Merge branch 'develop' into rheo

.github/release_steps.md

@@ -110,7 +110,7 @@ git clone -b release --depth 10 https://github.com/lammps/lammps.git lammps-rele
 cmake -S lammps-release/cmake -B build-release -G Ninja -D CMAKE_INSTALL_PREFIX=$PWD/lammps-static -D CMAKE_TOOLCHAIN_FILE=/usr/musl/share/cmake/linux-musl.cmake -C lammps-release/cmake/presets/most.cmake -C lammps-release/cmake/presets/kokkos-openmp.cmake -D DOWNLOAD_POTENTIALS=OFF -D BUILD_MPI=OFF -D BUILD_TESTING=OFF -D CMAKE_BUILD_TYPE=Release -D PKG_ATC=ON -D PKG_AWPMD=ON -D PKG_MANIFOLD=ON -D PKG_MESONT=ON -D PKG_MGPT=ON -D PKG_ML-PACE=ON -D PKG_ML-RANN=ON -D PKG_MOLFILE=ON -D PKG_PTM=ON -D PKG_QTB=ON -D PKG_SMTBQ=ON
 cmake --build build-release --target all
 cmake --build build-release --target install
-/usr/musl/bin/x86_64-linux-musl-strip lammps-static/bin/*
+/usr/musl/bin/x86_64-linux-musl-strip -g lammps-static/bin/*
 tar -czvvf ../lammps-linux-x86_64-4Feb2025.tar.gz lammps-static
 exit # fedora 41 container
 cd ..

.github/workflows/check-cpp23.yml

@@ -55,8 +55,8 @@ jobs:
       uses: actions/cache@v4
       with:
         path: ${{ env.CCACHE_DIR }}
-        key: linux-cpp23-ccache-${{ github.sha }}
+        key: linux-cpp23-ccache-${{ matrix.idx }}-${{ github.sha }}
-        restore-keys: linux-cpp23-ccache-
+        restore-keys: linux-cpp23-ccache-${{ matrix.idx }}
 
     - name: Building LAMMPS via CMake
       shell: bash

cmake/CMakeLists.txt

@@ -244,15 +244,6 @@ option(CMAKE_POSITION_INDEPENDENT_CODE "Create object compatible with shared lib
 option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
 option(BUILD_LAMMPS_GUI "Build and install the LAMMPS GUI" OFF)
 
-# Support using clang-tidy for C++ files with selected options
-set(ENABLE_CLANG_TIDY OFF CACHE BOOL "Include clang-tidy processing when compiling")
-if(ENABLE_CLANG_TIDY)
-  set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=-*,performance-trivially-destructible,performance-unnecessary-copy-initialization,performance-unnecessary-value-param,readability-redundant-control-flow,readability-redundant-declaration,readability-redundant-function-ptr-dereference,readability-redundant-member-init,readability-redundant-string-cstr,readability-redundant-string-init,readability-simplify-boolean-expr,readability-static-accessed-through-instance,readability-static-definition-in-anonymous-namespace,readability-qualified-auto,misc-unused-parameters,modernize-deprecated-ios-base-aliases,modernize-loop-convert,modernize-shrink-to-fit,modernize-use-auto,modernize-use-using,modernize-use-override,modernize-use-bool-literals,modernize-use-emplace,modernize-return-braced-init-list,modernize-use-equals-default,modernize-use-equals-delete,modernize-replace-random-shuffle,modernize-deprecated-headers,modernize-use-nullptr,modernize-use-noexcept,modernize-redundant-void-arg;-fix;-header-filter=.*,header-filter=library.h,header-filter=fmt/*.h" CACHE STRING "clang-tidy settings")
-else()
-  unset(CMAKE_CXX_CLANG_TIDY CACHE)
-endif()
-
-
 file(GLOB ALL_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
 file(GLOB MAIN_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/main.cpp)
 list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
@@ -277,6 +268,7 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
 set(STANDARD_PACKAGES
   ADIOS
   AMOEBA
+  APIP
   ASPHERE
   ATC
   AWPMD
@@ -476,6 +468,7 @@ pkg_depends(ELECTRODE KSPACE)
 pkg_depends(EXTRA-MOLECULE MOLECULE)
 pkg_depends(MESONT MOLECULE)
 pkg_depends(RHEO BPM)
+pkg_depends(APIP ML-PACE)
 
 # detect if we may enable OpenMP support by default
 set(BUILD_OMP_DEFAULT OFF)

cmake/Modules/Packages/ML-PACE.cmake

@@ -53,7 +53,13 @@ else()
       add_library(yaml-cpp::yaml-cpp ALIAS yaml-cpp)
     endif()
 
-    add_subdirectory(${lib-pace} build-pace)
+    # fixup yaml-cpp/emitterutils.cpp for GCC 15+ until patch is applied
+    file(READ ${lib-pace}/yaml-cpp/src/emitterutils.cpp yaml_emitterutils)
+    string(REPLACE "#include <sstream>" "#include <sstream>\n#include <cinttypes>" yaml_tmp_emitterutils "${yaml_emitterutils}")
+    string(REPLACE "#include <cinttypes>\n#include <cinttypes>" "#include <cinttypes>" yaml_emitterutils "${yaml_tmp_emitterutils}")
+    file(WRITE ${lib-pace}/yaml-cpp/src/emitterutils.cpp "${yaml_emitterutils}")
+
+    add_subdirectory(${lib-pace} build-pace EXCLUDE_FROM_ALL)
     set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
 
     if(CMAKE_PROJECT_NAME STREQUAL "lammps")

cmake/Modules/Tools.cmake

@@ -6,6 +6,10 @@ if(BUILD_TOOLS)
   add_executable(stl_bin2txt ${LAMMPS_TOOLS_DIR}/stl_bin2txt.cpp)
   install(TARGETS stl_bin2txt DESTINATION ${CMAKE_INSTALL_BINDIR})
 
+  add_executable(reformat-json ${LAMMPS_TOOLS_DIR}/json/reformat-json.cpp)
+  target_include_directories(reformat-json PRIVATE ${LAMMPS_SOURCE_DIR})
+  install(TARGETS reformat-json DESTINATION ${CMAKE_INSTALL_BINDIR})
+
   include(CheckGeneratorSupport)
   if(CMAKE_GENERATOR_SUPPORT_FORTRAN)
     include(CheckLanguage)

cmake/presets/all_off.cmake

@@ -4,6 +4,7 @@
 set(ALL_PACKAGES
   ADIOS
   AMOEBA
+  APIP
   ASPHERE
   ATC
   AWPMD

cmake/presets/all_on.cmake

@@ -6,6 +6,7 @@
 set(ALL_PACKAGES
   ADIOS
   AMOEBA
+  APIP
   ASPHERE
   ATC
   AWPMD

cmake/presets/kokkos-cuda.cmake

@@ -1,9 +1,8 @@
 # preset that enables KOKKOS and selects CUDA compilation with OpenMP
-# enabled as well. The GPU architecture *must* match your hardware
+# enabled as well. The GPU architecture *must* match your hardware (If not manually set, Kokkos will try to autodetect it).
 set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_CUDA   ON CACHE BOOL "" FORCE)
-set(Kokkos_ARCH_PASCAL60 ON CACHE BOOL "" FORCE)
 set(BUILD_OMP ON CACHE BOOL "" FORCE)
 get_filename_component(NVCC_WRAPPER_CMD ${CMAKE_CURRENT_SOURCE_DIR}/../lib/kokkos/bin/nvcc_wrapper ABSOLUTE)
 set(CMAKE_CXX_COMPILER ${NVCC_WRAPPER_CMD} CACHE FILEPATH "" FORCE)

cmake/presets/nolib.cmake

@@ -3,6 +3,7 @@
 
 set(PACKAGES_WITH_LIB
   ADIOS
+  APIP
   ATC
   AWPMD
   COMPRESS

doc/Makefile

@@ -99,8 +99,6 @@ html: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJ
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build -E $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
-		touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
-		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
 		ln -sf Manual.html html/index.html;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
@@ -162,8 +160,6 @@ epub: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build -E $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
-		touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
-		sphinx-build $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		deactivate ;\
 	)
@@ -183,8 +179,6 @@ pdf: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build -E $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
-		touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
-		sphinx-build  $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		rst_anchor_check src/*.rst ;\

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "2 April 2025" "2025-04-02"
+.TH LAMMPS "1" "12 June 2025" "2025-06-12"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 2 April 2025
+\- Molecular Dynamics Simulator.  Version 12 June 2025
 
 .SH SYNOPSIS
 .B lmp

doc/src/Build_development.rst

@@ -28,28 +28,6 @@ variable VERBOSE set to 1:
 
 ----------
 
-.. _clang-tidy:
-
-Enable static code analysis with clang-tidy (CMake only)
---------------------------------------------------------
-
-The `clang-tidy tool <https://clang.llvm.org/extra/clang-tidy/>`_ is a
-static code analysis tool to diagnose (and potentially fix) typical
-programming errors or coding style violations.  It has a modular framework
-of tests that can be adjusted to help identifying problems before they
-become bugs and also assist in modernizing large code bases (like LAMMPS).
-It can be enabled for all C++ code with the following CMake flag
-
-.. code-block:: bash
-
-   -D ENABLE_CLANG_TIDY=value    # value = no (default) or yes
-
-With this flag enabled all source files will be processed twice, first to
-be compiled and then to be analyzed. Please note that the analysis can be
-significantly more time-consuming than the compilation itself.
-
-----------
-
 .. _iwyu_processing:
 
 Report missing and unneeded '#include' statements (CMake only)

doc/src/Build_extras.rst

@@ -35,6 +35,7 @@ This is the list of packages that may require additional steps.
    :columns: 6
 
    * :ref:`ADIOS <adios>`
+   * :ref:`APIP <apip>`
    * :ref:`ATC <atc>`
    * :ref:`AWPMD <awpmd>`
    * :ref:`COLVARS <colvar>`
@@ -1272,6 +1273,34 @@ systems.
 
 ----------
 
+.. _apip:
+
+APIP package
+-----------------------------
+
+The APIP package depends on the library of the
+:ref:`ML-PACE <ml-pace>` 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
+
+      No additional settings are needed besides ``-D PKG_APIP=yes``
+      and ``-D PKG_ML-PACE=yes``.
+      One can use a local version of the ML-PACE library instead of
+      automatically downloading the library as described :ref:`here <ml-pace>`.
+
+
+   .. tab:: Traditional make
+
+      You need to install the ML-PACE package *first* and follow
+      the instructions :ref:`here <ml-pace>` before installing
+      the APIP package.
+
+----------
+
 .. _atc:
 
 ATC package

doc/src/Commands_fix.rst

@@ -22,6 +22,7 @@ OPT.
    * :doc:`append/atoms <fix_append_atoms>`
    * :doc:`atc <fix_atc>`
    * :doc:`atom/swap <fix_atom_swap>`
+   * :doc:`atom_weight/apip <fix_atom_weight_apip>`
    * :doc:`ave/atom <fix_ave_atom>`
    * :doc:`ave/chunk <fix_ave_chunk>`
    * :doc:`ave/correlate <fix_ave_correlate>`
@@ -91,6 +92,8 @@ OPT.
    * :doc:`imd <fix_imd>`
    * :doc:`indent <fix_indent>`
    * :doc:`ipi <fix_ipi>`
+   * :doc:`lambda/apip <fix_lambda_apip>`
+   * :doc:`lambda_thermostat/apip <fix_lambda_thermostat_apip>`
    * :doc:`langevin (k) <fix_langevin>`
    * :doc:`langevin/drude <fix_langevin_drude>`
    * :doc:`langevin/eff <fix_langevin_eff>`
@@ -113,7 +116,6 @@ OPT.
    * :doc:`mvv/tdpd <fix_mvv_dpd>`
    * :doc:`neb <fix_neb>`
    * :doc:`neb/spin <fix_neb_spin>`
-   * :doc:`neighbor/swap <fix_neighbor_swap>`
    * :doc:`nonaffine/displacement <fix_nonaffine_displacement>`
    * :doc:`nph (ko) <fix_nh>`
    * :doc:`nph/asphere (o) <fix_nph_asphere>`

doc/src/Commands_kspace.rst

@@ -31,3 +31,5 @@ OPT.
    * :doc:`pppm/dielectric <kspace_style>`
    * :doc:`pppm/electrode (i) <kspace_style>`
    * :doc:`scafacos <kspace_style>`
+   * :doc:`zero <kspace_style>`
+

doc/src/Commands_pair.rst

@@ -96,7 +96,9 @@ OPT.
    * :doc:`eam/cd <pair_eam>`
    * :doc:`eam/cd/old <pair_eam>`
    * :doc:`eam/fs (gikot) <pair_eam>`
+   * :doc:`eam/fs/apip <pair_eam_apip>`
    * :doc:`eam/he <pair_eam>`
+   * :doc:`eam/apip <pair_eam_apip>`
    * :doc:`edip (o) <pair_edip>`
    * :doc:`edip/multi <pair_edip>`
    * :doc:`edpd (g) <pair_mesodpd>`
@@ -124,6 +126,9 @@ OPT.
    * :doc:`ilp/tmd (t) <pair_ilp_tmd>`
    * :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
    * :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`
+   * :doc:`lambda/input/apip <pair_lambda_input_apip>`
+   * :doc:`lambda/input/csp/apip <pair_lambda_input_apip>`
+   * :doc:`lambda/zone/apip <pair_lambda_zone_apip>`
    * :doc:`lcbop <pair_lcbop>`
    * :doc:`lebedeva/z <pair_lebedeva_z>`
    * :doc:`lennard/mdf <pair_mdf>`
@@ -237,6 +242,9 @@ OPT.
    * :doc:`oxrna2/coaxstk <pair_oxrna2>`
    * :doc:`pace (k) <pair_pace>`
    * :doc:`pace/extrapolation (k) <pair_pace>`
+   * :doc:`pace/apip <pair_pace_apip>`
+   * :doc:`pace/fast/apip <pair_pace_apip>`
+   * :doc:`pace/precise/apip <pair_pace_apip>`
    * :doc:`pedone (o) <pair_pedone>`
    * :doc:`pod (k) <pair_pod>`
    * :doc:`peri/eps <pair_peri>`

doc/src/Commands_removed.rst

@@ -15,7 +15,7 @@ with the direct alternative (if available) and print a warning.
 GJF formulation in fix langevin
 -------------------------------
 
-.. deprecated:: TBD
+.. deprecated:: 12Jun2025
 
 The *gjf* keyword in fix langevin is deprecated and will be removed
 soon.  The GJF functionality has been moved to its own fix style

doc/src/Developer_plugins.rst

@@ -68,24 +68,25 @@ 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, improper, kspace, or command styles
+     - Pointer to factory function for pair, bond, angle, dihedral, improper, kspace, command, or minimize styles
    * - creator.v2
-     - Pointer to factory function for compute, fix, or region styles
+     - Pointer to factory function for compute, fix, region, or run styles
    * - handle
      - Pointer to the open DSO file handle
 
 Only one of the two alternate creator entries can be used at a time and
 which of those is determined by the style of plugin. The "creator.v1"
 element is for factory functions of supported styles computing forces
-(i.e. pair, bond, angle, dihedral, or improper styles) or command styles
+(i.e. pair, bond, angle, dihedral, or improper styles), command styles,
-and the function takes as single argument the pointer to the LAMMPS
+or minimize styles and the function takes as single argument the pointer
-instance. The factory function is cast to the ``lammpsplugin_factory1``
+to the LAMMPS instance. The factory function is cast to the
-type before assignment.  The "creator.v2" element is for factory
+``lammpsplugin_factory1`` type before assignment.  The "creator.v2"
-functions creating an instance of a fix, compute, or region style and
+element is for factory functions creating an instance of a fix, compute,
-takes three arguments: a pointer to the LAMMPS instance, an integer with
+region, or run style and takes three arguments: a pointer to the LAMMPS
-the length of the argument list and a ``char **`` pointer to the list of
+instance, an integer with the length of the argument list and a ``char
-arguments. The factory function pointer needs to be cast to the
+**`` pointer to the list of arguments. The factory function pointer
-``lammpsplugin_factory2`` type before assignment.
+needs to be cast to the ``lammpsplugin_factory2`` type before
+assignment.
 
 Pair style example
 ^^^^^^^^^^^^^^^^^^
@@ -247,8 +248,8 @@ DSO handle.  The registration function is called with a pointer to the address
 of this struct and the pointer of the LAMMPS class.  The registration function
 will then add the factory function of the plugin style to the respective
 style map under the provided name.  It will also make a copy of the struct
-in a list of all loaded plugins and update the reference counter for loaded
+in a global list of all loaded plugins and update the reference counter for
-plugins from this specific DSO file.
+loaded plugins from this specific DSO file.
 
 The pair style itself (i.e. the PairMorse2 class in this example) can be
 written just like any other pair style that is included in LAMMPS.  For
@@ -263,6 +264,21 @@ the plugin will override the existing code.  This can be used to modify
 the behavior of existing styles or to debug new versions of them without
 having to re-compile or re-install all of LAMMPS.
 
+.. versionchanged:: 12Jun2025
+
+When using the :doc:`clear <clear>` command, plugins are not unloaded
+but restored to their respective style maps.  This also applies when
+multiple LAMMPS instances are created and deleted through the library
+interface.  The :doc:`plugin load <plugin>` load command may be issued
+again, but for existing plugins they will be skipped.  To replace
+plugins they must be explicitly unloaded with :doc:`plugin unload
+<plugin>`.  When multiple LAMMPS instances are created concurrently, any
+loaded plugins will be added to the global list of plugins, but are not
+immediately available to any LAMMPS instance that was created before
+loading the plugin.  To "import" such plugins, the :doc:`plugin restore
+<plugin>` may be used.  Plugins are only removed when they are explicitly
+unloaded or the LAMMPS interface is "finalized".
+
 Compiling plugins
 ^^^^^^^^^^^^^^^^^
 

doc/src/Developer_updating.rst

@@ -615,7 +615,7 @@ This change is **required** or else the code will not compile.
 FLERR as first argument to minimum image functions in Domain class
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. versionchanged:: TBD
+.. versionchanged:: 12Jun2025
 
 The ``Domain::minimum_image()`` and ``Domain::minimum_image_big()``
 functions were changed to take the ``FLERR`` macros as first argument.

doc/src/Errors_common.rst

@@ -1,48 +1,66 @@
-Common problems
+Common issues that are often regarded as bugs
-===============
+=============================================
 
-If two LAMMPS runs do not produce the exact same answer on different
+The list below are some random notes on behavior of LAMMPS that is
+sometimes unexpected or even considered a bug.  Most of the time, these
+are just issues of understanding how LAMMPS is implemented and
+parallelized.  Please also have a look at the :doc:`Error details
+discussions page <Errors_details>` that contains recommendations for
+tracking down issues and explanations for error messages that may
+sometimes be confusing or need additional explanations.
+
+- A LAMMPS simulation typically has two stages, 1) issuing commands
+  and 2) run or minimize.  Most LAMMPS errors are detected in stage 1),
+  others at the beginning of stage 2), and finally others like a bond
+  stretching too far may or lost atoms or bonds may not occur until the
+  middle of a run.
+
+- If two LAMMPS runs do not produce the exact same answer on different
   machines or different numbers of processors, this is typically not a
   bug.  In theory you should get identical answers on any number of
   processors and on any machine.  In practice, numerical round-off can
   cause slight differences and eventual divergence of molecular dynamics
   phase space trajectories within a few 100s or few 1000s of timesteps.
+  This can be triggered by different ordering of atoms due to different
+  domain decompositions, but also through different CPU architectures,
+  different operating systems, different compilers or compiler versions,
+  different compiler optimization levels, different FFT libraries.
   However, the statistical properties of the two runs (e.g. average
   energy or temperature) should still be the same.
 
-If the :doc:`velocity <velocity>` command is used to set initial atom
+- If the :doc:`velocity <velocity>` command is used to set initial atom
   velocities, a particular atom can be assigned a different velocity
   when the problem is run on a different number of processors or on
   different machines.  If this happens, the phase space trajectories of
   the two simulations will rapidly diverge.  See the discussion of the
-*loop* option in the :doc:`velocity <velocity>` command for details and
+  *loop* option in the :doc:`velocity <velocity>` command for details
-options that avoid this issue.
+  and options that avoid this issue.
 
-Similarly, the :doc:`create_atoms <create_atoms>` command generates a
+- Similarly, the :doc:`create_atoms <create_atoms>` command generates a
   lattice of atoms.  For the same physical system, the ordering and
   numbering of atoms by atom ID may be different depending on the number
   of processors.
 
-Some commands use random number generators which may be setup to
+- Some commands use random number generators which may be setup to
   produce different random number streams on each processor and hence
   will produce different effects when run on different numbers of
-processors.  A commonly-used example is the :doc:`fix langevin <fix_langevin>` command for thermostatting.
+  processors.  A commonly-used example is the :doc:`fix langevin
+  <fix_langevin>` command for thermostatting.
 
-A LAMMPS simulation typically has two stages, setup and run.  Most
+- LAMMPS tries to flag errors and print informative error messages so
-LAMMPS errors are detected at setup time; others like a bond
-stretching too far may not occur until the middle of a run.
-
-LAMMPS tries to flag errors and print informative error messages so
   you can fix the problem.  For most errors it will also print the last
-input script command that it was processing.  Of course, LAMMPS cannot
+  input script command that it was processing or even point to the
-figure out your physics or numerical mistakes, like choosing too big a
+  keyword that is causing troubles.  Of course, LAMMPS cannot figure out
-timestep, specifying erroneous force field coefficients, or putting 2
+  your physics or numerical mistakes, like choosing too big a timestep,
-atoms on top of each other!  If you run into errors that LAMMPS
+  specifying erroneous force field coefficients, or putting 2 atoms on
-does not catch that you think it should flag, please send an email to
+  top of each other!  Also, LAMMPS does not know what you *intend* to
-the `developers <https://www.lammps.org/authors.html>`_ or create an new
+  do, but very strictly applies the syntax as described in the
-topic on the dedicated `MatSci forum section <https://matsci.org/lammps/>`_.
+  documentation.  If you run into errors that LAMMPS does not catch that
+  you think it should flag, please send an email to the `developers
+  <https://www.lammps.org/authors.html>`_ or create an new topic on the
+  dedicated `MatSci forum section <https://matsci.org/lammps/>`_.
 
-If you get an error message about an invalid command in your input
+- If you get an error message about an invalid command in your input
   script, you can determine what command is causing the problem by
   looking in the log.lammps file or using the :doc:`echo command <echo>`
   to see it on the screen.  If you get an error like "Invalid ...
@@ -51,31 +69,31 @@ mistyped the style name or that the command is part of an optional
   package which was not compiled into your executable.  The list of
   available styles in your executable can be listed by using
   :doc:`the -h command-line switch <Run_options>`.  The installation and
-compilation of optional packages is explained on the
+  compilation of optional packages is explained on the :doc:`Build
-:doc:`Build packages <Build_package>` doc page.
+  packages <Build_package>` doc page.
 
-For a given command, LAMMPS expects certain arguments in a specified
+- For a given command, LAMMPS expects certain arguments in a specified
   order.  If you mess this up, LAMMPS will often flag the error, but it
   may also simply read a bogus argument and assign a value that is
   valid, but not what you wanted.  E.g. trying to read the string "abc"
   as an integer value of 0.  Careful reading of the associated doc page
   for the command should allow you to fix these problems. In most cases,
-where LAMMPS expects to read a number, either integer or floating point,
+  where LAMMPS expects to read a number, either integer or floating
-it performs a stringent test on whether the provided input actually
+  point, it performs a stringent test on whether the provided input
-is an integer or floating-point number, respectively, and reject the
+  actually is an integer or floating-point number, respectively, and
-input with an error message (for instance, when an integer is required,
+  reject the input with an error message (for instance, when an integer
-but a floating-point number 1.0 is provided):
+  is required, but a floating-point number 1.0 is provided):
 
   .. parsed-literal::
 
      ERROR: Expected integer parameter instead of '1.0' in input script or data file
 
-Some commands allow for using variable references in place of numeric
+- Some commands allow for using variable references in place of numeric
   constants so that the value can be evaluated and may change over the
-course of a run.  This is typically done with the syntax *v_name* for a
+  course of a run.  This is typically done with the syntax *v_name* for
-parameter, where name is the name of the variable. On the other hand,
+  a parameter, where name is the name of the variable. On the other
-immediate variable expansion with the syntax ${name} is performed while
+  hand, immediate variable expansion with the syntax ${name} is
-reading the input and before parsing commands,
+  performed while reading the input and before parsing commands,
 
   .. note::
 
@@ -87,17 +105,24 @@ reading the input and before parsing commands,
 
      ERROR: Expected floating point parameter instead of 'v_name' in input script or data file
 
-Generally, LAMMPS will print a message to the screen and logfile and
+- Generally, LAMMPS will print a message to the screen and logfile and
-exit gracefully when it encounters a fatal error.  Sometimes it will
+  exit gracefully when it encounters a fatal error.  When running in
-print a WARNING to the screen and logfile and continue on; you can
+  parallel this message may be stuck in an I/O buffer and LAMMPS will be
-decide if the WARNING is important or not.  A WARNING message that is
+  terminated before that buffer is printed.  In that case you can try
-generated in the middle of a run is only printed to the screen, not to
+  adding the ``-nonblock`` or ``-nb`` command-line flag to turn off that
-the logfile, to avoid cluttering up thermodynamic output.  If LAMMPS
+  buffering.  Please note that this should not be used for production
-crashes or hangs without spitting out an error message first then it
+  runs, since turning off buffering usually has a significant negative
-could be a bug (see :doc:`this section <Errors_bugs>`) or one of the following
+  impact on performance (even worse than :doc:`thermo_modify flush yes
-cases:
+  <thermo_modify>`).  Sometimes LAMMPS will print a WARNING to the
+  screen and logfile and continue on; you can decide if the WARNING is
+  important or not, but as a general rule do not ignore warnings that
+  you not understand.  A WARNING message that is generated in the middle
+  of a run is only printed to the screen, not to the logfile, to avoid
+  cluttering up thermodynamic output.  If LAMMPS crashes or hangs
+  without generating an error message first then it could be a bug
+  (see :doc:`this section <Errors_bugs>`).
 
-LAMMPS runs in the available memory a processor allows to be
+- LAMMPS runs in the available memory a processor allows to be
   allocated.  Most reasonable MD runs are compute limited, not memory
   limited, so this should not be a bottleneck on most platforms.  Almost
   all large memory allocations in the code are done via C-style malloc's
@@ -105,9 +130,9 @@ which will generate an error message if you run out of memory.
   Smaller chunks of memory are allocated via C++ "new" statements.  If
   you are unlucky you could run out of memory just when one of these
   small requests is made, in which case the code will crash or hang (in
-parallel), since LAMMPS does not trap on those errors.
+  parallel).
 
-Illegal arithmetic can cause LAMMPS to run slow or crash.  This is
+- Illegal arithmetic can cause LAMMPS to run slow or crash.  This is
   typically due to invalid physics and numerics that your simulation is
   computing.  If you see wild thermodynamic values or NaN values in your
   LAMMPS output, something is wrong with your simulation.  If you
@@ -117,8 +142,8 @@ thermodynamic info frequently (e.g. every timestep) via the
   Visualizing the atom movement is also a good idea to ensure your model
   is behaving as you expect.
 
-In parallel, one way LAMMPS can hang is due to how different MPI
+- When running in parallel with MPI, one way LAMMPS can hang is because
-implementations handle buffering of messages.  If the code hangs
+  LAMMPS has come across an error condition, but only on one or a few
-without an error message, it may be that you need to specify an MPI
+  MPI processes and not all of them.  LAMMPS has two different "stop
-setting or two (usually via an environment variable) to enable
+  with an error message" functions and the correct one has to be called
-buffering or boost the sizes of messages that can be buffered.
+  or else it will hang.

doc/src/Errors_details.rst

@@ -51,8 +51,11 @@ Parallel versus serial
 ^^^^^^^^^^^^^^^^^^^^^^
 
 Issues where something is "lost" or "missing" often exhibit that issue
-only when running in parallel.  That doesn't mean there is no problem,
+*only* when running in parallel.  That doesn't mean there is no problem
-only the symptoms are not triggering an error quickly.  Correspondingly,
+when running in serial, only the symptoms are not triggering an error.
+This may be because there is no domain decomposition with just one
+processor and thus all atoms are accessible, or it may be because the
+problem will manifest faster with smaller subdomains.  Correspondingly,
 errors may be triggered faster with more processors and thus smaller
 sub-domains.
 
@@ -244,6 +247,25 @@ equal style (or similar) variables can only be expanded before the box
 is defined if they do not reference anything that cannot be defined
 before the box (e.g. a compute or fix reference or a thermo keyword).
 
+.. _hint13:
+
+Illegal ... command
+^^^^^^^^^^^^^^^^^^^
+
+These are a catchall error messages that used to be used a lot in LAMMPS
+(also programmers are sometimes lazy).  They usually include the name of
+the source file and the line where the error happened.  This can be used
+to track down what caused the error (most often some form of syntax error)
+by looking at the source code.  However, this has two disadvantages: 1. one
+has to check the source file from the exact same LAMMPS version, or else
+the line number would be different or the core may have been rewritten and
+that specific error does not exist anymore.
+
+The LAMMPS developers are committed to replace these too generic error
+messages with more descriptive errors, e.g. listing *which* keyword was
+causing the error, so that it will be much simpler to look up the
+correct syntax in the manual (and without referring to the source code).
+
 ------
 
 .. _err0001:
@@ -1029,13 +1051,15 @@ Even though the LAMMPS error message recommends to increase the "one"
 parameter, this may not always be the correct solution.  The neighbor
 list overflow can also be a symptom for some other error that cannot be
 easily detected.  For example, a frequent reason for an (unexpected)
-high density are incorrect box boundaries (since LAMMPS wraps atoms back
+high density are incorrect box dimensions (since LAMMPS wraps atoms back
 into the principal box with periodic boundaries) or coordinates provided
-as fractional coordinates.  In both cases, LAMMPS cannot easily know
+as fractional coordinates (LAMMPS does not support this for data files).
-whether the input geometry has such a high density (and thus requiring
+In both cases, LAMMPS cannot easily know whether the input geometry has
-more neighbor list storage per atom) by intention.  Rather than blindly
+such a high density (and thus requiring more neighbor list storage per
-increasing the "one" parameter, it is thus worth checking if this is
+atom) on purpose or by accident.  Rather than blindly increasing the
-justified by the combination of density and cutoff.
+"one" parameter, it is thus worth checking if this is justified by the
+combination of density and cutoff.  This is particularly recommended
+when using some tool(s) to convert input or data files.
 
 When boosting (= increasing) the "one" parameter, it is recommended to
 also increase the value for the "page" parameter to maintain the ratio

doc/src/Fortran.rst

@@ -69,10 +69,11 @@ statement.  Internally, it will call either
 :cpp:func:`lammps_open_fortran` or :cpp:func:`lammps_open_no_mpi` from
 the C library API to create the class instance.  All arguments are
 optional and :cpp:func:`lammps_mpi_init` will be called automatically
-if it is needed.  Similarly, a possible call to
+if it is needed.  Similarly, optional calls to
-:cpp:func:`lammps_mpi_finalize` is integrated into the :f:func:`close`
+:cpp:func:`lammps_mpi_finalize`, :cpp:func:`lammps_kokkos_finalize`,
-function and triggered with the optional logical argument set to
+:cpp:func:`lammps_python_finalize`, and :cpp:func:`lammps_plugin_finalize`
-``.TRUE.``. Here is a simple example:
+are integrated into the :f:func:`close` function and triggered with the
+optional logical argument set to ``.TRUE.``. Here is a simple example:
 
 .. code-block:: fortran
 
@@ -521,8 +522,8 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    This method will close down the LAMMPS instance through calling
    :cpp:func:`lammps_close`.  If the *finalize* argument is present and
    has a value of ``.TRUE.``, then this subroutine also calls
-   :cpp:func:`lammps_kokkos_finalize` and
+   :cpp:func:`lammps_kokkos_finalize`, :cpp:func:`lammps_mpi_finalize`,
-   :cpp:func:`lammps_mpi_finalize`.
+   :cpp:func:`lammps_python_finalize`, and :cpp:func:`lammps_plugin_finalize`.
 
    :o finalize: shut down the MPI environment of the LAMMPS
     library if ``.TRUE.``.
@@ -530,6 +531,8 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    :to: :cpp:func:`lammps_close`
    :to: :cpp:func:`lammps_mpi_finalize`
    :to: :cpp:func:`lammps_kokkos_finalize`
+   :to: :cpp:func:`lammps_python_finalize`
+   :to: :cpp:func:`lammps_plugin_finalize`
 
 --------
 
@@ -2096,7 +2099,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
 --------
 
-.. f:subroutine:: create_atoms([id,] type, x, [v,] [image,] [bexpand])
+.. f:function:: create_atoms([id,] type, x, [v,] [image,] [bexpand])
 
    This method calls :cpp:func:`lammps_create_atoms` to create additional atoms
    from a given list of coordinates and a list of atom types. Additionally,
@@ -2125,6 +2128,8 @@ Procedures Bound to the :f:type:`lammps` Derived Type
     will be created, not dropped, and the box dimensions will be extended.
     Default is ``.FALSE.``
    :otype bexpand: logical,optional
+   :r atoms: number of created atoms
+   :rtype atoms: integer(c_int)
    :to: :cpp:func:`lammps_create_atoms`
 
    .. note::
@@ -2149,6 +2154,18 @@ Procedures Bound to the :f:type:`lammps` Derived Type
 
 --------
 
+.. f:subroutine:: create_molecule(id, jsonstr)
+
+   Add molecule template from string with JSON data
+
+   .. versionadded:: TBD
+
+   :p character(len=\*) id: desired molecule-ID
+   :p character(len=\*) jsonstr: string with JSON data defining the molecule template
+   :to: :cpp:func:`lammps_create_molecule`
+
+--------
+
 .. f:function:: find_pair_neighlist(style[, exact][, nsub][, reqid])
 
    Find index of a neighbor list requested by a pair style.

doc/src/Howto.rst

@@ -93,6 +93,7 @@ Packages howto
    Howto_manifold
    Howto_rheo
    Howto_spins
+   Howto_apip
 
 Tutorials howto
 ===============

doc/src/Howto_apip.rst

@@ -0,0 +1,225 @@
+Adaptive-precision interatomic potentials (APIP)
+================================================
+
+The :ref:`PKG-APIP <PKG-APIP>` enables use of adaptive-precision potentials
+as described in :ref:`(Immel) <Immel2025_1>`.
+In the context of this package, precision refers to the accuracy of an interatomic
+potential.
+
+Modern machine-learning (ML) potentials translate the accuracy of DFT
+simulations into MD simulations, i.e., ML potentials are more accurate
+compared to traditional empirical potentials.
+However, this accuracy comes at a cost: there is a considerable performance
+gap between the evaluation of classical and ML potentials, e.g., the force
+calculation of a classical EAM potential is 100-1000 times faster compared
+to the ML-based ACE method.
+The evaluation time difference results in a conflict between large time and
+length scales on the one hand and accuracy on the other.
+This conflict is resolved by an APIP model for simulations, in which the highest precision
+is required only locally but not globally.
+
+An APIP model uses a precise but
+expensive ML potential only for a subset of atoms, while a fast
+potential is used for the remaining atoms.
+Whether the precise or the fast potential is used is determined
+by a continuous switching parameter :math:`\lambda_i` that can be defined for each
+atom :math:`i`.
+The switching parameter can be adjusted dynamically during a simulation or
+kept constant as explained below.
+
+The potential energy :math:`E_i` of an atom :math:`i` described by an
+adaptive-precision
+interatomic potential is given by :ref:`(Immel) <Immel2025_1>`
+
+.. math::
+
+   E_i = \lambda_i E_i^\text{(fast)} + (1-\lambda_i) E_i^\text{(precise)},
+
+whereas :math:`E_i^\text{(fast)}` is the potential energy of atom :math:`i`
+according to a fast interatomic potential,
+:math:`E_i^\text{(precise)}` is the potential energy according to a precise
+interatomic potential and :math:`\lambda_i\in[0,1]` is the
+switching parameter that decides how the potential energies are weighted.
+
+Adaptive-precision saves computation time when the computation of the
+precise potential is not required for many atoms, i.e., when
+:math:`\lambda_i=1` applies for many atoms.
+
+The currently implemented potentials are:
+
+.. list-table::
+   :header-rows: 1
+
+   * - Fast potential
+     - Precise potential
+   * - :doc:`ACE <pair_pace_apip>`
+     - :doc:`ACE <pair_pace_apip>`
+   * - :doc:`EAM <pair_eam_apip>`
+     -
+
+In theory, any short-range potential can be used for an adaptive-precision
+interatomic potential. How to implement a new (fast or precise)
+adaptive-precision
+potential is explained in :ref:`here <implementing_new_apip_styles>`.
+
+The switching parameter :math:`\lambda_i` that combines the two potentials
+can be dynamically calculated during a
+simulation.
+Alternatively, one can set a constant switching parameter before the start
+of a simulation.
+To run a simulation with an adaptive-precision potential, one needs the
+following components:
+
+.. tabs::
+
+   .. tab:: dynamic switching parameter
+
+        #. :doc:`atom_style apip <atom_style>` so that the switching parameter :math:`\lambda_i` can be stored.
+        #. A fast potential: :doc:`eam/apip <pair_eam_apip>` or :doc:`pace/fast/apip <pair_pace_apip>`.
+        #. A precise potential: :doc:`pace/precise/apip <pair_pace_apip>`.
+        #. :doc:`pair_style lambda/input/apip  <pair_lambda_input_apip>` to calculate :math:`\lambda_i^\text{input}`, from which :math:`\lambda_i` is calculated.
+        #. :doc:`fix lambda/apip <fix_lambda_apip>` to calculate the switching parameter :math:`\lambda_i`.
+        #. :doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>` to calculate the spatial transition zone of the switching parameter.
+        #. :doc:`pair_style hybrid/overlay <pair_hybrid>` to combine the previously mentioned pair_styles.
+        #. :doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>` to conserve the energy when switching parameters change.
+        #. :doc:`fix atom_weight/apip <fix_atom_weight_apip>` to approximate the load caused by every atom, as the computations of the pair_styles are only required for a subset of atoms.
+        #. :doc:`fix balance <fix_balance>` to perform dynamic load balancing with the calculated load.
+
+   .. tab:: constant switching parameter
+
+        #. :doc:`atom_style apip <atom_style>` so that the switching parameter :math:`\lambda_i` can be stored.
+        #. A fast potential: :doc:`eam/apip <pair_eam_apip>` or :doc:`pace/fast/apip <pair_pace_apip>`.
+        #. A precise potential: :doc:`pace/precise/apip <pair_pace_apip>`.
+        #. :doc:`set <set>` command to set the switching parameter :math:`\lambda_i`.
+        #. :doc:`pair_style hybrid/overlay <pair_hybrid>` to combine the previously mentioned pair_styles.
+        #. :doc:`fix atom_weight/apip <fix_atom_weight_apip>` to approximate the load caused by every atom, as the computations of the pair_styles are only required for a subset of atoms.
+        #. :doc:`fix balance <fix_balance>` to perform dynamic load balancing with the calculated load.
+
+----------
+
+Example
+"""""""
+.. note::
+
+   How to select the values of the parameters of an adaptive-precision
+   interatomic potential is discussed in detail in :ref:`(Immel) <Immel2025_1>`.
+
+
+.. tabs::
+
+   .. tab:: dynamic switching parameter
+
+      Lines like these would appear in the input script:
+
+
+      .. code-block:: LAMMPS
+
+         atom_style apip
+         comm_style tiled
+
+         pair_style hybrid/overlay eam/fs/apip pace/precise/apip lambda/input/csp/apip fcc cutoff 5.0 lambda/zone/apip 12.0
+         pair_coeff * * eam/fs/apip Cu.eam.fs Cu
+         pair_coeff * * pace/precise/apip Cu.yace Cu
+         pair_coeff * * lambda/input/csp/apip
+         pair_coeff * * lambda/zone/apip
+
+         fix 2 all lambda/apip 2.5 3.0 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
+         fix 3 all lambda_thermostat/apip N_rescaling 200
+         fix 4 all atom_weight/apip 100 eam ace lambda/input lambda/zone all
+
+         variable myweight atom f_4
+
+         fix 5 all balance 100 1.1 rcb weight var myweight
+
+      First, the :doc:`atom_style apip <atom_style>` and the communication style are set.
+
+      .. note::
+         Note, that :doc:`comm_style <comm_style>` *tiled* is required for the style *rcb* of
+         :doc:`fix balance <fix_balance>`, but not for APIP.
+         However, the flexibility offered by the balancing style *rcb*, compared to the
+         balancing style *shift*, is advantageous for APIP.
+
+      An adaptive-precision EAM-ACE potential, for which the switching parameter
+      :math:`\lambda` is calculated from the CSP, is defined via
+      :doc:`pair_style hybrid/overlay <pair_hybrid>`.
+      The fixes ensure that the switching parameter is calculated, the energy conserved,
+      the weight for the load balancing calculated and the load-balancing itself is done.
+
+   .. tab:: constant switching parameter
+
+      Lines like these would appear in the input script:
+
+      .. code-block:: LAMMPS
+
+         atom_style apip
+         comm_style tiled
+
+         pair_style hybrid/overlay eam/fs/apip pace/precise/apip
+         pair_coeff * * eam/fs/apip Cu.eam.fs Cu
+         pair_coeff * * pace/precise/apip Cu.yace Cu
+
+         # calculate lambda somehow
+         variable lambda atom ...
+         set group all apip/lambda v_lambda
+
+         fix 4 all atom_weight/apip 100 eam ace lambda/input lambda/zone all
+
+         variable myweight atom f_4
+
+         fix 5 all balance 100 1.1 rcb weight var myweight
+
+      First, the :doc:`atom_style apip <atom_style>` and the communication style are set.
+
+      .. note::
+         Note, that :doc:`comm_style <comm_style>` *tiled* is required for the style *rcb* of
+         :doc:`fix balance <fix_balance>`, but not for APIP.
+         However, the flexibility offered by the balancing style *rcb*, compared to the
+         balancing style *shift*, is advantageous for APIP.
+
+      An adaptive-precision EAM-ACE potential is defined via
+      :doc:`pair_style hybrid/overlay <pair_hybrid>`.
+      The switching parameter :math:`\lambda_i` of the adaptive-precision
+      EAM-ACE potential is set via the :doc:`set command <set>`.
+      The parameter is not updated during the simulation.
+      Therefore, the potential is conservative.
+      The fixes ensure that the weight for the load balancing is calculated
+      and the load-balancing itself is done.
+
+----------
+
+.. _implementing_new_apip_styles:
+
+Implementing new APIP pair styles
+"""""""""""""""""""""""""""""""""
+
+One can introduce adaptive-precision to an existing pair style by modifying
+the original pair style.
+One should calculate the force
+:math:`F_i = - \nabla_i \sum_j E_j^\text{original}` for a fast potential or
+:math:`F_i = - (1-\nabla_i) \sum_j E_j^\text{original}` for a precise
+potential from the original potential
+energy :math:`E_j^\text{original}` to see where the switching parameter
+:math:`\lambda_i` needs to be introduced in the force calculation.
+The switching parameter :math:`\lambda_i` is known for all atoms :math:`i`
+in force calculation routine.
+One needs to introduce an abortion criterion based on :math:`\lambda_i` to
+ensure that all not required calculations are skipped and compute time can
+be saved.
+Furthermore, one needs to provide the number of calculations and measure the
+computation time.
+Communication within the force calculation needs to be prevented to allow
+effective load-balancing.
+With communication, the load balancer cannot balance few calculations of the
+precise potential on one processor with many computations of the fast
+potential on another processor.
+
+All changes in the pair_style pace/apip compared to the pair_style pace
+are annotated and commented.
+Thus, the pair_style pace/apip can serve as an example for the implementation
+of new adaptive-precision potentials.
+
+----------
+
+.. _Immel2025_1:
+
+**(Immel)** Immel, Drautz and Sutmann, J Chem Phys, 162, 114119 (2025)

doc/src/Howto_spc.rst

@@ -8,6 +8,18 @@ the two O-H bonds and the H-O-H angle rigid.  A bond style of
 *harmonic* and an angle style of *harmonic* or *charmm* should also be
 used.
 
