1000   0.25950416   0.95256449           32           48          134           86            0            0 
+    1100   0.22561248    1.0102255           32           48          147           99            0            0 
+    1200    0.1734754   0.99475154           33           47          157          110            0            0 
+    1300   0.20081084   0.99873599           36           44          160          116            0            0 
+    1400   0.14240417   0.99442152           36           44          164          121            1            0 
+    1500   0.15314186   0.94559876           39           41          167          126            0            0 
+    1600   0.13574107    1.0484195           43           37          164          127            0            0 
+    1700   0.14477789    1.0105172           42           38          166          128            0            0 
+    1800   0.13493107    1.0349667           41           39          171          132            0            0 
+    1900   0.14849779    0.9994329           33           47          178          131            0            0 
+    2000   0.14485171   0.99739608           34           46          183          137            0            0 
+Loop time of 3.18871 on 4 procs for 2000 steps with 400 atoms
+
+Performance: 270955.695 tau/day, 627.212 timesteps/s
+94.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.086456   | 0.11738    | 0.18562    |  11.8 |  3.68
+Bond    | 0.00099182 | 0.0018544  | 0.0030079  |   1.8 |  0.06
+Kspace  | 0.77406    | 0.79354    | 0.80895    |   1.5 | 24.89
+Neigh   | 0.017894   | 0.017948   | 0.018002   |   0.0 |  0.56
+Comm    | 0.029044   | 0.07885    | 0.11432    |  11.3 |  2.47
+Output  | 0.00054932 | 0.0009656  | 0.0021319  |   0.0 |  0.03
+Modify  | 2.1676     | 2.1706     | 2.1733     |   0.2 | 68.07
+Other   |            | 0.007591   |            |       |  0.24
+
+Nlocal:        100.000 ave         110 max          89 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Nghost:        415.000 ave         418 max         411 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+Neighs:        1360.75 ave        1872 max        1018 min
+Histogram: 1 1 0 0 1 0 0 0 0 1
+
+Total # of neighbors = 5443
+Ave neighs/atom = 13.607500
+Ave special neighs/atom = 1.1700000
+Neighbor list builds = 1492
+Dangerous builds = 0
+Total wall time: 0:00:03

examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1

@@ -0,0 +1,145 @@
+LAMMPS (10 Feb 2021)
+# Charge regulation lammps for simple weak electrolyte
+
+units           real
+atom_style      charge
+neighbor        10.0 bin
+read_data       data.chreg-acid-real
+Reading data file ...
+  orthogonal box = (-180.00000 -180.00000 -180.00000) to (180.00000 180.00000 180.00000)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  219 atoms
+  read_data CPU = 0.002 seconds
+
+#real units
+variable 	sigma equal 7.2	              # particle diameter 0.72 nm
+variable	temperature equal 298         # temperature 298 K
+variable        kb index 0.0019872067         # kB in Kcal/mol/K
+variable 	epsilon equal ${kb}*${temperature}
+variable 	epsilon equal 0.0019872067*${temperature}
+variable 	epsilon equal 0.0019872067*298
+variable	tunit   equal 	2000          # time unit is 2000 fs
+variable	timestep equal 0.005*${tunit}
+variable	timestep equal 0.005*2000
+
+variable        cut_long equal 12.5*${sigma}
+variable        cut_long equal 12.5*7.2
+variable        nevery equal 100
+variable        nmc equal 100
+variable        pH equal 7.0
+variable        pKa equal 6.0
+variable        pIm equal 3.0
+variable        pIp equal 3.0
+
+variable        cut_lj equal 2^(1.0/6.0)*${sigma}
+variable        cut_lj equal 2^(1.0/6.0)*7.2
+velocity        all create ${temperature} 8008 loop geom
+velocity        all create 298 8008 loop geom
+
+pair_style      lj/cut/coul/long ${cut_lj} ${cut_long}
+pair_style      lj/cut/coul/long 8.08172674782749 ${cut_long}
+pair_style      lj/cut/coul/long 8.08172674782749 90
+pair_coeff      * *  ${epsilon} ${sigma}
+pair_coeff      * *  0.5921875966 ${sigma}
+pair_coeff      * *  0.5921875966 7.2
+kspace_style    pppm 1.0e-3
+dielectric	78
+pair_modify     shift yes
+
+#########  VERLET INTEGRATION WITH LANGEVIN THERMOSTAT  ###########
+fix             fnve all nve
+compute         dtemp all temp
+compute_modify  dtemp dynamic yes
+fix             fT all langevin $(v_temperature) $(v_temperature) $(v_tunit) 123
+fix             fT all langevin 298 $(v_temperature) $(v_tunit) 123
+fix             fT all langevin 298 298 $(v_tunit) 123
+fix             fT all langevin 298 298 2000 123
+fix_modify      fT temp dtemp
+
+fix chareg      all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc 100 seed 2345 tempfixid fT
+thermo          100
+thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
+timestep        ${timestep}
+timestep        10
+run             2000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:339)
+  G vector (1/distance) = 0.019408615
+  grid = 8 8 8
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00012527706
+  estimated relative force accuracy = 3.7726815e-07
+  using double precision KISS FFT
+  3d grid and FFT values/proc = 2197 512
+0 atoms in group FixChargeRegulation:exclusion_group:chareg
+WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:486)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 100
+  ghost atom cutoff = 100
+  binsize = 50, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.708 | 3.708 | 3.708 Mbytes
+Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] 
+       0   -6.4798431          298            0            0            1           99            0            0          109           10 
+     100   -6.9219668    306.44177          100           77           15           85            0            0           94            9 
+     200   -6.8175255    306.64254          200          164           23           77            0            0           87           10 
+     300   -5.2482381    331.67831          300          248           21           79            0            0           85            6 
+     400   -7.4531538     285.3495          400          326           17           83            0            0           89            6 
+     500   -6.9662528     286.2123          500          408           14           86            0            0           95            9 
+     600    -6.528214    291.41762          600          492           14           86            0            0           95            9 
+     700    -6.290871    271.50948          700          567           14           86            0            0           96           10 
+     800   -6.4944741    300.66261          800          650           23           77            0            0           83            6 
+     900   -8.0414672     305.6179          900          731           25           75            0            0           84            9 
+    1000   -8.5694583    298.73349         1000          810           25           75            0            0           83            8 
+    1100   -8.6677368    269.67435         1100          894           22           78            0            0           87            9 
+    1200   -8.2246183    284.14886         1200          969           22           78            0            0           88           10 
+    1300   -7.7674621    320.04838         1300         1040           23           77            0            0           85            8 
+    1400   -9.5186335    303.48091         1400         1124           18           82            0            0           93           11 
+    1500   -5.8437493    271.40712         1500         1204           25           75            0            0           83            8 
+    1600   -5.9149181    268.24708         1600         1285           23           77            0            0           90           13 
+    1700   -6.5047738    303.79732         1700         1369           27           73            0            0           84           11 
+    1800   -7.3010139    308.98213         1800         1450           22           78            0            0           83            5 
+    1900   -6.3505397    306.94357         1900         1527           22           78            0            0           86            8 
+    2000   -5.7144173    287.06184         2000         1605           27           73            0            0           80            7 
+Loop time of 1.17189 on 1 procs for 2000 steps with 187 atoms
+
+Performance: 1474.535 ns/day, 0.016 hours/ns, 1706.638 timesteps/s
+99.6% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.035807   | 0.035807   | 0.035807   |   0.0 |  3.06
+Kspace  | 0.37689    | 0.37689    | 0.37689    |   0.0 | 32.16
+Neigh   | 0.008694   | 0.008694   | 0.008694   |   0.0 |  0.74
+Comm    | 0.004793   | 0.004793   | 0.004793   |   0.0 |  0.41
+Output  | 0.000746   | 0.000746   | 0.000746   |   0.0 |  0.06
+Modify  | 0.74292    | 0.74292    | 0.74292    |   0.0 | 63.39
+Other   |            | 0.00205    |            |       |  0.17
+
+Nlocal:        187.000 ave         187 max         187 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        437.000 ave         437 max         437 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:        1500.00 ave        1500 max        1500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1500
+Ave neighs/atom = 8.0213904
+Neighbor list builds = 2080
+Dangerous builds = 0
+Total wall time: 0:00:01

examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4

@@ -0,0 +1,145 @@
+LAMMPS (10 Feb 2021)
+# Charge regulation lammps for simple weak electrolyte
+
+units           real
+atom_style      charge
+neighbor        10.0 bin
+read_data       data.chreg-acid-real
+Reading data file ...
+  orthogonal box = (-180.00000 -180.00000 -180.00000) to (180.00000 180.00000 180.00000)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  219 atoms
+  read_data CPU = 0.002 seconds
+
+#real units
+variable 	sigma equal 7.2	              # particle diameter 0.72 nm
+variable	temperature equal 298         # temperature 298 K
+variable        kb index 0.0019872067         # kB in Kcal/mol/K
+variable 	epsilon equal ${kb}*${temperature}
+variable 	epsilon equal 0.0019872067*${temperature}
+variable 	epsilon equal 0.0019872067*298
+variable	tunit   equal 	2000          # time unit is 2000 fs
+variable	timestep equal 0.005*${tunit}
+variable	timestep equal 0.005*2000
+
+variable        cut_long equal 12.5*${sigma}
+variable        cut_long equal 12.5*7.2
+variable        nevery equal 100
+variable        nmc equal 100
+variable        pH equal 7.0
+variable        pKa equal 6.0
+variable        pIm equal 3.0
+variable        pIp equal 3.0
+
+variable        cut_lj equal 2^(1.0/6.0)*${sigma}
+variable        cut_lj equal 2^(1.0/6.0)*7.2
+velocity        all create ${temperature} 8008 loop geom
+velocity        all create 298 8008 loop geom
+
+pair_style      lj/cut/coul/long ${cut_lj} ${cut_long}
+pair_style      lj/cut/coul/long 8.08172674782749 ${cut_long}
+pair_style      lj/cut/coul/long 8.08172674782749 90
+pair_coeff      * *  ${epsilon} ${sigma}
+pair_coeff      * *  0.5921875966 ${sigma}
+pair_coeff      * *  0.5921875966 7.2
+kspace_style    pppm 1.0e-3
+dielectric	78
+pair_modify     shift yes
+
+#########  VERLET INTEGRATION WITH LANGEVIN THERMOSTAT  ###########
+fix             fnve all nve
+compute         dtemp all temp
+compute_modify  dtemp dynamic yes
+fix             fT all langevin $(v_temperature) $(v_temperature) $(v_tunit) 123
+fix             fT all langevin 298 $(v_temperature) $(v_tunit) 123
+fix             fT all langevin 298 298 $(v_tunit) 123
+fix             fT all langevin 298 298 2000 123
+fix_modify      fT temp dtemp
+
+fix chareg      all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc ${nmc} seed 2345 tempfixid fT
+fix chareg      all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc 100 seed 2345 tempfixid fT
+thermo          100
+thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
+timestep        ${timestep}
+timestep        10
+run             2000
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (../kspace.cpp:339)
+  G vector (1/distance) = 0.019408615
+  grid = 8 8 8
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.00012527706
+  estimated relative force accuracy = 3.7726815e-07
+  using double precision KISS FFT
+  3d grid and FFT values/proc = 1053 128
+0 atoms in group FixChargeRegulation:exclusion_group:chareg
+WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:486)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 100
+  ghost atom cutoff = 100
+  binsize = 50, bins = 8 8 8
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.624 | 3.624 | 3.624 Mbytes
+Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] 
+       0   -6.4798431          298            0            0            1           99            0            0          109           10 
+     100   -7.6327126    304.68909          100           73           15           85            0            0           94            9 
+     200   -6.1699041    272.19597          200          156           24           76            0            0           87           11 
+     300   -7.7876571    288.90801          300          240           20           80            0            0           87            7 
+     400   -6.3239918    274.65708          400          315           16           84            0            0           90            6 
+     500   -5.3978659    257.49208          500          398           15           85            0            0           93            8 
+     600   -5.6433949    322.52048          600          477           18           82            0            0           90            8 
+     700   -6.5351367    269.20244          700          558           18           82            0            0           91            9 
+     800   -6.2093085    315.21326          800          638           24           76            0            0           83            7 
+     900   -7.0795998    311.93228          900          719           28           72            0            0           82           10 
+    1000   -6.4668438    281.72674         1000          796           27           73            0            0           81            8 
+    1100   -6.2377994    318.48594         1100          875           25           75            0            0           84            9 
+    1200   -6.6305072     304.9091         1200          950           23           77            0            0           87           10 
+    1300   -5.9624552    286.05027         1300         1029           22           78            0            0           86            8 
+    1400   -4.4695814    261.81053         1400         1111           20           80            0            0           90           10 
+    1500   -5.6928652    293.72403         1500         1191           24           76            0            0           86           10 
+    1600   -6.8715413    290.47065         1600         1275           22           78            0            0           90           12 
+    1700   -6.5067505    292.74735         1700         1356           25           75            0            0           85           10 
+    1800   -5.3902702    307.79012         1800         1434           22           78            0            0           83            5 
+    1900   -5.1407153    318.48918         1900         1510           21           79            0            0           87            8 
+    2000   -4.9514719    281.87771         2000         1589           25           75            0            0           82            7 
+Loop time of 0.562889 on 4 procs for 2000 steps with 189 atoms
+
+Performance: 3069.876 ns/day, 0.008 hours/ns, 3553.097 timesteps/s
+99.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.008399   | 0.010383   | 0.011765   |   1.2 |  1.84
+Kspace  | 0.17501    | 0.17543    | 0.1757     |   0.1 | 31.17
+Neigh   | 0.001833   | 0.0021325  | 0.002293   |   0.4 |  0.38
+Comm    | 0.023099   | 0.024255   | 0.026645   |   0.9 |  4.31
+Output  | 0.000465   | 0.000546   | 0.000783   |   0.0 |  0.10
+Modify  | 0.3464     | 0.34669    | 0.34698    |   0.0 | 61.59
+Other   |            | 0.003452   |            |       |  0.61
+
+Nlocal:        47.2500 ave          57 max          41 min
+Histogram: 1 1 0 1 0 0 0 0 0 1
+Nghost:        285.750 ave         303 max         263 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Neighs:        403.500 ave         548 max         324 min
+Histogram: 2 0 0 1 0 0 0 0 0 1
+
+Total # of neighbors = 1614
+Ave neighs/atom = 8.5396825
+Neighbor list builds = 2081
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/USER/pace/Cu-PBE-core-rep.ace