+One suitable pair style with cutoff Coulomb would for instance be:
+
+* :doc:`pair_style lj/cut/coul/cut <pair_lj_cut_coul>`
+
+These commands are examples for a long-range Coulomb model:
+
+* :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`
+* :doc:`pair_style lj/cut/coul/long/soft <pair_fep_soft>`
+* :doc:`kspace_style pppm <kspace_style>`
+* :doc:`pair_style lj/long/coul/long <pair_lj_long>`
+* :doc:`kspace_style pppm/disp <kspace_style>`
+
 These are the additional parameters (in real units) to set for O and H
 atoms and the water molecule to run a rigid SPC model.
 
@@ -39,7 +51,9 @@ the SPC and SPC/E models.
 Below is the code for a LAMMPS input file and a molecule file
 (``spce.mol``) of SPC/E water for use with the :doc:`molecule command
 <molecule>` demonstrating how to set up a small bulk water system for
-SPC/E with rigid bonds.
+SPC/E with rigid bonds.  For simplicity and speed the example uses a
+cutoff Coulomb.  Most production simulations require long-range Coulomb
+instead.
 
 .. code-block:: LAMMPS
 

doc/src/Howto_tip3p.rst

@@ -5,17 +5,24 @@ The TIP3P water model as implemented in CHARMM :ref:`(MacKerell)
 <howto-tip3p>` specifies a 3-site rigid water molecule with charges and
 Lennard-Jones parameters assigned to each of the three atoms.
 
-A suitable pair style with cutoff Coulomb would be:
+One suitable pair style with cutoff Coulomb would for instance be:
 
 * :doc:`pair_style lj/cut/coul/cut <pair_lj_cut_coul>`
 
-or these commands for a long-range Coulomb model:
+These commands are examples for a long-range Coulomb model:
 
 * :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`
 * :doc:`pair_style lj/cut/coul/long/soft <pair_fep_soft>`
 * :doc:`kspace_style pppm <kspace_style>`
+* :doc:`pair_style lj/long/coul/long <pair_lj_long>`
 * :doc:`kspace_style pppm/disp <kspace_style>`
 
+And these pair styles are compatible with the CHARMM force field:
+
+* :doc:`pair_style lj/charmm/coul/charmm <pair_charmm>`
+* :doc:`pair_style lj/charmm/coul/long <pair_charmm>`
+* :doc:`pair_style lj/charmmfsw/coul/long <pair_charmm>`
+
 In LAMMPS the :doc:`fix shake or fix rattle <fix_shake>` command can be
 used to hold the two O-H bonds and the H-O-H angle rigid.  A bond style
 of :doc:`harmonic <bond_harmonic>` and an angle style of :doc:`harmonic
@@ -100,7 +107,9 @@ ignored.
 Below is the code for a LAMMPS input file and a molecule file
 (``tip3p.mol``) of TIP3P water for use with the :doc:`molecule command
 <molecule>` demonstrating how to set up a small bulk water system for
-TIP3P with rigid bonds.
+TIP3P with rigid bonds.  For simplicity and speed the example uses a
+cutoff Coulomb.  Most production simulations require long-range Coulomb
+instead.
 
 .. code-block:: LAMMPS
 

doc/src/Howto_tip4p.rst

@@ -167,7 +167,9 @@ cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long
 Below is the code for a LAMMPS input file using the implicit method and
 the :ref:`TIP3P molecule file <tip3p_molecule>`.  Because the TIP4P
 charges are different from TIP3P they need to be reset (or the molecule
-file changed):
+file changed).  For simplicity and speed the example uses a cutoff
+Coulomb.  Most production simulations require long-range Coulomb
+instead.
 
 .. code-block:: LAMMPS
 

doc/src/Howto_tip5p.rst

@@ -87,7 +87,9 @@ atom style full or use :doc:`fix property/atom mol <fix_property_atom>`
 so that fix rigid/small can identify rigid bodies by their molecule ID.
 Also a :doc:`neigh_modify exclude <neigh_modify>` command is added to
 exclude computing intramolecular non-bonded interactions, since those
-are removed by the rigid fix anyway:
+are removed by the rigid fix anyway.  For simplicity and speed the
+example uses a cutoff Coulomb.  Most production simulations require
+long-range Coulomb instead.
 
 .. code-block:: LAMMPS
 

doc/src/Install_git.rst

@@ -21,8 +21,8 @@ You can follow the LAMMPS development on 4 different git branches:
 
 * **develop** : this branch follows the ongoing development and is
   updated with every merge commit of a pull request
-* **release** : this branch is updated with every "feature release";
+* **release** : this branch is updated with every "feature release"
-   updates are always "fast-forward" merges from *develop*
+  and updates are always "fast-forward" merges from *develop*
 * **maintenance** : this branch collects back-ported bug fixes from the
   *develop* branch to the *stable* branch.  It is used to update the
   *stable* branch for "stable update releases".

doc/src/Library_create.rst

@@ -11,6 +11,7 @@ This section documents the following functions:
 - :cpp:func:`lammps_mpi_finalize`
 - :cpp:func:`lammps_kokkos_finalize`
 - :cpp:func:`lammps_python_finalize`
+- :cpp:func:`lammps_plugin_finalize`
 - :cpp:func:`lammps_error`
 
 --------------------
@@ -119,5 +120,10 @@ calling program.
 
 -----------------------
 
+.. doxygenfunction:: lammps_plugin_finalize
+   :project: progguide
+
+-----------------------
+
 .. doxygenfunction:: lammps_error
    :project: progguide

doc/src/Library_scatter.rst

@@ -27,6 +27,7 @@ It documents the following functions:
 - :cpp:func:`lammps_scatter`
 - :cpp:func:`lammps_scatter_subset`
 - :cpp:func:`lammps_create_atoms`
+- :cpp:func:`lammps_create_molecule`
 
 -----------------------
 
@@ -103,4 +104,8 @@ It documents the following functions:
 .. doxygenfunction:: lammps_create_atoms(void *handle, int n, const int *id, const int *type, const double *x, const double *v, const int *image, int bexpand)
    :project: progguide
 
+-----------------------
+
+.. doxygenfunction:: lammps_create_molecule
+   :project: progguide
 

doc/src/Packages_details.rst

@@ -28,6 +28,7 @@ gives those details.
 
    * :ref:`ADIOS <PKG-ADIOS>`
    * :ref:`AMOEBA <PKG-AMOEBA>`
+   * :ref:`APIP <PKG-APIP>`
    * :ref:`ASPHERE <PKG-ASPHERE>`
    * :ref:`ATC <PKG-ATC>`
    * :ref:`AWPMD <PKG-AWPMD>`
@@ -186,6 +187,60 @@ provided by the Ponder group in their
 
 ----------
 
+.. _PKG-APIP:
+
+APIP package
+------------
+
+**Contents:**
+
+This package provides adaptive-precision interatomic potentials (APIP) as
+described in:
+
+D. Immel, R. Drautz and G. Sutmann, "Adaptive-precision potentials for
+large-scale atomistic simulations", J. Chem. Phys. 162, 114119 (2025)
+`link <immel2025_doi_>`_
+
+Adaptive-precision means, that a fast interatomic potential, such as EAM,
+is coupled to a precise interatomic potential, such as ACE.
+This package provides the required pair_styles and fixes to run an efficient,
+energy-conserving adaptive-precision simulation.
+
+In the context of this package, precision refers to the accuracy of an interatomic
+potential.
+
+.. _immel2025_doi: https://doi.org/10.1063/5.0245877
+
+**Authors:**
+
+This package was written by David Immel^1,
+Ralf Drautz^2 and Godehard Sutmann^1^2.
+
+ ^1: Forschungszentrum Juelich, Juelich, Germany
+
+ ^2: Ruhr-University Bochum, Bochum, Germany
+
+**Install:**
+
+The APIP package requires also the installation of ML-PACE, which has
+:ref:`specific installation instructions <ml-pace>` on the
+:doc:`Build extras <Build_extras>` page.
+
+**Supporting info:**
+
+* ``src/APIP``: filenames -> commands
+* :doc:`Howto APIP <Howto_apip>`
+* ``examples/PACKAGES/apip``
+* :doc:`fix atom_weight/apip <fix_atom_weight_apip>`
+* :doc:`fix lambda/apip <fix_lambda_apip>`
+* :doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`
+* :doc:`pair_style eam/apip <pair_eam_apip>`
+* :doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`
+* :doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`
+* :doc:`pair_style pace/apip <pair_pace_apip>`
+
+----------
+
 .. _PKG-ASPHERE:
 
 ASPHERE package

doc/src/Packages_list.rst

@@ -38,6 +38,11 @@ whether an extra library is needed to build and use the package:
      - :doc:`AMOEBA and HIPPO howto <Howto_amoeba>`
      - amoeba
      - no
+   * - :ref:`APIP <PKG-APIP>`
+     - adaptive-precision interatomic potentials
+     - :doc:`Howto APIP <Howto_apip>`
+     - ``PACKAGES/apip``
+     - ext
    * - :ref:`ASPHERE <PKG-ASPHERE>`
      - aspherical particle models
      - :doc:`Howto spherical <Howto_spherical>`

doc/src/Python_call.rst

@@ -5,18 +5,28 @@ LAMMPS has several commands which can be used to invoke Python
 code directly from an input script:
 
 * :doc:`python <python>`
-* :doc:`variable python <variable>`
+* :doc:`python-style variables <variable>`
+* :doc:`equal-style and atom-style variables with formulas containing Python function wrappers <variable>`
 * :doc:`fix python/invoke <fix_python_invoke>`
 * :doc:`pair_style python <pair_python>`
 
-The :doc:`python <python>` command which can be used to define and
+The :doc:`python <python>` command can be used to define and execute a
-execute a Python function that you write the code for.  The Python
+Python function that you write the code for.  The Python function can
-function can also be assigned to a LAMMPS python-style variable via
+also be assigned to a LAMMPS python-style variable via the
-the :doc:`variable <variable>` command.  Each time the variable is
+:doc:`variable <variable>` command.  Each time the variable is
 evaluated, either in the LAMMPS input script itself, or by another
 LAMMPS command that uses the variable, this will trigger the Python
 function to be invoked.
 
+The Python function can also be referenced in the formula used to
+define an :doc:`equal-style or atom-style variable <variable>`, using
+the syntax for a :doc:`Python function wrapper <variable>`.  This make
+it easy to pass LAMMPS-related arguments to the Python function, as
+well as to invoke it whenever the equal- or atom-style variable is
+evaluated.  For an atom-style variable it means the Python function
+can be invoked once per atom, using per-atom properties as arguments
+to the function.
+
 The Python code for the function can be included directly in the input
 script or in an auxiliary file.  The function can have arguments which
 are mapped to LAMMPS variables (also defined in the input script) and

doc/src/Tools.rst

@@ -92,6 +92,7 @@ Miscellaneous tools
    * :ref:`LAMMPS coding standards <coding_standard>`
    * :ref:`emacs <emacs>`
    * :ref:`i-PI <ipi>`
+   * :ref:`JSON support <json>`
    * :ref:`kate <kate>`
    * :ref:`LAMMPS-GUI <lammps_gui>`
    * :ref:`LAMMPS magic patterns for file(1) <magic>`
@@ -364,7 +365,7 @@ These tools were provided by Aidan Thompson at Sandia
 .. _fep:
 
 fep tool
-------------------
+--------
 
 The tools/fep directory contains Python scripts useful for
 post-processing results from performing free-energy perturbation
@@ -379,7 +380,7 @@ See README file in the tools/fep directory.
 .. _ipi:
 
 i-PI tool
--------------------
+---------
 
 .. versionchanged:: 27June2024
 
@@ -432,6 +433,87 @@ tools/createatoms tool's input file.
 
 ----------
 
+.. _json:
+
+JSON support files
+------------------
+
+.. versionadded:: 12June2025
+
+The ``tools/json`` directory contains files and tools to support
+using `JSON format <https://www.json.org/>`_ files in LAMMPS.
+Currently only the :doc:`molecule command <molecule>` supports
+files in JSON format directly, but this is planned to be expanded
+in the future.
+
+JSON file validation
+^^^^^^^^^^^^^^^^^^^^
+
+The JSON syntax is independent of its content, and thus the data in the
+file must follow suitable conventions to be correctly parsed during
+input.  This can be done in a portable fashion using a `JSON schema file
+<https://json-schema.org/>`_ (which is in JSON format as well) to define
+those conventions.  A suitable JSON validator software can then validate
+JSON files against the requirements.  Validating a particular JSON file
+against a schema ensures that both, the syntax *and* the conventions
+are followed.  This is useful when writing or editing JSON files in a
+text editor or when writing a pre-processing script or tool to create
+JSON files for a specific purpose in LAMMPS.  It **cannot** check
+whether the file contents are physically meaningful, though.
+
+One such validator tool is `check-jsonschema
+<https://check-jsonschema.readthedocs.io/>`_ which is written in Python
+and can be installed using the `pip Python package manager
+<https://pypi.org/>`_, best in a virtual environment as shown below (for
+a Bourne Shell command line):
+
+.. code-block:: sh
+
+   python -m venv validate-json
+   source validate-json/bin/activate
+   pip install --upgrade pip
+   pip install check-jsonschema
+
+To validate a specific JSON file against a provided schema (here for
+a :doc:`molecule command file <molecule>` you would then run for example:
+
+.. code-block:: sh
+
+   check-jsonschema --schemafile molecule-schema.json tip3p.json
+
+The latest schema files are also maintained and available for download
+at https://download.lammps.org/json .  This enables validation of JSON
+files even if the LAMMPS sources are not locally available. Example:
+
+.. code-block:: sh
+
+   check-jsonschema --schemafile https://download.lammps.org/json/molecule-schema.json tip3p.json
+
+JSON file format normalization
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+There are extensions to the strict JSON format that allow for comments
+or ignore additional (dangling) commas. The ``reformat-json.cpp`` tool
+will read JSON files in relaxed format, but write it out in strict format.
+It is also possible to change the level of indentation from -1 (all data
+one long line) to any positive integer value.  The original file will be
+backed up (.bak added to file name) and then overwritten.
+
+Manual compilation (it will be automatically included in the CMake build
+if building tools is requested during CMake configuration):
+
+.. code-block:: sh
+
+   g++ -I <path/to/lammps/src> -o reformat-json reformat-json.cpp
+
+Usage:
+
+.. parsed-literal::
+
+   reformat-json <indent-width> <json-file-1> [<json-file-2> ...]
+
+----------
+
 .. _kate:
 
 kate tool

doc/src/atom_style.rst

@@ -10,7 +10,7 @@ Syntax
 
    atom_style style args
 
-* style = *amoeba* or *angle* or *atomic* or *body* or *bond* or *charge* or *dielectric* or *dipole* or  *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or *bpm/sphere* or *spin* or *tdpd* or *tri* or *template* or *wavepacket* or *hybrid*
+* style = *amoeba* or *angle* or *apip* or *atomic* or *body* or *bond* or *charge* or *dielectric* or *dipole* or  *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or *bpm/sphere* or *spin* or *tdpd* or *tri* or *template* or *wavepacket* or *hybrid*
 
   .. parsed-literal::
 
@@ -117,6 +117,10 @@ the Additional Information section below.
      - *bond* + "angle data"
      - :ref:`MOLECULE <PKG-MOLECULE>`
      - bead-spring polymers with stiffness
+   * - *apip*
+     - *atomic* + apip_lambda, apip_lambda_required, apip_lambda_input, apip_lambda_const, apip_lambda_input_ta, apip_e_fast, apip_e_precise, apip_f_const_lambda, apip_f_dyn_lambda
+     - :ref:`APIP <PKG-APIP>`
+     - adaptive-precision interatomic potentials(APIP), see :doc:`APIP howto <Howto_apip>`
    * - *atomic*
      - tag, type, x, v, f, image, mask
      -

doc/src/compute_angle_local.rst

@@ -53,15 +53,17 @@ The value *eng* is the interaction energy for the angle.
 
 The value *v_name* can be used together with the *set* keyword to
 compute a user-specified function of the angle theta.  The *name*
-specified for the *v_name* value is the name of an :doc:`equal-style variable <variable>` which should evaluate a formula based on a
+specified for the *v_name* value is the name of an :doc:`equal-style
+variable <variable>` which should evaluate a formula based on a
 variable which will store the angle theta.  This other variable must
-be an :doc:`internal-style variable <variable>` defined in the input
+be an :doc:`internal-style variable <variable>` specified by the *set*
-script; its initial numeric value can be anything.  It must be an
+keyword.  It is an internal-style variable, because this command
-internal-style variable, because this command resets its value
+resets its value directly.  The internal-style variable does not need
-directly.  The *set* keyword is used to identify the name of this
+to be defined in the input script (though it can be); if it is not
-other variable associated with theta.
+defined, then the *set* option creates an :doc:`internal-style
+variable <variable>` with the specified name.
 
-Note that the value of theta for each angle which stored in the
+Note that the value of theta for each angle which is stored in the
 internal variable is in radians, not degrees.
 
 As an example, these commands can be added to the bench/in.rhodo
@@ -70,7 +72,6 @@ system and output the statistics in various ways:
 
 .. code-block:: LAMMPS
 
-   variable t internal 0.0
    variable cos equal cos(v_t)
    variable cossq equal cos(v_t)*cos(v_t)
 

doc/src/compute_bond_local.rst

@@ -64,7 +64,7 @@ All these properties are computed for the pair of atoms in a bond,
 whether the two atoms represent a simple diatomic molecule, or are part
 of some larger molecule.
 
-.. versionchanged:: TBD
+.. versionchanged:: 12Jun2025
 
    The sign of *dx*, *dy*, *dz* is no longer determined by the atom IDs
    of the bonded atoms but by their order in the bond list to be
@@ -130,13 +130,15 @@ moving apart.
 
 The value *v_name* can be used together with the *set* keyword to
 compute a user-specified function of the bond distance.  The *name*
-specified for the *v_name* value is the name of an :doc:`equal-style variable <variable>` which should evaluate a formula based on a
+specified for the *v_name* value is the name of an :doc:`equal-style
-variable which will store the bond distance.  This other variable must
+variable <variable>` which should evaluate a formula based on a
-be an :doc:`internal-style variable <variable>` defined in the input
+variable which stores the bond distance.  This other variable must be
-script; its initial numeric value can be anything.  It must be an
+the :doc:`internal-style variable <variable>` specified by the *set*
-internal-style variable, because this command resets its value
+keyword.  It is an internal-style variable, because this command
-directly.  The *set* keyword is used to identify the name of this
+resets its value directly.  The internal-style variable does not need
-other variable associated with theta.
+to be defined in the input script (though it can be); if it is not
+defined, then the *set* option creates an :doc:`internal-style
+variable <variable>` with the specified name.
 
 As an example, these commands can be added to the bench/in.rhodo
 script to compute the length\ :math:`^2` of every bond in the system and
@@ -144,7 +146,6 @@ output the statistics in various ways:
 
 .. code-block:: LAMMPS
 
-   variable d internal 0.0
    variable dsq equal v_d*v_d
 
    compute 1 all property/local batom1 batom2 btype

doc/src/compute_dihedral_local.rst

@@ -45,30 +45,31 @@ interactions.  The number of datums generated, aggregated across all
 processors, equals the number of dihedral angles in the system, modified
 by the group parameter as explained below.
 
-The value *phi* (:math:`\phi`) is the dihedral angle, as defined in the diagram
+The value *phi* (:math:`\phi`) is the dihedral angle, as defined in
-on the :doc:`dihedral_style <dihedral_style>` doc page.
+the diagram on the :doc:`dihedral_style <dihedral_style>` doc page.
 
-The value *v_name* can be used together with the *set* keyword to compute a
+The value *v_name* can be used together with the *set* keyword to
-user-specified function of the dihedral angle :math:`\phi`.  The *name*
+compute a user-specified function of the dihedral angle :math:`\phi`.
-specified for the *v_name* value is the name of an
+The *name* specified for the *v_name* value is the name of an
-:doc:`equal-style variable <variable>` which should evaluate a formula based on
+:doc:`equal-style variable <variable>` which should evaluate a formula
-a variable which will store the angle :math:`\phi`.  This other variable must
+based on a variable which will store the angle :math:`\phi`.  This
-be an :doc:`internal-style variable <variable>` defined in the input
+other variable must be an :doc:`internal-style variable <variable>`
-script; its initial numeric value can be anything.  It must be an
+specified by the *set* keyword.  It is an internal-style variable,
-internal-style variable, because this command resets its value
+because this command resets its value directly.  The internal-style
-directly.  The *set* keyword is used to identify the name of this
+variable does not need to be defined in the input script (though it
-other variable associated with :math:`\phi`.
+can be); if it is not defined, then the *set* option creates an
+:doc:`internal-style variable <variable>` with the specified name.
 
-Note that the value of :math:`\phi` for each angle which stored in the internal
+Note that the value of :math:`\phi` for each angle which stored in the
-variable is in radians, not degrees.
+internal variable is in radians, not degrees.
 
 As an example, these commands can be added to the bench/in.rhodo
-script to compute the :math:`\cos\phi` and :math:`\cos^2\phi` of every dihedral
+script to compute the :math:`\cos\phi` and :math:`\cos^2\phi` of every
-angle in the system and output the statistics in various ways:
+dihedral angle in the system and output the statistics in various
+ways:
 
 .. code-block:: LAMMPS
 
-   variable p internal 0.0
    variable cos equal cos(v_p)
    variable cossq equal cos(v_p)*cos(v_p)
 
@@ -100,10 +101,10 @@ no consistent ordering of the entries within the local vector or array
 from one timestep to the next.  The only consistency that is
 guaranteed is that the ordering on a particular timestep will be the
 same for local vectors or arrays generated by other compute commands.
-For example, dihedral output from the
+For example, dihedral output from the :doc:`compute property/local
-:doc:`compute property/local <compute_property_local>` command can be combined
+<compute_property_local>` command can be combined with data from this
-with data from this command and output by the :doc:`dump local <dump>`
+command and output by the :doc:`dump local <dump>` command in a
-command in a consistent way.
+consistent way.
 
 Here is an example of how to do this:
 

doc/src/compute_msd.rst

@@ -49,8 +49,6 @@ proportional to the diffusion coefficient of the diffusing atoms.
 The displacement of an atom is from its reference position. This is
 normally the original position at the time
 the compute command was issued, unless the *average* keyword is set to *yes*\ .
-The value of the displacement will be
-0.0 for atoms not in the specified compute group.
 
 If the *com* option is set to *yes* then the effect of any drift in
 the center-of-mass of the group of atoms is subtracted out before the
@@ -111,7 +109,10 @@ distance\ :math:`^2` :doc:`units <units>`.
 Restrictions
 """"""""""""
 
-Compute *msd* cannot be used with a dynamic group.
+Compute *msd* cannot be used with a dynamic group and the number of
+atoms in the compute group must not be changed by some fixes like,
+for example, :doc:`fix deposit <fix_deposit>` or
+:doc:`fix evaporate <fix_evaporate>`.
 
 Related commands
 """"""""""""""""

doc/src/compute_pair_local.rst

@@ -56,7 +56,7 @@ force cutoff distance for that interaction, as defined by the
 :doc:`pair_style <pair_style>` and :doc:`pair_coeff <pair_coeff>`
 commands.
 
-.. versionchanged:: TBD
+.. versionchanged:: 12Jun2025
 
    The sign of *dx*, *dy*, *dz* is no longer determined by the value of
    their atom-IDs but by their order in the neighbor list to be

doc/src/compute_property_atom.rst

@@ -34,6 +34,8 @@ Syntax
                              i_name, d_name, i2_name[I], d2_name[I],
                              vfrac, s0, espin, eradius, ervel, erforce,
                              rho, drho, e, de, cv, buckling,
+                             apip_lambda, apip_lambda_input, apip_e_fast,
+                             apip_e_precise
 
   .. parsed-literal::
 
@@ -70,6 +72,13 @@ Syntax
            *i2_name[I]* = Ith column of custom integer array with name
            *d2_name[I]* = Ith column of custom floating-point array with name
 
+  .. parsed-literal::
+
+           APIP package per-atom properties:
+           *apip_lambda* = switching parameter
+           *apip_lambda_input* = input used to calculate the switching parameter
+           *apip_e_fast,apip_e_precise* = potential energies mixed by the adaptive-precision potential
+
   .. parsed-literal::
 
            PERI package per-atom properties:
@@ -162,6 +171,22 @@ segment particles and define the end points of each line segment.
 *corner2z*, *corner3x*, *corner3y*, *corner3z*, are defined for
 triangular particles and define the corner points of each triangle.
 
+The accessible quantities from the :doc:`APIP package <Howto_apip>` are
+explained in the doc pages of this package in detail.
+In short: *apip_lambda* is the switching parameter :math:`\lambda\in[0,1]`,
+that is calculated from *apip_lambda_input* and that mixes the energies
+of a fast (*apip_e_fast*) and a precise (*apip_e_precise*) potential
+into an adaptive-precision energy.
+
+.. note::
+
+   The energy according to the fast and the precise potential are only
+   computed for the subset of atoms, for which it is required, i.e.,
+   for an atom :math:`i` with :math:`\lambda_i=1` one does not need
+   :math:`E_i^\text{precise}` and with :math:`\lambda_i=0` one does
+   not need :math:`E_i^\text{fast}`.
+
+
 In addition, the various per-atom quantities listed above for specific
 packages are only accessible by this command.
 

doc/src/create_atoms.rst

@@ -396,7 +396,7 @@ correct number of particles are inserted, in a perfectly random
 fashion.  Which lattice sites are selected will change with the number
 of processors used.
 
-.. versionadded:: TBD
+.. versionadded:: 12Jun2025
 
 The *group* keyword adds the newly created atoms to the named
 :doc:`group <group>`.  If the group does not yet exist it will be
@@ -416,24 +416,23 @@ atom, based on its coordinates.  They apply to all styles except
 *single*.  The *name* specified for the *var* keyword is the name of
 an :doc:`equal-style variable <variable>` that should evaluate to a
 zero or non-zero value based on one or two or three variables that
-will store the *x*, *y*, or *z* coordinates of an atom (one variable per
+will store the *x*, *y*, or *z* coordinates of an atom (one variable
-coordinate).  If used, these other variables must be
+per coordinate).  If used, these other variables must be specified by
-:doc:`internal-style variables <variable>` defined in the input
+the *set* keyword.  They are internal-style variable, because this
-script; their initial numeric value can be anything.  They must be
+command resets their values directly.  The internal-style variables do
-internal-style variables, because this command resets their values
+not need to be defined in the input script (though they can be); if
-directly.  The *set* keyword is used to identify the names of these
+one (or more) is not defined, then the *set* option creates an
-other variables, one variable for the *x*-coordinate of a created atom,
+:doc:`internal-style variable <variable>` with the specified name.
-one for *y*, and one for *z*.
 
 .. figure:: img/sinusoid.jpg
             :figwidth: 50%
             :align: right
             :target: _images/sinusoid.jpg
 
-When an atom is created, its :math:`(x,y,z)` coordinates become the values for
+When an atom is about to be created, its :math:`(x,y,z)` coordinates
-any *set* variable that is defined.  The *var* variable is then
+become the values for any *set* variable that is defined.  The *var*
-evaluated.  If the returned value is 0.0, the atom is not created.  If
+variable is then evaluated.  If the returned value is 0.0, the atom is
-it is non-zero, the atom is created.
+not created.  If it is non-zero, the atom is created.
 
 As an example, these commands can be used in a 2d simulation, to
 create a sinusoidal surface.  Note that the surface is "rough" due to
@@ -456,8 +455,6 @@ converts lattice spacings to distance.
    region      box block 0 $x 0 $y -0.5 0.5
    create_box  1 box
 
-   variable    xx internal 0.0
-   variable    yy internal 0.0
    variable    v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0"
    create_atoms  1 box var v set x xx set y yy
    write_dump  all atom sinusoid.lammpstrj

doc/src/fix.rst

@@ -201,6 +201,7 @@ accelerated styles exist.
 * :doc:`append/atoms <fix_append_atoms>` - append atoms to a running simulation
 * :doc:`atc <fix_atc>` - initiates a coupled MD/FE simulation
 * :doc:`atom/swap <fix_atom_swap>` - Monte Carlo atom type swapping
+* :doc:`atom_weight/apip <fix_atom_weight_apip>` - compute atomic load of an :doc:`APIP potential <Howto_apip>` for load balancing
 * :doc:`ave/atom <fix_ave_atom>` - compute per-atom time-averaged quantities
 * :doc:`ave/chunk <fix_ave_chunk>` - compute per-chunk time-averaged quantities
 * :doc:`ave/correlate <fix_ave_correlate>` - compute/output time correlations
@@ -270,6 +271,7 @@ accelerated styles exist.
 * :doc:`imd <fix_imd>` - implements the "Interactive MD" (IMD) protocol
 * :doc:`indent <fix_indent>` - impose force due to an indenter
 * :doc:`ipi <fix_ipi>` - enable LAMMPS to run as a client for i-PI path-integral simulations
+* :doc:`lambda/apip <fix_lambda_apip>` - compute switching parameter, that controls the precision of an :doc:`APIP potential <Howto_apip>`
 * :doc:`langevin <fix_langevin>` - Langevin temperature control
 * :doc:`langevin/drude <fix_langevin_drude>` - Langevin temperature control of Drude oscillators
 * :doc:`langevin/eff <fix_langevin_eff>` - Langevin temperature control for the electron force field model
@@ -278,6 +280,7 @@ accelerated styles exist.
 * :doc:`lb/momentum <fix_lb_momentum>` - :doc:`fix momentum <fix_momentum>` replacement for use with a lattice-Boltzmann fluid
 * :doc:`lb/viscous <fix_lb_viscous>` - :doc:`fix viscous <fix_viscous>` replacement for use with a lattice-Boltzmann fluid
 * :doc:`lineforce <fix_lineforce>` - constrain atoms to move in a line
+* :doc:`lambda_thermostat/apip <fix_lambda_thermostat_apip>` - apply energy conserving correction for an :doc:`APIP potential <Howto_apip>`
 * :doc:`manifoldforce <fix_manifoldforce>` - restrain atoms to a manifold during minimization
 * :doc:`mdi/qm <fix_mdi_qm>` - LAMMPS operates as a client for a quantum code via the MolSSI Driver Interface (MDI)
 * :doc:`mdi/qmmm <fix_mdi_qmmm>` - LAMMPS operates as client for QM/MM simulation with a quantum code via the MolSSI Driver Interface (MDI)
@@ -292,7 +295,6 @@ accelerated styles exist.
 * :doc:`mvv/tdpd <fix_mvv_dpd>` - constant temperature DPD using the modified velocity-Verlet algorithm
 * :doc:`neb <fix_neb>` - nudged elastic band (NEB) spring forces
 * :doc:`neb/spin <fix_neb_spin>` - nudged elastic band (NEB) spring forces for spins
-* :doc:`neighbor/swap <fix_neighbor_swap>` - kinetic Monte Carlo (kMC) atom swapping
 * :doc:`nonaffine/displacement <fix_nonaffine_displacement>` - calculate nonaffine displacement of atoms
 * :doc:`nph <fix_nh>` - constant NPH time integration via Nose/Hoover
 * :doc:`nph/asphere <fix_nph_asphere>` - NPH for aspherical particles

doc/src/fix_adapt.rst

@@ -440,7 +440,7 @@ this fix uses to reset theta0 needs to generate values in radians.
 
 ----------
 
-.. versionadded:: TBD
+.. versionadded:: 12Jun2025
 
 The *dihedral* keyword uses the specified variable to change the value of
 a dihedral coefficient over time, very similar to how the *angle* keyword

doc/src/fix_atom_weight_apip.rst

@@ -0,0 +1,143 @@
+.. index:: fix atom_weight/apip
+
+fix atom_weight/apip command
+============================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   fix ID group-ID atom_weight/apip nevery fast_potential precise_potential lambda_input lambda_zone group_lambda_input [no_rescale]
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* atom_weight/apip = style name of this fix command
+* nevery = perform load calculation every this many steps
+* fast_potential = *eam* or *ace* for time measurements of the corresponding pair_style or float for constant time
+* precise_potential = *ace* for a time measurement of the pair_style pace/apip or float for constant time
+* lambda_input = *lambda/input* for a time measurement of pair_style lambda/input/apip or float for constant time
+* lambda_zone = *lambda/zone* for a time measurement of pair_style lambda/zone/apip or float for constant time
+* group_lambda_input = group-ID of the group for which lambda_input is computed
+* no_rescale = do not rescale the work per processor to the measured total force-computation time
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 2 all atom_weight/apip 50 eam ace lambda/input lambda/zone all
+   fix 2 all atom_weight/apip 50 1e-05 0.0004 4e-06 4e-06 all
+   fix 2 all atom_weight/apip 50 ace ace 4e-06 4e-06 all no_rescale
+
+Description
+"""""""""""
+
+This command approximates the load every atom causes when an
+adaptive-precision interatomic potential (APIP) according to
+:ref:`(Immel) <Immel2025_2>` is used.
+This approximated load can be saved as atomic variable and
+used as input for the dynamic load balancing via the
+:doc:`fix balance <fix_balance>` command.
+
+An adaptive-precision potential like :doc:`eam/apip <pair_eam_apip>`
+and :doc:`pace/apip <pair_pace_apip>` is calculated only
+for a subset of atoms.
+The switching parameter that determines per atom, which potential energy is
+used, can be also calculated by
+:doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`.
+A spatial switching zone, that ensures a smooth transition between two
+different interatomic potentials, can be calculated by
+:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`.
+Thus, there are up to four force-subroutines, that are computed only for a
+subset of atoms and combined via the pair_style :doc:`hybrid/overlay <pair_hybrid>`.
+For all four force-subroutines, the average work per atom is be measured
+per processor by the corresponding pair_style.
+This fix extracts these measurements of the pair styles every *nevery*
+steps. The average compute times are used to calculates a per-atom vector with
+the approximated atomic weight, whereas the average compute time of the four
+subroutines contributes only to the load of atoms, for which the corresponding
+subroutine was calculated.
+If not disabled via *no_rescale*, the so calculated load is
+rescaled per processor so that the total atomic compute time matches the
+also measured total compute time of the whole pair_style.
+This atomic weight is intended to be used
+as input for :doc:`fix balance <fix_balance>`:
+
+.. code-block:: LAMMPS
+
+   variable nevery equal 10
+   fix weight_atom all atom_weight/apip ${nevery} eam ace lambda/input lambda/zone all
+   variable myweight atom f_weight_atom
+   fix balance all balance ${nevery} 1.1 rcb weight var myweight
+
+Furthermore, this fix provides the over the processors averaged compute time of the
+four pair_styles, which are used to approximate the atomic weight, as vector.
+
+----------
+
+Restart, fix_modify, output, run start/stop, minimize info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+No information about this fix is written to
+:doc:`binary restart files <restart>`.  None of the
+:doc:`fix_modify <fix_modify>` options are relevant to this fix.
+
+This fix produces a per-atom vector that contains the atomic
+weight of each atom.
+The per-atom vector can only be accessed on timesteps that are multiples
+of *nevery*.
+
+Furthermore, this fix computes a global vector of length 4 with
+statistical information about the four different (possibly)
+measured compute times per force subroutine. The four
+values in the vector are as follows:
+
+  #. average compute time for one atom using the fast pair_style
+  #. average compute time for one atom using the precise pair_style
+  #. average compute time of lambda/input/apip for one atom
+  #. average compute time of lambda/zone/apip for one atom
+
+The compute times are computed as average of all processors that
+measured at least one computation of the corresponding style.
+The vector values calculated by this fix are "intensive" and
+updated whenever the per-atom vector is computed, i.e., in
+timesteps that are multiples of *nevery*.
+
+The vector and the per-atom vector can be accessed by various
+:doc:`output commands <Howto_output>`.
+
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
+
+----------
+
+Restrictions
+""""""""""""
+
+This fix is part of the APIP package. It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package
+<Build_package>` page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix balance <fix_balance>`,
+:doc:`fix lambda/apip <fix_lambda_apip>`,
+:doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`,
+:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`,
+:doc:`pair_style lambda/input/apip  <pair_lambda_input_apip>`,
+:doc:`pair_style eam/apip <pair_eam_apip>`,
+:doc:`pair_style pace/apip  <pair_pace_apip>`,
+
+Default
+"""""""
+
+*no_rescale* is not used by default.
+
+----------
+
+.. _Immel2025_2:
+
+**(Immel)** Immel, Drautz and Sutmann, J Chem Phys, 162, 114119 (2025)

doc/src/fix_ave_moments.rst

@@ -50,7 +50,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 12Jun2025
 
 Using one or more values as input, calculate the moments of the underlying
 (population) distributions based on samples collected every few time

doc/src/fix_controller.rst

@@ -98,52 +98,53 @@ the following dynamic equation:
 
    \frac{dc}{dt}  = -\alpha (K_p e + K_i \int_0^t e \, dt + K_d \frac{de}{dt} )
 
-where *c* is the continuous time analog of the control variable,
+where *c* is the continuous time analog of the control variable, *e*
-*e* =\ *pvar*\ -\ *setpoint* is the error in the process variable, and
+=\ *pvar*\ -\ *setpoint* is the error in the process variable, and
-:math:`\alpha`, :math:`K_p`, :math:`K_i` , and :math:`K_d` are constants
+:math:`\alpha`, :math:`K_p`, :math:`K_i` , and :math:`K_d` are
-set by the corresponding
+constants set by the corresponding keywords described above. The
-keywords described above. The discretized version of this equation is:
+discretized version of this equation is:
 
 .. math::
 
    c_n  = c_{n-1} -\alpha \left( K_p \tau e_n + K_i \tau^2 \sum_{i=1}^n e_i + K_d (e_n - e_{n-1}) \right)
 
-where :math:`\tau = \mathtt{Nevery} \cdot \mathtt{timestep}` is the time
+where :math:`\tau = \mathtt{Nevery} \cdot \mathtt{timestep}` is the
-interval between updates,
+time interval between updates, and the subscripted variables indicate
-and the subscripted variables indicate the values of *c* and *e* at
+the values of *c* and *e* at successive updates.
-successive updates.
 
 From the first equation, it is clear that if the three gain values
 :math:`K_p`, :math:`K_i`, :math:`K_d` are dimensionless constants,
-then :math:`\alpha` must have
+then :math:`\alpha` must have units of [unit *cvar*\ ]/[unit *pvar*\
-units of [unit *cvar*\ ]/[unit *pvar*\ ]/[unit time] e.g. [ eV/K/ps
+]/[unit time] e.g. [ eV/K/ps ]. The advantage of this unit scheme is
-]. The advantage of this unit scheme is that the value of the
+that the value of the constants should be invariant under a change of
-constants should be invariant under a change of either the MD timestep
+either the MD timestep size or the value of *Nevery*\ . Similarly, if
-size or the value of *Nevery*\ . Similarly, if the LAMMPS :doc:`unit style <units>` is changed, it should only be necessary to change
+the LAMMPS :doc:`unit style <units>` is changed, it should only be
-the value of :math:`\alpha` to reflect this, while leaving :math:`K_p`,
+necessary to change the value of :math:`\alpha` to reflect this, while
-:math:`K_i`, and :math:`K_d` unaltered.
+leaving :math:`K_p`, :math:`K_i`, and :math:`K_d` unaltered.
 
 When choosing the values of the four constants, it is best to first
 pick a value and sign for :math:`\alpha` that is consistent with the
-magnitudes and signs of *pvar* and *cvar*\ .  The magnitude of :math:`K_p`
+magnitudes and signs of *pvar* and *cvar*\ .  The magnitude of
-should then be tested over a large positive range keeping :math:`K_i = K_d =0`.
+:math:`K_p` should then be tested over a large positive range keeping
-A good value for :math:`K_p` will produce a fast response in *pvar*,
+:math:`K_i = K_d =0`.  A good value for :math:`K_p` will produce a
-without overshooting the *setpoint*\ .  For many applications, proportional
+fast response in *pvar*, without overshooting the *setpoint*\ .  For
-feedback is sufficient, and so :math:`K_i = K_d =0` can be used. In cases
+many applications, proportional feedback is sufficient, and so
-where there is a substantial lag time in the response of *pvar* to a change
+:math:`K_i = K_d =0` can be used. In cases where there is a
-in *cvar*, this can be counteracted by increasing :math:`K_d`. In situations
+substantial lag time in the response of *pvar* to a change in *cvar*,
+this can be counteracted by increasing :math:`K_d`. In situations
 where *pvar* plateaus without reaching *setpoint*, this can be
-counteracted by increasing :math:`K_i`.  In the language of Charles Dickens,
+counteracted by increasing :math:`K_i`.  In the language of Charles
-:math:`K_p` represents the error of the present, :math:`K_i` the error of
+Dickens, :math:`K_p` represents the error of the present, :math:`K_i`
-the past, and :math:`K_d` the error yet to come.
+the error of the past, and :math:`K_d` the error yet to come.
 
 Because this fix updates *cvar*, but does not initialize its value,
-the initial value :math:`c_0` is that assigned by the user in the input script via
+the initial value :math:`c_0` is that assigned by the user in the
-the :doc:`internal-style variable <variable>` command.  This value is
+input script via the :doc:`internal-style variable <variable>`
-used (by every other LAMMPS command that uses the variable) until this
+command.  This value is used (by every other LAMMPS command that uses
-fix performs its first update of *cvar* after *Nevery* timesteps.  On
+the variable) until this fix performs its first update of *cvar* after
-the first update, the value of the derivative term is set to zero,
+*Nevery* timesteps.  On the first update, the value of the derivative
-because the value of :math:`e_{n-1}` is not yet defined.
+term is set to zero, because the value of :math:`e_{n-1}` is not yet
+defined.
 
 ----------
 
@@ -154,21 +155,23 @@ must produce a global quantity, not a per-atom or local quantity.
 
 If *pvar* begins with "c\_", a compute ID must follow which has been
 previously defined in the input script and which generates a global
-scalar or vector.  See the individual :doc:`compute <compute>` doc page
+scalar or vector.  See the individual :doc:`compute <compute>` doc
-for details.  If no bracketed integer is appended, the scalar
+page for details.  If no bracketed integer is appended, the scalar
 calculated by the compute is used.  If a bracketed integer is
 appended, the Ith value of the vector calculated by the compute is
-used.  Users can also write code for their own compute styles and :doc:`add them to LAMMPS <Modify>`.
+used.  Users can also write code for their own compute styles and
+:doc:`add them to LAMMPS <Modify>`.
 
 If *pvar* begins with "f\_", a fix ID must follow which has been
 previously defined in the input script and which generates a global
 scalar or vector.  See the individual :doc:`fix <fix>` page for
 details.  Note that some fixes only produce their values on certain
 timesteps, which must be compatible with when fix controller
-references the values, or else an error results.  If no bracketed integer
+references the values, or else an error results.  If no bracketed
-is appended, the scalar calculated by the fix is used.  If a bracketed
+integer is appended, the scalar calculated by the fix is used.  If a
-integer is appended, the Ith value of the vector calculated by the fix
+bracketed integer is appended, the Ith value of the vector calculated
-is used.  Users can also write code for their own fix style and :doc:`add them to LAMMPS <Modify>`.
+by the fix is used.  Users can also write code for their own fix style
+and :doc:`add them to LAMMPS <Modify>`.
 
 If *pvar* begins with "v\_", a variable name must follow which has been
 previously defined in the input script.  Only equal-style variables
@@ -182,19 +185,21 @@ variable.
 The target value *setpoint* for the process variable must be a numeric
 value, in whatever units *pvar* is defined for.
 
-The control variable *cvar* must be the name of an :doc:`internal-style variable <variable>` previously defined in the input script.  Note
+The control variable *cvar* must be the name of an
-that it is not specified with a "v\_" prefix, just the name of the
+:doc:`internal-style variable <variable>` previously defined in the
-variable.  It must be an internal-style variable, because this fix
+input script.  Note that it is not specified with a "v\_" prefix, just
-updates its value directly.  Note that other commands can use an
+the name of the variable.  It must be an internal-style variable,
-equal-style versus internal-style variable interchangeably.
+because this fix updates its value directly.  Note that other commands
+can use an equal-style versus internal-style variable interchangeably.
 