@@ -0,0 +1 @@
+../../../potentials/Cu-PBE-core-rep.ace

examples/USER/pace/in.pace.product

@@ -0,0 +1,38 @@
+# simple test of fcc Cu with ACE product  
+
+units		metal
+atom_style	atomic
+
+neighbor	0.3 bin
+neigh_modify	 every 2 delay 10 check yes
+
+variable	a equal 3.597
+lattice		fcc $a 
+region		box block 0 4 0 4 0 4
+create_box	1 box
+create_atoms	1 box
+
+mass		1 26.98
+
+group		Al type 1
+
+pair_style 	pace product
+pair_coeff  * * Cu-PBE-core-rep.ace Cu
+
+velocity        all create 300 8728 loop geom
+timestep        0.0005
+fix		1 all nve
+
+compute  	eatom all pe/atom
+compute  	energy all reduce sum c_eatom
+variable 	delenergy equal c_energy-pe
+
+compute  	satom all stress/atom NULL
+compute  	str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable 	delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
+
+thermo 		10
+thermo_style    custom step temp epair etotal press v_delenergy v_delpress
+
+run		100
+

examples/USER/pace/in.pace.recursive

@@ -0,0 +1,38 @@
+# simple test of fcc Cu with ACE recursive 
+
+units		metal
+atom_style	atomic
+
+neighbor	0.3 bin
+neigh_modify	 every 2 delay 10 check yes
+
+variable	a equal 3.597
+lattice		fcc $a 
+region		box block 0 4 0 4 0 4
+create_box	1 box
+create_atoms	1 box
+
+mass		1 26.98
+
+group		Al type 1
+
+pair_style 	pace recursive
+pair_coeff  * * Cu-PBE-core-rep.ace Cu
+
+velocity        all create 300 8728 loop geom
+timestep        0.0005
+fix		1 all nve
+
+compute  	eatom all pe/atom
+compute  	energy all reduce sum c_eatom
+variable 	delenergy equal c_energy-pe
+
+compute  	satom all stress/atom NULL
+compute  	str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable 	delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
+
+thermo 		10
+thermo_style    custom step temp epair etotal press v_delenergy v_delpress
+
+run		100
+

examples/USER/pace/log.03Feb2021.pace.product.g++.1

@@ -0,0 +1,108 @@
+LAMMPS (24 Dec 2020)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
+  using 1 OpenMP thread(s) per MPI task
+# simple test of fcc Cu with ACE product
+
+units		metal
+atom_style	atomic
+
+neighbor	0.3 bin
+neigh_modify	 every 2 delay 10 check yes
+
+variable	a equal 3.597
+lattice		fcc $a
+lattice		fcc 3.597
+Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000
+region		box block 0 4 0 4 0 4
+create_box	1 box
+Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 256 atoms
+  create_atoms CPU = 0.000 seconds
+
+mass		1 26.98
+
+group		Al type 1
+256 atoms in group Al
+
+pair_style 	pace product
+ACE version: 2021.2.3
+Product evaluator is used
+pair_coeff  * * Cu-PBE-core-rep.ace Cu
+Loading Cu-PBE-core-rep.ace
+Total number of basis functions
+	Cu: 16 (r=1) 726 (r>1)
+Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
+
+velocity        all create 300 8728 loop geom
+timestep        0.0005
+fix		1 all nve
+
+compute  	eatom all pe/atom
+compute  	energy all reduce sum c_eatom
+variable 	delenergy equal c_energy-pe
+
+compute  	satom all stress/atom NULL
+compute  	str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable 	delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
+
+thermo 		10
+thermo_style    custom step temp epair etotal press v_delenergy v_delpress
+
+run		100
+Neighbor list info ...
+  update every 2 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.7
+  ghost atom cutoff = 7.7
+  binsize = 3.85, bins = 4 4 4
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair pace, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.036 | 4.036 | 4.036 Mbytes
+Step Temp E_pair TotEng Press v_delenergy v_delpress 
+       0          300    -945.9873    -936.0989    45359.818            0 2.1827873e-11 
+      10    280.68558   -945.35055   -936.09878    46326.919            0 2.910383e-11 
+      20    228.73618   -943.63789   -936.09844    48903.598            0 -2.910383e-11 
+      30    160.53661   -941.38948   -936.09798    52222.083            0 -2.910383e-11 
+      40    97.732944   -939.31899   -936.09758    55176.875            0 2.1827873e-11 
+      50    59.165961   -938.04759    -936.0974    56850.103            0 2.910383e-11 
+      60    53.124678   -937.84857   -936.09751    56878.948            0            0 
+      70    74.623347    -938.5575   -936.09782    55565.237            0 4.3655746e-11 
+      80     109.4762   -939.70663   -936.09815    53665.652            0 2.910383e-11 
+      90    142.02657   -940.77975   -936.09837      52001.1            0            0 
+     100    161.73598   -941.42945   -936.09842    51114.997            0 1.4551915e-11 
+Loop time of 11.4718 on 1 procs for 100 steps with 256 atoms
+
+Performance: 0.377 ns/day, 63.732 hours/ns, 8.717 timesteps/s
+99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 11.468     | 11.468     | 11.468     |   0.0 | 99.96
+Neigh   | 0.001181   | 0.001181   | 0.001181   |   0.0 |  0.01
+Comm    | 0.001207   | 0.001207   | 0.001207   |   0.0 |  0.01
+Output  | 0.000876   | 0.000876   | 0.000876   |   0.0 |  0.01
+Modify  | 0.000455   | 0.000455   | 0.000455   |   0.0 |  0.00
+Other   |            | 0.000397   |            |       |  0.00
+
+Nlocal:        256.000 ave         256 max         256 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        2201.00 ave        2201 max        2201 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:         0.00000 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:      43118.0 ave       43118 max       43118 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 43118
+Ave neighs/atom = 168.42969
+Neighbor list builds = 1
+Dangerous builds = 0
+
+Total wall time: 0:00:11

examples/USER/pace/log.03Feb2021.pace.product.g++.4

@@ -0,0 +1,108 @@
+LAMMPS (24 Dec 2020)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
+  using 1 OpenMP thread(s) per MPI task
+# simple test of fcc Cu with ACE product
+
+units		metal
+atom_style	atomic
+
+neighbor	0.3 bin
+neigh_modify	 every 2 delay 10 check yes
+
+variable	a equal 3.597
+lattice		fcc $a
+lattice		fcc 3.597
+Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000
+region		box block 0 4 0 4 0 4
+create_box	1 box
+Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 256 atoms
+  create_atoms CPU = 0.000 seconds
+
+mass		1 26.98
+
+group		Al type 1
+256 atoms in group Al
+
+pair_style 	pace product
+ACE version: 2021.2.3
+Product evaluator is used
+pair_coeff  * * Cu-PBE-core-rep.ace Cu
+Loading Cu-PBE-core-rep.ace
+Total number of basis functions
+	Cu: 16 (r=1) 726 (r>1)
+Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
+
+velocity        all create 300 8728 loop geom
+timestep        0.0005
+fix		1 all nve
+
+compute  	eatom all pe/atom
+compute  	energy all reduce sum c_eatom
+variable 	delenergy equal c_energy-pe
+
+compute  	satom all stress/atom NULL
+compute  	str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable 	delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
+
+thermo 		10
+thermo_style    custom step temp epair etotal press v_delenergy v_delpress
+
+run		100
+Neighbor list info ...
+  update every 2 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.7
+  ghost atom cutoff = 7.7
+  binsize = 3.85, bins = 4 4 4
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair pace, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.005 | 4.005 | 4.005 Mbytes
+Step Temp E_pair TotEng Press v_delenergy v_delpress 
+       0          300    -945.9873    -936.0989    45359.818            0 -1.4551915e-11 
+      10    280.68558   -945.35055   -936.09878    46326.919            0 2.910383e-11 
+      20    228.73618   -943.63789   -936.09844    48903.598            0            0 
+      30    160.53661   -941.38948   -936.09798    52222.083            0 -2.910383e-11 
+      40    97.732944   -939.31899   -936.09758    55176.875            0 2.1827873e-11 
+      50    59.165961   -938.04759    -936.0974    56850.103            0 -1.4551915e-11 
+      60    53.124678   -937.84857   -936.09751    56878.948            0 7.2759576e-12 
+      70    74.623347    -938.5575   -936.09782    55565.237            0            0 
+      80     109.4762   -939.70663   -936.09815    53665.652            0 2.1827873e-11 
+      90    142.02657   -940.77975   -936.09837      52001.1            0 -1.4551915e-11 
+     100    161.73598   -941.42945   -936.09842    51114.997            0 1.4551915e-11 
+Loop time of 3.54317 on 4 procs for 100 steps with 256 atoms
+
+Performance: 1.219 ns/day, 19.684 hours/ns, 28.223 timesteps/s
+98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.1375     | 3.3058     | 3.469      |   6.5 | 93.30
+Neigh   | 0.000284   | 0.00031975 | 0.000352   |   0.0 |  0.01
+Comm    | 0.071607   | 0.23492    | 0.40336    |  24.6 |  6.63
+Output  | 0.001189   | 0.0012315  | 0.001347   |   0.2 |  0.03
+Modify  | 0.000311   | 0.00032725 | 0.000351   |   0.0 |  0.01
+Other   |            | 0.0005298  |            |       |  0.01
+
+Nlocal:        64.0000 ave          71 max          57 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Nghost:        1373.00 ave        1380 max        1366 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Neighs:         0.00000 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:      10779.5 ave       11978 max        9604 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+
+Total # of neighbors = 43118
+Ave neighs/atom = 168.42969
+Neighbor list builds = 1
+Dangerous builds = 0
+
+Total wall time: 0:00:03