 ----------
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-Currently, no information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
+Currently, no information about this fix is written to :doc:`binary
-are relevant to this fix.
+restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>`
+options are relevant to this fix.
 
 This fix produces a global vector with 3 values which can be accessed
 by various :doc:`output commands <Howto_output>`.  The values can be
@@ -211,7 +216,8 @@ variable is in.  The vector values calculated by this fix are
 "extensive".
 
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""

doc/src/fix_deposit.rst

@@ -225,22 +225,25 @@ rotated configuration of the molecule.
 
 .. versionadded:: 21Nov2023
 
-The *var* and *set* keywords can be used together to provide a criterion
+The *var* and *set* keywords can be used together to provide a
-for accepting or rejecting the addition of an individual atom, based on its
+criterion for accepting or rejecting the addition of an individual
-coordinates.  The *name* specified for the *var* keyword is the name of an
+atom, based on its coordinates.  The *name* specified for the *var*
-:doc:`equal-style variable <variable>` that should evaluate to a zero or
+keyword is the name of an :doc:`equal-style variable <variable>` that
-non-zero value based on one or two or three variables that will store the
+should evaluate to a zero or non-zero value based on one or two or
-*x*, *y*, or *z* coordinates of an atom (one variable per coordinate).  If
+three variables that will store the *x*, *y*, or *z* coordinates of an
-used, these other variables must be :doc:`internal-style variables
+atom (one variable per coordinate).  If used, these other variables
-<variable>` defined in the input script; their initial numeric value can be
+must be :doc:`internal-style variables <variable>` specified by the
-anything. They must be internal-style variables, because this command
+*set* keyword.  They must be internal-style variables, because this
-resets their values directly.  The *set* keyword is used to identify the
+command resets their values directly.  The internal-style variables do
-names of these other variables, one variable for the *x*-coordinate of a
+not need to be defined in the input script (though they can be); if
-created atom, one for *y*, and one for *z*.  When an atom is created, its
+one (or more) is not defined, then the *set* option creates an
-:math:`(x,y,z)` coordinates become the values for any *set* variable that
+:doc:`internal-style variable <variable>` with the specified name.
-is defined.  The *var* variable is then evaluated.  If the returned value
+
-is 0.0, the atom is not created.  If it is non-zero, the atom is created.
+When an atom is about to be created, its :math:`(x,y,z)` coordinates
-For an example of how to use these keywords, see the
+become the values for any *set* variable that is defined.  The *var*
+variable is then evaluated.  If the returned value is 0.0, the atom is
+not created.  If it is non-zero, the atom is created.  For an example
+of how to use the set/var keywords in a similar context, see the
 :doc:`create_atoms <create_atoms>` command.
 
 The *rate* option moves the insertion volume in the z direction (3d)
@@ -304,12 +307,13 @@ units of distance or velocity.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the state of the deposition to :doc:`binary restart files <restart>`.  This includes information about how many
+This fix writes the state of the deposition to :doc:`binary restart
-particles have been deposited, the random number generator seed, the
+files <restart>`.  This includes information about how many particles
-next timestep for deposition, etc.  See the
+have been deposited, the random number generator seed, the next
-:doc:`read_restart <read_restart>` command for info on how to re-specify
+timestep for deposition, etc.  See the :doc:`read_restart
-a fix in an input script that reads a restart file, so that the
+<read_restart>` command for info on how to re-specify a fix in an
-operation of the fix continues in an uninterrupted fashion.
+input script that reads a restart file, so that the operation of the
+fix continues in an uninterrupted fashion.
 
 .. note::
 

doc/src/fix_gjf.rst

@@ -39,7 +39,7 @@ Examples
 
 Description
 """""""""""
-.. versionadded:: TBD
+.. versionadded:: 12Jun2025
 
 Apply a Langevin thermostat as described in :ref:`(Gronbech-Jensen-2020) <Gronbech-Jensen-2020>`
 to a group of atoms which models an interaction with a background

doc/src/fix_lambda_apip.rst

@@ -0,0 +1,262 @@
+.. index:: fix lambda/apip
+
+fix lambda/apip command
+=======================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   fix ID group-ID lambda/apip thr_lo thr_hi keyword args ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* lambda/apip = style name of this fix command
+* thr_lo = value below which :math:`\lambda_i^\text{input}` results in a switching parameter of 1
+* thr_hi = value above which :math:`\lambda_i^\text{input}` results in a switching parameter of 0
+* zero or one keyword/args pairs may be appended
+* keyword = *time_averaged_zone* or *min_delta_lambda* or *lambda_non_group* or *store_atomic_stats* or *dump_atomic_history* or *group_fast* or *group_precise* or *group_ignore_lambda_input*
+
+  .. parsed-literal::
+
+       *time_averaged_zone* args = cut_lo cut_hi history_len_lambda_input history_len_lambda
+         cut_lo = distance at which the radial function decreases from 1
+         cut_hi = distance from which on the radial function is 0
+         history_len_lambda_input = number of time steps for which lambda_input is averaged
+         history_len_lambda = number of time steps for which the switching parameter is averaged
+       *min_delta_lambda* args = delta
+         delta = value below which changes of the switching parameter are neglected (>= 0)
+       *lambda_non_group* args = lambda_ng
+         lambda_ng = *precise* or *fast* or float
+           *precise* = assign a constant switching parameter of 0 to atoms, that are not in the group specified by group-ID
+           *fast* = assign a constant switching parameter of 1 to atoms, that are not in the group specified by group-ID
+           float = assign this constant switching parameter to atoms, that are not in the group specified by group-ID (0 <= float <= 1)
+       *group_fast* args = group-ID-fast
+         group-ID-fast = the switching parameter of 1 is used instead of the one computed by lambda_input for atoms in the group specified by group-ID-fast
+       *group_precise* args = group-ID-precise
+         group-ID-precise = the switching parameter of 0 is used instead of the one computed by lambda_input for atoms in the group specified by group-ID-precise
+       *group_ignore_lambda_input* args = group-ID-ignore-lambda-input
+         group-ID-ignore-lambda-input = the switching parameter of lambda_ng is used instead of the one computed by lambda_input for atoms in the group specified by group-ID-ignore-lambda-input
+       *store_atomic_stats* args = none
+       *dump_atomic_history* args = none
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 2 all lambda/apip 3.0 3.5 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
+   fix 2 mobile lambda/apip 3.0 3.5 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01 group_ignore_lambda_input immobile lambda_non_group fast
+
+Description
+"""""""""""
+The potential energy :math:`E_i` of an atom :math:`i` of an adaptive-precision
+potential according to :ref:`(Immel) <Immel2025_3>` is given by
+
+.. math::
+
+   E_i = \lambda_i E_i^\text{(fast)} + (1-\lambda_i) E_i^\text{(precise)},
+
+whereas :math:`E_i^\text{(fast)}` is the potential energy of atom :math:`i`
+according to a fast interatomic potential like EAM,
+:math:`E_i^\text{(precise)}` is the potential energy according to a precise
+interatomic potential such as ACE and :math:`\lambda_i\in[0,1]` is the
+switching parameter that decides which potential energy is used.
+This fix calculates the switching parameter :math:`\lambda_i` based on the
+input provided from :doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`.
+
+The calculation of the switching parameter is described in detail in
+:ref:`(Immel) <Immel2025_3>`.
+This fix calculates the switching parameter for all atoms in the
+:doc:`group <group>`
+described by group-ID, while the value of *lambda_non_group* is used
+as switching parameter for all other atoms.
+
+First, this fix calculates per atom :math:`i` the time averaged input
+:math:`\lambda^\text{input}_{\text{avg},i}` from
+:math:`\lambda^\text{input}_{i}`, whereas the number of averaged timesteps
+can be set via *time_averaged_zone*.
+
+.. note::
+
+   :math:`\lambda^\text{input}_{i}` is calculated by
+   :doc:`pair_style lambda/input/apip <pair_lambda_input_apip>`, which needs to be included
+   in the input script as well.
+
+The time averaged input :math:`\lambda^\text{input}_{\text{avg},i}` is then
+used to calculate the switching parameter
+
+.. math::
+
+   \lambda_{0,i}(t) = f^\text{(cut)} \left(\frac{\lambda_{\text{avg},i}^\text{input}(t) - \lambda_\text{lo}^\text{input}}{\lambda_\text{hi}^\text{input} - \lambda_\text{lo}^\text{input}} \right)\,,
+
+whereas the thresholds :math:`\lambda_\text{hi}^\text{input}`
+and  :math:`\lambda_\text{lo}^\text{input}` are set by the
+values provided as *thr_lo* and *thr_hi* and :math:`f^\text{(cut)}(x)` is a cutoff function
+that is 1 for :math:`x\leq 0`, decays from 1 to 0 for :math:`x\in[0,1]`, and
+is 0 for :math:`x\geq 1`.
+If the *group_precise* argument is used, :math:`\lambda_{0,i}=0` is used for all
+atoms :math:`i` assigned to the corresponding :doc:`group <group>`.
+If the *group_fast* argument is used, :math:`\lambda_{0,i}=1` is used for all
+atoms :math:`i` assigned to the corresponding :doc:`group <group>`.
+If an atom is in the groups *group_fast* and *group_precise*,
+:math:`\lambda_{0,i}=0` is used.
+If the *group_ignore_lambda_input* argument is used,
+:math:`\lambda_i^\text{input}` is not computed for all atoms :math:`i` assigned
+to the corresponding :doc:`group <group>`; instead, if the value is not already
+set by *group_fast* or *group_precise*, the value of *lambda_non_group* is
+used.
+
+.. note::
+
+   The computation of :math:`\lambda_i^\text{input}` is not required for
+   atoms that are in the groups *group_fast* and *group_precise*.
+   Thus, one should use *group_ignore_lambda_input* and prevent the
+   computation of :math:`\lambda_i^\text{input}` for all atoms, for
+   which a constant input is used.
+
+A spatial transition zone between the fast and the precise potential is
+introduced via
+
+.. math::
+
+   \lambda_{\text{min},i}(t) = \text{min}\left(\left\{1 - (1 -\lambda_{0,j}(t)) f^\text{(cut)}\left(\frac{r_{ij}(t)-r_{\lambda,\text{lo}}}{r_{\lambda,\text{hi}} - r_{\lambda,\text{lo}}}\right) : j \in \Omega_{\lambda,i} \right\}\right)\,,
+
+whereas the thresholds :math:`r_{\lambda,\text{lo}}` and
+:math:`r_{\lambda,\text{hi}}`
+of the cutoff function are set via *time_averaged_zone* and
+:math:`\Omega_{\lambda,i}` is the set of
+neighboring atoms of atom :math:`i`.
+
+.. note::
+
+   :math:`\lambda_{\text{min},i}` is calculated by
+   :doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`, which needs to be included
+   in the input script as well.
+
+The switching parameter is smoothed by the calculation of the time average
+
+.. math::
+
+   \lambda_{\text{avg},i}(t) = \frac{1}{N_{\lambda,\text{avg}}} \sum_{n=1}^{N_{\lambda,\text{avg}}} \lambda_{\text{min},i}(t - n \Delta t)\,,
+
+whereas :math:`\Delta t` is the :doc:`timestep <timestep>` and
+:math:`N_{\lambda,\text{avg}}` is the number of averaged timesteps, that
+can be set via *time_averaged_zone*.
+
+Finally, numerical fluctuations of the switching parameter are suppressed by the usage of
+
+.. math::
+
+   \lambda_{i}(t) = \left\{
+   \begin{array}{ll}
+   \lambda_{\text{avg},i}(t) & \text{ for } \left|\lambda_{\text{avg},i}(t) - \lambda_{i}(t-\Delta t)\right|\geq \Delta\lambda_\text{min} \text{ or } \lambda_{\text{avg},i}(t)\in\{0,1\}, \\
+   \lambda_{i}(t-\Delta t) & \text{ otherwise}\,,
+   \end{array}
+   \right.
+
+whereas the minimum change :math:`\Delta\lambda_\text{min}` is set by the
+*min_delta_lambda* argument.
+
+.. note::
+
+   *group_fast* affects only :math:`\lambda_{0,i}(t)`. The switching parameter
+   of atoms in this :doc:`group <group>` may change due to the calculation of the
+   spatial switching zone.
+   A switching parameter of 1 can be enforced by excluding the corresponding
+   atoms from the :doc:`group <group>` described by group-ID and using *lambda_non_group* 1
+   as argument.
+
+----------
+
+A code example for the calculation of the switching parameter for an
+adaptive-precision potential is given in the following:
+The adaptive-precision potential is created
+by combining :doc:`pair_style eam/fs/apip <pair_eam_apip>`
+and :doc:`pair_style pace/precise/apip <pair_pace_apip>`.
+The input, from which the switching parameter is calculated, is provided
+by :doc:`pair lambda/input/csp/apip <pair_lambda_input_apip>`.
+The switching parameter is calculated by this fix, whereas the spatial
+transition zone of the switching parameter is calculated by
+:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`.
+
+.. code-block:: LAMMPS
+
+   pair_style hybrid/overlay eam/fs/apip pace/precise/apip lambda/input/csp/apip fcc cutoff 5.0 lambda/zone/apip 12.0
+   pair_coeff * * eam/fs/apip Cu.eam.fs Cu
+   pair_coeff * * pace/precise/apip Cu_precise.yace Cu
+   pair_coeff * * lambda/input/csp/apip
+   pair_coeff * * lambda/zone/apip
+   fix 2 all lambda/apip 3.0 3.5 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
+
+
+----------
+
+Restart, fix_modify, output, run start/stop, minimize info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+The saved history of the switching parameter :math:`\lambda_i`
+and the saved history of
+:math:`\lambda_i^\text{input}` are written to
+:doc:`binary restart files <restart>` allow a smooth restart of a simulation.
+None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix.
+
+If the *store_atomic_stats* argument is used, basic statistics is provided as
+per-atom array:
+
+  #. :math:`\lambda_i^\text{input}(t)`
+  #. :math:`\lambda_{\text{avg},i}^\text{input}(t)`
+  #. :math:`\lambda_{0,i}(t)`
+  #. :math:`\lambda_{\text{min},i}(t)`
+  #. :math:`\lambda_{i}(t)`
+
+If the *dump_atomic_history* argument is used, the whole saved history
+of :math:`\lambda_i^\text{input}(t)` is appended to the previously
+mentioned array per atom.
+
+The per-atom vector can be accessed by various
+:doc:`output commands <Howto_output>`.
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
+
+----------
+
+Restrictions
+""""""""""""
+
+This fix is part of the APIP package. It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package
+<Build_package>` page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`,
+:doc:`pair_style lambda/input/apip  <pair_lambda_input_apip>`,
+:doc:`pair_style eam/apip <pair_eam_apip>`,
+:doc:`pair_style pace/apip  <pair_pace_apip>`,
+:doc:`fix atom_weight/apip <fix_atom_weight_apip>`
+:doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`,
+
+Default
+"""""""
+
+*min_delta_lambda* = 0,
+*lambda_non_group* = 1,
+*cut_lo* = 4.0,
+*cut_hi* = 12.0,
+*history_len_lambda_input* = 100,
+*history_len_lambda* = 100,
+*store_atomic_stats* is not used,
+*dump_atomic_history* is not used,
+*group_fast* is not used,
+*group_precise* is not used,
+*group_ignore_lambda_input* is not used
+
+----------
+
+.. _Immel2025_3:
+
+**(Immel)** Immel, Drautz and Sutmann, J Chem Phys, 162, 114119 (2025)

doc/src/fix_lambda_thermostat_apip.rst

@@ -0,0 +1,176 @@
+.. index:: fix lambda_thermostat/apip
+
+fix lambda_thermostat/apip command
+==================================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   fix ID group-ID lambda_thermostat/apip keyword values ...
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* lambda_thermostat/apip = style name of this fix command
+* zero or more keyword/value pairs may be appended
+* keyword = *seed* or *store_atomic_forces* or *N_rescaling*
+
+  .. parsed-literal::
+
+       *seed* value = integer
+         integer = integer that is used as seed for the random number generator (> 0)
+       *store_atomic_forces* value = nevery
+         nevery = provide per-atom output every this many steps
+       *N_rescaling* value = groupsize
+         groupsize = rescale this many neighboring atoms (> 1)
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 2 all lambda_thermostat/apip
+   fix 2 all lambda_thermostat/apip N_rescaling 100
+   fix 2 all lambda_thermostat/apip seed 42
+   fix 2 all lambda_thermostat/apip seed 42 store_atomic_forces 1000
+
+Description
+"""""""""""
+
+This command applies the local thermostat described in
+:ref:`(Immel) <Immel2025_4>`
+to conserve the energy when the switching parameters of an
+:doc:`adaptive-precision interatomic potential <Howto_apip>` (APIP)
+are updated while the gradient
+of the switching parameter is neglected in the force calculation.
+
+.. warning::
+
+   The temperature change caused by this fix is only the means to the end of
+   conserving the energy. Thus, this fix is not a classical thermostat, that
+   ensures a given temperature in the system.
+   All available thermostats are listed :doc:`here <Howto_thermostat>`.
+
+The potential energy :math:`E_i` of an atom :math:`i` is given by the formula from
+:ref:`(Immel) <Immel2025_4>`
+
+.. math::
+
+   E_i = \lambda_i E_i^\text{(fast)} + (1-\lambda_i) E_i^\text{(precise)},
+
+whereas :math:`E_i^\text{(fast)}` is the potential energy of atom :math:`i`
+according to a fast interatomic potential like EAM,
+:math:`E_i^\text{(precise)}` is the potential energy according to a precise
+interatomic potential such as ACE and :math:`\lambda_i\in[0,1]` is the
+switching parameter that decides which potential energy is used.
+This potential energy and the corresponding forces are conservative when
+the switching parameter :math:`\lambda_i` is constant in time for all atoms
+:math:`i`.
+
+For a conservative force calculation and dynamic switching parameters,
+the atomic force on an atom is given by
+:math:`F_i = -\nabla_i \sum_j E_j` and includes the derivative of the switching
+parameter :math:`\lambda_i`.
+The force contribution of this gradient of the switching function can cause
+large forces which are not similar to the forces of the fast or the precise
+interatomic potential as discussed in :ref:`(Immel) <Immel2025_4>`.
+Thus, one can neglect the gradient of the switching parameter in the force
+calculation and compensate for the violation of energy conservation by
+the application of the local thermostat implemented in this fix.
+One can compute the violation of the energy conservation :math:`\Delta H_i`
+for all atoms :math:`i` as discussed in :ref:`(Immel) <Immel2025_4>`.
+To locally correct this energy violation :math:`\Delta H_i`, one
+can rescale the velocity of atom :math:`i`  and of neighboring atoms.
+The rescaling is done relative to the center-of-mass velocity of the
+group and, thus, conserves the momentum.
+
+.. note::
+
+   This local thermostat provides the NVE ensemble rather than the NVT
+   ensemble as
+   the energy :math:`\Delta H_i` determines the rescaling factor rather than
+   a temperature.
+
+Velocities :math:`v` are updated by the integrator according to
+:math:`\Delta v_i = (F_i/m_i)\Delta t`, whereas `m` denotes the mass of atom
+:math:`i` and :math:`\Delta t` is the time step.
+One can interpret the velocity difference :math:`\Delta v` caused by the
+rescaling as the application of an additional force which is given by
+:math:`F^\text{lt}_i = (v^\text{unscaled}_i - v^\text{rescaled}_i) m_i
+/ \Delta t` :ref:`(Immel) <Immel2025_4>`.
+This additional force is computed when the *store_atomic_forces* option
+is used.
+
+The local thermostat is not appropriate for simulations at a temperature of 0K.
+
+.. note::
+
+   The maximum decrease of the kinetic energy is achieved with a rescaling
+   factor of 0, i.e., the relative velocity of the group of rescaled atoms
+   is set to zero. One cannot decrease the energy further. Thus, the
+   local thermostat can fail, which is, however, reported by the returned
+   vector.
+
+----------
+
+Restart, fix_modify, output, run start/stop, minimize info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+No information about this fix is written to
+:doc:`binary restart files <restart>`.  None of the
+:doc:`fix_modify <fix_modify>` options are relevant to this fix.
+
+If the *store_atomic_forces* option is used, this fix produces every
+*nevery* time steps a per-atom array that contains the theoretical force
+applied by the local thermostat in all three spatial dimensions in the first
+three components. :math:`\Delta H_i` is the fourth component of the per-atom
+array.
+The per-atom array can only be accessed on timesteps that are multiples
+of *nevery*.
+
+Furthermore, this fix computes a global vector of length 6 with
+information about the rescaling:
+
+  #. number of atoms whose energy changed due to the last :math:`\lambda` update
+  #. contribution of the potential energy to the last computed :math:`\Delta H`
+  #. contribution of the kinetic energy to the last computed :math:`\Delta H`
+  #. sum over all atoms of the absolute energy change caused by the last rescaling step
+  #. energy change that could not be compensated accumulated over all timesteps
+  #. number of atoms whose energy change could not be compensated accumulated over all timesteps
+
+The vector and the per-atom vector can be accessed by various
+:doc:`output commands <Howto_output>`.
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
+
+----------
+
+Restrictions
+""""""""""""
+
+This fix is part of the APIP package. It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package
+<Build_package>` page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix lambda/apip <fix_lambda_apip>`,
+:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`,
+:doc:`pair_style lambda/input/apip  <pair_lambda_input_apip>`,
+:doc:`pair_style eam/apip <pair_eam_apip>`,
+:doc:`pair_style pace/apip  <pair_pace_apip>`,
+:doc:`fix atom_weight/apip <fix_atom_weight_apip>`
+
+Default
+"""""""
+
+seed = 42, N_rescaling = 200, *store_atomic_forces* is not used
+
+----------
+
+.. _Immel2025_4:
+
+**(Immel)** Immel, Drautz and Sutmann, J Chem Phys, 162, 114119 (2025)

doc/src/fix_neighbor_swap.rst

@@ -1,264 +0,0 @@
-.. index:: fix neighbor/swap
-
-fix neighbor/swap command
-=========================
-
-Syntax
-""""""
-
-.. code-block:: LAMMPS
-
-   fix ID group-ID neighbor/swap N X seed T R0 voro-ID keyword values ...
-
-* ID, group-ID are documented in :doc:`fix <fix>` command
-* neighbor/swap = style name of this fix command
-* N = invoke this fix every N steps
-* X = number of swaps to attempt every N steps
-* seed = random # seed (positive integer)
-* T = scaling temperature of the MC swaps (temperature units)
-* R0 = scaling swap probability of the MC swaps (distance units)
-* voro-ID = valid voronoi compute id (compute voronoi/atom)
-* one or more keyword/value pairs may be appended to args
-* keywords *types* and *diff* are mutually exclusive, but one must be specified
-* keyword = *types* or *diff* or *ke* or *region* or *rates*
-
-  .. parsed-literal::
-
-       *types* values = two or more atom types (Integers in range [1,Ntypes] or type labels)
-       *diff* values = one atom type
-       *ke* value = *yes* or *no*
-         *yes* = kinetic energy is conserved after atom swaps
-         *no* = no conservation of kinetic energy after atom swaps
-       *region* value = region-ID
-         region-ID = ID of region to use as an exchange/move volume
-       *rates* values = V1 V2 . . . Vntypes values to conduct variable diffusion for different atom types (unitless)
-
-Examples
-""""""""
-
-.. code-block:: LAMMPS
-
-   compute voroN all voronoi/atom neighbors yes
-   fix mc all neighbor/swap 10 160 15238 1000.0 3.0 voroN diff 2
-   fix myFix all neighbor/swap 100 1 12345 298.0 3.0 voroN region my_swap_region types 5 6
-   fix kmc all neighbor/swap 1 100 345 1.0 3.0 voroN diff 3 rates 3 1 6
-
-Description
-"""""""""""
-
-.. versionadded:: TBD
-
-This fix performs Monte-Carlo (MC) evaluations to enable kinetic
-Monte Carlo (kMC)-type behavior during MD simulation by allowing
-neighboring atoms to swap their positions. In contrast to the :doc:`fix
-atom/swap <fix_atom_swap>` command which swaps pairs of atoms anywhere
-in the simulation domain, the restriction of the MC swapping to
-neighbors enables a hybrid MD/kMC-like simulation.
-
-Neighboring atoms are defined by using a Voronoi tesselation performed
-by the :doc:`compute voronoi/atom <compute_voronoi_atom>` command.
-Two atoms are neighbors if their Voronoi cells share a common face
-(3d) or edge (2d).
-
-The selection of a swap neighbor is made using a distance-based
-criterion for weighting the selection probability of each swap, in the
-same manner as kMC selects a next event using relative probabilities.
-The acceptance or rejection of each swap is determined via the
-Metropolis criterion after evaluating the change in system energy due
-to the swap.
-
-A detailed explanation of the original implementation of this
-algorithm can be found in :ref:`(Tavenner 2023) <TavennerMDkMC>`
-where it was used to simulated accelerated diffusion in an MD context.
-
-Simulating inherently kinetically-limited behaviors which rely on rare
-events (such as atomic diffusion in a solid) is challenging for
-traditional MD since its relatively short timescale will not naturally
-sample many events. This fix addresses this challenge by allowing rare
-neighbor hopping events to be sampled in a kMC-like fashion at a much
-faster rate (set by the specified *N* and *X* parameters).  This enables
-the processes of atomic diffusion to be approximated during an MD
-simulation, effectively decoupling the MD atomic vibrational timescale
-and the atomic hopping (kMC event) timescale.
-
-The algorithm implemented by this fix is as follows:
-
-   - The MD simulation is paused every *N* steps
-   - A Voronoi tesselation is performed for the current atom configuration.
-   - Then *X* atom swaps are attempted, one after the other.
-   - For each swap, an atom *I* is selected randomly from the list of
-     atom types specified by either the *types* or *diff* keywords.
-   - One of *I*'s Voronoi neighbors *J* is selected using the
-     distance-weighted probability for each neighbor detailed below.
-   - The *I,J* atom IDs are communicated to all processors so that a
-     global energy evaluation can be performed for the post-swap state
-     of the system.
-   - The swap is accepted or rejected based on the Metropolis criterion
-     using the energy change of the system and the specified temperature
-     *T*.
-
-Here are a few comments on the computational cost of the swapping
-algorithm.
-
-   1. The cost of a global energy evaluation is similar to that of an MD
-      timestep.
-
-   2. Similar to other MC algorithms in LAMMPS, improved parallel
-      efficiency is achieved with a smaller number of atoms per
-      processor than would typically be used in an standard MD
-      simulation. This is because the per-energy evaluation cost
-      increases relative to the balance of MD/MC steps as indicated by
-      1., but the communication cost remains relatively constant for a
-      given number of MD steps.
-
-   3. The MC portion of the simulation will run dramatically slower if
-      the pair style uses different cutoffs for different atom types (or
-      type pairs).  This is because each atom swap then requires a
-      rebuild of the neighbor list to ensure the post-swap global energy
-      can be computed correctly.
-
-Limitations are imposed on selection of *I,J* atom pairs to avoid
-swapping of atoms which are outside of a reasonable cutoff (e.g. due to
-a Voronoi tesselation near free surfaces) though the use of a
-distance-weighted probability scaling.
-
-----------
-
-This section gives more details on other arguments and keywords.
-
-The random number generator (RNG) used by all the processors for MC
-operations is initialized with the specified *seed*.
-
-The distance-based probability is weighted by the specified *R0* which
-sets the radius :math:`r_0` in this formula
-
-.. math::
-
-    p_{ij} = e^{(\frac{r_{ij}}{r_0})^2}
-
-where :math:`p_{ij}` is the probability of selecting atom :math:`j` to
-swap with atom :math:`i`.  Typically, a value for *R0* around the
-average nearest-neighbor spacing is appropriate.  Since this is simply a
-probability weighting, the swapping behavior is not very sensitive to
-the exact value of *R0*.
-
-The required *voro-ID* value is the compute-ID of a
-:doc:`compute voronoi/atom <compute_voronoi_atom>` command like
-this:
-
-.. code-block:: LAMMPS
-
-    compute compute-ID group-ID voronoi/atom neighbors yes
-
-It must return per-atom list of valid neighbor IDs as in the
-:doc:`compute voronoi/atom <compute_voronoi_atom>` command.
-
-The keyword *types* takes two or more atom types as its values.  Only
-atoms *I* of the first atom type will be selected.  Only atoms *J* of the
-remaining atom types will be considered as potential swap partners.
-
-The keyword *diff* take a single atom type as its value.  Only atoms
-*I* of the that atom type will be selected.  Atoms *J* of all
-remaining atom types will be considered as potential swap partners.
-This includes the atom type specified with the *diff* keyword to
-account for self-diffusive hops between two atoms of the same type.
-
-Note that the *neighbors yes* option must be enabled for use with this
-fix. The group-ID should include all the atoms which this fix will
-potentially select. I.e. the group-ID used in the voronoi compute should
-include the same atoms as that indicated by the *types* keyword. If the
-*diff* keyword is used, the group-ID should include atoms of all types
-in the simulation.
-
-The keyword *ke* takes *yes* (default) or *no* as its value.  It two
-atoms are swapped with different masses, then a value of *yes* will
-rescale their respective velocities to conserve the kinetic energy of
-the system.  A value of *no* will perform no rescaling, so that
-kinetic energy is not conserved.  See the restriction on this keyword
-below.
-
-The *region* keyword takes a *region-ID* as its value.  If specified,
-then only atoms *I* and *J* within the geometric region will be
-considered as swap partners.  See the :doc:`region <region>` command
-for details.  This means the group-ID for the :doc:`compute
-voronoi/atom <compute_voronoi_atom>` command also need only contain
-atoms within the region.
-
-The keyword *rates* can modify the swap rate based on the type of atom
-*J*.  Ntype values must be specified, where Ntype = the number of atom
-types in the system.  Each value is used to scale the probability
-weighting given by the equation above.  In the third example command
-above, a simulation has 3 atoms types.  Atom *I*s of type 1 are
-eligible for swapping.  Swaps may occur with atom *J*s of all 3 types.
-Assuming all *J* atoms are equidistant from an atom *I*, *J* atoms of
-type 1 will be 3x more likely to be selected as a swap partner than
-atoms of type 2.  And *J* atoms of type 3 will be 6.5x more likely to
-be selected than atoms of type 2.  If the *rates* keyword is not used,
-all atom types will be treated with the same probability during selection
-of swap attempts.
-
-
-Restart, fix_modify, output, run start/stop, minimize info
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-
-This fix writes the state of the fix to :doc:`binary restart files
-<restart>`.  This includes information about the random number generator
-seed, the next timestep for MC exchanges, and the number of exchange
-attempts and successes.  See the :doc:`read_restart <read_restart>`
-command for info on how to re-specify a fix in an input script that
-reads a restart file, so that the operation of the fix continues in an
-uninterrupted fashion.
-
-None of the :doc:`fix_modify <fix_modify>` options are relevant to this
-fix.
-
-This fix computes a global vector of length 2, which can be accessed
-by various :doc:`output commands <Howto_output>`.  The vector values are
-the following global cumulative quantities:
-
-  #. swap attempts
-  #. swap accepts
-
-The vector values calculated by this fix are "intensive".
-
-No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during
-:doc:`energy minimization <minimize>`.
-
-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.  Also this fix requires that the :ref:`VORONOI
-package <PKG-VORONOI>` is installed, otherwise the fix will not be
-compiled.
-
-The :doc:`compute voronoi/atom <compute_voronoi_atom>` command
-referenced by the required voro-ID must return neighboring atoms as
-illustrated in the examples above.
-
-If this fix is used with systems that do not have per-type masses
-(e.g. atom style sphere), the *ke* keyword must be set to *off* since
-the implemented algorithm will not be able to re-scale velocities
-properly.
-
-Related commands
-""""""""""""""""
-
-:doc:`fix nvt <fix_nh>`, :doc:`compute voronoi/atom <compute_voronoi_atom>`
-:doc:`delete_atoms <delete_atoms>`, :doc:`fix gcmc <fix_gcmc>`,
-:doc:`fix atom/swap <fix_atom_swap>`, :doc:`fix mol/swap <fix_mol_swap>`,
-:doc:`fix sgcmc <fix_sgcmc>`
-
-Default
-"""""""
-
-The option defaults are *ke* = yes and *rates* = 1 for all atom types.
-
-----------
-
-.. _TavennerMDkMC:
-
-**(Tavenner 2023)** J Tavenner, M Mendelev, J Lawson, Computational
- Materials Science, 218, 111929 (2023).

doc/src/fix_set.rst

@@ -27,6 +27,8 @@ Examples
 Description
 """""""""""
 
+.. versionadded:: 12Jun2025
+
 Reset one or more properties of one or more atoms once every *Nfreq*
 steps during a simulation.
 

doc/src/kspace_style.rst

@@ -32,6 +32,7 @@
 .. index:: kspace_style msm/cg/omp
 .. index:: kspace_style msm/dielectric
 .. index:: kspace_style scafacos
+.. index:: kspace_style zero
 
 kspace_style command
 ====================
@@ -43,7 +44,7 @@ Syntax
 
    kspace_style style value
 
-* style = *none* or *ewald* or *ewald/dipole* or *ewald/dipole/spin* or *ewald/disp* or *ewald/disp/dipole* or *ewald/omp* or *ewald/electrode* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/intel* or *pppm/disp/intel* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/disp/tip4p/omp* or *pppm/tip4p/omp* or *pppm/dielectic* or *pppm/disp/dielectric* or *pppm/electrode* or *pppm/electrode/intel* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *msm/dielectric* or *scafacos*
+* style = *none* or *ewald* or *ewald/dipole* or *ewald/dipole/spin* or *ewald/disp* or *ewald/disp/dipole* or *ewald/omp* or *ewald/electrode* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/intel* or *pppm/disp/intel* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/disp/tip4p/omp* or *pppm/tip4p/omp* or *pppm/dielectic* or *pppm/disp/dielectric* or *pppm/electrode* or *pppm/electrode/intel* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *msm/dielectric* or *scafacos* or *zero*
 
   .. parsed-literal::
 
@@ -121,6 +122,7 @@ Syntax
        *scafacos* values = method accuracy
          method = fmm or p2nfft or p3m or ewald or direct
          accuracy = desired relative error in forces
+       *zero* value = none
 
 Examples
 """"""""
@@ -132,6 +134,7 @@ Examples
    kspace_style msm 1.0e-4
    kspace_style scafacos fmm 1.0e-4
    kspace_style none
+   kspace_style zero
 
 Used in input scripts:
 
@@ -375,6 +378,13 @@ other ScaFaCoS options currently exposed to LAMMPS.
 
 ----------
 
+.. versionadded:: 12Jun2025
+
+The *zero* style does not do any calculations, but is compatible
+with all pair styles that require some version of a kspace style.
+
+----------
+
 The specified *accuracy* determines the relative RMS error in per-atom
 forces calculated by the long-range solver.  It is set as a
 dimensionless number, relative to the force that two unit point

doc/src/molecule.rst

@@ -34,7 +34,7 @@ Syntax
        *ioff* value = Ioff
          Ioff = offset to add to improper types
        *scale* value = sfactor
-         sfactor = scale factor to apply to the size and mass of the molecule
+         sfactor = scale factor to apply to the size, mass, and dipole of the molecule
 
 Examples
 """"""""
@@ -42,6 +42,7 @@ Examples
 .. code-block:: LAMMPS
 
    molecule 1 mymol.txt
+   molecule water tip3p.json
    molecule 1 co2.txt h2o.txt
    molecule CO2 co2.txt boff 3 aoff 2
    molecule 1 mymol.txt offset 6 9 18 23 14
@@ -65,7 +66,7 @@ templates include:
 * :doc:`atom_style template <atom_style>`
 
 The ID of a molecule template can only contain alphanumeric characters
-and underscores.
+and underscores, same as other IDs in LAMMPS.
 
 A single template can contain multiple molecules, listed one per file.
 Some of the commands listed above currently use only the first
@@ -74,6 +75,13 @@ contains multiple molecules.  The :doc:`atom_style template
 <atom_style>` command allows multiple-molecule templates to define a
 system with more than one templated molecule.
 
+The molecule file can be either in a *native* format or in `JSON format
+<https://www.json.org/>`_.  JSON formal filenames **must** have the
+extension ".json".  Files with any other name will be assumed to be in
+the "native" format.  The details of the two formats are described
+below.  When referencing multiple molecule files in a single *molecule*
+command, each of those files may be either format.
+
 Each filename can be followed by optional keywords which are applied
 only to the molecule in the file as used in this template.  This is to
 make it easy to use the same molecule file in different molecule
@@ -95,40 +103,45 @@ use that attribute (e.g. no bonds).
    labels will determine the actual types directly depending on the
    current :doc:`labelmap <labelmap>` settings.
 
-The *scale* keyword scales the size of the molecule.  This can be
+The *scale* keyword scales the size of the molecule.  This can be useful
-useful for modeling polydisperse granular rigid bodies.  The scale
+for modeling polydisperse granular rigid bodies.  The scale factor is
-factor is applied to each of these properties in the molecule file, if
+applied to each of these properties in the molecule file, if they are
-they are defined: the individual particle coordinates (Coords
+defined: the individual particle coordinates (Coords or "coords"
-section), the individual mass of each particle (Masses section), the
+section), the individual mass of each particle (Masses or "masses"
-individual diameters of each particle (Diameters section), the total
+section), the individual diameters of each particle (Diameters or
-mass of the molecule (header keyword = mass), the center-of-mass of
+"diameters" section), the per-atom dipoles (Dipoles or "dipoles"
-the molecule (header keyword = com), and the moments of inertia of the
+section) the total mass of the molecule (header keyword = mass), the
-molecule (header keyword = inertia).
+center-of-mass of the molecule (header keyword = com), and the moments
+of inertia of the molecule (header keyword = inertia).
 
 .. note::
 
    The molecule command can be used to define molecules with bonds,
-   angles, dihedrals, impropers, or special bond lists of neighbors
+   angles, dihedrals, impropers, and special bond lists of neighbors
    within a molecular topology, so that you can later add the molecules
    to your simulation, via one or more of the commands listed above.
-   Since this topology-related information requires that suitable storage
+   Since this topology-related information requires that suitable
-   is reserved when LAMMPS creates the simulation box (e.g. when using
+   storage is reserved when LAMMPS creates the simulation box (e.g. when
-   the :doc:`create_box <create_box>` command or the
+   using the :doc:`create_box <create_box>` command or the
-   :doc:`read_data <read_data>` command) suitable space has to be reserved
+   :doc:`read_data <read_data>` command) suitable space has to be
-   so you do not overflow those pre-allocated data structures when adding
+   reserved at that step so you do not overflow those pre-allocated data
-   molecules later.  Both the :doc:`create_box <create_box>` command and
+   structures when adding molecules later.  Both the :doc:`create_box
-   the :doc:`read_data <read_data>` command have "extra" options which
+   <create_box>` command and the :doc:`read_data <read_data>` command
-   ensure space is allocated for storing topology info for molecules that
+   have "extra" options which ensure extra space is allocated for
-   are added later.
+   storing topology info for molecules that are added later.  This
+   feature is *not* available for the :doc:`read_restart command
+   <read_restart>`, thus binary restart files need to be converted
+   to data files first.
 
 ----------
 
-Format of a molecule file
+Format of a native molecule file
-"""""""""""""""""""""""""
+""""""""""""""""""""""""""""""""
 
-The format of an individual molecule file looks similar but is
+The format of an "native" individual molecule file looks similar but is
-different than that of a data file read by the :doc:`read_data <read_data>`
+*different* from that of a data file read by the :doc:`read_data
-commands.  Here is a simple example for a TIP3P water molecule:
+<read_data>` commands.  Here is a simple example for a TIP3P water
+molecule:
 
 .. code-block::
 
@@ -196,7 +209,7 @@ defining a *body* particle, which requires setting the number of
 
 .. list-table::
       :header-rows: 1
-      :widths: 20 13 42 15
+      :widths: 21 12 47 20
 
       * - Number(s)
         - Keyword
@@ -205,7 +218,7 @@ defining a *body* particle, which requires setting the number of
       * - N
         - atoms
         - # of atoms N in molecule
-        - 0
+        - keyword is *required*
       * - Nb
         - bonds
         - # of bonds Nb in molecule
@@ -228,8 +241,8 @@ defining a *body* particle, which requires setting the number of
         - 0
       * - Ninteger Ndouble
         - body
-        - # of integer and floating-point values in body particle
+        - # of integer and floating-point values in :doc:`body particle <Howto_body>`
-        - 0
+        - 0 0
       * - Mtotal
         - mass
         - total mass of molecule
@@ -669,6 +682,343 @@ the file format.
 
 ----------
 
+Format of a JSON molecule file
+""""""""""""""""""""""""""""""
+
+.. versionadded:: 12Jun2025
+
+The format of a JSON format individual molecule file must follow the
+`JSON format <https://www.json.org/>`_, which evolved from the
+JavaScript programming language as a programming-language-neutral data
+interchange language.  The JSON syntax is independent of its content,
+and thus the data in the file must follow suitable conventions to be
+correctly processed.  LAMMPS provides a `JSON schema file
+<https://json-schema.org/>`_ for JSON format molecule files in the
+:ref:`tools/json folder <json>` to represent those conventions.  Using
+the schema file any JSON format molecule files can be validated.  Please
+note that the format requirement for JSON are very strict and the JSON
+reader in LAMMPS does not accept files with extensions like comments.
+Validating a particular JSON format molecule file against this schema
+ensures that both, the JSON syntax requirement *and* the LAMMPS
+conventions for molecule template files are followed.  LAMMPS should be
+able to read and parse any JSON file that passes the schema check.  This
+is a formal check only and thus it **cannot** check whether the file
+contents are consistent or physically meaningful.
+
+Here is a simple example for the same TIP3P water molecule from above in
+JSON format and also using :doc:`type labels <labelmap>` instead of
+numeric types:
+
+.. code-block:: json
+
+   {
+       "application": "LAMMPS",
+       "format": "molecule",
+       "revision": 1,
+       "title": "Water molecule. TIP3P geometry",
+       "schema": "https://download.lammps.org/json/molecule-schema.json",
+       "units": "real",
+       "coords": {
+           "format": ["atom-id", "x", "y", "z"],
+           "data": [
+               [1,  0.00000, -0.06556,  0.00000],
+               [2,  0.75695,  0.52032,  0.00000],
+               [3, -0.75695,  0.52032,  0.00000]
+           ]
+       },
+       "types": {
+           "format": ["atom-id", "type"],
+           "data": [
+               [1,  "OW"],
+               [2,  "HO1"],
+               [3,  "HO1"]
+           ]
+       },
+       "charges": {
+           "format": ["atom-id", "charge"],
+           "data": [
+               [1, -0.834],
+               [2,  0.417],
+               [3,  0.417]
+           ]
+       },
+       "bonds": {
+           "format": ["bond-type", "atom1", "atom2"],
+           "data": [
+               ["OW-HO1",  1,  2],
+               ["OW-HO1",  1,  3]
+           ]
+       },
+       "angles": {
+           "format": ["angle-type", "atom1", "atom2", "atom3"],
+           "data": [
+               ["HO1-OW-HO1",  2,  1,  3]
+           ]
+       }
+   }
+
+Unlike with the native molecule file format, there are no header or body
+sections, just a list of keywords with associated data.  JSON format
+data is read, parsed, and stored in an internal dictionary data
+structure in one step and thus the order of keywords is not relevant.
+
+Data for keywords is either provided directly following the keyword or
+as a *data block*.  A *data block* is a list that has to include two
+keywords, "format" and "data", where the former lists keywords of the
+properties that are stored in the columns of the "data" lists.  The
+names and order of entries in the "format" list (and thus how the data
+is interpreted) are currently fixed.
+
+Since the length of the various lists can be easily obtained from the
+internal data structure, several header keywords of the "native" molecule
+file are not needed.  On the other hand, some additional keywords are
+required to identify the conventions applied to the generic JSON file
+format.  The structure of the data itself mostly follows what is used
+for the "native" molecule file format.
+
+.. list-table::
+   :header-rows: 1
+
+   * - Keyword
+     - Argument(s)
+     - Required
+     - Description
+   * - application
+     - "LAMMPS"
+     - yes
+     - indicates a LAMMPS JSON file; files from other applications may be accepted in the future
+   * - format
+     - "molecule"
+     - yes
+     - indicates a molecule template file
+   * - revision
+     - an integer
+     - yes
+     - currently 1, to facility backward compatibility on changes to the conventions
+   * - title
+     - a string
+     - no
+     - information about the template which will echoed to the screen and log
+   * - schema
+     - URL as string
+     - no
+     - location of a JSON schema file for validating the molecule file format
+   * - units
+     - a string
+     - no
+     - indicates :doc:`units settings <units>` for this molecule template
+   * - com
+     - list with 3 doubles
+     - no
+     - overrides the auto-computed center-of-mass for the template
+   * - masstotal
+     - double
+     - no
+     - overrides the auto-computed total mass for the template
+   * - inertia
+     - list with 6 doubles
+     - no
+     - overrides the auto-computed moments of inertia
+   * - coords
+     - a data block
+     - no
+     - contains atom positions with the format "atom-id", "x", "y", "z" (same as Coords)
+   * - types
+     - a data block
+     - yes
+     - assigns atom types to atoms with the format "atom-id", "type" (same as Types)
+   * - molecule
+     - a data block
+     - no
+     - assigns molecule-IDs to atoms with the format "atom-id", "molecule-id" (same as Molecules)
+   * - fragments
+     - a data block
+     - no
+     - assigns atom-ids to fragment-IDs with the format "fragment-id", "atom-id-list" (same as Fragments)
+   * - charges
+     - a data block
+     - no
+     - assigns charges to atoms with the format "atom-id", "charge" (same as Charges)
+   * - dipoles
+     - a data block
+     - no
+     - assigns point dipoles to atoms with the format "atom-id", "mux", "muy", "muz" (same as Dipoles)
+   * - diameters
+     - a data block
+     - no
+     - assigns diameters to atoms with the format "atom-id", "diameter" (same as Diameters)
+   * - masses
+     - a data block
+     - no
+     - assigns per-atom masses to atoms with the format "atom-id", "mass" (same as Masses)
+   * - bonds
+     - a data block
+     - no
+     - defines bonds in the molecule template with the format "bond-type", "atom1", "atom2" (same as Bonds without bond-ID)
+   * - angles
+     - a data block
+     - no
+     - defines angles in the molecule template with the format "angle-type", "atom1", "atom2", "atom3" (same as Angles without angle-ID)
+   * - dihedrals
+     - a data block
+     - no
+     - defines dihedrals in the molecule template with the format "dihedral-type", "atom1", "atom2", "atom3", "atom4" (same as Dihedrals without dihedral-ID)
+   * - impropers
+     - a data block
+     - no
+     - defines impropers in the molecule template with the format "improper-type", "atom1", "atom2", "atom3", "atom4" (same as Impropers without improper-ID)
+   * - shake
+     - 3 JSON objects
+     - no
+     - contains the sub-sections "flags", "atoms", "bonds" described below
+   * - special
+     - 2 JSON objects
+     - no
+     - contains the sub-sections "counts" and "bonds" described below
+   * - body
+     - 2 JSON objects
+     - no
+     - contains the "integers" and "doubles" sub-sections with arrays with the same data as Body Integers and Body Doubles, respectively
+
+The following table describes the sub-sections for the "special" entry from above:
+
+.. list-table::
+   :header-rows: 1
+
+   * - Subsection
+     - Argument(s)
+     - Required
+     - Description
+   * - counts
+     - a data block
+     - yes
+     - contains the counts of 1-2, 1-3, and 1-4 special neighbors with the format "atom-id", "n12", "n13", "n14" (same as Special Bond Counts)
+   * - bonds
+     - a data block
+     - yes
+     - contains the lists of special neighbors to atoms with the format "atom-id", "atom-id-list" (same as Special Bonds)
+
+The following table describes the sub-sections for the "shake" entry from above:
+
+.. list-table::
+   :header-rows: 1
+
+   * - Subsection
+     - Argument(s)
+     - Required
+     - Description
+   * - flags
+     - a data block
+     - yes
+     - contains the counts shake flags for atoms with the format "atom-id", "flag" (same as Shake Flags)
+   * - atoms
+     - a data block
+     - yes
+     - contains the lists of shake cluster atom-ids for atoms with the format "atom-id", "atom-id-list" (same as Shake Atoms)
+   * - bonds
+     - a data block
+     - yes
+     - contains the lists of shake bond or angle types for atoms with the format "atom-id", "type-list" (same as Shake Bonds)
+
+The "special" and "shake" sections are usually not needed, since the
+data can be auto-generated as soon as the simulation box is defined.
+Below is an example for what would have to be *added* to the example
+JSON file above in case the molecule command needs to be issued earlier.
+
+.. code-block:: json
+
+   "special": {
+       "counts": {
+           "format": ["atom-id", "n12", "n13", "n14"],
+           "data": [
+               [1, 2, 0, 0],
+               [2, 1, 1, 0],
+               [3, 1, 1, 0]
+           ]
+       },
+       "bonds": {
+           "format": ["atom-id", "atom-id-list"],
+           "data": [
+               [1,  [2, 3]],
+               [2,  [1, 3]],
+               [3,  [1, 2]]
+           ]
+       }
+   },
+   "shake": {
+       "flags": {
+           "format": ["atom-id", "flag"],
+           "data": [
+               [1, 1],
+               [2, 1],
+               [3, 1]
+           ]
+       },
+       "atoms": {
+           "format": ["atom-id", "atom-id-list"],
+           "data": [
+               [1,  [1, 2, 3]],
+               [2,  [1, 2, 3]],
+               [3,  [1, 2, 3]]
+           ]
+       },
+       "types": {
+           "format": ["atom-id", "type-list"],
+           "data": [
+               [1,  ["OW-HO1",  "OW-HO1", "HO1-OW-HO1"]],
+               [2,  ["OW-HO1",  "OW-HO1", "HO1-OW-HO1"]],
+               [3,  ["OW-HO1",  "OW-HO1", "HO1-OW-HO1"]]
+           ]
+       }
+   }
+
+
+Below is a minimal example of a JSON format molecule template for a body
+particle for :doc:`pair style body/nparticle
+<pair_body_nparticle>`. Molecule templates for body particles must
+contain only one atom:
+
+.. code-block:: json
+
+   {
+       "application": "LAMMPS",
+       "format": "molecule",
+       "revision": 1,
+       "title": "Square body for body/nparticles",
+       "schema": "https://download.lammps.org/json/molecule-schema.json",
+       "units": "real",
+       "coords": {
+           "format": ["atom-id", "x", "y", "z"],
+           "data": [
+               [1,  0.00000,  0.00000,  0.00000]
+           ]
+       },
+       "types": {
+           "format": ["atom-id", "type"],
+           "data": [
+               [1,  1]
+           ]
+       },
+       "masses": {
+           "format": ["atom-id", "mass"],
+           "data": [
+               [1,  1.0]
+           ]
+       },
+       "body": {
+           "integers": [4],
+           "doubles": [
+               1.0, 1.0, 4.0, 0.0, 0.0, 0.0,
+               -0.70710678118654752440, -0.70710678118654752440, 0.0,
+               -0.70710678118654752440,  0.70710678118654752440, 0.0,
+               0.70710678118654752440,  0.70710678118654752440, 0.0,
+               0.70710678118654752440, -0.70710678118654752440, 0.0
+           ]
+       }
+   }
+
+----------
+
 Restrictions
 """"""""""""
 

doc/src/pair_eam_apip.rst

@@ -0,0 +1,127 @@
+.. index:: pair_style eam/apip
+.. index:: pair_style eam/fs/apip
+
+pair_style eam/apip command
+=============================
+
+Constant precision variant: *eam*
+
+pair_style eam/fs/apip command
+================================
+
+Constant precision variant: *eam/fs*
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style eam/apip
+   pair_style eam/fs/apip
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style hybrid/overlay eam/fs/apip pace/precise/apip lambda/input/csp/apip fcc cutoff 5.0 lambda/zone/apip 12.0
+   pair_coeff * * eam/fs/apip Cu.eam.fs Cu
+   pair_coeff * * pace/precise/apip Cu_precise.yace Cu
+   pair_coeff * * lambda/input/csp/apip
+   pair_coeff * * lambda/zone/apip
+
+
+Description
+"""""""""""
+Style *eam* computes pairwise interactions for metals and metal alloys
+using embedded-atom method (EAM) potentials :ref:`(Daw) <Daw2>`.  The total
+energy :math:`E_i` of an atom :math:`i` is given by
+
+.. math::
+
+   E_i^\text{EAM} = F_\alpha \left(\sum_{j \neq i}\ \rho_\beta (r_{ij})\right) +
+         \frac{1}{2} \sum_{j \neq i} \phi_{\alpha\beta} (r_{ij})
+
+where :math:`F` is the embedding energy which is a function of the atomic
+electron density :math:`\rho`, :math:`\phi` is a pair potential interaction,
+and :math:`\alpha` and :math:`\beta` are the element types of atoms
+:math:`i` and :math:`j`.  The multi-body nature of the EAM potential is a
+result of the embedding energy term. Both summations in the formula are over
+all neighbors :math:`j` of atom :math:`i` within the cutoff distance.
+EAM is documented in detail in :doc:`pair_style eam <pair_eam>`.
+
+The potential energy :math:`E_i` of an atom :math:`i` of an adaptive-precision
+interatomic potential (APIP) according to :ref:`(Immel) <Immel2025_5>` is given by
+
+.. math::
+
+   E_i^\text{APIP} = \lambda_i E_i^\text{(fast)} + (1-\lambda_i) E_i^\text{(precise)}\,,
+
+whereas the switching parameter :math:`\lambda_i` is computed
+dynamically during a simulation by :doc:`fix lambda/apip <fix_lambda_apip>`
+or set prior to a simulation via :doc:`set <set>`.
+
+The pair style *eam/fs/apip* computes the potential energy
+:math:`\lambda_i E_i^\text{EAM}` and the
+corresponding force and should be combined
+with a precise potential like
+:doc:`pair_style pace/precise/apip <pair_pace_apip>` that computes the
+potential energy :math:`(1-\lambda_i) E_i^\text{(precise)}` and the
+corresponding force via :doc:`pair_style hybrid/overlay <pair_hybrid>`.
+
+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 as
+described above with the individual styles.  You never need to specify
+a pair_coeff command with I != J arguments for the eam/apip styles.
+
+This pair style does not support the :doc:`pair_modify <pair_modify>`
+shift, table, and tail options.
+
+The eam/apip pair styles do not write their information to :doc:`binary
+restart files <restart>`, since it is stored in tabulated potential
+files.  Thus, you need to re-specify the pair_style and pair_coeff
+commands in an input script that reads a restart file.
+
+The eam/apip pair styles can only be used via the *pair* keyword of the
+:doc:`run_style respa <run_style>` command.  They do not support the
+*inner*, *middle*, *outer* keywords.
+
+----------
+
+Restrictions
+""""""""""""
+
+This pair styles are part of the APIP package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair_style eam  <pair_eam>`,
+:doc:`pair_style hybrid/overlay <pair_hybrid>`,
+:doc:`fix lambda/apip <fix_lambda_apip>`,
+:doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`,
+:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`,
+:doc:`pair_style lambda/input/apip  <pair_lambda_input_apip>`,
+:doc:`pair_style pace/apip <pair_pace_apip>`,
+:doc:`fix atom_weight/apip <fix_atom_weight_apip>`
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _Immel2025_5:
+
+**(Immel)** Immel, Drautz and Sutmann, J Chem Phys, 162, 114119 (2025)
+
+.. _Daw2:
+
+**(Daw)** Daw, Baskes, Phys Rev Lett, 50, 1285 (1983).
+Daw, Baskes, Phys Rev B, 29, 6443 (1984).

doc/src/pair_lambda_input_apip.rst

@@ -0,0 +1,151 @@
+.. index:: pair_style lambda/input/apip
+.. index:: pair_style lambda/input/csp/apip
+
+pair_style lambda/input/apip command
+====================================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style lambda/input/apip cutoff
+
+* lambda/input/apip = style name of this pair style
+* cutoff = global cutoff (distance units)
+
+pair_style lambda/input/csp/apip command
+========================================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style lambda/input/csp/apip lattice keyword args
+
+* lambda/input/csp/apip = style name of this pair style
+* lattice = *fcc* or *bcc* or integer
+
+  .. parsed-literal::
+
+       *fcc* = use 12 nearest neighbors to calculate the CSP like in a perfect fcc lattice
+       *bcc* = use 8 nearest neighbors to calculate the CSP like in a perfect bcc lattice
+       integer = use N nearest neighbors to calculate the CSP
+
+* zero or more keyword/args pairs may be appended
+* keyword = *cutoff* or *N_buffer*
+
+  .. parsed-literal::
+
+       *cutoff* args = cutoff
+         cutoff = distance in which neighboring atoms are considered (> 0)
+       *N_buffer* args = N_buffer
+         N_buffer = number of additional neighbors, which are included in the j-j+N/2 calculation
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style lambda/input/csp/apip fcc
+   pair_style lambda/input/csp/apip fcc cutoff 5.0
+   pair_style lambda/input/csp/apip bcc cutoff 5.0 N_buffer 2
+   pair_style lambda/input/csp/apip 14
+
+Description
+"""""""""""
+
+This pair_styles calculates :math:`\lambda_i^\text{input}(t)`, which
+is required for :doc:`fix lambda/apip <fix_lambda_apip>`.
+
+The pair_style lambda_input sets :math:`\lambda_i^\text{input}(t) = 0`.
+
+The pair_style lambda_input/csp calculates
+:math:`\lambda_i^\text{input}(t) = \text{CSP}_i(t)`.
+The centro-symmetry parameter (CSP) :ref:`(Kelchner) <Kelchner_2>` is described
+in :doc:`compute centro/atom <compute_centro_atom>`.
+
+The lattice argument is described in
+:doc:`compute centro/atom <compute_centro_atom>` and determines
+the number of neighboring atoms that are used to compute the CSP.
+The *N_buffer* argument allows to include more neighboring atoms in
+the calculation of the contributions from the pair j,j+N/2 to the CSP as
+discussed in :ref:`(Immel) <Immel2025_6>`.
+
+The computation of :math:`\lambda_i^\text{input}(t)` is done by this
+pair_style instead of by :doc:`fix lambda/apip <fix_lambda_apip>`, as this computation
+takes time and this pair_style can be included in the load-balancing via
+:doc:`fix atom_weight/apip <fix_atom_weight_apip>`.
+
+A code example for the calculation of the switching parameter for an adaptive-
+precision potential is given in the following:
+The adaptive-precision potential is created
+by combining :doc:`pair_style eam/fs/apip <pair_eam_apip>`
+and :doc:`pair_style pace/precise/apip <pair_pace_apip>`.
+The input, from which the switching parameter is calculated, is provided
+by this pair_style.
+The switching parameter is calculated by :doc:`fix lambda/apip <fix_lambda_apip>`,
+whereas the spatial
+transition zone of the switching parameter is calculated by
+:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`.
+
+.. code-block:: LAMMPS
+
+   pair_style hybrid/overlay eam/fs/apip pace/precise/apip lambda/input/csp/apip fcc cutoff 5.0 lambda/zone/apip 12.0
+   pair_coeff * * eam/fs/apip Cu.eam.fs Cu
+   pair_coeff * * pace/precise/apip Cu_precise.yace Cu
+   pair_coeff * * lambda/input/csp/apip
+   pair_coeff * * lambda/zone/apip
+   fix 2 all lambda/apip 3.0 3.5 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
+
+----------
+
+Mixing, shift, table, tail correction, restart, rRESPA info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+The cutoff distance for this pair style can be mixed.  The default mix
+value is *geometric*\ .  See the "pair_modify" command for details.
+
+This pair style does not support the :doc:`pair_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style writes no information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands need
+to be specified in an input script that reads a restart file.
+
+This pair style does not support the use of the *inner*, *middle*,
+and *outer* keywords of the :doc:`run_style respa <run_style>` command.
+
+----------
+
+Restrictions
+""""""""""""
+This fix is part of the APIP package. It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package
+<Build_package>` page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute centro/atom <compute_centro_atom>`,
+:doc:`fix lambda/apip <fix_lambda_apip>`,
+:doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`,
+:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`,
+:doc:`pair_style eam/apip <pair_eam_apip>`,
+:doc:`pair_style pace/apip  <pair_pace_apip>`,
+:doc:`fix atom_weight/apip <fix_atom_weight_apip>`
+
+Default
+"""""""
+
+N_buffer=0, cutoff=5.0
+
+----------
+
+.. _Kelchner_2:
+
+**(Kelchner)** Kelchner, Plimpton, Hamilton, Phys Rev B, 58, 11085 (1998).
+
+.. _Immel2025_6:
+
+**(Immel)** Immel, Drautz and Sutmann, J Chem Phys, 162, 114119 (2025)

doc/src/pair_lambda_zone_apip.rst

@@ -0,0 +1,106 @@
+.. index:: pair_style lambda/zone/apip
+
+pair_style lambda/zone/apip command
+===================================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style lambda/zone/apip cutoff
+
+* lambda/zone/apip = style name of this pair style
+* cutoff = global cutoff (distance units)
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style lambda/zone/apip 12.0
+
+Description
+"""""""""""
+
+This pair_style calculates :math:`\lambda_{\text{min},i}`, which
+is required for :doc:`fix lambda/apip <fix_lambda_apip>`.
+The meaning of :math:`\lambda_{\text{min},i}` is documented in
+:doc:`fix lambda/apip <fix_lambda_apip>`, as this pair_style is for use with
+:doc:`fix lambda/apip <fix_lambda_apip>` only.
+
+This pair_style requires only the global cutoff as argument.
+The remaining quantities, that are required to calculate
+:math:`\lambda_{\text{min},i}` are extracted from
+:doc:`fix lambda/apip <fix_lambda_apip>` and, thus,
+do not need to be passed to this pair_style as arguments.
+
+.. warning::
+
+   The cutoff given as argument to this pair style is only relevant for the
+   neighbor list creation. The radii, which define :math:`r_{\lambda,\text{hi}}` and :math:`r_{\lambda,\text{lo}}` are defined by :doc:`fix lambda/apip <fix_lambda_apip>`.
+
+The computation of :math:`\lambda_{\text{min},i}` is done by this
+pair_style instead of by :doc:`fix lambda/apip <fix_lambda_apip>`, as this computation
+takes time and this pair_style can be included in the load-balancing via
+:doc:`fix atom_weight/apip <fix_atom_weight_apip>`.
+
+A code example for the calculation of the switching parameter for an
+adaptive-precision interatomic potential (APIP) is given in the following:
+The adaptive-precision potential is created
+by combining :doc:`pair_style eam/fs/apip <pair_eam_apip>`
+and :doc:`pair_style pace/precise/apip <pair_pace_apip>`.
+The input, from which the switching parameter is calculated, is provided
+by :doc:`pair lambda/input/csp/apip <pair_lambda_input_apip>`.
+The switching parameter is calculated by :doc:`fix lambda/apip <fix_lambda_apip>`,
+whereas the spatial transition zone of the switching parameter is calculated
+by this pair style.
+
+.. code-block:: LAMMPS
+
+   pair_style hybrid/overlay eam/fs/apip pace/precise/apip lambda/input/csp/apip fcc cutoff 5.0 lambda/zone/apip 12.0
+   pair_coeff * * eam/fs/apip Cu.eam.fs Cu
+   pair_coeff * * pace/precise/apip Cu_precise.yace Cu
+   pair_coeff * * lambda/input/csp/apip
+   pair_coeff * * lambda/zone/apip
+   fix 2 all lambda/apip 3.0 3.5 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
+
+----------
+
+Mixing, shift, table, tail correction, restart, rRESPA info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+The cutoff distance for this pair style can be mixed.  The default mix
+value is *geometric*\ .  See the "pair_modify" command for details.
+
+This pair style does not support the :doc:`pair_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair style writes no information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands need
+to be specified in an input script that reads a restart file.
+
+This pair style does not support the use of the *inner*, *middle*,
+and *outer* keywords of the :doc:`run_style respa <run_style>` command.
+
+----------
+
+Restrictions
+""""""""""""
+This fix is part of the APIP package. It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package
+<Build_package>` page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix lambda/apip <fix_lambda_apip>`,
+:doc:`fix atom_weight/apip <fix_atom_weight_apip>`
+:doc:`pair_style lambda/input/apip  <pair_lambda_input_apip>`,
+:doc:`pair_style eam/apip <pair_eam_apip>`,
+:doc:`pair_style pace/apip  <pair_pace_apip>`,
+:doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`,
+
+Default
+"""""""
+
+none

doc/src/pair_lj_pirani.rst

@@ -27,7 +27,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 12Jun2025
 
 Pair style *lj/pirani* computes pairwise interactions from an Improved
 Lennard-Jones (ILJ) potential according to :ref:`(Pirani) <Pirani>`.

doc/src/pair_pace_apip.rst

@@ -0,0 +1,147 @@
+.. index:: pair_style pace/apip
+.. index:: pair_style pace/fast/apip
+.. index:: pair_style pace/precise/apip
+
+pair_style pace/apip command
+============================
+
+pair_style pace/fast/apip command
+=================================
+
+pair_style pace/precise/apip command
+====================================
+
+Constant precision variant: *pace*
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style pace/apip ... keyword values ...
+   pair_style pace/fast/apip ... keyword values ...
+   pair_style pace/precise/apip ... keyword values ...
+
+* one or more keyword/value pairs may be appended
+
+  .. parsed-literal::
+
+     keyword = keywords of :doc:`pair pace <pair_pace>`
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style hybrid/overlay pace/fast/apip pace/precise/apip lambda/input/csp/apip fcc cutoff 5.0 lambda/zone/apip 12.0
+   pair_coeff * * pace/fast/apip Cu_fast.yace Cu
+   pair_coeff * * pace/precise/apip Cu_precise.yace Cu
+   pair_coeff * * lambda/input/csp/apip
+   pair_coeff * * lambda/zone/apip
+
+   pair_style hybrid/overlay eam/fs/apip pace/precise/apip lambda/input/csp/apip fcc cutoff 5.0 lambda/zone/apip 12.0
+   pair_coeff * * eam/fs/apip Cu.eam.fs Cu
+   pair_coeff * * pace/precise/apip Cu_precise.yace Cu
+   pair_coeff * * lambda/input/csp/apip
+   pair_coeff * * lambda/zone/apip
+
+
+Description
+"""""""""""
+
+Pair style :doc:`pace <pair_pace>` computes interactions using the Atomic
+Cluster Expansion (ACE), which is a general expansion of the atomic energy in
+multi-body basis functions :ref:`(Drautz19) <Drautz2019_2>`.  The *pace*
+pair style provides an efficient implementation that is described in
+this paper :ref:`(Lysogorskiy21) <Lysogorskiy20211_2>`.
+
+The potential energy :math:`E_i` of an atom :math:`i` of an adaptive-precision
+interatomic potential (APIP) according to
+:ref:`(Immel25) <Immel2025_7>` is given by
+
+.. math::
+
+   E_i^\text{APIP} = \lambda_i E_i^\text{(fast)} + (1-\lambda_i) E_i^\text{(precise)}\,,
+
+whereas the switching parameter :math:`\lambda_i` is computed
+dynamically during a simulation by :doc:`fix lambda/apip <fix_lambda_apip>`
+or set prior to a simulation via :doc:`set <set>`.
+
+The pair style *pace/precise/apip* computes the potential energy
+:math:`(1-\lambda_i) E_i^\text{(pace)}` and the
+corresponding force and should be combined
+with a fast potential that computes the potential energy
+:math:`\lambda_i E_i^\text{(fast)}` and the corresponding force
+via :doc:`pair_style hybrid/overlay <pair_hybrid>`.
+
+The pair style *pace/fast/apip* computes the potential energy
+:math:`\lambda_i E_i^\text{(pace)}` and the
+corresponding force and should be combined
+with a precise potential that computes the potential energy
+:math:`(1-\lambda_i) E_i^\text{(precise)}` and the corresponding force
+via :doc:`pair_style hybrid/overlay <pair_hybrid>`.
+
+The pair_styles *pace/fast/apip* and *pace/precise/apip*
+commands may be followed by the optional keywords of
+:doc:`pair_style pace <pair_pace>`, which are described
+:doc:`here <pair_pace>`.
+
+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 styles does not support the :doc:`pair_modify <pair_modify>`
+shift, table, and tail options.
+
+This pair styles 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 styles 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 styles are part of the APIP package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair_style pace  <pair_pace>`,
+:doc:`pair_style hybrid/overlay <pair_hybrid>`,
+:doc:`fix lambda/apip <fix_lambda_apip>`,
+:doc:`fix lambda_thermostat/apip <fix_lambda_thermostat_apip>`,
+:doc:`pair_style lambda/zone/apip <pair_lambda_zone_apip>`,
+:doc:`pair_style lambda/input/apip  <pair_lambda_input_apip>`,
+:doc:`pair_style eam/apip <pair_eam_apip>`,
+:doc:`fix atom_weight/apip <fix_atom_weight_apip>`
+
+Default
+"""""""
+
+See :doc:`pair_style pace <pair_pace>`.
+
+----------
+
+.. _Drautz2019_2:
+
+**(Drautz19)** Drautz, Phys Rev B, 99, 014104 (2019).
+
+.. _Lysogorskiy20211_2:
+
+**(Lysogorskiy21)** Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, npj Comp Mat, 7, 97 (2021).
+
+.. _Immel2025_7:
+
+**(Immel25)** Immel, Drautz and Sutmann, J Chem Phys, 162, 114119 (2025)

doc/src/pair_style.rst

@@ -188,7 +188,9 @@ accelerated styles exist.
 * :doc:`eam/cd <pair_eam>` - concentration-dependent EAM
 * :doc:`eam/cd/old <pair_eam>` - older two-site model for concentration-dependent EAM
 * :doc:`eam/fs <pair_eam>` - Finnis-Sinclair EAM
+* :doc:`eam/fs/apip <pair_eam_apip>` - :doc:`adaptive precision <Howto_apip>` version of FS EAM, used as fast potential
 * :doc:`eam/he <pair_eam>` - Finnis-Sinclair EAM modified for Helium in metals
+* :doc:`eam/apip <pair_eam_apip>` - :doc:`adaptive-precision <Howto_apip>` version of EAM, used as fast potential
 * :doc:`edip <pair_edip>` - three-body EDIP potential
 * :doc:`edip/multi <pair_edip>` - multi-element EDIP potential
 * :doc:`edpd <pair_mesodpd>` - eDPD particle interactions
@@ -217,6 +219,9 @@ accelerated styles exist.
 * :doc:`kim <pair_kim>` - interface to potentials provided by KIM project
 * :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>` - Kolmogorov-Crespi (KC) potential with no simplifications
 * :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>` - Kolmogorov-Crespi (KC) potential with normals along z-axis
+* :doc:`lambda/input/apip <pair_lambda_input_apip>` - constant as input for the precision calculation of an :doc:`adaptive-precision interatomic potential (APIP) <Howto_apip>`
+* :doc:`lambda/input/csp/apip <pair_lambda_input_apip>` - CSP as input for the precision calculation of an :doc:`adaptive-precision interatomic potential (APIP) <Howto_apip>`
+* :doc:`lambda/zone/apip <pair_lambda_zone_apip>` - transition zone of an :doc:`adaptive-precision interatomic potential <Howto_apip>`
 * :doc:`lcbop <pair_lcbop>` - long-range bond-order potential (LCBOP)
 * :doc:`lebedeva/z <pair_lebedeva_z>` - Lebedeva interlayer potential for graphene with normals along z-axis
 * :doc:`lennard/mdf <pair_mdf>` - LJ potential in A/B form with a taper function
@@ -330,6 +335,9 @@ accelerated styles exist.
 * :doc:`oxrna2/xstk <pair_oxrna2>` -
 * :doc:`pace <pair_pace>` - Atomic Cluster Expansion (ACE) machine-learning potential
 * :doc:`pace/extrapolation <pair_pace>` - Atomic Cluster Expansion (ACE) machine-learning potential with extrapolation grades
+* :doc:`pace/apip <pair_pace_apip>` - :doc:`adaptive-precision <Howto_apip>` version of ACE, used as precise potential
+* :doc:`pace/fast/apip <pair_pace_apip>` - :doc:`adaptive-precision <Howto_apip>` version of ACE, used as fast potential
+* :doc:`pace/precise/apip <pair_pace_apip>` - :doc:`adaptive-precision <Howto_apip>` version of ACE, used as precise potential
 * :doc:`pedone <pair_pedone>` - Pedone (PMMCS) potential (non-Coulomb part)
 * :doc:`pod <pair_pod>` - Proper orthogonal decomposition (POD) machine-learning potential
 * :doc:`peri/eps <pair_peri>` - Peridynamic EPS potential

doc/src/plugin.rst

@@ -10,16 +10,17 @@ Syntax
 
    plugin command args
 
-* command = *load* or *unload* or *list* or *clear*
+* command = *load* or *unload* or *list* or *clear* or *restore*
 * args = list of arguments for a particular plugin command
 
   .. parsed-literal::
 
      *load* file = load plugin(s) from shared object in *file*
      *unload* style name = unload plugin *name* of style *style*
-         *style* = *pair* or *bond* or *angle* or *dihedral* or *improper* or *kspace* or *compute* or *fix* or *region* or *command*
+         *style* = *pair* or *bond* or *angle* or *dihedral* or *improper* or *kspace* or *compute* or *fix* or *region* or *command* or *run* or *min*
      *list* = print a list of currently loaded plugins
      *clear* = unload all currently loaded plugins
+     *restore* = restore all loaded plugins
 
 Examples
 """"""""
@@ -31,6 +32,7 @@ Examples
    plugin unload command hello
    plugin list
    plugin clear
+   plugin restore
 
 Description
 """""""""""
@@ -40,22 +42,46 @@ commands into a LAMMPS binary from so-called dynamic shared object (DSO)
 files.  This enables to add new functionality to an existing LAMMPS
 binary without having to recompile and link the entire executable.
 
+.. admonition:: Plugins are a global, per-executable property
+   :class: Hint
+
+   Unlike most settings in LAMMPS, plugins are a per-executable global
+   property.  Loading a plugin means that it is not only available for
+   the current LAMMPS instance but for all *future* LAMMPS instances.
+
+   After a :doc:`clear <clear>` command, all currently loaded plugins
+   will be restored and do not need to be loaded again.
+
+   When using the library interface or the Python or Fortran module
+   to create multiple concurrent LAMMPS instances, all plugins should
+   be loaded by the first created LAMMPS instance as all future instances
+   will inherit them.  To import plugins that were loaded by a different
+   LAMMPS instance, use the *restore* command.
+
+
 The *load* command will load and initialize all plugins contained in the
-plugin DSO with the given filename.  A message with information the
+plugin DSO with the given filename.  A message with information about
-plugin style and name and more will be printed.  Individual DSO files
+the plugin style and name and more will be printed.  Individual DSO
-may contain multiple plugins.  More details about how to write and
+files may contain multiple plugins.  If a plugin is already loaded
+it will be skipped.  More details about how to write and
 compile the plugin DSO is given in programmer's guide part of the manual
 under :doc:`Developer_plugins`.
 
 The *unload* command will remove the given style or the given name from
 the list of available styles.  If the plugin style is currently in use,
-that style instance will be deleted.
+that style instance will be deleted and replaced by the default setting
+for that style.
 
 The *list* command will print a list of the loaded plugins and their
 styles and names.
 
 The *clear* command will unload all currently loaded plugins.
 
+.. versionadded:: 12Jun2025
+
+The *restore* command will restore all currently loaded plugins.
+This allows to "import" plugins into a different LAMMPS instance.
+
 .. admonition:: Automatic loading of plugins
    :class: note
 

doc/src/python.rst

@@ -10,7 +10,7 @@ Syntax
 
    python mode keyword args ...
 
-* mode = *source* or name of Python function
+* mode = *source* or *name* of Python function
 
   if mode is *source*:
 
@@ -18,35 +18,39 @@ Syntax
 
      keyword = *here* or name of a *Python file*
        *here* arg = inline
-         inline = one or more lines of Python code which defines func
+         inline = one or more lines of Python code which will be executed immediately
                   must be a single argument, typically enclosed between triple quotes
        *Python file* = name of a file with Python code which will be executed immediately
 
-* if *mode* is the name of a Python function, one or more keywords with/without arguments must be appended
+* if *mode* is *name* of a Python function:
 
   .. parsed-literal::
 
+     one or more keywords with/without arguments must be appended
      keyword = *invoke* or *input* or *return* or *format* or *length* or *file* or *here* or *exists*
-       *invoke* arg = none = invoke the previously defined Python function
+       *invoke* arg = logreturn (optional)
+         invoke the previously-defined Python function
+         if logreturn is specified, print the return value of the invoked function to the screen and logfile
        *input* args = N i1 i2 ... iN
          N = # of inputs to function
          i1,...,iN = value, SELF, or LAMMPS variable name
            value = integer number, floating point number, or string
-           SELF = reference to LAMMPS itself which can be accessed by Python function
+           SELF = reference to LAMMPS itself which can then be accessed by Python function
-           variable = v_name, where name = name of LAMMPS variable, e.g. v_abc
+           variable = v_name, where name = name of a LAMMPS variable, e.g. v_abc
+           internal variable = iv_name, where name = name of a LAMMPS internal-style variable, e.g. iv_xyz
        *return* arg = varReturn
          varReturn = v_name  = LAMMPS variable name which the return value of the Python function will be assigned to
        *format* arg = fstring with M characters
          M = N if no return value, where N = # of inputs
          M = N+1 if there is a return value
-         fstring = each character (i,f,s,p) corresponds in order to an input or return value
+         fstring = each character (i,f,s,p) corresponds (in order) to an input or return value
            'i' = integer, 'f' = floating point, 's' = string, 'p' = SELF
        *length* arg = Nlen
          Nlen = max length of string returned from Python function
        *file* arg = filename
-         filename = file of Python code, which defines func
+         filename = file of Python code, which defines the Python function
        *here* arg = inline
-         inline = one or more lines of Python code which defines func
+         inline = one or more lines of Python code which defines the Python function
                   must be a single argument, typically enclosed between triple quotes
        *exists* arg = none = Python code has been loaded by previous python command
 
@@ -56,7 +60,7 @@ Examples
 .. code-block:: LAMMPS
 
    python pForce input 2 v_x 20.0 return v_f format fff file force.py
-   python pForce invoke
+   python pForce invoke logreturn
 
    python factorial input 1 myN return v_fac format ii here """
    def factorial(n):
@@ -87,75 +91,149 @@ Examples
 Description
 """""""""""
 
-The *python* command allows interfacing LAMMPS with an embedded Python
+The *python* command interfaces LAMMPS with an embedded Python
-interpreter and enables either executing arbitrary python code in that
+interpreter and enables executing arbitrary python code in that
-interpreter, registering a Python function for future execution (as a
+interpreter.  This can be done immediately, by using *mode* = *source*.
-python style variable, from a fix interfaced with python, or for direct
+Or execution can be deferred, by registering a Python function for later
-invocation), or invoking such a previously registered function.
+execution, by using *mode* = *name* of a Python function.
 
-Arguments, including LAMMPS variables, can be passed to the function
+Later execution can be triggered in one of two ways.  One is to use the
-from the LAMMPS input script and a value returned by the Python function
+python command again with its *invoke* keyword.  The other is to trigger
-assigned to a LAMMPS variable.  The Python code for the function can be included
+the evaluation of a python-style, equal-style, vector-style, or
-directly in the input script or in a separate Python file.  The function
+atom-style variable.  A python-style variable invokes its associated
-can be standard Python code or it can make "callbacks" to LAMMPS through
+Python function; its return value becomes the value of the python-style
-its library interface to query or set internal values within LAMMPS.
+variable.  Equal-, vector-, and atom-style variables can use a Python
-This is a powerful mechanism for performing complex operations in a
+function wrapper in their formulas which encodes the python-style
-LAMMPS input script that are not possible with the simple input script
+variable name, and specifies arguments (which themselves can be numeric
-and variable syntax which LAMMPS defines.  Thus your input script can
+formulas) to pass to the Python function associated with the
-operate more like a true programming language.
+python-style variable.
+
+As explained on the :doc:`variable <variable>` doc page, the definition
+of a python-style variable associates a Python function name with the
+variable.  Its specification must match the *mode* argument of the
+*python* command for the Python function name.  For example these two
+commands would be consistent:
+
+.. code-block:: LAMMPS
+
+   variable foo python myMultiply
+   python myMultiply return v_foo format f file funcs.py
+
+The two commands can appear in either order in the input script so long
+as both are specified before the Python function is invoked for the
+first time.
+
+Note that python-style, equal-style, vector-style, and atom-style
+variables can be used in many different ways within LAMMPS.  They can be
+evaluated directly in an input script, effectively replacing the
+variable with its value.  Or they can be passed to various commands as
+arguments, so that the variable is evaluated multiple times during a
+simulation run.  See the :doc:`variable <variable>` command doc page for
+more details on variable styles which enable Python function evaluation.
+
+The Python code for a Python function can be included directly in the
+input script or in a separate Python file.  The function can be standard
+Python code or it can make "callbacks" to LAMMPS through its library
+interface to query or set internal values within LAMMPS.  This is a
+powerful mechanism for performing complex operations in a LAMMPS input
+script that are not possible with the simple input script and variable
+syntax which LAMMPS defines.  Thus your input script can operate more
+like a true programming language.
 
 Use of this command requires building LAMMPS with the PYTHON package
 which links to the Python library so that the Python interpreter is
 embedded in LAMMPS.  More details about this process are given below.
 
-There are two ways to invoke a Python function once it has been
-registered.  One is using the *invoke* keyword.  The other is to assign
-the function to a :doc:`python-style variable <variable>` defined in
-your input script.  Whenever the variable is evaluated, it will execute
-the Python function to assign a value to the variable.  Note that
-variables can be evaluated in many different ways within LAMMPS.  They
-can be substituted with their result directly in an input script, or
-they can be passed to various commands as arguments, so that the
-variable is evaluated during a simulation run.
-
 A broader overview of how Python can be used with LAMMPS is given in the
 :doc:`Use Python with LAMMPS <Python_head>` section of the
-documentation.  There also is an ``examples/python`` directory which
+documentation.  There is also an ``examples/python`` directory which
 illustrates use of the python command.
 
 ----------
 
-The first argument of the *python* command is either the *source*
+The first argument to the *python* command is the *mode* setting, which
-keyword or the name of a Python function.  This defines the mode
+is either *source* or the *name* of a Python function.
-of the python command.
 
 .. versionchanged:: 22Dec2022
 
-If the *source* keyword is used, it is followed by either a file name or
+If *source* is used, it is followed by either the *here* keyword or a
-the *here* keyword.  No other keywords can be used.  The *here* keyword
+file name containing Python code.  The *here* keyword is followed by a
-is followed by a string with python commands, either on a single line
+single *inline* argument which is a string containing one or more python
-enclosed in quotes, or as multiple lines enclosed in triple quotes.
+commands.  The string can either be on the same line as the *python*
-These Python commands will be passed to the python interpreter and
+command, enclosed in quotes, or it can be multiple lines enclosed in
-executed immediately without registering a Python function for future
+triple quotes.
-execution.  The code will be loaded into and run in the "main" module of
-the Python interpreter.  This allows running arbitrary Python code at
-any time while processing the LAMMPS input file.  This can be used to
-pre-load Python modules, initialize global variables, define functions
-or classes, or perform operations using the python programming language.
-The Python code will be executed in parallel on all MPI processes.  No
-arguments can be passed.
 
-In all other cases, the first argument is the name of a Python function
+In either case, the in-line code or the file contents are passed to the
-that will be registered with LAMMPS for future execution.  The function
+python interpreter and executed immediately.  The code will be loaded
-may already be defined (see *exists* keyword) or must be defined using
+into and run in the "main" module of the Python interpreter.  This
-the *file* or *here* keywords as explained below.
+allows running arbitrary Python code at any time while processing the
+LAMMPS input file.  This can be used to pre-load Python modules,
+initialize global variables, define functions or classes, or perform
+operations using the Python programming language.  The Python code will
+be executed in parallel on all the MPI processes being used to run
+LAMMPS.  Note that no arguments can be passed to the executed Python
+code.
 
-If the *invoke* keyword is used, no other keywords can be used, and a
+If the *mode* setting is the *name* of a Python function, then it will
+be registered with LAMMPS for future execution (or can already be
+defined, see the *exists* keyword).  One or more keywords must follow
+the *mode* function name.  One of the keywords must be *invoke*, *file*,
+*here*, or *exists*, which specifies what Python code to load into the
+Python interpreter.  Note that only one of those 4 keywords is allowed
+since their operations are mutually exclusive.
+
+----------
+
+If the *invoke* keyword is used, no other keywords can be used.  A
 previous *python* command must have registered the Python function
-referenced by this command.  This invokes the Python function with the
+referenced by this command, which can then be invoked multiple times in
-previously defined arguments and the return value is processed as
+an input script via the *invoke* keyword.  Each invocation passes
-explained below.  You can invoke the function as many times as you wish
+current values for arguments to the Python function.  A return value of
-in your input script.
+the Python function will be ignored unless the Python function is linked
+to a :doc:`python style variable <variable>` with the *return* keyword.
+This return value can be logged to the screen and logfile by adding the
+optional *logreturn* argument to the *invoke* keyword.  In that case a
+message with the name of the python command and the return value is
+printed.  Note that return values of python functions are otherwise
+*only* accessible when the function is invoked indirectly by evaluating
+its associated :doc:`python style variable <variable>`, as described
+below.
+
+The *file* keyword gives the name of a file containing Python code,
+which should end with a ".py" suffix.  The code will be immediately
+loaded into and run in the "main" module of the Python interpreter.  The
+Python code will be executed in parallel on all MPI processes.  Note
+that Python code which contains a function definition does NOT "execute"
+the function when it is run; it simply defines the function so that it
+can be invoked later.
+
+The *here* keyword does the same thing, except that the Python code
+follows as a single argument to the *here* keyword.  This can be done
+using triple quotes as delimiters, as in the examples above and below.
+This allows Python code to be listed verbatim in your input script, with
+proper indentation, blank lines, and comments, as desired.  See the
+:doc:`Commands parse <Commands_parse>` doc page, for an explanation of
+how triple quotes can be used as part of input script syntax.
+
+The *exists* keyword takes no argument.  It simply means that Python
+code containing the needed Python function has already been loaded into
+the LAMMPS Python interpreter, for example by previous *python source*
+command or in a file that was loaded previously with the *file*
+keyword. This allows use of a single file of Python code which contains
+multiple functions, any of which can be used in the same (or different)
+input scripts (see below).
+
+Note that the Python code that is loaded and run by the *file* or *here*
+keyword must contain a function with the specified function *name*.  To
+operate properly when the function is later invoked, the code for the
+function must match the *input* and *return* and *format* keywords
+specified by the python command.  Otherwise Python will generate an
+error.
+
+----------
+
+The other keywords which can be used with the *python* command are
+*input*, *return*, *format*, and *length*.
 