examples/USER/pace/log.03Feb2021.pace.recursive.g++.1

@@ -0,0 +1,108 @@
+LAMMPS (24 Dec 2020)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
+  using 1 OpenMP thread(s) per MPI task
+# simple test of fcc Cu with ACE recursive
+
+units		metal
+atom_style	atomic
+
+neighbor	0.3 bin
+neigh_modify	 every 2 delay 10 check yes
+
+variable	a equal 3.597
+lattice		fcc $a
+lattice		fcc 3.597
+Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000
+region		box block 0 4 0 4 0 4
+create_box	1 box
+Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000)
+  1 by 1 by 1 MPI processor grid
+create_atoms	1 box
+Created 256 atoms
+  create_atoms CPU = 0.000 seconds
+
+mass		1 26.98
+
+group		Al type 1
+256 atoms in group Al
+
+pair_style 	pace recursive
+ACE version: 2021.2.3
+Recursive evaluator is used
+pair_coeff  * * Cu-PBE-core-rep.ace Cu
+Loading Cu-PBE-core-rep.ace
+Total number of basis functions
+	Cu: 16 (r=1) 726 (r>1)
+Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
+
+velocity        all create 300 8728 loop geom
+timestep        0.0005
+fix		1 all nve
+
+compute  	eatom all pe/atom
+compute  	energy all reduce sum c_eatom
+variable 	delenergy equal c_energy-pe
+
+compute  	satom all stress/atom NULL
+compute  	str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable 	delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
+
+thermo 		10
+thermo_style    custom step temp epair etotal press v_delenergy v_delpress
+
+run		100
+Neighbor list info ...
+  update every 2 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.7
+  ghost atom cutoff = 7.7
+  binsize = 3.85, bins = 4 4 4
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair pace, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.036 | 4.036 | 4.036 Mbytes
+Step Temp E_pair TotEng Press v_delenergy v_delpress 
+       0          300    -945.9873    -936.0989    45359.818            0            0 
+      10    280.68558   -945.35055   -936.09878    46326.919            0 5.8207661e-11 
+      20    228.73618   -943.63789   -936.09844    48903.598            0 1.4551915e-11 
+      30    160.53661   -941.38948   -936.09798    52222.083            0 7.2759576e-11 
+      40    97.732944   -939.31899   -936.09758    55176.875            0 -5.8207661e-11 
+      50    59.165961   -938.04759    -936.0974    56850.103            0            0 
+      60    53.124678   -937.84857   -936.09751    56878.948            0 8.7311491e-11 
+      70    74.623347    -938.5575   -936.09782    55565.237            0 -1.4551915e-11 
+      80     109.4762   -939.70663   -936.09815    53665.652            0 2.1827873e-11 
+      90    142.02657   -940.77975   -936.09837      52001.1            0 2.910383e-11 
+     100    161.73598   -941.42945   -936.09842    51114.997            0            0 
+Loop time of 9.31437 on 1 procs for 100 steps with 256 atoms
+
+Performance: 0.464 ns/day, 51.746 hours/ns, 10.736 timesteps/s
+99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 9.3103     | 9.3103     | 9.3103     |   0.0 | 99.96
+Neigh   | 0.001214   | 0.001214   | 0.001214   |   0.0 |  0.01
+Comm    | 0.001176   | 0.001176   | 0.001176   |   0.0 |  0.01
+Output  | 0.000827   | 0.000827   | 0.000827   |   0.0 |  0.01
+Modify  | 0.000479   | 0.000479   | 0.000479   |   0.0 |  0.01
+Other   |            | 0.000363   |            |       |  0.00
+
+Nlocal:        256.000 ave         256 max         256 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        2201.00 ave        2201 max        2201 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:         0.00000 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:      43118.0 ave       43118 max       43118 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 43118
+Ave neighs/atom = 168.42969
+Neighbor list builds = 1
+Dangerous builds = 0
+
+Total wall time: 0:00:09

examples/USER/pace/log.03Feb2021.pace.recursive.g++.4

@@ -0,0 +1,108 @@
+LAMMPS (24 Dec 2020)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94)
+  using 1 OpenMP thread(s) per MPI task
+# simple test of fcc Cu with ACE recursive
+
+units		metal
+atom_style	atomic
+
+neighbor	0.3 bin
+neigh_modify	 every 2 delay 10 check yes
+
+variable	a equal 3.597
+lattice		fcc $a
+lattice		fcc 3.597
+Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000
+region		box block 0 4 0 4 0 4
+create_box	1 box
+Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 256 atoms
+  create_atoms CPU = 0.000 seconds
+
+mass		1 26.98
+
+group		Al type 1
+256 atoms in group Al
+
+pair_style 	pace recursive
+ACE version: 2021.2.3
+Recursive evaluator is used
+pair_coeff  * * Cu-PBE-core-rep.ace Cu
+Loading Cu-PBE-core-rep.ace
+Total number of basis functions
+	Cu: 16 (r=1) 726 (r>1)
+Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
+
+velocity        all create 300 8728 loop geom
+timestep        0.0005
+fix		1 all nve
+
+compute  	eatom all pe/atom
+compute  	energy all reduce sum c_eatom
+variable 	delenergy equal c_energy-pe
+
+compute  	satom all stress/atom NULL
+compute  	str all reduce sum c_satom[1] c_satom[2] c_satom[3]
+variable 	delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press
+
+thermo 		10
+thermo_style    custom step temp epair etotal press v_delenergy v_delpress
+
+run		100
+Neighbor list info ...
+  update every 2 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.7
+  ghost atom cutoff = 7.7
+  binsize = 3.85, bins = 4 4 4
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair pace, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.005 | 4.005 | 4.005 Mbytes
+Step Temp E_pair TotEng Press v_delenergy v_delpress 
+       0          300    -945.9873    -936.0989    45359.818            0 -5.0931703e-11 
+      10    280.68558   -945.35055   -936.09878    46326.919            0 1.4551915e-11 
+      20    228.73618   -943.63789   -936.09844    48903.598            0            0 
+      30    160.53661   -941.38948   -936.09798    52222.083            0 -2.910383e-11 
+      40    97.732944   -939.31899   -936.09758    55176.875            0            0 
+      50    59.165961   -938.04759    -936.0974    56850.103            0 -2.910383e-11 
+      60    53.124678   -937.84857   -936.09751    56878.948            0 1.4551915e-11 
+      70    74.623347    -938.5575   -936.09782    55565.237            0 3.6379788e-11 
+      80     109.4762   -939.70663   -936.09815    53665.652            0 -7.2759576e-12 
+      90    142.02657   -940.77975   -936.09837      52001.1            0 -2.910383e-11 
+     100    161.73598   -941.42945   -936.09842    51114.997            0 7.2759576e-12 
+Loop time of 2.91339 on 4 procs for 100 steps with 256 atoms
+
+Performance: 1.483 ns/day, 16.185 hours/ns, 34.324 timesteps/s
+98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.5753     | 2.723      | 2.8656     |   6.3 | 93.46
+Neigh   | 0.000308   | 0.000365   | 0.00046    |   0.0 |  0.01
+Comm    | 0.045106   | 0.18792    | 0.33552    |  24.1 |  6.45
+Output  | 0.001213   | 0.001259   | 0.001388   |   0.2 |  0.04
+Modify  | 0.000304   | 0.00033    | 0.00037    |   0.0 |  0.01
+Other   |            | 0.0005595  |            |       |  0.02
+
+Nlocal:        64.0000 ave          71 max          57 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Nghost:        1373.00 ave        1380 max        1366 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+Neighs:         0.00000 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:      10779.5 ave       11978 max        9604 min
+Histogram: 1 0 0 0 1 1 0 0 0 1
+
+Total # of neighbors = 43118
+Ave neighs/atom = 168.42969
+Neighbor list builds = 1
+Dangerous builds = 0
+
+Total wall time: 0:00:03

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);
+    return new Hello(lmp);
-    hello.command(argc,argv);
 }
 
 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);
 }

lib/pace/.gitignore

@@ -0,0 +1,2 @@
+/src
+/libpace.a

lib/pace/Install.py

@@ -0,0 +1,105 @@
+# TODO#!/usr/bin/env python
+
+"""
+Install.py tool to download, compile, and setup the pace library
+used to automate the steps described in the README file in this dir
+"""
+
+from __future__ import print_function
+import sys, os, subprocess, shutil
+from argparse import ArgumentParser
+
+sys.path.append('..')
+from install_helpers import fullpath, geturl, checkmd5sum
+
+# settings
+
+thisdir = fullpath('.')
+version = 'v.2021.4.9'
+
+# known checksums for different PACE versions. used to validate the download.
+checksums = { \
+        'v.2021.2.3.upd2' : '8fd1162724d349b930e474927197f20d', 
+        'v.2021.4.9'      : '4db54962fbd6adcf8c18d46e1798ceb5',          
+        }
+
+
+parser = ArgumentParser(prog='Install.py',
+                        description="LAMMPS library build wrapper script")
+
+
+# help message
+
+HELP = """
+Syntax from src dir: make lib-pace args="-b"
+                 or: make lib-pace args="-b -v version"
+Syntax from lib dir: python Install.py -b 
+                 or: python Install.py -b -v version 
+
+Examples:
+
+make lib-pace args="-b" # install default version of PACE lib
+make lib-pace args="-b -v version" # install specified version of PACE lib
+
+
+"""
+
+pgroup = parser.add_mutually_exclusive_group()
+pgroup.add_argument("-b", "--build", action="store_true",
+                    help="download and build base PACE  library")
+parser.add_argument("-v", "--version", default=version, choices=checksums.keys(),
+                    help="set version of PACE library to download and build (default: %s)" % version)
+parser.add_argument("-vv", "--verbose", action="store_true",
+                    help="be more verbose about is happening while this script runs")
+
+args = parser.parse_args()
+
+# print help message and exit, if neither build nor path options are given
+if not args.build:
+  parser.print_help()
+  sys.exit(HELP)
+
+buildflag = args.build
+
+verboseflag = args.verbose
+version = args.version
+
+
+archive_extension = "tar.gz"
+url = "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/%s.%s" % (version, archive_extension)
+unarchived_folder_name = "lammps-user-pace-%s"%(version)
+
+# download PACE tarball, unpack, build PACE
+if buildflag:
+
+  # download entire tarball
+
+  print("Downloading pace tarball ...")
+  archive_filename = "%s.%s" % (version, archive_extension)
+  download_filename = "%s/%s" % (thisdir, archive_filename)
+  print("Downloading from ",url," to ",download_filename, end=" ")
+  geturl(url, download_filename)
+  print(" done")
+
+  # verify downloaded archive integrity via md5 checksum, if known.
+  if version in checksums:
+    if not checkmd5sum(checksums[version], archive_filename):
+      sys.exit("Checksum for pace library does not match")
+
+  print("Unpacking pace tarball ...")
+  src_folder = thisdir+"/src"
+  cmd = 'cd "%s"; rm -rf "%s"; tar -xvf %s; mv %s %s' % (thisdir, src_folder, archive_filename, unarchived_folder_name, src_folder)
+  subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
+
+  # build
+  print("Building libpace ...")
+  cmd = 'make lib -j2'
+  txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
+  if verboseflag:
+    print(txt.decode("UTF-8"))
+
+#   remove source files
+
+  print("Removing pace build files and archive ...")
+  cmd = 'rm %s; make clean-build' % (download_filename)
+  subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)

lib/pace/Makefile

@@ -0,0 +1,37 @@
+SHELL = /bin/sh
+
+# ------ FILES ------
+
+SRC_FILES = $(wildcard src/USER-PACE/*.cpp)
+SRC = $(filter-out src/USER-PACE/pair_pace.cpp, $(SRC_FILES))
+
+# ------ DEFINITIONS ------
+
+LIB = libpace.a
+OBJ =   $(SRC:.cpp=.o)
+
+
+# ------ SETTINGS ------
+CXXFLAGS = -O3 -fPIC -Isrc/USER-PACE
+
+ARCHIVE =	ar
+ARCHFLAG =	-rc
+USRLIB =
+SYSLIB =
+
+# ------ MAKE PROCEDURE ------
+
+lib: $(OBJ)
+	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
+
+# ------ COMPILE RULES ------
+
+%.o: %.cpp
+	$(CXX) $(CXXFLAGS) -c $< -o $@
+
+# ------ CLEAN ------
+clean-all:
+	-rm -f *~ $(OBJ) $(LIB)
+
+clean-build:
+	-rm -f *~ $(OBJ)

lib/pace/Makefile.lammps

@@ -0,0 +1,3 @@
+pace_SYSINC =-I../../lib/pace/src/USER-PACE
+pace_SYSLIB = -L../../lib/pace/ -lpace
+pace_SYSPATH =

lib/pace/README

@@ -0,0 +1,18 @@
+This directory contains files required to use the USER-PACE package,
+which 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. 
+This package was written by Yury Lysogorskiy and others
+at ICAMS, the Interdisciplinary Centre for Advanced Materials Simulation, 
+Ruhr University Bochum, Germany, http://www.icams.de
+
+You can type "make lib-pace" from the src directory to see help on
+how to download and build this library via make commands, or you can
+do the same thing by typing "python Install.py" from within this
+directory.
+
+More information about the USER-PACE implementation of ACE 
+is available here:
+
+https://github.com/ICAMS/lammps-user-pace