 The *input* keyword defines how many arguments *N* the Python function
 expects.  If it takes no arguments, then the *input* keyword should not
@@ -169,35 +247,63 @@ itself using the :doc:`LAMMPS Python module <Python_module>`.  This
 enables the function to call back to LAMMPS through its library
 interface as explained below.  This allows the Python function to query
 or set values internal to LAMMPS which can affect the subsequent
-execution of the input script.  A LAMMPS variable can also be used as an
+execution of the input script.
-argument, specified as v_name, where "name" is the name of the variable.
+
-Any style of LAMMPS variable returning a scalar or a string can be used,
+A LAMMPS variable can also be used as an *input* argument, specified as
-as defined by the :doc:`variable <variable>` command.  The *format*
+v_name, where "name" is the name of the variable defined in the input
-keyword must be used to set the type of data that is passed to Python.
+script.  Any style of LAMMPS variable returning a scalar or a string can
-Each time the Python function is invoked, the LAMMPS variable is
+be used, as defined by the :doc:`variable <variable>` command.  The
-evaluated and its value is passed to the Python function.
+style of variable must be consistent with the *format* keyword
+specification for the type of data that is passed to Python.  Each time
+the Python function is invoked, the LAMMPS variable is evaluated and its
+value is passed as an argument to the Python function.  Note that a
+python-style variable can be used as an argument, which means that the a
+Python function can use arguments which invoke other Python functions.
+
+A LAMMPS internal-style variable can also be used as an *input*
+argument, specified as iv_name, where "name" is the name of the
+internal-style variable.  The internal-style variable does not have to
+be defined in the input script (though it can be); if it is not defined,
+this command creates an :doc:`internal-style variable <variable>` with
+the specified name.
+
+An internal-style variable must be used when an equal-style,
+vector-style, or atom-style variable triggers the invocation of the
+Python function defined by this command, by including a Python function
+wrapper with arguments in its formula.  Each of the arguments must be
+specified as an internal-style variable via the *input* keyword.
+
+In brief, the syntax for a Python function wrapper in a variable formula
+is ``py_varname(arg1,arg2,...argN)``, where "varname" is the name of a
+python-style variable associated with a Python function defined by this
+command.  One or more arguments to the function wrapper can themselves
+be sub-formulas which the variable command will evaluate and pass as
+arguments to the Python function.  This is done by assigning the numeric
+result for each argument to an internal-style variable; thus the *input*
+keyword must specify the arguments as internal-style variables and their
+format (see below) as "f" for floating point.  This is because LAMMPS
+variable formulas are calculated with floating point arithmetic (any
+integer values are converted to floating point).  Note that the Python
+function can also have additional inputs, also specified by the *input*
+keyword, which are NOT arguments in the Python function wrapper.  See
+the example below for the ``mixedargs`` Python function.
+
+See the :doc:`variable <variable>` command doc page for full details on
+formula syntax including for Python function wrappers.  Examples using
+Python function wrappers are shown below.  Note that as explained above
+with python-style variables, Python function wrappers can be nested; a
+sub-formula for an argument can contain its own Python function wrapper
+which invokes another Python function.
 
 The *return* keyword is only needed if the Python function returns a
-value.  The specified *varReturn* must be of the form v_name, where
+value.  The specified *varReturn* is of the form v_name, where "name" is
-"name" is the name of a python-style LAMMPS variable, defined by the
+the name of a python-style LAMMPS variable, defined by the
 :doc:`variable <variable>` command.  The Python function can return a
-numeric or string value, as specified by the *format* keyword.
+numeric or string value, as specified by the *format* keyword.  This
-
+return value is *only* accessible when its associated python-style
-As explained on the :doc:`variable <variable>` doc page, the definition
+variable is evaluated.  When the *invoke* keyword is used, the return
-of a python-style variable associates a Python function name with the
+value of the python function is ignored unless the optional *logreturn*
-variable.  This must match the *Python function name* first argument of
+argument is specified.
-the *python* command.  For example these two commands would be
-consistent:
-
-.. code-block:: LAMMPS
-
-   variable foo python myMultiply
-   python myMultiply return v_foo format f file funcs.py
-
-The two commands can appear in either order in the input script so
-long as both are specified before the Python function is invoked for
-the first time.  Afterwards, the variable 'foo' is associated with
-the Python function 'myMultiply'.
 
 The *format* keyword must be used if the *input* or *return* keywords
 are used.  It defines an *fstring* with M characters, where M = sum of
@@ -214,47 +320,16 @@ but only if the output of the Python function is flagged as a numeric
 value ("i" or "f") via the *format* keyword.
 
 If the *return* keyword is used and the *format* keyword specifies the
-output as a string, then the default maximum length of that string is
+output as a string, then the default maximum length of that string is 63
-63 characters (64-1 for the string terminator).  If you want to return
+characters (64-1 for the string terminator).  If you want to return a
-a longer string, the *length* keyword can be specified with its *Nlen*
+longer string, the *length* keyword can be specified with its *Nlen*
-value set to a larger number (the code allocates space for Nlen+1 to
+value set to a larger number.  LAMMPS will then allocate Nlen+1 space to
-include the string terminator).  If the Python function generates a
+include the string terminator.  If the Python function generates a
 string longer than the default 63 or the specified *Nlen*, it will be
 truncated.
 
 ----------
 
-Either the *file*, *here*, or *exists* keyword must be used, but only
-one of them.  These keywords specify what Python code to load into the
-Python interpreter.  The *file* keyword gives the name of a file
-containing Python code, which should end with a ".py" suffix.  The code
-will be immediately loaded into and run in the "main" module of the
-Python interpreter.  The Python code will be executed in parallel on all
-MPI processes.  Note that Python code which contains a function
-definition does not "execute" the function when it is run; it simply
-defines the function so that it can be invoked later.
-
-The *here* keyword does the same thing, except that the Python code
-follows as a single argument to the *here* keyword.  This can be done
-using triple quotes as delimiters, as in the examples above.  This
-allows Python code to be listed verbatim in your input script, with
-proper indentation, blank lines, and comments, as desired.  See the
-:doc:`Commands parse <Commands_parse>` doc page, for an explanation of
-how triple quotes can be used as part of input script syntax.
-
-The *exists* keyword takes no argument.  It means that Python code
-containing the required Python function with the given name has already
-been executed, for example by a *python source* command or in the same
-file that was used previously with the *file* keyword.
-
-Note that the Python code that is loaded and run must contain a function
-with the specified function name.  To operate properly when later
-invoked, the function code must match the *input* and *return* and
-*format* keywords specified by the python command.  Otherwise Python
-will generate an error.
-
-----------
-
 This section describes how Python code can be written to work with
 LAMMPS.
 
@@ -275,16 +350,16 @@ keyword once to load several functions, and the *exists* keyword
 thereafter in subsequent python commands to register the other functions
 that were previously loaded with LAMMPS.
 
-A Python function you define (or more generally, the code you load)
+A Python function you define (or more generally, the code you load) can
-can import other Python modules or classes, it can make calls to other
+import other Python modules or classes, it can make calls to other
 system functions or functions you define, and it can access or modify
 global variables (in the "main" module) which will persist between
 successive function calls.  The latter can be useful, for example, to
 prevent a function from being invoke multiple times per timestep by
 different commands in a LAMMPS input script that access the returned
 python-style variable associated with the function.  For example,
-consider this function loaded with two global variables defined
+consider this function loaded with two global variables defined outside
-outside the function:
+the function:
 
 .. code-block:: python
 
@@ -308,32 +383,33 @@ previous value is simply returned, without re-computing it.  The
 "global" statement inside the Python function allows it to overwrite the
 global variables from within the local context of the function.
 
-Note that if you load Python code multiple times (via multiple python
+Also note that if you load Python code multiple times (via multiple
-commands), you can overwrite previously loaded variables and functions
+python commands), you can overwrite previously loaded variables and
-if you are not careful.  E.g. if the code above were loaded twice, the
+functions if you are not careful.  E.g. if the code above were loaded
-global variables would be re-initialized, which might not be what you
+twice, the global variables would be re-initialized, which might not be
-want.  Likewise, if a function with the same name exists in two chunks
+what you want.  Likewise, if a function with the same name exists in two
-of Python code you load, the function loaded second will override the
+chunks of Python code you load, the function loaded second will override
-function loaded first.
+the function loaded first.
 
 It's important to realize that if you are running LAMMPS in parallel,
-each MPI task will load the Python interpreter and execute a local
+each MPI task will load the Python interpreter and execute a local copy
-copy of the Python function(s) you define.  There is no connection
+of the Python function(s) you define.  There is no connection between
-between the Python interpreters running on different processors.
+the Python interpreters running on different processors.  This implies
-This implies three important things.
+three important things.
 
 First, if you put a print or other statement creating output to the
 screen in your Python function, you will see P copies of the output,
 when running on P processors.  If the prints occur at (nearly) the same
-time, the P copies of the output may be mixed together.  When loading
+time, the P copies of the output may be mixed together.
-the LAMMPS Python module into the embedded Python interpreter, it is
+
-possible to pass the pointer to the current LAMMPS class instance and
+It is possible to avoid this issue, by passing the pointer to the
-via the Python interface to the LAMMPS library interface, it is possible
+current LAMMPS class instance to the Python function via the {input}
-to determine the MPI rank of the current process and thus adapt the
+SELF argument described above.  The Python function can then use the
-Python code so that output will only appear on MPI rank 0.  The
+Python interface to the LAMMPS library interface, and determine the MPI
-following LAMMPS input demonstrates how this could be done. The text
+rank of the current process.  The Python code can then ensure output
-'Hello, LAMMPS!' should be printed only once, even when running LAMMPS
+will only appear on MPI rank 0.  The following LAMMPS input demonstrates
-in parallel.
+how this could be done. The text 'Hello, LAMPS!' should be printed only
+once, even when running LAMMPS in parallel.
 
 .. code-block:: LAMMPS
 
@@ -348,27 +424,26 @@ in parallel.
 
    python python_hello invoke
 
-If your Python code loads Python modules that are not pre-loaded by the
+Second, if your Python code loads Python modules that are not pre-loaded
-Python library, then it will load the module from disk.  This may be a
+by the Python library, then it will load the module from disk.  This may
-bottleneck if 1000s of processors try to load a module at the same time.
+be a bottleneck if 1000s of processors try to load a module at the same
-On some large supercomputers, loading of modules from disk by Python may
+time.  On some large supercomputers, loading of modules from disk by
-be disabled.  In this case you would need to pre-build a Python library
+Python may be disabled.  In this case you would need to pre-build a
-that has the required modules pre-loaded and link LAMMPS with that
+Python library that has the required modules pre-loaded and link LAMMPS
-library.
+with that library.
 
-Third, if your Python code calls back to LAMMPS (discussed in the
+Third, if your Python code calls back to LAMMPS (discussed in the next
-next section) and causes LAMMPS to perform an MPI operation requires
+section) and causes LAMMPS to perform an MPI operation requires global
-global communication (e.g. via MPI_Allreduce), such as computing the
+communication (e.g. via MPI_Allreduce), such as computing the global
-global temperature of the system, then you must ensure all your Python
+temperature of the system, then you must ensure all your Python
 functions (running independently on different processors) call back to
 LAMMPS.  Otherwise the code may hang.
 
 ----------
 
-Your Python function can "call back" to LAMMPS through its
+As mentioned above, a Python function can "call back" to LAMMPS through
-library interface, if you use the SELF input to pass Python
+its library interface, if the SELF input is used to pass Python a
-a pointer to LAMMPS.  The mechanism for doing this in your
+pointer to LAMMPS.  The mechanism for doing this is as follows:
-Python function is as follows:
 
 .. code-block:: python
 
@@ -393,15 +468,15 @@ appeared in your input script.  In this case, LAMMPS should output
    Hello from inside Python
 
 to the screen and log file.  Note that since the LAMMPS print command
-itself takes a string in quotes as its argument, the Python string
+itself takes a string in quotes as its argument, the Python string must
-must be delimited with a different style of quotes.
+be delimited with a different style of quotes.
 
-The :doc:`Python_head` page describes the syntax
+The :doc:`Python_head` page describes the syntax for how Python wraps
-for how Python wraps the various functions included in the LAMMPS
+the various functions included in the LAMMPS library interface.
-library interface.
 
-A more interesting example is in the ``examples/python/in.python`` script
+A more interesting example is in the ``examples/python/in.python``
-which loads and runs the following function from ``examples/python/funcs.py``:
+script which loads and runs the following function from
+``examples/python/funcs.py``:
 
 .. code-block:: python
 
@@ -416,7 +491,7 @@ which loads and runs the following function from ``examples/python/funcs.py``:
 
        lmp.set_variable("cut",cut)                 # set a variable in LAMMPS
        lmp.command("pair_style lj/cut ${cut}")     # LAMMPS command
-       #lmp.command("pair_style lj/cut %d" % cut)  # LAMMPS command option
+       #lmp.command("pair_style lj/cut %d" % cut)  # alternate form of LAMMPS command
 
        lmp.command("pair_coeff * * 1.0 1.0")       # ditto
        lmp.command("run 10")                       # ditto
@@ -432,51 +507,160 @@ with these input script commands:
    python          loop invoke
 
 This has the effect of looping over a series of 10 short runs (10
-timesteps each) where the pair style cutoff is increased from a value
+timesteps each) where the pair style cutoff is increased from a value of
-of 1.0 in distance units, in increments of 0.1.  The looping stops
+1.0 in distance units, in increments of 0.1.  The looping stops when the
-when the per-atom potential energy falls below a threshold of -4.0 in
+per-atom potential energy falls below a threshold of -4.0 in energy
-energy units.  More generally, Python can be used to implement a loop
+units.  More generally, Python can be used to implement a loop with
-with complex logic, much more so than can be created using the LAMMPS
+complex logic, much more so than can be created using the LAMMPS
 :doc:`jump <jump>` and :doc:`if <if>` commands.
 
 Several LAMMPS library functions are called from the loop function.
 Get_natoms() returns the number of atoms in the simulation, so that it
 can be used to normalize the potential energy that is returned by
-extract_compute() for the "thermo_pe" compute that is defined by
+extract_compute() for the "thermo_pe" compute that is defined by default
-default for LAMMPS thermodynamic output.  Set_variable() sets the
+for LAMMPS thermodynamic output.  Set_variable() sets the value of a
-value of a string variable defined in LAMMPS.  This library function
+string variable defined in LAMMPS.  This library function is a useful
-is a useful way for a Python function to return multiple values to
+way for a Python function to return multiple values to LAMMPS, more than
-LAMMPS, more than the single value that can be passed back via a
+the single value that can be passed back via a return statement.  This
-return statement.  This cutoff value in the "cut" variable is then
+cutoff value in the "cut" variable is then substituted (by LAMMPS) in
-substituted (by LAMMPS) in the pair_style command that is executed
+the pair_style command that is executed next.  Alternatively, the
-next.  Alternatively, the "LAMMPS command option" line could be used
+"alternate form of LAMMPS command" line could be used in place of the 2
-in place of the 2 preceding lines, to have Python insert the value
+preceding lines, to have Python insert the value into the LAMMPS command
-into the LAMMPS command string.
+string.
 
 .. note::
 
    When using the callback mechanism just described, recognize that
-   there are some operations you should not attempt because LAMMPS cannot
+   there are some operations you should not attempt because LAMMPS
-   execute them correctly.  If the Python function is invoked between
+   cannot execute them correctly.  If the Python function is invoked
-   runs in the LAMMPS input script, then it should be OK to invoke any
+   between runs in the LAMMPS input script, then it should be OK to
-   LAMMPS input script command via the library interface command() or
+   invoke any LAMMPS input script command via the library interface
-   file() functions, so long as the command would work if it were
+   command() or file() functions, so long as the command would work if
-   executed in the LAMMPS input script directly at the same point.
+   it were executed in the LAMMPS input script directly at the same
+   point.
 
-However, a Python function can also be invoked during a run, whenever
-an associated LAMMPS variable it is assigned to is evaluated.  If the
-variable is an input argument to another LAMMPS command (e.g. :doc:`fix setforce <fix_setforce>`), then the Python function will be invoked
-inside the class for that command, in one of its methods that is
-invoked in the middle of a timestep.  You cannot execute arbitrary
-input script commands from the Python function (again, via the
-command() or file() functions) at that point in the run and expect it
-to work.  Other library functions such as those that invoke computes
-or other variables may have hidden side effects as well.  In these
-cases, LAMMPS has no simple way to check that something illogical is
-being attempted.
 
-The same applies to Python functions called during a simulation run at
+----------
-each time step using :doc:`fix python/invoke <fix_python_invoke>`.
+
+As noted above, a Python function can be invoked during a run, whenever
+an associated python-style variable it is assigned to is evaluated.
+
+If the variable is an input argument to another LAMMPS command
+(e.g. :doc:`fix setforce <fix_setforce>`), then the Python function will
+be invoked inside the class for that command, possibly in one of its
+methods that is invoked in the middle of a timestep.  You cannot execute
+arbitrary input script commands from the Python function (again, via the
+command() or file() functions) at that point in the run and expect it to
+work.  Other library functions such as those that invoke computes or
+other variables may have hidden side effects as well.  In these cases,
+LAMMPS has no simple way to check that something illogical is being
+attempted.
+
+The same constraints apply to Python functions called during a
+simulation run at each time step using the :doc:`fix python/invoke
+<fix_python_invoke>` command.
+
+----------
+
+As noted above, a Python function can also be invoked within the formula
+for an equal-style, vector-style, or atom-style variable.  This means
+the Python function will be invoked whenever that variable is invoked.
+In the case of a vector-style variable, the Python function can be
+invoked once per element of the global vector.  In the case of an
+atom-style variable, the Python function can be invoked once per atom.
+
+Here are three simple examples using equal-, vector-, and atom-style
+variables to trigger execution of a Python function:
+
+.. code-block:: LAMMPS
+
+   variable        foo python truncate
+   python          truncate return v_foo input 1 iv_arg format fi here """
+   def truncate(x):
+     return int(x)
+   """
+   variable        ptrunc equal py_foo(press)
+   print           "TRUNCATED pressure = ${ptrunc}"
+
+The Python ``truncate`` function simply converts a floating-point value
+to an integer value.  When the LAMMPS print command evaluates the
+equal-style ``ptrunc`` variable, the current thermodynamic pressure is
+passed to the Python function.  The truncated value is output to the
+screen and logfile by the print command.  Note that the *input* keyword
+for the *python* command, specifies an internal-style variable named
+"arg" as iv_arg which is required to invoke the Python function from a
+Python function wrapper.
+
+The last 2 lines can be replaced by these to define a vector-style
+variable which invokes the same Python ``truncate`` function:
+
+.. code-block:: LAMMPS
+
+  compute         ke all temp
+  variable        ke vector c_ke
+  variable        ketrunc vector py_foo(v_ke)
+  thermo_style    custom step temp epair v_ketrunc[*6]
+
+The vector-style variable ``ketrunc`` invokes the Python ``truncate``
+function on each of the 6 components of the global kinetic energy tensor
+calculated by the :doc:`compute ke <compute_ke>` command.  The 6
+truncated values will be printed with thermo output to the screen and
+log file.
+
+Or the last 2 lines of the equal-style variable example can be replaced
+by these to define atom-style variables which invoke the same Python
+``truncate`` function:
+
+.. code-block:: LAMMPS
+
+   variable        xtrunc atom py_foo(x)
+   variable        ytrunc atom py_foo(y)
+   variable        ztrunc atom py_foo(z)
+   dump            1 all custom 100 tmp.dump id x y z v_xtrunc v_ytrunc v_ztrunc
+
+When the dump command invokes the 3 atom-style variables, their
+arguments x,y,z to the Python function wrapper are the current per-atom
+coordinates of each atom.  The Python ``truncate`` function is thus
+invoked 3 times for each atom, and the truncated coordinate values for
+each atom are written to the dump file.
+
+Note that when using a Python function wrapper in a variable, arguments
+can be passed to the Python function either from the variable formula or
+by *input* keyword to the :doc:`python command <python>`.  For example,
+consider these (made up) commands:
+
+.. code-block:: LAMMPS
+
+   variable        foo python mixedargs
+   python          mixedargs return v_foo input 6 7.5 v_myValue iv_arg1 iv_argy iv_argz v_flag &
+                   format fffffsf here """
+   def mixedargs(a,b,x,y,z,flag):
+     ...
+     return result
+   """
+   variable        flag string optionABC
+   variable        myValue equal "2.0*temp*c_pe"
+   compute         pe all pe
+   compute         peatom all pe/atom
+   variable        field atom py_foo(x+3.0,sqrt(y),(z-zlo)*c_peatom)
+
+They define a Python ``mixedargs`` function with 6 arguments.  Three of
+them are internal-style variables, which the variable formula calculates
+as numeric values for each atom and passes to the function.  In this
+example, these arguments are themselves small formulas containing the
+x,y,z coordinates of each atom as well as a per-atom compute (c_peratom)
+and thermodynamic keyword (zlo).
+
+The other three arguments ``(7.5,v_myValue,v_flag)`` are defined by the
+*python* command.  The first and last are constant values ("7.5" and the
+``optionABC`` string).  The second argument (``myValue``) is the result
+of an equal-style variable formula which accesses the system temperature
+and potential energy.
+
+The "result" returned by each invocation of the Python ``mixedargs``
+function becomes the per-atom value in the atom-style "field" variable,
+which could be output to a dump file or used elsewhere in the input
+script.
 
 ----------
 
@@ -485,12 +669,11 @@ interactively or by using Python to launch a Python script stored in a
 file, and your code has an error, you will typically see informative
 error messages.  That is not the case when you run Python code from
 LAMMPS using an embedded Python interpreter.  The code will typically
-fail silently.  LAMMPS will catch some errors but cannot tell you
+fail silently.  LAMMPS will catch some errors but cannot tell you where
-where in the Python code the problem occurred.  For example, if the
+in the Python code the problem occurred.  For example, if the Python
-Python code cannot be loaded and run because it has syntax or other
+code cannot be loaded and run because it has syntax or other logic
-logic errors, you may get an error from Python pointing to the
+errors, you may get an error from Python pointing to the offending line,
-offending line, or you may get one of these generic errors from
+or you may get one of these generic errors from LAMMPS:
-LAMMPS:
 
 .. parsed-literal::
 
@@ -504,16 +687,16 @@ you will typically get this generic error from LAMMPS:
 
    Python function evaluation failed
 
-Here are three suggestions for debugging your Python code while
+Here are three suggestions for debugging your Python code while running
-running it under LAMMPS.
+it under LAMMPS.
 
 First, don't run it under LAMMPS, at least to start with!  Debug it
 using plain Python.  Load and invoke your function, pass it arguments,
 check return values, etc.
 
-Second, add Python print statements to the function to check how far
+Second, add Python print statements to the function to check how far it
-it gets and intermediate values it calculates.  See the discussion
+gets and intermediate values it calculates.  See the discussion above
-above about printing from Python when running in parallel.
+about printing from Python when running in parallel.
 
 Third, use Python exception handling.  For example, say this statement
 in your Python function is failing, because you have not initialized the
@@ -523,8 +706,7 @@ variable foo:
 
    foo += 1
 
-If you put one (or more) statements inside a "try" statement,
+If you put one (or more) statements inside a "try" statement, like this:
-like this:
 
 .. code-block:: python
 
@@ -563,13 +745,15 @@ If you use Python code which calls back to LAMMPS, via the SELF input
 argument explained above, there is an extra step required when building
 LAMMPS.  LAMMPS must also be built as a shared library and your Python
 function must be able to load the :doc:`"lammps" Python module
-<Python_module>` that wraps the LAMMPS library interface.  These are the
+<Python_module>` that wraps the LAMMPS library interface.
-same steps required to use Python by itself to wrap LAMMPS.  Details on
+
-these steps are explained on the :doc:`Python <Python_head>` doc page.
+These are the same steps required to use Python by itself to wrap
-Note that it is important that the stand-alone LAMMPS executable and the
+LAMMPS.  Details on these steps are explained on the :doc:`Python
-LAMMPS shared library be consistent (built from the same source code
+<Python_head>` doc page.  Note that it is important that the stand-alone
-files) in order for this to work.  If the two have been built at
+LAMMPS executable and the LAMMPS shared library be consistent (built
-different times using different source files, problems may occur.
+from the same source code files) in order for this to work.  If the two
+have been built at different times using different source files,
+problems may occur.
 
 Another limitation of calling back to Python from the LAMMPS module
 using the *python* command in a LAMMPS input is that both, the Python
@@ -583,7 +767,8 @@ global variables will become invisible.
 Related commands
 """"""""""""""""
 
-:doc:`shell <shell>`, :doc:`variable <variable>`, :doc:`fix python/invoke <fix_python_invoke>`
+:doc:`shell <shell>`, :doc:`variable <variable>`,
+:doc:`fix python/invoke <fix_python_invoke>`
 
 Default
 """""""

doc/src/read_dump.rst

@@ -16,12 +16,13 @@ Syntax
 
   .. parsed-literal::
 
-     field = *x* or *y* or *z* or *vx* or *vy* or *vz* or *q* or *ix* or *iy* or *iz* or *fx* or *fy* or *fz*
+     field = *x* or *y* or *z* or *vx* or *vy* or *vz* or *q* or *ix* or *iy* or *iz* or *fx* or *fy* or *fz* or *apip_lambda*
        *x*,\ *y*,\ *z* = atom coordinates
        *vx*,\ *vy*,\ *vz* = velocity components
        *q* = charge
        *ix*,\ *iy*,\ *iz* = image flags in each dimension
        *fx*,\ *fy*,\ *fz* = force components
+       *apip_lambda* = switching parameter of an :doc:`adaptive-precision interatomic potential <Howto_apip>`
 
 * zero or more keyword/value pairs may be appended
 * keyword = *nfile* or *box* or *timestep* or *replace* or *purge* or *trim* or *add* or *label* or *scaled* or *wrapped* or *format*

doc/src/set.rst

@@ -23,8 +23,8 @@ Syntax
 
 * one or more keyword/value pairs may be appended
 
-* keyword = *angle* or *angmom* or *bond* or *cc* or *charge* or
+* keyword = *angle* or *angmom* or *apip/lambda* or *bond* or *cc* or *charge*
-  *density* or *density/disc* or *diameter* or *dihedral* or *dipole*
+  or *density* or *density/disc* or *diameter* or *dihedral* or *dipole*
   or *dipole/random* or *dpd/theta* or *edpd/cv* or *edpd/temp* or
   *epsilon* or *image* or *improper* or *length* or *mass* or *mol* or
   *omega* or *quat* or *quat/random* or *radius/electron* or *shape* or
@@ -41,6 +41,10 @@ Syntax
        *angmom* values = Lx Ly Lz
          Lx,Ly,Lz = components of angular momentum vector (distance-mass-velocity units)
          any of Lx,Ly,Lz can be an atom-style variable (see below)
+       *apip/lambda* value = fast or precise or float
+         fast = switching parameter of fast potential (1)
+         precise = switching parameter of fast potential (0)
+         float = constant float or atom-style variable (between 0 and 1)
        *bond* value = numeric bond type or bond type label, for all bonds between selected atoms
        *cc* values = index cc
          index = index of a chemical species (1 to Nspecies)
@@ -632,6 +636,13 @@ atoms.
 
 Keywords *x*, *y*, *z* set the coordinates of all selected atoms.
 
+Keyword *apip/lambda* sets the switching parameter of an
+adaptive-precision interatomic potential (:doc:`APIP <Howto_apip>`).
+The precise potential is used for an atom when its switching parameter
+:math:`\lambda` is 0. The fast potential is used for an atom when its
+switching parameter :math:`\lambda` is 1. Both potentials are partially
+used for :math:`\lambda\in(0,1)`.
+
 Keywords *i_name*, *d_name*, *i2_name*, *d2_name* refer to custom
 per-atom integer and floating-point vectors or arrays that have been
 added via the :doc:`fix property/atom <fix_property_atom>` command.

doc/src/variable.rst

@@ -45,7 +45,8 @@ Syntax
        *universe* args = one or more strings
        *world* args = one string for each partition of processors
 
-       *equal* or *vector* or *atom* args = one formula containing numbers, thermo keywords, math operations, built-in functions, atom values and vectors, compute/fix/variable references
+       *equal* or *vector* or *atom* args = one formula containing numbers, thermo keywords,
+           math operations, built-in functions, atom values and vectors, compute/fix/variable references
          numbers = 0.0, 100, -5.4, 2.8e-4, etc
          constants = PI, version, on, off, true, false, yes, no
          thermo keywords = vol, ke, press, etc from :doc:`thermo_style <thermo_style>`
@@ -67,8 +68,13 @@ Syntax
                            bound(group,dir,region), gyration(group,region), ke(group,reigon),
                            angmom(group,dim,region), torque(group,dim,region),
                            inertia(group,dimdim,region), omega(group,dim,region)
-         special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), sort(x), rsort(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label), is_typelabel(kind,label), is_timeout()
+         special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), sort(x), rsort(x),
-         feature functions = is_available(category,feature), is_active(category,feature), is_defined(category,id)
+                             gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name),
+                             extract_setting(name), label2type(kind,label),
+                             is_typelabel(kind,label), is_timeout()
+         feature functions = is_available(category,feature), is_active(category,feature),
+                             is_defined(category,id)
+         python function wrapper = py_varname(x,y,z,...)
          atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
          atom vector = id, mass, type, mol, radius, q, x, y, z, vx, vy, vz, fx, fy, fz
          custom atom property = i_name, d_name, i_name[i], d_name[i], i2_name[i], d2_name[i], i2_name[i][j], d2_name[i][j]
@@ -127,18 +133,21 @@ command), or used as input to an averaging fix (see the :doc:`fix
 ave/time <fix_ave_time>` command).  Variables of style *vector* store
 a formula which produces a vector of such values which can be used as
 input to various averaging fixes, or elements of which can be part of
-thermodynamic output.  Variables of style *atom* store a formula which
+thermodynamic output.
-when evaluated produces one numeric value per atom which can be output
+
-to a dump file (see the :doc:`dump custom <dump>` command) or used as
+Variables of style *atom* store a formula which when evaluated
-input to an averaging fix (see the :doc:`fix ave/chunk
+produces one numeric value per atom which can be output to a dump file
-<fix_ave_chunk>` and :doc:`fix ave/atom <fix_ave_atom>` commands).
+(see the :doc:`dump custom <dump>` command) or used as input to an
-Variables of style *atomfile* can be used anywhere in an input script
+averaging fix (see the :doc:`fix ave/chunk <fix_ave_chunk>` and
-that atom-style variables are used; they get their per-atom values
+:doc:`fix ave/atom <fix_ave_atom>` commands).  Variables of style
-from a file rather than from a formula.  Variables of style *python*
+*atomfile* can be used anywhere in an input script that atom-style
-can be hooked to Python functions using code you provide, so that the
+variables are used; they get their per-atom values from a file rather
-variable gets its value from the evaluation of the Python code.
+than from a formula.
-Variables of style *internal* are used by a few commands which set
+
-their value directly.
+Variables of style *python* can be hooked to Python functions using
+Python code you provide, so that the variable gets its value from the
+evaluation of the Python code.  Variables of style *internal* are used
+by a few commands which set their value directly.
 
 .. note::
 
@@ -166,15 +175,16 @@ simulation.
 
 .. note::
 
-   When an input script line is encountered that defines a variable
+   When an input script line is encountered that defines a variable of
-   of style *equal* or *vector* or *atom* or *python* that contains a
+   style *equal* or *vector* or *atom* or *python* that contains a
-   formula or Python code, the formula is NOT immediately evaluated.  It
+   formula or links to Python code, the formula or Python code is NOT
-   will be evaluated every time when the variable is **used** instead.  If
+   immediately evaluated.  Instead, it is evaluated each time the
-   you simply want to evaluate a formula in place you can use as
+   variable is **used**.  If you simply want to evaluate a formula in
-   so-called. See the section below about "Immediate Evaluation of
+   place you can use a so-called immediate variable. as described in
-   Variables" for more details on the topic.  This is also true of a
+   the preceding note.  Or see the section below about "Immediate
-   *format* style variable since it evaluates another variable when it is
+   Evaluation of Variables" for more details on the topic.  This is
-   invoked.
+   also true of a *format* style variable since it evaluates another
+   variable when it is invoked.
 
 Variables of style *equal* and *vector* and *atom* can be used as
 inputs to various other commands which evaluate their formulas as
@@ -183,12 +193,12 @@ this context, variables of style *timer* or *internal* or *python* can
 be used in place of an equal-style variable, with the following two
 caveats.
 
-First, internal-style variables can be used except by commands that
+First, internal-style variables require their values be set by code
-set the value stored by the internal variable.  When the LAMMPS
+elsewhere in LAMMPS.  When a LAMMPS input script or command evaluates
-command evaluates the internal-style variable, it will use the value
+an internal-style variable, it must have a current value set
-set (internally) by another command.  Second, python-style variables
+(internally) via that mechanism.  Second, python-style variables can
-can be used so long as the associated Python function, as defined by
+be used so long as the associated Python function, as defined by the
-the :doc:`python <python>` command, returns a numeric value.  When the
+:doc:`python <python>` command, returns a numeric value.  When the
 LAMMPS command evaluates the python-style variable, the Python
 function will be executed.
 
@@ -388,13 +398,24 @@ using the :doc:`command-line switch -var <Run_options>`.
 
 For the *internal* style a numeric value is provided.  This value will
 be assigned to the variable until a LAMMPS command sets it to a new
-value.  There are currently only two LAMMPS commands that require
+value.
-*internal* variables as inputs, because they reset them:
+
-:doc:`create_atoms <create_atoms>` and :doc:`fix controller
+Note however, that most commands which use internal-style variables do
-<fix_controller>`.  As mentioned above, an internal-style variable can
+not require them to be defined in the input script.  They create one or
-be used in place of an equal-style variable anywhere else in an input
+more internal-style variables if they do not already exist.  Examples
-script, e.g. as an argument to another command that allows for
+are these commands:
-equal-style variables.
+
+* :doc:`create_atoms <create_atoms>`
+* :doc:`fix deposit <fix_deposit>`
+* :doc:`compute bond/local <compute_bond_local>`
+* :doc:`compute angle/local <compute_angle_local>`
+* :doc:`compute dihedral/local <compute_dihedral_local>`
+* :doc:`python <python>` command in conjunction with Python function wrappers used in equal- and atom-style variable formulas
+
+A command which does require an internal-style variable to be defined in
+the input script is the :doc:`fix controller <fix_controller>` command,
+because another (arbitrary) command typically also references the
+variable.
 
 ----------
 
@@ -439,6 +460,15 @@ python-style variable can be used in place of an equal-style variable
 anywhere in an input script, e.g. as an argument to another command
 that allows for equal-style variables.
 
+A python-style variable can also be used within the formula for an
+equal-style or atom-style formula in a Python function wrapper, as
+explained below for variable formulas.  In this context, the usage
+syntax is py_varname(arg1,arg2,...), where varname is the name of the
+python-style variable.  When a Python wrapper function is used in an
+atom-style formula, it can be invoked once per atom using arguments
+specific to each atom.  The resulting values in the atom-style
+variable can thus be calculated by Python code.
+
 ----------
 
 For the *string* style, a single string is assigned to the variable.
@@ -528,9 +558,9 @@ is a valid (though strange) variable formula:
 
 Specifically, a formula can contain numbers, constants, thermo
 keywords, math operators, math functions, group functions, region
-functions, special functions, feature functions, atom values, atom
+functions, special functions, feature functions, Python function
-vectors, custom atom properties, compute references, fix references, and references to other
+wrappers, atom values, atom vectors, custom atom properties, compute
-variables.
+references, fix references, and references to other variables.
 
 +------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Number                 | 0.2, 100, 1.0e20, -15.4, etc                                                                                                                                                                                                                                                                                                                               |
@@ -551,6 +581,8 @@ variables.
 +------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Feature functions      | is_available(category,feature), is_active(category,feature), is_defined(category,id)                                                                                                                                                                                                                                                                       |
 +------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
+| Python func wrapper    | py_varname(x,y,z,...)                                                                                                                                                                                                                                                                                                                                      |
++------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Atom values            | id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]                                                                                                                                                                                                                                                          |
 +------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Atom vectors           | id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q                                                                                                                                                                                                                                                                                                    |
@@ -1161,6 +1193,84 @@ variable name.
 
 ----------
 
+Python Function wrapper
+------------------------
+
+A Python function wrapper enables the formula for an equal-style or
+atom-style variable to invoke functions coded in Python.  In the case
+of an equal-style variable, the Python-coded function will be invoked
+once.  In the case of an atom-style variable, it can be invoked once
+per atom, if one or more of its arguments include a per-atom quantity,
+e.g. the position of an atom.  As illustrated below, the reason to use
+a Python function wrapper is to make it easy to pass LAMMPS-related
+arguments to the Python-coded function associated with a python-style
+variable.
+
+The syntax for defining a Python function wrapper is
+
+.. code-block:: LAMMPS
+
+   py_varname(arg1,arg2,...argN)
+
+where *varname* is the name of a python-style variable which couples
+to a Python-coded function.  The function will be passed the zero or
+more arguments listed in parentheses: *arg1*, *arg2*, ... *argN*.  As
+with Math Functions, each argument can itself be an arbitrarily
+complex formula.
+
+A Python function wrapper can be used in the following manner by an
+input script:
+
+.. code-block:: LAMMPS
+
+   variable        foo python truncate
+   python          truncate return v_foo input 1 v_arg format fi here """
+   def truncate(x):
+    return int(x)
+   """
+   variable        xtrunc atom py_foo(x)
+   variable        ytrunc atom py_foo(y)
+   variable        ztrunc atom py_foo(z)
+   dump            1 all custom 100 tmp.dump id x y z v_xtrunc v_ytrunc v_ztrunc
+
+The first two commands define a python-style variable *foo* and couple
+it to the Python-coded function *truncate()* which takes a single
+floating point argument, and returns its truncated integer value.  In
+this case, the Python code for truncate() is included in the *python*
+command; it could also be contained in a file.  See the :doc:`python
+<python>` command doc page for details.
+
+The next three commands define atom-style variables *xtrunc*,
+*ytrunc*, and *ztrunc*.  Each of them include the same Python function
+wrapper in their formula, with a different argument.  The atom-style
+variable *xtrunc* will invoke the python-style variable *foo*, which
+will in turn invoke the Python-coded *truncate()* method.  Because
+*xtrunc* is an atom-style variable, and the argument *x* in the Python
+function wrapper is a per-atom quantity (the x-coord of each atom),
+each processor will invoke the *truncate()* method once per atom, for
+the atoms it owns.
+
+When invoked for the Ith atom, the value of the *arg* internal-style
+variable, defined by the *python* command, is set to the x-coord of
+the Ith atom.  The call via python-style variable *foo* to the Python
+*truncate()* function passes the value of the *arg* variable as the
+function's first (and only) argument.  Likewise, the return value of
+the Python function is stored by the python-style variable *foo* and
+used in the *xtrunc* atom-style variable formula for the Ith atom.
+
+The resulting per-atom vector for *xtrunc* will thus contain the
+truncated x-coord of every atom in the system.  The dump command
+includes the truncated xyz coords for each atom in its output.
+
+See the :doc:`python <python>` command for more details on options the
+*python* command can specify as well as examples of more complex Python
+functions which can be wrapped in this manner.  In particular, the
+Python function can take a variety of arguments, some generated by the
+*python* command, and others by the arguments of the Python function
+wrapper.
+
+----------
+
 Atom Values and Vectors
 -----------------------
 

doc/utils/requirements.txt

@@ -2,6 +2,7 @@ Sphinx >= 5.3.0, <8.3.0
 sphinxcontrib-spelling
 sphinxcontrib-jquery
 sphinx-design
+sphinx-toolbox
 git+https://github.com/akohlmey/sphinx-fortran@parallel-read
 sphinx-tabs>=3.4.1
 breathe
@@ -10,3 +11,4 @@ six
 pyyaml
 linkchecker
 ipython
+numpy

doc/utils/sphinx-config/conf.py.in

@@ -50,6 +50,7 @@ extensions = [
     'sphinx.ext.mathjax',
     'sphinx.ext.imgmath',
     'sphinx.ext.autodoc',
+    'sphinx_toolbox.collapse',
     'lammps_theme',
     'sphinxcontrib.jquery',
     'sphinxfortran.fortran_domain',
@@ -370,6 +371,17 @@ latex_elements = {
 {%
   \hypersetup{pageanchor=false}% avoid duplicate destination warnings
   \begin{titlepage}%
+    \sffamily\Large
+    The LAMMPS developers are thinking about dropping the PDF format version of
+    the LAMMPS manual.  This would allow us to focus on the HTML version, use
+    HTML-only features, and skip checking if the documentation source files,
+    especially the embedded mathematical expressions, are compatible with \LaTeX{} output.
+
+    Please let us know how you feel about this change by sending an email to
+    \texttt{developers@lammps.org} stating whether you agree or disagree with
+    removing support for the PDF format version of the  manual and optionally
+    provide arguments for your preference.
+    \clearpage
     \sffamily\bfseries
     \begingroup % for PDF information dictionary
       \def\endgraf{ }\def\and{\& }%

doc/utils/sphinx-config/false_positives.txt

@@ -33,6 +33,7 @@ activationfunctions
 acylindricity
 addforce
 Addington
+addstep
 addtorque
 adf
 Adhikari
@@ -135,6 +136,8 @@ anton
 Antonelli
 anysize
 api
+apip
+APIP
 apolar
 Apoorva
 Appl
@@ -230,6 +233,7 @@ Bagi
 Bagnold
 Baig
 Bajaj
+bak
 Bal
 balancer
 Balankura
@@ -529,6 +533,7 @@ civ
 CKD
 ckk
 Clang
+clearstep
 clearstore
 Cleary
 Clebsch
@@ -653,6 +658,7 @@ CSiC
 csld
 cslib
 CSlib
+csp
 cstdio
 cstdlib
 cstring
@@ -1383,6 +1389,7 @@ gmres
 gname
 gneb
 GNEB
+Godehard
 Goerigk
 Goga
 Goldfarb
@@ -1618,6 +1625,7 @@ Imageint
 Imagemagick
 imagename
 imd
+Immel
 Impey
 impl
 improperlist
@@ -3129,6 +3137,7 @@ Pxy
 pxz
 py
 Py
+pyargs
 pydir
 pylammps
 PyLammps
@@ -3845,6 +3854,7 @@ Thiaville
 Thibaudeau
 Thijsse
 Thirumalai
+thr
 Threadripper
 threebody
 thrid
@@ -4071,6 +4081,7 @@ Vaiwala
 valent
 Valeriu
 valgrind
+validator
 Valone
 valuev
 Valuev
@@ -4080,6 +4091,7 @@ Vanduyfhuys
 varargs
 varavg
 variational
+varname
 Varshalovich
 Varshney
 vashishta

examples/COUPLE/plugin/liblammpsplugin.c

@@ -79,6 +79,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
   ADDSYM(mpi_finalize);
   ADDSYM(kokkos_finalize);
   ADDSYM(python_finalize);
+  ADDSYM(plugin_finalize);
 
   ADDSYM(error);
   ADDSYM(expand);
@@ -140,6 +141,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
   ADDSYM(scatter_subset);
 
   ADDSYM(create_atoms);
+  ADDSYM(create_molecule);
 