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

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)
 

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()

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,
 )

src/.gitignore

@@ -32,6 +32,9 @@
 /pair_kim.cpp
 /pair_kim.h
 
+/pair_pace.cpp
+/pair_pace.h
+
 /superpose3d.h
 
 /kokkos.cpp

src/COMPRESS/dump_atom_gz.cpp

@@ -11,24 +11,18 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "dump_atom_gz.h"
 #include "domain.h"
+#include "dump_atom_gz.h"
 #include "error.h"
 #include "update.h"
 
-
 #include <cstring>
 
-
 using namespace LAMMPS_NS;
 
 DumpAtomGZ::DumpAtomGZ(LAMMPS *lmp, int narg, char **arg) :
   DumpAtom(lmp, narg, arg)
 {
-  gzFp = nullptr;
-
-  compression_level = Z_BEST_COMPRESSION;
-
   if (!compressed)
     error->all(FLERR,"Dump atom/gz only writes compressed files");
 }
@@ -37,9 +31,6 @@ DumpAtomGZ::DumpAtomGZ(LAMMPS *lmp, int narg, char **arg) :
 
 DumpAtomGZ::~DumpAtomGZ()
 {
-  if (gzFp) gzclose(gzFp);
-  gzFp = nullptr;
-  fp = nullptr;
 }
 
 /* ----------------------------------------------------------------------
@@ -80,7 +71,9 @@ void DumpAtomGZ::openfile()
         nameslist[numfiles] = utils::strdup(filecurrent);
         ++numfiles;
       } else {
-        remove(nameslist[fileidx]);
+        if (remove(nameslist[fileidx]) != 0) {
+          error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx]));
+        }
         delete[] nameslist[fileidx];
         nameslist[fileidx] = utils::strdup(filecurrent);
         fileidx = (fileidx + 1) % maxfiles;
@@ -91,17 +84,12 @@ void DumpAtomGZ::openfile()
   // each proc with filewriter = 1 opens a file
 
   if (filewriter) {
-    std::string mode;
+    try {
-    if (append_flag) {
+      writer.open(filecurrent, append_flag);
-      mode = fmt::format("ab{}", compression_level);
+    } catch (FileWriterException &e) {
-    } else {
+      error->one(FLERR, e.what());
-      mode = fmt::format("wb{}", compression_level);
+    }
   }
-
-    gzFp = gzopen(filecurrent, mode.c_str());
-
-    if (gzFp == nullptr) error->one(FLERR,"Cannot open dump file");
-  } else gzFp = nullptr;
 
   // delete string with timestep replaced
 
@@ -112,29 +100,34 @@ void DumpAtomGZ::openfile()
 
 void DumpAtomGZ::write_header(bigint ndump)
 {
+  std::string header;
+
   if ((multiproc) || (!multiproc && me == 0)) {
     if (unit_flag && !unit_count) {
       ++unit_count;
-      gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style);
+      header = fmt::format("ITEM: UNITS\n{}\n",update->unit_style);
     }
-    if (time_flag) gzprintf(gzFp,"ITEM: TIME\n%.16g\n",compute_time());
 
-    gzprintf(gzFp,"ITEM: TIMESTEP\n");
+    if (time_flag) {
-    gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
+      header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time());
-    gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");
-    gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
-    if (domain->triclinic == 0) {
-      gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr);
-      gzprintf(gzFp,"%-1.16e %-1.16e\n",boxxlo,boxxhi);
-      gzprintf(gzFp,"%-1.16e %-1.16e\n",boxylo,boxyhi);
-      gzprintf(gzFp,"%-1.16e %-1.16e\n",boxzlo,boxzhi);
-    } else {
-      gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);
-      gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxxlo,boxxhi,boxxy);
-      gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxylo,boxyhi,boxxz);
-      gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxzlo,boxzhi,boxyz);
     }
-    gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);
+
+    header += fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep);
+    header += fmt::format("ITEM: NUMBER OF ATOMS\n{}\n", ndump);
+    if (domain->triclinic == 0) {
+      header += fmt::format("ITEM: BOX BOUNDS {}\n", boundstr);
+      header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxxlo, boxxhi);
+      header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxylo, boxyhi);
+      header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxzlo, boxzhi);
+    } else {
+      header += fmt::format("ITEM: BOX BOUNDS xy xz yz {}\n", boundstr);
+      header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxxlo, boxxhi, boxxy);
+      header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxylo, boxyhi, boxxz);
+      header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxzlo, boxzhi, boxyz);
+    }
+    header += fmt::format("ITEM: ATOMS {}\n", columns);
+
+    writer.write(header.c_str(), header.length());
   }
 }
 
@@ -142,7 +135,33 @@ void DumpAtomGZ::write_header(bigint ndump)
 
 void DumpAtomGZ::write_data(int n, double *mybuf)
 {
-  gzwrite(gzFp,mybuf,sizeof(char)*n);
+  if (buffer_flag == 1) {
+    writer.write(mybuf, n);
+  } else {
+    constexpr size_t VBUFFER_SIZE = 256;
+    char vbuffer[VBUFFER_SIZE];
+    int m = 0;
+    for (int i = 0; i < n; i++) {
+      int written = 0;
+      if (image_flag == 1) {
+        written = snprintf(vbuffer, VBUFFER_SIZE, format,
+              static_cast<tagint> (mybuf[m]), static_cast<int> (mybuf[m+1]),
+              mybuf[m+2],mybuf[m+3],mybuf[m+4], static_cast<int> (mybuf[m+5]),
+              static_cast<int> (mybuf[m+6]), static_cast<int> (mybuf[m+7]));
+      } else {
+        written = snprintf(vbuffer, VBUFFER_SIZE, format,
+              static_cast<tagint> (mybuf[m]), static_cast<int> (mybuf[m+1]),
+              mybuf[m+2],mybuf[m+3],mybuf[m+4]);
+      }
+      if (written > 0) {
+        writer.write(vbuffer, written);
+      } else if (written < 0) {
+        error->one(FLERR, "Error while writing dump atom/gz output");
+      }
+
+      m += size_one;
+    }
+  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -152,11 +171,11 @@ void DumpAtomGZ::write()
   DumpAtom::write();
   if (filewriter) {
     if (multifile) {
-      gzclose(gzFp);
+      writer.close();
-      gzFp = nullptr;
     } else {
-      if (flush_flag)
+      if (flush_flag && writer.isopen()) {
-        gzflush(gzFp,Z_SYNC_FLUSH);
+        writer.flush();
+      }
     }
   }
 }
@@ -167,15 +186,16 @@ int DumpAtomGZ::modify_param(int narg, char **arg)
 {
   int consumed = DumpAtom::modify_param(narg, arg);
   if (consumed == 0) {
+    try {
       if (strcmp(arg[0],"compression_level") == 0) {
         if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
-      int min_level = Z_DEFAULT_COMPRESSION;
+        int compression_level = utils::inumeric(FLERR, arg[1], false, lmp);
-      int max_level = Z_BEST_COMPRESSION;
+        writer.setCompressionLevel(compression_level);
-      compression_level = utils::inumeric(FLERR, arg[1], false, lmp);
-      if (compression_level < min_level || compression_level > max_level)
-        error->all(FLERR, fmt::format("Illegal dump_modify command: compression level must in the range of [{}, {}]", min_level, max_level));
         return 2;
       }
+    } catch (FileWriterException &e) {
+      error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what()));
+    }
   }
   return consumed;
 }

src/COMPRESS/dump_atom_gz.h

@@ -21,7 +21,7 @@ DumpStyle(atom/gz,DumpAtomGZ)
 #define LMP_DUMP_ATOM_GZ_H
 
 #include "dump_atom.h"
-#include <zlib.h>
+#include "gz_file_writer.h"
 
 namespace LAMMPS_NS {
 
@@ -31,8 +31,7 @@ class DumpAtomGZ : public DumpAtom {
   virtual ~DumpAtomGZ();
 
  protected:
-  int compression_level;
+  GzFileWriter writer;
-  gzFile gzFp;  // file pointer for the compressed output stream
 
   virtual void openfile();
   virtual void write_header(bigint);

src/COMPRESS/dump_atom_zstd.cpp

@@ -43,7 +43,7 @@ DumpAtomZstd::~DumpAtomZstd()
 
 /* ----------------------------------------------------------------------
    generic opening of a dump file
-   ASCII or binary or zstdipped
+   ASCII or binary or compressed
    some derived classes override this function
 ------------------------------------------------------------------------- */
 
@@ -79,7 +79,9 @@ void DumpAtomZstd::openfile()
         nameslist[numfiles] = utils::strdup(filecurrent);
         ++numfiles;
       } else {
-        remove(nameslist[fileidx]);
+        if (remove(nameslist[fileidx]) != 0) {
+          error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx]));
+        }
         delete[] nameslist[fileidx];
         nameslist[fileidx] = utils::strdup(filecurrent);
         fileidx = (fileidx + 1) % maxfiles;
@@ -90,12 +92,8 @@ void DumpAtomZstd::openfile()
   // each proc with filewriter = 1 opens a file
 
   if (filewriter) {
-    if (append_flag) {
-      error->one(FLERR, "dump/zstd currently doesn't support append");
-    }
-
     try {
-      writer.open(filecurrent);
+      writer.open(filecurrent, append_flag);
     } catch (FileWriterException &e) {
       error->one(FLERR, e.what());
     }
@@ -145,7 +143,33 @@ void DumpAtomZstd::write_header(bigint ndump)
 
 void DumpAtomZstd::write_data(int n, double *mybuf)
 {
+  if (buffer_flag == 1) {
     writer.write(mybuf, n);
+  } else {
+    constexpr size_t VBUFFER_SIZE = 256;
+    char vbuffer[VBUFFER_SIZE];
+    int m = 0;
+    for (int i = 0; i < n; i++) {
+      int written = 0;
+      if (image_flag == 1) {
+        written = snprintf(vbuffer, VBUFFER_SIZE, format,
+              static_cast<tagint> (mybuf[m]), static_cast<int> (mybuf[m+1]),
+              mybuf[m+2],mybuf[m+3],mybuf[m+4], static_cast<int> (mybuf[m+5]),
+              static_cast<int> (mybuf[m+6]), static_cast<int> (mybuf[m+7]));
+      } else {
+        written = snprintf(vbuffer, VBUFFER_SIZE, format,
+              static_cast<tagint> (mybuf[m]), static_cast<int> (mybuf[m+1]),
+              mybuf[m+2],mybuf[m+3],mybuf[m+4]);
+      }
+      if (written > 0) {
+        writer.write(vbuffer, written);
+      } else if (written < 0) {
+        error->one(FLERR, "Error while writing dump atom/gz output");
+      }
+
+      m += size_one;
+    }
+  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -184,7 +208,7 @@ int DumpAtomZstd::modify_param(int narg, char **arg)
         return 2;
       }
     } catch (FileWriterException &e) {
-      error->one(FLERR, e.what());
+      error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what()));
     }
   }
   return consumed;

src/COMPRESS/dump_cfg_gz.cpp

@@ -11,41 +11,30 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "dump_cfg_gz.h"
 #include "atom.h"
 #include "domain.h"
+#include "dump_cfg_gz.h"
 #include "error.h"
 #include "update.h"
 
-
 #include <cstring>
 
-
 using namespace LAMMPS_NS;
 #define UNWRAPEXPAND 10.0
 
 DumpCFGGZ::DumpCFGGZ(LAMMPS *lmp, int narg, char **arg) :
   DumpCFG(lmp, narg, arg)
 {
-  gzFp = nullptr;
-
-  compression_level = Z_BEST_COMPRESSION;
-
   if (!compressed)
     error->all(FLERR,"Dump cfg/gz only writes compressed files");
 }
 
-
 /* ---------------------------------------------------------------------- */
 
 DumpCFGGZ::~DumpCFGGZ()
 {
-  if (gzFp) gzclose(gzFp);
-  gzFp = nullptr;
-  fp = nullptr;
 }
 
-
 /* ----------------------------------------------------------------------
    generic opening of a dump file
    ASCII or binary or gzipped
@@ -84,7 +73,9 @@ void DumpCFGGZ::openfile()
         nameslist[numfiles] = utils::strdup(filecurrent);
         ++numfiles;
       } else {
-        remove(nameslist[fileidx]);
+        if (remove(nameslist[fileidx]) != 0) {
+          error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx]));
+        }
         delete[] nameslist[fileidx];
         nameslist[fileidx] = utils::strdup(filecurrent);
         fileidx = (fileidx + 1) % maxfiles;
@@ -95,17 +86,12 @@ void DumpCFGGZ::openfile()
   // each proc with filewriter = 1 opens a file
 
   if (filewriter) {
-    std::string mode;
+    try {
-    if (append_flag) {
+      writer.open(filecurrent, append_flag);
-      mode = fmt::format("ab{}", compression_level);
+    } catch (FileWriterException &e) {
-    } else {
+      error->one(FLERR, e.what());
-      mode = fmt::format("wb{}", compression_level);
+    }
   }
-
-    gzFp = gzopen(filecurrent, mode.c_str());
-
-    if (gzFp == nullptr) error->one(FLERR,"Cannot open dump file");
-  } else gzFp = nullptr;
 
   // delete string with timestep replaced
 
@@ -127,30 +113,95 @@ void DumpCFGGZ::write_header(bigint n)
   if (atom->peri_flag) scale = atom->pdscale;
   else if (unwrapflag == 1) scale = UNWRAPEXPAND;
 
-  char str[64];
+  std::string header = fmt::format("Number of particles = {}\n", n);
-  sprintf(str,"Number of particles = %s\n",BIGINT_FORMAT);
+  header += fmt::format("A = {0:g} Angstrom (basic length-scale)\n", scale);
-  gzprintf(gzFp,str,n);
+  header += fmt::format("H0(1,1) = {0:g} A\n",domain->xprd);
-  gzprintf(gzFp,"A = %g Angstrom (basic length-scale)\n",scale);
+  header += fmt::format("H0(1,2) = 0 A \n");
-  gzprintf(gzFp,"H0(1,1) = %g A\n",domain->xprd);
+  header += fmt::format("H0(1,3) = 0 A \n");
-  gzprintf(gzFp,"H0(1,2) = 0 A \n");
+  header += fmt::format("H0(2,1) = {0:g} A \n",domain->xy);
-  gzprintf(gzFp,"H0(1,3) = 0 A \n");
+  header += fmt::format("H0(2,2) = {0:g} A\n",domain->yprd);
-  gzprintf(gzFp,"H0(2,1) = %g A \n",domain->xy);
+  header += fmt::format("H0(2,3) = 0 A \n");
-  gzprintf(gzFp,"H0(2,2) = %g A\n",domain->yprd);
+  header += fmt::format("H0(3,1) = {0:g} A \n",domain->xz);
-  gzprintf(gzFp,"H0(2,3) = 0 A \n");
+  header += fmt::format("H0(3,2) = {0:g} A \n",domain->yz);
-  gzprintf(gzFp,"H0(3,1) = %g A \n",domain->xz);
+  header += fmt::format("H0(3,3) = {0:g} A\n",domain->zprd);
-  gzprintf(gzFp,"H0(3,2) = %g A \n",domain->yz);
+  header += fmt::format(".NO_VELOCITY.\n");
-  gzprintf(gzFp,"H0(3,3) = %g A\n",domain->zprd);
+  header += fmt::format("entry_count = {}\n",nfield-2);
-  gzprintf(gzFp,".NO_VELOCITY.\n");
-  gzprintf(gzFp,"entry_count = %d\n",nfield-2);
   for (int i = 0; i < nfield-5; i++)
-    gzprintf(gzFp,"auxiliary[%d] = %s\n",i,auxname[i]);
+    header += fmt::format("auxiliary[{}] = {}\n",i,auxname[i]);
+
+  writer.write(header.c_str(), header.length());
 }
 
 /* ---------------------------------------------------------------------- */
 
 void DumpCFGGZ::write_data(int n, double *mybuf)
 {
-  gzwrite(gzFp,mybuf,sizeof(char)*n);
+  if (buffer_flag) {
+    writer.write(mybuf, n);
+  } else {
+    constexpr size_t VBUFFER_SIZE = 256;
+    char vbuffer[VBUFFER_SIZE];
+    if (unwrapflag == 0) {
+      int m = 0;
+      for (int i = 0; i < n; i++) {
+        for (int j = 0; j < size_one; j++) {
+          int written = 0;
+          if (j == 0) {
+            written = snprintf(vbuffer, VBUFFER_SIZE, "%f \n", mybuf[m]);
+          } else if (j == 1) {
+            written = snprintf(vbuffer, VBUFFER_SIZE, "%s \n", typenames[(int) mybuf[m]]);
+          } else if (j >= 2) {
+            if (vtype[j] == Dump::INT)
+              written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int> (mybuf[m]));
+            else if (vtype[j] == Dump::DOUBLE)
+              written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]);
+            else if (vtype[j] == Dump::STRING)
+              written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], typenames[(int) mybuf[m]]);
+            else if (vtype[j] == Dump::BIGINT)
+              written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<bigint> (mybuf[m]));
+          }
+          if (written > 0) {
+            writer.write(vbuffer, written);
+          } else if (written < 0) {
+            error->one(FLERR, "Error while writing dump cfg/gz output");
+          }
+          m++;
+        }
+        writer.write("\n", 1);
+      }
+    } else if (unwrapflag == 1) {
+      int m = 0;
+      for (int i = 0; i < n; i++) {
+        for (int j = 0; j < size_one; j++) {
+          int written = 0;
+          if (j == 0) {
+            written = snprintf(vbuffer, VBUFFER_SIZE, "%f \n", mybuf[m]);
+          } else if (j == 1) {
+            written = snprintf(vbuffer, VBUFFER_SIZE, "%s \n", typenames[(int) mybuf[m]]);
+          } else if (j >= 2 && j <= 4) {
+            double unwrap_coord = (mybuf[m] - 0.5)/UNWRAPEXPAND + 0.5;
+            written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], unwrap_coord);
+          } else if (j >= 5) {
+            if (vtype[j] == Dump::INT)
+              written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int> (mybuf[m]));
+            else if (vtype[j] == Dump::DOUBLE)
+              written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]);
+            else if (vtype[j] == Dump::STRING)
+              written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], typenames[(int) mybuf[m]]);
+            else if (vtype[j] == Dump::BIGINT)
+              written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<bigint> (mybuf[m]));
+          }
+          if (written > 0) {
+            writer.write(vbuffer, written);
+          } else if (written < 0) {
+            error->one(FLERR, "Error while writing dump cfg/gz output");
+          }
+          m++;
+        }
+        writer.write("\n", 1);
+      }
+    }
+  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -160,11 +211,11 @@ void DumpCFGGZ::write()
   DumpCFG::write();
   if (filewriter) {
     if (multifile) {
-      gzclose(gzFp);
+      writer.close();
-      gzFp = nullptr;
     } else {
-      if (flush_flag)
+      if (flush_flag && writer.isopen()) {
-        gzflush(gzFp,Z_SYNC_FLUSH);
+        writer.flush();
+      }
     }
   }
 }
@@ -175,16 +226,16 @@ int DumpCFGGZ::modify_param(int narg, char **arg)
 {
   int consumed = DumpCFG::modify_param(narg, arg);
   if (consumed == 0) {
+    try {
       if (strcmp(arg[0],"compression_level") == 0) {
         if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
-      int min_level = Z_DEFAULT_COMPRESSION;
+        int compression_level = utils::inumeric(FLERR, arg[1], false, lmp);
-      int max_level = Z_BEST_COMPRESSION;
+        writer.setCompressionLevel(compression_level);
-      compression_level = utils::inumeric(FLERR, arg[1], false, lmp);
-      if (compression_level < min_level || compression_level > max_level)
-        error->all(FLERR, fmt::format("Illegal dump_modify command: compression level must in the range of [{}, {}]", min_level, max_level));
         return 2;
       }
+    } catch (FileWriterException &e) {
+      error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what()));
+    }
   }
   return consumed;
 }
-

src/COMPRESS/dump_cfg_gz.h

@@ -21,7 +21,7 @@ DumpStyle(cfg/gz,DumpCFGGZ)
 #define LMP_DUMP_CFG_GZ_H
 
 #include "dump_cfg.h"
-#include <zlib.h>
+#include "gz_file_writer.h"
 
 namespace LAMMPS_NS {
 
@@ -31,8 +31,7 @@ class DumpCFGGZ : public DumpCFG {
   virtual ~DumpCFGGZ();
 
  protected:
-  int compression_level;
+  GzFileWriter writer;
-  gzFile gzFp;  // file pointer for the compressed output stream
 
   virtual void openfile();
   virtual void write_header(bigint);

src/COMPRESS/dump_cfg_zstd.cpp

@@ -21,7 +21,6 @@
 #include "domain.h"
 #include "dump_cfg_zstd.h"
 #include "error.h"
-#include "file_writer.h"
 #include "update.h"
 
 #include <cstring>
@@ -46,7 +45,7 @@ DumpCFGZstd::~DumpCFGZstd()
 
 /* ----------------------------------------------------------------------
    generic opening of a dump file
-   ASCII or binary or zstdipped
+   ASCII or binary or compressed
    some derived classes override this function
 ------------------------------------------------------------------------- */
 
@@ -82,7 +81,9 @@ void DumpCFGZstd::openfile()
         nameslist[numfiles] = utils::strdup(filecurrent);
         ++numfiles;
       } else {
-        remove(nameslist[fileidx]);
+        if (remove(nameslist[fileidx]) != 0) {
+          error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx]));
+        }
         delete[] nameslist[fileidx];
         nameslist[fileidx] = utils::strdup(filecurrent);
         fileidx = (fileidx + 1) % maxfiles;
@@ -147,7 +148,72 @@ void DumpCFGZstd::write_header(bigint n)
 
 void DumpCFGZstd::write_data(int n, double *mybuf)
 {
+  if (buffer_flag) {
     writer.write(mybuf, n);
+  } else {
+    constexpr size_t VBUFFER_SIZE = 256;
+    char vbuffer[VBUFFER_SIZE];
+    if (unwrapflag == 0) {
+      int m = 0;
+      for (int i = 0; i < n; i++) {
+        for (int j = 0; j < size_one; j++) {
+          int written = 0;
+          if (j == 0) {
+            written = snprintf(vbuffer, VBUFFER_SIZE, "%f \n", mybuf[m]);
+          } else if (j == 1) {
+            written = snprintf(vbuffer, VBUFFER_SIZE, "%s \n", typenames[(int) mybuf[m]]);
+          } else if (j >= 2) {
+            if (vtype[j] == Dump::INT)
+              written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int> (mybuf[m]));
+            else if (vtype[j] == Dump::DOUBLE)
+              written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]);
+            else if (vtype[j] == Dump::STRING)
+              written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], typenames[(int) mybuf[m]]);
+            else if (vtype[j] == Dump::BIGINT)
+              written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<bigint> (mybuf[m]));
+          }
+          if (written > 0) {
+            writer.write(vbuffer, written);
+          } else if (written < 0) {
+            error->one(FLERR, "Error while writing dump cfg/gz output");
+          }
+          m++;
+        }
+        writer.write("\n", 1);
+      }
+    } else if (unwrapflag == 1) {
+      int m = 0;
+      for (int i = 0; i < n; i++) {
+        for (int j = 0; j < size_one; j++) {
+          int written = 0;
+          if (j == 0) {
+            written = snprintf(vbuffer, VBUFFER_SIZE, "%f \n", mybuf[m]);
+          } else if (j == 1) {
+            written = snprintf(vbuffer, VBUFFER_SIZE, "%s \n", typenames[(int) mybuf[m]]);
+          } else if (j >= 2 && j <= 4) {
+            double unwrap_coord = (mybuf[m] - 0.5)/UNWRAPEXPAND + 0.5;
+            written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], unwrap_coord);
+          } else if (j >= 5) {
+            if (vtype[j] == Dump::INT)
+              written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int> (mybuf[m]));
+            else if (vtype[j] == Dump::DOUBLE)
+              written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]);
+            else if (vtype[j] == Dump::STRING)
+              written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], typenames[(int) mybuf[m]]);
+            else if (vtype[j] == Dump::BIGINT)
+              written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<bigint> (mybuf[m]));
+          }
+          if (written > 0) {
+            writer.write(vbuffer, written);
+          } else if (written < 0) {
+            error->one(FLERR, "Error while writing dump cfg/gz output");
+          }
+          m++;
+        }
+        writer.write("\n", 1);
+      }
+    }
+  }
 }
 