   ADDSYM(find_pair_neighlist);
   ADDSYM(find_fix_neighlist);

examples/COUPLE/plugin/liblammpsplugin.h

@@ -134,6 +134,7 @@ struct _liblammpsplugin {
   void (*mpi_finalize)();
   void (*kokkos_finalize)();
   void (*python_finalize)();
+  void (*plugin_finalize)();
 
   void (*error)(void *, int, const char *);
   char *(*expand)(void *, const char *);
@@ -206,6 +207,7 @@ struct _liblammpsplugin {
   int (*create_atoms)(void *, int, const int64_t *, const int *, const double *, const double *,
                       const int64_t *, int);
 #endif
+  int (*create_molecule)(void *, const char *, const char *);
 
   int (*find_pair_neighlist)(void *, const char *, int, int, int);
   int (*find_fix_neighlist)(void *, const char *, int);

examples/PACKAGES/apip/Cu-1.yace

@@ -0,0 +1,34 @@
+NOTE: This is a simple potential for the example. Production usage without testing is not recommended. Provided by Yury Lysogorskiy (ICAMS, RUB, Germany).
+elements: [Cu]
+E0: [0]
+deltaSplineBins: 0.001
+embeddings:
+  0: {ndensity: 2, FS_parameters: [1, 1, 1, 0.5], npoti: FinnisSinclairShiftedScaled, rho_core_cutoff: 100000, drho_core_cutoff: 250}
+bonds:
+  [0, 0]: {nradmax: 2, lmax: 2, nradbasemax: 15, radbasename: ChebPow, radparameters: [2], radcoefficients: [[[0.99440439385969503, -0.085048653403583918, -0.23248632054717755, -0.22732701549371864, 0.026354948476648921, 0.21853318667456997, 0.05745747498169812, -0.19717925712228765, -0.11474256770370879, 0.12738668745839368, 0.053777769435472259, -0.11094768379576209, 0.072620812391582482, -0.058715761632824881, 0.030359986427775303], [0.96259704765772924, -0.10129488003029259, -0.10345557604916655, -0.020393848425879282, 0.076671442494272601, 0.10318554794001746, 0.0555341702761026, 0.00083194423680727696, -0.018184436957498409, -0.021866885826555403, -0.020179969116479776, 0.021880011516616484, 0.053112509345249602, -0.083707026393616657, 0.020611714544479017], [1.001530579978529, -0.030080648426358471, -0.13318582671063051, -0.24371635685809706, -0.22760541127468878, -0.041144767051648642, 0.18080289144697201, 0.24543156067198274, 0.11014559411659355, -0.069512010077804498, -0.1172049950938457, -0.027509386703874331, 0.056985864219913585, 0.037536629112081353, -0.044222474537374087]], [[0.25716120576634355, 1.7485527550537943, 0.91889737965719875, 0.50902244208852199, -0.15895537149482841, -0.48109723575282892, -0.17843605933015286, 0.39450608859531944, 0.59293909285591195, 0.18268386912819001, -0.34706543720907351, -0.3210061634328315, 0.21678650779400246, 0.39500148786376449, -0.31820913370341625], [0.0079213202761679105, 1.0212489038630681, 0.011530454475879359, -0.049445152058907642, -0.15268524878755677, -0.2319378608755131, -0.20612580998548105, -0.067027395211212315, 0.08241096034972574, 0.11288597065081186, 0.01355948960244063, -0.074722461388416803, -0.022724332047049267, 0.088871664887057056, 0.031667459613258314], [-0.0069872405356639312, 0.9939655327342134, 0.035044055182587928, 0.099765277857093104, 0.11687607289674087, 0.030241996404391416, -0.12367698594314165, -0.22480900218170197, -0.17727517861619441, -0.015144941558075584, 0.11375495728241894, 0.090680932947050971, -0.041190210394591399, -0.10085768296286811, 0.055789864104988186]]], prehc: 0, lambdahc: 0, rcut: 3.8999999999999999, dcut: 0.01, rcut_in: 0, dcut_in: 0, inner_cutoff_type: density}
+functions:
+  0:
+    - {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [1], ls: [0], ms_combs: [0], ctildes: [0.26072556900842869, -0.03073189825062177]}
+    - {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [2], ls: [0], ms_combs: [0], ctildes: [0.64429175483702295, -0.1630534353246999]}
+    - {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [3], ls: [0], ms_combs: [0], ctildes: [0.51856313423563594, -0.4259316875879266]}
+    - {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [4], ls: [0], ms_combs: [0], ctildes: [-0.078113533662468398, -0.70352070540668643]}
+    - {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [5], ls: [0], ms_combs: [0], ctildes: [-0.45633111544093646, -0.7859368117550467]}
+    - {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [6], ls: [0], ms_combs: [0], ctildes: [-0.19608401600520556, -0.59151667874441172]}
+    - {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [7], ls: [0], ms_combs: [0], ctildes: [0.30580228338697285, -0.29248216980800118]}
+    - {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [8], ls: [0], ms_combs: [0], ctildes: [0.40167461008815436, -0.15647925731818518]}
+    - {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [9], ls: [0], ms_combs: [0], ctildes: [0.053519057558225343, -0.25900906688118652]}
+    - {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [10], ls: [0], ms_combs: [0], ctildes: [-0.20446546815457517, -0.40019216010057629]}
+    - {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [11], ls: [0], ms_combs: [0], ctildes: [-0.070020661105060208, -0.33441939205411986]}
+    - {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [12], ls: [0], ms_combs: [0], ctildes: [0.15734064575001952, -0.055233119903794807]}
+    - {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [13], ls: [0], ms_combs: [0], ctildes: [0.10021406559793103, 0.18641744536767416]}
+    - {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [14], ls: [0], ms_combs: [0], ctildes: [-0.14066730990975543, 0.14711096149210373]}
+    - {mu0: 0, rank: 1, ndensity: 2, num_ms_combs: 1, mus: [0], ns: [15], ls: [0], ms_combs: [0], ctildes: [0.031100766650549283, -0.13720067925313634]}
+    - {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 1, mus: [0, 0], ns: [1, 1], ls: [0, 0], ms_combs: [0, 0], ctildes: [1.0984212008195524, 0.49756623164565855]}
+    - {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 2, mus: [0, 0], ns: [1, 1], ls: [1, 1], ms_combs: [0, 0, 1, -1], ctildes: [0.2591109116320176, 0.21348077494861176, -0.5182218232640351, -0.4269615498972234]}
+    - {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 3, mus: [0, 0], ns: [1, 1], ls: [2, 2], ms_combs: [0, 0, 1, -1, 2, -2], ctildes: [0.015905361441871636, 0.023783303055646809, -0.031810722883743273, -0.047566606111293624, 0.031810722883743286, 0.047566606111293638]}
+    - {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 1, mus: [0, 0], ns: [2, 1], ls: [0, 0], ms_combs: [0, 0], ctildes: [0.63958612617724186, 1.6623415103929948]}
+    - {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 2, mus: [0, 0], ns: [2, 1], ls: [1, 1], ms_combs: [0, 0, 1, -1], ctildes: [0.14199022782503917, 0.0069900458821809735, -0.28398045565007829, -0.013980091764361944]}
+    - {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 3, mus: [0, 0], ns: [2, 1], ls: [2, 2], ms_combs: [0, 0, 1, -1, 2, -2], ctildes: [0.028732470496968317, -0.037173039560267927, -0.05746494099393664, 0.074346079120535868, 0.057464940993936654, -0.074346079120535882]}
+    - {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 1, mus: [0, 0], ns: [2, 2], ls: [0, 0], ms_combs: [0, 0], ctildes: [0.056442895466964321, 0.0054387873274233034]}
+    - {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 2, mus: [0, 0], ns: [2, 2], ls: [1, 1], ms_combs: [0, 0, 1, -1], ctildes: [0.025326283180140272, -0.19511149476156769, -0.050652566360280531, 0.39022298952313533]}
+    - {mu0: 0, rank: 2, ndensity: 2, num_ms_combs: 3, mus: [0, 0], ns: [2, 2], ls: [2, 2], ms_combs: [0, 0, 1, -1, 2, -2], ctildes: [0.012754475331985416, -0.058934602152610385, -0.025508950663970836, 0.11786920430522078, 0.025508950663970843, -0.11786920430522081]}

examples/PACKAGES/apip/README

@@ -0,0 +1,11 @@
+The APIP package is based on the paper:
+
+David Immel, Ralf Drautz, Godehard Sutmann; Adaptive-precision potentials for large-scale atomistic simulations. J. Chem. Phys. 14 March 2025; 162 (11): 114119. https://doi.org/10.1063/5.0245877
+
+The pair_style pace/apip requires the installation of lib/pace of the ML-PACE package.
+The installation of lib/pace is described in src/ML-PACE/README .
+
+Examples of how to use an adaptive-precision potential are provided in examples/PACKAGES/apip .
+
+in.vacancy contains a small example that can be used to visualize the transition region and get a visual impression of the selected parameters.
+in.surface.balance in a more realistic example, in which a surface is simulated and the benefit of fix apip_atom_weight and fix balance for adaptive-precision interatomic potentials is demonstrated.

examples/PACKAGES/apip/data.validate

@@ -0,0 +1,80 @@
+LAMMPS data file via write_data, version 2 Apr 2025, timestep = 0, units = metal
+
+31 atoms
+1 atom types
+
+0 7.23 xlo xhi
+0 7.23 ylo yhi
+0 7.23 zlo zhi
+
+Masses
+
+1 63.546
+
+Atoms # apip
+
+1 1 3.255649577011424 2.1469408310018205 1.596546647595962 0 0 0
+2 1 5.312133977687514 0.2962629940541289 1.7986410677440656 0 0 0
+3 1 0.3570136530341179 1.9589665444185802 1.8227120430766197 0 0 0
+4 1 1.538770434276094 1.8506888783106994 3.5984777679252336 0 0 0
+5 1 5.414379916412933 1.9802551521608864 3.5428423680157133 0 0 0
+6 1 3.3396207511420926 0.34696444514694835 3.3284295847601864 0 0 0
+7 1 0.04692381499727436 3.470558659189874 0.20838500420697273 0 0 0
+8 1 3.5507628116865004 3.419576015011443 0.09808429731968064 0 0 0
+9 1 3.4359438466091845 3.3442299605630015 3.344947182361245 0 0 0
+10 1 3.262172986855113 1.8898900738753799 5.6074716235080135 0 0 0
+11 1 5.616180533384058 0.24272458584617107 5.728614316596936 0 0 0
+12 1 0.3320737270957668 2.133631298552561 5.648234772896504 0 0 0
+13 1 7.193910458696732 0.040079315967661934 7.007063468494249 -1 0 -1
+14 1 1.9428459507398523 2.008894084694746 6.974381464595852 0 0 -1
+15 1 5.17195441765988 1.6398976096007498 7.144624559798802 0 0 -1
+16 1 3.828212487222493 0.27427274843853566 7.084083006467942 0 0 -1
+17 1 0.3576896118392189 3.5593061817506357 3.8539966829342287 0 0 0
+18 1 5.549388330643712 3.3771731288636446 5.733276811271104 0 0 0
+19 1 1.474782367736 3.311754538948766 5.203036111913638 0 0 0
+20 1 3.353885621487343 5.483140337766679 1.559656844576661 0 0 0
+21 1 1.4600851633288363 5.3693400677513985 0.16901869775192754 0 0 0
+22 1 1.865319826459661 3.680823307523189 1.909829542233995 0 0 0
+23 1 6.919428313555163 5.704165921616911 1.5626446154218376 -1 0 0
+24 1 5.286111954406888 3.9741177165543746 1.894962129368895 0 0 0
+25 1 5.661441532175263 5.770831269632481 0.2726487131030991 0 0 0
+26 1 5.749451385769738 5.694440631979816 3.315201684766776 0 0 0
+27 1 2.1656354707333425 5.630356615286487 3.525133119978771 0 0 0
+28 1 3.4802512558478638 5.136357035041954 5.613687950103865 0 0 0
+29 1 6.9476459434582605 5.669871702976 5.748711917622347 -1 0 0
+30 1 0.3145319513743893 6.992506749359428 3.748936483911442 0 -1 0
+31 1 2.0688280140984934 7.144932953378388 5.071647430554334 0 -1 0
+
+Velocities
+
+1 0 0 0
+2 0 0 0
+3 0 0 0
+4 0 0 0
+5 0 0 0
+6 0 0 0
+7 0 0 0
+8 0 0 0
+9 0 0 0
+10 0 0 0
+11 0 0 0
+12 0 0 0
+13 0 0 0
+14 0 0 0
+15 0 0 0
+16 0 0 0
+17 0 0 0
+18 0 0 0
+19 0 0 0
+20 0 0 0
+21 0 0 0
+22 0 0 0
+23 0 0 0
+24 0 0 0
+25 0 0 0
+26 0 0 0
+27 0 0 0
+28 0 0 0
+29 0 0 0
+30 0 0 0
+31 0 0 0

examples/PACKAGES/apip/in.surface.balance

@@ -0,0 +1,75 @@
+##################################################
+# parameters of the adaptive-precision potential #
+##################################################
+# We couple an EAM potential with an ACE potential.
+variable	eamfs_file string "Cu_300K_Immel_2023.eam.fs"
+variable	ace_file1 string "Cu-1.yace"
+variable	ace_file2 string "../../../potentials/Cu-PBE-core-rep.ace"
+# The csp is used as detection mechanism for atoms of interest.
+variable	csp_lattice string "fcc"
+variable	csp_cutoff equal 6.0
+# The range [r_sw_lo, r_sw_hi] determines where the switching parameter changes from 0 to 1.
+variable	r_sw_lo equal 4.0
+variable	r_sw_hi equal 12.0
+# Thresholds between which the switching parameter changes from 1 to 0 based on the csp.
+variable	lambda_input_thr_lo equal 7.5
+variable	lambda_input_thr_hi equal 8.0
+# Number of averaged steps.
+variable	lambda_input_histlen equal 110
+variable	lambda_histlen equal 110
+# Minimum required change of the switching parameter
+variable	min_delta_lambda equal 1/${lambda_histlen}
+# number of atoms rescaled by the lambda_thermostat
+variable	N_rescaling equal 600
+
+
+
+# basic stuff
+units		metal
+dimension	3
+boundary	p p s
+atom_style	apip # own atom style required for APIP
+timestep	0.001
+
+read_data	data.surface.balance
+
+fix		nve all nve
+comm_style	tiled
+
+
+# Only the upper surface should be treated precisely.
+# Thus, we create group, for whose atoms the csp is ignored, as the corresponding
+# argument of fix lambda is used.
+region		bottom block INF INF INF INF INF 0 units box
+group		group_ignore_csp region bottom
+
+
+# use adaptive-precision eam-ace potential with lambda_thermostat
+pair_style	hybrid/overlay eam/fs/apip pace/apip lambda/input/csp/apip ${csp_lattice} cutoff ${csp_cutoff} lambda/zone/apip ${r_sw_hi}
+pair_coeff	* * eam/fs/apip ${eamfs_file} Cu
+pair_coeff	* * pace/apip ${ace_file2} Cu
+pair_coeff	* * lambda/input/csp/apip
+pair_coeff	* * lambda/zone/apip
+fix		lambda all lambda/apip ${lambda_input_thr_lo} ${lambda_input_thr_hi} time_averaged_zone ${r_sw_lo} ${r_sw_hi} ${lambda_input_histlen} ${lambda_histlen} min_delta_lambda ${min_delta_lambda} group_ignore_lambda_input group_ignore_csp
+fix		lambda_thermostat all lambda_thermostat/apip N_rescaling ${N_rescaling}
+fix		weight_atom all atom_weight/apip 10 eam ace lambda/input lambda/zone all
+
+# store weight in variable
+fix		property_atom all property/atom d_usedweight
+variable	myweight atom f_weight_atom
+#compute		lambda all property/atom apip_lambda
+#compute		lambda_input all property/atom apip_lambda_input
+#dump		1 all custom 10 dump/surface_ap_balance.dump.* id type x y z c_lambda c_lambda_input f_weight_atom proc d_usedweight
+
+
+## apply load balancing
+## no load-balancing
+#fix		balance all balance 10 0.9 report weight time 1.0 weight store usedweight
+## load balancing with times per atom per processor
+#fix		balance all balance 10 0.9 rcb weight time 1.0 weight store usedweight
+## load balancing with an approximated load per atom by fix apip_atom_weight
+fix		balance all balance 10 0.9 rcb weight var myweight weight store usedweight
+
+thermo_style	custom step f_balance spcpu f_weight_atom[*]
+thermo		10
+run		100

examples/PACKAGES/apip/in.vacancy.const.lambda

@@ -0,0 +1,54 @@
+##################################################
+# parameters of the adaptive-precision potential #
+##################################################
+# We couple an EAM potential with an ACE potential.
+variable	eamfs_file string "Cu_300K_Immel_2023.eam.fs"
+variable	ace_file1 string "Cu-1.yace"
+variable	ace_file2 string "../../../potentials/Cu-PBE-core-rep.ace"
+
+
+## basic stuff
+units		metal
+atom_style	apip # own atom style required for APIP
+timestep	0.001
+
+# copper at room temperature with a vacancy
+read_data	data.vacancy
+
+
+# set lambda
+group		vacancy id 145 147 148 149 150 994 997 995 1024 1026 1028 1922
+group		transition id 77 79 81 84 88 151 152 153 154 155 158 1089 188 189 192 1033 1039 1964 1022 1021 999 998 996 948 950 952 992 993 139 1025 1027 1029 1034 1035 1038 1088 1920 1921 1923 1924 1925 1930
+group		bulk subtract all vacancy transition
+set		group vacancy apip/lambda precise
+set		group transition apip/lambda 0.5
+set		group bulk apip/lambda fast
+
+
+fix		nve all nve
+
+
+# Use adaptive-precision eam-ace potential with constant lambda.
+# Calculate atomic weight that could be used for load balancing.
+pair_style	hybrid/overlay eam/fs/apip pace/apip
+pair_coeff	* * eam/fs/apip ${eamfs_file} Cu
+pair_coeff	* * pace/apip ${ace_file2} Cu
+fix		weight_atom all atom_weight/apip 50 eam ace 0.5 0 all
+
+
+# get statistics about lambda
+compute		lambda all property/atom apip_lambda
+compute		lambda_input all property/atom apip_lambda_input
+variable	flag_simple atom c_lambda==1
+variable	flag_switch atom c_lambda<1&&c_lambda>0
+variable	flag_complex atom c_lambda==0
+compute		lambda_types all reduce sum v_flag_simple v_flag_switch v_flag_complex
+
+
+thermo_style	custom step etotal c_lambda_types[*]
+thermo		1
+
+run		100
+
+# dump atoms
+#write_dump	all custom dump.vacancy.* id type x y z fx fy fz c_lambda c_lambda_input f_weight_atom

examples/PACKAGES/apip/in.vacancy.dynamic.lambda

@@ -0,0 +1,101 @@
+##################################################
+# parameters of the adaptive-precision potential #
+##################################################
+# We couple an EAM potential with an ACE potential.
+variable	eamfs_file string "Cu_300K_Immel_2023.eam.fs"
+variable	ace_file1 string "Cu-1.yace"
+variable	ace_file2 string "../../../potentials/Cu-PBE-core-rep.ace"
+# The csp is used as detection mechanism for atoms of interest.
+variable	csp_lattice string "fcc"
+variable	csp_cutoff equal 6.0
+# The range [r_sw_lo, r_sw_hi] determines where the switching parameter changes from 0 to 1.
+variable	r_sw_lo equal 2.0
+variable	r_sw_hi equal 3.0
+# Thresholds between which the switching parameter changes from 1 to 0 based on the csp.
+variable	lambda_input_thr_lo equal 2.5
+variable	lambda_input_thr_hi equal 3.0
+# Number of averaged steps.
+variable	lambda_input_histlen equal 110
+variable	lambda_histlen equal 110
+# Minimum required change of the switching parameter
+variable	min_delta_lambda equal 1/${lambda_histlen}
+# number of atoms rescaled by the lambda_thermostat
+variable	N_rescaling equal 600
+
+
+
+## basic stuff
+units		metal
+atom_style	apip # own atom style required for APIP
+timestep	0.001
+
+# copper at room temperature with a vacancy
+read_data	data.vacancy
+
+fix		nve all nve
+
+
+## Use adaptive-precision ace-ace potential without lambda_thermostat.
+## Calculate atomic weight that could be used for load balancing.
+#pair_style	hybrid/overlay pace/fast/apip pace/precise/apip lambda/input/csp/apip ${csp_lattice} cutoff ${csp_cutoff} lambda/zone/apip ${r_sw_hi}
+#pair_coeff	* * pace/fast/apip ${ace_file1} Cu
+#pair_coeff	* * pace/precise/apip ${ace_file2} Cu
+#pair_coeff	* * lambda/input/csp/apip
+#pair_coeff	* * lambda/zone/apip
+#fix		lambda all lambda/apip ${lambda_input_thr_lo} ${lambda_input_thr_hi} time_averaged_zone ${r_sw_lo} ${r_sw_hi} ${lambda_input_histlen} ${lambda_histlen} min_delta_lambda ${min_delta_lambda}
+#fix		weight_atom all atom_weight/apip 100 ace ace lambda/input lambda/zone all
+
+
+# Use adaptive-precision eam-ace potential without lambda_thermostat.
+# Calculate atomic weight that could be used for load balancing.
+pair_style	hybrid/overlay eam/fs/apip pace/apip lambda/input/csp/apip ${csp_lattice} cutoff ${csp_cutoff} lambda/zone/apip ${r_sw_hi}
+pair_coeff	* * eam/fs/apip ${eamfs_file} Cu
+pair_coeff	* * pace/apip ${ace_file2} Cu
+pair_coeff	* * lambda/input/csp/apip
+pair_coeff	* * lambda/zone/apip
+fix		lambda all lambda/apip ${lambda_input_thr_lo} ${lambda_input_thr_hi} time_averaged_zone ${r_sw_lo} ${r_sw_hi} ${lambda_input_histlen} ${lambda_histlen} min_delta_lambda ${min_delta_lambda}
+fix		weight_atom all atom_weight/apip 100 eam ace lambda/input lambda/zone all
+
+
+## One can comment out fix lambda_thermostat to see the energy change caused by the neglection of the
+## gradient of the switching function. This neglection can be compensated by the local thermostat and the
+## energy can be conserved within numerical precision.
+fix		lambda_thermostat all lambda_thermostat/apip N_rescaling ${N_rescaling} store_atomic_forces 100
+
+
+# get statistics about lambda
+compute		lambda all property/atom apip_lambda
+compute		lambda_input all property/atom apip_lambda_input
+variable	flag_simple atom c_lambda==1
+variable	flag_switch atom c_lambda<1&&c_lambda>0
+variable	flag_complex atom c_lambda==0
+compute		lambda_types all reduce sum v_flag_simple v_flag_switch v_flag_complex
+
+
+thermo_style	custom step etotal c_lambda_types[*]
+thermo		1
+
+run		100
+
+# dump atoms
+#write_dump	all custom dump/vacancy.dump.* id type x y z fx fy fz c_lambda c_lambda_input f_weight_atom f_lambda_thermostat[*]
+
+
+
+## A smooth restart of the simulation is possible as the history of lambda and lambda_input is stored.
+
+#write_restart	vacancy_ap.restart
+#clear
+#read_restart	vacancy_ap.restart
+#pair_style	hybrid/overlay eam/fs/apip pace/apip lambda/input/csp/apip fcc cutoff 6.0 lambda/zone/apip 12.0
+#pair_coeff	* * eam/fs/apip "Cu_300K_Immel_2023.eam.fs" Cu
+#pair_coeff	* * pace/apip "../../../potentials/Cu-PBE-core-rep.ace" Cu
+#pair_coeff	* * lambda/input/csp/apip
+#pair_coeff	* * lambda/zone/apip
+#fix		lambda all lambda/apip 2.5 3.0 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda $(1/110)
+#fix		lambda_thermostat all lambda_thermostat/apip N_rescaling ${N_rescaling} store_atomic_forces 100
+#fix		nve all nve
+#thermo_style	custom step etotal
+#thermo		1
+#run		10
+#shell		rm vacancy_ap.restart

examples/PACKAGES/apip/in.validate

@@ -0,0 +1,51 @@
+##################################################
+# parameters of the adaptive-precision potential #
+##################################################
+# We couple an EAM potential with an ACE potential.
+variable	eamfs_file string "Cu_300K_Immel_2023.eam.fs"
+variable	ace_file string "Cu-1.yace"
+
+
+## basic stuff
+units		metal
+atom_style	apip # own atom style required for APIP
+timestep	0.001
+
+## copper with a vacancy
+#lattice		fcc 3.615
+#region		box block 0 2 0 2 0 2 units lattice
+#create_box	1 box
+#create_atoms	1 box
+#mass		1 63.546
+#displace_atoms	all random 0.1 0.1 0.1 42 units lattice
+#delete_atoms	random count 1 yes all NULL 42
+#write_data	data.validate
+read_data	data.validate
+
+
+fix		1 all nve
+thermo_style	custom step pe fnorm fmax
+
+
+# use ACE potential
+pair_style	pace
+pair_coeff	* * ${ace_file} Cu
+run		0
+
+# use adaptive-precision EAM-ACE potential with constant lambda
+pair_style	hybrid/overlay eam/fs/apip pace/apip
+pair_coeff	* * eam/fs/apip ${eamfs_file} Cu
+pair_coeff	* * pace/apip ${ace_file} Cu
+
+# use ACE of adaptive-precision potential
+set		group all apip/lambda precise
+run		0
+
+# use EAM of adaptive-precision potential
+set		group all apip/lambda fast
+run		0
+
+# Use EAM potential
+pair_style	eam/fs
+pair_coeff	* * ${eamfs_file} Cu
+run		0

examples/PACKAGES/apip/log.02Apr25.surface.balance.nolb.g++.4

@@ -0,0 +1,108 @@
+LAMMPS (2 Apr 2025 - Development - )
+Reading data file ...
+  orthogonal box = (0 0 -1.1656272) to (36.15 36.15 362.81506)
+  1 by 1 by 4 MPI processor grid
+  reading atoms ...
+  40200 atoms
+  reading velocities ...
+  40200 velocities
+  read_data CPU = 0.135 seconds
+200 atoms in group group_ignore_csp
+ACE version: 2023.11.25
+Recursive evaluator is used by ACE
+Loading ../../../potentials/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
+atomic load lambda:
+	fast potential: extract eam/apip:time_per_atom
+	precise potential: extract pace/apip:time_per_atom
+	lambda_input: extract lambda/input/apip:time_per_atom
+	lambda: extract lambda/zone/apip:time_per_atom
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+- fix lambda command: doi.org/10.1063/5.0245877
+The log file lists these citations in BibTeX format.
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 14
+  ghost atom cutoff = 14
+  binsize = 7, bins = 6 6 52
+  5 neighbor lists, perpetual/occasional/extra = 5 0 0
+  (1) pair eam/fs/apip, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair pace/apip, perpetual, trim from (4)
+      attributes: full, newton on, cut 9.4
+      pair build: trim
+      stencil: none
+      bin: none
+  (3) pair lambda/input/csp/apip, perpetual, trim from (2)
+      attributes: full, newton on, cut 8
+      pair build: trim
+      stencil: none
+      bin: none
+  (4) pair lambda/zone/apip, perpetual
+      attributes: full, newton on, ghost, cut 14
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (5) fix lambda_thermostat/apip, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Setting up Verlet run ...
+  Unit style    : metal
+  Current step  : 0
+  Time step     : 0.001
+Per MPI rank memory allocation (min/avg/max) = 297.9 | 306.9 | 315.9 Mbytes
+   Step       f_balance        S/CPU      f_weight_atom[1] f_weight_atom[2] f_weight_atom[3] f_weight_atom[4]
+         0   1.0139303      0              0              0              0              0            
+        10   2.6176099      0.23789922     3.4933844e-05  0.0018769787   2.0912678e-05  3.414976e-05 
+        20   2.1242027      0.2259695      4.2800036e-05  0.0022124427   2.4613899e-05  4.0819606e-05
+        30   2.1197082      0.22281117     4.3885117e-05  0.0022416604   2.4808124e-05  4.081464e-05 
+        40   2.1149313      0.2245266      4.3328755e-05  0.0022134411   2.4645468e-05  4.0892224e-05
+        50   2.1066618      0.22308398     4.3884622e-05  0.0022085846   2.464161e-05   4.0909229e-05
+        60   2.1000306      0.22186291     4.4839801e-05  0.0022299631   2.4816945e-05  4.1173119e-05
+        70   2.1062658      0.22406791     4.3740709e-05  0.0022049729   2.4693417e-05  4.0963037e-05
+        80   2.1072933      0.22241288     4.4160464e-05  0.0022245226   2.4854938e-05  4.2491144e-05
+        90   2.0981181      0.22412189     4.3990788e-05  0.0022086162   2.4710948e-05  4.09478e-05  
+       100   2.1033304      0.2237968      4.3982714e-05  0.0022112815   2.4658851e-05  4.1060551e-05
+Loop time of 444.499 on 4 procs for 100 steps with 40200 atoms
+
+Performance: 0.019 ns/day, 1234.721 hours/ns, 0.225 timesteps/s, 9.044 katom-step/s
+99.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 67.764     | 146.15     | 378.03     |1107.5 | 32.88
+Neigh   | 55.764     | 59.579     | 62.94      |  43.1 | 13.40
+Comm    | 0.6589     | 153.57     | 302.72     |1199.1 | 34.55
+Output  | 0.0032423  | 6.1068     | 24.01      | 418.3 |  1.37
+Modify  | 8.0892     | 16.162     | 38.588     | 322.6 |  3.64
+Other   |            | 62.93      |            |       | 14.16
+
+Nlocal:          10050 ave       10180 max       10000 min
+Histogram: 2 1 0 0 0 0 0 0 0 1
+Nghost:        27854.5 ave       30385 max       25525 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  9.49222e+06 ave 9.76687e+06 max 9.29466e+06 min
+Histogram: 2 0 0 0 0 0 1 0 0 1
+
+Total # of neighbors = 37968882
+Ave neighs/atom = 944.49955
+Neighbor list builds = 10
+Dangerous builds = 0
+Total wall time: 0:07:25

examples/PACKAGES/apip/log.02Apr25.surface.balance.rcb.myweight.g++.4

@@ -0,0 +1,108 @@
+LAMMPS (2 Apr 2025 - Development - )
+Reading data file ...
+  orthogonal box = (0 0 -1.1656272) to (36.15 36.15 362.81506)
+  1 by 1 by 4 MPI processor grid
+  reading atoms ...
+  40200 atoms
+  reading velocities ...
+  40200 velocities
+  read_data CPU = 0.161 seconds
+200 atoms in group group_ignore_csp
+ACE version: 2023.11.25
+Recursive evaluator is used by ACE
+Loading ../../../potentials/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
+atomic load lambda:
+	fast potential: extract eam/apip:time_per_atom
+	precise potential: extract pace/apip:time_per_atom
+	lambda_input: extract lambda/input/apip:time_per_atom
+	lambda: extract lambda/zone/apip:time_per_atom
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+- fix lambda command: doi.org/10.1063/5.0245877
+The log file lists these citations in BibTeX format.
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 14
+  ghost atom cutoff = 14
+  binsize = 7, bins = 6 6 52
+  5 neighbor lists, perpetual/occasional/extra = 5 0 0
+  (1) pair eam/fs/apip, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair pace/apip, perpetual, trim from (4)
+      attributes: full, newton on, cut 9.4
+      pair build: trim
+      stencil: none
+      bin: none
+  (3) pair lambda/input/csp/apip, perpetual, trim from (2)
+      attributes: full, newton on, cut 8
+      pair build: trim
+      stencil: none
+      bin: none
+  (4) pair lambda/zone/apip, perpetual
+      attributes: full, newton on, ghost, cut 14
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (5) fix lambda_thermostat/apip, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Setting up Verlet run ...
+  Unit style    : metal
+  Current step  : 0
+  Time step     : 0.001
+Per MPI rank memory allocation (min/avg/max) = 298.1 | 306.3 | 314.5 Mbytes
+   Step       f_balance        S/CPU      f_weight_atom[1] f_weight_atom[2] f_weight_atom[3] f_weight_atom[4]
+         0   1              0              0              0              0              0            
+        10   1.0018226      0.21929744     4.2082278e-05  0.0022147425   2.472285e-05   4.0694771e-05
+        20   1.002451       0.38193369     4.9389333e-05  0.0023722824   2.4776133e-05  2.168819e-05 
+        30   1.0004234      0.39492198     4.8977088e-05  0.002249832    2.4610967e-05  2.1465621e-05
+        40   1.0012276      0.39068387     4.9886201e-05  0.0022529811   2.4663509e-05  2.1540032e-05
+        50   1.0013752      0.39170654     5.0527084e-05  0.002253323    2.4721079e-05  2.153442e-05 
+        60   1.0007053      0.3758265      5.0935226e-05  0.0022581901   2.4772692e-05  2.1596641e-05
+        70   1.0003982      0.38524379     5.1685387e-05  0.002263544    2.495032e-05   2.1714264e-05
+        80   1.0022848      0.38409158     5.1897166e-05  0.0022557711   2.4755235e-05  2.1595246e-05
+        90   1.0012911      0.38122934     5.2440631e-05  0.0022574019   2.4795351e-05  2.1615786e-05
+       100   1.0005279      0.37983246     5.2871808e-05  0.0022583136   2.484618e-05   2.1569403e-05
+Loop time of 279.389 on 4 procs for 100 steps with 40200 atoms
+
+Performance: 0.031 ns/day, 776.081 hours/ns, 0.358 timesteps/s, 14.389 katom-step/s
+98.6% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 148.19     | 155.34     | 175.77     |  94.7 | 55.60
+Neigh   | 87.542     | 87.924     | 88.444     |   3.6 | 31.47
+Comm    | 4.9019     | 18.932     | 33.429     | 322.2 |  6.78
+Output  | 0.01326    | 0.04615    | 0.075485   |  10.3 |  0.02
+Modify  | 9.5358     | 10.391     | 12.424     |  36.6 |  3.72
+Other   |            | 6.756      |            |       |  2.42
+
+Nlocal:          10050 ave       10283 max        9838 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Nghost:          52763 ave       52975 max       52530 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  9.49222e+06 ave 9.71459e+06 max 9.29015e+06 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+
+Total # of neighbors = 37968882
+Ave neighs/atom = 944.49955
+Neighbor list builds = 10
+Dangerous builds = 0
+Total wall time: 0:04:48

examples/PACKAGES/apip/log.02Apr25.surface.balance.rcb.time.g++.4

@@ -0,0 +1,108 @@
+LAMMPS (2 Apr 2025 - Development - )
+Reading data file ...
+  orthogonal box = (0 0 -1.1656272) to (36.15 36.15 362.81506)
+  1 by 1 by 4 MPI processor grid
+  reading atoms ...
+  40200 atoms
+  reading velocities ...
+  40200 velocities
+  read_data CPU = 0.134 seconds
+200 atoms in group group_ignore_csp
+ACE version: 2023.11.25
+Recursive evaluator is used by ACE
+Loading ../../../potentials/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
+atomic load lambda:
+	fast potential: extract eam/apip:time_per_atom
+	precise potential: extract pace/apip:time_per_atom
+	lambda_input: extract lambda/input/apip:time_per_atom
+	lambda: extract lambda/zone/apip:time_per_atom
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+- fix lambda command: doi.org/10.1063/5.0245877
+The log file lists these citations in BibTeX format.
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 14
+  ghost atom cutoff = 14
+  binsize = 7, bins = 6 6 52
+  5 neighbor lists, perpetual/occasional/extra = 5 0 0
+  (1) pair eam/fs/apip, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair pace/apip, perpetual, trim from (4)
+      attributes: full, newton on, cut 9.4
+      pair build: trim
+      stencil: none
+      bin: none
+  (3) pair lambda/input/csp/apip, perpetual, trim from (2)
+      attributes: full, newton on, cut 8
+      pair build: trim
+      stencil: none
+      bin: none
+  (4) pair lambda/zone/apip, perpetual
+      attributes: full, newton on, ghost, cut 14
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (5) fix lambda_thermostat/apip, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Setting up Verlet run ...
+  Unit style    : metal
+  Current step  : 0
+  Time step     : 0.001
+Per MPI rank memory allocation (min/avg/max) = 298.1 | 306.3 | 314.5 Mbytes
+   Step       f_balance        S/CPU      f_weight_atom[1] f_weight_atom[2] f_weight_atom[3] f_weight_atom[4]
+         0   1              0              0              0              0              0            
+        10   1.000245       0.23168829     2.8965377e-05  0.0016346261   1.8194173e-05  2.8621987e-05
+        20   1.0001156      0.23012235     4.2703387e-05  0.0022174634   2.4522315e-05  4.0198928e-05
+        30   1.0003479      0.24170843     4.2900821e-05  0.0022358654   2.4496934e-05  4.0262644e-05
+        40   1.0000952      0.34743014     4.4687983e-05  0.0022336389   2.4626704e-05  2.8362965e-05
+        50   1.000399       0.23273413     4.4278568e-05  0.0022319529   2.4645291e-05  4.0394287e-05
+        60   1.000137       0.23531789     4.5212176e-05  0.0022671271   2.4758267e-05  4.0607561e-05
+        70   1.0001901      0.34359487     4.5647742e-05  0.0022386998   2.473236e-05   2.8357019e-05
+        80   1.0003173      0.23324348     4.5372627e-05  0.0022272881   2.4704053e-05  4.0760615e-05
+        90   1.0009828      0.2360927      4.5867574e-05  0.0022616272   2.4715122e-05  4.0548519e-05
+       100   1.0005337      0.34332801     4.6171376e-05  0.0022394199   2.4724815e-05  2.8552653e-05
+Loop time of 385.695 on 4 procs for 100 steps with 40200 atoms
+
+Performance: 0.022 ns/day, 1071.376 hours/ns, 0.259 timesteps/s, 10.423 katom-step/s
+98.9% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 80.949     | 145.84     | 287.45     | 683.6 | 37.81
+Neigh   | 21.125     | 61.121     | 98.27      | 452.7 | 15.85
+Comm    | 23.839     | 129.54     | 261.28     | 833.4 | 33.59
+Output  | 0.10319    | 2.5231     | 8.6153     | 222.9 |  0.65
+Modify  | 5.3228     | 13.101     | 29.2       | 267.2 |  3.40
+Other   |            | 33.57      |            |       |  8.70
+
+Nlocal:          10050 ave       16825 max        3772 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:        27618.8 ave       41748 max       12149 min
+Histogram: 1 1 0 0 0 0 0 0 0 2
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  9.49222e+06 ave 1.58445e+07 max   3.337e+06 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 37968882
+Ave neighs/atom = 944.49955
+Neighbor list builds = 10
+Dangerous builds = 0
+Total wall time: 0:06:27

examples/PACKAGES/apip/log.02Apr25.vacancy.const.lambda.g++.1

@@ -0,0 +1,182 @@
+LAMMPS (2 Apr 2025 - Development - )
+Reading data file ...
+  orthogonal box = (0 0 0) to (28.92 28.92 28.92)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  2047 atoms
+  reading velocities ...
+  2047 velocities
+  read_data CPU = 0.009 seconds
+12 atoms in group vacancy
+42 atoms in group transition
+1993 atoms in group bulk
+Setting atom values ...
+  12 settings made for apip/lambda
+Setting atom values ...
+  42 settings made for apip/lambda
+Setting atom values ...
+  1993 settings made for apip/lambda
+ACE version: 2023.11.25
+Recursive evaluator is used by ACE
+Loading ../../../potentials/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
+atomic load lambda:
+	fast potential: extract eam/apip:time_per_atom
+	precise potential: extract pace/apip:time_per_atom
+	lambda_input: const 0.5
+	lambda: const 0
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 9.4
+  ghost atom cutoff = 9.4
+  binsize = 4.7, bins = 7 7 7
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/fs/apip, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair pace/apip, perpetual
+      attributes: full, newton on, cut 9.4
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Setting up Verlet run ...
+  Unit style    : metal
+  Current step  : 0
+  Time step     : 0.001
+Per MPI rank memory allocation (min/avg/max) = 11.08 | 11.08 | 11.08 Mbytes
+   Step         TotEng     c_lambda_types[1] c_lambda_types[2] c_lambda_types[3]
+         0  -7408.6798      1993           42             12           
+         1  -7408.6798      1993           42             12           
+         2  -7408.6798      1993           42             12           
+         3  -7408.6798      1993           42             12           
+         4  -7408.6798      1993           42             12           
+         5  -7408.6798      1993           42             12           
+         6  -7408.6799      1993           42             12           
+         7  -7408.6799      1993           42             12           
+         8  -7408.6799      1993           42             12           
+         9  -7408.6799      1993           42             12           
+        10  -7408.6799      1993           42             12           
+        11  -7408.68        1993           42             12           
+        12  -7408.68        1993           42             12           
+        13  -7408.68        1993           42             12           
+        14  -7408.68        1993           42             12           
+        15  -7408.68        1993           42             12           
+        16  -7408.68        1993           42             12           
+        17  -7408.6801      1993           42             12           
+        18  -7408.6801      1993           42             12           
+        19  -7408.6801      1993           42             12           
+        20  -7408.6801      1993           42             12           
+        21  -7408.6801      1993           42             12           
+        22  -7408.6801      1993           42             12           
+        23  -7408.6801      1993           42             12           
+        24  -7408.6801      1993           42             12           
+        25  -7408.6801      1993           42             12           
+        26  -7408.6801      1993           42             12           
+        27  -7408.6801      1993           42             12           
+        28  -7408.6801      1993           42             12           
+        29  -7408.6801      1993           42             12           
+        30  -7408.6801      1993           42             12           
+        31  -7408.6801      1993           42             12           
+        32  -7408.68        1993           42             12           
+        33  -7408.68        1993           42             12           
+        34  -7408.68        1993           42             12           
+        35  -7408.68        1993           42             12           
+        36  -7408.68        1993           42             12           
+        37  -7408.68        1993           42             12           
+        38  -7408.68        1993           42             12           
+        39  -7408.68        1993           42             12           
+        40  -7408.6801      1993           42             12           
+        41  -7408.6801      1993           42             12           
+        42  -7408.6801      1993           42             12           
+        43  -7408.6801      1993           42             12           
+        44  -7408.6801      1993           42             12           
+        45  -7408.6801      1993           42             12           
+        46  -7408.6801      1993           42             12           
+        47  -7408.6801      1993           42             12           
+        48  -7408.6801      1993           42             12           
+        49  -7408.6802      1993           42             12           
+        50  -7408.6802      1993           42             12           
+        51  -7408.6802      1993           42             12           
+        52  -7408.6802      1993           42             12           
+        53  -7408.6802      1993           42             12           
+        54  -7408.6802      1993           42             12           
+        55  -7408.6802      1993           42             12           
+        56  -7408.6802      1993           42             12           
+        57  -7408.6802      1993           42             12           
+        58  -7408.6802      1993           42             12           
+        59  -7408.6801      1993           42             12           
+        60  -7408.6801      1993           42             12           
+        61  -7408.6801      1993           42             12           
+        62  -7408.6801      1993           42             12           
+        63  -7408.6801      1993           42             12           
+        64  -7408.68        1993           42             12           
+        65  -7408.68        1993           42             12           
+        66  -7408.68        1993           42             12           
+        67  -7408.68        1993           42             12           
+        68  -7408.68        1993           42             12           
+        69  -7408.6799      1993           42             12           
+        70  -7408.6799      1993           42             12           
+        71  -7408.6799      1993           42             12           
+        72  -7408.6799      1993           42             12           
+        73  -7408.6799      1993           42             12           
+        74  -7408.6799      1993           42             12           
+        75  -7408.6798      1993           42             12           
+        76  -7408.6798      1993           42             12           
+        77  -7408.6798      1993           42             12           
+        78  -7408.6798      1993           42             12           
+        79  -7408.6798      1993           42             12           
+        80  -7408.6798      1993           42             12           
+        81  -7408.6799      1993           42             12           
+        82  -7408.6799      1993           42             12           
+        83  -7408.6799      1993           42             12           
+        84  -7408.6799      1993           42             12           
+        85  -7408.6799      1993           42             12           
+        86  -7408.6799      1993           42             12           
+        87  -7408.6799      1993           42             12           
+        88  -7408.68        1993           42             12           
+        89  -7408.68        1993           42             12           
+        90  -7408.68        1993           42             12           
+        91  -7408.68        1993           42             12           
+        92  -7408.68        1993           42             12           
+        93  -7408.68        1993           42             12           
+        94  -7408.68        1993           42             12           
+        95  -7408.68        1993           42             12           
+        96  -7408.68        1993           42             12           
+        97  -7408.6801      1993           42             12           
+        98  -7408.6801      1993           42             12           
+        99  -7408.6801      1993           42             12           
+       100  -7408.6801      1993           42             12           
+Loop time of 1.65093 on 1 procs for 100 steps with 2047 atoms
+
+Performance: 5.233 ns/day, 4.586 hours/ns, 60.572 timesteps/s, 123.991 katom-step/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.6272     | 1.6272     | 1.6272     |   0.0 | 98.56
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.012716   | 0.012716   | 0.012716   |   0.0 |  0.77
+Output  | 0.0078409  | 0.0078409  | 0.0078409  |   0.0 |  0.47
+Modify  | 0.0013654  | 0.0013654  | 0.0013654  |   0.0 |  0.08
+Other   |            | 0.001839   |            |       |  0.11
+
+Nlocal:           2047 ave        2047 max        2047 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           7790 ave        7790 max        7790 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:       648022 ave      648022 max      648022 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 648022
+Ave neighs/atom = 316.57157
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:01