 /* ---------------------------------------------------------------------- */

src/COMPRESS/dump_custom_gz.cpp

@@ -11,39 +11,28 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "dump_custom_gz.h"
 #include "domain.h"
+#include "dump_custom_gz.h"
 #include "error.h"
 #include "update.h"
 
-
 #include <cstring>
 
-
 using namespace LAMMPS_NS;
 
 DumpCustomGZ::DumpCustomGZ(LAMMPS *lmp, int narg, char **arg) :
   DumpCustom(lmp, narg, arg)
 {
-  gzFp = nullptr;
-
-  compression_level = Z_BEST_COMPRESSION;
-
   if (!compressed)
     error->all(FLERR,"Dump custom/gz only writes compressed files");
 }
 
-
 /* ---------------------------------------------------------------------- */
 
 DumpCustomGZ::~DumpCustomGZ()
 {
-  if (gzFp) gzclose(gzFp);
-  gzFp = nullptr;
-  fp = nullptr;
 }
 
-
 /* ----------------------------------------------------------------------
    generic opening of a dump file
    ASCII or binary or gzipped
@@ -82,7 +71,9 @@ void DumpCustomGZ::openfile()
         nameslist[numfiles] = utils::strdup(filecurrent);
         ++numfiles;
       } else {
-        remove(nameslist[fileidx]);
+        if (remove(nameslist[fileidx]) != 0) {
+          error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx]));
+        }
         delete[] nameslist[fileidx];
         nameslist[fileidx] = utils::strdup(filecurrent);
         fileidx = (fileidx + 1) % maxfiles;
@@ -93,17 +84,12 @@ void DumpCustomGZ::openfile()
   // each proc with filewriter = 1 opens a file
 
   if (filewriter) {
-    std::string mode;
+    try {
-    if (append_flag) {
+      writer.open(filecurrent, append_flag);
-      mode = fmt::format("ab{}", compression_level);
+    } catch (FileWriterException &e) {
-    } else {
+      error->one(FLERR, e.what());
-      mode = fmt::format("wb{}", compression_level);
+    }
   }
-
-    gzFp = gzopen(filecurrent, mode.c_str());
-
-    if (gzFp == nullptr) error->one(FLERR,"Cannot open dump file");
-  } else gzFp = nullptr;
 
   // delete string with timestep replaced
 
@@ -112,29 +98,34 @@ void DumpCustomGZ::openfile()
 
 void DumpCustomGZ::write_header(bigint ndump)
 {
+  std::string header;
+
   if ((multiproc) || (!multiproc && me == 0)) {
     if (unit_flag && !unit_count) {
       ++unit_count;
-      gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style);
+      header = fmt::format("ITEM: UNITS\n{}\n",update->unit_style);
     }
-    if (time_flag) gzprintf(gzFp,"ITEM: TIME\n%.16g\n",compute_time());
 
-    gzprintf(gzFp,"ITEM: TIMESTEP\n");
+    if (time_flag) {
-    gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
+      header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time());
-    gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n");
-    gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
-    if (domain->triclinic == 0) {
-      gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr);
-      gzprintf(gzFp,"%-1.16e %-1.16e\n",boxxlo,boxxhi);
-      gzprintf(gzFp,"%-1.16e %-1.16e\n",boxylo,boxyhi);
-      gzprintf(gzFp,"%-1.16e %-1.16e\n",boxzlo,boxzhi);
-    } else {
-      gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);
-      gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxxlo,boxxhi,boxxy);
-      gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxylo,boxyhi,boxxz);
-      gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxzlo,boxzhi,boxyz);
     }
-    gzprintf(gzFp,"ITEM: ATOMS %s\n",columns);
+
+    header += fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep);
+    header += fmt::format("ITEM: NUMBER OF ATOMS\n{}\n", ndump);
+    if (domain->triclinic == 0) {
+      header += fmt::format("ITEM: BOX BOUNDS {}\n", boundstr);
+      header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxxlo, boxxhi);
+      header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxylo, boxyhi);
+      header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxzlo, boxzhi);
+    } else {
+      header += fmt::format("ITEM: BOX BOUNDS xy xz yz {}\n", boundstr);
+      header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxxlo, boxxhi, boxxy);
+      header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxylo, boxyhi, boxxz);
+      header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxzlo, boxzhi, boxyz);
+    }
+    header += fmt::format("ITEM: ATOMS {}\n", columns);
+
+    writer.write(header.c_str(), header.length());
   }
 }
 
@@ -142,7 +133,35 @@ void DumpCustomGZ::write_header(bigint ndump)
 
 void DumpCustomGZ::write_data(int n, double *mybuf)
 {
-  gzwrite(gzFp,mybuf,sizeof(char)*n);
+  if (buffer_flag == 1) {
+    writer.write(mybuf, n);
+  } else {
+    constexpr size_t VBUFFER_SIZE = 256;
+    char vbuffer[VBUFFER_SIZE];
+    int m = 0;
+    for (int i = 0; i < n; i++) {
+      for (int j = 0; j < nfield; j++) {
+        int written = 0;
+        if (vtype[j] == Dump::INT) {
+          written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int> (mybuf[m]));
+        } else if (vtype[j] == Dump::DOUBLE) {
+          written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]);
+        } else if (vtype[j] == Dump::STRING) {
+          written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], typenames[(int) mybuf[m]]);
+        } else if (vtype[j] == Dump::BIGINT) {
+          written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<bigint> (mybuf[m]));
+        }
+
+        if (written > 0) {
+          writer.write(vbuffer, written);
+        } else if (written < 0) {
+          error->one(FLERR, "Error while writing dump custom/gz output");
+        }
+        m++;
+      }
+      writer.write("\n", 1);
+    }
+  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -152,11 +171,11 @@ void DumpCustomGZ::write()
   DumpCustom::write();
   if (filewriter) {
     if (multifile) {
-      gzclose(gzFp);
+      writer.close();
-      gzFp = nullptr;
     } else {
-      if (flush_flag)
+      if (flush_flag && writer.isopen()) {
-        gzflush(gzFp,Z_SYNC_FLUSH);
+        writer.flush();
+      }
     }
   }
 }
@@ -167,15 +186,16 @@ int DumpCustomGZ::modify_param(int narg, char **arg)
 {
   int consumed = DumpCustom::modify_param(narg, arg);
   if (consumed == 0) {
+    try {
       if (strcmp(arg[0],"compression_level") == 0) {
         if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
-      int min_level = Z_DEFAULT_COMPRESSION;
+        int compression_level = utils::inumeric(FLERR, arg[1], false, lmp);
-      int max_level = Z_BEST_COMPRESSION;
+        writer.setCompressionLevel(compression_level);
-      compression_level = utils::inumeric(FLERR, arg[1], false, lmp);
-      if (compression_level < min_level || compression_level > max_level)
-        error->all(FLERR, fmt::format("Illegal dump_modify command: compression level must in the range of [{}, {}]", min_level, max_level));
         return 2;
       }
+    } catch (FileWriterException &e) {
+      error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what()));
+    }
   }
   return consumed;
 }

src/COMPRESS/dump_custom_gz.h

@@ -21,7 +21,7 @@ DumpStyle(custom/gz,DumpCustomGZ)
 #define LMP_DUMP_CUSTOM_GZ_H
 
 #include "dump_custom.h"
-#include <zlib.h>
+#include "gz_file_writer.h"
 
 namespace LAMMPS_NS {
 
@@ -31,8 +31,7 @@ class DumpCustomGZ : public DumpCustom {
   virtual ~DumpCustomGZ();
 
  protected:
-  int compression_level;
+  GzFileWriter writer;
-  gzFile gzFp;  // file pointer for the compressed output stream
 
   virtual void openfile();
   virtual void write_header(bigint);

src/COMPRESS/dump_custom_zstd.cpp

@@ -20,7 +20,6 @@
 #include "domain.h"
 #include "dump_custom_zstd.h"
 #include "error.h"
-#include "file_writer.h"
 #include "update.h"
 
 #include <cstring>
@@ -79,7 +78,9 @@ void DumpCustomZstd::openfile()
         nameslist[numfiles] = utils::strdup(filecurrent);
         ++numfiles;
       } else {
-        remove(nameslist[fileidx]);
+        if (remove(nameslist[fileidx]) != 0) {
+          error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx]));
+        }
         delete[] nameslist[fileidx];
         nameslist[fileidx] = utils::strdup(filecurrent);
         fileidx = (fileidx + 1) % maxfiles;
@@ -145,7 +146,35 @@ void DumpCustomZstd::write_header(bigint ndump)
 
 void DumpCustomZstd::write_data(int n, double *mybuf)
 {
+  if (buffer_flag == 1) {
     writer.write(mybuf, n);
+  } else {
+    constexpr size_t VBUFFER_SIZE = 256;
+    char vbuffer[VBUFFER_SIZE];
+    int m = 0;
+    for (int i = 0; i < n; i++) {
+      for (int j = 0; j < nfield; j++) {
+        int written = 0;
+        if (vtype[j] == Dump::INT) {
+          written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int> (mybuf[m]));
+        } else if (vtype[j] == Dump::DOUBLE) {
+          written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]);
+        } else if (vtype[j] == Dump::STRING) {
+          written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], typenames[(int) mybuf[m]]);
+        } else if (vtype[j] == Dump::BIGINT) {
+          written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<bigint> (mybuf[m]));
+        }
+
+        if (written > 0) {
+          writer.write(vbuffer, written);
+        } else if (written < 0) {
+          error->one(FLERR, "Error while writing dump custom/gz output");
+        }
+        m++;
+      }
+      writer.write("\n", 1);
+    }
+  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -184,7 +213,7 @@ int DumpCustomZstd::modify_param(int narg, char **arg)
         return 2;
       }
     } catch (FileWriterException &e) {
-      error->one(FLERR, e.what());
+      error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what()));
     }
   }
   return consumed;

src/COMPRESS/dump_local_gz.cpp

@@ -11,39 +11,28 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "dump_local_gz.h"
 #include "domain.h"
+#include "dump_local_gz.h"
 #include "error.h"
 #include "update.h"
 
-
 #include <cstring>
 
-
 using namespace LAMMPS_NS;
 
 DumpLocalGZ::DumpLocalGZ(LAMMPS *lmp, int narg, char **arg) :
   DumpLocal(lmp, narg, arg)
 {
-  gzFp = nullptr;
-
-  compression_level = Z_BEST_COMPRESSION;
-
   if (!compressed)
     error->all(FLERR,"Dump local/gz only writes compressed files");
 }
 
-
 /* ---------------------------------------------------------------------- */
 
 DumpLocalGZ::~DumpLocalGZ()
 {
-  if (gzFp) gzclose(gzFp);
-  gzFp = nullptr;
-  fp = nullptr;
 }
 
-
 /* ----------------------------------------------------------------------
    generic opening of a dump file
    ASCII or binary or gzipped
@@ -82,7 +71,9 @@ void DumpLocalGZ::openfile()
         nameslist[numfiles] = utils::strdup(filecurrent);
         ++numfiles;
       } else {
-        remove(nameslist[fileidx]);
+        if (remove(nameslist[fileidx]) != 0) {
+          error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx]));
+        }
         delete[] nameslist[fileidx];
         nameslist[fileidx] = utils::strdup(filecurrent);
         fileidx = (fileidx + 1) % maxfiles;
@@ -93,17 +84,12 @@ void DumpLocalGZ::openfile()
   // each proc with filewriter = 1 opens a file
 
   if (filewriter) {
-    std::string mode;
+    try {
-    if (append_flag) {
+      writer.open(filecurrent, append_flag);
-      mode = fmt::format("ab{}", compression_level);
+    } catch (FileWriterException &e) {
-    } else {
+      error->one(FLERR, e.what());
-      mode = fmt::format("wb{}", compression_level);
+    }
   }
-
-    gzFp = gzopen(filecurrent, mode.c_str());
-
-    if (gzFp == nullptr) error->one(FLERR,"Cannot open dump file");
-  } else gzFp = nullptr;
 
   // delete string with timestep replaced
 
@@ -112,29 +98,34 @@ void DumpLocalGZ::openfile()
 
 void DumpLocalGZ::write_header(bigint ndump)
 {
+  std::string header;
+
   if ((multiproc) || (!multiproc && me == 0)) {
     if (unit_flag && !unit_count) {
       ++unit_count;
-      gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style);
+      header = fmt::format("ITEM: UNITS\n{}\n",update->unit_style);
     }
-    if (time_flag) gzprintf(gzFp,"ITEM: TIME\n%.16g\n",compute_time());
 
-    gzprintf(gzFp,"ITEM: TIMESTEP\n");
+    if (time_flag) {
-    gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep);
+      header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time());
-    gzprintf(gzFp,"ITEM: NUMBER OF %s\n",label);
-    gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
-    if (domain->triclinic) {
-      gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);
-      gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxxlo,boxxhi,boxxy);
-      gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxylo,boxyhi,boxxz);
-      gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxzlo,boxzhi,boxyz);
-    } else {
-      gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr);
-      gzprintf(gzFp,"%-1.16e %-1.16e\n",boxxlo,boxxhi);
-      gzprintf(gzFp,"%-1.16e %-1.16e\n",boxylo,boxyhi);
-      gzprintf(gzFp,"%-1.16e %-1.16e\n",boxzlo,boxzhi);
     }
-    gzprintf(gzFp,"ITEM: %s %s\n",label,columns);
+
+    header += fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep);
+    header += fmt::format("ITEM: NUMBER OF {}\n{}\n", label, ndump);
+    if (domain->triclinic == 0) {
+      header += fmt::format("ITEM: BOX BOUNDS {}\n", boundstr);
+      header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxxlo, boxxhi);
+      header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxylo, boxyhi);
+      header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxzlo, boxzhi);
+    } else {
+      header += fmt::format("ITEM: BOX BOUNDS xy xz yz {}\n", boundstr);
+      header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxxlo, boxxhi, boxxy);
+      header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxylo, boxyhi, boxxz);
+      header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxzlo, boxzhi, boxyz);
+    }
+    header += fmt::format("ITEM: {} {}\n", label, columns);
+
+    writer.write(header.c_str(), header.length());
   }
 }
 
@@ -143,19 +134,32 @@ void DumpLocalGZ::write_header(bigint ndump)
 void DumpLocalGZ::write_data(int n, double *mybuf)
 {
   if (buffer_flag == 1) {
-    gzwrite(gzFp,mybuf,sizeof(char)*n);
+    writer.write(mybuf, sizeof(char)*n);
-
   } else {
-    int i,j;
+    constexpr size_t VBUFFER_SIZE = 256;
+    char vbuffer[VBUFFER_SIZE];
     int m = 0;
-    for (i = 0; i < n; i++) {
+    for (int i = 0; i < n; i++) {
-      for (j = 0; j < size_one; j++) {
+      for (int j = 0; j < size_one; j++) {
-        if (vtype[j] == INT)
+        int written = 0;
-          gzprintf(gzFp,vformat[j],static_cast<int> (mybuf[m]));
+        if (vtype[j] == Dump::INT) {
-        else gzprintf(gzFp,vformat[j],mybuf[m]);
+          written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int> (mybuf[m]));
+        } else if (vtype[j] == Dump::DOUBLE) {
+          written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]);
+        } else if (vtype[j] == Dump::BIGINT) {
+          written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<bigint> (mybuf[m]));
+        } else {
+          written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]);
+        }
+
+        if (written > 0) {
+          writer.write(vbuffer, written);
+        } else if (written < 0) {
+          error->one(FLERR, "Error while writing dump local/gz output");
+        }
         m++;
       }
-      gzprintf(gzFp,"\n");
+      writer.write("\n", 1);
     }
   }
 }
@@ -167,11 +171,11 @@ void DumpLocalGZ::write()
   DumpLocal::write();
   if (filewriter) {
     if (multifile) {
-      gzclose(gzFp);
+      writer.close();
-      gzFp = nullptr;
     } else {
-      if (flush_flag)
+      if (flush_flag && writer.isopen()) {
-        gzflush(gzFp,Z_SYNC_FLUSH);
+        writer.flush();
+      }
     }
   }
 }
@@ -182,15 +186,16 @@ int DumpLocalGZ::modify_param(int narg, char **arg)
 {
   int consumed = DumpLocal::modify_param(narg, arg);
   if (consumed == 0) {
+    try {
       if (strcmp(arg[0],"compression_level") == 0) {
         if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
-      int min_level = Z_DEFAULT_COMPRESSION;
+        int compression_level = utils::inumeric(FLERR, arg[1], false, lmp);
-      int max_level = Z_BEST_COMPRESSION;
+        writer.setCompressionLevel(compression_level);
-      compression_level = utils::inumeric(FLERR, arg[1], false, lmp);
-      if (compression_level < min_level || compression_level > max_level)
-        error->all(FLERR, fmt::format("Illegal dump_modify command: compression level must in the range of [{}, {}]", min_level, max_level));
         return 2;
       }
+    } catch (FileWriterException &e) {
+      error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what()));
+    }
   }
   return consumed;
 }

src/COMPRESS/dump_local_gz.h

@@ -21,7 +21,7 @@ DumpStyle(local/gz,DumpLocalGZ)
 #define LMP_DUMP_LOCAL_GZ_H
 
 #include "dump_local.h"
-#include <zlib.h>
+#include "gz_file_writer.h"
 
 namespace LAMMPS_NS {
 
@@ -31,8 +31,7 @@ class DumpLocalGZ : public DumpLocal {
   virtual ~DumpLocalGZ();
 
  protected:
-  int compression_level;
+  GzFileWriter writer;
-  gzFile gzFp;  // file pointer for the compressed output stream
 
   virtual void openfile();
   virtual void write_header(bigint);

src/COMPRESS/dump_local_zstd.cpp

@@ -17,15 +17,13 @@
 
 #ifdef LAMMPS_ZSTD
 
-#include "dump_local_zstd.h"
 #include "domain.h"
+#include "dump_local_zstd.h"
 #include "error.h"
 #include "update.h"
 
-
 #include <cstring>
 
-
 using namespace LAMMPS_NS;
 
 DumpLocalZstd::DumpLocalZstd(LAMMPS *lmp, int narg, char **arg) :
@@ -42,7 +40,6 @@ DumpLocalZstd::~DumpLocalZstd()
 {
 }
 
-
 /* ----------------------------------------------------------------------
    generic opening of a dump file
    ASCII or binary or gzipped
@@ -81,7 +78,9 @@ void DumpLocalZstd::openfile()
         nameslist[numfiles] = utils::strdup(filecurrent);
         ++numfiles;
       } else {
-        remove(nameslist[fileidx]);
+        if (remove(nameslist[fileidx]) != 0) {
+          error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx]));
+        }
         delete[] nameslist[fileidx];
         nameslist[fileidx] = utils::strdup(filecurrent);
         fileidx = (fileidx + 1) % maxfiles;
@@ -145,7 +144,35 @@ void DumpLocalZstd::write_header(bigint ndump)
 
 void DumpLocalZstd::write_data(int n, double *mybuf)
 {
+  if (buffer_flag == 1) {
     writer.write(mybuf, sizeof(char)*n);
+  } else {
+    constexpr size_t VBUFFER_SIZE = 256;
+    char vbuffer[VBUFFER_SIZE];
+    int m = 0;
+    for (int i = 0; i < n; i++) {
+      for (int j = 0; j < size_one; j++) {
+        int written = 0;
+        if (vtype[j] == Dump::INT) {
+          written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<int> (mybuf[m]));
+        } else if (vtype[j] == Dump::DOUBLE) {
+          written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]);
+        } else if (vtype[j] == Dump::BIGINT) {
+          written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast<bigint> (mybuf[m]));
+        } else {
+          written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]);
+        }
+
+        if (written > 0) {
+          writer.write(vbuffer, written);
+        } else if (written < 0) {
+          error->one(FLERR, "Error while writing dump local/gz output");
+        }
+        m++;
+      }
+      writer.write("\n", 1);
+    }
+  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -184,7 +211,7 @@ int DumpLocalZstd::modify_param(int narg, char **arg)
         return 2;
       }
     } catch (FileWriterException &e) {
-      error->one(FLERR, e.what());
+      error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what()));
     }
   }
   return consumed;

src/COMPRESS/dump_xyz_gz.cpp

@@ -15,19 +15,13 @@
 #include "error.h"
 #include "update.h"
 
-
 #include <cstring>
 
-
 using namespace LAMMPS_NS;
 
 DumpXYZGZ::DumpXYZGZ(LAMMPS *lmp, int narg, char **arg) :
   DumpXYZ(lmp, narg, arg)
 {
-  gzFp = nullptr;
-
-  compression_level = Z_BEST_COMPRESSION;
-
   if (!compressed)
     error->all(FLERR,"Dump xyz/gz only writes compressed files");
 }
@@ -37,12 +31,8 @@ DumpXYZGZ::DumpXYZGZ(LAMMPS *lmp, int narg, char **arg) :
 
 DumpXYZGZ::~DumpXYZGZ()
 {
-  if (gzFp) gzclose(gzFp);
-  gzFp = nullptr;
-  fp = nullptr;
 }
 
-
 /* ----------------------------------------------------------------------
    generic opening of a dump file
    ASCII or binary or gzipped
@@ -81,7 +71,9 @@ void DumpXYZGZ::openfile()
         nameslist[numfiles] = utils::strdup(filecurrent);
         ++numfiles;
       } else {
-        remove(nameslist[fileidx]);
+        if (remove(nameslist[fileidx]) != 0) {
+          error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx]));
+        }
         delete[] nameslist[fileidx];
         nameslist[fileidx] = utils::strdup(filecurrent);
         fileidx = (fileidx + 1) % maxfiles;
@@ -92,17 +84,12 @@ void DumpXYZGZ::openfile()
   // each proc with filewriter = 1 opens a file
 
   if (filewriter) {
-    std::string mode;
+    try {
-    if (append_flag) {
+      writer.open(filecurrent, append_flag);
-      mode = fmt::format("ab{}", compression_level);
+    } catch (FileWriterException &e) {
-    } else {
+      error->one(FLERR, e.what());
-      mode = fmt::format("wb{}", compression_level);
+    }
   }
-
-    gzFp = gzopen(filecurrent, mode.c_str());
-
-    if (gzFp == nullptr) error->one(FLERR,"Cannot open dump file");
-  } else gzFp = nullptr;
 
   // delete string with timestep replaced
 
@@ -112,8 +99,9 @@ void DumpXYZGZ::openfile()
 void DumpXYZGZ::write_header(bigint ndump)
 {
   if (me == 0) {
-    gzprintf(gzFp,BIGINT_FORMAT "\n",ndump);
+    std::string header = fmt::format("{}\n", ndump);
-    gzprintf(gzFp,"Atoms. Timestep: " BIGINT_FORMAT "\n",update->ntimestep);
+    header += fmt::format("Atoms. Timestep: {}\n", update->ntimestep);
+    writer.write(header.c_str(), header.length());
   }
 }
 