examples/PACKAGES/apip/log.02Apr25.vacancy.dynamic.lambda.no.thermostat.g++.1

@@ -0,0 +1,193 @@
+LAMMPS (2 Apr 2025 - Development - )
+Reading data file ...
+  orthogonal box = (0 0 0) to (28.92 28.92 28.92)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  2047 atoms
+  reading velocities ...
+  2047 velocities
+  read_data CPU = 0.009 seconds
+ACE version: 2023.11.25
+Recursive evaluator is used by ACE
+Loading ../../../potentials/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
+atomic load lambda:
+	fast potential: extract eam/apip:time_per_atom
+	precise potential: extract pace/apip:time_per_atom
+	lambda_input: extract lambda/input/apip:time_per_atom
+	lambda: extract lambda/zone/apip:time_per_atom
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+- fix lambda command: doi.org/10.1063/5.0245877
+The log file lists these citations in BibTeX format.
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+WARNING: The energy is not conserved when lambda changes as fix lambda_thermostat/apip is not used. (../fix_lambda_apip.cpp:248)
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 9.4
+  ghost atom cutoff = 9.4
+  binsize = 4.7, bins = 7 7 7
+  4 neighbor lists, perpetual/occasional/extra = 4 0 0
+  (1) pair eam/fs/apip, perpetual, trim from (3)
+      attributes: full, newton on, cut 7.50679
+      pair build: trim
+      stencil: none
+      bin: none
+  (2) pair pace/apip, perpetual
+      attributes: full, newton on, cut 9.4
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) pair lambda/input/csp/apip, perpetual, trim from (2)
+      attributes: full, newton on, cut 8
+      pair build: trim
+      stencil: none
+      bin: none
+  (4) pair lambda/zone/apip, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+Setting up Verlet run ...
+  Unit style    : metal
+  Current step  : 0
+  Time step     : 0.001
+Per MPI rank memory allocation (min/avg/max) = 49.37 | 49.37 | 49.37 Mbytes
+   Step         TotEng     c_lambda_types[1] c_lambda_types[2] c_lambda_types[3]
+         0  -7408.7649      1993           42             12           
+         1  -7408.7649      1993           42             12           
+         2  -7408.7649      1993           42             12           
+         3  -7408.765       1993           42             12           
+         4  -7408.7657      1993           42             12           
+         5  -7408.7785      1993           42             12           
+         6  -7408.7769      1993           42             12           
+         7  -7408.778       1993           42             12           
+         8  -7408.7862      1993           42             12           
+         9  -7408.79        1993           42             12           
+        10  -7408.7912      1993           42             12           
+        11  -7408.8005      1993           42             12           
+        12  -7408.8012      1993           42             12           
+        13  -7408.8016      1993           42             12           
+        14  -7408.8123      1993           42             12           
+        15  -7408.8154      1993           42             12           
+        16  -7408.8144      1993           42             12           
+        17  -7408.8271      1993           42             12           
+        18  -7408.8277      1993           42             12           
+        19  -7408.8289      1993           42             12           
+        20  -7408.8352      1993           42             12           
+        21  -7408.8376      1993           42             12           
+        22  -7408.841       1993           42             12           
+        23  -7408.8507      1993           42             12           
+        24  -7408.8496      1993           42             12           
+        25  -7408.8544      1993           42             12           
+        26  -7408.8645      1993           42             12           
+        27  -7408.8665      1993           42             12           
+        28  -7408.8713      1993           42             12           
+        29  -7408.8763      1993           42             12           
+        30  -7408.8812      1993           42             12           
+        31  -7408.8842      1993           42             12           
+        32  -7408.8905      1993           42             12           
+        33  -7408.8947      1993           42             12           
+        34  -7408.9048      1993           42             12           
+        35  -7408.9099      1993           42             12           
+        36  -7408.9101      1993           42             12           
+        37  -7408.9159      1993           42             12           
+        38  -7408.9256      1993           42             12           
+        39  -7408.9241      1993           42             12           
+        40  -7408.9342      1993           42             12           
+        41  -7408.9423      1993           42             12           
+        42  -7408.9402      1993           42             12           
+        43  -7408.9452      1993           42             12           
+        44  -7408.9548      1993           42             12           
+        45  -7408.9543      1993           42             12           
+        46  -7408.9607      1993           42             12           
+        47  -7408.9699      1993           42             12           
+        48  -7408.9751      1993           42             12           
+        49  -7408.978       1993           42             12           
+        50  -7408.9797      1993           42             12           
+        51  -7408.9851      1993           42             12           
+        52  -7408.9937      1993           42             12           
+        53  -7408.9977      1993           42             12           
+        54  -7408.9961      1993           42             12           
+        55  -7409.0011      1993           42             12           
+        56  -7409.0098      1993           42             12           
+        57  -7409.0132      1993           42             12           
+        58  -7409.0173      1993           42             12           
+        59  -7409.0174      1993           42             12           
+        60  -7409.0204      1993           42             12           
+        61  -7409.0259      1993           42             12           
+        62  -7409.0324      1993           42             12           
+        63  -7409.0365      1993           42             12           
+        64  -7409.0407      1993           42             12           
+        65  -7409.0407      1993           42             12           
+        66  -7409.0428      1993           42             12           
+        67  -7409.0437      1993           42             12           
+        68  -7409.0437      1993           42             12           
+        69  -7409.0502      1993           42             12           
+        70  -7409.0558      1993           42             12           
+        71  -7409.0572      1993           42             12           
+        72  -7409.0624      1993           42             12           
+        73  -7409.0686      1993           42             12           
+        74  -7409.0721      1993           42             12           
+        75  -7409.075       1993           42             12           
+        76  -7409.0751      1993           42             12           
+        77  -7409.0728      1993           42             12           
+        78  -7409.0732      1993           42             12           
+        79  -7409.0764      1993           42             12           
+        80  -7409.077       1993           42             12           
+        81  -7409.0879      1993           42             12           
+        82  -7409.0898      1993           42             12           
+        83  -7409.0922      1993           42             12           
+        84  -7409.0916      1993           42             12           
+        85  -7409.0928      1993           42             12           
+        86  -7409.0944      1993           42             12           
+        87  -7409.1058      1993           42             12           
+        88  -7409.1084      1993           42             12           
+        89  -7409.1103      1993           42             12           
+        90  -7409.1121      1993           42             12           
+        91  -7409.1145      1993           42             12           
+        92  -7409.1133      1993           42             12           
+        93  -7409.1166      1993           42             12           
+        94  -7409.12        1993           42             12           
+        95  -7409.119       1993           42             12           
+        96  -7409.1208      1993           42             12           
+        97  -7409.1217      1993           42             12           
+        98  -7409.1229      1993           42             12           
+        99  -7409.1235      1993           42             12           
+       100  -7409.1206      1993           42             12           
+Loop time of 2.01276 on 1 procs for 100 steps with 2047 atoms
+
+Performance: 4.293 ns/day, 5.591 hours/ns, 49.683 timesteps/s, 101.701 katom-step/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.985      | 1.985      | 1.985      |   0.0 | 98.62
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.012367   | 0.012367   | 0.012367   |   0.0 |  0.61
+Output  | 0.0080612  | 0.0080612  | 0.0080612  |   0.0 |  0.40
+Modify  | 0.0053111  | 0.0053111  | 0.0053111  |   0.0 |  0.26
+Other   |            | 0.002      |            |       |  0.10
+
+Nlocal:           2047 ave        2047 max        2047 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           7790 ave        7790 max        7790 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:       291196 ave      291196 max      291196 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 291196
+Ave neighs/atom = 142.25501
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:02

examples/PACKAGES/apip/log.02Apr25.vacancy.dynamic.lambda.thermostat.g++.1

@@ -0,0 +1,197 @@
+LAMMPS (2 Apr 2025 - Development - )
+Reading data file ...
+  orthogonal box = (0 0 0) to (28.92 28.92 28.92)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  2047 atoms
+  reading velocities ...
+  2047 velocities
+  read_data CPU = 0.009 seconds
+ACE version: 2023.11.25
+Recursive evaluator is used by ACE
+Loading ../../../potentials/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
+atomic load lambda:
+	fast potential: extract eam/apip:time_per_atom
+	precise potential: extract pace/apip:time_per_atom
+	lambda_input: extract lambda/input/apip:time_per_atom
+	lambda: extract lambda/zone/apip:time_per_atom
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+- fix lambda command: doi.org/10.1063/5.0245877
+The log file lists these citations in BibTeX format.
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 9.4
+  ghost atom cutoff = 9.4
+  binsize = 4.7, bins = 7 7 7
+  5 neighbor lists, perpetual/occasional/extra = 5 0 0
+  (1) pair eam/fs/apip, perpetual, trim from (3)
+      attributes: full, newton on, cut 7.50679
+      pair build: trim
+      stencil: none
+      bin: none
+  (2) pair pace/apip, perpetual
+      attributes: full, newton on, cut 9.4
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) pair lambda/input/csp/apip, perpetual, trim from (2)
+      attributes: full, newton on, cut 8
+      pair build: trim
+      stencil: none
+      bin: none
+  (4) pair lambda/zone/apip, perpetual
+      attributes: full, newton on, ghost
+      pair build: full/bin/ghost
+      stencil: full/ghost/bin/3d
+      bin: standard
+  (5) fix lambda_thermostat/apip, perpetual, copy from (2)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Setting up Verlet run ...
+  Unit style    : metal
+  Current step  : 0
+  Time step     : 0.001
+Per MPI rank memory allocation (min/avg/max) = 52.93 | 52.93 | 52.93 Mbytes
+   Step         TotEng     c_lambda_types[1] c_lambda_types[2] c_lambda_types[3]
+         0  -7408.7649      1993           42             12           
+         1  -7408.7649      1993           42             12           
+         2  -7408.7649      1993           42             12           
+         3  -7408.765       1993           42             12           
+         4  -7408.765       1993           42             12           
+         5  -7408.765       1993           42             12           
+         6  -7408.765       1993           42             12           
+         7  -7408.765       1993           42             12           
+         8  -7408.765       1993           42             12           
+         9  -7408.765       1993           42             12           
+        10  -7408.7651      1993           42             12           
+        11  -7408.7651      1993           42             12           
+        12  -7408.7651      1993           42             12           
+        13  -7408.7651      1993           42             12           
+        14  -7408.7651      1993           42             12           
+        15  -7408.7651      1993           42             12           
+        16  -7408.7652      1993           42             12           
+        17  -7408.7652      1993           42             12           
+        18  -7408.7652      1993           42             12           
+        19  -7408.7652      1993           42             12           
+        20  -7408.7652      1993           42             12           
+        21  -7408.7652      1993           42             12           
+        22  -7408.7652      1993           42             12           
+        23  -7408.7652      1993           42             12           
+        24  -7408.7652      1993           42             12           
+        25  -7408.7652      1993           42             12           
+        26  -7408.7652      1993           42             12           
+        27  -7408.7652      1993           42             12           
+        28  -7408.7652      1993           42             12           
+        29  -7408.7652      1993           42             12           
+        30  -7408.7652      1993           42             12           
+        31  -7408.7652      1993           42             12           
+        32  -7408.7652      1993           42             12           
+        33  -7408.7652      1993           42             12           
+        34  -7408.7652      1993           42             12           
+        35  -7408.7652      1993           42             12           
+        36  -7408.7652      1993           42             12           
+        37  -7408.7652      1993           42             12           
+        38  -7408.7652      1993           42             12           
+        39  -7408.7652      1993           42             12           
+        40  -7408.7652      1993           42             12           
+        41  -7408.7652      1993           42             12           
+        42  -7408.7652      1993           42             12           
+        43  -7408.7652      1993           42             12           
+        44  -7408.7652      1993           42             12           
+        45  -7408.7652      1993           42             12           
+        46  -7408.7652      1993           42             12           
+        47  -7408.7653      1993           42             12           
+        48  -7408.7653      1993           42             12           
+        49  -7408.7653      1993           42             12           
+        50  -7408.7653      1993           42             12           
+        51  -7408.7653      1993           42             12           
+        52  -7408.7653      1993           42             12           
+        53  -7408.7653      1993           42             12           
+        54  -7408.7653      1993           42             12           
+        55  -7408.7653      1993           42             12           
+        56  -7408.7653      1993           42             12           
+        57  -7408.7653      1993           42             12           
+        58  -7408.7653      1993           42             12           
+        59  -7408.7653      1993           42             12           
+        60  -7408.7652      1993           42             12           
+        61  -7408.7652      1993           42             12           
+        62  -7408.7652      1993           42             12           
+        63  -7408.7652      1993           42             12           
+        64  -7408.7652      1993           42             12           
+        65  -7408.7651      1993           42             12           
+        66  -7408.7651      1993           42             12           
+        67  -7408.7651      1993           42             12           
+        68  -7408.7651      1993           42             12           
+        69  -7408.7651      1993           42             12           
+        70  -7408.765       1993           42             12           
+        71  -7408.765       1993           42             12           
+        72  -7408.765       1993           42             12           
+        73  -7408.765       1993           42             12           
+        74  -7408.765       1993           42             12           
+        75  -7408.765       1993           42             12           
+        76  -7408.765       1993           42             12           
+        77  -7408.765       1993           42             12           
+        78  -7408.765       1993           42             12           
+        79  -7408.765       1993           42             12           
+        80  -7408.765       1993           42             12           
+        81  -7408.765       1993           42             12           
+        82  -7408.765       1993           42             12           
+        83  -7408.765       1993           42             12           
+        84  -7408.765       1993           42             12           
+        85  -7408.765       1993           42             12           
+        86  -7408.765       1993           42             12           
+        87  -7408.765       1993           42             12           
+        88  -7408.765       1993           42             12           
+        89  -7408.7651      1993           42             12           
+        90  -7408.7651      1993           42             12           
+        91  -7408.7651      1993           42             12           
+        92  -7408.7651      1993           42             12           
+        93  -7408.7651      1993           42             12           
+        94  -7408.7651      1993           42             12           
+        95  -7408.7651      1993           42             12           
+        96  -7408.7651      1993           42             12           
+        97  -7408.7651      1993           42             12           
+        98  -7408.7651      1993           42             12           
+        99  -7408.7651      1993           42             12           
+       100  -7408.7651      1993           42             12           
+Loop time of 2.19492 on 1 procs for 100 steps with 2047 atoms
+
+Performance: 3.936 ns/day, 6.097 hours/ns, 45.560 timesteps/s, 93.261 katom-step/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.0683     | 2.0683     | 2.0683     |   0.0 | 94.23
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.012156   | 0.012156   | 0.012156   |   0.0 |  0.55
+Output  | 0.0084851  | 0.0084851  | 0.0084851  |   0.0 |  0.39
+Modify  | 0.10386    | 0.10386    | 0.10386    |   0.0 |  4.73
+Other   |            | 0.002096   |            |       |  0.10
+
+Nlocal:           2047 ave        2047 max        2047 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           7790 ave        7790 max        7790 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:       291196 ave      291196 max      291196 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 291196
+Ave neighs/atom = 142.25501
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:02

examples/PACKAGES/apip/log.02Apr25.validate.g++.1

@@ -0,0 +1,201 @@
+LAMMPS (2 Apr 2025 - Development - )
+Reading data file ...
+  orthogonal box = (0 0 0) to (7.23 7.23 7.23)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  31 atoms
+  reading velocities ...
+  31 velocities
+  read_data CPU = 0.002 seconds
+ACE version: 2023.11.25
+Recursive evaluator is used
+Loading Cu-1.yace
+Total number of basis functions
+	Cu: 15 (r=1) 9 (r>1)
+Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.9
+  ghost atom cutoff = 5.9
+  binsize = 2.95, bins = 3 3 3
+  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
+Setting up Verlet run ...
+  Unit style    : metal
+  Current step  : 0
+  Time step     : 0.001
+Per MPI rank memory allocation (min/avg/max) = 4.908 | 4.908 | 4.908 Mbytes
+   Step         PotEng         Fnorm           Fmax     
+         0  -98.699376      49.367618      19.563052    
+Loop time of 6.74e-07 on 1 procs for 0 steps with 31 atoms
+
+148.4% 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          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 6.74e-07   |            |       |100.00
+
+Nlocal:             31 ave          31 max          31 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            616 ave         616 max         616 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:         2132 ave        2132 max        2132 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2132
+Ave neighs/atom = 68.774194
+Neighbor list builds = 0
+Dangerous builds = 0
+ACE version: 2023.11.25
+Recursive evaluator is used by ACE
+Loading Cu-1.yace
+Total number of basis functions
+	Cu: 15 (r=1) 9 (r>1)
+Mapping LAMMPS atom type #1(Cu) -> ACE species type #0
+Setting atom values ...
+  31 settings made for apip/lambda
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.50679
+  ghost atom cutoff = 7.50679
+  binsize = 3.753395, bins = 2 2 2
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/fs/apip, perpetual
+      attributes: full, newton on, cut 7.50679
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (2) pair pace/apip, perpetual, copy from (1)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Setting up Verlet run ...
+  Unit style    : metal
+  Current step  : 0
+  Time step     : 0.001
+Per MPI rank memory allocation (min/avg/max) = 5.564 | 5.564 | 5.564 Mbytes
+   Step         PotEng         Fnorm           Fmax     
+         0  -98.699376      49.367618      19.563052    
+Loop time of 5.62e-07 on 1 procs for 0 steps with 31 atoms
+
+177.9% 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          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 5.62e-07   |            |       |100.00
+
+Nlocal:             31 ave          31 max          31 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            957 ave         957 max         957 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:         4558 ave        4558 max        4558 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 4558
+Ave neighs/atom = 147.03226
+Neighbor list builds = 0
+Dangerous builds = 0
+Setting atom values ...
+  31 settings made for apip/lambda
+Setting up Verlet run ...
+  Unit style    : metal
+  Current step  : 0
+  Time step     : 0.001
+Per MPI rank memory allocation (min/avg/max) = 5.564 | 5.564 | 5.564 Mbytes
+   Step         PotEng         Fnorm           Fmax     
+         0  -85.025323      53.839249      22.182149    
+Loop time of 5.49e-07 on 1 procs for 0 steps with 31 atoms
+
+182.1% 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          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 5.49e-07   |            |       |100.00
+
+Nlocal:             31 ave          31 max          31 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            957 ave         957 max         957 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:         4558 ave        4558 max        4558 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 4558
+Ave neighs/atom = 147.03226
+Neighbor list builds = 0
+Dangerous builds = 0
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.50679
+  ghost atom cutoff = 7.50679
+  binsize = 3.753395, bins = 2 2 2
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair eam/fs, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Setting up Verlet run ...
+  Unit style    : metal
+  Current step  : 0
+  Time step     : 0.001
+Per MPI rank memory allocation (min/avg/max) = 5.183 | 5.183 | 5.183 Mbytes
+   Step         PotEng         Fnorm           Fmax     
+         0  -85.025323      53.839249      22.182149    
+Loop time of 4.77e-07 on 1 procs for 0 steps with 31 atoms
+
+0.0% 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          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 4.77e-07   |            |       |100.00
+
+Nlocal:             31 ave          31 max          31 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            957 ave         957 max         957 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           2279 ave        2279 max        2279 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 2279
+Ave neighs/atom = 73.516129
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00

examples/PACKAGES/neighbor-swap/MoCoNiVFeAlCr_2nn.meam

@@ -1 +0,0 @@
-../../../potentials/MoCoNiVFeAlCr_2nn.meam

examples/PACKAGES/neighbor-swap/in.KMC_pulse_center

@@ -1,46 +0,0 @@
-# May 2025
-# Test script for MD-KMC accelerated diffusion testing in LAMMPS
-# Created by Jacob Tavenner, Baylor University
-
-# Initiation -------------------------------------
-units           metal
-dimension       3
-boundary        p p p
-atom_style      atomic
-
-# Atom Definition --------------------------------
-lattice fcc 3.762
-region          whole block 0 1 0 1 0 1
-create_box      2 whole
-create_atoms    1 region whole
-
-replicate 6 16 6
-
-region      puck block INF INF 7 9 INF INF 
-set         region puck type 2
-
-# Force Fields -----------------------------------
-pair_style      meam
-pair_coeff      * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
-
-# Settings ---------------------------------------
-timestep        0.002
-thermo          100
-
-# Computations -----------------------------------
-compute         voroN all voronoi/atom neighbors yes
-
-run             0
-thermo_style    custom step temp press pxx pyy pzz lx ly lz vol pe
-
-# Execution --------------------------------------
-
-velocity    all create 2400 908124 loop geom
-fix         temp all npt temp 1000 1000 1000 aniso 0 0 1
-fix         mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
-thermo_style    custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
-#dump           dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
-
-run 1000
-
-#write_data     pulse_center.data

examples/PACKAGES/neighbor-swap/in.KMC_pulse_edge

@@ -1,47 +0,0 @@
-# May 2025
-# Test script for MD-KMC accelerated diffusion testing in LAMMPS
-# Created by Jacob Tavenner, Baylor University
-
-# Initiation -------------------------------------
-units           metal
-dimension       3
-boundary        p p p
-atom_style      atomic
-
-
-# Atom Definition --------------------------------
-lattice fcc 3.762
-region          whole block 0 1 0 1 0 1
-create_box      2 whole
-create_atoms    1 region whole
-
-replicate 6 16 6
-
-region      puck block INF INF INF 2 INF INF 
-set         region puck type 2
-
-# Force Fields -----------------------------------
-pair_style      meam
-pair_coeff      * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
-
-# Settings ---------------------------------------
-timestep        0.002
-thermo          100
-
-# Computations -----------------------------------
-compute         voroN all voronoi/atom neighbors yes
-
-run             0
-thermo_style    custom step temp press pxx pyy pzz lx ly lz vol pe
-
-# Execution --------------------------------------
-
-velocity    all create 2400 908124 loop geom
-fix         temp all npt temp 1000 1000 1000 aniso 0 0 1
-fix         mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
-thermo_style    custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
-#dump           dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
-
-run 1000
-
-#write_data     pulse_end.data

examples/PACKAGES/neighbor-swap/library_2nn.meam

@@ -1 +0,0 @@
-../../../potentials/library_2nn.meam

examples/PACKAGES/neighbor-swap/log.22May22.KMC_pulse_center.g++.1

@@ -1,154 +0,0 @@
-LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-384-g88bc7dc720-modified)
-  using 1 OpenMP thread(s) per MPI task
-# May 2025
-# Test script for MD-KMC accelerated diffusion testing in LAMMPS
-# Created by Jacob Tavenner, Baylor University
-
-# Initiation -------------------------------------
-units		metal
-dimension	3
-boundary	p p p
-atom_style	atomic
-
-# Atom Definition --------------------------------
-lattice	fcc 3.762
-Lattice spacing in x,y,z = 3.762 3.762 3.762
-region		whole block 0 1 0 1 0 1
-create_box	2 whole
-Created orthogonal box = (0 0 0) to (3.762 3.762 3.762)
-  1 by 1 by 1 MPI processor grid
-create_atoms	1 region whole
-Created 4 atoms
-  using lattice units in orthogonal box = (0 0 0) to (3.762 3.762 3.762)
-  create_atoms CPU = 0.000 seconds
-
-replicate 6 16 6
-Replication is creating a 6x16x6 = 576 times larger system...
-  orthogonal box = (0 0 0) to (22.572 60.192 22.572)
-  1 by 1 by 1 MPI processor grid
-  2304 atoms
-  replicate CPU = 0.000 seconds
-
-region      puck block INF INF 7 9 INF INF
-set         region puck type 2
-Setting atom values ...
-  360 settings made for type
-
-# Force Fields -----------------------------------
-pair_style	meam
-pair_coeff	* * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
-Reading MEAM library file library_2nn.meam with DATE: 2024-08-08
-Reading MEAM potential file MoCoNiVFeAlCr_2nn.meam with DATE: 2024-08-08
-
-# Settings ---------------------------------------
-timestep	0.002
-thermo		100
-
-# Computations -----------------------------------
-compute		voroN all voronoi/atom neighbors yes
-
-run		0
-WARNING: No fixes with time integration, atoms won't move
-For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
-Neighbor list info ...
-  update: every = 1 steps, delay = 0 steps, check = yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.8
-  ghost atom cutoff = 6.8
-  binsize = 3.4, bins = 7 18 7
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair meam, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-  (2) pair meam, perpetual, half/full from (1)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes
-   Step          Temp          E_pair         E_mol          TotEng         Press     
-         0   0             -9674.3728      0             -9674.3728     -212400.94    
-Loop time of 1.202e-06 on 1 procs for 0 steps with 2304 atoms
-
-0.0% 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          | 0          | 0          |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0          | 0          | 0          |   0.0 |  0.00
-Output  | 0          | 0          | 0          |   0.0 |  0.00
-Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 1.202e-06  |            |       |100.00
-
-Nlocal:           2304 ave        2304 max        2304 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:           4735 ave        4735 max        4735 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:          99072 ave       99072 max       99072 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:       198144 ave      198144 max      198144 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 198144
-Ave neighs/atom = 86
-Neighbor list builds = 0
-Dangerous builds = 0
-thermo_style	custom step temp press pxx pyy pzz lx ly lz vol pe
-
-# Execution --------------------------------------
-
-velocity    all create 2400 908124
-fix         temp all npt temp 1000 1000 1000 aniso 0 0 1
-fix         mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
-thermo_style	custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
-#dump		dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
-
-run 1000
-Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes
-   Step          Temp          Press           Pxx            Pyy            Pzz             Lx             Ly             Lz           Volume         PotEng        f_mc[1]        f_mc[2]    
-         0   2400          -187517.52     -187403.07     -187750.14     -187399.35      22.572         60.192         22.572         30667.534     -9674.3728      0              0            
-       100   1664.9956      14000          14280.682      15095.077      12624.241      21.635315      57.726568      21.64791       27036.778     -9592.8978      24             22           
-       200   1560.0093     -5452.2434     -5749.5816     -2957.4228     -7649.7258      21.734212      58.085959      21.724853      27426.596     -9562.8822      48             45           
-       300   1586.4553      2030.9253      2776.4677      775.50538      2540.803       21.678654      58.101753      21.654423      27275.215     -9571.1308      72             66           
-       400   1603.6896     -223.16773      156.17673     -478.47929     -347.20061      21.701021      58.098904      21.657752      27306.213     -9576.4456      96             90           
-       500   1618.236      -925.51874     -1640.9078      451.6228      -1587.2713      21.718334      58.042685      21.666081      27312.054     -9581.2045      120            110          
-       600   1581.9995      290.10126      1359.1314      1407.5434     -1896.371       21.679813      58.086147      21.692118      27316.815     -9570.4803      144            132          
-       700   1568.3261      1387.3472      938.81523      2159.3686      1063.8577      21.685928      58.075626      21.67273       27295.153     -9566.2914      168            155          
-       800   1607.1531      46.792964     -453.90265     -1533.3908      2127.6723      21.685188      58.202356      21.628338      27297.753     -9577.7848      192            177          
-       900   1573.4747     -84.225488      548.90935     -1356.7479      555.16208      21.69634       58.150052      21.651847      27316.908     -9567.7039      216            196          
-      1000   1609.2136      1215.0833      764.08936      3301.0811     -419.92053      21.683731      58.000401      21.68726       27275.31      -9578.2843      240            219          
-Loop time of 31.6263 on 1 procs for 1000 steps with 2304 atoms
-
-Performance: 5.464 ns/day, 4.393 hours/ns, 31.619 timesteps/s, 72.851 katom-step/s
-99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 28.487     | 28.487     | 28.487     |   0.0 | 90.07
-Neigh   | 0.22789    | 0.22789    | 0.22789    |   0.0 |  0.72
-Comm    | 0.010808   | 0.010808   | 0.010808   |   0.0 |  0.03
-Output  | 0.00033526 | 0.00033526 | 0.00033526 |   0.0 |  0.00
-Modify  | 2.8963     | 2.8963     | 2.8963     |   0.0 |  9.16
-Other   |            | 0.003905   |            |       |  0.01
-
-Nlocal:           2304 ave        2304 max        2304 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:           4750 ave        4750 max        4750 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:         130023 ave      130023 max      130023 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:       260046 ave      260046 max      260046 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 260046
-Ave neighs/atom = 112.86719
-Neighbor list builds = 65
-Dangerous builds = 0
-
-#write_data	pulse_center.data
-Total wall time: 0:00:31

examples/PACKAGES/neighbor-swap/log.22May22.KMC_pulse_center.g++.4

@@ -1,154 +0,0 @@
-LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-384-g88bc7dc720-modified)
-  using 1 OpenMP thread(s) per MPI task
-# May 2025
-# Test script for MD-KMC accelerated diffusion testing in LAMMPS
-# Created by Jacob Tavenner, Baylor University
-
-# Initiation -------------------------------------
-units		metal
-dimension	3
-boundary	p p p
-atom_style	atomic
-
-# Atom Definition --------------------------------
-lattice	fcc 3.762
-Lattice spacing in x,y,z = 3.762 3.762 3.762
-region		whole block 0 1 0 1 0 1
-create_box	2 whole
-Created orthogonal box = (0 0 0) to (3.762 3.762 3.762)
-  1 by 2 by 2 MPI processor grid
-create_atoms	1 region whole
-Created 4 atoms
-  using lattice units in orthogonal box = (0 0 0) to (3.762 3.762 3.762)
-  create_atoms CPU = 0.000 seconds
-
-replicate 6 16 6
-Replication is creating a 6x16x6 = 576 times larger system...
-  orthogonal box = (0 0 0) to (22.572 60.192 22.572)
-  1 by 4 by 1 MPI processor grid
-  2304 atoms
-  replicate CPU = 0.000 seconds
-
-region      puck block INF INF 7 9 INF INF
-set         region puck type 2
-Setting atom values ...
-  360 settings made for type
-
-# Force Fields -----------------------------------
-pair_style	meam
-pair_coeff	* * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
-Reading MEAM library file library_2nn.meam with DATE: 2024-08-08
-Reading MEAM potential file MoCoNiVFeAlCr_2nn.meam with DATE: 2024-08-08
-
-# Settings ---------------------------------------
-timestep	0.002
-thermo		100
-
-# Computations -----------------------------------
-compute		voroN all voronoi/atom neighbors yes
-
-run		0
-WARNING: No fixes with time integration, atoms won't move
-For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
-Neighbor list info ...
-  update: every = 1 steps, delay = 0 steps, check = yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.8
-  ghost atom cutoff = 6.8
-  binsize = 3.4, bins = 7 18 7
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair meam, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-  (2) pair meam, perpetual, half/full from (1)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 9.636 | 9.636 | 9.636 Mbytes
-   Step          Temp          E_pair         E_mol          TotEng         Press     
-         0   0             -9674.3728      0             -9674.3728     -212400.94    
-Loop time of 1.422e-06 on 4 procs for 0 steps with 2304 atoms
-
-35.2% 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          | 0          | 0          |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0          | 0          | 0          |   0.0 |  0.00
-Output  | 0          | 0          | 0          |   0.0 |  0.00
-Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 1.422e-06  |            |       |100.00
-
-Nlocal:            576 ave         576 max         576 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Nghost:           2131 ave        2131 max        2131 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Neighs:          24768 ave       24768 max       24768 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-FullNghs:        49536 ave       49536 max       49536 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 198144
-Ave neighs/atom = 86
-Neighbor list builds = 0
-Dangerous builds = 0
-thermo_style	custom step temp press pxx pyy pzz lx ly lz vol pe
-
-# Execution --------------------------------------
-
-velocity    all create 2400 908124
-fix         temp all npt temp 1000 1000 1000 aniso 0 0 1
-fix         mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
-thermo_style	custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
-#dump		dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
-
-run 1000
-Per MPI rank memory allocation (min/avg/max) = 9.636 | 9.636 | 9.636 Mbytes
-   Step          Temp          Press           Pxx            Pyy            Pzz             Lx             Ly             Lz           Volume         PotEng        f_mc[1]        f_mc[2]    
-         0   2400          -187517.52     -187403.09     -187750.05     -187399.42      22.572         60.192         22.572         30667.534     -9674.3728      0              0            
-       100   1668.8754      13300.763      12419.304      15568.772      11914.212      21.636248      57.724775      21.647685      27036.823     -9594.7526      24             23           
-       200   1584.9699     -5686.0414     -4741.8496     -5914.7681     -6401.5064      21.729384      58.060532      21.730736      27415.923     -9571.0639      48             46           
-       300   1582.0473      2806.2983      3413.4122      2716.0124      2289.4702      21.6679        58.033587      21.694744      27280.402     -9570.5549      72             69           
-       400   1582.5825      845.29268     -849.61221      2123.5339      1261.9563      21.676298      58.14253       21.656418      27293.905     -9570.7948      96             93           
-       500   1591.7285     -501.17955      1151.9743     -1719.3712     -936.14174      21.696367      58.157211      21.648308      27315.839     -9573.5089      120            116          
-       600   1610.708      -821.74669     -1002.4957      291.88502     -1754.6294      21.730338      58.008213      21.661226      27304.8       -9579.5573      144            138          
-       700   1598.5176     -590.00633     -1844.42        408.97706     -334.57602      21.712908      57.96131       21.698129      27307.281     -9575.8973      168            162          
-       800   1584.3478      330.16711      666.88818      74.698331      248.91482      21.650908      58.045055      21.719838      27295.933     -9571.9268      192            186          
-       900   1557.9946      1471.1207      2124.6512      1526.9937      761.71731      21.645578      58.156083      21.681637      27293.323     -9564.4385      216            207          
-      1000   1582.5312      379.57005     -602.96446      2696.737      -955.06238      21.655418      58.231248      21.649581      27300.598     -9571.9879      240            227          
-Loop time of 9.1632 on 4 procs for 1000 steps with 2304 atoms
-
-Performance: 18.858 ns/day, 1.273 hours/ns, 109.132 timesteps/s, 251.440 katom-step/s
-98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 7.867      | 7.9923     | 8.1311     |   4.3 | 87.22
-Neigh   | 0.054997   | 0.057518   | 0.060145   |   1.0 |  0.63
-Comm    | 0.017529   | 0.14801    | 0.27408    |  29.5 |  1.62
-Output  | 0.00015963 | 0.00017216 | 0.00020869 |   0.0 |  0.00
-Modify  | 0.95227    | 0.96325    | 0.9917     |   1.7 | 10.51
-Other   |            | 0.001983   |            |       |  0.02
-
-Nlocal:            576 ave         609 max         540 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Nghost:         2161.5 ave        2173 max        2151 min
-Histogram: 1 0 1 0 0 0 1 0 0 1
-Neighs:        32450.2 ave       35422 max       29271 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-FullNghs:      64900.5 ave       70800 max       58684 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-
-Total # of neighbors = 259602
-Ave neighs/atom = 112.67448
-Neighbor list builds = 62
-Dangerous builds = 0
-
-#write_data	pulse_center.data
-Total wall time: 0:00:09

examples/PACKAGES/neighbor-swap/log.22May22.KMC_pulse_edge.g++.1

@@ -1,155 +0,0 @@
-LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-384-g88bc7dc720-modified)
-  using 1 OpenMP thread(s) per MPI task
-# May 2025
-# Test script for MD-KMC accelerated diffusion testing in LAMMPS
-# Created by Jacob Tavenner, Baylor University
-
-# Initiation -------------------------------------
-units		metal
-dimension	3
-boundary	p p p
-atom_style	atomic
-
-
-# Atom Definition --------------------------------
-lattice	fcc 3.762
-Lattice spacing in x,y,z = 3.762 3.762 3.762
-region		whole block 0 1 0 1 0 1
-create_box	2 whole
-Created orthogonal box = (0 0 0) to (3.762 3.762 3.762)
-  1 by 1 by 1 MPI processor grid
-create_atoms	1 region whole
-Created 4 atoms
-  using lattice units in orthogonal box = (0 0 0) to (3.762 3.762 3.762)
-  create_atoms CPU = 0.000 seconds
-
-replicate 6 16 6
-Replication is creating a 6x16x6 = 576 times larger system...
-  orthogonal box = (0 0 0) to (22.572 60.192 22.572)
-  1 by 1 by 1 MPI processor grid
-  2304 atoms
-  replicate CPU = 0.000 seconds
-
-region      puck block INF INF INF 2 INF INF
-set         region puck type 2
-Setting atom values ...
-  360 settings made for type
-
-# Force Fields -----------------------------------
-pair_style	meam
-pair_coeff	* * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
-Reading MEAM library file library_2nn.meam with DATE: 2024-08-08
-Reading MEAM potential file MoCoNiVFeAlCr_2nn.meam with DATE: 2024-08-08
-
-# Settings ---------------------------------------
-timestep	0.002
-thermo		100
-
-# Computations -----------------------------------
-compute		voroN all voronoi/atom neighbors yes
-
-run		0
-WARNING: No fixes with time integration, atoms won't move
-For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
-Neighbor list info ...
-  update: every = 1 steps, delay = 0 steps, check = yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.8
-  ghost atom cutoff = 6.8
-  binsize = 3.4, bins = 7 18 7
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair meam, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-  (2) pair meam, perpetual, half/full from (1)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes
-   Step          Temp          E_pair         E_mol          TotEng         Press     
-         0   0             -9674.3728      0             -9674.3728     -212400.94    
-Loop time of 1.232e-06 on 1 procs for 0 steps with 2304 atoms
-
-81.2% 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          | 0          | 0          |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0          | 0          | 0          |   0.0 |  0.00
-Output  | 0          | 0          | 0          |   0.0 |  0.00
-Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 1.232e-06  |            |       |100.00
-
-Nlocal:           2304 ave        2304 max        2304 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:           4735 ave        4735 max        4735 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:          99072 ave       99072 max       99072 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:       198144 ave      198144 max      198144 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 198144
-Ave neighs/atom = 86
-Neighbor list builds = 0
-Dangerous builds = 0
-thermo_style	custom step temp press pxx pyy pzz lx ly lz vol pe
-
-# Execution --------------------------------------
-
-velocity    all create 2400 908124 loop geom
-fix         temp all npt temp 1000 1000 1000 aniso 0 0 1
-fix         mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
-thermo_style	custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
-#dump		dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
-
-run 1000
-Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes
-   Step          Temp          Press           Pxx            Pyy            Pzz             Lx             Ly             Lz           Volume         PotEng        f_mc[1]        f_mc[2]    
-         0   2400          -187517.52     -187464.47     -188202.62     -186885.48      22.572         60.192         22.572         30667.534     -9674.3728      0              0            
-       100   1665.6154      14281.316      14426.547      14555.867      13861.534      21.637238      57.719793      21.637281      27022.733     -9594.4303      24             24           
-       200   1603.3309     -7325.7341     -8878.1524     -5333.0485     -7766.0015      21.710246      58.122827      21.725933      27415.106     -9577.4545      48             48           
-       300   1603.2974      207.19165      1983.4565     -1841.9518      480.07024      21.678227      58.079126      21.674033      27288.745     -9577.6391      72             69           
-       400   1600.1515      810.95054      1087.969       802.04946      542.83316      21.683731      58.045848      21.678505      27285.662     -9576.6508      96             92           
-       500   1629.8313     -2808.1005     -3197.9357      310.89931     -5537.265       21.683924      58.090375      21.697076      27330.229     -9585.5435      120            113          
-       600   1598.8232     -67.845623     -1573.0718     -1526.7607      2896.2957      21.70213       58.12191       21.653853      27313.504     -9576.4147      144            137          
-       700   1607.2185      154.66718     -1777.2469      2566.4705     -325.22208      21.712408      57.971553      21.678708      27287.033     -9579.1772      168            158          
-       800   1582.559      -891.23631     -632.46037     -636.88203     -1404.3665      21.671936      58.127004      21.678224      27308.594     -9571.6663      192            180          
-       900   1586.7172     -617.17083     -2495.5378     -2302.8766      2946.9018      21.658489      58.181921      21.668968      27305.771     -9572.9641      216            204          
-      1000   1607.563      -389.8113       810.4908       298.84287     -2278.7676      21.624573      58.076745      21.724272      27283.183     -9579.5034      240            227          
-Loop time of 31.7733 on 1 procs for 1000 steps with 2304 atoms
-
-Performance: 5.439 ns/day, 4.413 hours/ns, 31.473 timesteps/s, 72.514 katom-step/s
-99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 28.604     | 28.604     | 28.604     |   0.0 | 90.02
-Neigh   | 0.21293    | 0.21293    | 0.21293    |   0.0 |  0.67
-Comm    | 0.010645   | 0.010645   | 0.010645   |   0.0 |  0.03
-Output  | 0.00033194 | 0.00033194 | 0.00033194 |   0.0 |  0.00
-Modify  | 2.9411     | 2.9411     | 2.9411     |   0.0 |  9.26
-Other   |            | 0.00448    |            |       |  0.01
-
-Nlocal:           2304 ave        2304 max        2304 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:           4748 ave        4748 max        4748 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:         130301 ave      130301 max      130301 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:       260602 ave      260602 max      260602 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 260602
-Ave neighs/atom = 113.10851
-Neighbor list builds = 62
-Dangerous builds = 0
-
-#write_data	pulse_end.data
-Total wall time: 0:00:31

examples/PACKAGES/neighbor-swap/log.22May22.KMC_pulse_edge.g++.4

@@ -1,155 +0,0 @@
-LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-384-g88bc7dc720-modified)
-  using 1 OpenMP thread(s) per MPI task
-# May 2025
-# Test script for MD-KMC accelerated diffusion testing in LAMMPS
-# Created by Jacob Tavenner, Baylor University
-
-# Initiation -------------------------------------
-units		metal
-dimension	3
-boundary	p p p
-atom_style	atomic
-
-
-# Atom Definition --------------------------------
-lattice	fcc 3.762
-Lattice spacing in x,y,z = 3.762 3.762 3.762
-region		whole block 0 1 0 1 0 1
-create_box	2 whole
-Created orthogonal box = (0 0 0) to (3.762 3.762 3.762)
-  1 by 2 by 2 MPI processor grid
-create_atoms	1 region whole
-Created 4 atoms
-  using lattice units in orthogonal box = (0 0 0) to (3.762 3.762 3.762)
-  create_atoms CPU = 0.000 seconds
-
-replicate 6 16 6
-Replication is creating a 6x16x6 = 576 times larger system...
-  orthogonal box = (0 0 0) to (22.572 60.192 22.572)
-  1 by 4 by 1 MPI processor grid
-  2304 atoms
-  replicate CPU = 0.000 seconds
-
-region      puck block INF INF INF 2 INF INF
-set         region puck type 2
-Setting atom values ...
-  360 settings made for type
-
-# Force Fields -----------------------------------
-pair_style	meam
-pair_coeff	* * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
-Reading MEAM library file library_2nn.meam with DATE: 2024-08-08
-Reading MEAM potential file MoCoNiVFeAlCr_2nn.meam with DATE: 2024-08-08
-
-# Settings ---------------------------------------
-timestep	0.002
-thermo		100
-
-# Computations -----------------------------------
-compute		voroN all voronoi/atom neighbors yes
-
-run		0
-WARNING: No fixes with time integration, atoms won't move
-For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
-Neighbor list info ...
-  update: every = 1 steps, delay = 0 steps, check = yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 6.8
-  ghost atom cutoff = 6.8
-  binsize = 3.4, bins = 7 18 7
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair meam, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-  (2) pair meam, perpetual, half/full from (1)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 9.636 | 9.636 | 9.636 Mbytes
-   Step          Temp          E_pair         E_mol          TotEng         Press     
-         0   0             -9674.3728      0             -9674.3728     -212400.94    
-Loop time of 1.53e-06 on 4 procs for 0 steps with 2304 atoms
-
-65.4% 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          | 0          | 0          |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0          | 0          | 0          |   0.0 |  0.00
-Output  | 0          | 0          | 0          |   0.0 |  0.00
-Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 1.53e-06   |            |       |100.00
-
-Nlocal:            576 ave         576 max         576 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Nghost:           2131 ave        2131 max        2131 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Neighs:          24768 ave       24768 max       24768 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-FullNghs:        49536 ave       49536 max       49536 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 198144
-Ave neighs/atom = 86
-Neighbor list builds = 0
-Dangerous builds = 0
-thermo_style	custom step temp press pxx pyy pzz lx ly lz vol pe
-
-# Execution --------------------------------------
-
-velocity    all create 2400 908124 loop geom
-fix         temp all npt temp 1000 1000 1000 aniso 0 0 1
-fix         mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
-thermo_style	custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
-#dump		dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym
-
-run 1000
-Per MPI rank memory allocation (min/avg/max) = 9.636 | 9.636 | 9.636 Mbytes
-   Step          Temp          Press           Pxx            Pyy            Pzz             Lx             Ly             Lz           Volume         PotEng        f_mc[1]        f_mc[2]    
-         0   2400          -187517.52     -187464.47     -188202.62     -186885.48      22.572         60.192         22.572         30667.534     -9674.3728      0              0            
-       100   1665.569       14271.813      14638.855      14316.569      13860.016      21.63675       57.721065      21.637799      27023.366     -9594.291       24             24           
-       200   1598.6479     -6990.8349     -8574.1986     -5033.6147     -7364.6916      21.708963      58.123129      21.724821      27412.223     -9575.7322      48             47           
-       300   1604.388       456.43285      1926.408      -1214.1721      657.0626       21.673369      58.090421      21.671716      27285.018     -9577.698       72             70           
-       400   1601.1591      1303.6721      703.88473      1137.6607      2069.471       21.684004      58.049595      21.671161      27278.522     -9576.4811      96             94           
-       500   1623.6044     -2243.2478     -2084.532       320.87709     -4966.0885      21.686171      58.097101      21.695911      27334.758     -9583.1878      120            118          
-       600   1587.2041      421.60034      190.88741     -328.76599      1402.6796      21.712439      58.086039      21.655927      27312.229     -9572.559       144            141          
-       700   1591.2923      32.327829     -2893.2353      1839.7574      1150.4614      21.719102      57.999862      21.666164      27292.974     -9573.9009      168            165          
-       800   1580.8587     -105.51079      654.26389     -160.04168     -810.75457      21.670225      58.109245      21.684683      27306.229     -9570.6482      192            186          
-       900   1570.7648      1290.088       1252.3689      255.62548      2362.2695      21.68101       58.100507      21.658755      27283.051     -9567.9864      216            209          
-      1000   1598.1483     -125.35291     -3626.5479      3404.789      -154.29983      21.720146      57.952942      21.686111      27297.313     -9576.2975      240            231          
-Loop time of 9.17241 on 4 procs for 1000 steps with 2304 atoms
-
-Performance: 18.839 ns/day, 1.274 hours/ns, 109.023 timesteps/s, 251.188 katom-step/s
-98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 7.7477     | 8.0143     | 8.1344     |   5.5 | 87.37
-Neigh   | 0.050543   | 0.056882   | 0.05986    |   1.6 |  0.62
-Comm    | 0.069784   | 0.16898    | 0.40996    |  34.2 |  1.84
-Output  | 0.00015612 | 0.0001707  | 0.00021249 |   0.0 |  0.00
-Modify  | 0.90628    | 0.93003    | 0.96157    |   2.2 | 10.14
-Other   |            | 0.002053   |            |       |  0.02
-
-Nlocal:            576 ave         614 max         505 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-Nghost:        2165.75 ave        2204 max        2132 min
-Histogram: 1 0 0 0 2 0 0 0 0 1
-Neighs:        32430.8 ave       35552 max       26564 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-FullNghs:      64861.5 ave       71111 max       53164 min
-Histogram: 1 0 0 0 0 0 1 0 0 2
-
-Total # of neighbors = 259446
-Ave neighs/atom = 112.60677
-Neighbor list builds = 62
-Dangerous builds = 0
-
-#write_data	pulse_end.data
-Total wall time: 0:00:09

examples/PACKAGES/reaction/tiny_nylon_json/in.tiny_nylon.stabilized

@@ -0,0 +1,61 @@
+# two monomer nylon example
+# reaction produces a condensed water molecule
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+special_bonds lj/coul 0 0 1
+pair_modify tail yes mix sixthpower
+
+read_data tiny_nylon.data &
+  extra/bond/per/atom 5  &
+  extra/angle/per/atom 15 &
+  extra/dihedral/per/atom 15 &
+  extra/improper/per/atom 25 &
+  extra/special/per/atom 25
+
+velocity all create 300.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_unreacted.json
+molecule mol2 rxn1_stp1_reacted.json
+molecule mol3 rxn1_stp2_unreacted.json
+molecule mol4 rxn1_stp2_reacted.json
+
+thermo 50
+
+# dump 1 all xyz 1 test_vis.xyz
+# dump_modify 1 types labels
+
+fix myrxns all bond/react stabilization yes statted_grp .03 &
+  react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
+  react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map rescale_charges yes
+
+fix 1 statted_grp_REACT nvt temp 300 300 100
+
+# optionally, you can customize behavior of reacting atoms,
+# by using the internally-created 'bond_react_MASTER_group', like so:
+fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
+
+thermo_style custom step temp press density f_myrxns[*]
+
+# restart 100 restart1 restart2
+
+run 10000
+
+# write_restart restart_longrun
+# write_data restart_longrun.data

examples/PACKAGES/reaction/tiny_nylon_json/log.tiny_nylon.stabilized.12Jun2025.g++.1