@@ -121,7 +109,24 @@ void DumpXYZGZ::write_header(bigint ndump)
 
 void DumpXYZGZ::write_data(int n, double *mybuf)
 {
-  gzwrite(gzFp,mybuf,sizeof(char)*n);
+  if (buffer_flag) {
+    writer.write(mybuf, n);
+  } else {
+    constexpr size_t VBUFFER_SIZE = 256;
+    char vbuffer[VBUFFER_SIZE];
+    int m = 0;
+    for (int i = 0; i < n; i++) {
+      int written = snprintf(vbuffer, VBUFFER_SIZE, format,
+              typenames[static_cast<int> (mybuf[m+1])],
+              mybuf[m+2],mybuf[m+3],mybuf[m+4]);
+      if (written > 0) {
+        writer.write(vbuffer, written);
+      } else if (written < 0) {
+        error->one(FLERR, "Error while writing dump xyz/gz output");
+      }
+      m += size_one;
+    }
+  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -131,11 +136,11 @@ void DumpXYZGZ::write()
   DumpXYZ::write();
   if (filewriter) {
     if (multifile) {
-      gzclose(gzFp);
+      writer.close();
-      gzFp = nullptr;
     } else {
-      if (flush_flag)
+      if (flush_flag && writer.isopen()) {
-        gzflush(gzFp,Z_SYNC_FLUSH);
+        writer.flush();
+      }
     }
   }
 }
@@ -146,15 +151,16 @@ int DumpXYZGZ::modify_param(int narg, char **arg)
 {
   int consumed = DumpXYZ::modify_param(narg, arg);
   if (consumed == 0) {
+    try {
       if (strcmp(arg[0],"compression_level") == 0) {
         if (narg < 2) error->all(FLERR,"Illegal dump_modify command");
-      int min_level = Z_DEFAULT_COMPRESSION;
+        int compression_level = utils::inumeric(FLERR, arg[1], false, lmp);
-      int max_level = Z_BEST_COMPRESSION;
+        writer.setCompressionLevel(compression_level);
-      compression_level = utils::inumeric(FLERR, arg[1], false, lmp);
-      if (compression_level < min_level || compression_level > max_level)
-        error->all(FLERR, fmt::format("Illegal dump_modify command: compression level must in the range of [{}, {}]", min_level, max_level));
         return 2;
       }
+    } catch (FileWriterException &e) {
+      error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what()));
+    }
   }
   return consumed;
 }

src/COMPRESS/dump_xyz_gz.h

@@ -21,7 +21,7 @@ DumpStyle(xyz/gz,DumpXYZGZ)
 #define LMP_DUMP_XYZ_GZ_H
 
 #include "dump_xyz.h"
-#include <zlib.h>
+#include "gz_file_writer.h"
 
 namespace LAMMPS_NS {
 
@@ -31,8 +31,7 @@ class DumpXYZGZ : public DumpXYZ {
   virtual ~DumpXYZGZ();
 
  protected:
-  int compression_level;
+  GzFileWriter writer;
-  gzFile gzFp;  // file pointer for the compressed output stream
 
   virtual void openfile();
   virtual void write_header(bigint);

src/COMPRESS/dump_xyz_zstd.cpp

@@ -19,7 +19,6 @@
 
 #include "dump_xyz_zstd.h"
 #include "error.h"
-#include "file_writer.h"
 #include "update.h"
 
 #include <cstring>
@@ -79,7 +78,9 @@ void DumpXYZZstd::openfile()
         nameslist[numfiles] = utils::strdup(filecurrent);
         ++numfiles;
       } else {
-        remove(nameslist[fileidx]);
+        if (remove(nameslist[fileidx]) != 0) {
+          error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx]));
+        }
         delete[] nameslist[fileidx];
         nameslist[fileidx] = utils::strdup(filecurrent);
         fileidx = (fileidx + 1) % maxfiles;
@@ -119,7 +120,24 @@ void DumpXYZZstd::write_header(bigint ndump)
 
 void DumpXYZZstd::write_data(int n, double *mybuf)
 {
+  if (buffer_flag) {
     writer.write(mybuf, n);
+  } else {
+    constexpr size_t VBUFFER_SIZE = 256;
+    char vbuffer[VBUFFER_SIZE];
+    int m = 0;
+    for (int i = 0; i < n; i++) {
+      int written = snprintf(vbuffer, VBUFFER_SIZE, format,
+              typenames[static_cast<int> (mybuf[m+1])],
+              mybuf[m+2],mybuf[m+3],mybuf[m+4]);
+      if (written > 0) {
+        writer.write(vbuffer, written);
+      } else if (written < 0) {
+        error->one(FLERR, "Error while writing dump xyz/gz output");
+      }
+      m += size_one;
+    }
+  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -158,7 +176,7 @@ int DumpXYZZstd::modify_param(int narg, char **arg)
         return 2;
       }
     } catch (FileWriterException &e) {
-      error->one(FLERR, e.what());
+      error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what()));
     }
   }
   return consumed;

src/COMPRESS/gz_file_writer.cpp

@@ -0,0 +1,105 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://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.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Richard Berger (Temple U)
+------------------------------------------------------------------------- */
+
+#include "gz_file_writer.h"
+#include <stdio.h>
+#include "fmt/format.h"
+
+using namespace LAMMPS_NS;
+
+GzFileWriter::GzFileWriter() : FileWriter(),
+    compression_level(Z_BEST_COMPRESSION),
+    gzFp(nullptr)
+{
+}
+
+/* ---------------------------------------------------------------------- */
+
+GzFileWriter::~GzFileWriter()
+{
+  close();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GzFileWriter::open(const std::string &path, bool append)
+{
+    if (isopen()) return;
+
+    std::string mode;
+    if (append) {
+      mode = fmt::format("ab{}", mode, compression_level);
+    } else {
+      mode = fmt::format("wb{}", mode, compression_level);
+    }
+
+    gzFp = gzopen(path.c_str(), mode.c_str());
+
+    if (gzFp == nullptr)
+      throw FileWriterException(fmt::format("Could not open file '{}'", path));
+}
+
+/* ---------------------------------------------------------------------- */
+
+size_t GzFileWriter::write(const void * buffer, size_t length)
+{
+  if (!isopen()) return 0;
+
+  return gzwrite(gzFp, buffer, length);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GzFileWriter::flush()
+{
+  if (!isopen()) return;
+
+  gzflush(gzFp, Z_SYNC_FLUSH);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GzFileWriter::close()
+{
+  if (!isopen()) return;
+
+  gzclose(gzFp);
+  gzFp = nullptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
+bool GzFileWriter::isopen() const
+{
+  return gzFp;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void GzFileWriter::setCompressionLevel(int level)
+{
+  if (isopen())
+    throw FileWriterException("Compression level can not be changed while file is open");
+
+  const int min_level = Z_DEFAULT_COMPRESSION;
+  const int max_level = Z_BEST_COMPRESSION;
+
+  if (level < min_level || level > max_level)
+    throw FileWriterException(fmt::format("Compression level must in the range of [{}, {}]", min_level, max_level));
+
+  compression_level = level;
+}

src/COMPRESS/gz_file_writer.h

@@ -0,0 +1,47 @@
+/* -*- 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.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Richard Berger (Temple U)
+------------------------------------------------------------------------- */
+
+#ifndef LMP_GZ_FILE_WRITER_H
+#define LMP_GZ_FILE_WRITER_H
+
+#include "file_writer.h"
+#include <string>
+#include <zlib.h>
+#include <exception>
+
+namespace LAMMPS_NS {
+
+class GzFileWriter : public FileWriter {
+  int compression_level;
+
+  gzFile gzFp;  // file pointer for the compressed output stream
+public:
+    GzFileWriter();
+    virtual ~GzFileWriter();
+    virtual void open(const std::string &path, bool append = false) override;
+    virtual void close() override;
+    virtual void flush() override;
+    virtual size_t write(const void * buffer, size_t length) override;
+    virtual bool isopen() const override;
+
+    void setCompressionLevel(int level);
+};
+
+
+}
+
+#endif

src/COMPRESS/zstd_file_writer.cpp

@@ -46,11 +46,15 @@ ZstdFileWriter::~ZstdFileWriter()
 
 /* ---------------------------------------------------------------------- */
 
-void ZstdFileWriter::open(const std::string &path)
+void ZstdFileWriter::open(const std::string &path, bool append)
 {
     if (isopen()) return;
 
+    if (append) {
+      fp = fopen(path.c_str(), "ab");
+    } else {
       fp = fopen(path.c_str(), "wb");
+    }
 
     if (!fp) {
         throw FileWriterException(fmt::format("Could not open file '{}'", path));

src/COMPRESS/zstd_file_writer.h

@@ -38,7 +38,7 @@ class ZstdFileWriter : public FileWriter {
 public:
     ZstdFileWriter();
     virtual ~ZstdFileWriter();
-    virtual void open(const std::string &path) override;
+    virtual void open(const std::string &path, bool append = false) override;
     virtual void close() override;
     virtual void flush() override;
     virtual size_t write(const void * buffer, size_t length) override;

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 **);
 };
 

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

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);

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,

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.
+
+*/

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

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);
+      }
     }
   }
 }

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");
 
@@ -207,11 +205,14 @@ void FixQEQComb::post_force(int /*vflag*/)
   if (comb) {
     inum = comb->list->inum;
     ilist = comb->list->ilist;
-  }
+  } else if (comb3) {
-  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;

src/MC/fix_charge_regulation.h

@@ -0,0 +1,118 @@
+/* -*- 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.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing author: Tine Curk (tcurk5@gmail.com) and Jiaxing Yuan (yuanjiaxing123@hotmail.com)
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(charge/regulation,FixChargeRegulation)
+
+#else
+
+#ifndef LMP_FIX_CHARGE_REGULATION_H
+#define LMP_FIX_CHARGE_REGULATION_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+  class FixChargeRegulation : public Fix {
+  public:
+    FixChargeRegulation(class LAMMPS *, int, char **);
+    ~FixChargeRegulation();
+    int setmask();
+    void init();
+    void pre_exchange();
+    void forward_acid();
+    void backward_acid();
+    void forward_base();
+    void backward_base();
+    void forward_ions();
+    void forward_ions_multival();
+    void backward_ions();
+    void backward_ions_multival();
+    int get_random_particle(int, double, double, double *);
+    int insert_particle(int, double, double, double *);
+    double energy_full();
+    int particle_number(int, double);
+    int particle_number_xrd(int, double, double, double *);
+    double compute_vector(int n);
+    void assign_tags();
+    void options(int, char **);
+    void setThermoTemperaturePointer();
+    double memory_usage();
+
+  private:
+    int exclusion_group, exclusion_group_bit;
+    int nevery, seed;         // begin MC cycle every nevery MD timesteps, random seed
+    int nmc;                  // MC move attempts per cycle
+    double llength_unit_in_nm ; // LAMMPS unit of length in nm, needed since chemical potentials are in units of mol/l
+    double pH, pKa, pKb, pKs, pI_plus, pI_minus; // chemical potentials and equilibrium constant in log10 base
+    double c10pH, c10pKa, c10pKb, c10pOH, c10pI_plus, c10pI_minus; // 10 raised to chemical potential value, in units of concentration [mol/liter]
+    double pmcmoves[3];       // mc move attempt probability: acid, base, ion pair exchange
+    double pmcc;              // mc move cumulative attempt probability
+    int npart_xrd;            // # of particles (ions) within xrd
+    int npart_xrd2;           // # of particles (ions) within xrd
+    double vlocal_xrd;        // # local volume within xrd
+    bool only_salt_flag;      // true if performing only salt insertion/deletion, no acid/base dissociation.
+    bool add_tags_flag;       // true if each inserted atom gets its unique atom tag
+    int groupbitall;          // group bitmask for inserted atoms
+    int ngroups;              // number of group-ids for inserted atoms
+    char **groupstrings;      // list of group-ids for inserted atoms
+
+    // counters
+    unsigned long int nacid_attempts, nacid_successes, nbase_attempts, nbase_successes, nsalt_attempts, nsalt_successes;
+    int nacid_neutral, nacid_charged, nbase_neutral, nbase_charged, ncation, nanion; // particle type counts
+    int cr_nmax;              //  max number of local particles
+    double reservoir_temperature;
+    double beta, sigma, volume, volume_rx; // inverse temperature, speed, total volume, reacting volume
+    int salt_charge[2];       // charge of salt ions: [0] - cation, [1] - anion
+    int salt_charge_ratio;    // charge ratio when using multivalent ion exchange
+    double xlo, xhi, ylo, yhi, zlo, zhi; // box size
+    double energy_stored;     // full energy of old/current configuration
+    int triclinic;            // 0 = orthog box, 1 = triclinic
+    double *sublo, *subhi;    // triclinic size
+    int *ptype_ID;            // particle ID array
+    double overlap_cutoffsq;  // square distance cutoff for overlap
+    int overlap_flag;
+    int acid_type, cation_type, base_type, anion_type; // reacting atom types
+    int reaction_distance_flag;  // radial reaction restriction flag
+    double reaction_distance;    // max radial distance from acid/base for ion insertion
+
+
+    class Pair *pair;
+    class Compute *c_pe;         // energy compute pointer
+    class RanPark *random_equal; // random number generator
+    class RanPark *random_unequal; // random number generator
+    char *idftemp;               // pointer to the temperature fix
+    double *target_temperature_tcp;  // current temperature of the thermostat
+
+  };
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory.  Check the input script syntax and compare to the
+documentation for the command.  You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+Self-explanatory.
+
+*/

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;
+    neighbor->modify_params(fmt::format("exclude group {} all",group_id));
-    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;
   }
 
   // create a new group for temporary use with selected molecules

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;
+    neighbor->modify_params(fmt::format("exclude group {} all",group_id));
-    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;
   }
 
   // create a new group for temporary use with selected molecules