@@ -0,0 +1,444 @@
+LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-583-g5868aa095d-modified)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
+  using 1 OpenMP thread(s) per MPI task
+# two monomer nylon example
+# reaction produces a condensed water molecule
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+special_bonds lj/coul 0 0 1
+pair_modify tail yes mix sixthpower
+
+read_data tiny_nylon.data   extra/bond/per/atom 5    extra/angle/per/atom 15   extra/dihedral/per/atom 15   extra/improper/per/atom 25   extra/special/per/atom 25
+Reading data file ...
+  orthogonal box = (-25 -25 -25) to (25 25 25)
+  1 by 1 by 1 MPI processor grid
+  reading atom labelmap ...
+  reading bond labelmap ...
+  reading angle labelmap ...
+  reading dihedral labelmap ...
+  reading improper labelmap ...
+  reading atoms ...
+  44 atoms
+  reading velocities ...
+  44 velocities
+  scanning bonds ...
+  9 = max bonds/atom
+  scanning angles ...
+  21 = max angles/atom
+  scanning dihedrals ...
+  29 = max dihedrals/atom
+  scanning impropers ...
+  29 = max impropers/atom
+  orthogonal box = (-25 -25 -25) to (25 25 25)
+  1 by 1 by 1 MPI processor grid
+  reading bonds ...
+  42 bonds
+  reading angles ...
+  74 angles
+  reading dihedrals ...
+  100 dihedrals
+  reading impropers ...
+  16 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        1       
+  special bond factors coul:  0        0        1       
+     4 = max # of 1-2 neighbors
+     6 = max # of 1-3 neighbors
+    35 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.005 seconds
+
+velocity all create 300.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_unreacted.json
+Read molecule template mol1:
+(no title)
+  1 molecules
+  0 fragments
+  18 atoms with max type 0
+  16 bonds with max type 8
+  25 angles with max type 25
+  23 dihedrals with max type 33
+  2 impropers with max type 3
+molecule mol2 rxn1_stp1_reacted.json
+Read molecule template mol2:
+(no title)
+  1 molecules
+  0 fragments
+  18 atoms with max type 0
+  17 bonds with max type 11
+  31 angles with max type 24
+  39 dihedrals with max type 30
+  0 impropers with max type 0
+molecule mol3 rxn1_stp2_unreacted.json
+Read molecule template mol3:
+(no title)
+  1 molecules
+  0 fragments
+  15 atoms with max type 0
+  14 bonds with max type 11
+  25 angles with max type 24
+  30 dihedrals with max type 30
+  0 impropers with max type 0
+molecule mol4 rxn1_stp2_reacted.json
+Read molecule template mol4:
+(no title)
+  1 molecules
+  0 fragments
+  15 atoms with max type 0
+  13 bonds with max type 13
+  19 angles with max type 26
+  16 dihedrals with max type 29
+  2 impropers with max type 5
+
+thermo 50
+
+# dump 1 all xyz 1 test_vis.xyz
+# dump_modify 1 types labels
+
+fix myrxns all bond/react stabilization yes statted_grp .03   react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map rescale_charges yes
+WARNING: Fix bond/react: Atom affected by reaction rxn1 is too close to template edge (src/REACTION/fix_bond_react.cpp:2708)
+WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (src/REACTION/fix_bond_react.cpp:2708)
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp_REACT defined
+
+fix 1 statted_grp_REACT nvt temp 300 300 100
+
+# optionally, you can customize behavior of reacting atoms,
+# by using the internally-created 'bond_react_MASTER_group', like so:
+fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
+
+thermo_style custom step temp press density f_myrxns[*]
+
+# restart 100 restart1 restart2
+
+run 10000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
+
+@Article{Gissinger24,
+ author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
+ title = {Type Label Framework for Bonded Force Fields in LAMMPS},
+ journal = {J. Phys. Chem. B},
+ year =    2024,
+ volume =  128,
+ number =  13,
+ pages =   {3282--3297}
+}
+
+- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012, doi:10.1016/j.cpc.2024.109287
+
+@Article{Gissinger17,
+ author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
+ title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
+ journal = {Polymer},
+ year =    2017,
+ volume =  128,
+ pages =   {211--217}
+}
+
+@Article{Gissinger20,
+ author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
+ title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
+ journal = {Macromolecules},
+ year =    2020,
+ volume =  53,
+ number =  22,
+ pages =   {9953--9961}
+}
+
+@Article{Gissinger24,
+ author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
+ title = {Molecular Modeling of Reactive Systems with REACTER},
+ journal = {Computer Physics Communications},
+ year =    2024,
+ volume =  304,
+ number =  109287
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
+  G vector (1/distance) = 0.23408048
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.018627396
+  estimated relative force accuracy = 5.6095851e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 8000 3375
+Generated 55 of 55 mixed pair_coeff terms from sixthpower/sixthpower mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.5
+  ghost atom cutoff = 10.5
+  binsize = 5.25, bins = 10 10 10
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/class2/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+  (2) fix bond/react, occasional, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 34 | 34 | 34 Mbytes
+   Step          Temp          Press         Density      f_myrxns[1]    f_myrxns[2]  
+         0   300            357.25588      0.0034851739   0              0            
+        50   328.952       -39.291672      0.0034851739   1              0            
+       100   311.59495      29.741131      0.0034851739   1              1            
+       150   325.04965     -19.624049      0.0034851739   1              1            
+       200   313.15254      15.730975      0.0034851739   1              1            
+       250   307.88805     -22.944869      0.0034851739   1              1            
+       300   287.9343       6.7916738      0.0034851739   1              1            
+       350   314.40601      12.913246      0.0034851739   1              1            
+       400   304.58587      6.9804459      0.0034851739   1              1            
+       450   300.97668      14.68689       0.0034851739   1              1            
+       500   345.19498     -29.961085      0.0034851739   1              1            
+       550   229.37329      12.88087       0.0034851739   1              1            
+       600   239.75504     -3.575567       0.0034851739   1              1            
+       650   257.58951     -5.0844118      0.0034851739   1              1            
+       700   249.84121      22.825491      0.0034851739   1              1            
+       750   287.62022      28.059197      0.0034851739   1              1            
+       800   352.31339     -50.233738      0.0034851739   1              1            
+       850   316.12821      22.493396      0.0034851739   1              1            
+       900   283.85252      26.129698      0.0034851739   1              1            
+       950   290.30591     -25.743121      0.0034851739   1              1            
+      1000   346.57856     -2.1188627      0.0034851739   1              1            
+      1050   251.23391      20.636107      0.0034851739   1              1            
+      1100   267.48303     -15.912571      0.0034851739   1              1            
+      1150   282.66256      14.019753      0.0034851739   1              1            
+      1200   227.56518     -27.076623      0.0034851739   1              1            
+      1250   232.7204      -1.0387593      0.0034851739   1              1            
+      1300   277.28783      32.449571      0.0034851739   1              1            
+      1350   308.5732      -11.129035      0.0034851739   1              1            
+      1400   264.96641     -20.93416       0.0034851739   1              1            
+      1450   262.83931      30.82366       0.0034851739   1              1            
+      1500   276.23182     -24.480049      0.0034851739   1              1            
+      1550   319.00599     -9.8372065      0.0034851739   1              1            
+      1600   316.48228     -15.940319      0.0034851739   1              1            
+      1650   277.213        1.3856424      0.0034851739   1              1            
+      1700   302.34736     -27.623644      0.0034851739   1              1            
+      1750   312.06738     -52.786773      0.0034851739   1              1            
+      1800   232.82457     -8.2208725      0.0034851739   1              1            
+      1850   219.66312      0.0019676295   0.0034851739   1              1            
+      1900   245.49515     -24.208901      0.0034851739   1              1            
+      1950   262.40648     -1.8634047      0.0034851739   1              1            
+      2000   307.5184       10.588572      0.0034851739   1              1            
+      2050   316.54878      8.3925575      0.0034851739   1              1            
+      2100   318.99324      29.042199      0.0034851739   1              1            
+      2150   352.69886      18.443891      0.0034851739   1              1            
+      2200   326.32556     -38.670826      0.0034851739   1              1            
+      2250   333.73083      15.388091      0.0034851739   1              1            
+      2300   258.51644     -42.524581      0.0034851739   1              1            
+      2350   259.55019     -23.484535      0.0034851739   1              1            
+      2400   289.75114      28.367986      0.0034851739   1              1            
+      2450   312.34376      10.345659      0.0034851739   1              1            
+      2500   298.65847     -14.077573      0.0034851739   1              1            
+      2550   237.48617     -55.545493      0.0034851739   1              1            
+      2600   266.79718     -17.165884      0.0034851739   1              1            
+      2650   297.32794     -30.336059      0.0034851739   1              1            
+      2700   258.77594     -1.3622741      0.0034851739   1              1            
+      2750   240.05564     -0.4418629      0.0034851739   1              1            
+      2800   189.88737     -13.20747       0.0034851739   1              1            
+      2850   260.84014     -18.597276      0.0034851739   1              1            
+      2900   299.99473     -7.3249394      0.0034851739   1              1            
+      2950   377.90497      18.041664      0.0034851739   1              1            
+      3000   263.92156     -54.260856      0.0034851739   1              1            
+      3050   273.64003      26.973976      0.0034851739   1              1            
+      3100   276.52232     -3.8583179      0.0034851739   1              1            
+      3150   351.27802      84.899229      0.0034851739   1              1            
+      3200   327.48822     -10.339189      0.0034851739   1              1            
+      3250   356.11987      16.719201      0.0034851739   1              1            
+      3300   263.01966     -18.033913      0.0034851739   1              1            
+      3350   285.41196     -24.466282      0.0034851739   1              1            
+      3400   233.65271     -39.293739      0.0034851739   1              1            
+      3450   276.32895      44.300639      0.0034851739   1              1            
+      3500   300.42687      28.489275      0.0034851739   1              1            
+      3550   254.03142     -24.335427      0.0034851739   1              1            
+      3600   304.6963       4.5827938      0.0034851739   1              1            
+      3650   321.1785      -15.477109      0.0034851739   1              1            
+      3700   256.00258      25.354176      0.0034851739   1              1            
+      3750   356.60667     -5.4004451      0.0034851739   1              1            
+      3800   361.31092     -1.481153       0.0034851739   1              1            
+      3850   253.80196     -1.2120222      0.0034851739   1              1            
+      3900   258.01895      19.280499      0.0034851739   1              1            
+      3950   261.55352     -47.57161       0.0034851739   1              1            
+      4000   254.54757     -8.6460339      0.0034851739   1              1            
+      4050   301.56201      22.484551      0.0034851739   1              1            
+      4100   304.73035     -31.321217      0.0034851739   1              1            
+      4150   307.14343      0.5455717      0.0034851739   1              1            
+      4200   291.05765      51.79974       0.0034851739   1              1            
+      4250   333.73864     -24.668278      0.0034851739   1              1            
+      4300   370.55562     -11.922425      0.0034851739   1              1            
+      4350   408.03441      8.5963114      0.0034851739   1              1            
+      4400   329.13138     -25.679871      0.0034851739   1              1            
+      4450   366.98033      26.287047      0.0034851739   1              1            
+      4500   311.80954      31.766893      0.0034851739   1              1            
+      4550   292.28765      13.064974      0.0034851739   1              1            
+      4600   320.72746     -49.078838      0.0034851739   1              1            
+      4650   271.7173      -3.6846681      0.0034851739   1              1            
+      4700   305.69502      37.947369      0.0034851739   1              1            
+      4750   304.57521      52.411498      0.0034851739   1              1            
+      4800   299.22173      12.555443      0.0034851739   1              1            
+      4850   317.1756      -14.332118      0.0034851739   1              1            
+      4900   330.62798      23.762097      0.0034851739   1              1            
+      4950   342.34292     -21.428049      0.0034851739   1              1            
+      5000   415.76656      10.136854      0.0034851739   1              1            
+      5050   381.90086      18.17029       0.0034851739   1              1            
+      5100   380.63709      28.042746      0.0034851739   1              1            
+      5150   321.578        31.648896      0.0034851739   1              1            
+      5200   301.22258     -29.246031      0.0034851739   1              1            
+      5250   277.39891     -33.660526      0.0034851739   1              1            
+      5300   259.34417     -47.78529       0.0034851739   1              1            
+      5350   254.36079      10.616064      0.0034851739   1              1            
+      5400   242.39213      29.468553      0.0034851739   1              1            
+      5450   273.79403     -21.736668      0.0034851739   1              1            
+      5500   367.30713     -6.0185517      0.0034851739   1              1            
+      5550   309.52317      20.860119      0.0034851739   1              1            
+      5600   316.82746     -10.339826      0.0034851739   1              1            
+      5650   248.8707       33.659016      0.0034851739   1              1            
+      5700   314.30152      19.05817       0.0034851739   1              1            
+      5750   307.09966      14.458312      0.0034851739   1              1            
+      5800   313.07936      15.825371      0.0034851739   1              1            
+      5850   255.76382      23.890796      0.0034851739   1              1            
+      5900   274.57947     -0.19520339     0.0034851739   1              1            
+      5950   286.72486     -0.92397306     0.0034851739   1              1            
+      6000   304.60873     -4.3983652      0.0034851739   1              1            
+      6050   271.84784     -60.940602      0.0034851739   1              1            
+      6100   283.48258     -8.2903551      0.0034851739   1              1            
+      6150   336.07933     -8.2576526      0.0034851739   1              1            
+      6200   363.09919     -17.309847      0.0034851739   1              1            
+      6250   305.63822      14.475989      0.0034851739   1              1            
+      6300   274.59195      49.13711       0.0034851739   1              1            
+      6350   302.91015     -21.034604      0.0034851739   1              1            
+      6400   293.87945      0.74647589     0.0034851739   1              1            
+      6450   320.03843      47.624624      0.0034851739   1              1            
+      6500   329.4551      -52.788127      0.0034851739   1              1            
+      6550   320.74765      7.9598838      0.0034851739   1              1            
+      6600   290.63144     -19.66089       0.0034851739   1              1            
+      6650   266.9576       18.962642      0.0034851739   1              1            
+      6700   274.61389     -9.823603       0.0034851739   1              1            
+      6750   210.31417     -4.5767817      0.0034851739   1              1            
+      6800   258.23732      44.233497      0.0034851739   1              1            
+      6850   269.33119     -41.097429      0.0034851739   1              1            
+      6900   318.88077     -21.601871      0.0034851739   1              1            
+      6950   333.85796      26.067522      0.0034851739   1              1            
+      7000   320.59631     -44.226656      0.0034851739   1              1            
+      7050   348.15593      56.564077      0.0034851739   1              1            
+      7100   291.30894      7.6597589      0.0034851739   1              1            
+      7150   261.87574     -1.926724       0.0034851739   1              1            
+      7200   318.17418      61.577301      0.0034851739   1              1            
+      7250   269.73912     -41.921242      0.0034851739   1              1            
+      7300   235.40776     -7.8606915      0.0034851739   1              1            
+      7350   344.03017      73.910798      0.0034851739   1              1            
+      7400   335.03212      13.288114      0.0034851739   1              1            
+      7450   350.0822      -22.899498      0.0034851739   1              1            
+      7500   360.69025     -78.556242      0.0034851739   1              1            
+      7550   316.85895     -26.533434      0.0034851739   1              1            
+      7600   271.65568      32.425371      0.0034851739   1              1            
+      7650   264.7899      -40.230568      0.0034851739   1              1            
+      7700   281.36612      8.9888402      0.0034851739   1              1            
+      7750   276.96176      1.8256977      0.0034851739   1              1            
+      7800   330.1516      -19.751957      0.0034851739   1              1            
+      7850   325.80791     -12.52799       0.0034851739   1              1            
+      7900   322.07086      35.21732       0.0034851739   1              1            
+      7950   310.09493     -37.779071      0.0034851739   1              1            
+      8000   309.87152      40.561377      0.0034851739   1              1            
+      8050   252.91862     -27.545616      0.0034851739   1              1            
+      8100   308.23471     -25.313089      0.0034851739   1              1            
+      8150   278.69561      19.299388      0.0034851739   1              1            
+      8200   270.81879      33.341696      0.0034851739   1              1            
+      8250   312.58182      19.404863      0.0034851739   1              1            
+      8300   302.20303      19.388391      0.0034851739   1              1            
+      8350   299.55144     -12.952851      0.0034851739   1              1            
+      8400   330.13129     -34.998178      0.0034851739   1              1            
+      8450   281.66968      24.865214      0.0034851739   1              1            
+      8500   262.4416       1.0196786      0.0034851739   1              1            
+      8550   268.47784      44.761905      0.0034851739   1              1            
+      8600   274.80898      8.6257741      0.0034851739   1              1            
+      8650   264.82423     -3.9236534      0.0034851739   1              1            
+      8700   268.88205      3.7102664      0.0034851739   1              1            
+      8750   315.78315     -44.215318      0.0034851739   1              1            
+      8800   280.19362     -4.2172962      0.0034851739   1              1            
+      8850   331.88665      58.274571      0.0034851739   1              1            
+      8900   314.70472      36.746006      0.0034851739   1              1            
+      8950   395.82228      53.308443      0.0034851739   1              1            
+      9000   351.95636      29.133084      0.0034851739   1              1            
+      9050   369.74695     -37.487774      0.0034851739   1              1            
+      9100   259.4453      -2.1826545      0.0034851739   1              1            
+      9150   294.9952      -44.357151      0.0034851739   1              1            
+      9200   273.94092      12.07438       0.0034851739   1              1            
+      9250   257.18809     -29.792606      0.0034851739   1              1            
+      9300   269.54343     -19.617554      0.0034851739   1              1            
+      9350   301.09849     -26.979046      0.0034851739   1              1            
+      9400   316.93675     -46.890327      0.0034851739   1              1            
+      9450   304.52185     -8.8525101      0.0034851739   1              1            
+      9500   371.73494      11.979311      0.0034851739   1              1            
+      9550   291.23417      8.1900851      0.0034851739   1              1            
+      9600   359.20912      38.693544      0.0034851739   1              1            
+      9650   321.73443      33.448943      0.0034851739   1              1            
+      9700   362.4237       36.54429       0.0034851739   1              1            
+      9750   296.19875     -11.425255      0.0034851739   1              1            
+      9800   329.9426       16.039783      0.0034851739   1              1            
+      9850   296.79216      40.176303      0.0034851739   1              1            
+      9900   345.63868      43.479483      0.0034851739   1              1            
+      9950   282.27772     -49.08352       0.0034851739   1              1            
+     10000   286.24393     -12.060687      0.0034851739   1              1            
+Loop time of 1.29509 on 1 procs for 10000 steps with 44 atoms
+
+Performance: 667.133 ns/day, 0.036 hours/ns, 7721.451 timesteps/s, 339.744 katom-step/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    | 0.065326   | 0.065326   | 0.065326   |   0.0 |  5.04
+Bond    | 0.23111    | 0.23111    | 0.23111    |   0.0 | 17.84
+Kspace  | 0.94073    | 0.94073    | 0.94073    |   0.0 | 72.64
+Neigh   | 0.0032599  | 0.0032599  | 0.0032599  |   0.0 |  0.25
+Comm    | 0.0013719  | 0.0013719  | 0.0013719  |   0.0 |  0.11
+Output  | 0.00093869 | 0.00093869 | 0.00093869 |   0.0 |  0.07
+Modify  | 0.049692   | 0.049692   | 0.049692   |   0.0 |  3.84
+Other   |            | 0.002667   |            |       |  0.21
+
+Nlocal:             44 ave          44 max          44 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:             14 ave          14 max          14 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:            869 ave         869 max         869 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 869
+Ave neighs/atom = 19.75
+Ave special neighs/atom = 6.4090909
+Neighbor list builds = 209
+Dangerous builds = 0
+
+# write_restart restart_longrun
+# write_data restart_longrun.data
+Total wall time: 0:00:01

examples/PACKAGES/reaction/tiny_nylon_json/log.tiny_nylon.stabilized.12Jun2025.g++.4

@@ -0,0 +1,444 @@
+LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-583-g5868aa095d-modified)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
+  using 1 OpenMP thread(s) per MPI task
+# two monomer nylon example
+# reaction produces a condensed water molecule
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+special_bonds lj/coul 0 0 1
+pair_modify tail yes mix sixthpower
+
+read_data tiny_nylon.data   extra/bond/per/atom 5    extra/angle/per/atom 15   extra/dihedral/per/atom 15   extra/improper/per/atom 25   extra/special/per/atom 25
+Reading data file ...
+  orthogonal box = (-25 -25 -25) to (25 25 25)
+  1 by 2 by 2 MPI processor grid
+  reading atom labelmap ...
+  reading bond labelmap ...
+  reading angle labelmap ...
+  reading dihedral labelmap ...
+  reading improper labelmap ...
+  reading atoms ...
+  44 atoms
+  reading velocities ...
+  44 velocities
+  scanning bonds ...
+  9 = max bonds/atom
+  scanning angles ...
+  21 = max angles/atom
+  scanning dihedrals ...
+  29 = max dihedrals/atom
+  scanning impropers ...
+  29 = max impropers/atom
+  orthogonal box = (-25 -25 -25) to (25 25 25)
+  1 by 2 by 2 MPI processor grid
+  reading bonds ...
+  42 bonds
+  reading angles ...
+  74 angles
+  reading dihedrals ...
+  100 dihedrals
+  reading impropers ...
+  16 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        1       
+  special bond factors coul:  0        0        1       
+     4 = max # of 1-2 neighbors
+     6 = max # of 1-3 neighbors
+    35 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.006 seconds
+
+velocity all create 300.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_unreacted.json
+Read molecule template mol1:
+(no title)
+  1 molecules
+  0 fragments
+  18 atoms with max type 0
+  16 bonds with max type 8
+  25 angles with max type 25
+  23 dihedrals with max type 33
+  2 impropers with max type 3
+molecule mol2 rxn1_stp1_reacted.json
+Read molecule template mol2:
+(no title)
+  1 molecules
+  0 fragments
+  18 atoms with max type 0
+  17 bonds with max type 11
+  31 angles with max type 24
+  39 dihedrals with max type 30
+  0 impropers with max type 0
+molecule mol3 rxn1_stp2_unreacted.json
+Read molecule template mol3:
+(no title)
+  1 molecules
+  0 fragments
+  15 atoms with max type 0
+  14 bonds with max type 11
+  25 angles with max type 24
+  30 dihedrals with max type 30
+  0 impropers with max type 0
+molecule mol4 rxn1_stp2_reacted.json
+Read molecule template mol4:
+(no title)
+  1 molecules
+  0 fragments
+  15 atoms with max type 0
+  13 bonds with max type 13
+  19 angles with max type 26
+  16 dihedrals with max type 29
+  2 impropers with max type 5
+
+thermo 50
+
+# dump 1 all xyz 1 test_vis.xyz
+# dump_modify 1 types labels
+
+fix myrxns all bond/react stabilization yes statted_grp .03   react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map rescale_charges yes
+WARNING: Fix bond/react: Atom affected by reaction rxn1 is too close to template edge (src/REACTION/fix_bond_react.cpp:2708)
+WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (src/REACTION/fix_bond_react.cpp:2708)
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp_REACT defined
+
+fix 1 statted_grp_REACT nvt temp 300 300 100
+
+# optionally, you can customize behavior of reacting atoms,
+# by using the internally-created 'bond_react_MASTER_group', like so:
+fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
+
+thermo_style custom step temp press density f_myrxns[*]
+
+# restart 100 restart1 restart2
+
+run 10000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
+
+@Article{Gissinger24,
+ author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
+ title = {Type Label Framework for Bonded Force Fields in LAMMPS},
+ journal = {J. Phys. Chem. B},
+ year =    2024,
+ volume =  128,
+ number =  13,
+ pages =   {3282--3297}
+}
+
+- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012, doi:10.1016/j.cpc.2024.109287
+
+@Article{Gissinger17,
+ author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
+ title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
+ journal = {Polymer},
+ year =    2017,
+ volume =  128,
+ pages =   {211--217}
+}
+
+@Article{Gissinger20,
+ author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
+ title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
+ journal = {Macromolecules},
+ year =    2020,
+ volume =  53,
+ number =  22,
+ pages =   {9953--9961}
+}
+
+@Article{Gissinger24,
+ author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
+ title = {Molecular Modeling of Reactive Systems with REACTER},
+ journal = {Computer Physics Communications},
+ year =    2024,
+ volume =  304,
+ number =  109287
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
+  G vector (1/distance) = 0.23408048
+  grid = 15 15 15
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.018627396
+  estimated relative force accuracy = 5.6095851e-05
+  using double precision FFTW3
+  3d grid and FFT values/proc = 3380 960
+Generated 55 of 55 mixed pair_coeff terms from sixthpower/sixthpower mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10.5
+  ghost atom cutoff = 10.5
+  binsize = 5.25, bins = 10 10 10
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/class2/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+  (2) fix bond/react, occasional, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 33.49 | 33.72 | 34.28 Mbytes
+   Step          Temp          Press         Density      f_myrxns[1]    f_myrxns[2]  
+         0   300            357.25588      0.0034851739   0              0            
+        50   328.952       -39.291672      0.0034851739   1              0            
+       100   311.59495      29.741131      0.0034851739   1              1            
+       150   325.04965     -19.624049      0.0034851739   1              1            
+       200   313.15254      15.730975      0.0034851739   1              1            
+       250   307.88805     -22.944869      0.0034851739   1              1            
+       300   287.9343       6.7916738      0.0034851739   1              1            
+       350   314.40601      12.913246      0.0034851739   1              1            
+       400   304.58587      6.9804459      0.0034851739   1              1            
+       450   300.97668      14.68689       0.0034851739   1              1            
+       500   345.19498     -29.961085      0.0034851739   1              1            
+       550   229.37329      12.88087       0.0034851739   1              1            
+       600   239.75504     -3.575567       0.0034851739   1              1            
+       650   257.58951     -5.0844118      0.0034851739   1              1            
+       700   249.84121      22.825491      0.0034851739   1              1            
+       750   287.62022      28.059197      0.0034851739   1              1            
+       800   352.31339     -50.233738      0.0034851739   1              1            
+       850   316.12821      22.493396      0.0034851739   1              1            
+       900   283.85252      26.129698      0.0034851739   1              1            
+       950   290.30591     -25.743121      0.0034851739   1              1            
+      1000   346.57856     -2.1188627      0.0034851739   1              1            
+      1050   251.23391      20.636107      0.0034851739   1              1            
+      1100   267.48303     -15.912571      0.0034851739   1              1            
+      1150   282.66256      14.019753      0.0034851739   1              1            
+      1200   227.56518     -27.076623      0.0034851739   1              1            
+      1250   232.7204      -1.0387593      0.0034851739   1              1            
+      1300   277.28783      32.449571      0.0034851739   1              1            
+      1350   308.5732      -11.129035      0.0034851739   1              1            
+      1400   264.96641     -20.93416       0.0034851739   1              1            
+      1450   262.83931      30.82366       0.0034851739   1              1            
+      1500   276.23182     -24.480049      0.0034851739   1              1            
+      1550   319.00599     -9.8372065      0.0034851739   1              1            
+      1600   316.48228     -15.940319      0.0034851739   1              1            
+      1650   277.213        1.3856424      0.0034851739   1              1            
+      1700   302.34736     -27.623644      0.0034851739   1              1            
+      1750   312.06738     -52.786773      0.0034851739   1              1            
+      1800   232.82457     -8.2208725      0.0034851739   1              1            
+      1850   219.66312      0.0019675712   0.0034851739   1              1            
+      1900   245.49515     -24.2089        0.0034851739   1              1            
+      1950   262.40648     -1.8634053      0.0034851739   1              1            
+      2000   307.5184       10.588572      0.0034851739   1              1            
+      2050   316.54878      8.3925573      0.0034851739   1              1            
+      2100   318.99324      29.042199      0.0034851739   1              1            
+      2150   352.69886      18.443891      0.0034851739   1              1            
+      2200   326.32556     -38.670827      0.0034851739   1              1            
+      2250   333.73083      15.388091      0.0034851739   1              1            
+      2300   258.51644     -42.524579      0.0034851739   1              1            
+      2350   259.55019     -23.484534      0.0034851739   1              1            
+      2400   289.75114      28.367991      0.0034851739   1              1            
+      2450   312.34376      10.34566       0.0034851739   1              1            
+      2500   298.65847     -14.077574      0.0034851739   1              1            
+      2550   237.48617     -55.545492      0.0034851739   1              1            
+      2600   266.79719     -17.165888      0.0034851739   1              1            
+      2650   297.32793     -30.336065      0.0034851739   1              1            
+      2700   258.77594     -1.3622773      0.0034851739   1              1            
+      2750   240.05564     -0.44186476     0.0034851739   1              1            
+      2800   189.88736     -13.20747       0.0034851739   1              1            
+      2850   260.84014     -18.597268      0.0034851739   1              1            
+      2900   299.99469     -7.3249657      0.0034851739   1              1            
+      2950   377.90515      18.041562      0.0034851739   1              1            
+      3000   263.92164     -54.260872      0.0034851739   1              1            
+      3050   273.63965      26.974167      0.0034851739   1              1            
+      3100   276.52188     -3.8587984      0.0034851739   1              1            
+      3150   351.27821      84.898762      0.0034851739   1              1            
+      3200   327.48898     -10.338223      0.0034851739   1              1            
+      3250   356.1212       16.719521      0.0034851739   1              1            
+      3300   263.02135     -18.034405      0.0034851739   1              1            
+      3350   285.4132      -24.466598      0.0034851739   1              1            
+      3400   233.65385     -39.293822      0.0034851739   1              1            
+      3450   276.32817      44.300742      0.0034851739   1              1            
+      3500   300.43096      28.490491      0.0034851739   1              1            
+      3550   254.03694     -24.336803      0.0034851739   1              1            
+      3600   304.68561      4.5774591      0.0034851739   1              1            
+      3650   321.19694     -15.472971      0.0034851739   1              1            
+      3700   256.01801      25.355422      0.0034851739   1              1            
+      3750   356.6048      -5.4033701      0.0034851739   1              1            
+      3800   361.31685     -1.4920086      0.0034851739   1              1            
+      3850   253.81335     -1.20491        0.0034851739   1              1            
+      3900   257.99176      19.272863      0.0034851739   1              1            
+      3950   261.56599     -47.578625      0.0034851739   1              1            
+      4000   254.55501     -8.6462427      0.0034851739   1              1            
+      4050   301.57465      22.466646      0.0034851739   1              1            
+      4100   304.71812     -31.337506      0.0034851739   1              1            
+      4150   307.05688      0.54710967     0.0034851739   1              1            
+      4200   291.11678      51.789059      0.0034851739   1              1            
+      4250   333.71702     -24.64525       0.0034851739   1              1            
+      4300   370.53725     -11.852814      0.0034851739   1              1            
+      4350   407.98596      8.5128018      0.0034851739   1              1            
+      4400   329.43106     -25.637208      0.0034851739   1              1            
+      4450   366.91557      26.250029      0.0034851739   1              1            
+      4500   311.63134      31.61568       0.0034851739   1              1            
+      4550   292.18008      13.020734      0.0034851739   1              1            
+      4600   320.76549     -49.324846      0.0034851739   1              1            
+      4650   271.72115     -3.6666938      0.0034851739   1              1            
+      4700   305.52974      38.114013      0.0034851739   1              1            
+      4750   304.37057      52.050863      0.0034851739   1              1            
+      4800   300.50548      13.158616      0.0034851739   1              1            
+      4850   317.66606     -14.951608      0.0034851739   1              1            
+      4900   331.39591      23.823575      0.0034851739   1              1            
+      4950   340.899       -19.557136      0.0034851739   1              1            
+      5000   414.45112      8.7124515      0.0034851739   1              1            
+      5050   382.95479      18.555744      0.0034851739   1              1            
+      5100   381.26344      22.674486      0.0034851739   1              1            
+      5150   309.88477      36.184971      0.0034851739   1              1            
+      5200   312.4976      -31.403643      0.0034851739   1              1            
+      5250   285.1896      -36.180241      0.0034851739   1              1            
+      5300   249.68604     -55.078779      0.0034851739   1              1            
+      5350   251.76542      12.156887      0.0034851739   1              1            
+      5400   278.40908      15.846527      0.0034851739   1              1            
+      5450   281.22116     -12.005198      0.0034851739   1              1            
+      5500   362.38064     -14.608206      0.0034851739   1              1            
+      5550   287.39255      38.446058      0.0034851739   1              1            
+      5600   264.87699     -20.21112       0.0034851739   1              1            
+      5650   300.31424     -15.899086      0.0034851739   1              1            
+      5700   318.6444       18.688317      0.0034851739   1              1            
+      5750   321.74224     -7.5355749      0.0034851739   1              1            
+      5800   314.65871      33.512178      0.0034851739   1              1            
+      5850   307.11597     -16.492491      0.0034851739   1              1            
+      5900   259.10441     -49.668159      0.0034851739   1              1            
+      5950   292.09045     -22.04962       0.0034851739   1              1            
+      6000   243.99229     -15.110485      0.0034851739   1              1            
+      6050   276.66494     -21.052012      0.0034851739   1              1            
+      6100   328.39444      64.522811      0.0034851739   1              1            
+      6150   289.49991     -18.518616      0.0034851739   1              1            
+      6200   358.50076     -9.3115021      0.0034851739   1              1            
+      6250   303.15143     -42.618735      0.0034851739   1              1            
+      6300   297.17364      18.116143      0.0034851739   1              1            
+      6350   254.2382       2.4963759      0.0034851739   1              1            
+      6400   227.56255      23.535315      0.0034851739   1              1            
+      6450   280.70805      13.243012      0.0034851739   1              1            
+      6500   251.14485     -18.466759      0.0034851739   1              1            
+      6550   284.32321      9.0351234      0.0034851739   1              1            
+      6600   284.03779     -10.683306      0.0034851739   1              1            
+      6650   315.1569      -39.736019      0.0034851739   1              1            
+      6700   302.50424      5.9013011      0.0034851739   1              1            
+      6750   368.279        44.343503      0.0034851739   1              1            
+      6800   279.67266     -35.967233      0.0034851739   1              1            
+      6850   298.98045      3.0539699      0.0034851739   1              1            
+      6900   236.94852      0.55971293     0.0034851739   1              1            
+      6950   303.38382     -9.1880246      0.0034851739   1              1            
+      7000   264.56096      3.904024       0.0034851739   1              1            
+      7050   272.26968     -44.608801      0.0034851739   1              1            
+      7100   235.38132      13.141913      0.0034851739   1              1            
+      7150   272.0985       26.601686      0.0034851739   1              1            
+      7200   314.41177     -7.6236617      0.0034851739   1              1            
+      7250   313.29915     -45.214663      0.0034851739   1              1            
+      7300   309.20548     -11.691744      0.0034851739   1              1            
+      7350   342.22769      18.805899      0.0034851739   1              1            
+      7400   301.02701      32.830071      0.0034851739   1              1            
+      7450   318.19524      48.620851      0.0034851739   1              1            
+      7500   290.00663     -9.1444424      0.0034851739   1              1            
+      7550   238.07666      32.654941      0.0034851739   1              1            
+      7600   275.95317     -23.982336      0.0034851739   1              1            
+      7650   274.54472     -29.183684      0.0034851739   1              1            
+      7700   307.25317      11.981268      0.0034851739   1              1            
+      7750   299.40271     -19.390542      0.0034851739   1              1            
+      7800   314.18813     -6.0794802      0.0034851739   1              1            
+      7850   271.14043      40.491364      0.0034851739   1              1            
+      7900   266.43792      37.250574      0.0034851739   1              1            
+      7950   330.21996      31.783381      0.0034851739   1              1            
+      8000   313.80294      44.878972      0.0034851739   1              1            
+      8050   331.1094       1.9597746      0.0034851739   1              1            
+      8100   267.80448      26.159121      0.0034851739   1              1            
+      8150   267.17305      16.135234      0.0034851739   1              1            
+      8200   290.248       -13.058622      0.0034851739   1              1            
+      8250   231.77635     -42.850795      0.0034851739   1              1            
+      8300   233.58288      29.137765      0.0034851739   1              1            
+      8350   270.2913      -11.177011      0.0034851739   1              1            
+      8400   254.69873      3.1775639      0.0034851739   1              1            
+      8450   334.88277     -27.336924      0.0034851739   1              1            
+      8500   354.95137     -9.751911       0.0034851739   1              1            
+      8550   327.78998      8.2348621      0.0034851739   1              1            
+      8600   306.15772      1.3756734      0.0034851739   1              1            
+      8650   325.68699      6.5939205      0.0034851739   1              1            
+      8700   302.84804      13.912169      0.0034851739   1              1            
+      8750   299.34988      10.311212      0.0034851739   1              1            
+      8800   258.77684     -8.0783535      0.0034851739   1              1            
+      8850   299.8835      -9.61362        0.0034851739   1              1            
+      8900   350.28205     -34.897861      0.0034851739   1              1            
+      8950   316.90133     -52.845562      0.0034851739   1              1            
+      9000   337.50548      18.172556      0.0034851739   1              1            
+      9050   306.67254      37.062973      0.0034851739   1              1            
+      9100   310.74844      58.178538      0.0034851739   1              1            
+      9150   301.53463      5.9650738      0.0034851739   1              1            
+      9200   284.61384      10.677528      0.0034851739   1              1            
+      9250   247.86475     -15.325203      0.0034851739   1              1            
+      9300   309.74481     -60.070902      0.0034851739   1              1            
+      9350   290.17111      5.6049467      0.0034851739   1              1            
+      9400   268.79925     -9.2423032      0.0034851739   1              1            
+      9450   315.80445      18.124612      0.0034851739   1              1            
+      9500   351.58161     -14.465115      0.0034851739   1              1            
+      9550   344.93028      43.161438      0.0034851739   1              1            
+      9600   265.92273      0.3396608      0.0034851739   1              1            
+      9650   261.1649      -20.46043       0.0034851739   1              1            
+      9700   262.05627      27.187613      0.0034851739   1              1            
+      9750   249.12463      15.911339      0.0034851739   1              1            
+      9800   262.40626     -16.159153      0.0034851739   1              1            
+      9850   267.48677      0.32143902     0.0034851739   1              1            
+      9900   316.15674      40.664589      0.0034851739   1              1            
+      9950   323.94181      20.356291      0.0034851739   1              1            
+     10000   307.90841      4.8392456      0.0034851739   1              1            
+Loop time of 0.937214 on 4 procs for 10000 steps with 44 atoms
+
+Performance: 921.881 ns/day, 0.026 hours/ns, 10669.916 timesteps/s, 469.476 katom-step/s
+96.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00042896 | 0.01827    | 0.04944    |  14.9 |  1.95
+Bond    | 0.00067626 | 0.061292   | 0.18867    |  31.0 |  6.54
+Kspace  | 0.50738    | 0.64527    | 0.7136     |  10.4 | 68.85
+Neigh   | 0.0031476  | 0.0031815  | 0.0032165  |   0.0 |  0.34
+Comm    | 0.01335    | 0.020817   | 0.035424   |   6.1 |  2.22
+Output  | 0.0010449  | 0.0012202  | 0.0016969  |   0.8 |  0.13
+Modify  | 0.16314    | 0.18266    | 0.20201    |   4.3 | 19.49
+Other   |            | 0.004499   |            |       |  0.48
+
+Nlocal:             11 ave          40 max           0 min
+Histogram: 2 1 0 0 0 0 0 0 0 1
+Nghost:             22 ave          40 max           4 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Neighs:          216.5 ave         845 max           0 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 866
+Ave neighs/atom = 19.681818
+Ave special neighs/atom = 6.4090909
+Neighbor list builds = 212
+Dangerous builds = 0
+
+# write_restart restart_longrun
+# write_data restart_longrun.data
+Total wall time: 0:00:00